Citrus Sinensis ID: 018065

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Local Sequence Feature Prediction

Residue Number Marker
--------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-------350-------360-
Protein Sequence
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccHHHHHHHcccccHHHHHHHHccccccHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHccccHHHHHHHHHHHHccccccccccccccHHHHHHHHcccccccccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHcccccccccccccccccccccccccccccccccccccccccEcccccccHHccccccEEcccccccccccHcccHccccHHHHHcccccccEEEcccccccccHcHHHHHHHHHHHHcccHcccccccccccccccccccccccccccccccccccHHHHHHHHHHcccHHHHHHccccccccccccccccccccccccccccEEEcHHHHHHHHHHHHccHHHcccccccccccccHHHccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHcc
Coil and Loop (DISEMBL)
meagrnllssppsfpsrtrvkhslsssasssssssVLMHneqsapavasvptssvarhfptsvllqeqrdeyrpllhmfkedktsqatsdsrnIETEAFFveeknsgdlDQLVQDLEHqflhwpdlwnlsppmkrgedpsvsltmqslsndteesvdaepfDAVALARKALSASKEAAslaenpklngaeftdisltsslgypleevkqfsqprflerrskkrkvskpqvtnhetynSRKASVKKKLsegfdrndplrlflwgpetrklltaDEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRdlkselhsgnssREKLINANLRLVVHVAKQyqgrgislHDLLQI
Flexible Loop (DISEMBL)
meagrnllssppsfpsrtrVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMfkedktsqatsdsrNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAAslaenpklngaeFTDISLTSslgypleevkqfsqprflerrskkrkvskpqvtnhetynsrkasvkkklsegfdrndplrlfLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLqsqfgreptLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKqyqgrgislhdllqi
Low Complexity Region (SEG)
MEAGRNLLSSPPSFPSRTRVKHslsssasssssssVLMHNEQsapavasvptssvaRHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDavalarkalsaskeaaslaeNPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI
Disordered region (IsUnstruct)
**************************************************************************************************FFV******DLDQLVQDLEHQFLHWPDLWNL******************************************************************************************************************************PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLE*********FGREPTLIEWAKAIGLSCRDL************KLINANLRLVVHVAKQYQGRGISLH*****
Disordered Region (DISOPRED)
**********PP****************************EQSAPAV*SVPTSSVARHFPTSVLLQE*************************************************EHQFLH***************************************************************************************************************************************RLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQ******PTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI
Disordered Region (DISEMBL)
******************************************************VARHFPTSVLLQEQRDEYRPLLHMFKED*********RNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQS**********AEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLE*************TNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLK********SREKLINANLRLVVHVAKQYQGRGISLHDLLQI
Disordered Region (DISPRO)
***************************************************TSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPM********************ESVDAEPFDAVALARKALSASKEAASLAENPKLN*******************VKQFSQPRFLERRSKKR*****************************RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFExxxxxxxxxxxxxxxxxxxxxFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	361	2.2.26 [Sep-21-2011]
Q9LD95	547	RNA polymerase sigma fact	yes	no	0.914	0.603	0.467	1e-70
O22056	572	RNA polymerase sigma fact	no	no	0.407	0.256	0.378	5e-23
P26683	390	RNA polymerase sigma fact	yes	no	0.393	0.364	0.354	3e-17
Q31ME3	320	RNA polymerase sigma fact	yes	no	0.293	0.331	0.396	3e-14
P38023	399	RNA polymerase sigma fact	no	no	0.293	0.265	0.415	3e-14
Q31QG5	320	RNA polymerase sigma fact	no	no	0.296	0.334	0.416	1e-13
Q03065	332	RNA polymerase sigma-B fa	no	no	0.293	0.319	0.358	2e-10
P74565	425	RNA polymerase sigma fact	N/A	no	0.324	0.275	0.293	2e-08
Q59996	404	Probable RNA polymerase s	N/A	no	0.296	0.264	0.302	2e-08
P52322	416	RNA polymerase sigma fact	no	no	0.293	0.254	0.296	4e-08

>sp|Q9LD95|SIGF_ARATH RNA polymerase sigma factor sigF, chloroplastic OS=Arabidopsis thaliana GN=SIGF PE=1 SV=1

 Score =  267 bits (682), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 172/368 (46%), Positives = 226/368 (61%), Gaps = 38/368 (10%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           MEA RNL+SS PSF ++T +K     S+ SS SS V++H++ + P V S   +S++RHFP
Sbjct: 1   MEATRNLVSSSPSFQTKTHLK-----SSYSSPSSVVMLHDQTTTPVVNSRHLNSLSRHFP 55

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV-----QD 115
            SVL QE R+E RPL H  ++D+TSQ T + R                 D+LV     + 
Sbjct: 56  ASVLSQEPREESRPLSHALRDDRTSQLTLERRQ---------------FDELVSSREDEK 100

Query: 116 LEHQFLHWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSA 173
            E Q LH   LWNL  SP     + P+V   +           DAE  D VALA+KALSA
Sbjct: 101 FEQQLLHSTGLWNLLISPLTSETKLPAVVSPL----------ADAELCDVVALAQKALSA 150

Query: 174 SKEAASLAENPKLNGAE-FTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTN 232
           SK+AA L ++ + N ++   D   TSS     E+       R LERR+K R+  K    +
Sbjct: 151 SKQAALLVDDTEANPSDNIKDSLSTSSSMSLPEKGNIVRSKRQLERRAKNRRAPKSNDVD 210

Query: 233 HETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 292
            E Y  +K S KKK  +G D +D L+LFLWGPET++LLTA EE ELI+ IQ L++LEK K
Sbjct: 211 DEGYVPQKTSAKKKYKQGADNDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVK 270

Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 352
           +KL+SQ G EPT+ EWA+A+G+S   LKS++H G SSREKLI ANLRLVVH+AKQYQ RG
Sbjct: 271 TKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRG 330

Query: 353 ISLHDLLQ 360
           ++  DLLQ
Sbjct: 331 LNFQDLLQ 338

Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released. Regulates transcription in chloroplast in a DG1-dependent manner. Involved in light-dependent chloroplast development. Required during early plant development and primary leaf formation.
Arabidopsis thaliana (taxid: 3702)

>sp|O22056|SIGB_ARATH RNA polymerase sigma factor sigB OS=Arabidopsis thaliana GN=SIGB PE=2 SV=2

 Score =  108 bits (271), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 56/148 (37%), Positives = 92/148 (62%), Gaps = 1/148 (0%)

Query: 214 RFLERRSKKRKVSKPQVTNHETYNSRKASVKKKL-SEGFDRNDPLRLFLWGPETRKLLTA 272
           R  ER++++ K  +   +   +  +  +  KK+L ++  D NDPLR       + KLLT 
Sbjct: 216 RQTERKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTV 275

Query: 273 DEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332
            EE EL A IQDL++LE+ +++L  + GR+PT  +WA A G+  + L+  +H G   ++K
Sbjct: 276 REEHELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDK 335

Query: 333 LINANLRLVVHVAKQYQGRGISLHDLLQ 360
           +I +N+RLV+ +AK YQG G++L DL+Q
Sbjct: 336 MIKSNIRLVISIAKNYQGAGMNLQDLVQ 363

Required for the transition of plastids into chloroplasts by coordinating nuclear and chloroplastic genomes under light conditions. Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released. Promotes the biosynthesis of plastid-encoded tRNAs (e.g. trnE-UUC and trnV-UAC).

Arabidopsis thaliana (taxid: 3702)

>sp|P26683|RPOD_NOSS1 RNA polymerase sigma factor RpoD OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=rpoD PE=3 SV=1

 Score = 89.7 bits (221), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 55/155 (35%), Positives = 87/155 (56%), Gaps = 13/155 (8%)

Query: 206 EVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPE 265
           ++ +F +P+  E  +K  K +K +         R  S KK  +E     D +RL+L    
Sbjct: 44  DIDEFLEPQTDEDDAKSGKAAKSR--------RRTQSKKKHYTE-----DSIRLYLQEIG 90

Query: 266 TRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325
             +LL ADEE EL  +I DL+ LE+ + +L  +  R+P   EWA+A+ L     +  LH 
Sbjct: 91  RIRLLRADEEIELARKIADLLELERVRERLSEKLERDPRDSEWAEAVQLPLPAFRYRLHI 150

Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           G  +++K++ +NLRLVV +AK+Y  RG+S  DL+Q
Sbjct: 151 GRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQ 185

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

>sp|Q31ME3|RPOD2_SYNE7 RNA polymerase sigma factor rpoD2 OS=Synechococcus elongatus (strain PCC 7942) GN=rpoD2 PE=1 SV=1

 Score = 80.1 bits (196), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 42/106 (39%), Positives = 65/106 (61%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 314
           D +R +L      +LLTA+EE     Q+Q L+ L   +++L+ + G EP+  EWA A+ L
Sbjct: 11  DLVRAYLQEIGRVRLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEWAAAVDL 70

Query: 315 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           +  DL  ++  G  ++ K+I ANLRLVV +AK+YQ R +   DL+Q
Sbjct: 71  NLEDLDRQIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQ 116

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released (By similarity). This sigma factor is a component of the biological clock pathway that affects the circadian expression of a subset of genes in this bacterium.

Synechococcus elongatus (strain PCC 7942) (taxid: 1140)

>sp|P38023|RPOD1_SYNE7 RNA polymerase sigma factor rpoD1 OS=Synechococcus elongatus (strain PCC 7942) GN=rpoD1 PE=3 SV=2

 Score = 79.7 bits (195), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 44/106 (41%), Positives = 65/106 (61%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 314
           D +RL+L      +LL ADEE EL  QI DL+ LE+ + +L  Q  R P+  EWA A+  
Sbjct: 89  DSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAVDS 148

Query: 315 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
              + +  L  G  +++K++ +NLRLVV +AK+Y  RG+S  DL+Q
Sbjct: 149 PLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQ 194

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.

Synechococcus elongatus (strain PCC 7942) (taxid: 1140)

>sp|Q31QG5|RPOD3_SYNE7 RNA polymerase sigma factor rpoD3 OS=Synechococcus elongatus (strain PCC 7942) GN=rpoD3 PE=3 SV=1

 Score = 77.8 bits (190), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 45/108 (41%), Positives = 69/108 (63%), Gaps = 1/108 (0%)

Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG-REPTLIEWAKAI 312
           +D +R +L       LLT +EE  L  ++Q  ++L++ +  LQS+ G R+P+ +EWA A 
Sbjct: 9   SDLVRTYLREIGRVPLLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWAAAA 68

Query: 313 GLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           GLS  +L+ + H G  ++ K+I ANLRLVV VAK+Y  R + L DL+Q
Sbjct: 69  GLSIEELRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQ 116

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

Synechococcus elongatus (strain PCC 7942) (taxid: 1140)

>sp|Q03065|RPSB_NOSS1 RNA polymerase sigma-B factor OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=sigB PE=3 SV=1

 Score = 67.4 bits (163), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 38/106 (35%), Positives = 60/106 (56%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 314
           D + ++L       LL+ ++E     Q+Q ++ +   K +L  +  REPTL EWA  + L
Sbjct: 23  DAVSIYLHKIGRVPLLSHEQEIFFAQQVQQMMVMFTAKEELAEKLQREPTLQEWADKMQL 82

Query: 315 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
               L  +L  G  +++K+I ANLRLVV +AK+YQ R +   DL+Q
Sbjct: 83  KEDVLLQQLSQGQIAKQKMIQANLRLVVSIAKKYQKRNLEFLDLIQ 128

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

Nostoc sp. (strain PCC 7120 / UTEX 2576) (taxid: 103690)

>sp|P74565|RPOD_SYNY3 RNA polymerase sigma factor RpoD OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=rpoD PE=3 SV=1

 Score = 60.5 bits (145), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 49/167 (29%), Positives = 77/167 (46%), Gaps = 50/167 (29%)

Query: 239 RKASVKKK-LSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS 297
           RK +VKKK  +E     D +R++L      +LL A+EE EL  QI DL+ LE  +  L  
Sbjct: 59  RKDAVKKKPYTE-----DSIRIYLQEIGRIRLLRAEEEIELARQIADLLELELIRDNLTL 113

Query: 298 QFGREPTLIEWAKAI----------------GLSCRDLKSELHSGNS------------- 328
           Q  R+P+ +EW K +                    +D+ S L + ++             
Sbjct: 114 QLERQPSELEWGKQVWKLETAKQRLVGDKKKEPKKKDIDSYLANPDNELSLENEWSQQPN 173

Query: 329 ---------------SREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
                          +++K++ +NLRLVV +AK+Y  RG+S  DL+Q
Sbjct: 174 KNFAAFRRRLFLDRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQ 220

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.

Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)

>sp|Q59996|RPSC_SYNY3 Probable RNA polymerase sigma-C factor OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=sigC PE=3 SV=1

 Score = 60.5 bits (145), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 45/149 (30%), Positives = 64/149 (42%), Gaps = 42/149 (28%)

Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSK------------------- 294
            D +RL+L       LL  DEE  +  Q+Q  +RL + +++                   
Sbjct: 48  TDLVRLYLQDIGRIPLLKRDEEVHIAQQVQSYLRLVEIQNRAAESDAAIDQYQTAIAVHD 107

Query: 295 -LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN----------------------SSRE 331
            L  Q G  P+   WAK +G +   LK  L SG                       +++ 
Sbjct: 108 QLLVQLGHRPSYERWAKILGQTVATLKQTLKSGKKRWAELAGLTVEELENIEKQGITAKA 167

Query: 332 KLINANLRLVVHVAKQYQGRGISLHDLLQ 360
            +I ANLRLVV VAK+YQ RG+ L DL+Q
Sbjct: 168 HMIKANLRLVVSVAKKYQNRGLELLDLIQ 196

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)

>sp|P52322|RPOD_MICAE RNA polymerase sigma factor rpoD1 OS=Microcystis aeruginosa GN=rpoD1 PE=3 SV=1

 Score = 59.3 bits (142), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 43/145 (29%), Positives = 67/145 (46%), Gaps = 39/145 (26%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEK------------------------ 290
           D +R++L      +LL A+EE EL  +I DL++LE+                        
Sbjct: 67  DSIRIYLQEIGRIRLLRAEEEIELARKIADLLKLERIREDFCLYSDAEWGKQVFLFERIE 126

Query: 291 ----EKSK-------LQSQFGRE----PTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335
               EKS+       +++  G+     P L EW           K  L+ G  ++EK++ 
Sbjct: 127 KIIVEKSEKEPKLSDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQ 186

Query: 336 ANLRLVVHVAKQYQGRGISLHDLLQ 360
           +NLRLVV +AK+Y  RG+S  DL+Q
Sbjct: 187 SNLRLVVSIAKKYMNRGLSFQDLIQ 211

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.

