Citrus Sinensis ID: 020252

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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-------33
Protein Sequence
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHccccccccccccccccccccccHHHHHHHHHHHHcccEEccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHcccccccHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccHHHccccccccccccccccccccEEccccccccccHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHcccHHcccccccHcccccccccHHHHcccccccccEEEEccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHccHHHHHccc
Coil and Loop (DISEMBL)
mttvldveklrlpsleahSNAVAAnrqwtyfgavgpsteenlgtslatetltSDEAVIAAASAEAVALARAAVKVAKDAALMVnhhnsakpkskpaisssadtnTSMWAQLTERERAsiigdsviveaapeeeyseqqplnksadleptHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSvksgstsrrkrpsvqevdysdplrylrattsssrlltANEEMQLSAGIQDLLKLEGLREVlsercggsptFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH
Flexible Loop (DISEMBL)
mttvldveklrlpsleahsNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVnhhnsakpkskpaisssadtNTSMWAQLTERERASIIGDSVIVEAAPeeeyseqqplnkSADLEPTHEELKLLEeqvsqsiavrsrrqterkARRTRaaekaaanvmsvksgstsrrkrpsvqevdysdplrylRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAaaagvdqrelRRRLNYGilckdkmitsNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH
Low Complexity Region (SEG)
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTsdeaviaaasaeavalaraavkvakdaalMVNHHNsakpkskpaisssaDTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSrrqterkarrtraaekaaaNVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH
Disordered region (IsUnstruct)
*******************NAVAANRQWTYFGAVGP*********LATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMV************************************I******************************************************************************************************************LSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYL****
Disordered Region (DISOPRED)
**T*LD*EKLRL***********************************************************************************************************************************************************************************************************YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVL**********AQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA*
Disordered Region (DISEMBL)
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHH******************TSMWAQLTERERASIIGDSVIVEAAP***********KSADLEPTHEELKLLEEQVSQS********************************************VDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH
Disordered Region (DISPRO)
**TVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNH*****************TNTSMWAQLTERERASIIGDSVIVEAAP*******************************QSIAVRSRRQTERKARRT******************************YSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNM**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH
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	328	2.2.26 [Sep-21-2011]
O22056	572	RNA polymerase sigma fact	yes	no	0.939	0.538	0.580	6e-79
Q9LD95	547	RNA polymerase sigma fact	no	no	0.460	0.276	0.388	5e-21
P26683	390	RNA polymerase sigma fact	yes	no	0.381	0.320	0.425	6e-18
P38023	399	RNA polymerase sigma fact	yes	no	0.323	0.265	0.462	5e-14
Q31QG5	320	RNA polymerase sigma fact	no	no	0.335	0.343	0.433	1e-12
Q31ME3	320	RNA polymerase sigma fact	no	no	0.283	0.290	0.419	3e-12
O24621	571	RNA polymerase sigma fact	no	no	0.262	0.150	0.372	3e-12
P52322	416	RNA polymerase sigma fact	no	no	0.323	0.254	0.317	3e-10
Q03065	332	RNA polymerase sigma-B fa	no	no	0.292	0.289	0.343	9e-09
O24629	502	RNA polymerase sigma fact	no	no	0.399	0.260	0.307	4e-07

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

 Score =  294 bits (752), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 188/324 (58%), Positives = 233/324 (71%), Gaps = 16/324 (4%)

Query: 1   MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIA 59
           +T++LDV KLRLPS +  S+++ ++RQWTY    GPSTE     +LA+ETL TSDEAV+ 
Sbjct: 49  LTSMLDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVV 108

Query: 60  AASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASI 119
           AA+AEAVALARAAVKVAKDA L  N +N+        ++SS     S W Q TE+ERA I
Sbjct: 109 AAAAEAVALARAAVKVAKDATLFKNSNNTN------LLTSSTADKRSKWDQFTEKERAGI 162

Query: 120 IG-----DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQV-SQSIAVRSRRQTE 173
           +G     D+ IV        S ++ +    DLE   +E   L E+  S S+AVRS RQTE
Sbjct: 163 LGHLAVSDNGIVSDKITASASNKESI---GDLESEKQEEVELLEEQPSVSLAVRSTRQTE 219

Query: 174 RKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEM 233
           RKARR +  EK A+ + SVK+GS+ ++KR   QEVD++DPLRYLR TTSSS+LLT  EE 
Sbjct: 220 RKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEH 279

Query: 234 QLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITS 293
           +LSAGIQDLLKLE L+  L+ER G  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI S
Sbjct: 280 ELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKS 339

Query: 294 NIRLVISIAKNYQGAGMNLQDLVQ 317
           NIRLVISIAKNYQGAGMNLQDLVQ
Sbjct: 340 NIRLVISIAKNYQGAGMNLQDLVQ 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|Q9LD95|SIGF_ARATH RNA polymerase sigma factor sigF, chloroplastic OS=Arabidopsis thaliana GN=SIGF PE=1 SV=1

 Score =  102 bits (253), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 59/152 (38%), Positives = 87/152 (57%), Gaps = 1/152 (0%)

Query: 166 VRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSR 225
           VRS+RQ ER+A+  RA +    +        TS +K+   Q  D  D L+       + +
Sbjct: 188 VRSKRQLERRAKNRRAPKSNDVDDEGYVPQKTSAKKKYK-QGADNDDALQLFLWGPETKQ 246

Query: 226 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 285
           LLTA EE +L + IQ LLKLE ++  L  + G  PT  +WA A G+    L+  ++ G  
Sbjct: 247 LLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRS 306

Query: 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
            ++K+IT+N+RLV+ IAK YQ  G+N QDL+Q
Sbjct: 307 SREKLITANLRLVVHIAKQYQNRGLNFQDLLQ 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|P26683|RPOD_NOSS1 RNA polymerase sigma factor RpoD OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=rpoD PE=3 SV=1

 Score = 91.7 bits (226), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 54/127 (42%), Positives = 76/127 (59%), Gaps = 2/127 (1%)

Query: 193 KSG--STSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE 250
           KSG  + SRR+  S ++    D +R         RLL A+EE++L+  I DLL+LE +RE
Sbjct: 59  KSGKAAKSRRRTQSKKKHYTEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRE 118

Query: 251 VLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGM 310
            LSE+    P  ++WA A  +     R RL+ G   KDKM+ SN+RLV+SIAK Y   G+
Sbjct: 119 RLSEKLERDPRDSEWAEAVQLPLPAFRYRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGL 178

Query: 311 NLQDLVQ 317
           + QDL+Q
Sbjct: 179 SFQDLIQ 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|P38023|RPOD1_SYNE7 RNA polymerase sigma factor rpoD1 OS=Synechococcus elongatus (strain PCC 7942) GN=rpoD1 PE=3 SV=2

 Score = 79.0 bits (193), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 49/106 (46%), Positives = 65/106 (61%)

Query: 212 DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGV 271
           D +R         RLL A+EE++L+  I DLL LE +R+ L E+    P+ A+WAAA   
Sbjct: 89  DSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAVDS 148

Query: 272 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
              E RRRL  G   KDKM+ SN+RLV+SIAK Y   G++ QDL+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 = 74.3 bits (181), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 49/113 (43%), Positives = 67/113 (59%), Gaps = 3/113 (2%)

Query: 207 EVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVL-SERCGGSPTFAQ 264
           E   SD +R YLR       LLT  EE+ L   +Q  +KL+ LR+ L SE     P+  +
Sbjct: 5   ETPTSDLVRTYLREIGRVP-LLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLE 63

Query: 265 WAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
           WAAAAG+   ELR++ + G   K KMI +N+RLV+S+AK Y    M+L DL+Q
Sbjct: 64  WAAAAGLSIEELRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQ 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|Q31ME3|RPOD2_SYNE7 RNA polymerase sigma factor rpoD2 OS=Synechococcus elongatus (strain PCC 7942) GN=rpoD2 PE=1 SV=1

 Score = 72.8 bits (177), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 39/93 (41%), Positives = 55/93 (59%)

Query: 225 RLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGI 284
           RLLTA EE+     +Q L+ L   +  L +R G  P+  +WAAA  ++  +L R++  G 
Sbjct: 24  RLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEWAAAVDLNLEDLDRQIEQGQ 83

Query: 285 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
             K KMI +N+RLV+SIAK YQ   M   DL+Q
Sbjct: 84  RAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQ 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|O24621|SIGC_ARATH RNA polymerase sigma factor sigC OS=Arabidopsis thaliana GN=SIGC PE=2 SV=1

