254780237

254780237

DNA-directed RNA polymerase subunit alpha

GeneID in NCBI database:8209218Locus tag:CLIBASIA_00610
Protein GI in NCBI database:254780237Protein Accession:YP_003064650.1
Gene range:-(129714, 130736)Protein Length:340aa
Gene description:DNA-directed RNA polymerase subunit alpha
COG prediction:[K] DNA-directed RNA polymerase, alpha subunit/40 kD subunit
KEGG prediction:rpoA; DNA-directed RNA polymerase subunit alpha (EC:2.7.7.6); K03040 DNA-directed RNA polymerase subunit alpha [EC:2.7.7.6]
SEED prediction:DNA-directed RNA polymerase alpha subunit (EC 2.7.7.6)
Pathway involved in KEGG:Purine metabolism [PATH:las00230]
Pyrimidine metabolism [PATH:las00240]
RNA polymerase [PATH:las03020]
Subsystem involved in SEED:RNA polymerase bacterial
sequencesequence profile

Prediction of Local Sequence Properties

SourceSummaryResult
scaler
NCBI Databasesequence
PSIPREDsecondary structure
SSPROsecondary structure
DISEMBLcoil and loop
DISEMBLflexible loop
SEGlow complexity
DISOPREDdisordered
DISEMBLmissing residues
DISPROdisordered
TMHMMnone TM-Helix
TOPPRED1 TM-Helix
HMMTOPnone TM-Helix
MEMSATnone TM-Helix
MEMSAT_SVMnone TM-Helix
PHOBIUSnone TM-Helix
SignalP_HMMno
SignalP_NNno
COILScoiled coil
70% MSAconservation map
90% MSAconservation map
  
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340
MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC
cccccHHHHccccccEEEEcccccccEEEEEEEEcccccccHHHHHHHHHHHHccccccEEEEEEccEEcccccccccHHHHHHHHHHHccEEEEEEccccEEEEEEEEccccEEEcccccccccEEEccccEEEEEccccEEEEEEEEEccccEEcccccccccccccEEEEccEEccEEEEEEEEEEcccccccccEEEEEEEEEcccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHcccHHHHcccHHHHHHHHHcccccHHHHHHccHHHHHccccccHHHHHHHHHHHHHccccccccccccccHHHHHHHHHccccc
cccccHHHHcccccEEEEEccccccccEEEEEccccccccccHHHHHHHHHHHHcccccEEEEEEccEEEEEcccccccHHHHHHHHHHcccEEEEcccccEEEEEEcccccEEEEcEEcccccEEEEcccEEEEEEccccEEEEEEEEEccccEEcccccccccccccEEEEcccccccEEEEEEEcccccccccccccEEEEEcccccccHHHHHHHHHHHHHHHHHHHcccccccccccHHcccccccccccHccccccccEEHEcHHHHHHcccEEHHHHHHHHHHHHHcccccccccHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHcc
MIQKNWQelikpnnieyIVLGQeeenrtlmiaeplprgfaHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGInlkmsgdshkrVTIFkrgpgvvtagdiqtvndievlnpdhvicnldVDAVVRMELTVskghgyvpakhhrtendpigLITIDALYSPIKKVSYTVEsaregqvldydklsmtidtdgsitgeDSVALASRILQDQLGmfinfeepkkevkedinvkslpfnpaLLKKVEELELSVRStnclrgenivyMGDLIQRTEADMLRMANFGRKSLVEIKGVLGtmglflgmnlpdwppeSIEELAKKYEDKC
miqknwqelikpnnieYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKrgpgvvtagDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSkghgyvpakhhrtendpiglITIDALYSPIKKVSYTVEsaregqvldydklSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEpkkevkedinvkslpfNPALLKKVEELELSvrstnclrgenivYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC
MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPAllkkveelelSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC
****NWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKH****NDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF*********************LLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIE**********
MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC
***KNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE*INVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
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MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC
MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC
MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC

Close Homologs Detected by BLAST or PSI-BLAST

Homolog within the Genome Detected by BLAST

No hits with e-value below 0.05

Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations

IdentityAlignment graphLength Definition Round E-value
Target340 DNA-directed RNA polymerase subunit alpha [Candidatus L
315122794340 DNA-directed RNA polymerase subunit alpha [Candidatus L 1 1e-177
222085699336 DNA-directed RNA polymerase, alpha subunit [Agrobacteri 1 1e-138
86357329336 DNA-directed RNA polymerase subunit alpha [Rhizobium et 1 1e-138
110634006336 DNA-directed RNA polymerase subunit alpha [Mesorhizobiu 1 1e-137
319783344336 DNA-directed RNA polymerase subunit alpha [Mesorhizobiu 1 1e-137
13470575336 DNA-directed RNA polymerase subunit alpha [Mesorhizobiu 1 1e-137
15965133336 DNA-directed RNA polymerase subunit alpha [Sinorhizobiu 1 1e-136
227821779336 DNA-directed RNA polymerase subunit alpha [Sinorhizobiu 1 1e-136
15889218336 DNA-directed RNA polymerase subunit alpha [Agrobacteriu 1 1e-136
222148390336 DNA-directed RNA polymerase subunit alpha [Agrobacteriu 1 1e-136
>gi|315122794|ref|YP_004063283.1| DNA-directed RNA polymerase subunit alpha [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 340 Back     alignment and organism information
 Score =  625 bits (1611), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 299/340 (87%), Positives = 321/340 (94%)

Query: 1   MIQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAI 60
           MIQKNWQELIKPNNIE+ VLG EEENRT+++AEP PRGFAHTLGNALRRVL+SSLRGAAI
Sbjct: 1   MIQKNWQELIKPNNIEFTVLGHEEENRTMVVAEPFPRGFAHTLGNALRRVLLSSLRGAAI 60

Query: 61  TAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQ 120
           TAVQIDGVLHEISSIKGV ED+TDIILNIKGINLKMS DS KRVTI+KRGPGVVTAGDIQ
Sbjct: 61  TAVQIDGVLHEISSIKGVREDITDIILNIKGINLKMSSDSSKRVTIYKRGPGVVTAGDIQ 120

Query: 121 TVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYSPI 180
           TVNDIE+LNPDHVICNLDVDAVVRMELTVSKG GYVPAKHHRTENDPIGLITIDALYSPI
Sbjct: 121 TVNDIEILNPDHVICNLDVDAVVRMELTVSKGQGYVPAKHHRTENDPIGLITIDALYSPI 180

Query: 181 KKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKE 240
           KKVSY VESAREGQ+LDYDKL+M IDTDGSI GED+VA ASRILQDQL +FINF+EP KE
Sbjct: 181 KKVSYKVESAREGQILDYDKLNMIIDTDGSIGGEDAVAFASRILQDQLNVFINFDEPTKE 240

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
            KED++V  LPFNPALLKKVEELELSVRS NCLRG+NI+Y+GDLIQ+TEA+MLR ANFGR
Sbjct: 241 EKEDMDVDRLPFNPALLKKVEELELSVRSANCLRGDNIIYIGDLIQKTEAEMLRTANFGR 300