Microcystis aeruginosa (taxid: 1126)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	361
224068757	535	predicted protein [Populus trichocarpa]	0.903	0.609	0.555	1e-102
297741628	561	unnamed protein product [Vitis vinifera]	0.958	0.616	0.560	1e-101
359481391	572	PREDICTED: RNA polymerase sigma factor r	0.983	0.620	0.554	1e-100
255556952	548	RNA polymerase sigma factor rpoD, putati	0.922	0.607	0.549	1e-98
356536959	571	PREDICTED: RNA polymerase sigma factor r	0.980	0.619	0.527	6e-86
356548319	574	PREDICTED: RNA polymerase sigma factor r	0.983	0.618	0.502	7e-85
449451030	562	PREDICTED: RNA polymerase sigma factor s	0.961	0.617	0.489	2e-77
312282671	547	unnamed protein product [Thellungiella h	0.914	0.603	0.480	5e-73
297827203	546	RNA polymerase sigma-70 factor [Arabidop	0.911	0.602	0.475	8e-72
18404292	547	RNApolymerase sigma-subunit F [Arabidops	0.914	0.603	0.467	6e-69

>gi|224068757|ref|XP_002326192.1| predicted protein [Populus trichocarpa] gi|222833385|gb|EEE71862.1| predicted protein [Populus trichocarpa]

 Score =  377 bits (968), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 200/360 (55%), Positives = 255/360 (70%), Gaps = 34/360 (9%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           MEAGR LLSS PSFP+RT +K+SL+SS        VL+  EQ+ PAV+S+PT+S A+HFP
Sbjct: 1   MEAGRTLLSSSPSFPTRTHLKNSLTSS--------VLILREQATPAVSSIPTTSTAQHFP 52

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQF 120
           TSVLLQEQRDE+RPL ++FKED+ SQAT D R  E      E K+S +LDQLV++ E+Q 
Sbjct: 53  TSVLLQEQRDEFRPLQNIFKEDRASQATLDRRKTEIGTSGHEGKDSDELDQLVENFEYQL 112

Query: 121 LHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASL 180
            HWP  WNL                      T++ +D EP + + LA++ALSASK AA L
Sbjct: 113 HHWPAYWNL----------------------TDKLIDVEPTNVINLAKRALSASKHAAFL 150

Query: 181 AENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRK 240
           A+N      +  +++ TSS  + LEEVK     R L R+S  R+  K +    ETY+S+ 
Sbjct: 151 ADN----NTDLDNLASTSSSSFSLEEVKIVRSRRHLARQSLNRRAPKTKDLIFETYDSKS 206

Query: 241 ASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG 300
           A ++K+LS+GFD NDPLRLFLWGPET++LLTA EEFELIAQIQDL+ LE  K++L+SQFG
Sbjct: 207 ADIQKRLSQGFDPNDPLRLFLWGPETKQLLTAKEEFELIAQIQDLMNLEGVKNRLESQFG 266

Query: 301 REPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           REPTL+EWA+A+GLSC  LK +LHSGN SREKLINANLR+VVH+AK+YQ RG+ L DLLQ
Sbjct: 267 REPTLVEWAQAVGLSCHVLKLQLHSGNRSREKLINANLRMVVHIAKRYQNRGLGLQDLLQ 326

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297741628|emb|CBI32760.3| unnamed protein product [Vitis vinifera]

 Score =  375 bits (964), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 205/366 (56%), Positives = 259/366 (70%), Gaps = 20/366 (5%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           MEAG N+LSS PSFP RT  +         +SSSSVLM ++Q APAVAS+PT+ +AR FP
Sbjct: 1   MEAGTNILSSTPSFPPRTHFR---------NSSSSVLMLHDQVAPAVASIPTT-IARKFP 50

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQF 120
           TSVLLQEQRDEYRP     K+++T QAT + R +E      +E+NS D +Q + + E Q 
Sbjct: 51  TSVLLQEQRDEYRPFPQALKDERTFQATLEKRQMEI-VVSADEENSDDHNQYMVNFERQL 109

Query: 121 LHWPDLWNLSPPMKRGE-DPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAAS 179
           L  P LW   P  + GE  P  S  M+S++ D E S+D +P D +ALA+KALSASK+A S
Sbjct: 110 LLQPGLWYSLPSSQTGEKSPFSSSIMKSITTDIENSMDVKPCDVLALAKKALSASKQAVS 169

Query: 180 LAENPKLNGAEFTD-----ISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHE 234
           L EN KL GA+  D     +   SS   PLEE K     R LERRSKKR+   P+V  HE
Sbjct: 170 LYENAKLLGADLEDSPSPSLGAISSPNLPLEE-KTVRSTRLLERRSKKRR--NPKVAVHE 226

Query: 235 TYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSK 294
            + SR+A V++K++EG+D  DPLRLFLWGPETRKLLTA EE ELI QIQ+L+RLE+ K +
Sbjct: 227 NHGSRRAEVQRKINEGYDPKDPLRLFLWGPETRKLLTAKEESELIVQIQELMRLEEVKKR 286

Query: 295 LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGIS 354
           LQS   REPT++EWA+A+GLSC+ L+S+LHSGN SR+KLI ANLR+VVH+AKQYQGRG++
Sbjct: 287 LQSHLKREPTVVEWAEAVGLSCQVLQSQLHSGNRSRQKLIYANLRMVVHIAKQYQGRGLN 346

Query: 355 LHDLLQ 360
           L DLLQ
Sbjct: 347 LQDLLQ 352

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359481391|ref|XP_002276710.2| PREDICTED: RNA polymerase sigma factor rpoD [Vitis vinifera]

 Score =  371 bits (952), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 204/368 (55%), Positives = 259/368 (70%), Gaps = 13/368 (3%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSS--VLMHNEQSAPAVASVPTSSVARH 58
           MEAG N+LSS PSFP RT  ++S SS  +        VLM ++Q APAVAS+PT+ +AR 
Sbjct: 1   MEAGTNILSSTPSFPPRTHFRNSSSSGNAFFFYVVLFVLMLHDQVAPAVASIPTT-IARK 59

Query: 59  FPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEH 118
           FPTSVLLQEQRDEYRP     K+++T QAT + R +E      +E+NS D +Q + + E 
Sbjct: 60  FPTSVLLQEQRDEYRPFPQALKDERTFQATLEKRQMEI-VVSADEENSDDHNQYMVNFER 118

Query: 119 QFLHWPDLWNLSPPMKRGE-DPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEA 177
           Q L  P LW   P  + GE  P  S  M+S++ D E S+D +P D +ALA+KALSASK+A
Sbjct: 119 QLLLQPGLWYSLPSSQTGEKSPFSSSIMKSITTDIENSMDVKPCDVLALAKKALSASKQA 178

Query: 178 ASLAENPKLNGAEFTD-----ISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTN 232
            SL EN KL GA+  D     +   SS   PLEE K     R LERRSKKR+   P+V  
Sbjct: 179 VSLYENAKLLGADLEDSPSPSLGAISSPNLPLEE-KTVRSTRLLERRSKKRR--NPKVAV 235

Query: 233 HETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 292
           HE + SR+A V++K++EG+D  DPLRLFLWGPETRKLLTA EE ELI QIQ+L+RLE+ K
Sbjct: 236 HENHGSRRAEVQRKINEGYDPKDPLRLFLWGPETRKLLTAKEESELIVQIQELMRLEEVK 295

Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 352
            +LQS   REPT++EWA+A+GLSC+ L+S+LHSGN SR+KLI ANLR+VVH+AKQYQGRG
Sbjct: 296 KRLQSHLKREPTVVEWAEAVGLSCQVLQSQLHSGNRSRQKLIYANLRMVVHIAKQYQGRG 355

Query: 353 ISLHDLLQ 360
           ++L DLLQ
Sbjct: 356 LNLQDLLQ 363

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255556952|ref|XP_002519509.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis] gi|223541372|gb|EEF42923.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]

 Score =  365 bits (938), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 201/366 (54%), Positives = 252/366 (68%), Gaps = 33/366 (9%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           ME  R  LSSPP FPSRT  K+SLSSS +   +   ++H EQ+ PAV S PT+S+AR+FP
Sbjct: 1   METARTFLSSPPPFPSRTHFKNSLSSSDAYVDNFVFMLH-EQAVPAVTSAPTTSIARNFP 59

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQF 120
           TSVLLQEQRDE+RPLL++FKEDKT QAT D++ ++      E   S  LDQL+    H  
Sbjct: 60  TSVLLQEQRDEFRPLLNIFKEDKTFQATVDTKQMDPGTSDQEGICSDVLDQLIL---HSN 116

Query: 121 LHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASL 180
           L W                  SLTMQS++ +T+E +  EP + + LARKALSASKEAA L
Sbjct: 117 LSW------------------SLTMQSITTNTDELMVVEPTNVIDLARKALSASKEAALL 158

Query: 181 AE------NPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHE 234
           A+      +    G E TD+S      + LEEVK     R LER+SK R+V+K +   HE
Sbjct: 159 AQKCANLDDTVSTGLEPTDLS-----NFSLEEVKTVRSTRRLERQSKNRRVTKTKEIFHE 213

Query: 235 TYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSK 294
            Y+SR+A V+KK++EGFD  DPLRLFLWGPET++LLTA EE ELI Q+QDL+ LE  K K
Sbjct: 214 PYSSRRAGVQKKINEGFDPKDPLRLFLWGPETKQLLTAKEESELIGQVQDLMSLENVKEK 273

Query: 295 LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGIS 354
            + QFGR+PTL+EWA A+GLS   ++S+LHSGN SREKLINANLR+VVH+AKQYQGRG+S
Sbjct: 274 FKLQFGRDPTLVEWADAVGLSYSVMQSQLHSGNRSREKLINANLRMVVHIAKQYQGRGLS 333

Query: 355 LHDLLQ 360
           L DLLQ
Sbjct: 334 LQDLLQ 339

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356536959|ref|XP_003536999.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max]

 Score =  323 bits (829), Expect = 6e-86,   Method: Compositional matrix adjust.
 Identities = 194/368 (52%), Positives = 251/368 (68%), Gaps = 14/368 (3%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           ME  R +  S P FP RT   H  S+  SSSS+SSVLM +EQ++P VAS  ++  A++FP
Sbjct: 1   MEFARTMFCSSPPFPPRTH--HPWSTLPSSSSTSSVLMLHEQASPTVASWSSNFSAQNFP 58

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQF 120
            SVLL EQRDEYRPLLHM KEDKTSQA   +R ++T     EE N+ + DQ+V D     
Sbjct: 59  ASVLLPEQRDEYRPLLHMSKEDKTSQAMLSTRQMDTVTVH-EENNTENADQVVLDFRKHL 117

Query: 121 LHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASL 180
            HWP+L   S  +  GE  + S T++ +S D E   +   F+ V+LA+KALS SK+ +S+
Sbjct: 118 HHWPNLQLTSSQI--GE-VAASSTLEHVSVDLERRPNGVQFNGVSLAKKALSTSKQESSV 174

Query: 181 AENPKLNGAEFTDISLTS-SLGYP-LEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNS 238
            E+ K   A+    SL S SL  P +   K     R LERRSK+RKV K +V + ETY +
Sbjct: 175 VEDLKSIKADDVPFSLASTSLADPSIGRNKTVRSTRLLERRSKQRKVPKSKVIDDETYLA 234

Query: 239 RKASVKKKL------SEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 292
           RK   ++KL      +E  D++DPLRLFLWGPET++LLT ++E +LI+QIQDL+RLE+ K
Sbjct: 235 RKDDAQEKLRAEKKKNEELDQDDPLRLFLWGPETKQLLTLEQESQLISQIQDLLRLEEVK 294

Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 352
           + LQSQFGREPT+ EWA+  GL+CR L+S+LHSGN SREKLI ANLR+VVHVAK YQGRG
Sbjct: 295 TNLQSQFGREPTMAEWAEGAGLNCRLLQSQLHSGNRSREKLIQANLRMVVHVAKSYQGRG 354

Query: 353 ISLHDLLQ 360
           +SL DLLQ
Sbjct: 355 LSLQDLLQ 362

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356548319|ref|XP_003542550.1| PREDICTED: RNA polymerase sigma factor rpoD [Glycine max]

 Score =  320 bits (820), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 186/370 (50%), Positives = 245/370 (66%), Gaps = 15/370 (4%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           ME  R +  S P FP RT   H   ++   SSS+SVLM  EQ++P VAS  ++  A++FP
Sbjct: 1   MEFSRTMFCSSPPFPPRT---HHPWNTLPLSSSTSVLMLREQASPTVASWSSNFSAQNFP 57

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQF 120
            SVLLQEQRDEYRPLLHM KEDKTSQA   +R ++T     EE N+ + DQ+V D     
Sbjct: 58  ASVLLQEQRDEYRPLLHMSKEDKTSQAMLSTRQMDT-VMVHEENNTENADQVVLDFRKHL 116

Query: 121 LHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASL 180
            +WP L NL    + GE  S S T+Q +S+D +   +    + V+LA+KALS SK+ +S+
Sbjct: 117 HYWPHLQNLLASSQTGE-ISASSTLQQVSSDLDRHTNGVQCNRVSLAKKALSTSKQGSSV 175

Query: 181 AENPKLNGAEFTDISL---TSSLGYP-LEEVKQFSQPRFLERRSKKRKVSKPQVTNHETY 236
            E+ K   A+   I     ++ L  P +   K     R LERRSK+RKV K +V + ETY
Sbjct: 176 VEDLKSIKADDDSIPFGLASTGLADPSIGRNKTVRSTRLLERRSKQRKVPKSKVIDDETY 235

Query: 237 NSRK------ASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEK 290
            +RK        V+KK +E  D+NDPL  FL GPET++LLT ++E +LI+QIQDL+RLE+
Sbjct: 236 LARKDDAHEKLRVEKKKNEELDQNDPLCFFLRGPETKQLLTLEQESQLISQIQDLLRLEE 295

Query: 291 EKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQG 350
            K+KLQSQFGREPT+ EWA+ +GL+CR L ++L SG+ SREKLI ANLR+VVHVAK YQG
Sbjct: 296 VKTKLQSQFGREPTMAEWAEGVGLNCRMLHAQLRSGSRSREKLIQANLRMVVHVAKSYQG 355

Query: 351 RGISLHDLLQ 360
           RG+SL DLLQ
Sbjct: 356 RGLSLQDLLQ 365

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449451030|ref|XP_004143265.1| PREDICTED: RNA polymerase sigma factor sigF, chloroplastic-like [Cucumis sativus] gi|449482444|ref|XP_004156283.1| PREDICTED: RNA polymerase sigma factor sigF, chloroplastic-like [Cucumis sativus]

 Score =  295 bits (756), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 180/368 (48%), Positives = 235/368 (63%), Gaps = 21/368 (5%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSS-------VLMHNEQSAPAVASVPTS 53
           MEAG NLLSS   F SR   +  L+ S SS++S S       V M  EQ++PA       
Sbjct: 1   MEAGLNLLSSSSPFISRCHPRSFLAPSCSSAASPSSSSSSSSVYMFPEQASPA------- 53

Query: 54  SVARHFPTSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV 113
              R+F TS L QEQ  E RP   + K+D++SQ T + R IE  +  ++E +  D D L+
Sbjct: 54  ---RYFSTSFLSQEQHHECRPQSQILKDDRSSQMTLERRLIE-RSVPIDEGSRDDHDHLI 109

Query: 114 QDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSA 173
            +L+HQ + WP L +  PP++  E    S+  +S +   E  V  EP + +ALA+KALSA
Sbjct: 110 WELKHQAVEWPGLLSSWPPVQMEEYKISSIEKESYNAAGEMLVKDEPENVIALAKKALSA 169

Query: 174 SKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNH 233
           SK+AA L +  +L G      SL  SL    +E +     R  +RRSKKRKV K   T  
Sbjct: 170 SKQAALLVDETELVGTSLDYSSLDDSLS---KEGRTVRSTRLQDRRSKKRKVPKHVTTID 226

Query: 234 ETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS 293
           E  N R    ++K SE FD NDPLRLFLWGPET+KLLTA EE ELI QIQDL+ L+  K+
Sbjct: 227 EISNFRGKDSRRKTSEKFDPNDPLRLFLWGPETKKLLTAQEESELIVQIQDLMILDNVKA 286

Query: 294 KLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGI 353
           +LQSQF REPTL+EWA+A+G++C+ L+S+LH   +SREKLINANLR+VVH+AKQYQGRG+
Sbjct: 287 RLQSQFDREPTLVEWAEALGITCQHLQSQLHVFQTSREKLINANLRMVVHIAKQYQGRGL 346

Query: 354 SLHDLLQI 361
           SLHDLLQ+
Sbjct: 347 SLHDLLQV 354

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312282671|dbj|BAJ34201.1| unnamed protein product [Thellungiella halophila]

 Score =  281 bits (718), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 177/368 (48%), Positives = 225/368 (61%), Gaps = 38/368 (10%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           MEA RNL+SS PSF ++T +K     S  SS SS V++H + + P V S   +S++RHFP
Sbjct: 1   MEATRNLVSSSPSFQTKTHLK-----SGFSSPSSVVMLHEQTATPVVNSRHLTSLSRHFP 55