 Score = 72.8 bits (177), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 32/86 (37%), Positives = 57/86 (66%)

Query: 232 EMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI 291
           E ++S G++ +  +E +R  L E  G   + + WAAAAG++++ L R L+YG  C+D+++
Sbjct: 278 ETEMSTGVKIVADMERIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELV 337

Query: 292 TSNIRLVISIAKNYQGAGMNLQDLVQ 317
            S   LV+ +A+NY+G G+  +DL+Q
Sbjct: 338 KSTRSLVLFLARNYRGLGIAHEDLIQ 363

Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 66.2 bits (160), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 46/145 (31%), Positives = 63/145 (43%), Gaps = 39/145 (26%)

Query: 212 DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE--------------VLSERCG 257
           D +R         RLL A EE++L+  I DLLKLE +RE               L ER  
Sbjct: 67  DSIRIYLQEIGRIRLLRAEEEIELARKIADLLKLERIREDFCLYSDAEWGKQVFLFERIE 126

Query: 258 G-------------------------SPTFAQWAAAAGVDQRELRRRLNYGILCKDKMIT 292
                                     +P   +W A +       +RRL +G   K+KM+ 
Sbjct: 127 KIIVEKSEKEPKLSDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQ 186

Query: 293 SNIRLVISIAKNYQGAGMNLQDLVQ 317
           SN+RLV+SIAK Y   G++ QDL+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)

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

 Score = 61.2 bits (147), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 33/96 (34%), Positives = 56/96 (58%)

Query: 226 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 285
           LL+  +E+  +  +Q ++ +   +E L+E+    PT  +WA    + +  L ++L+ G +
Sbjct: 37  LLSHEQEIFFAQQVQQMMVMFTAKEELAEKLQREPTLQEWADKMQLKEDVLLQQLSQGQI 96

Query: 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQAL 321
            K KMI +N+RLV+SIAK YQ   +   DL+Q  AL
Sbjct: 97  AKQKMIQANLRLVVSIAKKYQKRNLEFLDLIQEGAL 132

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|O24629|SIGA_ARATH RNA polymerase sigma factor sigA OS=Arabidopsis thaliana GN=SIGA PE=1 SV=1

 Score = 55.8 bits (133), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 44/143 (30%), Positives = 72/143 (50%), Gaps = 12/143 (8%)

Query: 176 ARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLR-YLRATTSSSRLLTANEEMQ 234
           AR+ R   K   N+  VK+          V +V     +R Y++   S   +L+  E ++
Sbjct: 159 ARQRRIGAKKKTNMTHVKA----------VSDVSSGKQVRGYVKGVISED-VLSHVEVVR 207

Query: 235 LSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSN 294
           LS  I+  L+L+  +  L +R G  P+  Q A +  + + EL+  L    L ++K+  SN
Sbjct: 208 LSKKIKSGLRLDDHKSRLKDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSN 267

Query: 295 IRLVISIAKNYQGAGMNLQDLVQ 317
           +RLV+SIA+ Y   G  + DLVQ
Sbjct: 268 VRLVMSIAQRYDNLGAEMSDLVQ 290

Essential protein. Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released. Controls the transcription of the psaA gene and thus modulates photosystem stoichiometry. Thereby maintains an harmonious electron flow and photosynthetic efficiency.

Arabidopsis thaliana (taxid: 3702)

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	328
255565968	569	RNA polymerase sigma factor rpoD1, putat	0.923	0.532	0.685	7e-98
224126061	567	predicted protein [Populus trichocarpa]	0.963	0.557	0.690	4e-91
449454538	580	PREDICTED: RNA polymerase sigma factor s	0.935	0.529	0.625	1e-90
224144900	564	predicted protein [Populus trichocarpa]	0.957	0.556	0.669	3e-90
296090195	575	unnamed protein product [Vitis vinifera]	0.963	0.549	0.704	5e-85
225436223	578	PREDICTED: RNA polymerase sigma factor r	0.963	0.546	0.704	5e-85
7363218	575	sigma factor 2 [Sinapis alba]	0.939	0.535	0.574	2e-79
297843640	572	hypothetical protein ARALYDRAFT_470915 [	0.948	0.543	0.595	6e-79
15223259	572	RNApolymerase sigma subunit 2 [Arabidops	0.939	0.538	0.580	4e-77
356509511	558	PREDICTED: RNA polymerase sigma factor r	0.902	0.530	0.572	6e-77

>gi|255565968|ref|XP_002523972.1| RNA polymerase sigma factor rpoD1, putative [Ricinus communis] gi|223536699|gb|EEF38340.1| RNA polymerase sigma factor rpoD1, putative [Ricinus communis]

 Score =  363 bits (931), Expect = 7e-98,   Method: Compositional matrix adjust.
 Identities = 216/315 (68%), Positives = 255/315 (80%), Gaps = 12/315 (3%)

Query: 4   VLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAAS 62
           VLD+EKLRLPS EA S+++A N  WTY            G++LATETL TSDEAVIAAA+
Sbjct: 59  VLDLEKLRLPSFEAPSDSIAPNSPWTY---------ATFGSTLATETLITSDEAVIAAAA 109

Query: 63  AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGD 122
           AEAVALARAAVKVAKDAAL+V +  SA+ +SK  ++S +  + S W Q TE ERA IIGD
Sbjct: 110 AEAVALARAAVKVAKDAALLVKNFPSAETESK--LTSPSTIDASRWPQFTETERARIIGD 167

Query: 123 SVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAA 182
           SV  E  P EE S Q  + +S  LE TH+EL+LL++Q+S+ IAVRSRRQTERKARR RA 
Sbjct: 168 SVATETGPREESSMQSSIKESDYLELTHKELELLQKQLSEGIAVRSRRQTERKARRARAV 227

Query: 183 EKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDL 242
           EKAA++V+SVK GSTS++KR S+QEVDYSDPLRYLR TTS+SRLLTA+EE++LSA IQDL
Sbjct: 228 EKAASSVVSVKPGSTSKKKRGSLQEVDYSDPLRYLRGTTSTSRLLTASEELELSAAIQDL 287

Query: 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 302
           LKLE L+E L+ER GG PTFAQWAAAAGVDQR LR+R+N+G +CKDKMI SNIRLVISIA
Sbjct: 288 LKLERLQEELAERYGGQPTFAQWAAAAGVDQRTLRKRINHGTICKDKMIKSNIRLVISIA 347

Query: 303 KNYQGAGMNLQDLVQ 317
           KNYQGAGMNLQDLVQ
Sbjct: 348 KNYQGAGMNLQDLVQ 362

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224126061|ref|XP_002319746.1| predicted protein [Populus trichocarpa] gi|222858122|gb|EEE95669.1| predicted protein [Populus trichocarpa]

 Score =  341 bits (874), Expect = 4e-91,   Method: Compositional matrix adjust.
 Identities = 219/317 (69%), Positives = 258/317 (81%), Gaps = 1/317 (0%)

Query: 2   TTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLT-SDEAVIAA 60
           T VLD+EKLRLPSLE HS++++ANR WTY G +GP  +   GTSLA ETL  +DEAVIAA
Sbjct: 44  TAVLDLEKLRLPSLEPHSDSISANRPWTYIGGIGPQKKPPFGTSLAAETLIANDEAVIAA 103

Query: 61  ASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASII 120
           A+AEAVALARAAVKVAKDAA M  +++S K ++K  I+S+ D+ +SMW+ LTE+ERA II
Sbjct: 104 AAAEAVALARAAVKVAKDAAEMAKNYSSMKKETKIPIASTTDSFSSMWSLLTEKERADII 163

Query: 121 GDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTR 180
           GDSV  E    EEYS Q P  +   LEPT EEL LL++Q+S+ IAVRS+RQTERKARR R
Sbjct: 164 GDSVSAETRLREEYSVQYPTEEYDCLEPTQEELALLQKQLSEGIAVRSKRQTERKARRAR 223

Query: 181 AAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQ 240
           AAEKAAANV+SVKSGSTS++KR  +QEVD SDPLR+ R  +SSSRLL+A EE++LS GIQ
Sbjct: 224 AAEKAAANVVSVKSGSTSKKKRVPLQEVDQSDPLRFFRGASSSSRLLSATEEVELSEGIQ 283

