geni-act - ubwp.buffalo.eduubwp.buffalo.edu/wnygirahcp/wp-content/uploads/sites/25/2017/11/... ·...

Stephen Koury ([email protected]) | profile | logout

[ ] geni-act

geni-act :: genomes :: Kytococcus sedentarius DSM 20547 CP001686 :: Ksed_00010 :: Lab Notebook 8ed2a45227a744df

Lab NotebookOrganism: Kytococcus sedentarius DSM 20547 CP001686Locus: Ksed_00010

[-] Basic Information

Module Instructions

DNA Coordinates

go to the Gene Page

DNA coordinates209..1729

DNA Sequence

go to the Gene Page

Nucleotide sequence (FASTA format; see module Quick Links for instructions)>Ksed_00010 nucleotide sequnce GTGAGCCAGACCCCCGACGACCACGCCACCGCCATCTGGCAGGAGGCCATGGTCCACCTCCAGGGAGCAGGCCTGGCCCCGCGCGACATCGGGGTGCTCCGGCTGGCCACGCTCGTGGGTCTGCTGGAGGGCACTGCCCTGCTCGCGGTGAAGTACGACCACGTCAAGGACGCCGTCGAGGGGCACCTGCGCGAGGACGTGTCCACCGCCCTGGCGGAGGTCCTGGACCGTGACATCCGGCTGGCCGTCTCGGTGGACCCCGATGCGGTGAGCGCCGCCCAGGAGGAGGCCGCACCCCCGGCCCCGTCCCCGGCCGATGAGGACGACCCGGCCACAGGTGAGGGACCGTTGTCCACAGCTGTGGACGGAGCCGTGGAAAAGCACGAGGGAAGCAGTCCGGCACGTGCCGGGGAATCGGTGGCGCCGGCCACGACGGCCAGCCTGACGGCGACAAACTCCTCACCCGGTGTGGAGCGCGATTACTCCGCGCTGAACCACAAGTACACTTTCGACACCTTCGTGCTGGGGTCGTCGAACCGTTTCGCCCACGCCGCAGCGACCGCCGTGGCCGAAGCCCCCGCCCGCGCCTACAACCCGCTGTTCATCTACGGCGGATCAGGTCTGGGCAAGACCCACCTGTTGCACGCCATCGGCCACTACGCCCGCACCCTGGATTCCTCGGTGCGCGTGAAGTACGTGAACTCGGAGGAGTTCACCAACCAGTTCATCAACGCGGTCTCGGCCGGCCAGGCGAATGCCTTCCAGCGCCAGTACCGCGATGTGGACGTCCTGCTCATCGACGACATCCAGTTCCTGCAGGGCAAGGAGCAGACGATGGAGGAGTTCTTCCACACCTTCAACACCCTGCACAACAGCGAGAAGCAGATCGTCATCACCTCCGACCAGCCCCCGAAGAAGCTCAGTGGCTTCGCCGAGCGCATGCGCTCGCGTTTCGAGTGGGGTCTGCTCACCGACGTGCAGCCGCCGGACCTGGAGACCCGCATCGCGATCCTCCGGCGCAAGGCAGCGGCCGACAAGCTGGACATCCCCGATGACGTGCTCCACCTCATCGCGTCGAAGATCTCCTCGAACATCCGCGAGCTCGAGGGGGCCCTGACCCGGGTGACGGCCTTCGCGAGCCTGTCCGGGTCGCCCCTGGACGAGTACCTGGCCCGCACGGTGCTCAAGGACGTGATGCCCGGCGGTGACAGCGGCCAGATCACGCCCACGATGATCCTGGAGGAGACCGCGGGGTACTTCGTCATCTCCGTCGAGGAGATCCAGGGCGCCTCCCGCTCGCGCAACCTGACCCGGGCCCGGCAGATCGCCATGTACCTGTGCCGCGAGCTCACGGACCTCTCGCTGCCGAAGATCGGCAAGGAGTTCGGCGGC

http://geni-act.org/lab_notebook/public/8ed2a45227a744df/ 11/7/15, 7:37 PM of 39

CGCGACCACACGACCGTCATGCACGCCGAGCGCAAGATCAAGCAGCTGCTCGGGGAGGACCGCCGGGTCTACGACGAGGTGAGCGAGCTCACCAGCATCATCCGCAAGAAGGCGGCGCGCGGCCGCTG A

Sequence Length1521 nucleotides

Protein Sequence

go to the Gene Page

Amino acid sequence

>Ksed_00010_amino acid seqMSQTPDDHATAIWQEAMVHLQGAGLAPRDIGVLRLATLVGLLEGTALLAVKYDHVKDAVEGHLREDVSTALAEVLDRDIRLAVSVDPDAVSAAQEEAAPPAPSPADEDDPATGEGPLSTAVDGAVEKHEGSSPARAGESVAPATTASLTATNSSPGVERDYSALNHKYTFDTFVLGSSNRFAHAAATAVAEAPARAYNPLFIYGGSGLGKTHLLHAIGHYARTLDSSVRVKYVNSEEFTNQFINAVSAGQANAFQRQYRDVDVLLIDDIQFLQGKEQTMEEFFHTFNTLHNSEKQIVITSDQPPKKLSGFAERMRSRFEWGLLTDVQPPDLETRIAILRRKAAADKLDIPDDVLHLIASKISSNIRELEGALTRVTAFASLSGSPLDEYLARTVLKDVMPGGDSGQITPTMILEETAGYFVISVEEIQGASRSRNLTRARQIAMYLCRELTDLSLPKIGKEFGGRDHTTVMHAERKIKQLLGEDRRVYDEVSELTSIIRKKAARGR

Sequence Length506 aa

[-] Sequence-based Similarity Data

Module Instructions

BLAST

go to BLAST at http://www.ncbi.nlm.nih.gov/blast

Gene product name (top hit)

Note that results from both the Swiss-Prot and nr databases have been recorded. The Swiss-Prot data for both tophits are shown in the "BLAST first hit" section of the notebook and the nr data are shown in the second hit section ofthe notebook.

Hit #1 Swis Prot Database - chromosomal replication initiator protein DnaA

Hit #2 Swis Prot Database - chromosomal replication initiator protein DnaA


Organism

Hit #1 Swis Prot Database - Kineococcus radiotolerans SRS30216

Hit #2 Swis Prot Database - Mycobacterium vanbaalenii PYR-1

Alignment Length

Hit #1 Swis Prot Database - 493

Hit #2 Swis Prot Database - 504

Score

See image files below for both SwissProt hits

E-value

See image files below for both SwissProt hits

Alignment of the top hit and the query sequence

SwissProt Database 2 top hits:


Gene product name (second hit)

Hit #1 nr Database - chromosomal replication initiator protein DnaA

Hit #2 nr Database - chromosomal replication initiator protein DnaA

Organism

Hit #1 nr Database - Ornithinimicrobium pekingense

Hit #2 nr Database- Serinicoccus profundi

Alignment Length

Hit #1 nr Database - 503

Hit #2 nr Database - 503

Score

See image files below for both nr hits

E-value

See image files below for both nr hits

Alignment of the second hit and the query sequence


CDD

click on the CDD search results at the top of the BLAST results page

COG number (top hit)COG0593

COG nameDnaA: Chromosomal replication initiation ATPase DnaA [Replication, recombination and repair]

E-value1.03e-153


COG number (second hit)No second found

COG name

E-value

T-Coffee

go to T-Coffee at http://www.ebi.ac.uk/Tools/msa/tcoffee

Sequences used for alignmentNote that the nr database BLAST results were used to select sequences for alginment since there were a much larger number of good hitsin those results.

>Kytococcus sedentarius DSM 20547]

MSQTPDDHATAIWQEAMVHLQGAGLAPRDIGVLRLATLVGLLEGTALLAVKYDHVKDAVEGHLREDVSTALAEVLDRDIR

LAVSVDPDAVSAAQEEAAPPAPSPADEDDPATGEGPLSTAVDGAVEKHEGSSPARAGESVAPATTASLTATNSSPGVERD

YSALNHKYTFDTFVLGSSNRFAHAAATAVAEAPARAYNPLFIYGGSGLGKTHLLHAIGHYARTLDSSVRVKYVNSEEFTN

QFINAVSAGQANAFQRQYRDVDVLLIDDIQFLQGKEQTMEEFFHTFNTLHNSEKQIVITSDQPPKKLSGFAERMRSRFEW

GLLTDVQPPDLETRIAILRRKAAADKLDIPDDVLHLIASKISSNIRELEGALTRVTAFASLSGSPLDEYLARTVLKDVMP

GGDSGQITPTMILEETAGYFVISVEEIQGASRSRNLTRARQIAMYLCRELTDLSLPKIGKEFGGRDHTTVMHAERKIKQL

LGEDRRVYDEVSELTSIIRKKAARGR

>gi|551300082|ref|WP_022920049.1| chromosomal replication initiator protein DnaA [Ornithinimicrobium pekingense]

MTSQSPAESAEVWQRVVSQLESQGVTARDRAFLRLTQLVGLLDTTALLAVPYQHTKETLETTLRQPIVDALAGELGHDVR

LAITVDEDLRRQVEDEGDPAPGPAVTEQVPSDPDRTPYRSNGAGPGEPRSDGHRTPSGAVQTASAEDARLNPKYTFDTFV

SGSSNRFAHAASLAVAESPARAYNPLFIYGESGLGKTHLLHAIGHYARSLYPGVRVRYVNSEEFTNDFINSIRDDKAGAF

QRRYRNVDFLLVDDIQFLQGKEQTVEEFFHTFNTLHNSEKQVVITSDQPPKRLSGFAERMRSRFEWGLLTDVQPPDLETR

IAILKKKAAQEGMQLPDEVLELIGSKISTNIRELEGALIRVTAFASLSSTPPDAALASHVLKDIIPNSESAAITVPTIMA

EVADYFQISNDDLCGTSRSRTLVNARQIAMYLCRELTDLSLPKIGQEFGGRDHTTVMHAERKIRQLIGERRALYDQITEL

TGIIRKASAR

>gi|497833122|ref|WP_010147278.1| chromosomal replication initiator protein DnaA [Serinicoccus profundi]

MSQPSTDSGDTWRRVVSELEDKGLGAREKAFLRLTTMVGVLDSTVLLAVPYPHTKEMLETTLRQPIVDLLSRELDREVRL

AITVDDDVRQRVEDEADDEADEDAQTRESLTRPASQPSSSAGAGVPGPSGNGIPRPATPAGPAVTGAADEARLNPKYSFD

TFVSGPSNRFAHAASLAVAESPARAYNPLFIYGESGLGKTHLLHAIGHYARKLYPGVRVRYVNSEEFTNDFINSIRDDKA

GAFQRRYRNVDFLLVDDIQFLQGKEQTVEEFFHTFNTLHNSEKQVVITSDQPPKRLSGFAERMRSRFEWGLLTDVQPPDL

ETRIAILRKKAAQEGMQLPDEVLEHIASRITTNIRELEGALIRVTAFASLSSQPADADLAAHVLKDIVPGSDTAQITVST


IIREVSEYFQISIDELCGTSRSRTLVNARQIAMYLCRELTDLSLPKIGQEFGGRDHTTVMHAERKIRAQIGERRALYDQI

AELTGTIRRASQR

>gi|737975618|ref|WP_035938084.1| chromosomal replication initiator protein DnaA [Knoellia aerolata] >gi|700180054|gb|KGN40755.1|chromosomal replication initiation protein [Knoellia aerolata DSM 18566]