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV-----QD 115
            SVL QE R+E +PL H  +ED+TSQ T + R                 D+LV     + 
Sbjct: 56  ASVLSQELREESKPLSHALREDRTSQLTLERRQ---------------FDELVSSREDEK 100

Query: 116 LEHQFLHWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSA 173
            E Q LH   LWNL  SP     + P+V             S DA+  D VALA+KALSA
Sbjct: 101 FEQQLLHSAGLWNLLISPLTTEKQLPAV----------VSPSADADLCDLVALAQKALSA 150

Query: 174 SKEAASLAENPKLNGAEF-TDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTN 232
           SK+AA L EN + +  +   D   TSS     E+       R LERR+K R+  K    +
Sbjct: 151 SKQAALLVENSEADPPDNPRDSLSTSSSMSLPEKGTIVRSKRQLERRAKNRRAPKSNNMD 210

Query: 233 HETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 292
            E Y  +K + KKK+ +GFD +D L+LFLWGPET++LLTA EE ELIA IQ LI+LEK K
Sbjct: 211 SEGYVPQKINAKKKMKQGFDTDDALQLFLWGPETKQLLTAKEEAELIAHIQHLIKLEKVK 270

Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 352
           +KL+SQ G EPT+ EWA+A+GLS   LKSE+H G SSREKLI ANLRLVVH+AKQYQ RG
Sbjct: 271 TKLESQNGCEPTIGEWAEAMGLSSPVLKSEIHRGRSSREKLITANLRLVVHIAKQYQNRG 330

Query: 353 ISLHDLLQ 360
           ++  DLLQ
Sbjct: 331 LNFQDLLQ 338

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297827203|ref|XP_002881484.1| RNA polymerase sigma-70 factor [Arabidopsis lyrata subsp. lyrata] gi|297327323|gb|EFH57743.1| RNA polymerase sigma-70 factor [Arabidopsis lyrata subsp. lyrata]

 Score =  276 bits (707), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 175/368 (47%), Positives = 229/368 (62%), Gaps = 39/368 (10%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           MEA RNL+SS PSF ++T +K      + SS SS V++H + + P V S   +S++RHFP
Sbjct: 1   MEATRNLVSSSPSFQTKTHLK------SYSSPSSVVMLHEQTTTPVVNSRHLNSLSRHFP 54

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV-----QD 115
            SVL QE R+E RPL H  +ED+TSQ T + R                 D+LV     + 
Sbjct: 55  ASVLSQEPREESRPLSHALREDRTSQLTLERRQ---------------FDELVSSREDEK 99

Query: 116 LEHQFLHWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSA 173
            E Q LH   LWNL  SP     + P V   +           DAE  D VALA+KALSA
Sbjct: 100 FEQQLLHSAGLWNLLISPLTAETKLPPVVPPL----------ADAELCDIVALAQKALSA 149

Query: 174 SKEAASLAENPKLNGAEFTDISLTSSLGYPLEEVKQFSQ-PRFLERRSKKRKVSKPQVTN 232
           SK+AA LA++ + N ++ T  SL++S    L E     +  R LERR+K R+  K    +
Sbjct: 150 SKQAALLADDTEANPSDNTRGSLSTSSSMSLPEKGAIVRSKRQLERRAKNRRAPKSNDVD 209

Query: 233 HETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 292
           +E Y  +K + KKK  +G D +D L+LFLWGPET++LLTA EE ELI+ IQ L++LEK K
Sbjct: 210 NEGYVPQKINAKKKFKQGVDTDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVK 269

Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 352
           +KL+SQ G EPT+ EWA+A+G+S  DLKSE+H G SSREKLI ANLRLVVH+AKQYQ RG
Sbjct: 270 TKLESQNGCEPTIGEWAEAMGISSPDLKSEIHRGRSSREKLITANLRLVVHIAKQYQNRG 329

Query: 353 ISLHDLLQ 360
           ++  DLLQ
Sbjct: 330 LNFQDLLQ 337

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18404292|ref|NP_565856.1| RNApolymerase sigma-subunit F [Arabidopsis thaliana] gi|75173811|sp|Q9LD95.1|SIGF_ARATH RecName: Full=RNA polymerase sigma factor sigF, chloroplastic; Short=Sigma factor F; Short=Sigma-F; AltName: Full=Protein SINGLET OXYGEN-LINKED DEATH ACTIVATOR 8; AltName: Full=RNA polymerase sigma factor sig6; Short=Atsig6; Short=Sigma factor 6; Flags: Precursor gi|7209640|dbj|BAA92288.1| SigF [Arabidopsis thaliana] gi|7688083|emb|CAB89775.1| sigma factor-like protein [Arabidopsis thaliana] gi|16604647|gb|AAL24116.1| putative RNA polymerase sigma-70 factor [Arabidopsis thaliana] gi|20197948|gb|AAD31584.2| putative RNA polymerase sigma-70 factor [Arabidopsis thaliana] gi|20259557|gb|AAM14121.1| putative RNA polymerase sigma-70 factor protein [Arabidopsis thaliana] gi|330254238|gb|AEC09332.1| RNApolymerase sigma-subunit F [Arabidopsis thaliana]

 Score =  267 bits (682), Expect = 6e-69,   Method: Compositional matrix adjust.
 Identities = 172/368 (46%), Positives = 226/368 (61%), Gaps = 38/368 (10%)

Query: 1   MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
           MEA RNL+SS PSF ++T +K     S+ SS SS V++H++ + P V S   +S++RHFP
Sbjct: 1   MEATRNLVSSSPSFQTKTHLK-----SSYSSPSSVVMLHDQTTTPVVNSRHLNSLSRHFP 55

Query: 61  TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV-----QD 115
            SVL QE R+E RPL H  ++D+TSQ T + R                 D+LV     + 
Sbjct: 56  ASVLSQEPREESRPLSHALRDDRTSQLTLERRQ---------------FDELVSSREDEK 100

Query: 116 LEHQFLHWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSA 173
            E Q LH   LWNL  SP     + P+V   +           DAE  D VALA+KALSA
Sbjct: 101 FEQQLLHSTGLWNLLISPLTSETKLPAVVSPL----------ADAELCDVVALAQKALSA 150

Query: 174 SKEAASLAENPKLNGAE-FTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTN 232
           SK+AA L ++ + N ++   D   TSS     E+       R LERR+K R+  K    +
Sbjct: 151 SKQAALLVDDTEANPSDNIKDSLSTSSSMSLPEKGNIVRSKRQLERRAKNRRAPKSNDVD 210

Query: 233 HETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 292
            E Y  +K S KKK  +G D +D L+LFLWGPET++LLTA EE ELI+ IQ L++LEK K
Sbjct: 211 DEGYVPQKTSAKKKYKQGADNDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVK 270

Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 352
           +KL+SQ G EPT+ EWA+A+G+S   LKS++H G SSREKLI ANLRLVVH+AKQYQ RG
Sbjct: 271 TKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRG 330

Query: 353 ISLHDLLQ 360
           ++  DLLQ
Sbjct: 331 LNFQDLLQ 338

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	361
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.725	0.478	0.425	1.5e-44
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.407	0.256	0.422	8e-28
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.407	0.256	0.378	1.5e-23
UNIPROTKB|O48655	519	rsigA "Plastid RNA polymerase	0.285	0.198	0.359	6.1e-11
TAIR|locus:2084420	571	SIGC "AT3G53920" [Arabidopsis	0.448	0.283	0.282	5.6e-06
TAIR|locus:2010871	502	SIGA "AT1G64860" [Arabidopsis	0.288	0.207	0.307	1.7e-05
UNIPROTKB|Q59563	323	mysB "RNA polymerase sigma fac	0.155	0.173	0.473	0.0001
TIGR_CMR|GSU_1525	328	GSU_1525 "RNA polymerase sigma	0.121	0.134	0.4	0.00022
TAIR|locus:2167413	517	SIGE "AT5G24120" [Arabidopsis	0.368	0.257	0.273	0.00023

TAIR|locus:2057996 SIGF "AT2G36990" [Arabidopsis thaliana (taxid:3702)]

 Score = 469 (170.2 bits), Expect = 1.5e-44, P = 1.5e-44
 Identities = 120/282 (42%), Positives = 159/282 (56%)

Query:    85 SQATSDSRNIETEAFFVEEKNSGDLDQLVQD--LEHQFLHWPDLWNL--SPPMKRGEDPS 140
             S A  D R   T    +E +   +L    +D   E Q LH   LWNL  SP     + P+
Sbjct:    71 SHALRDDR---TSQLTLERRQFDELVSSREDEKFEQQLLHSTGLWNLLISPLTSETKLPA 127

Query:   141 VSLTMQSLSNDTEESVDAEPFDXXXXXXXXXXXXXXXXXXXXNPKLNGAE-FTD-ISLTS 198
             V   +  L+       DAE  D                    + + N ++   D +S +S
Sbjct:   128 V---VSPLA-------DAELCDVVALAQKALSASKQAALLVDDTEANPSDNIKDSLSTSS 177

Query:   199 SLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLR 258
             S+  P E+       R LERR+K R+  K    + E Y  +K S KKK  +G D +D L+
Sbjct:   178 SMSLP-EKGNIVRSKRQLERRAKNRRAPKSNDVDDEGYVPQKTSAKKKYKQGADNDDALQ 236

Query:   259 LFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRD 318
             LFLWGPET++LLTA EE ELI+ IQ L++LEK K+KL+SQ G EPT+ EWA+A+G+S   
Sbjct:   237 LFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPV 296

Query:   319 LKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
             LKS++H G SSREKLI ANLRLVVH+AKQYQ RG++  DLLQ
Sbjct:   297 LKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQ 338

GO:0003677 "DNA binding" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISM

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0006352 "DNA-dependent transcription, initiation" evidence=TAS

GO:0009507 "chloroplast" evidence=IDA

GO:0009536 "plastid" evidence=IDA

GO:0016987 "sigma factor activity" evidence=ISS;IDA

GO:0071483 "cellular response to blue light" evidence=IEP

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA;IMP

GO:0071482 "cellular response to light stimulus" evidence=IMP

GO:0090351 "seedling development" evidence=IMP

GO:0001053 "plastid sigma factor activity" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0030154 "cell differentiation" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

UNIPROTKB|Q84LK8 SIG6 "Sig6" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 317 (116.6 bits), Expect = 8.0e-28, P = 8.0e-28
 Identities = 63/149 (42%), Positives = 97/149 (65%)

Query:   214 RFLERRSKKRKVSKPQVTNHETY--NSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLT 271
             R LERRSK+R   +  + +      NS+K    KK     + ++P +LFL   ET + LT
Sbjct:   216 RLLERRSKRRYAPRASIADVSCSADNSKKKEKSKKYGRVLEPDEPFKLFLRDRETTEFLT 275

Query:   272 ADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE 331
             A EE  L ++IQ L+++E+   KL+ Q GREPTL EWA+A+G+S ++L+S + +G   RE
Sbjct:   276 AKEERHLFSKIQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRRCRE 335

Query:   332 KLINANLRLVVHVAKQYQGRGISLHDLLQ 360
             K+  +N RLV+HVA++Y+G G+ + DL+Q
Sbjct:   336 KMARSNFRLVIHVARKYEGYGLDIQDLVQ 364

GO:0009536 "plastid" evidence=RCA

TAIR|locus:2025650 SIG2 "AT1G08540" [Arabidopsis thaliana (taxid:3702)]

 Score = 278 (102.9 bits), Expect = 1.5e-23, P = 1.5e-23
 Identities = 56/148 (37%), Positives = 92/148 (62%)

Query:   214 RFLERRSKKRKVSKPQVTNHETYNSRKASVKKKL-SEGFDRNDPLRLFLWGPETRKLLTA 272
             R  ER++++ K  +   +   +  +  +  KK+L ++  D NDPLR       + KLLT 
Sbjct:   216 RQTERKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTV 275

Query:   273 DEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332
              EE EL A IQDL++LE+ +++L  + GR+PT  +WA A G+  + L+  +H G   ++K
Sbjct:   276 REEHELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDK 335

Query:   333 LINANLRLVVHVAKQYQGRGISLHDLLQ 360
             +I +N+RLV+ +AK YQG G++L DL+Q
Sbjct:   336 MIKSNIRLVISIAKNYQGAGMNLQDLVQ 363

GO:0003677 "DNA binding" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0071482 "cellular response to light stimulus" evidence=IEP;IMP

GO:0006352 "DNA-dependent transcription, initiation" evidence=IDA;TAS

GO:0009658 "chloroplast organization" evidence=IMP

GO:0006399 "tRNA metabolic process" evidence=IMP

GO:0001053 "plastid sigma factor activity" evidence=IMP

GO:2001141 "regulation of RNA biosynthetic process" evidence=IMP

GO:0009637 "response to blue light" evidence=IGI;RCA

GO:0010114 "response to red light" evidence=IEP;RCA

GO:0006098 "pentose-phosphate shunt" evidence=RCA

GO:0006364 "rRNA processing" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010218 "response to far red light" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

GO:0019288 "isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0016987 "sigma factor activity" evidence=ISS

UNIPROTKB|O48655 rsigA "Plastid RNA polymerase sigma factor" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 178 (67.7 bits), Expect = 6.1e-11, P = 6.1e-11
 Identities = 37/103 (35%), Positives = 67/103 (65%)

Query:   258 RLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCR 317
             R++L G  +++LLT  +   L  +I+D I L++++SKL+ + G EP+  + A ++ +S  
Sbjct:   205 RIYLRGTVSKELLTHKQVVHLSHKIKDGIWLQQQRSKLKEKLGNEPSYKQLAHSLKISPP 264

Query:   318 DLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
             +L+S +H    +RE L  +NLRLV+ +A++Y   G+ L DL+Q
Sbjct:   265 ELRSRMHESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQ 307

GO:0009416 "response to light stimulus" evidence=IEP

TAIR|locus:2084420 SIGC "AT3G53920" [Arabidopsis thaliana (taxid:3702)]

 Score = 135 (52.6 bits), Expect = 5.6e-06, P = 5.6e-06
 Identities = 48/170 (28%), Positives = 87/170 (51%)

Query:   195 SLTSSLGYPLEEVKQF-SQPRFLERRSK-KRKVSKPQVTNHETYNSRKASVKKKLSEGFD 252
             S+TS L    E V    +Q  F+  R K K+K  +  VT     N  ++S+   L   ++
Sbjct:   198 SITSCLSDTTELVDTTPNQQVFVSSRRKVKKKARRSSVTAE---NGDQSSLPIGLRTTWN 254

Query:   253 RNDPLRLFLWGPETRKLLT--ADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAK 310
               D  R+    P+ RK     +  E E+   ++ +  +E+ +++L+ + G+  +L  WA 
Sbjct:   255 NIDVPRVRR-PPKYRKKRERISRNETEMSTGVKIVADMERIRTQLEEESGKVASLSCWAA 313

Query:   311 AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
             A G++ + L   LH G   R++L+ +   LV+ +A+ Y+G GI+  DL+Q
Sbjct:   314 AAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLGIAHEDLIQ 363

GO:0003677 "DNA binding" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS;IMP

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0019685 "photosynthesis, dark reaction" evidence=NAS

GO:0006352 "DNA-dependent transcription, initiation" evidence=IDA;TAS

GO:0071482 "cellular response to light stimulus" evidence=IEP

GO:0001053 "plastid sigma factor activity" evidence=IMP

GO:2001141 "regulation of RNA biosynthetic process" evidence=IMP

GO:0016987 "sigma factor activity" evidence=ISS

TAIR|locus:2010871 SIGA "AT1G64860" [Arabidopsis thaliana (taxid:3702)]

 Score = 130 (50.8 bits), Expect = 1.7e-05, P = 1.7e-05
 Identities = 32/104 (30%), Positives = 63/104 (60%)