Query: 301 KSLVEIKGVLGTMGLFLGMNLPDWPPESIEELAKKYEDKC 340
           KSL+EIKGVL TMGLFLGMNLPDWPPESIE+LAKKYEDKC
Sbjct: 301 KSLLEIKGVLATMGLFLGMNLPDWPPESIEDLAKKYEDKC 340


Species: Candidatus Liberibacter solanacearum
Genus: Candidatus Liberibacter
Family: Rhizobiaceae
Order: Rhizobiales
Class: Alphaproteobacteria
Phylum: Proteobacteria
Superkingdom: Bacteria
>gi|222085699|ref|YP_002544229.1| DNA-directed RNA polymerase, alpha subunit [Agrobacterium radiobacter K84] Length = 336 Back     alignment and organism information
>gi|86357329|ref|YP_469221.1| DNA-directed RNA polymerase subunit alpha [Rhizobium etli CFN 42] Length = 336 Back     alignment and organism information
>gi|110634006|ref|YP_674214.1| DNA-directed RNA polymerase subunit alpha [Mesorhizobium sp. BNC1] Length = 336 Back     alignment and organism information
>gi|319783344|ref|YP_004142820.1| DNA-directed RNA polymerase subunit alpha [Mesorhizobium ciceri biovar biserrulae WSM1271] Length = 336 Back     alignment and organism information
>gi|13470575|ref|NP_102144.1| DNA-directed RNA polymerase subunit alpha [Mesorhizobium loti MAFF303099] Length = 336 Back     alignment and organism information
>gi|15965133|ref|NP_385486.1| DNA-directed RNA polymerase subunit alpha [Sinorhizobium meliloti 1021] Length = 336 Back     alignment and organism information
>gi|227821779|ref|YP_002825749.1| DNA-directed RNA polymerase subunit alpha [Sinorhizobium fredii NGR234] Length = 336 Back     alignment and organism information
>gi|15889218|ref|NP_354899.1| DNA-directed RNA polymerase subunit alpha [Agrobacterium tumefaciens str. C58] Length = 336 Back     alignment and organism information
>gi|222148390|ref|YP_002549347.1| DNA-directed RNA polymerase subunit alpha [Agrobacterium vitis S4] Length = 336 Back     alignment and organism information

Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch

Conserved Domains in CDD Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target340 DNA-directed RNA polymerase subunit alpha [Candidatus L
PRK05182310 PRK05182, PRK05182, DNA-directed RNA polymerase subunit 1e-126
TIGR02027297 TIGR02027, rpoA, DNA-directed RNA polymerase, alpha sub 1e-102
CHL00013327 CHL00013, rpoA, RNA polymerase alpha subunit 1e-50
COG0202317 COG0202, RpoA, DNA-directed RNA polymerase, alpha subun 5e-83
cd06928215 cd06928, RNAP_alpha_NTD, N-terminal domain of the Alpha 1e-78
smart00662224 smart00662, RPOLD, RNA polymerases D 1e-46
pfam01000117 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA inse 7e-30
pfam0311862 pfam03118, RNA_pol_A_CTD, Bacterial RNA polymerase, alp 5e-17
pfam0119391 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimeriz 2e-10
cd0046086 cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits of RN 0.001
pfam0119391 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimeriz 7e-07
>gnl|CDD|179956 PRK05182, PRK05182, DNA-directed RNA polymerase subunit alpha; Provisional Back     alignment and domain information
>gnl|CDD|162666 TIGR02027, rpoA, DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type Back     alignment and domain information
>gnl|CDD|176956 CHL00013, rpoA, RNA polymerase alpha subunit Back     alignment and domain information
>gnl|CDD|30551 COG0202, RpoA, DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription] Back     alignment and domain information
>gnl|CDD|132904 cd06928, RNAP_alpha_NTD, N-terminal domain of the Alpha subunit of Bacterial RNA polymerase Back     alignment and domain information
>gnl|CDD|128908 smart00662, RPOLD, RNA polymerases D Back     alignment and domain information
>gnl|CDD|110031 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA insert domain Back     alignment and domain information
>gnl|CDD|145976 pfam03118, RNA_pol_A_CTD, Bacterial RNA polymerase, alpha chain C terminal domain Back     alignment and domain information
>gnl|CDD|144693 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerization domain Back     alignment and domain information
>gnl|CDD|132901 cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits of RNA polymerase Back     alignment and domain information
>gnl|CDD|144693 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerization domain Back     alignment and domain information

Conserved Domains in CDD Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target 340 DNA-directed RNA polymerase subunit alpha [Candidatus L
100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins , .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription DNA-dependent." target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=TIGR02027">TIGR02027324 rpoA DNA-directed RNA polymerase, alpha subunit; InterP 100.0
PRK05182306 DNA-directed RNA polymerase subunit alpha; Provisional 100.0
CHL00013333 rpoA RNA polymerase alpha subunit 100.0
COG0202317 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD s 100.0
cd06928215 RNAP_alpha_NTD N-terminal domain of the Alpha subunit o 100.0
smart00662224 RPOLD RNA polymerases D. DNA-directed RNA polymerase su 100.0
cd07030259 RNAP_D D subunit of Archaeal RNA polymerase. The D subu 99.89
PRK00783265 DNA-directed RNA polymerase subunit D; Provisional 99.88
pfam0119391 RNA_pol_L RNA polymerase Rpb3/Rpb11 dimerization domain 99.86
cd07028212 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The euka 99.78
cd07031265 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase 99.5
cd07032291 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymeras 99.48
KOG1522285 consensus 98.87
KOG1521338 consensus 97.82
pfam01000117 RNA_pol_A_bac RNA polymerase Rpb3/RpoA insert domain. M 100.0
pfam0311862 RNA_pol_A_CTD Bacterial RNA polymerase, alpha chain C t 99.76
PRK0775895 hypothetical protein; Provisional 97.99
PTZ00035 350 Rad51; Provisional 94.63
PRK07956 668 ligA NAD-dependent DNA ligase LigA; Validated 92.44
PRK02406355 DNA polymerase IV; Validated 91.35
cd0046086 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymera 99.61
PRK0377395 DNA-directed RNA polymerase subunit L; Provisional 95.98
cd0692783 RNAP_L L subunit of Archaeal RNA polymerase. The archae 95.3
cd0702783 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eu 94.2
cd0692693 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymeras 93.58
cd0702985 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymera 92.95
COG176199 RPB11 DNA-directed RNA polymerase, subunit L [Transcrip 92.39
PRK04301318 radA DNA repair and recombination protein RadA; Validat 95.96
cd0046086 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymera 94.17
cd0702783 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eu 93.1
cd0692783 RNAP_L L subunit of Archaeal RNA polymerase. The archae 92.36
cd0702985 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymera 91.86
PRK0377395 DNA-directed RNA polymerase subunit L; Provisional 91.42
cd0692693 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymeras 90.52
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit; InterPro: IPR011773 DNA-directed RNA polymerases 2 Back     alignment and domain information
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional Back     alignment and domain information
>CHL00013 rpoA RNA polymerase alpha subunit Back     alignment and domain information
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription] Back     alignment and domain information
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase Back     alignment and domain information
>smart00662 RPOLD RNA polymerases D Back     alignment and domain information
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase Back     alignment and domain information
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional Back     alignment and domain information
>pfam01193 RNA_pol_L RNA polymerase Rpb3/Rpb11 dimerization domain Back     alignment and domain information
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase Back     alignment and domain information
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II Back     alignment and domain information
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III Back     alignment and domain information
>KOG1522 consensus Back     alignment and domain information
>KOG1521 consensus Back     alignment and domain information
>pfam01000 RNA_pol_A_bac RNA polymerase Rpb3/RpoA insert domain Back     alignment and domain information
>pfam03118 RNA_pol_A_CTD Bacterial RNA polymerase, alpha chain C terminal domain Back     alignment and domain information
>PRK07758 hypothetical protein; Provisional Back     alignment and domain information
>PTZ00035 Rad51; Provisional Back     alignment and domain information
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated Back     alignment and domain information
>PRK02406 DNA polymerase IV; Validated Back     alignment and domain information
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase Back     alignment and domain information
>PRK03773 DNA-directed RNA polymerase subunit L; Provisional Back     alignment and domain information
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase Back     alignment and domain information
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase Back     alignment and domain information
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II Back     alignment and domain information
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III Back     alignment and domain information
>COG1761 RPB11 DNA-directed RNA polymerase, subunit L [Transcription] Back     alignment and domain information
>PRK04301 radA DNA repair and recombination protein RadA; Validated Back     alignment and domain information
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase Back     alignment and domain information
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase Back     alignment and domain information
>cd06927 RNAP_L L subunit of Archaeal RNA polymerase Back     alignment and domain information
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III Back     alignment and domain information
>PRK03773 DNA-directed RNA polymerase subunit L; Provisional Back     alignment and domain information
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II Back     alignment and domain information