Query: 241 DLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS 300
           DLLKLE + E L ER GG P+FAQWAAAAGVDQ  LR+RLNYGILCKDKMI SN+RLVIS
Sbjct: 284 DLLKLERIEEELKERFGGEPSFAQWAAAAGVDQLTLRKRLNYGILCKDKMIKSNVRLVIS 343

Query: 301 IAKNYQGAGMNLQDLVQ 317
           IAKNYQG GMNLQDLVQ
Sbjct: 344 IAKNYQGTGMNLQDLVQ 360

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449454538|ref|XP_004145011.1| PREDICTED: RNA polymerase sigma factor sigB-like [Cucumis sativus] gi|449473951|ref|XP_004154029.1| PREDICTED: RNA polymerase sigma factor sigB-like [Cucumis sativus]

 Score =  338 bits (868), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 197/315 (62%), Positives = 242/315 (76%), Gaps = 8/315 (2%)

Query: 3   TVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAAS 62
           T LDV++L+LP  + ++++V+  R  +Y GAV         +SLA+  LTS+EA IAAA+
Sbjct: 67  TTLDVDRLKLPPFDTNTDSVSVERLRSYLGAVE--------SSLASTLLTSEEASIAAAA 118

Query: 63  AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGD 122
           AEAV LA+AAVKVA+DAAL+ N+ NS++  +K   S   D     WAQ  E ERA IIG+
Sbjct: 119 AEAVTLAKAAVKVARDAALLANNINSSRAGTKSQSSPKPDALHFKWAQFMESERADIIGE 178

Query: 123 SVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAA 182
            V V   P E  + +    +S D+EPT EEL+LL++++S+SI V+S+RQTERKARRTRAA
Sbjct: 179 PVGVNKRPMEGDALEPSTTESDDMEPTSEELELLQDELSESITVKSKRQTERKARRTRAA 238

Query: 183 EKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDL 242
           EK   +V+S KSGS+SR+KR SVQEVDYSDPLRYLRATT++SRLLTA EE++LS GIQDL
Sbjct: 239 EKTVTSVLSFKSGSSSRKKRNSVQEVDYSDPLRYLRATTNTSRLLTATEELELSEGIQDL 298

Query: 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 302
           LKLE L+E L ER G  PTFAQWAAAAGV+QR LR+RLNYG LCKDKMI SNIRLVISIA
Sbjct: 299 LKLERLQEELGERYGNEPTFAQWAAAAGVNQRTLRKRLNYGTLCKDKMIKSNIRLVISIA 358

Query: 303 KNYQGAGMNLQDLVQ 317
           KNYQGAGMNLQDLVQ
Sbjct: 359 KNYQGAGMNLQDLVQ 373

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224144900|ref|XP_002325455.1| predicted protein [Populus trichocarpa] gi|222862330|gb|EEE99836.1| predicted protein [Populus trichocarpa]

 Score =  338 bits (866), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 211/315 (66%), Positives = 249/315 (79%), Gaps = 1/315 (0%)

Query: 4   VLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLT-SDEAVIAAAS 62
           VL++EKLRLPSLE+HS+++AANR WTY G +GP  E   GTSLATETL  +DEAVIAAA+
Sbjct: 43  VLNLEKLRLPSLESHSDSIAANRPWTYIGGIGPPKEPLFGTSLATETLIINDEAVIAAAA 102

Query: 63  AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGD 122
           AEAVALARAAVKVAKDAA M  ++ S   ++K  I+S+AD+ +SMW+ LT +ERA IIG 
Sbjct: 103 AEAVALARAAVKVAKDAAEMAKNYCSVNTETKIPIASTADSFSSMWSLLTGKERADIIGV 162

Query: 123 SVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAA 182
           S   E    EE S Q P  +S    PTHEEL LLE+Q+S+SI VRS+RQT+RKA+R RAA
Sbjct: 163 SFSAETGLREECSTQYPTEESDCFGPTHEELALLEKQLSESIVVRSKRQTQRKAKRARAA 222

Query: 183 EKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDL 242
           EKAAAN + +KSGS  ++KR  VQEVD SDPLR+ R  ++SSRLL+A EE++LS GIQDL
Sbjct: 223 EKAAANFVFMKSGSACKKKRVPVQEVDQSDPLRFFRGASTSSRLLSATEEVELSEGIQDL 282

Query: 243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 302
           LKLE + E L ER GG PTFAQWAAAA VDQ  LR+RLNY ILCKDKMI SNIRLVISIA
Sbjct: 283 LKLERIEEELKERFGGKPTFAQWAAAARVDQITLRKRLNYAILCKDKMIKSNIRLVISIA 342

Query: 303 KNYQGAGMNLQDLVQ 317
           KNYQGAGMNLQDLVQ
Sbjct: 343 KNYQGAGMNLQDLVQ 357

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296090195|emb|CBI40014.3| unnamed protein product [Vitis vinifera]

 Score =  320 bits (821), Expect = 5e-85,   Method: Compositional matrix adjust.
 Identities = 224/318 (70%), Positives = 252/318 (79%), Gaps = 2/318 (0%)

Query: 2   TTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAA 60
           T VLD+EKLRLPSLE+HSN+VAA+R WTY G VGP TE N   +LA ETL TS+EAVIAA
Sbjct: 51  TAVLDIEKLRLPSLESHSNSVAAHRPWTYIGVVGPPTEANFEATLARETLLTSEEAVIAA 110

Query: 61  ASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPA-ISSSADTNTSMWAQLTERERASI 119
           A+AEAVALA+AAVKVAKDAA +V  +NSAK ++KPA   S  DT+     Q TE ER  I
Sbjct: 111 AAAEAVALAKAAVKVAKDAARLVGKNNSAKSETKPASFLSGDDTSQFRRIQFTETERIGI 170

Query: 120 IGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRT 179
           +GDSV  E    +  S Q     S DLEPT EEL+LLE + S+SI VRS RQ ERKARR 
Sbjct: 171 LGDSVGAETGMVDYNSLQDVTEDSDDLEPTLEELELLEAEFSKSIVVRSNRQVERKARRA 230

Query: 180 RAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGI 239
           RAAEKA+A V+SV+SGSTSRRKR S+QEVDYSDPLRYLR TTS+SRLLTA EE++LS GI
Sbjct: 231 RAAEKASAGVVSVRSGSTSRRKRVSLQEVDYSDPLRYLRGTTSTSRLLTATEELELSEGI 290

Query: 240 QDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVI 299
           QDLLKLE L+E L ER G  PTFAQWAAAAGVDQ+ LRRR NYGI CKDKMI SNIRLVI
Sbjct: 291 QDLLKLEKLQEDLEERFGVKPTFAQWAAAAGVDQKTLRRRTNYGIRCKDKMIKSNIRLVI 350

Query: 300 SIAKNYQGAGMNLQDLVQ 317
           SIAKNYQGAGMN+QDLVQ
Sbjct: 351 SIAKNYQGAGMNIQDLVQ 368

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225436223|ref|XP_002273602.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Vitis vinifera]

 Score =  320 bits (820), Expect = 5e-85,   Method: Compositional matrix adjust.
 Identities = 224/318 (70%), Positives = 252/318 (79%), Gaps = 2/318 (0%)

Query: 2   TTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAA 60
           T VLD+EKLRLPSLE+HSN+VAA+R WTY G VGP TE N   +LA ETL TS+EAVIAA
Sbjct: 54  TAVLDIEKLRLPSLESHSNSVAAHRPWTYIGVVGPPTEANFEATLARETLLTSEEAVIAA 113

Query: 61  ASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPA-ISSSADTNTSMWAQLTERERASI 119
           A+AEAVALA+AAVKVAKDAA +V  +NSAK ++KPA   S  DT+     Q TE ER  I
Sbjct: 114 AAAEAVALAKAAVKVAKDAARLVGKNNSAKSETKPASFLSGDDTSQFRRIQFTETERIGI 173

Query: 120 IGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRT 179
           +GDSV  E    +  S Q     S DLEPT EEL+LLE + S+SI VRS RQ ERKARR 
Sbjct: 174 LGDSVGAETGMVDYNSLQDVTEDSDDLEPTLEELELLEAEFSKSIVVRSNRQVERKARRA 233

Query: 180 RAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGI 239
           RAAEKA+A V+SV+SGSTSRRKR S+QEVDYSDPLRYLR TTS+SRLLTA EE++LS GI
Sbjct: 234 RAAEKASAGVVSVRSGSTSRRKRVSLQEVDYSDPLRYLRGTTSTSRLLTATEELELSEGI 293