Query:   257 LRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSC 316
             +R ++ G  +  +L+  E   L  +I+  +RL+  KS+L+ + G EP+  + A ++ +S 
Sbjct:   187 VRGYVKGVISEDVLSHVEVVRLSKKIKSGLRLDDHKSRLKDRLGCEPSDEQLAVSLKISR 246

Query:   317 RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
              +L++ L   + +REKL  +N+RLV+ +A++Y   G  + DL+Q
Sbjct:   247 AELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQ 290

GO:0003677 "DNA binding" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS;IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0071482 "cellular response to light stimulus" evidence=IEP

GO:0006352 "DNA-dependent transcription, initiation" evidence=IDA;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0001053 "plastid sigma factor activity" evidence=IMP

GO:2001141 "regulation of RNA biosynthetic process" evidence=IMP

GO:0071461 "cellular response to redox state" evidence=IDA

GO:0080005 "photosystem stoichiometry adjustment" evidence=IDA

GO:0006833 "water transport" evidence=RCA

GO:0009651 "response to salt stress" evidence=RCA

GO:0009750 "response to fructose stimulus" evidence=RCA

GO:0016987 "sigma factor activity" evidence=ISS

UNIPROTKB|Q59563 mysB "RNA polymerase sigma factor" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 120 (47.3 bits), Expect = 0.00010, P = 0.00010
 Identities = 27/57 (47%), Positives = 39/57 (68%)

Query:   305 LIEWAKAIGLSC-RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
             L+E  K +G +  RDL + +  G ++R  L+ ANLRLVV +AK+Y GRG+ L DL+Q
Sbjct:    61 LLETRKRLGENRKRDLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQ 117

GO:0001666 "response to hypoxia" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009408 "response to heat" evidence=IEP

GO:0009410 "response to xenobiotic stimulus" evidence=IEP

GO:0016987 "sigma factor activity" evidence=IGI

GO:0019217 "regulation of fatty acid metabolic process" evidence=IDA

GO:0040007 "growth" evidence=IMP

GO:0043175 "RNA polymerase core enzyme binding" evidence=IDA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

GO:0050708 "regulation of protein secretion" evidence=IDA

TIGR_CMR|GSU_1525 GSU_1525 "RNA polymerase sigma-70 factor family" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 92 (37.4 bits), Expect = 0.00022, Sum P(2) = 0.00022
 Identities = 18/45 (40%), Positives = 32/45 (71%)

Query:   317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
             ++L   +  G+ ++R+K+I +NLRLVV +AK+Y  RG+   DL++
Sbjct:    79 KELAGRIAKGDKAARDKMIESNLRLVVKIAKRYINRGLPFLDLIE 123

GO:0006352 "DNA-dependent transcription, initiation" evidence=ISS

GO:0016987 "sigma factor activity" evidence=ISS

TAIR|locus:2167413 SIGE "AT5G24120" [Arabidopsis thaliana (taxid:3702)]

 Score = 120 (47.3 bits), Expect = 0.00023, P = 0.00023
 Identities = 38/139 (27%), Positives = 70/139 (50%)

Query:   216 LERR-SKKRKVS-KPQVTNHETYNSRKASVKKKLSE---GFDRNDPLRLFLWGP-ETRKL 269
             L++R + KR V  KP V + +   +++   ++K+      +  ++ +    W   +   +
Sbjct:   160 LDKRIALKRNVQEKPVVASVDKKVTKRQQEEEKIERLVRDYSASNDIVSLDWKKMKIPPV 219

Query:   270 LTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSS 329
             L++ E   L   +Q +  L + K  LQ   GREP   E A  I ++  ++K ++  G ++
Sbjct:   220 LSSTEHAWLFKLMQPMKALLEVKDVLQKSLGREPREAEIAGEINMTAGEVKKKIEIGRAA 279

Query:   330 REKLINANLRLVVHVAKQY 348
             R KLI  NLRLV+ V  +Y
Sbjct:   280 RNKLIKHNLRLVLFVMNKY 298


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.314   0.131   0.372    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      361       314   0.00081  116 3  11 23  0.45    34
                                                     33  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  9
  No. of states in DFA:  606 (64 KB)
  Total size of DFA:  213 KB (2119 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  27.78u 0.10s 27.88t   Elapsed:  00:00:01
  Total cpu time:  27.78u 0.10s 27.88t   Elapsed:  00:00:01
  Start:  Fri May 10 15:40:01 2013   End:  Fri May 10 15:40:02 2013

GO:0003677 "DNA binding" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS

GO:0006352 "DNA-dependent transcription, initiation" evidence=ISS;TAS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0016987 "sigma factor activity" evidence=ISS

GO:0071483 "cellular response to blue light" evidence=IEP

GO:0005739 "mitochondrion" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0001053 "plastid sigma factor activity" evidence=IMP

GO:0010207 "photosystem II assembly" evidence=IMP

GO:2001141 "regulation of RNA biosynthetic process" evidence=IMP

GO:0010114 "response to red light" evidence=IEP

GO:0010218 "response to far red light" evidence=IEP

GO:0009637 "response to blue light" evidence=IGI

GO:0009658 "chloroplast organization" evidence=IMP

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IMP

GO:0010264 "myo-inositol hexakisphosphate biosynthetic process" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	361
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	3e-26
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	5e-24
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	1e-21
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	8e-19
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	2e-13
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	8e-11
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	6e-09
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-08
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	2e-06
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	6e-06
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	5e-05
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	7e-05
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	1e-04
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	2e-04
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	2e-04
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	7e-04
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	0.002
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	0.002
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	0.002
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	0.002
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	0.004

>gnl|CDD|234082 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma factor, cyanobacterial RpoD-like family

 Score =  106 bits (266), Expect = 3e-26
 Identities = 48/92 (52%), Positives = 65/92 (70%)

Query: 269 LLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS 328
           LLT +EE EL  Q+Q ++ LE+ + +L+ Q GREP+  EWA A GLS  +L+  L  G  
Sbjct: 15  LLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQR 74

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           ++EK+I ANLRLVV VAK+YQ RG+ L DL+Q
Sbjct: 75  AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQ 106

This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393). Length = 298

>gnl|CDD|236012 PRK07406, PRK07406, RNA polymerase sigma factor RpoD; Validated

 Score =  101 bits (252), Expect = 5e-24
 Identities = 46/123 (37%), Positives = 72/123 (58%), Gaps = 5/123 (4%)

Query: 238 SRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS 297
             K   KK  +E     D +R++L      +LL  DEE EL  +I DL+ LE+ + + +S
Sbjct: 51  RIKIGPKKVYTE-----DSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFES 105

Query: 298 QFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHD 357
           + GREP+  EWA+ + +     +  L  G  ++EK++ +NLRLVV +AK+Y  RG+S  D
Sbjct: 106 ELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQD 165

Query: 358 LLQ 360
           L+Q
Sbjct: 166 LIQ 168

Length = 373

>gnl|CDD|180963 PRK07405, PRK07405, RNA polymerase sigma factor SigD; Validated

 Score = 93.3 bits (232), Expect = 1e-21
 Identities = 45/106 (42%), Positives = 66/106 (62%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 314
           D +R +L       LLT +EE     Q+Q L+ L++ + +L  + GREPT  EWAKA  L
Sbjct: 8   DLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKL 67

Query: 315 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           S  +L+S +  G +++ K++ ANLRLVV VAK+Y  R + L DL+Q
Sbjct: 68  SEEELRSAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQ 113

Length = 317

>gnl|CDD|180321 PRK05949, PRK05949, RNA polymerase sigma factor; Validated

 Score = 85.7 bits (212), Expect = 8e-19
 Identities = 41/92 (44%), Positives = 60/92 (65%)

Query: 269 LLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS 328
           LLT ++E     Q+Q ++ L + K  L  + GREP+L EWA+A+ LS  +LK  L  G  
Sbjct: 32  LLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKR 91

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           +++K+I ANLRLVV +AK+YQ R +   DL+Q
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQ 123

Length = 327

>gnl|CDD|236067 PRK07598, PRK07598, RNA polymerase sigma factor SigC; Validated

 Score = 70.3 bits (172), Expect = 2e-13
 Identities = 45/148 (30%), Positives = 63/148 (42%), Gaps = 42/148 (28%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKE--------------------KSK 294
           D +RL+L      +LL  DEE     ++Q  ++L                       + +
Sbjct: 60  DLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRER 119

Query: 295 LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS----------------------SREK 332
           L S+ G  P+L  WAK   +S  DLK  L  G                        ++E 
Sbjct: 120 LTSELGHRPSLERWAKTADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEH 179

Query: 333 LINANLRLVVHVAKQYQGRGISLHDLLQ 360
           +I ANLRLVV VAK+YQ RG+ L DL+Q
Sbjct: 180 MIKANLRLVVSVAKKYQNRGLELLDLVQ 207

Length = 415

>gnl|CDD|223642 COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]

 Score = 62.3 bits (152), Expect = 8e-11
 Identities = 36/112 (32%), Positives = 51/112 (45%), Gaps = 20/112 (17%)

Query: 269 LLTADEEFELIAQIQDLIRLEKEKSKL-QSQFGREPTL---------------IEWAKAI 312
           LL  + E EL  Q++D   L +    L   + GREP+                IE A  +
Sbjct: 23  LLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLL 82

Query: 313 GLS-CRDLKSELHSGNSSRE---KLINANLRLVVHVAKQYQGRGISLHDLLQ 360
                + L   L  G    +   KL+ +NLRLVV +AK+Y GRG+   DL+Q
Sbjct: 83  TPEEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQ 134

Length = 342

>gnl|CDD|181169 PRK07921, PRK07921, RNA polymerase sigma factor SigB; Reviewed

 Score = 56.3 bits (136), Expect = 6e-09
 Identities = 39/107 (36%), Positives = 60/107 (56%), Gaps = 15/107 (14%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 314
           D +R++L G     LLTA +E EL  +I+         + L ++      L+E  K +  
Sbjct: 26  DLVRVYLNGIGKTALLTAADEVELAKRIE---------AGLYAE-----HLLETRKRLSE 71

Query: 315 SC-RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           +  RDL + +  G ++R  L+ ANLRLVV +AK+Y GRG+ L DL+Q
Sbjct: 72  ARKRDLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQ 118

Length = 324

>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score = 56.2 bits (136), Expect = 1e-08
 Identities = 35/93 (37%), Positives = 46/93 (49%), Gaps = 13/93 (13%)

Query: 268 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN 327
           KLL A+EE EL        R+E         +  E  L E  K      RDL+     G 
Sbjct: 224 KLLNAEEEVELA------KRIEAG------LYAEE-LLAEGEKLDPELRRDLQWIGRDGK 270

Query: 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
            ++  L+ ANLRLVV +AK+Y  RG+S  DL+Q
Sbjct: 271 RAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQ 303

Length = 509

>gnl|CDD|213709 TIGR02393, RpoD_Cterm, RNA polymerase sigma factor RpoD, C-terminal domain

 Score = 48.5 bits (116), Expect = 2e-06
 Identities = 16/31 (51%), Positives = 25/31 (80%)

Query: 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           +++L+ +NLRLVV +AK+Y  RG+S  DL+Q
Sbjct: 2   KKQLVESNLRLVVSIAKKYTNRGLSFLDLIQ 32

This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc [Transcription, Transcription factors]. Length = 238

>gnl|CDD|236413 PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated

 Score = 47.3 bits (113), Expect = 6e-06
 Identities = 35/114 (30%), Positives = 48/114 (42%), Gaps = 42/114 (36%)

Query: 248 SEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIE 307
             G   NDP+R++L       LLTA+EE EL                             
Sbjct: 89  PPGVKINDPVRMYLKEIGRVPLLTAEEEIEL----------------------------- 119

Query: 308 WAKAIGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
            AK I             G+  ++++L  ANLRLVV +AK+Y GRG+   DL+Q
Sbjct: 120 -AKRIE-----------EGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQ 161

Length = 367

>gnl|CDD|181296 PRK08215, PRK08215, sporulation sigma factor SigG; Reviewed

 Score = 44.2 bits (105), Expect = 5e-05
 Identities = 20/46 (43%), Positives = 31/46 (67%), Gaps = 1/46 (2%)

Query: 317 RDLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI 361
           R+L   + +G   +REKLIN NLRLV+ V +++  RG ++ DL Q+
Sbjct: 25  RELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQV 70

Length = 258

>gnl|CDD|234078 TIGR02980, SigBFG, RNA polymerase sigma-70 factor, sigma-B/F/G subfamily

 Score = 43.4 bits (103), Expect = 7e-05
 Identities = 14/32 (43%), Positives = 22/32 (68%)

Query: 330 REKLINANLRLVVHVAKQYQGRGISLHDLLQI 361
           REKL+  NL LV  +A++++ RG    DL+Q+
Sbjct: 5   REKLVELNLPLVRSIARRFRNRGEPHEDLVQV 36

This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage. Length = 227

>gnl|CDD|131897 TIGR02850, spore_sigG, RNA polymerase sigma-G factor

 Score = 42.5 bits (100), Expect = 1e-04
 Identities = 21/46 (45%), Positives = 32/46 (69%), Gaps = 1/46 (2%)

Query: 317 RDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQI 361
           R+L   + SG+ ++REKLIN NLRLV+ V +++  RG  + DL Q+
Sbjct: 22  RELFIRMQSGDTTAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQV 67

Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 254

>gnl|CDD|131447 TIGR02394, rpoS_proteo, RNA polymerase sigma factor RpoS

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 16/32 (50%), Positives = 24/32 (75%)

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           +R+ +I +NLRLVV +AK Y  RG+ L DL++
Sbjct: 47  ARKVMIESNLRLVVSIAKHYVNRGLPLLDLIE 78

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393) [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]. Length = 285

>gnl|CDD|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated

 Score = 42.2 bits (100), Expect = 2e-04
 Identities = 16/31 (51%), Positives = 26/31 (83%)

Query: 328 SSREKLINANLRLVVHVAKQYQGRGISLHDL 358
           ++R+++I +NLRLVV +AK+Y  RG++L DL
Sbjct: 86  AARQRMIESNLRLVVKIAKRYLNRGLALLDL 116

Length = 325

>gnl|CDD|236228 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed

 Score = 40.2 bits (95), Expect = 7e-04
 Identities = 18/45 (40%), Positives = 30/45 (66%), Gaps = 1/45 (2%)

Query: 318 DLKSELHSG-NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI 361
            L ++L  G  + R  LI  NLRLVV++A++++  GI++ DL+ I
Sbjct: 41  YLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISI 85

Length = 234

>gnl|CDD|233844 TIGR02392, rpoH_proteo, alternative sigma factor RpoH

 Score = 39.2 bits (92), Expect = 0.002
 Identities = 13/29 (44%), Positives = 21/29 (72%)

Query: 332 KLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           KL+ ++LR VV +A+ Y+G G+   DL+Q
Sbjct: 39  KLVLSHLRFVVKIARGYRGYGLPQADLIQ 67

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]. Length = 270

>gnl|CDD|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score = 39.8 bits (94), Expect = 0.002
 Identities = 23/81 (28%), Positives = 42/81 (51%), Gaps = 8/81 (9%)

Query: 281 QIQDLIRLEKEKSKLQSQFGREPT-LIEWAKAIGLSCRDLKSELHSGNSSREKLINANLR 339
              ++ +L++E   ++ + G     L E  + I       K E  +  + +E ++ ANLR
Sbjct: 339 VYDEIKKLQQELEAIEEETGLTIEELKEINRQI------SKGEAKARRAKKE-MVEANLR 391

Query: 340 LVVHVAKQYQGRGISLHDLLQ 360
           LV+ +AK+Y  RG+   DL+Q
Sbjct: 392 LVISIAKKYTNRGLQFLDLIQ 412

Length = 619

>gnl|CDD|218138 pfam04542, Sigma70_r2, Sigma-70 region 2

 Score = 36.0 bits (84), Expect = 0.002
 Identities = 11/28 (39%), Positives = 16/28 (57%)