MDQIWRTTLDALDSDGIPVQQRAFLSLARLVGLLDETALIAVPNDFTKDIVETRLRDRVTETLSSQLGHTVRLAVTVDSS

LGDVPVLDPPADAPSGSTTTEPRPAAGTEGDGRHAERRAELDGIALVEDDDDGDSSRTGRSVAHTRSPGALRPRPGVTVP

EQVELTRLNPKYTFDTFVIGASNRFANAAALAVAETPAKAYNPLFIYGESGLGKTHLLHAIGHYARNLFPHVKVRYVNSE

EFTNDFINSIRDDKAANFQRRYRDVDVLLIDDIQFLQGKVQTQEEFFHTFNTLHNANKQVVITSDLPPKLLSGFEERMRS

RFEWGLMTDVQPPDLETRIAILRKKAAQEKLSVPDDVLEFIASRISTNIRELEGALIRVTAFASLNRQPVDISLAEIVLK

DLIPHDSSSQITSATIMAQTAAYFGLTLEDLQGQSRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGGRDHTTVMHADKK

IRQLMAERRAIYNQVTELTNRIKQQSR

>gi|914680953|ref|WP_050671265.1| chromosomal replication initiation protein [Luteipulveratus sp. C296001] >gi|912506872|gb|KNX38763.1|chromosomal replication initiation protein [Luteipulveratus sp. C296001]

MSEDKPDLAHVWHSTVMALEETGIAARDRAFLRLTRLVGLVDQTALLAVPFDHTKDILETSLREPVSSALSRLLDRDVRL

AVTVDPQLQQTVSASAEAKDAGIGEDEVAETDAEEAGTPAPALIRPVRASNRPPVEPVTDARLNPKYTFDTFVIGASNRF

AHAAAFAVAEAPAKSYNPLFVYGDSGLGKTHLLHAIGHYVRNLYPSMRVRYVNSEEFTNDFINSIRDDKASSFQKRYRDD

VDVLLIDDVQFLQGKDGTQEEFFHTFNALHDSEKQIVLTSDQPPKKLSGFADRMRSRFEWGLQTDVTPPDLETRIAILRK

KAIAERMNVPDDVLELIASKFSTNIRELEGALIRVMAFASLSQQPVDQQVAGYVLKDLVPSAGSSQITATLIMTKTAEYF

HVSVEELCGSSRSRTLVTARQIAMYLCRELTELSLPKIGQQFGGRDHTTVMHADRKIRQLIGERRPIYDQITELTGQITR

AAAG

>gi|497462772|ref|WP_009776970.1| chromosomal replication initiator protein DnaA [Janibacter sp. HTCC2649] >gi|84382082|gb|EAP97964.1|chromosomal replication initiator protein [Janibacter sp. HTCC2649]

MDQIWRTTLDALDSDGIPVQQRAFLSLAKLVGLLDETALIAVPNDFTKDIVETRLRDRVTETLSSQLGHDVRLAVTVDHS

LADVPVTIPADTTTVDGAGADQVPRTATTIGLEPGPADADGRRAKRRAELDGIALVEDDEGEDDSRNNGAIGRTRSPGAL

RPRPGATVPEQVELTRLNPKYTFDTFVIGASNRFANAAALAVAETPAKAYNPLFIYGESGLGKTHLLHAIGHYARNLYPH

VKVRYVNSEEFTNDFINSIRDDKAANFQRRYRDVDVLLIDDIQFLQGKVQTQEEFFHTFNTLHNANKQVVITSDLPPKLL

SGFEERMRSRFEWGLMTDVQPPDLETRIAILRKKAAQEKLSVPDDVLEFIASRISTNIRELEGALIRVTAFASLNRQPVD

ISLAEIVLKDLIPHDSANQITSATIMAQTAAYFGLTLEDLQGQSRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGGRDH

TTVMHADKKIRQLMAERRAIYNQVTELTNRIKQQSR

>gi|872700517|ref|WP_048552171.1| chromosomal replication initiation protein [Tetrasphaera japonica] >gi|665501165|emb|CCH80159.1|chromosomal replication initiator protein DnaA [Tetrasphaera japonica T1-X7]

MDYSRVWRTALDELDADGLPIQQRAFLSLARFVGLLDDTALIAVPNDYTKEFVETRVRQQLTQTLSNHAGRELRLAVTVD

PGLKAADEAEPTLGAPAEAWGPRPRAGIGPVDDEEDHEAQDVIDARGVDTFHIQRPTPGQRPVPELIENTRLNPKYTFDT

FVIGASNRFAHAAAVAVAEAPAKAYNPLFVYGDSGLGKTHLLHAIGHYARNLYPTVRVRYVNSEEFTNDFINSIRDDKAA

NFQSRYRDVDVLLIDDIQFLQGKVQTQEEFFHTFNTLHNANKQVVITSDVPPKLLSGFEERMRSRFEWGLLTDVQPPDLE

TRIAILRKKAIQERLSVPDDVLEFIASRISTNIRELEGALIRVTAFASLNRQPVDMSLAEIVLKDLIPSDGANQITSATI

MAQTATYFGLTVEDLQGASRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGGRDHTTVMHADKKIRQLMAERRAIYNQVT

ELTNRIKQQSR


>gi|656266264|ref|WP_029212190.1| chromosomal replication initiator protein DnaA [Arsenicicoccus bolidensis]

MTDAQVDVPRVWRDTLRALESGGISAQHRGFLRLSRLVGLLEGTALIAVPNDYTRDIVEKRIRTELVAALQEQLGRDVRL

AVTVDSSLELSEAEDRDDSTQRPGSPGEVPHVVTSSDPVRHDGERGGSDPRSTYGPRLVRDERVPRPVSTDASFGGERPY

ADPARHDGGPGHAPGIRPAQDDDADDDRELLAEGDGIREMFRKPFVPEDGRDAKLNPKYTFDTFVIGSSNRFAHAAAIAV

AEAPAKAYNPLFIYGGSGLGKTHLLHAIGHYAQQIYPNVRVKYVNSEEFTNDFINSIGANKASDFQRRYRDIDFLLIDDI

QFLQGKVQTQEEFFHTFNTLHNANKQVVITSDVAPKLLSGFEERMRSRFEWGLLTDVQPPDLETRIAILRKKAVQERMTA

PDDVLEFIASKISTNIRELEGALIRVTAFASLNHQGVDMTLAEVVLKDLIPADQTNQITPATIMAQTASYFGLTVDDLCG

TSRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGGRDHTTVMHADRKIRELMSERRAIYNQVTELTNRIKSNPS

>gi|918414635|ref|WP_052465811.1| chromosomal replication initiation protein [Mobilicoccus sp. SIT2]

MSGSGEPPTTPAVDDPARIWGATLRALDQAGIPAPQRAFLRQAMLVGVLDTTALIAVPDDFTKEIVESRARDYLVKALTE

QVGREVRLAVTVDASLREQIAAAEQPVLEGYADPDSDVAAAEPPAASPTAAAPASPPVEDSPAPVGERRPRPAPTGRREE

SSQLNPKYTFDTFVIGASNRFAHAAAVAVAEAPAKAYNPLFVYGDSGLGKTHLLHAIGHYARNLYPHVKVKYVNSEEFTN

DFINSIRDDKAAGFQRRYRDMDVLLIDDIQFLQGKMQTQEEFFHTFNTLHNSNKQVVITSDVPPKQLSGFEERMRSRFEW

GLLTDVQPPDLETRIAILRKKAVQEHLALPDEVMEFIASRISTNIRELEGALIRVTAFANLNRQPVEMSLAEIVLKDLIP

DKESSQITASMIMGQTAAYFGLSIDDLCGSSRSRGLVTARQIAMYLCRELTELSLPKIGQQFGGRDHTTVMHADRKIRQL

MAERRSVYNQVTELTTRIRSQAS

>gi|503647989|ref|WP_013882065.1| chromosomal replication initiator protein DnaA [[Cellvibrio] gilvus] >gi|336102716|gb|AEI10535.1| chromosomalreplication initiator protein DnaA [[Cellvibrio] gilvus ATCC 13127]

MAQDEELSRVWGHVVTTLEESPDITQRQLAFVRLAQPLGLLDGTIILAVGNEYTKEYLETKVRAEVTSALGSALGRDGRF

AITVDPSLVDDAPPAVRAMTSAPELGVVTDGTDERGAPNRTVPTDADTGRHERSPMLSESAEPTRPVRETASSRRPAAEP

ARLNPHYLFETFVIGSSNRFAHAAAVAVAEAPAKAYNPLFIYGDSGLGKTHLLHAIGHYAQNLYPSVRVRYVNSEEFTND

FINSISEGKAGAFQRRYREVDVLLIDDIQFLQGKEQTMEEFFHTFNTLHNANKQVVITSDLPPKQLNGFEDRMRSRFEWG

LITDVQPPDLETRIAILRKKAGGDNMQAPPDVLEYIASKISTNIRELEGALIRVTAFASLNRQQVDLSLAEIVLKDLITD

DQTTEITATQVIGQTAAYFGLSIEDLCGSSRSRVLVTARQIAMYLCRELTDLSLPKIGQAFGGRDHTTVMHANRKIRELM

AERRSIYNQVTELTNRIKQQSRG

>gi|739084600|ref|WP_036955733.1| chromosomal replication initiator protein DnaA [Promicromonosporaceae bacterium W15]