Query: 240 QDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVI 299
           QDLLKLE L+E L ER G  PTFAQWAAAAGVDQ+ LRRR NYGI CKDKMI SNIRLVI
Sbjct: 294 QDLLKLEKLQEDLEERFGVKPTFAQWAAAAGVDQKTLRRRTNYGIRCKDKMIKSNIRLVI 353

Query: 300 SIAKNYQGAGMNLQDLVQ 317
           SIAKNYQGAGMN+QDLVQ
Sbjct: 354 SIAKNYQGAGMNIQDLVQ 371

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|7363218|emb|CAB83106.1| sigma factor 2 [Sinapis alba]

 Score =  302 bits (773), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 186/324 (57%), Positives = 234/324 (72%), Gaps = 16/324 (4%)

Query: 1   MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIA 59
           +T+ LDV KLRLPS +  S++  ++R WTY   +GPSTE     +LA+ETL TSDEAV+A
Sbjct: 49  LTSTLDVAKLRLPSFDTDSDSRISDRPWTYTRTIGPSTEAKYLEALASETLLTSDEAVVA 108

Query: 60  AASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASI 119
           AA+AEAVALARAA+KVAKDA L  N HN+     K ++SS+AD   S W Q TE+ERA I
Sbjct: 109 AAAAEAVALARAALKVAKDATLFGNSHNT-----KLSVSSAADKR-SKWDQFTEKERAGI 162

Query: 120 IG-----DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTER 174
           +G     D+ +V        S +     S DL P  ++     E++S S AVRS RQTER
Sbjct: 163 LGHLAVSDTGVVSDRITAPGSLECNKEASDDLTPAEKQE---VEKLSVSSAVRSTRQTER 219

Query: 175 KARRTRAAEKAAANVMS-VKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEM 233
           KARR +  EK A+ + S VK+GS+SR+KR + QE+D++DPLRYLR TTSSS+LLTA EE 
Sbjct: 220 KARRVKGLEKTASGMQSSVKTGSSSRKKRVASQEIDHNDPLRYLRMTTSSSKLLTAREEQ 279

Query: 234 QLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITS 293
           QLS GIQDLLKLE L+  L+ERCG  PTF+QWA+AAGVD++ LR+R+ +G  CKD+MI S
Sbjct: 280 QLSEGIQDLLKLERLQAELTERCGHQPTFSQWASAAGVDKKTLRKRITHGTQCKDRMIKS 339

Query: 294 NIRLVISIAKNYQGAGMNLQDLVQ 317
           NIRLVISIAKNYQGAGM+ QDLVQ
Sbjct: 340 NIRLVISIAKNYQGAGMDFQDLVQ 363

Source: Sinapis alba

Species: Sinapis alba

Genus: Sinapis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297843640|ref|XP_002889701.1| hypothetical protein ARALYDRAFT_470915 [Arabidopsis lyrata subsp. lyrata] gi|297335543|gb|EFH65960.1| hypothetical protein ARALYDRAFT_470915 [Arabidopsis lyrata subsp. lyrata]

 Score =  300 bits (768), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 191/321 (59%), Positives = 232/321 (72%), Gaps = 10/321 (3%)

Query: 1   MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIA 59
           +T++LDV KLRLPS +  S++  ++RQWTY    GPSTE     +LA+ETL TSDEAV+ 
Sbjct: 49  LTSMLDVAKLRLPSFDTDSDSRISDRQWTYTRTDGPSTEAKYLEALASETLLTSDEAVVV 108

Query: 60  AASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASI 119
           AA+AEAVALARAAVKVAKDA L  N +N+        ISS+AD   S W Q TE+ERA I
Sbjct: 109 AAAAEAVALARAAVKVAKDATLFKNSNNT-----NLLISSTADKR-SKWDQFTEKERAGI 162

Query: 120 IGDSVIVEAAPEEEYSEQQPLNKSA--DLEPTHEELKLLEEQV-SQSIAVRSRRQTERKA 176
           +G   + +     +       NK +  DLE   +E   L E+  S S+AVRS RQTERKA
Sbjct: 163 LGHLAVSDNGIVSDKITAPASNKESPGDLESEKQEEVELLEEQPSVSLAVRSTRQTERKA 222

Query: 177 RRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLS 236
           RR +  EK A+ + SVK+GS  R+KR   QEVD++DPLRYLR TTSSS+LLT  EE +LS
Sbjct: 223 RRAKGLEKTASGIPSVKTGSNPRKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELS 282

Query: 237 AGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIR 296
           AGIQDLLKLE L+  L+ERCG  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI SNIR
Sbjct: 283 AGIQDLLKLERLQTELTERCGRQPTFAQWASAAGVDQKSLRKRIHHGTLCKDKMIKSNIR 342

Query: 297 LVISIAKNYQGAGMNLQDLVQ 317
           LVISIAKNYQGAGMNLQDLVQ
Sbjct: 343 LVISIAKNYQGAGMNLQDLVQ 363

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15223259|ref|NP_172330.1| RNApolymerase sigma subunit 2 [Arabidopsis thaliana] gi|75219074|sp|O22056.2|SIGB_ARATH RecName: Full=RNA polymerase sigma factor sigB; Short=Sigma factor B; Short=Sigma-B; AltName: Full=Protein ABERRANT CHLOROPLAST 1; AltName: Full=RNA polymerase sigma factor sig1; Short=Atsig1; Short=Sigma factor 1; AltName: Full=RNA polymerase sigma factor sig2; Short=Atsig2; Short=Sigma factor 2; AltName: Full=RNA polymerase sigma factor sigA; Short=Sigma factor A; Short=Sigma-A; Flags: Precursor gi|6664315|gb|AAF22897.1|AC006932_14 T27G7.22 [Arabidopsis thaliana] gi|9802550|gb|AAF99752.1|AC003981_2 F22O13.2 [Arabidopsis thaliana] gi|2443357|dbj|BAA22427.1| SigB [Arabidopsis thaliana] gi|2597831|emb|CAA75584.1| sigma factor [Arabidopsis thaliana] gi|2879922|dbj|BAA24825.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana] gi|5478446|dbj|BAA82449.1| sigma factor SigB [Arabidopsis thaliana] gi|133778838|gb|ABO38759.1| At1g08540 [Arabidopsis thaliana] gi|332190182|gb|AEE28303.1| RNApolymerase sigma subunit 2 [Arabidopsis thaliana]

 Score =  294 bits (752), Expect = 4e-77,   Method: Compositional matrix adjust.
 Identities = 188/324 (58%), Positives = 233/324 (71%), Gaps = 16/324 (4%)

Query: 1   MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIA 59
           +T++LDV KLRLPS +  S+++ ++RQWTY    GPSTE     +LA+ETL TSDEAV+ 
Sbjct: 49  LTSMLDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVV 108

Query: 60  AASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASI 119
           AA+AEAVALARAAVKVAKDA L  N +N+        ++SS     S W Q TE+ERA I
Sbjct: 109 AAAAEAVALARAAVKVAKDATLFKNSNNTN------LLTSSTADKRSKWDQFTEKERAGI 162

Query: 120 IG-----DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQV-SQSIAVRSRRQTE 173
           +G     D+ IV        S ++ +    DLE   +E   L E+  S S+AVRS RQTE
Sbjct: 163 LGHLAVSDNGIVSDKITASASNKESI---GDLESEKQEEVELLEEQPSVSLAVRSTRQTE 219

Query: 174 RKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEM 233
           RKARR +  EK A+ + SVK+GS+ ++KR   QEVD++DPLRYLR TTSSS+LLT  EE 
Sbjct: 220 RKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEH 279

Query: 234 QLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITS 293
           +LSAGIQDLLKLE L+  L+ER G  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI S
Sbjct: 280 ELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKS 339

Query: 294 NIRLVISIAKNYQGAGMNLQDLVQ 317
           NIRLVISIAKNYQGAGMNLQDLVQ
Sbjct: 340 NIRLVISIAKNYQGAGMNLQDLVQ 363

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356509511|ref|XP_003523491.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max]

 Score =  293 bits (751), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 186/325 (57%), Positives = 230/325 (70%), Gaps = 29/325 (8%)

Query: 2   TTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAA 60
           +T+L +EK +L +L+A S+    N  W Y  A       N  ++L+ E+L T++EAVI A
Sbjct: 47  STLLSLEK-KL-ALDAPSDP---NTSWPYIAAA------NFKSTLSAESLLTNEEAVIVA 95