Query: 333 LINANLRLVVHVAKQYQGRGISLHDLLQ 360
           L+   L LV  +A++Y G G    DL+Q
Sbjct: 1   LVERYLPLVYSLARRYLGDGADAEDLVQ 28

Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation. Length = 71

>gnl|CDD|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed

 Score = 38.8 bits (91), Expect = 0.002
 Identities = 14/33 (42%), Positives = 21/33 (63%)

Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQI 361
           +R  LI  NLRLV H+ K+++  G  + DL+ I
Sbjct: 50  ARNILIERNLRLVAHIVKKFENTGEDVDDLISI 82

Length = 233

>gnl|CDD|131882 TIGR02835, spore_sigmaE, RNA polymerase sigma-E factor

 Score = 37.9 bits (88), Expect = 0.004
 Identities = 15/35 (42%), Positives = 25/35 (71%)

Query: 327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI 361
            S++  LI  NLRLVV++A++++  GI + DL+ I
Sbjct: 51  ESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSI 85

Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 234

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	361
PRK07598	415	RNA polymerase sigma factor SigC; Validated	99.89
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	99.85
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	99.82
PRK05949	327	RNA polymerase sigma factor; Validated	99.79
PRK07405	317	RNA polymerase sigma factor SigD; Validated	99.79
PRK05901	509	RNA polymerase sigma factor; Provisional	99.59
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	99.51
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	99.38
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	98.97
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	98.79
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	98.64
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	98.61
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	98.54
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	98.29
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	98.1
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	98.1
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	98.07
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	97.8
PRK08215	258	sporulation sigma factor SigG; Reviewed	97.68
PRK05803	233	sporulation sigma factor SigK; Reviewed	97.49
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	97.13
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	96.86
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	96.71
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	96.49
PRK08583	257	RNA polymerase sigma factor SigB; Validated	96.42
PRK05572	252	sporulation sigma factor SigF; Validated	96.04
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	94.18
PRK08301	234	sporulation sigma factor SigE; Reviewed	92.41
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	90.42
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	86.21
PRK11922	231	RNA polymerase sigma factor; Provisional	86.1
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	82.09
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	81.99
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	80.86

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=99.89  E-value=3e-23  Score=208.63  Aligned_cols=109  Identities=41%  Similarity=0.642  Sum_probs=101.8

Q ss_pred             CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHHhhCCCCcHHHHHHHh
Q 018065          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR--------------------LEKEKSKLQSQFGREPTLIEWAKAI  312 (361)
Q Consensus       253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~--------------------LEkir~~Le~~lGrePT~~EWA~Aa  312 (361)
                      .+|+++.||++|++.||||++||++|+++||++++                    |++++.+|++++|++||..|||.++
T Consensus        58 ~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~  137 (415)
T PRK07598         58 STDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTA  137 (415)
T ss_pred             CCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHh
Confidence            57999999999999999999999999999999999                    8999999999999999999999888


Q ss_pred             ccchhhhhhhc----------------------cccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065          313 GLSCRDLKSEL----------------------HSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI  361 (361)
Q Consensus       313 G~d~~~Lr~~L----------------------~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQi  361 (361)
                      |+++.+|+.+|                      ..|..|+++||++|+|||++||++|.|+|+.++||||.
T Consensus       138 ~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQE  208 (415)
T PRK07598        138 DISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQE  208 (415)
T ss_pred             CCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHH
Confidence            77766666665                      57889999999999999999999999999999999993

>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family

Probab=99.85  E-value=2.1e-21  Score=185.07  Aligned_cols=106  Identities=49%  Similarity=0.758  Sum_probs=103.6

Q ss_pred             cHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHH
Q 018065          255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLI  334 (361)
Q Consensus       255 D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI  334 (361)
                      |++..||++++++|+||++||.+|+++|++++.+++++.+|++++|++||..+||+++|++..+|..++..|..|+++||
T Consensus         1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv   80 (298)
T TIGR02997         1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI   80 (298)
T ss_pred             CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence            46788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhHHHHHHHHHhcCCCCCCccCccC
Q 018065          335 NANLRLVVHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       335 ~sNLRLVVSIAKrY~grGLsfqDLIQ  360 (361)
                      .+|+|||++||++|.|+|++++||||
T Consensus        81 ~~~lrlV~~iA~~y~~~~~~~eDLiQ  106 (298)
T TIGR02997        81 KANLRLVVSVAKKYQNRGLELLDLIQ  106 (298)
T ss_pred             HHhHHHHHHHHHHHhcCCCCHHHHHH
Confidence            99999999999999999999999998

This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=99.82  E-value=5e-20  Score=182.97  Aligned_cols=109  Identities=39%  Similarity=0.693  Sum_probs=106.2

Q ss_pred             CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHH
Q 018065          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (361)
Q Consensus       253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARek  332 (361)
                      ..|++..||++++++|+||++||++|+++|++++.|++++.+|++.+|++|+..+||.++|++..+|++++..|..|+++
T Consensus        61 ~~d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~  140 (373)
T PRK07406         61 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEK  140 (373)
T ss_pred             CCCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHH
Confidence            46789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065          333 LINANLRLVVHVAKQYQGRGISLHDLLQI  361 (361)
Q Consensus       333 LI~sNLRLVVSIAKrY~grGLsfqDLIQi  361 (361)
                      ||.+|++||++||++|.|+|++++||||.
T Consensus       141 Li~~~l~lV~~iA~ry~~~~~~~eDLiQE  169 (373)
T PRK07406        141 MVQSNLRLVVSIAKKYMNRGLSFQDLIQE  169 (373)
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            99999999999999999999999999983

>PRK05949 RNA polymerase sigma factor; Validated

Probab=99.79  E-value=5.2e-19  Score=172.31  Aligned_cols=108  Identities=41%  Similarity=0.643  Sum_probs=105.8

Q ss_pred             CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHH
Q 018065          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (361)
Q Consensus       253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARek  332 (361)
                      ..|++..||++|+++|+||++||++|++.|+.++.+++.+..|+..+|++|+..+||.++|++..+|...+..|..|+++
T Consensus        16 ~~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~   95 (327)
T PRK05949         16 SADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQK   95 (327)
T ss_pred             CCCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065          333 LINANLRLVVHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       333 LI~sNLRLVVSIAKrY~grGLsfqDLIQ  360 (361)
                      ||.+|+++|++||++|.|.|++++||||
T Consensus        96 Li~~~~~~V~~iA~~y~~~~~~~eDLvQ  123 (327)
T PRK05949         96 MIEANLRLVVAIAKKYQKRNMEFLDLIQ  123 (327)
T ss_pred             HHHHHHHHHHHHHHHHccCCCCHHHHHH
Confidence            9999999999999999999999999998

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=99.79  E-value=4.4e-19  Score=171.71  Aligned_cols=108  Identities=42%  Similarity=0.625  Sum_probs=105.5

Q ss_pred             CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHH
Q 018065          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (361)
Q Consensus       253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARek  332 (361)
                      .+|++..||++++++|+||++||++|+++|++++.+++++..|++++|++|+..+||.++|++...|...+..|..|+++
T Consensus         6 ~~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~   85 (317)
T PRK07405          6 STDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK   85 (317)
T ss_pred             CCcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHH
Confidence            36789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065          333 LINANLRLVVHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       333 LI~sNLRLVVSIAKrY~grGLsfqDLIQ  360 (361)
                      ||.+|+++|+++|++|.|.|.+++||||
T Consensus        86 L~~~~~~~V~~~a~~~~~~~~~~eDLvQ  113 (317)
T PRK07405         86 MVEANLRLVVSVAKKYLKRNVDLLDLIQ  113 (317)
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence            9999999999999999999999999998

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=99.59  E-value=1.2e-15  Score=157.37  Aligned_cols=96  Identities=38%  Similarity=0.507  Sum_probs=80.6

Q ss_pred             CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHH
Q 018065          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (361)
Q Consensus       253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARek  332 (361)
                      ..|+++.||++|+++|+||++||++|+++|+.+..++..   +++  |     .+|+.   ....+|+.+++.|..||++
T Consensus       209 ~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~~--~-----~~~~~---~~~~~l~~~~~~g~~Ar~~  275 (509)
T PRK05901        209 TADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LAE--G-----EKLDP---ELRRDLQWIGRDGKRAKNH  275 (509)
T ss_pred             cccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hhh--c-----ccchh---hhhhhhhhhccchHHHHHH
Confidence            578999999999999999999999999999986443321   111  1     23442   2567899999999999999


Q ss_pred             HHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065          333 LINANLRLVVHVAKQYQGRGISLHDLLQI  361 (361)
Q Consensus       333 LI~sNLRLVVSIAKrY~grGLsfqDLIQi  361 (361)
                      ||.+|||||++||++|.|+|++|+||||.
T Consensus       276 LI~sNLrLVvsIAkrY~~~Gl~~eDLIQE  304 (509)
T PRK05901        276 LLEANLRLVVSLAKRYTNRGLSFLDLIQE  304 (509)
T ss_pred             HHHHhHHHHHHHHHHHhcCCCCHHHHHHH
Confidence            99999999999999999999999999994

>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]

Probab=99.51  E-value=1.6e-14  Score=142.80  Aligned_cols=108  Identities=35%  Similarity=0.517  Sum_probs=94.4

Q ss_pred             CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-hhCCCCcHH---------------HHHHHhccch
Q 018065          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS-QFGREPTLI---------------EWAKAIGLSC  316 (361)
Q Consensus       253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~-~lGrePT~~---------------EWA~AaG~d~  316 (361)
                      ..|.+..|+.+++..++++.++|.++.+.+++...+......|.. ..|..|+..               +|+.....++
T Consensus         7 ~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E   86 (342)
T COG0568           7 SADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE   86 (342)
T ss_pred             chhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence            467899999999999999999999999999988888777777777 678888886               6665555544


Q ss_pred             -hhhhhhccccHH---HHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065          317 -RDLKSELHSGNS---SREKLINANLRLVVHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       317 -~~Lr~~L~~G~~---ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ  360 (361)
                       ..|..++..|..   |+.+||.+||||||+|||+|.|+|++|.||||
T Consensus        87 e~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQ  134 (342)
T COG0568          87 EKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQ  134 (342)
T ss_pred             HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHh
Confidence             778888888865   99999999999999999999999999999999

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=99.38  E-value=5.5e-13  Score=130.39  Aligned_cols=96  Identities=38%  Similarity=0.523  Sum_probs=80.7

Q ss_pred             CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHH
Q 018065          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (361)
Q Consensus       253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARek  332 (361)
                      ..|++..||++++++|+||++||.+|+++|+.+..++..           |+..+|+...  ...+|+.+++.|..|+++
T Consensus        24 ~~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~   90 (324)
T PRK07921         24 AADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRH   90 (324)
T ss_pred             CCChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHH
Confidence            357899999999999999999999999999987665543           2223333111  456789999999999999


Q ss_pred             HHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065          333 LINANLRLVVHVAKQYQGRGISLHDLLQI  361 (361)
Q Consensus       333 LI~sNLRLVVSIAKrY~grGLsfqDLIQi  361 (361)
                      ||.+|+++|++||++|.|.|++++||||.
T Consensus        91 Lv~~~~~lV~~iA~r~~~~~~~~eDLvQE  119 (324)
T PRK07921         91 LLEANLRLVVSLAKRYTGRGMPLLDLIQE  119 (324)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence            99999999999999999999999999983

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=98.97  E-value=6.6e-10  Score=110.04  Aligned_cols=70  Identities=46%  Similarity=0.734  Sum_probs=64.5

Q ss_pred             CCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHH
Q 018065          252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE  331 (361)
Q Consensus       252 ~~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARe  331 (361)
                      ..+|+++.||++|+++|+||.+||.+|++.++.               |                         +..|++
T Consensus        93 ~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~---------------G-------------------------d~~A~~  132 (367)
T PRK09210         93 KINDPVRMYLKEIGRVPLLTAEEEIELAKRIEE---------------G-------------------------DEEAKQ  132 (367)
T ss_pred             ccCcHHHHHHHHhhccCCCCHHHHHHHHHHHHh---------------h-------------------------HHHHHH
Confidence            357899999999999999999999999998875               4                         467999


Q ss_pred             HHHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065          332 KLINANLRLVVHVAKQYQGRGISLHDLLQI  361 (361)
Q Consensus       332 kLI~sNLRLVVSIAKrY~grGLsfqDLIQi  361 (361)
                      +||..|+++|++||++|.|+|+.++||||.
T Consensus       133 ~Li~~~~~lV~~iA~~~~~~~~~~eDLiQE  162 (367)
T PRK09210        133 RLAEANLRLVVSIAKRYVGRGMLFLDLIQE  162 (367)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence            999999999999999999999999999983

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=98.79  E-value=3.4e-09  Score=111.35  Aligned_cols=35  Identities=40%  Similarity=0.787  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI  361 (361)
Q Consensus       327 ~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQi  361 (361)
                      ..|+++||.+|||||++|||+|.|+|++|.||||.
T Consensus       379 ~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQe  413 (619)
T PRK05658        379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE  413 (619)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHH
Confidence            47999999999999999999999999999999994

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=98.64  E-value=4.4e-08  Score=93.75  Aligned_cols=71  Identities=30%  Similarity=0.551  Sum_probs=63.2

Q ss_pred             CCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHH
Q 018065          252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE  331 (361)
Q Consensus       252 ~~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARe  331 (361)
                      .+.+++..|+++++++|+|+.++|.+|+..++.              .|                         +..|++
T Consensus        11 ~~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~--------------~G-------------------------d~~a~~   51 (284)
T PRK06596         11 SPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLRE--------------HG-------------------------DLEAAK   51 (284)
T ss_pred             CCccHHHHHHHHHhccCCCCHHHHHHHHHHHHH--------------cC-------------------------CHHHHH
Confidence            356799999999999999999999999986542              14                         578999


Q ss_pred             HHHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065          332 KLINANLRLVVHVAKQYQGRGISLHDLLQI  361 (361)
Q Consensus       332 kLI~sNLRLVVSIAKrY~grGLsfqDLIQi  361 (361)
                      +||..|++||.+||++|.+.|++++||||.
T Consensus        52 ~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQe   81 (284)
T PRK06596         52 QLVLSHLRFVVHIARGYRGYGLPQADLIQE   81 (284)
T ss_pred             HHHHHhHHHHHHHHHHhcCCCCCHHHHHHH
Confidence            999999999999999999999999999984

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=98.61  E-value=5.1e-08  Score=92.17  Aligned_cols=67  Identities=30%  Similarity=0.582  Sum_probs=60.0

Q ss_pred             HHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHH
Q 018065          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (361)
Q Consensus       256 ~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~  335 (361)
                      ++..||++++++|+|+.++|.+|+..+..              .|                         +..|+++||.
T Consensus         2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~--------------~g-------------------------d~~a~~~Lv~   42 (270)
T TIGR02392         2 SLDAYIRAVNRIPMLTPEEEYQLAKRLRE--------------HG-------------------------DLDAAKKLVL   42 (270)
T ss_pred             hHHHHHHHHhcCCCCCHHHHHHHHHHHHH--------------CC-------------------------CHHHHHHHHH
Confidence            57889999999999999999999986432              13                         6789999999


Q ss_pred             HhHHHHHHHHHhcCCCCCCccCccCC
Q 018065          336 ANLRLVVHVAKQYQGRGISLHDLLQI  361 (361)
Q Consensus       336 sNLRLVVSIAKrY~grGLsfqDLIQi  361 (361)
                      .|+++|.++|++|.+.|.+++||||.
T Consensus        43 ~~~~lV~~~a~~~~~~~~~~eDLvQe   68 (270)
T TIGR02392        43 SHLRFVVKIARGYRGYGLPQADLIQE   68 (270)
T ss_pred             HhHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            99999999999999999999999984

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=98.54  E-value=1.1e-07  Score=91.32  Aligned_cols=69  Identities=23%  Similarity=0.403  Sum_probs=61.6