Homologous Structures in PDB Database
Detected by PSI-BLAST, RPS-BLAST and HHsearch

Homologous Structures Detected by PSI-BLAST against Nonredundant Database

IdentityAlignment graphLength Definition E-value
Target340 DNA-directed RNA polymerase subunit alpha [Candidatus L
3iyd_A329 Three-Dimensional Em Structure Of An Intact Activat 9e-99
1hqm_A313 Crystal Structure Of Thermus Aquaticus Core Rna Pol 4e-76
1l9u_A314 Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A 4e-76
1i6v_A314 Thermus Aquaticus Core Rna Polymerase-Rifampicin Co 1e-75
1iw7_A315 Crystal Structure Of The Rna Polymerase Holoenzyme 2e-73
1bdf_A235 Structure Of Escherichia Coli Rna Polymerase Alpha 7e-65
1xs9_D84 A Model Of The Ternary Complex Formed Between Mara, 1e-24
2jzb_A99 Solution Structure Of The Complex Between E.Coli Nu 1e-24
1lb2_B84 Structure Of The E. Coli Alpha C-Terminal Domain Of 2e-24
1coo_A98 The Cooh-Terminal Domain Of Rna Polymerase Alpha Su 3e-24
3k4g_A86 Crystal Structure Of E. Coli Rna Polymerase Alpha S 1e-20
3ihq_B75 Crystal Structure Of Reduced C10s Spx In Complex Wi 4e-16
3gfk_B79 Crystal Structure Of Bacillus Subtilis SpxRNA POLYM 6e-16
1z3e_B73 Crystal Structure Of Spx In Complex With The C-Term 7e-16
1doq_A69 The C-Terminal Domain Of The Rna Polymerase Alpha S 7e-05
3h0g_C297 Rna Polymerase Ii From Schizosaccharomyces Pombe Le 0.002
gi|266618715|pdb|3IYD|A Chain A, Three-Dimensional Em Structure Of An Intact Activator- Dependent Transcription Initiation Complex Length = 329 Back     alignment and structure
 Score =  364 bits (935), Expect = 9e-99,   Method: Composition-based stats.
 Identities = 146/334 (43%), Positives = 220/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++   +         +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIEQVSS---THAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAK---HHRTENDPIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++    ++  +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQP---EVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>gi|13096176|pdb|1HQM|A Chain A, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase- Includes Complete Structure With Side-Chains (Except For Disordered Regions)-Further Refined From Original Deposition-Contains Additional Sequence Information Length = 313 Back     alignment and structure
gi|21466003|pdb|1L9U|A Chain A, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 314 Back     alignment and structure
>gi|14278481|pdb|1I6V|A Chain A, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex Length = 314 Back     alignment and structure
gi|21730337|pdb|1IW7|A Chain A, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 315 Back     alignment and structure
>gi|5107487|pdb|1BDF|A Chain A, Structure Of Escherichia Coli Rna Polymerase Alpha Subunit N-Terminal Domain Length = 235 Back     alignment and structure
>gi|56554702|pdb|1XS9|D Chain D, A Model Of The Ternary Complex Formed Between Mara, The Alpha-Ctd Of Rna Polymerase And Dna Length = 84 Back     alignment and structure
>gi|228311784|pdb|2JZB|A Chain A, Solution Structure Of The Complex Between E.Coli Nusa-Ar2 And Rnap-Actd Length = 99 Back     alignment and structure
>gi|24158833|pdb|1LB2|B Chain B, Structure Of The E. Coli Alpha C-Terminal Domain Of Rna Polymerase In Complex With Cap And Dna Length = 84 Back     alignment and structure
>gi|157830665|pdb|1COO|A Chain A, The Cooh-Terminal Domain Of Rna Polymerase Alpha Subunit Length = 98 Back     alignment and structure
>gi|300193165|pdb|3K4G|A Chain A, Crystal Structure Of E. Coli Rna Polymerase Alpha Subunit C-Terminal Domain Length = 86 Back     alignment and structure
>gi|285803273|pdb|3IHQ|B Chain B, Crystal Structure Of Reduced C10s Spx In Complex With The Alpha C-Terminal Domain Of Rna Polymeras Length = 75 Back     alignment and structure
>gi|224983719|pdb|3GFK|B Chain B, Crystal Structure Of Bacillus Subtilis SpxRNA POLYMERASE Alpha Subunit C-Terminal Domain Complex Length = 79 Back     alignment and structure
>gi|82407558|pdb|1Z3E|B Chain B, Crystal Structure Of Spx In Complex With The C-Terminal Domain Of The Rna Polymerase Alpha Subunit Length = 73 Back     alignment and structure
>gi|159162213|pdb|1DOQ|A Chain A, The C-Terminal Domain Of The Rna Polymerase Alpha Subunit From Thermus Thermophilus Length = 69 Back     alignment and structure
gi|256599717|pdb|3H0G|C Chain C, Rna Polymerase Ii From Schizosaccharomyces Pombe Length = 297 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target340 DNA-directed RNA polymerase subunit alpha [Candidatus L
3lu0_A329 DNA-directed RNA polymerase subunit alpha; E. coli RNA 1e-105
3iyd_A329 DNA-directed RNA polymerase subunit alpha; transcriptio 3e-96
2a6h_A315 DNA-directed RNA polymerase alpha chain; RNA polymerase 2e-81
1bdf_A235 RNA polymerase alpha subunit; nucleotidyltransferase, a 1e-64
2pa8_D265 DNA-directed RNA polymerase subunit D; ferredoxin-like 8e-32
1twf_C318 B44.5, DNA-directed RNA polymerase II 45 kDa polypeptid 2e-31
3h0g_C297 DNA-directed RNA polymerase II subunit RPB3; transcript 9e-30
1lb2_B84 DNA-directed RNA polymerase alpha chain; protein-DNA co 3e-28
1coo_A98 RNA polymerase alpha subunit; transcription regulation, 2e-27
3k4g_A86 DNA-directed RNA polymerase subunit alpha; bacterial tr 3e-27
3gfk_B79 DNA-directed RNA polymerase subunit alpha; protein-prot 2e-20
1z3e_B73 DNA-directed RNA polymerase alpha chain; bacterial tran 3e-20
>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A Length = 329 Back     alignment and structure
 Score =  376 bits (966), Expect = e-105
 Identities = 146/334 (43%), Positives = 219/334 (65%), Gaps = 10/334 (2%)