MAEVWSAARIQLENDPDVTPRQRGYVRLVAPLAHIDDTVFLKVSDEPIRSFIETNLRADLVGALAGVLGYEPKLAISVDP

DLQIADDDTDPAAPVYARPAPTTATSPAAQRMPTDEPDHGLSNPVGFGATVGLPEAMPAAPGSARAAQHAPRHAEPTAPL

GENSRLNPKYLFETFVIGASNRFAHAAAVAVAEAPAKAYNPLFIYGDSGLGKTHLLHAIGHYAQSLYPNVRVRYVNSEEF

TNDFINSIGEGKAGAFQRRYRDVDVLLIDDIQFLQGKEQTMEEFFHTFNALHNANKQVVITSDLPPKQLNGFEDRLRSRF

EWGLITDVQPPDLETRIAILRKKALQERLDAPDDVLEYIASRISTNIRELEGALIRVTAFANLNRQPVDQSLAEIVLKDL

ITDDDAGEITAASVIAQTAAYFGLTIDDLCGSSRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGGRDHTTVMHANRKIS

EQMAERRSIYNQVTELTSRIKQQHRG

Multiple sequence alignment

[Kytococcus MSQTPDDHATAIWQEAMVHLQ-GAGLAPRDIGVLRLATLVGLLEGTALLAgi|478759289|emb|CCH68940.1| MADA---SMTSVWVRILRALD-REGVSHQERAFLSITRLAGVLDETALIA


gi|497462772|ref|WP_009776970.1| M--------DQIWRTTLDALD-SDGIPVQQRAFLSLAKLVGLLDETALIAgi|497833122|ref|WP_010147278.1| MSQ-PSTDSGDTWRRVVSELE-DKGLGAREKAFLRLTTMVGVLDSTVLLAgi|503647989|ref|WP_013882065.1| MAQD--EELSRVWGHVVTTLEESPDITQRQLAFVRLAQPLGLLDGTIILAgi|551300082|ref|WP_022920049.1| MTSQSPAESAEVWQRVVSQLE-SQGVTARDRAFLRLTQLVGLLDTTALLAgi|656266264|ref|WP_029212190.1| MTDA-QVDVPRVWRDTLRALE-SGGISAQHRGFLRLSRLVGLLEGTALIAgi|665501165|emb|CCH80159.1| MD------YSRVWRTALDELD-ADGLPIQQRAFLSLARFVGLLDDTALIAgi|737975618|ref|WP_035938084.1| M--------DQIWRTTLDALD-SDGIPVQQRAFLSLARLVGLLDETALIAgi|750471801|ref|WP_040753674.1| M--------TSVWVRILRALD-REGVSHQERAFLSITRLAGVLDETALIA * * : *: .: :. ..: :: *:*: * ::*

[Kytococcus VKYDHVKDAVEGHLREDVSTALAEVLDRDIRLAVSVDPDAVSAAQEEAAPgi|478759289|emb|CCH68940.1| VPNDFSKDIVETRLRGRISGHLTAELDRPLRLAVTVDPSLAEAEPLDLDAgi|497462772|ref|WP_009776970.1| VPNDFTKDIVETRLRDRVTETLSSQLGHDVRLAVTVDHSLADVPVTIPADgi|497833122|ref|WP_010147278.1| VPYPHTKEMLETTLRQPIVDLLSRELDREVRLAITVDDDVRQRVEDEADDgi|503647989|ref|WP_013882065.1| VGNEYTKEYLETKVRAEVTSALGSALGRDGRFAITVDPSLVDDAPPAVRAgi|551300082|ref|WP_022920049.1| VPYQHTKETLETTLRQPIVDALAGELGHDVRLAITVDEDLRRQVEDEGD-gi|656266264|ref|WP_029212190.1| VPNDYTRDIVEKRIRTELVAALQEQLGRDVRLAVTVDSSLELSEAEDRDDgi|665501165|emb|CCH80159.1| VPNDYTKEFVETRVRQQLTQTLSNHAGRELRLAVTVDPGLKAADEAEPTLgi|737975618|ref|WP_035938084.1| VPNDFTKDIVETRLRDRVTETLSSQLGHTVRLAVTVDSSLGDVPVLDPPAgi|750471801|ref|WP_040753674.1| VPNDFSKDIVETRLRGRISGHLTAELDRPLRLAVTVDPSLAEAEPLDLDA * . :: :* :* : * .: *:*::** .

[Kytococcus -PAP----------SPADEDDPATGEGPLS--------------------gi|478759289|emb|CCH68940.1| HDSQDHSLATD--PQRATQDDPALVNGVADL----AVVD-----------gi|497462772|ref|WP_009776970.1| -TTTVDGAGADQVPRTATTI--GLEPGP----------------------gi|497833122|ref|WP_010147278.1| -EAD----------EDAQTRESL---------------------------gi|503647989|ref|WP_013882065.1| M-------TSA--PELGVVTDGTDERGAPNR----TV-P-----------gi|551300082|ref|WP_022920049.1| -PAP----------GPAVTEQVP---------------------------gi|656266264|ref|WP_029212190.1| STQRPGSPGEV--PHVVTSSDPVRHDGERGGSDPRSTYGPRLVRDERVPRgi|665501165|emb|CCH80159.1| -GAPAEA--WG--PRPRA--------------------------------gi|737975618|ref|WP_035938084.1| -DAPSGSTTTE--PRPAA----G---------------------------gi|750471801|ref|WP_040753674.1| HDSQDHSLATD--PQRATQDDPALVNGVADL----AVVD-----------

[Kytococcus -------------------------TAVDG--AVEKHEGSSPARA-GESVgi|478759289|emb|CCH68940.1| ---L----------DDPEVRRAQRRLELDGL-------DADETPM-PRAAgi|497462772|ref|WP_009776970.1| --------------ADADGRRAKRRAELDGIALVEDDEGEDDSRN-NGAIgi|497833122|ref|WP_010147278.1| -----------------------------------TRPASQPSSSAGAGVgi|503647989|ref|WP_013882065.1| --------------TDADTGR------------------HERSPMLSESAgi|551300082|ref|WP_022920049.1| -----------------------------------SDPDRTPYRSNGAGPgi|656266264|ref|WP_029212190.1| PVSTDASFGGERPYADP-ARHDGGPGHAPGIRPAQDDD-ADDDRE-LL-Agi|665501165|emb|CCH80159.1| -----------------------------GIGPVDDEEDHEAQDV-IDA-gi|737975618|ref|WP_035938084.1| --------------TEGDGRHAERRAELDGIALVEDDDDGDSSRT-GRSVgi|750471801|ref|WP_040753674.1| ---L----------DDPEVRRAQRRLELDGL-------DADETPM-PRAA

[Kytococcus A-PATTASL---TATNSSPGVERDYSALNHKYTFDTFVLGSSNRFAHAAAgi|478759289|emb|CCH68940.1| EPTGIPANLR-----RGSNPENVELTRLNPKYTFETFVIGASNRFAHAAAgi|497462772|ref|WP_009776970.1| GRTRSPGALRP-RPG-ATVPEQVELTRLNPKYTFDTFVIGASNRFANAAAgi|497833122|ref|WP_010147278.1| PGPSGNGIPRPATPAGPAVTGAADEARLNPKYSFDTFVSGPSNRFAHAASgi|503647989|ref|WP_013882065.1| EPTR-PVRE----T-ASSRRPAAEPARLNPHYLFETFVIGSSNRFAHAAAgi|551300082|ref|WP_022920049.1| GEPRSDGHR---TPSGAVQTASAEDARLNPKYTFDTFVSGSSNRFAHAASgi|656266264|ref|WP_029212190.1| EGDGIREMFR-----KPFVPEDGRDAKLNPKYTFDTFVIGSSNRFAHAAAgi|665501165|emb|CCH80159.1| RGVDTFHIQRP-TPGQRPVPELIENTRLNPKYTFDTFVIGASNRFAHAAAgi|737975618|ref|WP_035938084.1| AHTRSPGALRP-RPG-VTVPEQVELTRLNPKYTFDTFVIGASNRFANAAAgi|750471801|ref|WP_040753674.1| EPTGIPANLR-----RGSNPENVELTRLNPKYTFETFVIGASNRFAHAAA : ** :* *:*** *.*****:**:

[Kytococcus TAVAEAPARAYNPLFIYGGSGLGKTHLLHAIGHYARTLDSSVRVKYVNSEgi|478759289|emb|CCH68940.1| TAVGETPAKAYNPLFIYGGSGLGKTHLLHAIGHYARSLYPNVKVRYVNSEgi|497462772|ref|WP_009776970.1| LAVAETPAKAYNPLFIYGESGLGKTHLLHAIGHYARNLYPHVKVRYVNSEgi|497833122|ref|WP_010147278.1| LAVAESPARAYNPLFIYGESGLGKTHLLHAIGHYARKLYPGVRVRYVNSEgi|503647989|ref|WP_013882065.1| VAVAEAPAKAYNPLFIYGDSGLGKTHLLHAIGHYAQNLYPSVRVRYVNSEgi|551300082|ref|WP_022920049.1| LAVAESPARAYNPLFIYGESGLGKTHLLHAIGHYARSLYPGVRVRYVNSEgi|656266264|ref|WP_029212190.1| IAVAEAPAKAYNPLFIYGGSGLGKTHLLHAIGHYAQQIYPNVRVKYVNSEgi|665501165|emb|CCH80159.1| VAVAEAPAKAYNPLFVYGDSGLGKTHLLHAIGHYARNLYPTVRVRYVNSEgi|737975618|ref|WP_035938084.1| LAVAETPAKAYNPLFIYGESGLGKTHLLHAIGHYARNLFPHVKVRYVNSEgi|750471801|ref|WP_040753674.1| TAVGETPAKAYNPLFIYGGSGLGKTHLLHAIGHYARSLYPNVKVRYVNSE **.*:**:******:** ****************: : . *:*:*****

[Kytococcus EFTNQFINAVSAGQANAFQRQYRDVDVLLIDDIQFLQGKEQTMEEFFHTFgi|478759289|emb|CCH68940.1| EFTNDFINSVRDGKAAEFQRRYRYVDVLLIDDIQFLQGKEQTQEEFFHTFgi|497462772|ref|WP_009776970.1| EFTNDFINSIRDDKAANFQRRYRDVDVLLIDDIQFLQGKVQTQEEFFHTFgi|497833122|ref|WP_010147278.1| EFTNDFINSIRDDKAGAFQRRYRNVDFLLVDDIQFLQGKEQTVEEFFHTFgi|503647989|ref|WP_013882065.1| EFTNDFINSISEGKAGAFQRRYREVDVLLIDDIQFLQGKEQTMEEFFHTFgi|551300082|ref|WP_022920049.1| EFTNDFINSIRDDKAGAFQRRYRNVDFLLVDDIQFLQGKEQTVEEFFHTFgi|656266264|ref|WP_029212190.1| EFTNDFINSIGANKASDFQRRYRDIDFLLIDDIQFLQGKVQTQEEFFHTFgi|665501165|emb|CCH80159.1| EFTNDFINSIRDDKAANFQSRYRDVDVLLIDDIQFLQGKVQTQEEFFHTFgi|737975618|ref|WP_035938084.1| EFTNDFINSIRDDKAANFQRRYRDVDVLLIDDIQFLQGKVQTQEEFFHTFgi|750471801|ref|WP_040753674.1| EFTNDFINSVRDGKAAEFQRRYRYVDVLLIDDIQFLQGKEQTQEEFFHTF ****:***:: .:* ** :** :*.**:********* ** *******

[Kytococcus NTLHNSEKQIVITSDQPPKKLSGFAERMRSRFEWGLLTDVQPPDLETRIAgi|478759289|emb|CCH68940.1| NALHNANKQVVVTSDVAPKQLAGMEERLRSRLEWGLLTDVQPPDLETRIAgi|497462772|ref|WP_009776970.1| NTLHNANKQVVITSDLPPKLLSGFEERMRSRFEWGLMTDVQPPDLETRIAgi|497833122|ref|WP_010147278.1| NTLHNSEKQVVITSDQPPKRLSGFAERMRSRFEWGLLTDVQPPDLETRIAgi|503647989|ref|WP_013882065.1| NTLHNANKQVVITSDLPPKQLNGFEDRMRSRFEWGLITDVQPPDLETRIAgi|551300082|ref|WP_022920049.1| NTLHNSEKQVVITSDQPPKRLSGFAERMRSRFEWGLLTDVQPPDLETRIAgi|656266264|ref|WP_029212190.1| NTLHNANKQVVITSDVAPKLLSGFEERMRSRFEWGLLTDVQPPDLETRIAgi|665501165|emb|CCH80159.1| NTLHNANKQVVITSDVPPKLLSGFEERMRSRFEWGLLTDVQPPDLETRIAgi|737975618|ref|WP_035938084.1| NTLHNANKQVVITSDLPPKLLSGFEERMRSRFEWGLMTDVQPPDLETRIAgi|750471801|ref|WP_040753674.1| NALHNANKQVVVTSDVAPKQLAGMEERLRSRLEWGLLTDVQPPDLETRIA *:***::**:*:*** .** * *: :*:***:****:*************