Q ss_pred             CcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHH
Q 018065          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKL  333 (361)
Q Consensus       254 ~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekL  333 (361)
                      .+.+..||+++.++|+||.++|.+|+..++.              .|                         +..|+++|
T Consensus         5 ~~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~--------------~g-------------------------d~~A~~~L   45 (289)
T PRK07500          5 ASADRSMIRSAMKAPYLEREEEHALAYRWKD--------------HR-------------------------DEDALHRI   45 (289)
T ss_pred             hhHHHHHHHHHhcCCCCCHHHHHHHHHHHHH--------------CC-------------------------CHHHHHHH
Confidence            3467789999999999999999999987753              13                         67899999


Q ss_pred             HHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065          334 INANLRLVVHVAKQYQGRGISLHDLLQI  361 (361)
Q Consensus       334 I~sNLRLVVSIAKrY~grGLsfqDLIQi  361 (361)
                      |..|+++|.++|++|.+.|.+++||||.
T Consensus        46 v~~~~~lV~~~a~~~~~~~~~~eDLvQe   73 (289)
T PRK07500         46 ISAHMRLVISMAGKFRRFGLPMNDLIQE   73 (289)
T ss_pred             HHHhHHHHHHHHHHHcCCCCCHHHHHHH
Confidence            9999999999999999999999999983

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=98.29  E-value=1e-06  Score=86.27  Aligned_cols=68  Identities=38%  Similarity=0.576  Sum_probs=62.9

Q ss_pred             CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHH
Q 018065          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK  332 (361)
Q Consensus       253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARek  332 (361)
                      ..|.+..|+.+|+..|+||+++|.+|+..++.               |                         +..|.++
T Consensus        51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~---------------G-------------------------d~~A~~~   90 (325)
T PRK05657         51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALR---------------G-------------------------DFAARQR   90 (325)
T ss_pred             cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHH
Confidence            36788999999999999999999999988775               4                         5789999


Q ss_pred             HHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065          333 LINANLRLVVHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       333 LI~sNLRLVVSIAKrY~grGLsfqDLIQ  360 (361)
                      ||..|+++|.++|++|.+.|.+.+||+|
T Consensus        91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQ  118 (325)
T PRK05657         91 MIESNLRLVVKIAKRYLNRGLALLDLIE  118 (325)
T ss_pred             HHHHhHHHHHHHHHHHhcCCCCHHHHHH
Confidence            9999999999999999999999999998

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=98.10  E-value=1.1e-06  Score=83.33  Aligned_cols=35  Identities=31%  Similarity=0.675  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065          327 NSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI  361 (361)
Q Consensus       327 ~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQi  361 (361)
                      ..+|++||.+|+|||++||++|.++|++++||||+
T Consensus        39 ~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQe   73 (264)
T PRK07122         39 QRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQV   73 (264)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHH
Confidence            56999999999999999999999999999999995

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=98.10  E-value=5.5e-06  Score=78.91  Aligned_cols=69  Identities=38%  Similarity=0.563  Sum_probs=63.9

Q ss_pred             CCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHH
Q 018065          252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSRE  331 (361)
Q Consensus       252 ~~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARe  331 (361)
                      -..|++..||.+|+..+.|+.++|.+|+..++.               |                         +..|.+
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~a~~   49 (285)
T TIGR02394        10 RVADVTQLYLREIGFKPLLTAEEEIAYARRALA---------------G-------------------------DFEARK   49 (285)
T ss_pred             CcchHHHHHHHHHhccCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHH
Confidence            357899999999999999999999999987775               4                         578999


Q ss_pred             HHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065          332 KLINANLRLVVHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       332 kLI~sNLRLVVSIAKrY~grGLsfqDLIQ  360 (361)
                      .||..+..+|..+|++|.+.|...+||+|
T Consensus        50 ~L~~~y~~~v~~~a~~~~~~~~~aeDLvQ   78 (285)
T TIGR02394        50 VMIESNLRLVVSIAKHYVNRGLPLLDLIE   78 (285)
T ss_pred             HHHHHhHHHHHHHHHHHhcCCCCHHHHHH
Confidence            99999999999999999999999999998

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=98.07  E-value=1.2e-06  Score=61.27  Aligned_cols=34  Identities=41%  Similarity=0.464  Sum_probs=30.3

Q ss_pred             CcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHH
Q 018065          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR  287 (361)
Q Consensus       254 ~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~  287 (361)
                      +|+++.||++|+++||||++||++|+++|+.+-.
T Consensus         1 ~D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~   34 (37)
T PF00140_consen    1 SDSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE   34 (37)
T ss_dssp             HHHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence            3789999999999999999999999999998654

2; InterPro: IPR009042 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1SMY_F 1IW7_P 1SIG_A 3IYD_F 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P 3DXJ_P ....

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=97.80  E-value=2.9e-05  Score=72.76  Aligned_cols=59  Identities=39%  Similarity=0.623  Sum_probs=52.3

Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHH
Q 018065          263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVV  342 (361)
Q Consensus       263 ei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVV  342 (361)
                      +.+++|+||+++|.+|+..++.               |                         +..|+++|+..|+++|.
T Consensus         9 ~~~~~~~l~~~~~~~li~~~~~---------------g-------------------------d~~a~~~L~~~~~~~v~   48 (254)
T TIGR02850         9 NTSKLPVLKNQEMRELFIRMQS---------------G-------------------------DTTAREKLINGNLRLVL   48 (254)
T ss_pred             cccCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhHHHHH
Confidence            3578999999999999877764               3                         56799999999999999


Q ss_pred             HHHHhcCCCCCCccCccCC
Q 018065          343 HVAKQYQGRGISLHDLLQI  361 (361)
Q Consensus       343 SIAKrY~grGLsfqDLIQi  361 (361)
                      ++|++|.+.+.+.+||+|.
T Consensus        49 ~~a~~~~~~~~~aeDlvQe   67 (254)
T TIGR02850        49 SVIQRFNNRGEYVDDLFQV   67 (254)
T ss_pred             HHHHHHhCCCCCHHHHHHH
Confidence            9999999999999999983

Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=97.68  E-value=5.6e-05  Score=70.86  Aligned_cols=59  Identities=39%  Similarity=0.657  Sum_probs=51.8

Q ss_pred             ccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHH
Q 018065          263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVV  342 (361)
Q Consensus       263 ei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVV  342 (361)
                      +..++|+|+++||..|+..++.               |                         +..++++||..|+++|.
T Consensus        12 ~~~~~~~l~~~~~~~l~~~~~~---------------g-------------------------d~~a~~~l~~~~~~~v~   51 (258)
T PRK08215         12 NTSKLPVLKNEEMRELFERMQN---------------G-------------------------DKEAREKLINGNLRLVL   51 (258)
T ss_pred             cCCCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHHHHHHH
Confidence            3467789999999999887764               3                         57899999999999999


Q ss_pred             HHHHhcCCCCCCccCccCC
Q 018065          343 HVAKQYQGRGISLHDLLQI  361 (361)
Q Consensus       343 SIAKrY~grGLsfqDLIQi  361 (361)
                      .+|++|.+.+.+.+||+|.
T Consensus        52 ~~a~~~~~~~~~aeDlvQe   70 (258)
T PRK08215         52 SVIQRFNNRGENVDDLFQV   70 (258)
T ss_pred             HHHHHHhCCCCCHHHHHHH
Confidence            9999999999999999983

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=97.49  E-value=0.0002  Score=66.15  Aligned_cols=65  Identities=28%  Similarity=0.496  Sum_probs=58.8

Q ss_pred             HHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHH
Q 018065          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (361)
Q Consensus       256 ~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~  335 (361)
                      ++..|+.+++..++||+++|..|...++.               |                         +..|.+.|+.
T Consensus        17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~---------------g-------------------------d~~a~~~l~~   56 (233)
T PRK05803         17 FLVSYVKNNSFPQPLSEEEERKYLELMKE---------------G-------------------------DEEARNILIE   56 (233)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHH
Confidence            67889999999999999999988876654               3                         5779999999


Q ss_pred             HhHHHHHHHHHhcCCCCCCccCccC
Q 018065          336 ANLRLVVHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       336 sNLRLVVSIAKrY~grGLsfqDLIQ  360 (361)
                      .+.++|..+|.+|.|.|.+.+||||
T Consensus        57 ~y~~~l~~~a~~~~~~~~daeDlvQ   81 (233)
T PRK05803         57 RNLRLVAHIVKKFENTGEDVDDLIS   81 (233)
T ss_pred             HhHHHHHHHHHHHhcCCCCHHHHHH
Confidence            9999999999999999999999998

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=97.13  E-value=0.00052  Score=64.87  Aligned_cols=59  Identities=25%  Similarity=0.286  Sum_probs=50.2

Q ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHH
Q 018065          264 PETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVH  343 (361)
Q Consensus       264 i~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVS  343 (361)
                      .|.+|+||.++|.+|+..++..              |                         +..+.+.|+..|++||..
T Consensus         6 ~~~~~~~~~~~e~~l~~~~~~~--------------~-------------------------d~~a~~~l~~~y~~lv~~   46 (268)
T PRK06288          6 SGKIPKYAQQDETELWREYKKT--------------G-------------------------DPKIREYLILKYSPLVKY   46 (268)
T ss_pred             cCCCccccchHHHHHHHHHHHc--------------C-------------------------CHHHHHHHHHHHHHHHHH
Confidence            3789999999999999877641              2                         578999999999999999


Q ss_pred             HHHhcC-C--CCCCccCccCC
Q 018065          344 VAKQYQ-G--RGISLHDLLQI  361 (361)
Q Consensus       344 IAKrY~-g--rGLsfqDLIQi  361 (361)
                      ||++|. |  .+.+.+||+|.
T Consensus        47 ~a~~~~~~~~~~~~~eDl~Qe   67 (268)
T PRK06288         47 VAGRIAVGMPQNVEFDDLVSY   67 (268)
T ss_pred             HHHHHHhcCCCCCCHHHHHHH
Confidence            999986 3  57789999983

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=96.86  E-value=0.001  Score=70.62  Aligned_cols=35  Identities=31%  Similarity=0.482  Sum_probs=32.9

Q ss_pred             CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHH
Q 018065          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIR  287 (361)
Q Consensus       253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~  287 (361)
                      .+||+++||++||..+|||+|+|++++++|..+.+
T Consensus       102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~  136 (619)
T PRK05658        102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGEN  136 (619)
T ss_pred             CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHH
Confidence            58999999999999999999999999999998764

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=96.71  E-value=0.0023  Score=59.77  Aligned_cols=54  Identities=30%  Similarity=0.401  Sum_probs=47.6

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHh
Q 018065          268 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ  347 (361)
Q Consensus       268 ~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKr  347 (361)
                      +.||.++|.+|...++..              |                         +..|.++|+..|.++|..+|++
T Consensus         8 ~~l~~~~~~~li~~~~~~--------------g-------------------------d~~a~~~l~~~y~~~v~~~a~~   48 (255)
T TIGR02941         8 TNLTKEDVIQWIAEFQQN--------------Q-------------------------NGEAQEKLVDHYQNLVYSIAYK   48 (255)
T ss_pred             CCCCHHHHHHHHHHHHHC--------------C-------------------------CHHHHHHHHHHhHHHHHHHHHH
Confidence            668999999888777641              2                         4779999999999999999999


Q ss_pred             cCCCCCCccCccC
Q 018065          348 YQGRGISLHDLLQ  360 (361)
Q Consensus       348 Y~grGLsfqDLIQ  360 (361)
                      |.+.|...+||+|
T Consensus        49 ~~~~~~~aeDlvQ   61 (255)
T TIGR02941        49 YSKGGPMHEDLVQ   61 (255)
T ss_pred             HhcCCCCHHHHHH
Confidence            9999999999998

This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=96.49  E-value=0.0038  Score=48.26  Aligned_cols=39  Identities=31%  Similarity=0.607  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhcc
Q 018065          286 IRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH  324 (361)
Q Consensus       286 ~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~  324 (361)
                      .++.+.+.+|+..+||+||..|.|+.+|++.+.++..+.
T Consensus         4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~   42 (78)
T PF04539_consen    4 RKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQ   42 (78)
T ss_dssp             HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHH
Confidence            456678899999999999999999999999988876554

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=96.42  E-value=0.0046  Score=57.86  Aligned_cols=54  Identities=30%  Similarity=0.327  Sum_probs=47.5

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHh
Q 018065          268 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQ  347 (361)
Q Consensus       268 ~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKr  347 (361)
                      +.|++++|.+|..+++..              |                         +..|.+.|+..|.++|..+|++
T Consensus         8 ~~l~~~e~~~li~~~~~~--------------g-------------------------d~~a~~~l~~~~~~~v~~~a~~   48 (257)
T PRK08583          8 TKLTKEEVNKWIAEYQEN--------------Q-------------------------DEEAQEKLVKHYKNLVESLAYK   48 (257)
T ss_pred             CcCChHHHHHHHHHHHHc--------------C-------------------------CHHHHHHHHHHHHHHHHHHHHH
Confidence            779999999888766530              2                         5779999999999999999999


Q ss_pred             cCCCCCCccCccC
Q 018065          348 YQGRGISLHDLLQ  360 (361)
Q Consensus       348 Y~grGLsfqDLIQ  360 (361)
                      |.+.+.+.+||+|
T Consensus        49 ~~~~~~~aeDlvQ   61 (257)
T PRK08583         49 YSKGQSHHEDLVQ   61 (257)
T ss_pred             HhcCCCCHHHHHH
Confidence            9999999999998

>PRK05572 sporulation sigma factor SigF; Validated

Probab=96.04  E-value=0.011  Score=55.40  Aligned_cols=59  Identities=36%  Similarity=0.553  Sum_probs=51.2

Q ss_pred             hccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHH
Q 018065          262 WGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLV  341 (361)
Q Consensus       262 kei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLV  341 (361)
                      ++-...|.||.+++.+|...++.               |                         +..|.++|+..+.++|
T Consensus         6 ~~~~~~~~l~~~~~~~li~~~~~---------------g-------------------------d~~a~~~L~~~y~~~v   45 (252)
T PRK05572          6 KNKKKKPQLKDEENKELIKKSQD---------------G-------------------------DQEARDTLVEKNLRLV   45 (252)
T ss_pred             ccCcCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhHHHH
Confidence            45567899999999988765553               3                         5679999999999999


Q ss_pred             HHHHHhcCCCCCCccCccC
Q 018065          342 VHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       342 VSIAKrY~grGLsfqDLIQ  360 (361)
                      ..+|++|.+.+.+.+||+|
T Consensus        46 ~~~a~~~~~~~~~aeDl~Q   64 (252)
T PRK05572         46 WSVVQRFLNRGYEPDDLFQ   64 (252)
T ss_pred             HHHHHHHccCCCCHHHHHH
Confidence            9999999999999999998

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=94.18  E-value=0.11  Score=47.92  Aligned_cols=64  Identities=28%  Similarity=0.517  Sum_probs=52.9

Q ss_pred             HHHHHh-ccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHH
Q 018065          257 LRLFLW-GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN  335 (361)
Q Consensus       257 l~~YLk-ei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~  335 (361)
                      +-.|.- +-+..+.|++.+|..|...++.               |                         +..|-+.|+.
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~af~~l~~   55 (227)
T TIGR02846        16 LVGYVTNNGSFPQPLSEEEEKKYLDRLKE---------------G-------------------------DEEARNVLIE   55 (227)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHH
Confidence            344664 3456678999999999877764               4                         5678999999


Q ss_pred             HhHHHHHHHHHhcCCCCCCccCccC
Q 018065          336 ANLRLVVHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       336 sNLRLVVSIAKrY~grGLsfqDLIQ  360 (361)
                      .+.++|..+|.+|.+.+.+.+||+|
T Consensus        56 ~y~~~v~~~~~~~~~~~~dAEDlvQ   80 (227)
T TIGR02846        56 RNLRLVAHIVKKFSNTGEDVDDLIS   80 (227)
T ss_pred             HhHHHHHHHHHHhcCCCCCHHHHHH
Confidence            9999999999999998999999998

The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=92.41  E-value=0.25  Score=45.47  Aligned_cols=35  Identities=40%  Similarity=0.728  Sum_probs=32.8

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       326 G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ  360 (361)
                      +..|.+.|+..+.++|..+|++|.+.+.+.+||+|
T Consensus        50 d~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQ   84 (234)
T PRK08301         50 DEAVRSLLIERNLRLVVYIARKFENTGINIEDLIS   84 (234)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHH
Confidence            56789999999999999999999999999999998

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=90.42  E-value=0.51  Score=43.78  Aligned_cols=56  Identities=36%  Similarity=0.623  Sum_probs=47.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHH
Q 018065          265 ETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHV  344 (361)
Q Consensus       265 ~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSI  344 (361)
                      ...+.|++++|.+|...++.               |                         +..|.+.|+..+.++|..+
T Consensus        29 ~~~~~~~~~~~~~l~~~~~~---------------~-------------------------d~~a~~~l~~~y~~~l~~~   68 (234)
T TIGR02835        29 ALPPPLTGEEEEALLQKLTQ---------------G-------------------------DESAKSTLIERNLRLVVYI   68 (234)
T ss_pred             cCCCcCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhHHHHHHH
Confidence            45678888888887765543               3                         5789999999999999999


Q ss_pred             HHhcCCCCCCccCccC
Q 018065          345 AKQYQGRGISLHDLLQ  360 (361)
Q Consensus       345 AKrY~grGLsfqDLIQ  360 (361)
                      |++|.+.+.+-+||+|
T Consensus        69 ~~~~~~~~~~AEDlvQ   84 (234)
T TIGR02835        69 ARKFENTGIGIEDLVS   84 (234)
T ss_pred             HHHhccCCCCHHHHHH
Confidence            9999999999999998

Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.