Query: 61  ASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASII 120
           A++EA+ALA+AA KVAKDAAL+V     A+ + K  +SS +D     W +  E     + 
Sbjct: 96  AASEALALAKAAAKVAKDAALLVKKKPPAEAEYKSHVSSKSDDLLLKWFKQMEEVEDGVA 155

Query: 121 GDSVI--------VEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQT 172
            +S+         V+ +P EE S         DLEP+HEEL+ L+EQ+S SIAVRSRRQT
Sbjct: 156 EESMGAGAEIMEGVDVSPSEEES---------DLEPSHEELERLQEQLSDSIAVRSRRQT 206

Query: 173 ERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEE 232
           ERKA+R RA EKA  N  S K GS+SRRKR S+QEVDYSDPLRYLR TTS+SRLLT  EE
Sbjct: 207 ERKAKRVRATEKATTNFTSFKPGSSSRRKRVSMQEVDYSDPLRYLRTTTSASRLLTPTEE 266

Query: 233 MQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMIT 292
           ++LSAGIQDLLKLE ++E L+ER G  PTFAQWAA AGVDQ+ LR+RLNYGI CKDKMI 
Sbjct: 267 IKLSAGIQDLLKLEKIQEDLAERFGSQPTFAQWAAVAGVDQKTLRKRLNYGIFCKDKMIK 326

Query: 293 SNIRLVISIAKNYQGAGMNLQDLVQ 317
           SNIRLVISIAKNYQG+GMNLQDLVQ
Sbjct: 327 SNIRLVISIAKNYQGSGMNLQDLVQ 351

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	328
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.951	0.545	0.465	6.7e-65
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.518	0.297	0.318	3.1e-18
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.365	0.219	0.404	2.7e-17
UNIPROTKB|O48655	519	rsigA "Plastid RNA polymerase	0.307	0.194	0.392	6.8e-11
TAIR|locus:2084420	571	SIGC "AT3G53920" [Arabidopsis	0.271	0.155	0.359	1.1e-10
TAIR|locus:2010871	502	SIGA "AT1G64860" [Arabidopsis	0.344	0.225	0.321	1.7e-06

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

 Score = 661 (237.7 bits), Expect = 6.7e-65, P = 6.7e-65
 Identities = 149/320 (46%), Positives = 188/320 (58%)

Query:     1 MTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTXXXXXXXX 60
             +T++LDV KLRLPS +  S+++ ++RQWTY    GPSTE     +LA+ETL         
Sbjct:    49 LTSMLDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVV 108

Query:    61 XXXXXXXXXXXXXXXXXXXXXMVNHHNXXXXXXXXXXXXXXDTNTSMWAQLTERERASII 120
                                  +  + N                  S W Q TE+ERA I+
Sbjct:   109 AAAAEAVALARAAVKVAKDATLFKNSNNTNLLTSSTAD-----KRSKWDQFTEKERAGIL 163

Query:   121 GDSVIVEAAPEEEYSEQQPLNKSA--DLEPT-HEELKLLEEQVSQSIAVRSXXXXXXXXX 177
             G   + +     +       NK +  DLE    EE++LLEEQ S S+AVRS         
Sbjct:   164 GHLAVSDNGIVSDKITASASNKESIGDLESEKQEEVELLEEQPSVSLAVRSTRQTERKAR 223

Query:   178 XXXXXXXXXXNVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSA 237
                        + SVK+GS+ ++KR   QEVD++DPLRYLR TTSSS+LLT  EE +LSA
Sbjct:   224 RAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSA 283

Query:   238 GIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRL 297
             GIQDLLKLE L+  L+ER G  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI SNIRL
Sbjct:   284 GIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRL 343

Query:   298 VISIAKNYQGAGMNLQDLVQ 317
             VISIAKNYQGAGMNLQDLVQ
Sbjct:   344 VISIAKNYQGAGMNLQDLVQ 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|Q84LK8 SIG6 "Sig6" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 229 (85.7 bits), Expect = 3.1e-18, P = 3.1e-18
 Identities = 56/176 (31%), Positives = 83/176 (47%)

Query:   143 SADLEPTHEELKLLEEQVSQSIAVRSXXXXXXXXXXXXXXXXXXXNVMSVKSGSTSRRKR 202
             S D   ++EEL     Q    + VRS                   +V      S  + K 
Sbjct:   194 SVDSSKSNEEL-----QSKGQVFVRSTRLLERRSKRRYAPRASIADVSCSADNSKKKEKS 248

Query:   203 PSVQEV-DYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPT 261
                  V +  +P +       ++  LTA EE  L + IQ L+K+E     L  +CG  PT
Sbjct:   249 KKYGRVLEPDEPFKLFLRDRETTEFLTAKEERHLFSKIQILMKIEEAHRKLEVQCGREPT 308

Query:   262 FAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
              A+WA A G+  +EL+  +  G  C++KM  SN RLVI +A+ Y+G G+++QDLVQ
Sbjct:   309 LAEWAEAVGMSSKELQSSIRTGRRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQ 364

GO:0009536 "plastid" evidence=RCA

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

 Score = 220 (82.5 bits), Expect = 2.7e-17, P = 2.7e-17
 Identities = 49/121 (40%), Positives = 72/121 (59%)

Query:   197 TSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERC 256
             TS +K+   Q  D  D L+       + +LLTA EE +L + IQ LLKLE ++  L  + 
Sbjct:   219 TSAKKKYK-QGADNDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQN 277

Query:   257 GGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLV 316
             G  PT  +WA A G+    L+  ++ G   ++K+IT+N+RLV+ IAK YQ  G+N QDL+
Sbjct:   278 GCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLL 337

Query:   317 Q 317
             Q
Sbjct:   338 Q 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|O48655 rsigA "Plastid RNA polymerase sigma factor" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 174 (66.3 bits), Expect = 6.8e-11, P = 6.8e-11
 Identities = 40/102 (39%), Positives = 59/102 (57%)

Query:   216 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRE 275
             YLR T S   LLT  + + LS  I+D + L+  R  L E+ G  P++ Q A +  +   E
Sbjct:   207 YLRGTVSKE-LLTHKQVVHLSHKIKDGIWLQQQRSKLKEKLGNEPSYKQLAHSLKISPPE 265

Query:   276 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
             LR R++   L ++ +  SN+RLVISIA+ Y   G+ L DL+Q
Sbjct:   266 LRSRMHESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQ 307

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

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

 Score = 173 (66.0 bits), Expect = 1.1e-10, P = 1.1e-10
 Identities = 32/89 (35%), Positives = 58/89 (65%)

Query:   229 ANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 288
             +  E ++S G++ +  +E +R  L E  G   + + WAAAAG++++ L R L+YG  C+D
Sbjct:   275 SRNETEMSTGVKIVADMERIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRD 334

Query:   289 KMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
             +++ S   LV+ +A+NY+G G+  +DL+Q
Sbjct:   335 ELVKSTRSLVLFLARNYRGLGIAHEDLIQ 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 = 137 (53.3 bits), Expect = 1.7e-06, P = 1.7e-06
 Identities = 37/115 (32%), Positives = 63/115 (54%)

Query:   204 SVQEVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTF 262
             +V +V     +R Y++   S   +L+  E ++LS  I+  L+L+  +  L +R G  P+ 
Sbjct:   177 AVSDVSSGKQVRGYVKGVISED-VLSHVEVVRLSKKIKSGLRLDDHKSRLKDRLGCEPSD 235

Query:   263 AQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
              Q A +  + + EL+  L    L ++K+  SN+RLV+SIA+ Y   G  + DLVQ
Sbjct:   236 EQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQ 290


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        0.312   0.126   0.344    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      328       266   0.00094  114 3  11 23  0.39    34
                                                     32  0.39    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:  6
  No. of states in DFA:  604 (64 KB)
  Total size of DFA:  180 KB (2104 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:  19.76u 0.10s 19.86t   Elapsed:  00:00:00
  Total cpu time:  19.76u 0.10s 19.86t   Elapsed:  00:00:00
  Start:  Sat May 11 09:49:42 2013   End:  Sat May 11 09:49:42 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: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