Query: 2   IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT 61
           +Q +  E +KP  ++     Q       +  EPL RGF HTLGNALRR+L+SS+ G A+T
Sbjct: 1   MQGSVTEFLKPRLVDIE---QVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVT 57

Query: 62  AVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQT 121
            V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA DI  
Sbjct: 58  EVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITH 117

Query: 122 VNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPAKHHRTEND---PIGLITIDALY 177
             D+E++ P HVIC+L D +A + M + V +G GYVPA       +   PIG + +DA Y
Sbjct: 118 DGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACY 177

Query: 178 SPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP 237
           SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + 
Sbjct: 178 SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV 237

Query: 238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMAN 297
           ++   ++   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N
Sbjct: 238 RQPEVKE---EKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPN 294

Query: 298 FGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
            G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 295 LGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 328


>3iyd_A DNA-directed RNA polymerase subunit alpha; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12} Length = 329 Back     alignment and structure
>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* 2gho_A 1hqm_A ... Length = 315 Back     alignment and structure
>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1 Length = 235 Back     alignment and structure
>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D Length = 265 Back     alignment and structure
>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ... Length = 318 Back     alignment and structure
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Length = 297 Back     alignment and structure
>1lb2_B DNA-directed RNA polymerase alpha chain; protein-DNA complex, gene-regulatory, gene regulation/DNA complex; HET: CMP; 3.10A {Escherichia coli} SCOP: a.60.3.1 PDB: 1xs9_D Length = 84 Back     alignment and structure
>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli K12} SCOP: a.60.3.1 PDB: 2jzb_A Length = 98 Back     alignment and structure
>3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription regulation, DNA-directed RNA polymer nucleotidyltransferase; HET: MLY; 2.05A {Escherichia coli k-12} PDB: 1lb2_B* 1xs9_D Length = 86 Back     alignment and structure
>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} Length = 79 Back     alignment and structure
>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} SCOP: a.60.3.1 Length = 73 Back     alignment and structure

Homologous Structures in PDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target340 DNA-directed RNA polymerase subunit alpha [Candidatus L
3lu0_A329 DNA-directed RNA polymerase subunit alpha; E. coli RNA 100.0
2a6h_A315 DNA-directed RNA polymerase alpha chain; RNA polymerase 100.0
1bdf_A235 RNA polymerase alpha subunit; nucleotidyltransferase, a 100.0
2pa8_D265 DNA-directed RNA polymerase subunit D; ferredoxin-like 100.0
3h0g_C297 DNA-directed RNA polymerase II subunit RPB3; transcript 99.97
1twf_C318 B44.5, DNA-directed RNA polymerase II 45 kDa polypeptid 99.97
1coo_A98 RNA polymerase alpha subunit; transcription regulation, 99.93
3k4g_A86 DNA-directed RNA polymerase subunit alpha; bacterial tr 99.93
3gfk_B79 DNA-directed RNA polymerase subunit alpha; protein-prot 99.85
1z3e_B73 DNA-directed RNA polymerase alpha chain; bacterial tran 99.85
1b22_A114 DNA repair protein RAD51; DNA binding, riken structural 96.53
3lda_A 400 DNA repair protein RAD51; DNA binding protein, ATP-bind 95.97
1pzn_A 349 RAD51, DNA repair and recombination protein RAD51, RADA 95.82
2zj8_A720 DNA helicase, putative SKI2-type helicase; RECA fold, A 94.93
1dgs_A 667 DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 92.62
2i1q_A322 DNA repair and recombination protein RADA; ATPase, reco 94.3
2pa8_L92 DNA-directed RNA polymerase subunit L; ferredoxin-like 93.02
2z43_A324 DNA repair and recombination protein RADA; archaea, fil 92.97
1v5w_A343 DMC1, meiotic recombination protein DMC1/LIM15 homolog; 91.21
1twf_K120 B13.6, DNA-directed RNA polymerase II 13.6 kDa polypept 90.48
3h0g_K123 DNA-directed RNA polymerase II subunit RPB11; transcrip 90.14
1vq8_Y241 50S ribosomal protein L32E; ribosome 50S, protein-prote 93.12
>3lu0_A DNA-directed RNA polymerase subunit alpha; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_A Back     alignment and structure
Probab=100.00  E-value=0  Score=810.30  Aligned_cols=324  Identities=45%  Similarity=0.798  Sum_probs=304.0

Q ss_pred             CCCHHHHCCCCCCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHH
Q ss_conf             52205751797420158636788815899996169756678889999987416983068899988714431466462444
Q gi|254780237|r    2 IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHED   81 (340)
Q Consensus         2 ~~~~~~~~~~P~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~ED   81 (340)
                      |+..|++|++|+.+++   ++.+++||||+++||+||||+|||||||||||||++|+|||+|||+||.|||++|+||+||
T Consensus         1 m~~~~~~~~~p~~i~~---~~~~~~yg~f~i~Ple~G~g~TlGnaLRRvLLssi~G~ait~vkI~gv~HEfsti~GV~Ed   77 (329)
T 3lu0_A            1 MQGSVTEFLKPRLVDI---EQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQED   77 (329)
T ss_dssp             CCCSTTTSSSCCCCCE---EECTTSEEEEEECCCCTTCHHHHHHHHHHHTTTSSCEEEEEEEEESSCSSTTCCCTTBSSC
T ss_pred             CCCHHHHHCCCCEEEE---ECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCCC
T ss_conf             9613666138857787---2268867899997688862636688999998856984588999989965545568996237


Q ss_pred             HHHHHHHHCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEEC-CCCEEEEEEEEECCCCCEECCC
Q ss_conf             999998401141777279827999999447169963351389859988880899977-8964999999746876320344
Q gi|254780237|r   82 LTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLD-VDAVVRMELTVSKGHGYVPAKH  160 (340)
Q Consensus        82 V~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~-~~~~l~iel~ie~G~GY~~~e~  160 (340)
                      |++|+||||+|+|+.+++.+..++|+++|||+|||+||++|++++|+||||||||++ +++.|+|+++|++|+||++++.
T Consensus        78 v~~IilNLK~i~~~~~~~~~~~~~l~~~Gpg~vtA~di~~p~~veivNpdq~IaTl~~~~~~l~~e~~i~~G~GY~~~~~  157 (329)
T 3lu0_A           78 ILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPAST  157 (329)
T ss_dssp             HHHHHHHHHSCCCEESSCSCEEEEECCCSSSCEETTSSCCCSSEECSCTTCEEECBCSSCCCCCEEEEEEEESSEECTTT
T ss_pred             HHHHHHHCCCCCEEECCCCCEEEEEEEECCCCEEECCCCCCCCEEEECCCEEEEEECCCCCEEEEEEEEEECCCEEECCC
T ss_conf             99999846733156426872589999616776681136667987995899889996588926999999990565264200