>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]

Probab=86.21  E-value=1.9  Score=43.90  Aligned_cols=33  Identities=24%  Similarity=0.326  Sum_probs=29.3

Q ss_pred             CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHH
Q 018065          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDL  285 (361)
Q Consensus       253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l  285 (361)
                      ..+.+..|+..+...++|+++||.+|+..++.+
T Consensus        65 ~~~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g   97 (342)
T COG0568          65 PAGRLSFYIRAIEAAPLLTPEEEKALARRLKRG   97 (342)
T ss_pred             hhhhHHHHHHHHhhhcccChHHHHHHHHHHHcC
Confidence            455778899999999999999999999999877

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=86.10  E-value=0.76  Score=42.46  Aligned_cols=56  Identities=21%  Similarity=0.293  Sum_probs=47.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccccHHHHHHHHHHhHHHHHHH
Q 018065          265 ETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHV  344 (361)
Q Consensus       265 ~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSI  344 (361)
                      ...|+|+...+..|...++.               |                         +..+-+.|+..+.++|..+
T Consensus         7 ~~~~~~~~~~~~~l~~~~~~---------------g-------------------------d~~a~~~l~~~y~~~l~~~   46 (231)
T PRK11922          7 SRPPPLSAASDRELVARVLA---------------G-------------------------DEAAFEALMRRHNRRLYRT   46 (231)
T ss_pred             CCCCCcCcccHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHHHHHHHHH
Confidence            56788999888888776654               3                         5778889999999999999


Q ss_pred             HHhcCCCCCCccCccC
Q 018065          345 AKQYQGRGISLHDLLQ  360 (361)
Q Consensus       345 AKrY~grGLsfqDLIQ  360 (361)
                      |++|.+.+-+-+||+|
T Consensus        47 a~~~~~~~~~AEDlvQ   62 (231)
T PRK11922         47 ARAILRNDAEAEDVVQ   62 (231)
T ss_pred             HHHHhCChhhHHHHHH
Confidence            9999998888899988

>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=82.09  E-value=0.58  Score=34.27  Aligned_cols=28  Identities=29%  Similarity=0.415  Sum_probs=26.3

Q ss_pred             HHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065          333 LINANLRLVVHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       333 LI~sNLRLVVSIAKrY~grGLsfqDLIQ  360 (361)
                      |++.+.++|..+|++|.+.+.+.+|++|
T Consensus         1 L~~~~~~~l~~~~~~~~~~~~~~eD~~q   28 (71)
T PF04542_consen    1 LYERYYPLLYRYARRYTGDPEDAEDLVQ   28 (71)
T ss_dssp             HHHHTHHHHHHHHHTCTTCSSHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhCCHhhHHHHhh
Confidence            6889999999999999999999999987

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....

>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]

Probab=81.99  E-value=2  Score=41.73  Aligned_cols=62  Identities=24%  Similarity=0.326  Sum_probs=42.8

Q ss_pred             HHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhccc
Q 018065          256 PLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS  325 (361)
Q Consensus       256 ~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~  325 (361)
                      -+..||++-.  ..--+---.+++.      +++....+|+..+||+||..|.|+..|++.+++...+..
T Consensus        88 ei~d~LR~~~--~v~vpR~~~~~~~------~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~  149 (247)
T COG1191          88 EILDYLRKND--SVKVPRSLRELGR------RIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLA  149 (247)
T ss_pred             HHHHHHHhCC--CccCcHHHHHHHH------HHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHH
Confidence            4556787766  2222223333333      345678889999999999999999999998877665543

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=80.86  E-value=3.1  Score=39.43  Aligned_cols=36  Identities=28%  Similarity=0.458  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhh
Q 018065          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE  322 (361)
Q Consensus       287 ~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~  322 (361)
                      ++.+...+|...+|++||..|.|+..|++.++++..
T Consensus       114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~  149 (256)
T PRK07408        114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI  149 (256)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence            445677889999999999999999999998877654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	361
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		2e-08
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		4e-07
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		7e-07
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		8e-07
3les_A	179	2f5 Epitope Scaffold Es2 Length = 179		8e-07
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		3e-06
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		3e-06
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		3e-06

>pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A Resolution Length = 332

Iteration: 1
 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 43/125 (34%), Positives = 67/125 (53%), Gaps = 21/125 (16%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 310
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 2   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 58
Query: 311 AIGLS------------CRDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISL 355
            +G +             ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S 
Sbjct: 59  ILGTARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSF 118
Query: 356 HDLLQ 360
            DL+Q
Sbjct: 119 LDLIQ 123

>pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction Promoter Dna Complex At 6.5 A Resolution Length = 438

Iteration: 1
 Score = 52.4 bits (124), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 43/140 (30%), Positives = 67/140 (47%), Gaps = 36/140 (25%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQD---LIRLEKEKSKLQSQFGREPTLIEWAK 310
           +DP+R +L       LLT +EE +L  ++++    I+   E + L  +  RE   +  AK
Sbjct: 93  SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIRE---VVRAK 149
Query: 311 AIGLS---------------------------CRDLKSELH---SGNSSREKLINANLRL 340
            +G +                            ++LK  LH    G ++R+ LI ANLRL
Sbjct: 150 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 209
Query: 341 VVHVAKQYQGRGISLHDLLQ 360
           VV +AK+Y GRG+S  DL+Q
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQ 229

>pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase Sigma Subunit Fragment Containing Regions 1.2 To 3.1 Length = 241

Iteration: 1
 Score = 51.6 bits (122), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 25/47 (53%), Positives = 34/47 (72%), Gaps = 3/47 (6%)
Query: 317 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+Q
Sbjct: 92  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 138

>pdb|3UGO|A Chain A, Crystal Structure Of Rna-Polymerase Sigma Subunit Domain 2 Complexed With -10 Promoter Element Ssdna Oligo (Tacaat) Length = 245

Iteration: 1
 Score = 51.6 bits (122), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 25/47 (53%), Positives = 34/47 (72%), Gaps = 3/47 (6%)
Query: 317 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+Q
Sbjct: 96  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 142

>pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2 Length = 179

Iteration: 1
 Score = 51.2 bits (121), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 25/47 (53%), Positives = 34/47 (72%), Gaps = 3/47 (6%)
Query: 317 RDLKSELH---SGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           ++LK  LH    G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+Q
Sbjct: 91  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 137

>pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme In Complex With The Antibiotic Myxopyronin Length = 423

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 21/35 (60%), Positives = 28/35 (80%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+Q
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 214

>pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From Thermus Thermophilus At 2.6a Resolution Length = 423

Iteration: 1
 Score = 49.7 bits (117), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 21/35 (60%), Positives = 28/35 (80%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+Q
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 214

>pdb|4G7H|F Chain F, Crystal Structure Of Thermus Thermophilus Transcription Initiation Complex Length = 443

Iteration: 1
 Score = 49.3 bits (116), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 21/35 (60%), Positives = 28/35 (80%)
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
           G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+Q
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 234

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	361
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-09
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	4e-09
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	5e-09
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	2e-08
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	7e-08
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	4e-06
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	2e-05
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	7e-04

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 59.1 bits (142), Expect = 1e-09
 Identities = 63/358 (17%), Positives = 118/358 (32%), Gaps = 78/358 (21%)

Query: 38  MHNEQSAPAVASVPTSSVARHFPTSVL---LQEQRDEYRPLLH-MFKEDKTSQATSDSRN 93
           ++N+            +V+R  P   L   L E R     L+  +    KT  A     +
Sbjct: 119 LYND-----NQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLS 173

Query: 94  IETEAFF--------VEEKNSGD--LDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVS- 142
            + +           ++  NS +  L+ L Q L +Q    P+  + S      +    S 
Sbjct: 174 YKVQCKMDFKIFWLNLKNCNSPETVLEML-QKLLYQID--PNWTSRSDHSSNIKLRIHSI 230

Query: 143 ---LTMQSLSNDTEES------V-DAEPFDAVALARKALSASKEAASLAENPKLNGAEFT 192
              L     S   E        V +A+ ++A  L+ K L  ++    + +   L+ A  T
Sbjct: 231 QAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFK-QVTD--FLSAATTT 287

Query: 193 DISLT-SSLGYPLEEVKQ-FSQPRFLERRSKK--RKVSK--PQVTNHETYNSRKASVKKK 246
            ISL   S+    +EVK      ++L+ R +   R+V    P+           + + + 
Sbjct: 288 HISLDHHSMTLTPDEVKSLLL--KYLDCRPQDLPREVLTTNPRRL---------SIIAES 336

Query: 247 LSEGFDRNDPLRLFLWGPETRKL---LTADEEFELIAQIQDLIRLEKEKSKLQSQFGREP 303
           + +G    D  +       T  +   L   E  E       L       + + +      
Sbjct: 337 IRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPS-AHIPTI----- 390

Query: 304 TL-IEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
            L + W   I      + ++LH     +  L+           KQ +   IS+  +  
Sbjct: 391 LLSLIWFDVIKSDVMVVVNKLH-----KYSLVE----------KQPKESTISIPSIYL 433

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 56.4 bits (135), Expect = 7e-09
 Identities = 47/358 (13%), Positives = 103/358 (28%), Gaps = 81/358 (22%)

Query: 58  HFPTSVLLQEQRDEYRPLLHMFK------------EDKTSQATSD--------SRNIETE 97
           H        E + +Y+ +L +F+            +D      S         S++  + 
Sbjct: 6   HMDFET--GEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSG 63

Query: 98  AFFV----EEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPMKRGEDPSVSLTM-----QSL 148
              +      K    + + V+++      +  L   SP       PS+   M       L
Sbjct: 64  TLRLFWTLLSKQEEMVQKFVEEVLRINYKF--LM--SPIKTEQRQPSMMTRMYIEQRDRL 119

Query: 149 SNDTEESVD-----AEPFDAVALARKALSASKEAASLAENPKLNG-AEFTDISLTSSLGY 202
            ND +          +P+  +   R+AL   + A ++     ++G        +   +  
Sbjct: 120 YNDNQVFAKYNVSRLQPYLKL---RQALLELRPAKNVL----IDGVLGSGKTWVALDVCL 172

Query: 203 PLEEVKQFSQPRF---LERRSKKRKVSKPQVT-------NHETYNSRKASVKKKLSEGFD 252
             +   +     F   L+  +    V +           N  + +   +++K ++     
Sbjct: 173 SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQA 232

Query: 253 RNDPLRLFLWGPETRKLLTAD--------EEFE-----LI----AQIQDLIRLEKEK--- 292
                RL    P    LL             F      L+     Q+ D +         
Sbjct: 233 E--LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHIS 290

Query: 293 -SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQ 349
                     +       K +    +DL  E+ + N  R  +I  ++R  +     ++
Sbjct: 291 LDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWK 348

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2 Length = 243

 Score = 55.3 bits (134), Expect = 4e-09
 Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 1/46 (2%)

Query: 317 RDLKSELHSGNSS-REKLINANLRLVVHVAKQYQGRGISLHDLLQI 361
           ++L      G+   R+++I  N+RLV  V +++  RG    DL QI
Sbjct: 16  KELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQI 61

>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 1ku2_A 3lev_A* 3les_A* Length = 245

 Score = 55.3 bits (133), Expect = 5e-09
 Identities = 36/139 (25%), Positives = 60/139 (43%), Gaps = 34/139 (24%)

Query: 254 NDPLRLFLWGPETRK--LLTADEEFELIAQI------------------QDLIRLEKEKS 293
           +DP+R +L   E  +  LLT +EE +L  ++                  + +  + + K 
Sbjct: 6   SDPVRQYLH--EIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKI 63

Query: 294 KLQSQFGREPTLIEWAKAIGLS------------CRDLKSELHSGNSSREKLINANLRLV 341
              ++  + P L E      +              +        G ++R+ LI ANLRLV
Sbjct: 64  LGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLV 123

Query: 342 VHVAKQYQGRGISLHDLLQ 360
           V +AK+Y GRG+S  DL+Q
Sbjct: 124 VSIAKKYTGRGLSFLDLIQ 142

>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H Length = 423

 Score = 54.9 bits (132), Expect = 2e-08
 Identities = 38/143 (26%), Positives = 60/143 (41%), Gaps = 30/143 (20%)

Query: 248 SEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQ---------------------DLI 286
                 +DP+R +L       LLT +EE EL  +++                     +++
Sbjct: 72  IPKISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVV 131

Query: 287 RLEKEKSKL--QSQFGREPTLIEWAKAIGLSCRDLKSEL-------HSGNSSREKLINAN 337
           R +   S         +E    +  + I    + L  E          G ++R+ LI AN
Sbjct: 132 RAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEAN 191

Query: 338 LRLVVHVAKQYQGRGISLHDLLQ 360
           LRLVV +AK+Y GRG+S  DL+Q
Sbjct: 192 LRLVVSIAKKYTGRGLSFLDLIQ 214

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1 Length = 438

 Score = 53.0 bits (127), Expect = 7e-08
 Identities = 29/98 (29%), Positives = 43/98 (43%), Gaps = 4/98 (4%)

Query: 263 GPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSE 322
           G +   +        L       I   KEK   ++    +  L    K +    +     
Sbjct: 136 GLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKEL----KRYLHI 191

Query: 323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ 360
              G ++R+ LI ANLRLVV +AK+Y GRG+S  DL+Q
Sbjct: 192 AREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 229

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1 Length = 339

 Score = 47.2 bits (112), Expect = 4e-06
 Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 10/81 (12%)

Query: 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK-------LINANLR 339
           +L     ++     +   L +  +  GL+   +K      +    K       ++ ANLR
Sbjct: 220 KLHDVSEEVHRALQK---LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLR 276

Query: 340 LVVHVAKQYQGRGISLHDLLQ 360
           LV+ +AK+Y  RG+   DL+Q
Sbjct: 277 LVISIAKKYTNRGLQFLDLIQ 297

>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12} Length = 613

 Score = 45.4 bits (107), Expect = 2e-05
 Identities = 47/311 (15%), Positives = 102/311 (32%), Gaps = 37/311 (11%)