---

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

Your Input:
	estExt_fgenesh4_pm.C_LG_XIII0293	hypothetical protein (568 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	eugene3.29520003	annotation not avaliable (742 aa)					•		•		0.499
	fgenesh4_pm.C_LG_X000986	hypothetical protein (932 aa)							•		0.472
	gw1.XIV.2088.1	hypothetical protein (955 aa)			•	•			•		0.429
	estExt_fgenesh4_pg.C_13160002	hypothetical protein (165 aa)			•				•		0.415
	estExt_Genewise1_v1.C_LG_X3691	SubName- Full=Putative uncharacterized protein; (165 aa)			•				•		0.410
	grail3.3134000101	Predicted protein (100 aa)							•		0.406
	eugene3.00020721	hypothetical protein (1053 aa)			•						0.404

---

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	328
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	6e-24
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	9e-23
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	5e-18
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	1e-14
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	2e-10
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	3e-10
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	2e-08
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	1e-07
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	1e-04
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	3e-04
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	5e-04
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	5e-04
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	7e-04
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	0.002

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

 Score = 98.9 bits (247), Expect = 6e-24
 Identities = 50/107 (46%), Positives = 71/107 (66%), Gaps = 2/107 (1%)

Query: 212 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAG 270
           D +R YL+       LLT  EE++L+  +Q ++ LE LRE L E+ G  P+  +WAAAAG
Sbjct: 1   DLVRLYLQ-EIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAG 59

Query: 271 VDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
           + + ELR+RL  G   K+KMI +N+RLV+S+AK YQ  G+ L DL+Q
Sbjct: 60  LSEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQ 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 = 97.2 bits (242), Expect = 9e-23
 Identities = 51/179 (28%), Positives = 76/179 (42%), Gaps = 11/179 (6%)

Query: 139 PLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTS 198
                 +L    E+ +        S                + A+  A            
Sbjct: 1   TPELEDELLLLEEDRQPAATDDLDSDEDEESSSENADELSEKEAKAKA-----------L 49

Query: 199 RRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGG 258
            R +   ++V   D +R         RLL  +EE++L+  I DLL+LE LRE      G 
Sbjct: 50  ARIKIGPKKVYTEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGR 109

Query: 259 SPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
            P+  +WA    +   + RRRL  G   K+KM+ SN+RLV+SIAK Y   G++ QDL+Q
Sbjct: 110 EPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQ 168

Length = 373

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

 Score = 82.9 bits (205), Expect = 5e-18
 Identities = 44/108 (40%), Positives = 64/108 (59%), Gaps = 2/108 (1%)

Query: 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAA 269
           +D +R YLR       LLT  EE+     +Q L+ L+ +RE L+E  G  PT A+WA AA
Sbjct: 7   TDLVRTYLREIGRVP-LLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAA 65

Query: 270 GVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
            + + ELR  +  G   K KM+ +N+RLV+S+AK Y    ++L DL+Q
Sbjct: 66  KLSEEELRSAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQ 113

Length = 317

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

 Score = 73.0 bits (179), Expect = 1e-14
 Identities = 34/92 (36%), Positives = 54/92 (58%)

Query: 226 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 285
           LLT  +E+     +Q ++ L   +E L+++ G  P+  +WA A  + + EL++ L  G  
Sbjct: 32  LLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKR 91

Query: 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
            K KMI +N+RLV++IAK YQ   M   DL+Q
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQ 123

Length = 327

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

 Score = 61.2 bits (149), Expect = 2e-10
 Identities = 53/284 (18%), Positives = 102/284 (35%), Gaps = 50/284 (17%)

Query: 44  TSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADT 103
           + +  +T  + E+ I     +  A A AA   AK         +S K + K A+    D 
Sbjct: 60  SGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLK-DELDSSKKAEKKNALDKDDDL 118

Query: 104 NTSMWAQLTE--RERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVS 161
           N      +     +      D  + +   +++  ++       D +   E+ +  E +  
Sbjct: 119 NYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKEL 178

Query: 162 QSIAVRSRRQTE-------RKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPL 214
           + ++       +       R+AR+       A                         DP+
Sbjct: 179 EKLSDDDDFVWDEDDSEALRQARKDAKLTATA-------------------------DPV 213

Query: 215 R-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQ 273
           + YL+      +LL A EE++L+  I+      GL        G               +
Sbjct: 214 KAYLK-QIGKVKLLNAEEEVELAKRIE-----AGLYAEELLAEGEKLDPEL--------R 259

Query: 274 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
           R+L+     G   K+ ++ +N+RLV+S+AK Y   G++  DL+Q
Sbjct: 260 RDLQWIGRDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQ 303

Length = 509

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

 Score = 60.3 bits (146), Expect = 3e-10
 Identities = 36/125 (28%), Positives = 57/125 (45%), Gaps = 28/125 (22%)

Query: 215 RYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQR 274
           RY++       ++ AN   +    I+  L+L  +RE L+   G  P+  +WA  A +   
Sbjct: 89  RYMKL------IVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADISLA 142

Query: 275 ELRRRLNY----------------------GILCKDKMITSNIRLVISIAKNYQGAGMNL 312
           +L+  L                        G+  K+ MI +N+RLV+S+AK YQ  G+ L
Sbjct: 143 DLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLEL 202

Query: 313 QDLVQ 317
            DLVQ
Sbjct: 203 LDLVQ 207

Length = 415

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

 Score = 55.0 bits (133), Expect = 2e-08
 Identities = 34/113 (30%), Positives = 49/113 (43%), Gaps = 20/113 (17%)

Query: 225 RLLTANEEMQLSAGIQDLLKLEGLREVL-SERCGGSPTFAQWAAAAGVDQ---------- 273
            LL    E++L+  ++D   L  L E L   + G  P+      A  +            
Sbjct: 22  PLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPL 81

Query: 274 ------RELRRRLNYGIL---CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
                 + L RRL  G      K K++ SN+RLV+SIAK Y G G+   DL+Q
Sbjct: 82  LTPEEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQ 134

Length = 342

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

 Score = 51.1 bits (123), Expect = 1e-07
 Identities = 15/31 (48%), Positives = 23/31 (74%)

Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
           K +++ SN+RLV+SIAK Y   G++  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|235549 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated

 Score = 43.6 bits (104), Expect = 1e-04
 Identities = 18/33 (54%), Positives = 23/33 (69%), Gaps = 4/33 (12%)

Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQ--DLVQ 317
           K +M+ +N+RLVISIAK Y   G  LQ  DL+Q
Sbjct: 382 KKEMVEANLRLVISIAKKYTNRG--LQFLDLIQ 412

Length = 619

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

 Score = 41.6 bits (98), Expect = 3e-04
 Identities = 16/31 (51%), Positives = 23/31 (74%)

Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
           +  MI SN+RLV+SIAK+Y   G+ L DL++
Sbjct: 48  RKVMIESNLRLVVSIAKHYVNRGLPLLDLIE 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|181169 PRK07921, PRK07921, RNA polymerase sigma factor SigB; Reviewed

 Score = 41.3 bits (97), Expect = 5e-04
 Identities = 29/96 (30%), Positives = 47/96 (48%), Gaps = 21/96 (21%)

Query: 226 LLTANEEMQLS----AGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN 281
           LLTA +E++L+    AG+     LE  + +   R                 +R+L   + 
Sbjct: 40  LLTAADEVELAKRIEAGLYAEHLLETRKRLSEAR-----------------KRDLAAVVR 82

Query: 282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
            G   +  ++ +N+RLV+S+AK Y G GM L DL+Q
Sbjct: 83  DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQ 118

Length = 324

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

 Score = 41.1 bits (97), Expect = 5e-04
 Identities = 16/31 (51%), Positives = 22/31 (70%)

Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
           K ++  +N+RLV+SIAK Y G GM   DL+Q
Sbjct: 131 KQRLAEANLRLVVSIAKRYVGRGMLFLDLIQ 161

Length = 367

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

 Score = 40.3 bits (95), Expect = 7e-04
 Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 2/47 (4%)

Query: 273 QRELRRRLNYG--ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
           + +L +RL     +    K++ S++R V+ IA+ Y+G G+   DL+Q
Sbjct: 21  EYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQ 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|235838 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed

 Score = 39.0 bits (92), Expect = 0.002
 Identities = 11/29 (37%), Positives = 21/29 (72%)

Query: 289 KMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
           +++ S++R V+ IA+ Y+G G+   DL+Q
Sbjct: 52  QLVLSHLRFVVHIARGYRGYGLPQADLIQ 80