Q ss_pred             CC---CCCCCCCEECCCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             44---655754302124311114422357764116887762189999993896177799999999999988876224444
Q gi|254780237|r  161 HR---TENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEP  237 (340)
Q Consensus       161 ~~---~~~~~ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~  237 (340)
                      ++   ....++|+||+||+||||+||||.|+++|+|++++||+|+|||||||||+|++||++||++|++||++|.++++.
T Consensus       158 ~~~~~~~~~~ig~i~iDa~FsPV~kVny~Ve~~rv~~~~~~e~L~lEI~TnGsI~P~eAl~~AakiL~~~f~~f~~~~~~  237 (329)
T 3lu0_A          158 RIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDV  237 (329)
T ss_dssp             SCCCSTTSSSCCCEECCEECCCEEEEEEEEEEECCSSCSCEEEEEEEEEECSSSCHHHHHHHHHHHHHHHTTTSSSCC--
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             23554334667834036655563789999864355667751038999983898898999999999999999976263101


Q ss_pred             CCCCCCHHHCCCCHHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             32210000000001123331112210110588898988398371888744988886188988644999999999808312
Q gi|254780237|r  238 KKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFL  317 (340)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~l  317 (340)
                      .....   ..+..+.++.+.++||+||||+||+||||||||+|||||+++|++||+++||||+||++||+++|+++||+|
T Consensus       238 ~~~~~---~~~~~~~~~~l~~~Ie~LeLSvRs~NcLkra~I~ti~dLv~~s~~dLl~ikNfGkKSl~EI~~kL~~~gl~l  314 (329)
T 3lu0_A          238 RQPEV---KEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSL  314 (329)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCCCC---CCCCCCCCHHHHCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHHHCCCCC
T ss_conf             34444---444444265763879885277888865757189189997647999995589976200999999999749777


Q ss_pred             CCCCCCCCHHHHHH
Q ss_conf             67687898677999
Q gi|254780237|r  318 GMNLPDWPPESIEE  331 (340)
Q Consensus       318 g~~l~~~~~~~~~~  331 (340)
                      ||++++|||+++++
T Consensus       315 gm~l~~~~~~~~~~  328 (329)
T 3lu0_A          315 GMRLENWPPASIAD  328 (329)
T ss_dssp             --------------
T ss_pred             CCCCCCCCCCCCCC
T ss_conf             78789999534356



>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: d.74.3.1 d.181.1.1 PDB: 1smy_A* 1zyr_A* 1iw7_A* 2a69_A* 2a6e_A 2a68_A* 2be5_A* 2cw0_A 2o5i_A 2o5j_A* 2ppb_A* 3dxj_A* 3eql_A* 1i6v_A* 1ynj_A* 1l9z_A 1l9u_A* 1ynn_A* 2gho_A 1hqm_A ... Back     alignment and structure
>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} SCOP: d.74.3.1 d.181.1.1 Back     alignment and structure
>2pa8_D DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D Back     alignment and structure
>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1twf_C B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.1 d.181.1.1 PDB: 1i3q_C 1i6h_C 1k83_C* 1nik_C 1nt9_C 1pqv_C 1r5u_C 1r9s_C* 1r9t_C* 1sfo_C* 1twa_C* 1twc_C* 1i50_C* 1twg_C* 1twh_C* 1wcm_C 1y1v_C 1y1w_C 1y1y_C 1y77_C* ... Back     alignment and structure
>1coo_A RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli K12} SCOP: a.60.3.1 PDB: 2jzb_A Back     alignment and structure
>3k4g_A DNA-directed RNA polymerase subunit alpha; bacterial transcription regulation, DNA-directed RNA polymer nucleotidyltransferase; HET: MLY; 2.05A {Escherichia coli k-12} PDB: 1lb2_B* 1xs9_D Back     alignment and structure
>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} Back     alignment and structure
>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} SCOP: a.60.3.1 PDB: 3ihq_B Back     alignment and structure
>1b22_A DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1 Back     alignment and structure
>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A* Back     alignment and structure
>1pzn_A RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} SCOP: a.60.4.1 c.37.1.11 Back     alignment and structure
>2zj8_A DNA helicase, putative SKI2-type helicase; RECA fold, ATP-binding, hydrolase, nucleotide- binding; 2.00A {Pyrococcus furiosus} PDB: 2zj5_A* 2zj2_A 2zja_A* Back     alignment and structure
>1dgs_A DNA ligase; AMP complex, NAD+-dependent; HET: DNA AMP; 2.90A {Thermus filiformis} SCOP: a.60.2.2 b.40.4.6 d.142.2.2 PDB: 1v9p_A* Back     alignment and structure
>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ewa_A* 3ew9_A* 3etl_A* 2gdj_A* Back     alignment and structure
>2pa8_L DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L Back     alignment and structure
>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular switch, RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus P2} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A* Back     alignment and structure
>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A Back     alignment and structure
>1twf_K B13.6, DNA-directed RNA polymerase II 13.6 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: d.74.3.2 PDB: 1i3q_K 1i6h_K 1k83_K* 1nik_K 1nt9_K 1pqv_K 1r5u_K 1r9s_K* 1r9t_K* 1sfo_K* 1twa_K* 1twc_K* 1i50_K* 1twg_K* 1twh_K* 1wcm_K 1y1v_K 1y1w_K 1y1y_K 1y77_K* ... Back     alignment and structure
>3h0g_K DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1vq8_Y 50S ribosomal protein L32E; ribosome 50S, protein-protein complex, RNA-RNA complex, protein-RNA complex, peptidyl transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A {Haloarcula marismortui} SCOP: c.9.2.1 PDB: 1vq4_Y* 1vq5_Y* 1vq6_Y* 1vq7_Y* 1s72_Y* 1vq9_Y* 1vqk_Y* 1vql_Y* 1vqm_Y* 1vqn_Y* 1vqo_Y* 1vqp_Y* 1yhq_Y* 1yi2_Y* 1yij_Y* 1yit_Y* 1yj9_Y* 1yjn_Y* 1yjw_Y* 2otj_Y* ... Back     alignment and structure