[Kytococcus ILRRKAAADKLDIPDDVLHLIASKISSNIRELEGALTRVTAFASLSGSPLgi|478759289|emb|CCH68940.1| ILRKKAIHERLSVPDDVMEFIASRISTNIRELEGALIRVTAFANLNRQPVgi|497462772|ref|WP_009776970.1| ILRKKAAQEKLSVPDDVLEFIASRISTNIRELEGALIRVTAFASLNRQPVgi|497833122|ref|WP_010147278.1| ILRKKAAQEGMQLPDEVLEHIASRITTNIRELEGALIRVTAFASLSSQPAgi|503647989|ref|WP_013882065.1| ILRKKAGGDNMQAPPDVLEYIASKISTNIRELEGALIRVTAFASLNRQQVgi|551300082|ref|WP_022920049.1| ILKKKAAQEGMQLPDEVLELIGSKISTNIRELEGALIRVTAFASLSSTPPgi|656266264|ref|WP_029212190.1| ILRKKAVQERMTAPDDVLEFIASKISTNIRELEGALIRVTAFASLNHQGVgi|665501165|emb|CCH80159.1| ILRKKAIQERLSVPDDVLEFIASRISTNIRELEGALIRVTAFASLNRQPVgi|737975618|ref|WP_035938084.1| ILRKKAAQEKLSVPDDVLEFIASRISTNIRELEGALIRVTAFASLNRQPVgi|750471801|ref|WP_040753674.1| ILRKKAIHERLSVPDDVMEFIASRISTNIRELEGALIRVTAFANLNRQPV **::** : : * :*:. *.*:*::********* ******.*.

[Kytococcus DEYLARTVLKDVMPGGDSGQITPTMILEETAGYFVISVEEIQGASRSRNLgi|478759289|emb|CCH68940.1| DLALAEIVLRDLIPTE-GGEITSATIMAQTAAYFGLTLEDLRGSSRSRVLgi|497462772|ref|WP_009776970.1| DISLAEIVLKDLIPHDSANQITSATIMAQTAAYFGLTLEDLQGQSRSRVLgi|497833122|ref|WP_010147278.1| DADLAAHVLKDIVPGSDTAQITVSTIIREVSEYFQISIDELCGTSRSRTLgi|503647989|ref|WP_013882065.1| DLSLAEIVLKDLITDDQTTEITATQVIGQTAAYFGLSIEDLCGSSRSRVLgi|551300082|ref|WP_022920049.1| DAALASHVLKDIIPNSESAAITVPTIMAEVADYFQISNDDLCGTSRSRTLgi|656266264|ref|WP_029212190.1| DMTLAEVVLKDLIPADQTNQITPATIMAQTASYFGLTVDDLCGTSRSRVLgi|665501165|emb|CCH80159.1| DMSLAEIVLKDLIPSDGANQITSATIMAQTATYFGLTVEDLQGASRSRVLgi|737975618|ref|WP_035938084.1| DISLAEIVLKDLIPHDSSSQITSATIMAQTAAYFGLTLEDLQGQSRSRVLgi|750471801|ref|WP_040753674.1| DLALAEIVLRDLIPTE-GGEITSATIMAQTAAYFGLTLEDLRGSSRSRVL * ** **:*::. ** . :: :.: ** :: ::: * **** *

[Kytococcus TRARQIAMYLCRELTDLSLPKIGKEFGGRDHTTVMHAERKIKQLLGEDRRgi|478759289|emb|CCH68940.1| VNARQIAMYLCRELTSMSLPEIGKEFN-KDHTTVMHANKKIGQLMAERRAgi|497462772|ref|WP_009776970.1| VTARQIAMYLCRELTDLSLPKIGQQFGGRDHTTVMHADKKIRQLMAERRAgi|497833122|ref|WP_010147278.1| VNARQIAMYLCRELTDLSLPKIGQEFGGRDHTTVMHAERKIRAQIGERRAgi|503647989|ref|WP_013882065.1| VTARQIAMYLCRELTDLSLPKIGQAFGGRDHTTVMHANRKIRELMAERRSgi|551300082|ref|WP_022920049.1| VNARQIAMYLCRELTDLSLPKIGQEFGGRDHTTVMHAERKIRQLIGERRAgi|656266264|ref|WP_029212190.1| VTARQIAMYLCRELTDLSLPKIGQQFGGRDHTTVMHADRKIRELMSERRAgi|665501165|emb|CCH80159.1| VTARQIAMYLCRELTDLSLPKIGQQFGGRDHTTVMHADKKIRQLMAERRAgi|737975618|ref|WP_035938084.1| VTARQIAMYLCRELTDLSLPKIGQQFGGRDHTTVMHADKKIRQLMAERRAgi|750471801|ref|WP_040753674.1| VNARQIAMYLCRELTSMSLPEIGKEFN-KDHTTVMHANKKIGQLMAERRA . *************.:***:**: *. :********::** :.* *

[Kytococcus VYDEVSELTSIIRKKAARGRgi|478759289|emb|CCH68940.1| IYNNVTELTGRIKQQS---Rgi|497462772|ref|WP_009776970.1| IYNQVTELTNRIKQQS---Rgi|497833122|ref|WP_010147278.1| LYDQIAELTGTIRRAS--QRgi|503647989|ref|WP_013882065.1| IYNQVTELTNRIKQQS--RGgi|551300082|ref|WP_022920049.1| LYDQITELTGIIRKAS--ARgi|656266264|ref|WP_029212190.1| IYNQVTELTNRIKSNP---Sgi|665501165|emb|CCH80159.1| IYNQVTELTNRIKQQS---Rgi|737975618|ref|WP_035938084.1| IYNQVTELTNRIKQQS---Rgi|750471801|ref|WP_040753674.1| IYNNVTELTGRIKQQS---R :*::::***. *: .

WebLogo

go to WebLogo at http://weblogo.berkeley.edu

Sequence Logo


Comments/observationsThe N-terminal end of this protein is indicated to be reasonably well conserved. There is a gap from positions 128 to 164 in the alignment showingthat gaps were added in this region of the alignment. The C-terminal end of the protein is highly conserved showing several regions with hydrophobicamino acids.

[-] Cellular Localization Data

Module Instructions

Gram Stain

go to NCBI Pubmed at http://www.ncbi.nlm.nih.gov/pubmed

Gram stain of the microbeGram Positive

TMHMM

go to TMHMM at http://www.cbs.dtu.dk/services/TMHMM

Number of predicted transmembrane helices0

Transmembrane topology graph


Comments/observationsNo transmembrane helicies were predicted by TMHMM, suggesting that Ksed_00010 does not reside within the cell membrane.

SignalP

go to SignalP at http://www.cbs.dtu.dk/services/SignalP

Signal peptide probabilityNo

0.131

Most likely cleavage site (between position # and #)N/A - no signal peptide is predicted, thus there is no predicted cleavage site.

Signal peptide graph


LipoP

Go to LipoP at http://www.cbs.dtu.dk/services/LipoP/

Best Prediction (options = cytoplasm, signal peptidase I, signal peptidases II)This was not done for Kytococcus since it only applies to Gram negative bacteria and Kytococcus is Gram positive.

Cleavage site, if predicted, after AA #

PSORT-B

go to PSORT-B at http://www.psort.org/psortb

Cytoplasmic score9.97

CytoplasmicMembrane score


0.00

Cellwall score

0.01

Periplasmic scoreN/A

OuterMembrane scoreN/A

Extracellular score0.02

PSORT-B final prediction

Phobius

go to Phobius at http://phobius.sbc.su.se

Phobius probability graph

The Phobius tool predicts that there is neither a signal peptide nor transmembrane helicies found in the amino acid sequence of Ksed_00010. Thestatement that amino acids 1-506 are "non cytoplasmic" in the Phobius probablilty graph is meaningless in predicting location.


Hypothesis

Based on the results of these tools, where do you expect to find this protein?TMHMM indicates that there are no transmembrane helices, Signal IP revelas low probability for signal peptide, pSORTB predicts Ksed_00010 to bea cytoplasmic protein . Phobius coroborates negative results for TMHs and Signal peptide. Taking all of these results into account, the final predictionfor localization is that Ksed_00010 is a cytoplasmic protein.

[-] Alternative Open Reading Frame

Module Instructions

DNA Coordinates

login to IMG/EDU and find the gene page for this gene

Proposed DNA coordinates (if different from those predicted by IMG)..


Explanation of choice

There is no shine dalgarno sequence upstream of the predicted start codon for Ksed_00010. No alternative start codons with a better start codonwere seen when 99 bases of upstream sequence was added, but a start codon with a shine-dalgarno sequence was found downstream of the startcodon called by the computer. This was tested as a potential alternative start codon (see image below).

The sequence tested was as follows:

>Ksed_00010_amino acid seq - downstream start codonMSQTPDDHATAIWQEAMVHLQGAGLAPRDIGVLRLATLVGLLEGTALLAVKYDHVKDAVEGHLREDVSTALAEVLDRDIRLAVSVDPDAVSAAQEEAAPPAPSPADEDDPATGEGPLSTAVDGAVEKHEGSSPARAGESVAPATTASLTATNSSPGVERDYSALNHKYTFDTFVLGSSNRFAHAAATAVAEAPARAYNPLFIYGGSGLGKTHLLHAIGHYARTLDSSVRVKYVNSEEFTNQFINAVSAGQANAFQRQYRDVDVLLIDDIQFLQGKEQTMEEFFHTFNTLHNSEKQIVITSDQPPKKLSGFAERMRSRFEWGLLTDVQPPDLETRIAILRRKAAADKLDIPDDVLHLIASKISSNIRELEGALTRVTAFASLSGSPLDEYLARTVLKDVMPGGDSGQITPTMILEETAGYFVISVEEIQGASRSRNLTRARQIAMYLCRELTDLSLPKIGKEFGGRDHTTVMHAERKIKQLLGEDRRVYDEVSELTSIIRKKAARGR

The BLAST scores for the sequence starting with the downstream start codon was less than that observed when the sequence beginning with the computer called start codon was used in either Swiss-Prot or nr databases. Therefore is no evidence to suggest the computer called start codon is incorrect.