Length = 284

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	328
PRK07598	415	RNA polymerase sigma factor SigC; Validated	99.95
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	99.93
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	99.91
PRK05949	327	RNA polymerase sigma factor; Validated	99.89
PRK07405	317	RNA polymerase sigma factor SigD; Validated	99.89
PRK05901	509	RNA polymerase sigma factor; Provisional	99.84
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	99.8
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	99.72
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	99.49
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	99.49
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	99.36
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	99.34
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	99.28
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	99.22
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	99.05
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	98.95
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	98.89
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	98.87
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	98.85
PRK08215	258	sporulation sigma factor SigG; Reviewed	98.82
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	98.66
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	98.57
PRK05803	233	sporulation sigma factor SigK; Reviewed	98.56
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	98.5
PRK08583	257	RNA polymerase sigma factor SigB; Validated	98.39
PRK05572	252	sporulation sigma factor SigF; Validated	98.07
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	98.03
PRK07670	251	RNA polymerase sigma factor SigD; Validated	97.88
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	97.79
PRK08301	234	sporulation sigma factor SigE; Reviewed	97.67
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	97.41
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	97.2
PRK11922	231	RNA polymerase sigma factor; Provisional	97.01
PRK05602	186	RNA polymerase sigma factor; Reviewed	96.78
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	96.71
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	96.7
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	96.67
PRK08295	208	RNA polymerase factor sigma-70; Validated	96.66
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	96.52
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	96.5
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	96.45
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	96.35
PRK12513	194	RNA polymerase sigma factor; Provisional	96.21
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	96.18
PRK13919	186	putative RNA polymerase sigma E protein; Provision	96.07
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	95.98
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	95.97
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	95.94
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	95.78
PRK06811	189	RNA polymerase factor sigma-70; Validated	95.44
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	95.35
PRK12519	194	RNA polymerase sigma factor; Provisional	95.18
PRK12514	179	RNA polymerase sigma factor; Provisional	95.16
PRK12534	187	RNA polymerase sigma factor; Provisional	95.0
PRK12524	196	RNA polymerase sigma factor; Provisional	94.88
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	94.19
PRK12531	194	RNA polymerase sigma factor; Provisional	93.26
PRK12515	189	RNA polymerase sigma factor; Provisional	93.14
PRK12538	233	RNA polymerase sigma factor; Provisional	93.0
PRK12537	182	RNA polymerase sigma factor; Provisional	92.25
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	92.06
PRK12512	184	RNA polymerase sigma factor; Provisional	91.9
PRK12526	206	RNA polymerase sigma factor; Provisional	91.28
PRK12536	181	RNA polymerase sigma factor; Provisional	91.26
PRK12539	184	RNA polymerase sigma factor; Provisional	90.86
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	84.84
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	83.95
PRK08241	339	RNA polymerase factor sigma-70; Validated	83.52
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	81.98

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=99.95  E-value=4.7e-27  Score=233.74  Aligned_cols=119  Identities=34%  Similarity=0.561  Sum_probs=110.1

Q ss_pred             CCCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHhhcCCCCchHHHHH
Q 020252          209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK--------------------LEGLREVLSERCGGSPTFAQWAA  267 (328)
Q Consensus       209 ~~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~--------------------Le~~r~~L~~~~GrePT~~eWA~  267 (328)
                      ..+|+++ ||++| |+.||||++||++|+++||+++.                    |++++.+|++++|++||..|||.
T Consensus        57 ~~~d~v~~yl~~i-gr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~  135 (415)
T PRK07598         57 RSTDLVRLYLQEI-GRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAK  135 (415)
T ss_pred             CCCChHHHHHHhc-ccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence            4479999 99999 99999999999999999999999                    89999999999999999999997


Q ss_pred             HhcCcHHHHHHh----------------------hhhhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHh
Q 020252          268 AAGVDQRELRRR----------------------LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLN  325 (328)
Q Consensus       268 a~g~d~~~L~~~----------------------L~~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmr  325 (328)
                      ++|+++.+|+.+                      +..|..|+++||.+|+|||++||++|.++|++++||||||+||||+
T Consensus       136 ~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~r  215 (415)
T PRK07598        136 TADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLER  215 (415)
T ss_pred             HhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHH
Confidence            777666666655                      4678899999999999999999999999999999999999999999


Q ss_pred             hhC
Q 020252          326 MAH  328 (328)
Q Consensus       326 Ave  328 (328)
                      |++
T Consensus       216 ave  218 (415)
T PRK07598        216 AVE  218 (415)
T ss_pred             HHH
Confidence            984

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

Probab=99.93  E-value=3.2e-25  Score=209.70  Aligned_cols=116  Identities=44%  Similarity=0.691  Sum_probs=112.9

Q ss_pred             ChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHH
Q 020252          212 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM  290 (328)
Q Consensus       212 d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~L  290 (328)
                      |++. ||+++ +++|+||++||.+|+++++.++.+++++.+|+++.|++||..+||+++|++..+|..++..|..|+++|
T Consensus         1 ~~~~~yl~~~-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~L   79 (298)
T TIGR02997         1 DLVRLYLQEI-GRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKM   79 (298)
T ss_pred             CcHHHHHHHc-cccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHH
Confidence            4677 99999 999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          291 ITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       291 I~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      |.+|+|+|++||++|.|+|.+++||||||++|||+|++
T Consensus        80 v~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~  117 (298)
T TIGR02997        80 IKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVE  117 (298)
T ss_pred             HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999974

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=99.91  E-value=5.9e-24  Score=209.05  Aligned_cols=118  Identities=41%  Similarity=0.651  Sum_probs=115.0

Q ss_pred             CCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHH
Q 020252          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  288 (328)
Q Consensus       210 ~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are  288 (328)
                      ..|++. ||++| +++|+||++||++|+++|++++.+++++.+|+++.|++|+..+||.++|++..+|++++..|..|++
T Consensus        61 ~~d~l~~Yl~~i-~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~  139 (373)
T PRK07406         61 TEDSIRVYLQEI-GRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKE  139 (373)
T ss_pred             CCCHHHHHHHHh-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHH
Confidence            468899 99999 9999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       289 ~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      +||.+|+++|++||++|.++|++++||||||+||||+|++
T Consensus       140 ~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~  179 (373)
T PRK07406        140 KMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAE  179 (373)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999974

>PRK05949 RNA polymerase sigma factor; Validated

Probab=99.89  E-value=1.5e-22  Score=195.46  Aligned_cols=118  Identities=33%  Similarity=0.545  Sum_probs=115.0

Q ss_pred             CCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHH
Q 020252          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  288 (328)
Q Consensus       210 ~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are  288 (328)
                      .+|++. ||++| +++|+||++||++|+++||.++.+++.+..|..++|++|+..+||.+++++..+|...+..|..|++
T Consensus        16 ~~d~~~~yl~~i-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~   94 (327)
T PRK05949         16 SADMVRTYLHEI-GRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQ   94 (327)
T ss_pred             CCCHHHHHHHHc-CCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHH
Confidence            478999 99999 9999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       289 ~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      +||.+|+++|++||++|.+.|.+++||||||++||+++++
T Consensus        95 ~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~  134 (327)
T PRK05949         95 KMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVE  134 (327)
T ss_pred             HHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999974

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=99.89  E-value=1.8e-22  Score=193.72  Aligned_cols=117  Identities=38%  Similarity=0.562  Sum_probs=114.2

Q ss_pred             CChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHH
Q 020252          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK  289 (328)
Q Consensus       211 ~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~  289 (328)
                      +|++. ||+++ +++|+||++||++|+++|++++.+++++..|++++|++|+..+||.+++++...|...+..|..|+++
T Consensus         7 ~~~~~~yl~~i-~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~   85 (317)
T PRK07405          7 TDLVRTYLREI-GRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRK   85 (317)
T ss_pred             CcHHHHHHHHc-cccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHH
Confidence            67899 99999 99999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          290 MITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       290 LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      ||.+|+++|+++|++|.+.|.+++||||||++||+++++
T Consensus        86 L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~  124 (317)
T PRK07405         86 MVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVE  124 (317)
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999974

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=3.8e-21  Score=195.74  Aligned_cols=107  Identities=31%  Similarity=0.478  Sum_probs=91.1