Homologous Domains in SCOP and MMDB Database
Detected by RPS-BLAST and HHsearch

Homologous Domains in SCOP70 (Version1.75) Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 340 DNA-directed RNA polymerase subunit alpha [Candidatus L
d1bdfa2126 d.181.1.1 (A:53-178) RNA polymerase alpha subunit {Esch 6e-32
d1smya2123 d.181.1.1 (A:50-172) RNA polymerase alpha subunit {Ther 2e-31
d1lb2b_72 a.60.3.1 (B:) C-terminal domain of RNA polymerase alpha 7e-25
d1z3eb167 a.60.3.1 (B:245-311) C-terminal domain of RNA polymeras 2e-19
d1doqa_69 a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha 1e-18
d1bdfa1105 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha {Esche 2e-19
d1smya1106 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Therm 2e-14
d1bdfa1105 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha {Esche 2e-10
d1smya1106 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Therm 5e-09
>d1bdfa2 d.181.1.1 (A:53-178) RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]} Length = 126 Back     information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Insert subdomain of RNA polymerase alpha subunit
superfamily: Insert subdomain of RNA polymerase alpha subunit
family: Insert subdomain of RNA polymerase alpha subunit
domain: RNA polymerase alpha subunit
species: Escherichia coli [TaxId: 562]
 Score =  132 bits (332), Expect = 6e-32
 Identities = 56/126 (44%), Positives = 81/126 (64%), Gaps = 4/126 (3%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA
Sbjct: 1   GCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPA---KHHRTENDPIGLIT 172
            DI    D+E++ P HVIC+L   +A + M + V +G GYVPA    H   +  PIG + 
Sbjct: 61  ADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLL 120

Query: 173 IDALYS 178
           +DA YS
Sbjct: 121 VDACYS 126


>d1smya2 d.181.1.1 (A:50-172) RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} Length = 123 Back     information, alignment and structure
>d1lb2b_ a.60.3.1 (B:) C-terminal domain of RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]} Length = 72 Back     information, alignment and structure
>d1z3eb1 a.60.3.1 (B:245-311) C-terminal domain of RNA polymerase alpha subunit {Bacillus subtilis [TaxId: 1423]} Length = 67 Back     information, alignment and structure
>d1doqa_ a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} Length = 69 Back     information, alignment and structure
>d1bdfa1 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha {Escherichia coli [TaxId: 562]} Length = 105 Back     information, alignment and structure
>d1smya1 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Thermus thermophilus [TaxId: 274]} Length = 106 Back     information, alignment and structure
>d1bdfa1 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha {Escherichia coli [TaxId: 562]} Length = 105 Back     information, alignment and structure
>d1smya1 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Thermus thermophilus [TaxId: 274]} Length = 106 Back     information, alignment and structure

Homologous Domains in SCOP70 (Version 1.75) Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target340 DNA-directed RNA polymerase subunit alpha [Candidatus L
d1bdfa2126 RNA polymerase alpha subunit {Escherichia coli [TaxId: 100.0
d1smya2123 RNA polymerase alpha subunit {Thermus thermophilus [Tax 100.0
d1bdfa1105 RNA polymerase alpha {Escherichia coli [TaxId: 562]} 99.96
d1smya1106 RNA polymerase alpha {Thermus thermophilus [TaxId: 274] 99.95
d1twfc1135 RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 97.96
d1lb2b_72 C-terminal domain of RNA polymerase alpha subunit {Esch 99.91
d1z3eb167 C-terminal domain of RNA polymerase alpha subunit {Baci 99.83
d1doqa_69 C-terminal domain of RNA polymerase alpha subunit {Ther 99.79
d1szpa164 DNA repair protein Rad51, N-terminal domain {Baker's ye 97.26
d1b22a_70 DNA repair protein Rad51, N-terminal domain {Human (Hom 96.95
d1pzna161 DNA repair protein Rad51, N-terminal domain {Archaeon P 94.86
d2i1qa160 DNA repair protein Rad51, N-terminal domain {Archaeon M 94.05
d1bdfa1105 RNA polymerase alpha {Escherichia coli [TaxId: 562]} 94.65
>d1bdfa2 d.181.1.1 (A:53-178) RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
class: Alpha and beta proteins (a+b)
fold: Insert subdomain of RNA polymerase alpha subunit
superfamily: Insert subdomain of RNA polymerase alpha subunit
family: Insert subdomain of RNA polymerase alpha subunit
domain: RNA polymerase alpha subunit
species: Escherichia coli [TaxId: 562]
Probab=100.00  E-value=5.3e-43  Score=295.72  Aligned_cols=122  Identities=45%  Similarity=0.807  Sum_probs=117.0

Q ss_pred             CEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEE
Q ss_conf             30688999887144314664624449999984011417772798279999994471699633513898599888808999
Q gi|254780237|r   57 GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICN  136 (340)
Q Consensus        57 G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaT  136 (340)
                      |+|||+|||+||.|||++||||+|||++|+||||+|+|++++++++.++|+++|||.|||+||++|+++||+||||||||
T Consensus         1 G~AIt~vkI~Gv~HEfsti~GV~EDV~~IiLNLK~i~~k~~~~~~~~~~l~~~gp~~VtA~di~~~~~veIvNpd~~Iat   80 (126)
T d1bdfa2           1 GCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICH   80 (126)
T ss_dssp             CEEEEEEEETTCCSTTCCCTTBSSCHHHHHHHHHTCCEECSSCSEEEEEEEEESSEEEEGGGBCCCSSCEESCTTCEEEE
T ss_pred             CCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCEEEECCCCCEEEEEEECCCCCEEEECCCCCCCEEEECCCEEEEE
T ss_conf             97779999889531021378814669999973435457851788638999935852389734137898799677639999


Q ss_pred             EC-CCCEEEEEEEEECCCCCEECCCCC---CCCCCCCEECCCCCHH
Q ss_conf             77-896499999974687632034444---6557543021243111
Q gi|254780237|r  137 LD-VDAVVRMELTVSKGHGYVPAKHHR---TENDPIGLITIDALYS  178 (340)
Q Consensus       137 l~-~~~~l~iel~ie~G~GY~~~e~~~---~~~~~ig~i~iDa~Fs  178 (340)
                      ++ +++.|+||++|++||||+|++.++   .+..++|+|++||+||
T Consensus        81 lt~~~~~l~mel~v~~GrGYv~ae~~~~~~~~~~~ig~I~iDa~FS  126 (126)
T d1bdfa2          81 LTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYS  126 (126)
T ss_dssp             ECSTTCEEEEEEEEEECCSEECGGGTC-----CCCCSCCBCCEECC
T ss_pred             EECCCCEEEEEEEEECCCCEECCCCCCCCCCCCCCCCEEEECCCCC
T ss_conf             8047850899999967877504421344555677664788677789



>d1smya2 d.181.1.1 (A:50-172) RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1bdfa1 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1smya1 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1twfc1 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1lb2b_ a.60.3.1 (B:) C-terminal domain of RNA polymerase alpha subunit {Escherichia coli [TaxId: 562]} Back     information, alignment and structure
>d1z3eb1 a.60.3.1 (B:245-311) C-terminal domain of RNA polymerase alpha subunit {Bacillus subtilis [TaxId: 1423]} Back     information, alignment and structure
>d1doqa_ a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha subunit {Thermus thermophilus [TaxId: 274]} Back     information, alignment and structure
>d1szpa1 a.60.4.1 (A:81-144) DNA repair protein Rad51, N-terminal domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Back     information, alignment and structure
>d1b22a_ a.60.4.1 (A:) DNA repair protein Rad51, N-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Back     information, alignment and structure
>d1pzna1 a.60.4.1 (A:35-95) DNA repair protein Rad51, N-terminal domain {Archaeon Pyrococcus furiosus [TaxId: 2261]} Back     information, alignment and structure
>d2i1qa1 a.60.4.1 (A:5-64) DNA repair protein Rad51, N-terminal domain {Archaeon Methanococcus voltae [TaxId: 2188]} Back     information, alignment and structure
>d1bdfa1 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha {Escherichia coli [TaxId: 562]} Back     information, alignment and structure