[-] Structure-based Evidence

Module Instructions

TIGRFAM

go to TIGRFAM at http://tigrblast.tigr.org/web-hmm

TIGRFAM numberFirst Hit: TIGR00362

Second Hit: TIGR03420

TIGRFAM name

First Hit: DnaA: chromosomal replication initiator protein DnaA

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

Second Hit: DnaA_homol_Hda: DnaA regulatory inactivator Hda

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

Score

First Hit: 740.9 Second Hit: 13.9

E-value

First Hit: 3.8e-220

Second Hit: 1.2e-13

Pfam

go to Pfam at http://pfam.sanger.ac.uk/search

Pfam number (PF#####) for top hit

PF00308


Pfam name

Bac_DnaA

The following was copied from the wiki link for PF00308. "DnaA is a protein that activates initiation of DNA replication in bacteria.[1] It is areplication initiation factor which promotes the unwinding of DNA at oriC.[1] The onset of the initiation phase of DNA replication is determined by theconcentration of DnaA.[1] DnaA accumulates during growth and then triggers the initiation of replication.[1]Replication begins with active DnaA bindingto 9-mer (9-bp) repeats upstream of oriC.[1] Binding of DnaA leads to strand separation at the 13-mer repeats.[1] This binding causes the DNA to loopin preparation for melting open by the helicase DnaB.[1]"

Clan name

P-loop_NTPase

P-loop containing nucleoside triphosphate hydrolase superfamilyAAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].

This clan contains 198 families and the total number of domains in the clan is 5072865. The clan was built by DJ Studholme.

Clan number (CL####)

CL0023

Score329.1

E-value1.3e-98

Pairwise alignment


HMM logo

Key functional/structural residues (e.g. I2, W7, F13)

There are a number of amino acicds that are predominant in the model HMM as indicated by the large wide letters atvarious postions in the logo ( L1, F7, F10, P36 etc). Comparing the pairwise alignment to the HMM logo, one call seethat L1, F7 and F10 (among many others) are exact matches of the Ksed_00010 amino acid sequence and the majoramino acid found at the same position in the HMM logo.appears to be significant variablity among other proteinsused to create this model HMM as indicated by the large number of smaller letters under the predominant aminoacids at those positions.

Pfam number (PF#####) for second hit

PF08299

Pfam name

Bac_DnaA_C

The following was copied from the wiki link for PF08299.

"The active form DnaA is bound to ATP.[1] Immediately after a cell has divided, the level of active DnaA within the cell is low.[1] Although the activeform of DnaA requires ATP, the formation of the oriC/DnaA complex and subsequent DNA unwinding does not require ATP hydrolysis.[2]

The oriC site in E. coli has three AT rich 13 base pair regions (DUEs) followed by four 9 bp regions with the sequence TTAT(C or A)CA(C or A)A.Around 10 DnaA molecules bind to the 9 bp regions, which wrap around the proteins causing the DNA at the AT-rich region to unwind. There are 8DnaA binding sites within oriC, to which DnaA binds with differential affinity. When DNA replication is about to commence, DnaA occupies all of thehigh and low affinity binding sites. The denatured AT-rich region allows for the recruitment of DnaB (helicase), which complexes with DnaC (helicaseloader). DnaC helps the helicase to bind to and to properly accommodate the ssDNA at the 13 bp region; this is accomplished by ATP hydrolysiswhich DnaC is released. Single-strand binding proteins (SSBs) stabilize the single DNA strands in order to maintain the replication bubble. DnaB5'â†’3' helicase, so it travels on the lagging strand. It associates with DnaG (a primase) to form the only primer for the leading strand and to add primers on the lagging strand. The interaction between DnaG and DnaB is necessary to control the longitude of Okazaki fragments on the laggingstrand. DNA polymerase III is then able to start DNA replication.

DnaA contains two conserved regions: the first is located in the central part of the protein and corresponds to the ATP-binding domain, the second is


located in the C-terminal half and is involved in DNA-binding.[4]"

Clan name

HTH

Helix-turn-helix clan This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif.

This clan contains 217 families and the total number of domains in the clan is 4270183. The clan was built by A Bateman.

Clan number (CL####)

CL0123

Score

101.8

E-value

1.4e-29

Pairwise alignment

HMM logo


Key functional/structural residues (e.g. I2, W7, F13)I4, V8, R24, R32, I50, G51, T61 and V62 are all exact matches for the HTH domain in Ksed_00010 and the model HMM

PDB

go to PDB at http://www.rcsb.org/pdb/home/home.do

PDB code2Z4R

PDB nameCrystal structure of domain III from the Thermotoga maritima replication initiation protein DnaA

Alignment length346

E-value9.20639E-59

Pairwise alignment


[-] Enzymatic Function

Module Instructions

KEGG


go to KEGG at http://www.genome.jp/kegg/pathway.html

KEGG pathway ID

ko02020 Two-component system

The following was obtained from a PubMedSearch:

Annu Rev Biochem. 2000;69:183-215.

Two-component signaltransduction.Stock AM 1, Robinson VL, Goudreau PN.

Author information

Abstract

Most prokaryotic signal-transduction systems and a few eukaryoticpathways use phosphotransfer schemes involving two conservedcomponents, a histidine protein kinase and a response regulatorprotein. The histidine protein kinase, which is regulated byenvironmental stimuli, autophosphorylates at a histidine residue,creating a high-energy phosphoryl group that is subsequentlytransferred to an aspartate residue in the response regulator protein.Phosphorylation induces a conformational change in the regulatorydomain that results in activation of an associated domain that effectsthe response. The basic scheme is highly adaptable, and numerousvariations have provided optimization within specific signaling systems.The domains of two-component proteins are modular and can beintegrated into proteins and pathways in a variety of ways, but the corestructures and activities are maintained. Thus detailed analyses of arelatively small number of representative proteins provide a foundationfor understanding this large family of signaling proteins.

Pathway map

Below is a portion of the general two component map that shows the location of DnaA


Below is the same section of the two component system, but with the genes called in Kytococcus highlighted in green. DnaA has been called by thecomputer. Clicking on the DnaA hyperlink confirmst that DnaA in Kytococcus is, in fact, Ksed_00010


MetaCyc

go to MetaCyc at http://metacyc.org

Pathway mapNot applicable: Ksed-00010 is not an enzyme and therefore not found in Metacyc

E.C. Number

go to ExPASy ENZYME at http://www.expasy.ch/enzyme/enzyme-search-ec.html

EC NumberNot applicable: Ksed-00010 is not an enzyme and therefore does not have an E.C. number or name

EC NameN/A

[-] Duplication and Degradation

Module Instructions

DNA Coordinates

Paralog gene product nameNo significant paralog hits were found.

Percent identity

Alignment length

E-value


Pairwise alignment

Pseudogene

Use the instructions provided by your professor

Is this a pseudogene?By the three criteria used in the project manual there no evidence that the Ksed_00010 is a pseudogene.

[-] Horizontal Gene Transfer

Module Instructions

Phylogenetic Tree

go to Phylogeny.fr at http://www.phylogeny.fr

Phylogenetic tree

Sequences used to contruct the tree:

>Kytococcus sedentarius DSM 20547] MSQTPDDHATAIWQEAMVHLQGAGLAPRDIGVLRLATLVGLLEGTALLAVKYDHVKDAVEGHLREDVSTALAEVLDRDIR LAVSVDPDAVSAAQEEAAPPAPSPADEDDPATGEGPLSTAVDGAVEKHEGSSPARAGESVAPATTASLTATNSSPGVERD YSALNHKYTFDTFVLGSSNRFAHAAATAVAEAPARAYNPLFIYGGSGLGKTHLLHAIGHYARTLDSSVRVKYVNSEEFTN QFINAVSAGQANAFQRQYRDVDVLLIDDIQFLQGKEQTMEEFFHTFNTLHNSEKQIVITSDQPPKKLSGFAERMRSRFEW GLLTDVQPPDLETRIAILRRKAAADKLDIPDDVLHLIASKISSNIRELEGALTRVTAFASLSGSPLDEYLARTVLKDVMP GGDSGQITPTMILEETAGYFVISVEEIQGASRSRNLTRARQIAMYLCRELTDLSLPKIGKEFGGRDHTTVMHAERKIKQL LGEDRRVYDEVSELTSIIRKKAARGR >Ornithinimicrobium pekingense] MTSQSPAESAEVWQRVVSQLESQGVTARDRAFLRLTQLVGLLDTTALLAVPYQHTKETLETTLRQPIVDALAGELGHDVR LAITVDEDLRRQVEDEGDPAPGPAVTEQVPSDPDRTPYRSNGAGPGEPRSDGHRTPSGAVQTASAEDARLNPKYTFDTFV SGSSNRFAHAASLAVAESPARAYNPLFIYGESGLGKTHLLHAIGHYARSLYPGVRVRYVNSEEFTNDFINSIRDDKAGAF QRRYRNVDFLLVDDIQFLQGKEQTVEEFFHTFNTLHNSEKQVVITSDQPPKRLSGFAERMRSRFEWGLLTDVQPPDLETR IAILKKKAAQEGMQLPDEVLELIGSKISTNIRELEGALIRVTAFASLSSTPPDAALASHVLKDIIPNSESAAITVPTIMA EVADYFQISNDDLCGTSRSRTLVNARQIAMYLCRELTDLSLPKIGQEFGGRDHTTVMHAERKIRQLIGERRALYDQITEL TGIIRKASAR >Serinicoccus profundi] MSQPSTDSGDTWRRVVSELEDKGLGAREKAFLRLTTMVGVLDSTVLLAVPYPHTKEMLETTLRQPIVDLLSRELDREVRL AITVDDDVRQRVEDEADDEADEDAQTRESLTRPASQPSSSAGAGVPGPSGNGIPRPATPAGPAVTGAADEARLNPKYSFD TFVSGPSNRFAHAASLAVAESPARAYNPLFIYGESGLGKTHLLHAIGHYARKLYPGVRVRYVNSEEFTNDFINSIRDDKA GAFQRRYRNVDFLLVDDIQFLQGKEQTVEEFFHTFNTLHNSEKQVVITSDQPPKRLSGFAERMRSRFEWGLLTDVQPPDL ETRIAILRKKAAQEGMQLPDEVLEHIASRITTNIRELEGALIRVTAFASLSSQPADADLAAHVLKDIVPGSDTAQITVST IIREVSEYFQISIDELCGTSRSRTLVNARQIAMYLCRELTDLSLPKIGQEFGGRDHTTVMHAERKIRAQIGERRALYDQI AELTGTIRRASQR >Knoellia aerolata] >gi|700180054|gb|KGN40755.1| chromosomal replication initiation protein [Knoellia aerolata DSM 18566] MDQIWRTTLDALDSDGIPVQQRAFLSLARLVGLLDETALIAVPNDFTKDIVETRLRDRVTETLSSQLGHTVRLAVTVDSS LGDVPVLDPPADAPSGSTTTEPRPAAGTEGDGRHAERRAELDGIALVEDDDDGDSSRTGRSVAHTRSPGALRPRPGVTVP EQVELTRLNPKYTFDTFVIGASNRFANAAALAVAETPAKAYNPLFIYGESGLGKTHLLHAIGHYARNLFPHVKVRYVNSE EFTNDFINSIRDDKAANFQRRYRDVDVLLIDDIQFLQGKVQTQEEFFHTFNTLHNANKQVVITSDLPPKLLSGFEERMRS