Query: 74  PLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLVQDLEHQFLHWPDLWNLSPPM 133
            LL    E   ++   D  N    +     +    L +    +E +     DL       
Sbjct: 109 ELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVDP 168

Query: 134 KRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSASKEAASLAENPKLNGAEFTD 193
              ED + + T        E+  D E  D      +           + +P+L   +F +
Sbjct: 169 NAEEDLAPTATHVGSELSQEDLDDDEDED-----EEDGDDDSADDDNSIDPELAREKFAE 223

Query: 194 ISLTSSLGYPLEEVKQFSQPRFLERRSK----------KRKVSKPQVTNHETYNSRKASV 243
           +     +     + K  S     E   K            K     V +      R  + 
Sbjct: 224 LRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQ 283

Query: 244 KKKLSE------GFDRNDPLRLFL-------WGPETRKLLTADEEFELIAQIQDLIRLEK 290
           ++ + +         + + + LF        W      +     E  L    +++ R  +
Sbjct: 284 ERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEK-LHDVSEEVHRALQ 342

Query: 291 EKSKLQSQFGREPT-LIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQ 349
           +  +++ + G     + +  + + +     +        ++++++ ANLRLV+ +AK+Y 
Sbjct: 343 KLQQIEEETGLTIEQVKDINRRMSIGEAKARR-------AKKEMVEANLRLVISIAKKYT 395

Query: 350 GRGISLHDLLQ 360
            RG+   DL+Q
Sbjct: 396 NRGLQFLDLIQ 406

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A Length = 239

 Score = 39.5 bits (93), Expect = 7e-04
 Identities = 11/41 (26%), Positives = 18/41 (43%), Gaps = 3/41 (7%)

Query: 324 HSGNSSREKLINANLRLVVHVAKQYQ---GRGISLHDLLQI 361
           +S    RE+LI   L LV  +A   +      + + DL+  
Sbjct: 8   YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISY 48

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	361
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	99.6
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	99.58
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	99.5
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	96.99
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	95.71
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	95.51
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	94.36

>3ugo_A RNA polymerase sigma factor; protein-DNA complex, bacterial promoter opening, G-quartet, quadruplex, DNA binding; 2.10A {Thermus aquaticus} PDB: 3ugp_A 4gor_A 1ku2_A 3lev_A* 3les_A*

Probab=99.60  E-value=1.3e-15  Score=141.30  Aligned_cols=108  Identities=33%  Similarity=0.475  Sum_probs=89.7

Q ss_pred             CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHH-HHHHH------H--HH-----------------hhCCCCcHH
Q 018065          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLE-KEKSK------L--QS-----------------QFGREPTLI  306 (361)
Q Consensus       253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LE-kir~~------L--e~-----------------~lGrePT~~  306 (361)
                      .+|+++.||++|+++||||++||++|+++|+.++... .+...      +  +.                 ..+.+|+..
T Consensus         5 ~~d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~~   84 (245)
T 3ugo_A            5 TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTV   84 (245)
T ss_dssp             CCHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHHHH
T ss_pred             CCCcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccchhH
Confidence            5899999999999999999999999999999987633 33221      0  00                 014689999


Q ss_pred             HHHHHhccchh----hhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065          307 EWAKAIGLSCR----DLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       307 EWA~AaG~d~~----~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ  360 (361)
                      +||.+.|++..    .|.+....|..|+++||..|+++|.++|++|.+.|.+++||+|
T Consensus        85 ~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQ  142 (245)
T 3ugo_A           85 EEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ  142 (245)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHH
T ss_pred             HHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHH
Confidence            99999999654    3444566788999999999999999999999999999999998

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1

Probab=99.58  E-value=1.9e-15  Score=151.57  Aligned_cols=109  Identities=33%  Similarity=0.494  Sum_probs=90.4

Q ss_pred             CCCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHH------------------HHHHhhCCCCcHHHHHH---
Q 018065          252 DRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKS------------------KLQSQFGREPTLIEWAK---  310 (361)
Q Consensus       252 ~~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~------------------~Le~~lGrePT~~EWA~---  310 (361)
                      ...|+++.||++|+++||||++||++|+++|+.++.++....                  .....+|+.|+..+|+.   
T Consensus        91 ~~~d~~~~Yl~ei~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  170 (438)
T 1l9z_H           91 STSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKT  170 (438)
T ss_pred             CCCChHHHHHHHhccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccchh
Confidence            467899999999999999999999999999999865443221                  12234567898888753   


Q ss_pred             ---------HhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065          311 ---------AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       311 ---------AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ  360 (361)
                               ++|++...|..++..|..|+++||.+|+|||++||++|.|+|++++||||
T Consensus       171 ~~~~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQ  229 (438)
T 1l9z_H          171 VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ  229 (438)
T ss_pred             hhhhhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence                     23556677888888899999999999999999999999999999999998

>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H

Probab=99.50  E-value=3.9e-15  Score=147.63  Aligned_cols=108  Identities=34%  Similarity=0.527  Sum_probs=85.7

Q ss_pred             CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH------------------HHhhCCCCcHHH-------
Q 018065          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKL------------------QSQFGREPTLIE-------  307 (361)
Q Consensus       253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~L------------------e~~lGrePT~~E-------  307 (361)
                      ..|+++.||++|+++|+||++||++|+++|+.+..++......                  ....|+.|+..+       
T Consensus        77 ~~d~~~~Yl~ei~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  156 (423)
T 2a6h_F           77 TSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTV  156 (423)
T ss_dssp             THHHHHHHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTHHH
T ss_pred             CCcHHHHHHHHhcccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhhhh
Confidence            5689999999999999999999999999999975443321110                  112235565444       


Q ss_pred             --HHH---HhccchhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065          308 --WAK---AIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       308 --WA~---AaG~d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ  360 (361)
                        |+.   ++|++...|..++..|..|+++||.+|+|||++||++|.|+|++++||||
T Consensus       157 ~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQ  214 (423)
T 2a6h_F          157 EEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ  214 (423)
T ss_dssp             HHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHH
T ss_pred             hhhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHH
Confidence              332   34667778888888899999999999999999999999999999999998

>1sig_A Sigma70, RNA polymerase primary sigma factor; RNA polymerase sigma factor, transcription regulation; 2.60A {Escherichia coli} SCOP: a.177.1.1

Probab=96.99  E-value=0.00024  Score=67.59  Aligned_cols=33  Identities=42%  Similarity=0.858  Sum_probs=32.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065          328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       328 ~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQ  360 (361)
                      .|.+.|+..|+++|+++|++|.+.|..++||+|
T Consensus       265 ~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQ  297 (339)
T 1sig_A          265 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ  297 (339)
T ss_dssp             HHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHH
Confidence            699999999999999999999999999999998

>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12}

Probab=95.71  E-value=0.0014  Score=67.58  Aligned_cols=34  Identities=32%  Similarity=0.570  Sum_probs=13.8

Q ss_pred             CCcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHH
Q 018065          253 RNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI  286 (361)
Q Consensus       253 ~~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~  286 (361)
                      .+||+++||++||..+|||+++|++|++.|..+.
T Consensus        94 ~~dpvrmyl~emg~~~ll~~~~e~~~ak~ie~g~  127 (613)
T 3iyd_F           94 TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI  127 (613)
T ss_dssp             -----------C--------CSSSTTTHHHHHHH
T ss_pred             CCCcHHHHHHHhcccccCCchhHHHHHHHHHHhH
Confidence            6899999999999999999999999999999864

>3iyd_F RNA polymerase sigma factor RPOD; transcription, initiation, class I, activator, RNA polymeras holoenzyme, sigma70, open complex, CAP, CRP; HET: DNA CMP; 19.80A {Escherichia coli k-12}

Probab=95.51  E-value=0.0045  Score=63.92  Aligned_cols=42  Identities=36%  Similarity=0.773  Sum_probs=35.3

Q ss_pred             hhhhccccH-HH---HHHHHHHhHHHHHHHHHhcCCCCCCccCccC
Q 018065          319 LKSELHSGN-SS---REKLINANLRLVVHVAKQYQGRGISLHDLLQ  360 (361)
Q Consensus       319 Lr~~L~~G~-~A---RekLI~sNLRLVVSIAKrY~grGLsfqDLIQ  360 (361)
                      |-.++..|. .|   ++.||..|+++|++||++|.++|..++||||
T Consensus       361 Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQ  406 (613)
T 3iyd_F          361 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ  406 (613)
T ss_dssp             HHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTH
T ss_pred             HHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            333444443 34   9999999999999999999999999999998

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=94.36  E-value=0.0073  Score=51.93  Aligned_cols=36  Identities=36%  Similarity=0.664  Sum_probs=0.0

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065          326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI  361 (361)
Q Consensus       326 G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQi  361 (361)
                      +..|.+.|+..|.++|..+|++|.+.+.+.+||+|.
T Consensus        26 d~~a~~~l~~~~~~~v~~~~~~~~~~~~~aeDl~Qe   61 (243)
T 1l0o_C           26 DQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQI   61 (243)
T ss_dssp             ------------------------------------
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHHhccCCCHHHHHHH
Confidence            467889999999999999999999999999999983

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	361
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	1e-08
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	7e-08
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	2e-06

>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Length = 180

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

 Score = 52.1 bits (124), Expect = 1e-08
 Identities = 37/137 (27%), Positives = 60/137 (43%), Gaps = 30/137 (21%)

Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIR------------------LEKEKSKLQ 296
           DP+R +L       LLT +EE +L  ++++ +                   + + K    
Sbjct: 2   DPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGT 61

Query: 297 SQFGREPTLIEWAKAIGLSCRDLKSE------------LHSGNSSREKLINANLRLVVHV 344
           ++  + P L E      +   D K +               G ++R+ LI ANLRLVV +
Sbjct: 62  ARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSI 121

Query: 345 AKQYQGRGISLHDLLQI 361
           AK+Y GRG+S  DL+Q 
Sbjct: 122 AKKYTGRGLSFLDLIQE 138

>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]} Length = 334

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma70
species: Escherichia coli [TaxId: 562]

 Score = 51.4 bits (122), Expect = 7e-08
 Identities = 27/154 (17%), Positives = 53/154 (34%)

Query: 208 KQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETR 267
           + F Q R + ++      S   + +      R             + + + LF     + 
Sbjct: 142 EVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSD 201

Query: 268 KLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN 327
               A          +     E+    LQ     E       + +    R +        
Sbjct: 202 TWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKAR 261

Query: 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQI 361
            ++++++ ANLRLV+ +AK+Y  RG+   DL+Q 
Sbjct: 262 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 295

>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 87

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 43.4 bits (102), Expect = 2e-06
 Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 3/40 (7%)

Query: 324 HSGNSSREKLINANLRLVVHVAKQYQGR---GISLHDLLQ 360
           +S    RE+LI   L LV  +A   +      + + DL+ 
Sbjct: 6   YSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLIS 45

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	361
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.79
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	98.76
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	97.48
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	96.82
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	96.77
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	96.2

>d1ku2a2 a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=99.79  E-value=1.4e-20  Score=163.10  Aligned_cols=108  Identities=33%  Similarity=0.508  Sum_probs=83.1

Q ss_pred             CcHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH------------------HhhCCCCcHHHHHHH----
Q 018065          254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQ------------------SQFGREPTLIEWAKA----  311 (361)
Q Consensus       254 ~D~l~~YLkei~~~~LLTaEEE~eL~~~IQ~l~~LEkir~~Le------------------~~lGrePT~~EWA~A----  311 (361)
                      +||++.||++|+++||||+|||++|+++|+.++.+.+...+..                  ...+..|...+|...    
T Consensus         1 tDpVr~YLreig~v~LLT~EEEieLAr~Ie~g~~~~~~~~e~~~~~~~l~~e~~~~~~~~~~~~~~~~~~~e~~~~~~~~   80 (180)
T d1ku2a2           1 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVE   80 (180)
T ss_dssp             CHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCSSCCCTTSCCSSCTTTHH
T ss_pred             CCcHHHHHHHhcCcCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHhhhHHHHhcchhhHHHhhHHHHH
Confidence            4899999999999999999999999999999877654432221                  122333443333322    


Q ss_pred             -----hcc---chhhhhhhccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065          312 -----IGL---SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI  361 (361)
Q Consensus       312 -----aG~---d~~~Lr~~L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQi  361 (361)
                           ...   ..+.+.+.+..|..||++||.+|+|||++||++|.|+|++|+||||.
T Consensus        81 ~~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl~q~  138 (180)
T d1ku2a2          81 EVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQE  138 (180)
T ss_dssp             HHHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHHHHH
Confidence                 222   23555667778999999999999999999999999999999999984

>d1siga_ a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma70
species: Escherichia coli [TaxId: 562]

Probab=98.76  E-value=9.2e-10  Score=100.95  Aligned_cols=39  Identities=36%  Similarity=0.681  Sum_probs=35.5

Q ss_pred             ccccHHHHHHHHHHhHHHHHHHHHhcCCCCCCccCccCC
Q 018065          323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQI  361 (361)
Q Consensus       323 L~~G~~ARekLI~sNLRLVVSIAKrY~grGLsfqDLIQi  361 (361)
                      -..+..||++||++|||||++||++|.|+|++|+||||.
T Consensus       257 e~~~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~  295 (334)
T d1siga_         257 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE  295 (334)
T ss_dssp             HHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHH
T ss_pred             HhhccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHh
Confidence            345567999999999999999999999999999999984

>d1rp3a3 a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.48  E-value=1.2e-05  Score=62.33  Aligned_cols=36  Identities=28%  Similarity=0.417  Sum_probs=31.8

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHhcCCC---CCCccCccCC
Q 018065          326 GNSSREKLINANLRLVVHVAKQYQGR---GISLHDLLQI  361 (361)
Q Consensus       326 G~~ARekLI~sNLRLVVSIAKrY~gr---GLsfqDLIQi  361 (361)
                      +...|++||..|++||.+||++|.++   |++++||||+
T Consensus         8 ~~~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~   46 (87)
T d1rp3a3           8 NQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISY   46 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHH
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHH
Confidence            34579999999999999999999765   8999999984

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=96.82  E-value=0.0008  Score=48.08  Aligned_cols=40  Identities=30%  Similarity=0.439  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhcccc
Q 018065          287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSG  326 (361)
Q Consensus       287 ~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~~G  326 (361)
                      ++.++..+|...+||+||..|.|+++|++.+++...|..+
T Consensus        16 ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~   55 (57)
T d1l0oc_          16 KIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAV   55 (57)
T ss_dssp             HHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHh
Confidence            4567889999999999999999999999999998776543

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.77  E-value=0.00082  Score=49.85  Aligned_cols=41  Identities=37%  Similarity=0.498  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHHhhCCCCcHHHHHHHhccchhhhhhhcc
Q 018065          284 DLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELH  324 (361)
Q Consensus       284 ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~d~~~Lr~~L~  324 (361)
                      ...++++...+|+..+||+||..|.|+.+||+.+++++.+.
T Consensus         8 ~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~   48 (77)
T d1rp3a1           8 KERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLD   48 (77)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34467789999999999999999999999999998876654

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor SigA
species: Thermus aquaticus [TaxId: 271]

Probab=96.20  E-value=0.0034  Score=45.41  Aligned_cols=42  Identities=29%  Similarity=0.526  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHHHhhCCCCcHHHHHHHhcc--chhhhhhhccc
Q 018065          284 DLIRLEKEKSKLQSQFGREPTLIEWAKAIGL--SCRDLKSELHS  325 (361)
Q Consensus       284 ~l~~LEkir~~Le~~lGrePT~~EWA~AaG~--d~~~Lr~~L~~  325 (361)
                      .+-++.++..+|.+.+||+||.+|.|+++|+  +.+.++..+..
T Consensus        10 ~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~~   53 (60)
T d1ku2a1          10 TINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKI   53 (60)
T ss_dssp             HHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGGG
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHH
Confidence            3445667889999999999999999999985  45667766654