Homologous Domains in MMDB70 Database Detected by RPS-BLAST

IdentityAlignment graphLength Definition E-value
Target 340 DNA-directed RNA polymerase subunit alpha [Candida
3iyd_A_49-180132 (A:49-180) DNA-directed RNA polymerase subunit alp 3e-39
2a6h_A_48-172125 (A:48-172) DNA-directed RNA polymerase alpha chain 5e-37
1bdf_A_51-178128 (A:51-178) RNA polymerase alpha subunit; nucleotid 7e-37
2a6h_A_1-47_173-315190 (A:1-47,A:173-315) DNA-directed RNA polymerase alp 3e-34
2a6h_A_1-47_173-315190 (A:1-47,A:173-315) DNA-directed RNA polymerase alp 3e-07
3iyd_A_1-48_181-246114 (A:1-48,A:181-246) DNA-directed RNA polymerase sub 2e-11
1bdf_A_1-50_179-235107 (A:1-50,A:179-235) RNA polymerase alpha subunit; n 2e-10
1coo_A_98 (A:) RNA polymerase alpha subunit; transcription r 2e-24
1lb2_B_84 (B:) DNA-directed RNA polymerase alpha chain; prot 7e-24
3gfk_B_79 (B:) DNA-directed RNA polymerase subunit alpha; pr 2e-18
1z3e_B_73 (B:) DNA-directed RNA polymerase alpha chain; bact 5e-18
3iyd_A_1-48_181-246114 (A:1-48,A:181-246) DNA-directed RNA polymerase sub 2e-17
1bdf_A_1-50_179-235107 (A:1-50,A:179-235) RNA polymerase alpha subunit; n 6e-17
>3iyd_A (A:49-180) DNA-directed RNA polymerase subunit alpha; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12}Length = 132 Back     alignment and structure
 Score =  156 bits (397), Expect = 3e-39
 Identities = 60/132 (45%), Positives = 87/132 (65%), Gaps = 4/132 (3%)

Query: 53  SSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G
Sbjct: 1   SSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIG 60

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA---KHHRTENDPI 168
            VTA DI    D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PI
Sbjct: 61  PVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPI 120

Query: 169 GLITIDALYSPI 180
           G + +DA YSP+
Sbjct: 121 GRLLVDACYSPV 132


>2a6h_A (A:48-172) DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus}Length = 125 Back     alignment and structure
>1bdf_A (A:51-178) RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli}Length = 128 Back     alignment and structure
>2a6h_A (A:1-47,A:173-315) DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus}Length = 190 Back     alignment and structure
>2a6h_A (A:1-47,A:173-315) DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus}Length = 190 Back     alignment and structure
>3iyd_A (A:1-48,A:181-246) DNA-directed RNA polymerase subunit alpha; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12}Length = 114 Back     alignment and structure
>1bdf_A (A:1-50,A:179-235) RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli}Length = 107 Back     alignment and structure
>1coo_A (A:) RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli K12}Length = 98 Back     alignment and structure
>1lb2_B (B:) DNA-directed RNA polymerase alpha chain; protein-DNA complex, gene-regulatory, gene regulation/DNA complex; HET: CMP; 3.10A {Escherichia coli}Length = 84 Back     alignment and structure
>3gfk_B (B:) DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis}Length = 79 Back     alignment and structure
>1z3e_B (B:) DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis}Length = 73 Back     alignment and structure
>3iyd_A (A:1-48,A:181-246) DNA-directed RNA polymerase subunit alpha; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12}Length = 114 Back     alignment and structure
>1bdf_A (A:1-50,A:179-235) RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli}Length = 107 Back     alignment and structure

Homologous Domains in MMDB70 Database Detected by HHsearch

IdentityAlignment graphLength Definition Probability
Target340 DNA-directed RNA polymerase subunit alpha [Candidatus L
2a6h_A_1-47_173-315190 DNA-directed RNA polymerase alpha chain; RNA polym 100.0
3iyd_A_49-180132 DNA-directed RNA polymerase subunit alpha; transcr 100.0
1bdf_A_51-178128 RNA polymerase alpha subunit; nucleotidyltransfera 100.0
2a6h_A_48-172125 DNA-directed RNA polymerase alpha chain; RNA polym 100.0
3iyd_A_1-48_181-246114 DNA-directed RNA polymerase subunit alpha; transcr 100.0
1bdf_A_1-50_179-235107 RNA polymerase alpha subunit; nucleotidyltransfera 99.97
1twf_C_1-40_169-318190 B44.5, DNA-directed RNA polymerase II 45 kDa polyp 95.24
1lb2_B_84 DNA-directed RNA polymerase alpha chain; protein-D 99.91
1coo_A_98 RNA polymerase alpha subunit; transcription regula 99.9
1z3e_B_73 DNA-directed RNA polymerase alpha chain; bacterial 99.86
3gfk_B_79 DNA-directed RNA polymerase subunit alpha; protein 99.85
1wcn_A_70 Transcription elongation protein NUSA; RNA-binding 95.7
1b22_A_114 DNA repair protein RAD51; DNA binding, riken struc 95.52
1pzn_A_1-9595 RAD51, DNA repair and recombination protein RAD51, 92.0
2pa8_D_36-153118 DNA-directed RNA polymerase subunit D; ferredoxin- 96.62
1twf_C_41-168128 B44.5, DNA-directed RNA polymerase II 45 kDa polyp 94.86
3h0g_C_39-170132 DNA-directed RNA polymerase II subunit RPB3; trans 93.59
1twf_K_120 B13.6, DNA-directed RNA polymerase II 13.6 kDa pol 95.07
2pa8_L_92 DNA-directed RNA polymerase subunit L; ferredoxin- 94.75
3h0g_K_123 DNA-directed RNA polymerase II subunit RPB11; tran 94.22
1xpp_A_115 TA1416, DNA-directed RNA polymerase subunit L; str 93.6
3h0g_C_1-38_171-297165 DNA-directed RNA polymerase II subunit RPB3; trans 93.59
1twf_C_1-40_169-318190 B44.5, DNA-directed RNA polymerase II 45 kDa polyp 94.47
1twf_K_120 B13.6, DNA-directed RNA polymerase II 13.6 kDa pol 94.4
2pa8_L_92 DNA-directed RNA polymerase subunit L; ferredoxin- 93.71
3h0g_K_123 DNA-directed RNA polymerase II subunit RPB11; tran 92.76
3h0g_C_1-38_171-297165 DNA-directed RNA polymerase II subunit RPB3; trans 92.68
>2a6h_A (A:1-47,A:173-315) DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} Back     alignment and structure
Probab=100.00  E-value=0  Score=394.12  Aligned_cols=181  Identities=34%  Similarity=0.467  Sum_probs=162.6