RFEWGLMTDVQPPDLETRIAILRKKAAQEKLSVPDDVLEFIASRISTNIRELEGALIRVTAFASLNRQPVDISLAEIVLK DLIPHDSSSQITSATIMAQTAAYFGLTLEDLQGQSRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGGRDHTTVMHADKK IRQLMAERRAIYNQVTELTNRIKQQSR >Luteipulveratus sp. C296001] MSEDKPDLAHVWHSTVMALEETGIAARDRAFLRLTRLVGLVDQTALLAVPFDHTKDILETSLREPVSSALSRLLDRDVRL AVTVDPQLQQTVSASAEAKDAGIGEDEVAETDAEEAGTPAPALIRPVRASNRPPVEPVTDARLNPKYTFDTFVIGASNRF AHAAAFAVAEAPAKSYNPLFVYGDSGLGKTHLLHAIGHYVRNLYPSMRVRYVNSEEFTNDFINSIRDDKASSFQKRYRDD VDVLLIDDVQFLQGKDGTQEEFFHTFNALHDSEKQIVLTSDQPPKKLSGFADRMRSRFEWGLQTDVTPPDLETRIAILRK KAIAERMNVPDDVLELIASKFSTNIRELEGALIRVMAFASLSQQPVDQQVAGYVLKDLVPSAGSSQITATLIMTKTAEYF HVSVEELCGSSRSRTLVTARQIAMYLCRELTELSLPKIGQQFGGRDHTTVMHADRKIRQLIGERRPIYDQITELTGQITR AAAG >Janibacter sp. HTCC2649] MDQIWRTTLDALDSDGIPVQQRAFLSLAKLVGLLDETALIAVPNDFTKDIVETRLRDRVTETLSSQLGHDVRLAVTVDHS LADVPVTIPADTTTVDGAGADQVPRTATTIGLEPGPADADGRRAKRRAELDGIALVEDDEGEDDSRNNGAIGRTRSPGAL RPRPGATVPEQVELTRLNPKYTFDTFVIGASNRFANAAALAVAETPAKAYNPLFIYGESGLGKTHLLHAIGHYARNLYPH VKVRYVNSEEFTNDFINSIRDDKAANFQRRYRDVDVLLIDDIQFLQGKVQTQEEFFHTFNTLHNANKQVVITSDLPPKLL SGFEERMRSRFEWGLMTDVQPPDLETRIAILRKKAAQEKLSVPDDVLEFIASRISTNIRELEGALIRVTAFASLNRQPVD ISLAEIVLKDLIPHDSANQITSATIMAQTAAYFGLTLEDLQGQSRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGGRDH TTVMHADKKIRQLMAERRAIYNQVTELTNRIKQQSR >Tetrasphaera japonica T1-X7] MDYSRVWRTALDELDADGLPIQQRAFLSLARFVGLLDDTALIAVPNDYTKEFVETRVRQQLTQTLSNHAGRELRLAVTVD PGLKAADEAEPTLGAPAEAWGPRPRAGIGPVDDEEDHEAQDVIDARGVDTFHIQRPTPGQRPVPELIENTRLNPKYTFDT FVIGASNRFAHAAAVAVAEAPAKAYNPLFVYGDSGLGKTHLLHAIGHYARNLYPTVRVRYVNSEEFTNDFINSIRDDKAA NFQSRYRDVDVLLIDDIQFLQGKVQTQEEFFHTFNTLHNANKQVVITSDVPPKLLSGFEERMRSRFEWGLLTDVQPPDLE TRIAILRKKAIQERLSVPDDVLEFIASRISTNIRELEGALIRVTAFASLNRQPVDMSLAEIVLKDLIPSDGANQITSATI MAQTATYFGLTVEDLQGASRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGGRDHTTVMHADKKIRQLMAERRAIYNQVT ELTNRIKQQSR >Arsenicicoccus bolidensis] MTDAQVDVPRVWRDTLRALESGGISAQHRGFLRLSRLVGLLEGTALIAVPNDYTRDIVEKRIRTELVAALQEQLGRDVRL AVTVDSSLELSEAEDRDDSTQRPGSPGEVPHVVTSSDPVRHDGERGGSDPRSTYGPRLVRDERVPRPVSTDASFGGERPY ADPARHDGGPGHAPGIRPAQDDDADDDRELLAEGDGIREMFRKPFVPEDGRDAKLNPKYTFDTFVIGSSNRFAHAAAIAV AEAPAKAYNPLFIYGGSGLGKTHLLHAIGHYAQQIYPNVRVKYVNSEEFTNDFINSIGANKASDFQRRYRDIDFLLIDDI QFLQGKVQTQEEFFHTFNTLHNANKQVVITSDVAPKLLSGFEERMRSRFEWGLLTDVQPPDLETRIAILRKKAVQERMTA PDDVLEFIASKISTNIRELEGALIRVTAFASLNHQGVDMTLAEVVLKDLIPADQTNQITPATIMAQTASYFGLTVDDLCG TSRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGGRDHTTVMHADRKIRELMSERRAIYNQVTELTNRIKSNPS >Mobilicoccus sp. SIT2] MSGSGEPPTTPAVDDPARIWGATLRALDQAGIPAPQRAFLRQAMLVGVLDTTALIAVPDDFTKEIVESRARDYLVKALTE QVGREVRLAVTVDASLREQIAAAEQPVLEGYADPDSDVAAAEPPAASPTAAAPASPPVEDSPAPVGERRPRPAPTGRREE SSQLNPKYTFDTFVIGASNRFAHAAAVAVAEAPAKAYNPLFVYGDSGLGKTHLLHAIGHYARNLYPHVKVKYVNSEEFTN DFINSIRDDKAAGFQRRYRDMDVLLIDDIQFLQGKMQTQEEFFHTFNTLHNSNKQVVITSDVPPKQLSGFEERMRSRFEW GLLTDVQPPDLETRIAILRKKAVQEHLALPDEVMEFIASRISTNIRELEGALIRVTAFANLNRQPVEMSLAEIVLKDLIP DKESSQITASMIMGQTAAYFGLSIDDLCGSSRSRGLVTARQIAMYLCRELTELSLPKIGQQFGGRDHTTVMHADRKIRQL MAERRSVYNQVTELTTRIRSQAS >Cellvibrio] gilvus ATCC 13127] MAQDEELSRVWGHVVTTLEESPDITQRQLAFVRLAQPLGLLDGTIILAVGNEYTKEYLETKVRAEVTSALGSALGRDGRF AITVDPSLVDDAPPAVRAMTSAPELGVVTDGTDERGAPNRTVPTDADTGRHERSPMLSESAEPTRPVRETASSRRPAAEP ARLNPHYLFETFVIGSSNRFAHAAAVAVAEAPAKAYNPLFIYGDSGLGKTHLLHAIGHYAQNLYPSVRVRYVNSEEFTND FINSISEGKAGAFQRRYREVDVLLIDDIQFLQGKEQTMEEFFHTFNTLHNANKQVVITSDLPPKQLNGFEDRMRSRFEWG LITDVQPPDLETRIAILRKKAGGDNMQAPPDVLEYIASKISTNIRELEGALIRVTAFASLNRQQVDLSLAEIVLKDLITD DQTTEITATQVIGQTAAYFGLSIEDLCGSSRSRVLVTARQIAMYLCRELTDLSLPKIGQAFGGRDHTTVMHANRKIRELM AERRSIYNQVTELTNRIKQQSRG >Promicromonosporaceae bacterium W15] MAEVWSAARIQLENDPDVTPRQRGYVRLVAPLAHIDDTVFLKVSDEPIRSFIETNLRADLVGALAGVLGYEPKLAISVDP DLQIADDDTDPAAPVYARPAPTTATSPAAQRMPTDEPDHGLSNPVGFGATVGLPEAMPAAPGSARAAQHAPRHAEPTAPL GENSRLNPKYLFETFVIGASNRFAHAAAVAVAEAPAKAYNPLFIYGDSGLGKTHLLHAIGHYAQSLYPNVRVRYVNSEEF TNDFINSIGEGKAGAFQRRYRDVDVLLIDDIQFLQGKEQTMEEFFHTFNALHNANKQVVITSDLPPKQLNGFEDRLRSRF EWGLITDVQPPDLETRIAILRKKALQERLDAPDDVLEYIASRISTNIRELEGALIRVTAFANLNRQPVDQSLAEIVLKDL ITDDDAGEITAASVIAQTAAYFGLTIDDLCGSSRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGGRDHTTVMHANRKIS EQMAERRSIYNQVTELTSRIKQQHRG >Nocardioides sp. Iso805N] METPPDNGQHDELGQAWQSVVAELQPHQRAWLTACQPEALHGTTVLVGVPNDFTRNQLEGRLRAELEDALSTRFGQEMRI AAIVKPELEDRPLEATTPAPAISDAPVAPIKPHIDLSTNRFGGSSHNDTPDSGGAAPNFQLPPLRHEAPETERTTSESRL NPKYTFETFVIGSSNRFPHAAAVAVAEAPGRAYNPLLVYGESGLGKTHLLHAIGHYVRSLYNGAKVRYVSSEEFTNEFIN AIRDDRQDRFKRKYRDIDVLLIDDIQFLEGKTQTQEEFFHTFNTLHNANKQIVLTSDRAPKRLEALEDRLRNRFEWGLIT DVQPPDVETRIAILRKKAAMERLKAPADVLEFIATKIQTNIRELEGALIRVTAFANLNRQEVDMTLAEIVLKDLIPEGGE


PEITAGLIIAQTAAYFGLSIDELTGPSRGRHLVMARQIAMYLCRELTDLSLPKIGQQFGGRDHTTVMYAERKINQLLAER RSVFNQVSELTNRVKMQARQA >Arthrobacter globiformis NBRC 12137] MTVDEANHANTVGSSWRRVVTLLEQDDRVSPRQRGFVILAQAQGLIGSTLLVAVPNELTREVLQTQVKDALDDALRNVFS DDIRCAIDVDTDLVPIHEEPEPAVELSLANDPSIEQKPQPMLPSTSHEFGRLNPKYVFDTFVIGSSNRFAHAAAVAVAEA PAKAYNPLFIYGDSGLGKTHLLHAIGHYARRLYSGIRVRYVNSEEFTNDFINSIRDDEGASFKTTYRNVDVLLIDDIQFL AGKDRTLEEFFHTFNSLHNNNKQVVITSDQPPKLLAGFEDRMKSRFEWGLLTDIQPPELETRIAILRKKALSEGLSAPDD ALEYIASKIASNIRELEGALIRVTAFASLNRQPVDVALAEMVLKDLITDDGAQEITSGQILQQTADYFKLSMEELCSKSR TRTLVTARQIAMYLCRELTDMSLPKIGQELGGRDHTTVIHADRKIRELMAERRVIYNQVTELTNRIKQQQRDS

The T-Coffee Alignment:

CLUSTAL W (1.83) multiple sequence alignment

Arsenicicoccus MTDA--------QVDVPRVWRDTLRALES-GGISAQHRGFLRLSRLVGLLArthrobacter MTVDE---AN-HANTVGSSWRRVVTLLEQDDRVSPRQRGFVILAQAQGLICellvibrio] MAQD---------EELSRVWGHVVTTLEESPDITQRQLAFVRLAQPLGLLJanibacter M---------------DQIWRTTLDALDS-DGIPVQQRAFLSLAKLVGLLKnoellia M---------------DQIWRTTLDALDS-DGIPVQQRAFLSLARLVGLLKytococcus MSQTP-------DDHATAIWQEAMVHLQG-AGLAPRDIGVLRLATLVGLLLuteipulveratus MSED--------KPDLAHVWHSTVMALEE-TGIAARDRAFLRLTRLVGLVMobilicoccus MSGSGEPPTTPAVDDPARIWGATLRALDQ-AGIPAPQRAFLRQAMLVGVLNocardioides METPP---DNGQHDELGQAWQSVVAELQ------PHQRAWLTACQPEALHOrnithinimicrobium MTSQS-------PAESAEVWQRVVSQLES-QGVTARDRAFLRLTQLVGLLPromicromonosporaceae M---------------AEVWSAARIQLENDPDVTPRQRGYVRLVAPLAHISerinicoccus MSQP--------STDSGDTWRRVVSELED-KGLGAREKAFLRLTTMVGVLTetrasphaera M-------------DYSRVWRTALDELDA-DGLPIQQRAFLSLARFVGLL * * . *: . . : .

Arsenicicoccus EGTALIAVPNDYTRDIVEKRIRTELVAALQEQLGRDVRLAVTVDSSLELSArthrobacter GSTLLVAVPNELTREVLQTQVKDALDDALRNVFSDDIRCAIDVDTDLVPICellvibrio] DGTIILAVGNEYTKEYLETKVRAEVTSALGSALGRDGRFAITVDPSLVDDJanibacter DETALIAVPNDFTKDIVETRLRDRVTETLSSQLGHDVRLAVTVDHSLADVKnoellia DETALIAVPNDFTKDIVETRLRDRVTETLSSQLGHTVRLAVTVDSSLGDVKytococcus EGTALLAVKYDHVKDAVEGHLREDVSTALAEVLDRDIRLAVSVDPDAVSALuteipulveratus DQTALLAVPFDHTKDILETSLREPVSSALSRLLDRDVRLAVTVDPQLQQTMobilicoccus DTTALIAVPDDFTKEIVESRARDYLVKALTEQVGREVRLAVTVDASLREQNocardioides GTTVLVGVPNDFTRNQLEGRLRAELEDALSTRFGQEMRIAAIVKPELEDROrnithinimicrobium DTTALLAVPYQHTKETLETTLRQPIVDALAGELGHDVRLAITVDEDLRRQPromicromonosporaceae DDTVFLKVSDEPIRSFIETNLRADLVGALAGVLGYEPKLAISVDPDLQIASerinicoccus DSTVLLAVPYPHTKEMLETTLRQPIVDLLSRELDREVRLAITVDDDVRQRTetrasphaera DDTALIAVPNDYTKEFVETRVRQQLTQTLSNHAGRELRLAVTVDPGLKAA * :: * :. :: : : * . : * *.

Arsenicicoccus EAEDR-DDSTQRPG-SPGEVPHVVT--SSDPVRHDGERGGSDPRSTYGPRArthrobacter HEE-P-EPAVE-----------LSL--ANDPS------------------Cellvibrio] ---APPA-VRAM---TS--APELGV--VTDGTDERG--------------Janibacter PVTI-PADTTTVDGAGADQVPRTATTIGLEPGPADA--------------Knoellia PVLDPPADAPS-----------GST--TTEPRPAAG----TE--------Kytococcus AQEEAAPPAPS-----------PAD--EDDPAT--G----E---------Luteipulveratus VSASAE--AKD-----------AGI--GEDEVA-----------------Mobilicoccus IAAAE-QPVL--EG-YADPDSDVAA--AEPPAASP---------------Nocardioides PLEAT-TPAPA-----------IS----DAPV------------------Ornithinimicrobium VEDEGDP-APG-----------PAV--TEQVPS-----------------Promicromonosporaceae DDDTDPA-APV----YA--RPAPTT--ATSPAA-----------------Serinicoccus VEDEADDEADE-----------DAQ--TRESLT-----------------Tetrasphaera DEAEPTLGAPA-----------EA----WGPRPRAG----I---------

Arsenicicoccus LVRDERVPRPVSTDASFGGERPYADPARHDGGPGHAPGIRPAQDDDADDDArthrobacter --------------------------------------------------Cellvibrio] --------------AP-NRTVP-------------------T-DA-DT--Janibacter -------------DGRRAKRRA------------ELDGIALVEDDEGEDDKnoellia ------------GDGRHAERRA------------ELDGIALVEDDDDGDSKytococcus -----------------GPLST---A---------VDG--AVEKHEGSSPLuteipulveratus -----------------ET-------------------------------Mobilicoccus --------------TAAAPASP---P---------------VED------Nocardioides -----------------APIKP---H---------IDL-S-TNRFGGSSHOrnithinimicrobium -----------------DPD---------------------------RTPPromicromonosporaceae ------------------QRMP-------------------T-DEPDHGLSerinicoccus -----------------RPA---------------------------SQPTetrasphaera ---------------------------------------GPVDDEEDHEA

Arsenicicoccus RE-----LLA-------------EGDGIR-EM-FRKPFVPEDGRDAKLNPArthrobacter --------------------------IEQKPQ-P--MLPSTSHEFGRLNPCellvibrio] -----------GRHERSPMLSESAEPTRPVR-ETA-SSRRPAAEPARLNPJanibacter SR---N-NGA---------IGRTRSPGALRPR-PG-ATVPEQVELTRLNPKnoellia SR---T-GRS---------VAHTRSPGALRPR-PG-VTVPEQVELTRLNPKytococcus AR---AGES-----------VAPATT---ASLTATNSSPGVERDYSALNHLuteipulveratus -D---AEEAG---------TPAP---ALIRPVRASNRPPVEPVTDARLNPMobilicoccus ---------------------SPAPVGERRPR-P--APTGRREESSQLNPNocardioides ND-----TPD---------SGGAAPNFQLPPLRHEAPETERTTSESRLNPOrnithinimicrobium YR---SNGAG---------PGEPRSDGHR---TPSGAVQTASAEDARLNPPromicromonosporaceae SNPVGF-GATVGLPEAMPAAPGSARAAQHAP-RHA-EPTAPLGENSRLNPSerinicoccus SS---SAGAG---------VPGPSGNGIPRPATPAGPAVTGAADEARLNP


Tetrasphaera QD-----VID---------ARGVDTFHIQRPT-PGQRPVPELIENTRLNP **

Arsenicicoccus KYTFDTFVIGSSNRFAHAAAIAVAEAPAKAYNPLFIYGGSGLGKTHLLHAArthrobacter KYVFDTFVIGSSNRFAHAAAVAVAEAPAKAYNPLFIYGDSGLGKTHLLHACellvibrio] HYLFETFVIGSSNRFAHAAAVAVAEAPAKAYNPLFIYGDSGLGKTHLLHAJanibacter KYTFDTFVIGASNRFANAAALAVAETPAKAYNPLFIYGESGLGKTHLLHAKnoellia KYTFDTFVIGASNRFANAAALAVAETPAKAYNPLFIYGESGLGKTHLLHAKytococcus KYTFDTFVLGSSNRFAHAAATAVAEAPARAYNPLFIYGGSGLGKTHLLHALuteipulveratus KYTFDTFVIGASNRFAHAAAFAVAEAPAKSYNPLFVYGDSGLGKTHLLHAMobilicoccus KYTFDTFVIGASNRFAHAAAVAVAEAPAKAYNPLFVYGDSGLGKTHLLHANocardioides KYTFETFVIGSSNRFPHAAAVAVAEAPGRAYNPLLVYGESGLGKTHLLHAOrnithinimicrobium KYTFDTFVSGSSNRFAHAASLAVAESPARAYNPLFIYGESGLGKTHLLHAPromicromonosporaceae KYLFETFVIGASNRFAHAAAVAVAEAPAKAYNPLFIYGDSGLGKTHLLHASerinicoccus KYSFDTFVSGPSNRFAHAASLAVAESPARAYNPLFIYGESGLGKTHLLHATetrasphaera KYTFDTFVIGASNRFAHAAAVAVAEAPAKAYNPLFVYGDSGLGKTHLLHA :* *:*** *.****.:**: ****:*.::****::** ***********

Arsenicicoccus IGHYAQQIYPNVRVKYVNSEEFTNDFINSIGANKASDFQRRYRD-IDFLLArthrobacter IGHYARRLYSGIRVRYVNSEEFTNDFINSIRDDEGASFKTTYRN-VDVLLCellvibrio] IGHYAQNLYPSVRVRYVNSEEFTNDFINSISEGKAGAFQRRYRE-VDVLLJanibacter IGHYARNLYPHVKVRYVNSEEFTNDFINSIRDDKAANFQRRYRD-VDVLLKnoellia IGHYARNLFPHVKVRYVNSEEFTNDFINSIRDDKAANFQRRYRD-VDVLLKytococcus IGHYARTLDSSVRVKYVNSEEFTNQFINAVSAGQANAFQRQYRD-VDVLLLuteipulveratus IGHYVRNLYPSMRVRYVNSEEFTNDFINSIRDDKASSFQKRYRDDVDVLLMobilicoccus IGHYARNLYPHVKVKYVNSEEFTNDFINSIRDDKAAGFQRRYRD-MDVLLNocardioides IGHYVRSLYNGAKVRYVSSEEFTNEFINAIRDDRQDRFKRKYRD-IDVLLOrnithinimicrobium IGHYARSLYPGVRVRYVNSEEFTNDFINSIRDDKAGAFQRRYRN-VDFLLPromicromonosporaceae IGHYAQSLYPNVRVRYVNSEEFTNDFINSIGEGKAGAFQRRYRD-VDVLLSerinicoccus IGHYARKLYPGVRVRYVNSEEFTNDFINSIRDDKAGAFQRRYRN-VDFLLTetrasphaera IGHYARNLYPTVRVRYVNSEEFTNDFINSIRDDKAANFQSRYRD-VDVLL ****.: : :*:**.******:***:: .. *: **: :*.**