Q ss_pred             CCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             42015863678881589999616975667888999998741698306889998871443146646244499999840114
Q gi|254780237|r   13 NNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGI   92 (340)
Q Consensus        13 ~~i~~~~~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I   92 (340)
                      ..++. ..++.+++||+|+++||+||||+||||||||||||                                       
T Consensus         7 ~~~e~-~~~~~~~~yg~f~~~Ple~G~g~TiGN~lRR~LLs---------------------------------------   46 (190)
T 2a6h_A            7 KAPVF-TVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLS---------------------------------------   46 (190)
T ss_dssp             SCCEE-EEEEETTTEEEEEEEEECTTCHHHHHHHHHHHHHH---------------------------------------
T ss_pred             CCCEE-EEEECCCCEEEEEEECCCCCCHHHHHHHHHHHHHH---------------------------------------
T ss_conf             89567-88756885689999568896175778899999885---------------------------------------


Q ss_pred             EEEECCCCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCCCEEC
Q ss_conf             17772798279999994471699633513898599888808999778964999999746876320344446557543021
Q gi|254780237|r   93 NLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT  172 (340)
Q Consensus        93 ~~k~~~~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~ig~i~  172 (340)
                                                                                                      
T Consensus        47 --------------------------------------------------------------------------------   46 (190)
T 2a6h_A           47 --------------------------------------------------------------------------------   46 (190)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             --------------------------------------------------------------------------------
T ss_conf             --------------------------------------------------------------------------------


Q ss_pred             CCCCHHEEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC--HHHCCCC
Q ss_conf             24311114422357764116887762189999993896177799999999999988876224444322100--0000000
Q gi|254780237|r  173 IDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKE--DINVKSL  250 (340)
Q Consensus       173 iDa~FsPV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f~~~~~~~~~~~~--~~~~~~~  250 (340)
                           |||++|||.|+++|||+.++||||+|||||||||+|++|+++||++|++||.+|.++.........  ....+..
T Consensus        47 -----sPV~kVnY~Ve~~~v~~~~~~ekL~leI~TdGsItP~eAl~~Aa~iL~~~~~~~~~~~~~~~~~~~~~~~~~~~~  121 (190)
T 2a6h_A           47 -----SPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAKEPEAPP  121 (190)
T ss_dssp             -----TCEEEEEEEEEECCBTTBCCCEEEEEEEEECSSSCHHHHHHHHHHHHHHHHHTTCSCC-----------------
T ss_pred             -----CHHHHEEEEEEEEECCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
T ss_conf             -----611104457888521777766610599954886452335999999999888763353212223442111111221


Q ss_pred             HHHHHHHCCHHHCCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             11233311122101105888989883983718887449888861889886449999999998083126
Q gi|254780237|r  251 PFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGTMGLFLG  318 (340)
Q Consensus       251 ~~~~~L~~~IeeLeLSvRs~NcLk~a~I~tigdLv~~s~~dLl~ikNfG~KSl~EI~~~L~~~gl~lg  318 (340)
                      ..+..+.++|++|+||+|++||||+|||+|||||+++|++||++++|||+||++||+++|+++||+|.
T Consensus       122 ~~~~~~~~~IeeL~Ls~R~~n~Lk~a~I~ti~dL~~~s~~dL~~i~n~G~ksl~EI~~~L~~~gl~L~  189 (190)
T 2a6h_A          122 EQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTLK  189 (190)
T ss_dssp             --------------------------------------------------------------------
T ss_pred             CHHHHHCCCHHHHCCCHHHHHHHHHCCCCCHHHHHHCCHHHHHCCCCCCCCCHHHHHHHHHHCCCCCC
T ss_conf             01354268599905878888678775894799988499999845999760559999999998599888



>3iyd_A (A:49-180) DNA-directed RNA polymerase subunit alpha; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12} Back     alignment and structure
>1bdf_A (A:51-178) RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} Back     alignment and structure
>2a6h_A (A:48-172) DNA-directed RNA polymerase alpha chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} Back     alignment and structure
>3iyd_A (A:1-48,A:181-246) DNA-directed RNA polymerase subunit alpha; transcription, initiation, class I, activator, RNA polymerase, holoenzyme, sigma70, open complex, CAP, CRP, CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli k-12} Back     alignment and structure
>1bdf_A (A:1-50,A:179-235) RNA polymerase alpha subunit; nucleotidyltransferase, assemble; 2.50A {Escherichia coli} Back     alignment and structure
>1twf_C (C:1-40,C:169-318) B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} Back     alignment and structure
>1lb2_B (B:) DNA-directed RNA polymerase alpha chain; protein-DNA complex, gene-regulatory, gene regulation/DNA complex; HET: CMP; 3.10A {Escherichia coli} Back     alignment and structure
>1coo_A (A:) RNA polymerase alpha subunit; transcription regulation, nucleotidyl transferase; NMR {Escherichia coli K12} Back     alignment and structure
>1z3e_B (B:) DNA-directed RNA polymerase alpha chain; bacterial transcription regulation, disulfide stress; 1.50A {Bacillus subtilis} Back     alignment and structure
>3gfk_B (B:) DNA-directed RNA polymerase subunit alpha; protein-protein complex, cytoplasm, redox-active center, stress response, transcription; 2.30A {Bacillus subtilis} Back     alignment and structure
>1wcn_A (A:) Transcription elongation protein NUSA; RNA-binding protein, escherichia coli NUSA, transcription regulation, regulation of RNA binding; NMR {Escherichia coli} PDB: 2jzb_B Back     alignment and structure
>1b22_A (A:) DNA repair protein RAD51; DNA binding, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: DNA; NMR {Homo sapiens} Back     alignment and structure
>1pzn_A (A:1-95) RAD51, DNA repair and recombination protein RAD51, RADA; heptameric ring, heptamer, ring, oligomer, RAD51 polymerization motif; HET: DNA; 2.85A {Pyrococcus furiosus} Back     alignment and structure
>2pa8_D (D:36-153) DNA-directed RNA polymerase subunit D; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_D 3hkz_D 2waq_D 2wb1_D Back     alignment and structure
>1twf_C (C:41-168) B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} Back     alignment and structure
>3h0g_C (C:39-170) DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1twf_K (K:) B13.6, DNA-directed RNA polymerase II 13.6 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} Back     alignment and structure
>2pa8_L (L:) DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L Back     alignment and structure
>3h0g_K (K:) DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1xpp_A (A:) TA1416, DNA-directed RNA polymerase subunit L; structural genomics, protein structure initiative, MCSG; 1.60A {Thermoplasma acidophilum} Back     alignment and structure
>3h0g_C (C:1-38,C:171-297) DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>1twf_C (C:1-40,C:169-318) B44.5, DNA-directed RNA polymerase II 45 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} Back     alignment and structure
>1twf_K (K:) B13.6, DNA-directed RNA polymerase II 13.6 kDa polypeptide; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} Back     alignment and structure
>2pa8_L (L:) DNA-directed RNA polymerase subunit L; ferredoxin-like Fe-S binding motif, platform for RNA polymerase assembly, transferase; 1.76A {Sulfolobus solfataricus P2} PDB: 2pmz_L 3hkz_L 2waq_L 2wb1_L Back     alignment and structure
>3h0g_K (K:) DNA-directed RNA polymerase II subunit RPB11; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure
>3h0g_C (C:1-38,C:171-297) DNA-directed RNA polymerase II subunit RPB3; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe} Back     alignment and structure