Arsenicicoccus IDDIQFLQGKVQTQEEFFHTFNTLHNANKQVVITSDVAPKLLSGFEERMRArthrobacter IDDIQFLAGKDRTLEEFFHTFNSLHNNNKQVVITSDQPPKLLAGFEDRMKCellvibrio] IDDIQFLQGKEQTMEEFFHTFNTLHNANKQVVITSDLPPKQLNGFEDRMRJanibacter IDDIQFLQGKVQTQEEFFHTFNTLHNANKQVVITSDLPPKLLSGFEERMRKnoellia IDDIQFLQGKVQTQEEFFHTFNTLHNANKQVVITSDLPPKLLSGFEERMRKytococcus IDDIQFLQGKEQTMEEFFHTFNTLHNSEKQIVITSDQPPKKLSGFAERMRLuteipulveratus IDDVQFLQGKDGTQEEFFHTFNALHDSEKQIVLTSDQPPKKLSGFADRMRMobilicoccus IDDIQFLQGKMQTQEEFFHTFNTLHNSNKQVVITSDVPPKQLSGFEERMRNocardioides IDDIQFLEGKTQTQEEFFHTFNTLHNANKQIVLTSDRAPKRLEALEDRLROrnithinimicrobium VDDIQFLQGKEQTVEEFFHTFNTLHNSEKQVVITSDQPPKRLSGFAERMRPromicromonosporaceae IDDIQFLQGKEQTMEEFFHTFNALHNANKQVVITSDLPPKQLNGFEDRLRSerinicoccus VDDIQFLQGKEQTVEEFFHTFNTLHNSEKQVVITSDQPPKRLSGFAERMRTetrasphaera IDDIQFLQGKVQTQEEFFHTFNTLHNANKQVVITSDVPPKLLSGFEERMR :**:*** ** * ********:**: :**:*:*** .** * .: :*::

Arsenicicoccus SRFEWGLLTDVQPPDLETRIAILRKKAVQERMTAPDDVLEFIASKISTNIArthrobacter SRFEWGLLTDIQPPELETRIAILRKKALSEGLSAPDDALEYIASKIASNICellvibrio] SRFEWGLITDVQPPDLETRIAILRKKAGGDNMQAPPDVLEYIASKISTNIJanibacter SRFEWGLMTDVQPPDLETRIAILRKKAAQEKLSVPDDVLEFIASRISTNIKnoellia SRFEWGLMTDVQPPDLETRIAILRKKAAQEKLSVPDDVLEFIASRISTNIKytococcus SRFEWGLLTDVQPPDLETRIAILRRKAAADKLDIPDDVLHLIASKISSNILuteipulveratus SRFEWGLQTDVTPPDLETRIAILRKKAIAERMNVPDDVLELIASKFSTNIMobilicoccus SRFEWGLLTDVQPPDLETRIAILRKKAVQEHLALPDEVMEFIASRISTNINocardioides NRFEWGLITDVQPPDVETRIAILRKKAAMERLKAPADVLEFIATKIQTNIOrnithinimicrobium SRFEWGLLTDVQPPDLETRIAILKKKAAQEGMQLPDEVLELIGSKISTNIPromicromonosporaceae SRFEWGLITDVQPPDLETRIAILRKKALQERLDAPDDVLEYIASRISTNISerinicoccus SRFEWGLLTDVQPPDLETRIAILRKKAAQEGMQLPDEVLEHIASRITTNITetrasphaera SRFEWGLLTDVQPPDLETRIAILRKKAIQERLSVPDDVLEFIASRISTNI .****** **: **::*******::** : : * :.:. *.::: :**

Arsenicicoccus RELEGALIRVTAFASLNHQGVDMTLAEVVLKDLIPADQTNQITPATIMAQArthrobacter RELEGALIRVTAFASLNRQPVDVALAEMVLKDLITDDGAQEITSGQILQQCellvibrio] RELEGALIRVTAFASLNRQQVDLSLAEIVLKDLITDDQTTEITATQVIGQJanibacter RELEGALIRVTAFASLNRQPVDISLAEIVLKDLIPHDSANQITSATIMAQKnoellia RELEGALIRVTAFASLNRQPVDISLAEIVLKDLIPHDSSSQITSATIMAQKytococcus RELEGALTRVTAFASLSGSPLDEYLARTVLKDVMPGGDSGQITPTMILEELuteipulveratus RELEGALIRVMAFASLSQQPVDQQVAGYVLKDLVPSAGSSQITATLIMTKMobilicoccus RELEGALIRVTAFANLNRQPVEMSLAEIVLKDLIPDKESSQITASMIMGQNocardioides RELEGALIRVTAFANLNRQEVDMTLAEIVLKDLIPEGGEPEITAGLIIAQOrnithinimicrobium RELEGALIRVTAFASLSSTPPDAALASHVLKDIIPNSESAAITVPTIMAEPromicromonosporaceae RELEGALIRVTAFANLNRQPVDQSLAEIVLKDLITDDDAGEITAASVIAQSerinicoccus RELEGALIRVTAFASLSSQPADADLAAHVLKDIVPGSDTAQITVSTIIRETetrasphaera RELEGALIRVTAFASLNRQPVDMSLAEIVLKDLIPSDGANQITSATIMAQ ******* ** ***.*. : :* ****::. ** :: :

Arsenicicoccus TASYFGLTVDDLCGTSRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGGRArthrobacter TADYFKLSMEELCSKSRTRTLVTARQIAMYLCRELTDMSLPKIGQELGGRCellvibrio] TAAYFGLSIEDLCGSSRSRVLVTARQIAMYLCRELTDLSLPKIGQAFGGRJanibacter TAAYFGLTLEDLQGQSRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGGRKnoellia TAAYFGLTLEDLQGQSRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGGRKytococcus TAGYFVISVEEIQGASRSRNLTRARQIAMYLCRELTDLSLPKIGKEFGGRLuteipulveratus TAEYFHVSVEELCGSSRSRTLVTARQIAMYLCRELTELSLPKIGQQFGGRMobilicoccus TAAYFGLSIDDLCGSSRSRGLVTARQIAMYLCRELTELSLPKIGQQFGGRNocardioides TAAYFGLSIDELTGPSRGRHLVMARQIAMYLCRELTDLSLPKIGQQFGGROrnithinimicrobium VADYFQISNDDLCGTSRSRTLVNARQIAMYLCRELTDLSLPKIGQEFGGRPromicromonosporaceae TAAYFGLTIDDLCGSSRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGGRSerinicoccus VSEYFQISIDELCGTSRSRTLVNARQIAMYLCRELTDLSLPKIGQEFGGRTetrasphaera TATYFGLTVEDLQGASRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGGR .: ** :: ::: . ** * *. *************::******: :***

Arsenicicoccus DHTTVMHADRKIRELMSERRAIYNQVTELTNRIKSNP---S


Arthrobacter DHTTVIHADRKIRELMAERRVIYNQVTELTNRIKQQQ-RDSCellvibrio] DHTTVMHANRKIRELMAERRSIYNQVTELTNRIKQQS--RGJanibacter DHTTVMHADKKIRQLMAERRAIYNQVTELTNRIKQQS---RKnoellia DHTTVMHADKKIRQLMAERRAIYNQVTELTNRIKQQS---RKytococcus DHTTVMHAERKIKQLLGEDRRVYDEVSELTSIIRKKAARGRLuteipulveratus DHTTVMHADRKIRQLIGERRPIYDQITELTGQITRAA--AGMobilicoccus DHTTVMHADRKIRQLMAERRSVYNQVTELTTRIRSQA---SNocardioides DHTTVMYAERKINQLLAERRSVFNQVSELTNRVKMQA-RQAOrnithinimicrobium DHTTVMHAERKIRQLIGERRALYDQITELTGIIRKAS--ARPromicromonosporaceae DHTTVMHANRKISEQMAERRSIYNQVTELTSRIKQQH--RGSerinicoccus DHTTVMHAERKIRAQIGERRALYDQIAELTGTIRRAS--QRTetrasphaera DHTTVMHADKKIRQLMAERRAIYNQVTELTNRIKQQS---R *****::*::** :.* * ::::::*** :

The Cladogram from T-COFFEE:

The Tree File in Newick Format from PhyML at Phylogeny.fr:

((((((Arsenicicoccus:0.363182,(Tetrasphaera:0.164269,(Knoellia:0.031567,Janibacter:0.053012)1.000000:0.157616)0.944000:0.077073)0.903000:0.074505,Mobilicoccus:0.285031)0.880000:0.062980,(Nocardioides:0.686282,((Promicromonosporaceae:0.278553,Cellvibrio:0.267551)0.969000:0.118671,Arthrobacter:0.550811)0.522000:0.056440)0.926000:0.080531)0.998000:0.210238,Luteipulveratus:0.307826)0.864000:0.084907,Kytococcus:0.618026)0.995000:0.205025,Serinicoccus:0.196835,Ornithinimicrobium:0.129401);

The phylogram from TreeDyn:


The radial version of the phlogenetic tree from TreeDyn:


Interpretation of phylogenetic treeLooking at the names of the different genera on the phylogenetic trees, it is clear that the three that are in a clade with Kytococcus are related torelated down to the same order or family. Since few closer relatives of Kytococcus have had their genomes sequenced, there is no evidencesuggesting that horizontal gene transfer of Ksed_00010 has occured. In fact, just about all of the genera in the tree have a realtionship to the sameorder, with the notable exception of Cellvibrio. Given that Ksed_00010 is an enzyme of DNA metabolism and the ecvalues and scores of all 100 hitsin the nr database are highly signficant, DnaA is likely very highly coserved across microbial species, and it would be hard to find evidence ofhorizontal transfer as a result.

Ornithinimicrobium - same order Serinicoccus - same order Luteipulveratus - same family


Cellvibrio - different phylum Promicromonosporaceae - same order Arsenicicoccus - same order Mobilicoccus - same order

Gene Context

login to IMG/ER and find the gene page for this gene

Ortholog Neighborhood Region of organism and examples of similarities or differences

Comment on the ortholog neighborhood regionsThe neighborhoods in the image above have similarity in the region immediately downstream of and including Ksed_00010 and are all as closelyrelated to Kytococcus sedentarius as we can expect to find. Therefore there is no evidence of horizontal gene transfer from th ortholog neighborhoodregions approach.

Chromosome Viewer GC Heat Map

go to the IMG Gene Detail page

Characteristic GC% of the genome72%


Average GC% of the geneKsed_00010 has a GC content of 68%. The average GC content of the genome of Kytococcus sedentarius is 72%. Therefore the GC content ofKsed_00010 is similar to that of the genome as a whole, and there is no evidence of horizontal gene transfer using the %GC approach.

[-] RNA

Module Instructions

Rfam

go to Rfam at http://rfam.sanger.ac.uk

Rfam number (RF#####)Not applicable. Ksed_00010 is not an RNA gene

Rfam name

Score

E-value

Pairwise Alignment

[-] Proposed Annotation

Proposed Annotation

Enter the proposed annotation for the gene

chromosomal replication initiator protein DnaA

The top two BLAST hits in both the nr and Swiss-prot databases have name of chromosomal replication initiatorprotein DnaA, the top COG hit is DnaA: Chromosomal replication initiation ATPase DnaA [Replication,recombination and repair]; the top TIGRFAM hit is DnaA: chromosomal replication initiator protein DnaA and the topPfam hit is Bac_DnaA. All of these findings support the annotation of Ksed_00010 as chromosomal replicationinitiator protein DnaA as indicated by the computer annotation.


Return to Gene Page


geni-act - ubwp.buffalo.eduubwp.buffalo.edu/wnygirahcp/wp-content/uploads/sites/25/2017/11/... ·...

Documents

Transcript of geni-act - ubwp.buffalo.eduubwp.buffalo.edu/wnygirahcp/wp-content/uploads/sites/25/2017/11/... ·...