Q ss_pred             CCCCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHH
Q 020252          208 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILC  286 (328)
Q Consensus       208 ~~~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~A  286 (328)
                      ....|+++ ||++| +++|+||++||++|+++|+.+..++..   +.+       ..+|+..   +..+|+++++.|..|
T Consensus       207 ~~~~d~l~~YL~~i-~~~~lLt~eEE~~La~~i~~g~~~~~~---~~~-------~~~~~~~---~~~~l~~~~~~g~~A  272 (509)
T PRK05901        207 TATADPVKAYLKQI-GKVKLLNAEEEVELAKRIEAGLYAEEL---LAE-------GEKLDPE---LRRDLQWIGRDGKRA  272 (509)
T ss_pred             cccccHHHHHHHHh-ccCCCCCHHHHHHHHHHHHhCCchhhh---hhh-------cccchhh---hhhhhhhhccchHHH
Confidence            44578999 99999 999999999999999999987544442   111       1234422   468899999999999


Q ss_pred             HHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       287 re~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      +++||.+|||||++||++|.++|++++|||||||||||+||+
T Consensus       273 r~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAve  314 (509)
T PRK05901        273 KNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVE  314 (509)
T ss_pred             HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999984

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

Probab=99.80  E-value=1.1e-19  Score=177.30  Aligned_cols=117  Identities=32%  Similarity=0.501  Sum_probs=103.5

Q ss_pred             CChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh-hcCCCCchH---------------HHHHHhcCcH
Q 020252          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSE-RCGGSPTFA---------------QWAAAAGVDQ  273 (328)
Q Consensus       211 ~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~-~~GrePT~~---------------eWA~a~g~d~  273 (328)
                      .|.+. |+.++ +..++++.++|..+...++....+......+.. ..+..|+..               +|+..+..+.
T Consensus         8 ~d~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E   86 (342)
T COG0568           8 ADAVRAYLDEI-GRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEE   86 (342)
T ss_pred             hhHHHHHHHHh-cchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHH
Confidence            56788 99999 999999999999999999988777777777776 678888887               7766666655


Q ss_pred             -HHHHHhhhhhHH---HHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          274 -RELRRRLNYGIL---CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       274 -~~L~~~L~~G~~---Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                       ..|..++..|..   |+.+||.+|||||++||++|.|+|++|.|||||||||||+||+
T Consensus        87 e~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVe  145 (342)
T COG0568          87 EKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVE  145 (342)
T ss_pred             HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHH
Confidence             778889988865   9999999999999999999999999999999999999999985

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=99.72  E-value=2.3e-17  Score=159.58  Aligned_cols=106  Identities=32%  Similarity=0.464  Sum_probs=90.4

Q ss_pred             CCCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHH
Q 020252          209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK  287 (328)
Q Consensus       209 ~~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Ar  287 (328)
                      ..+|++. ||+++ +++|+||++||.+|+++|+.+..++..           |+..+|....  ...+|+..++.|..|+
T Consensus        23 ~~~~~~~~Yl~~i-~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~   88 (324)
T PRK07921         23 PAADLVRVYLNGI-GKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAAR   88 (324)
T ss_pred             CCCChHHHHHHHh-cccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHH
Confidence            3468899 99999 999999999999999999987665553           2223332111  4568999999999999


Q ss_pred             HHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       288 e~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      ++||.+|+++|+++|++|.+.|++++||||||+|||++|++
T Consensus        89 ~~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~  129 (324)
T PRK07921         89 RHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAME  129 (324)
T ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999974

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=99.49  E-value=7.6e-14  Score=136.70  Aligned_cols=80  Identities=39%  Similarity=0.642  Sum_probs=73.7

Q ss_pred             CCCCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHH
Q 020252          208 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILC  286 (328)
Q Consensus       208 ~~~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~A  286 (328)
                      ...+|+++ ||++| ++.|+||++||.+|+++++.               |                         +..|
T Consensus        92 ~~~~d~~~~yl~~i-~~~~~l~~~ee~~L~~~~~~---------------G-------------------------d~~A  130 (367)
T PRK09210         92 VKINDPVRMYLKEI-GRVPLLTAEEEIELAKRIEE---------------G-------------------------DEEA  130 (367)
T ss_pred             cccCcHHHHHHHHh-hccCCCCHHHHHHHHHHHHh---------------h-------------------------HHHH
Confidence            34578999 99999 99999999999999998876               3                         3679


Q ss_pred             HHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       287 re~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      +++||.+|+++|++||++|.++|++++||||||+||||+|++
T Consensus       131 ~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~  172 (367)
T PRK09210        131 KQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVE  172 (367)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999974

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=99.49  E-value=4.6e-14  Score=146.37  Aligned_cols=45  Identities=36%  Similarity=0.580  Sum_probs=43.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       284 ~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      ..|+++||.+|||||++||++|.++|++|+|||||||||||+||+
T Consensus       379 ~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~  423 (619)
T PRK05658        379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD  423 (619)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHH
Confidence            368999999999999999999999999999999999999999985

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=99.36  E-value=2.5e-12  Score=121.74  Aligned_cols=80  Identities=26%  Similarity=0.499  Sum_probs=71.8

Q ss_pred             CCCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHH
Q 020252          209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK  287 (328)
Q Consensus       209 ~~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Ar  287 (328)
                      .+.+++. |++++ ++.|+|+.++|.+|+.+++.              .|                         +..++
T Consensus        11 ~~~~~~~~y~~~~-~~~~~l~~~~e~~l~~~~~~--------------~G-------------------------d~~a~   50 (284)
T PRK06596         11 SPEGNLDAYIQAV-NKIPMLTAEEEYMLAKRLRE--------------HG-------------------------DLEAA   50 (284)
T ss_pred             CCccHHHHHHHHH-hccCCCCHHHHHHHHHHHHH--------------cC-------------------------CHHHH
Confidence            4567899 99999 99999999999999987542              14                         47899


Q ss_pred             HHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          288 DKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       288 e~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      +.||..|+++|.+||++|.+.|++++||||||++||++|++
T Consensus        51 ~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~   91 (284)
T PRK06596         51 KQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVK   91 (284)
T ss_pred             HHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999974

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=99.34  E-value=3.2e-12  Score=119.63  Aligned_cols=76  Identities=30%  Similarity=0.564  Sum_probs=68.6

Q ss_pred             hhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHH
Q 020252          213 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI  291 (328)
Q Consensus       213 ~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI  291 (328)
                      ++. ||+++ ++.|+|+.++|.+|+.+++.              .|                         +..|+++||
T Consensus         2 ~~~~yl~~~-~~~~~l~~~~e~~l~~~~~~--------------~g-------------------------d~~a~~~Lv   41 (270)
T TIGR02392         2 SLDAYIRAV-NRIPMLTPEEEYQLAKRLRE--------------HG-------------------------DLDAAKKLV   41 (270)
T ss_pred             hHHHHHHHH-hcCCCCCHHHHHHHHHHHHH--------------CC-------------------------CHHHHHHHH
Confidence            577 99999 99999999999999887532              14                         478999999


Q ss_pred             HHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          292 TSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       292 ~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      ..|+++|.++|++|.+.|.+++||||+|++||++|++
T Consensus        42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~   78 (270)
T TIGR02392        42 LSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVK   78 (270)
T ss_pred             HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999974

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=99.28  E-value=1.3e-11  Score=117.27  Aligned_cols=78  Identities=26%  Similarity=0.364  Sum_probs=70.2

Q ss_pred             CChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHH
Q 020252          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK  289 (328)
Q Consensus       211 ~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~  289 (328)
                      .+.++ ||+++ .+.|+||.++|.+|+++++..              |                         +..|+++
T Consensus         5 ~~~~~~y~~~~-~~~~~l~~~~e~~L~~~~~~~--------------g-------------------------d~~A~~~   44 (289)
T PRK07500          5 ASADRSMIRSA-MKAPYLEREEEHALAYRWKDH--------------R-------------------------DEDALHR   44 (289)
T ss_pred             hhHHHHHHHHH-hcCCCCCHHHHHHHHHHHHHC--------------C-------------------------CHHHHHH
Confidence            34566 99999 999999999999999987531              4                         4789999


Q ss_pred             HHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          290 MITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       290 LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      ||..|+++|.++|++|.+.|.+.+||+|||++||++|++
T Consensus        45 Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~   83 (289)
T PRK07500         45 IISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAA   83 (289)
T ss_pred             HHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999974

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=99.22  E-value=9.1e-12  Score=116.83  Aligned_cols=45  Identities=27%  Similarity=0.433  Sum_probs=43.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       284 ~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      ..++++||.+|+|||++||++|.++|++++||||+|+||||+|++
T Consensus        39 ~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~Aie   83 (264)
T PRK07122         39 QRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVN   83 (264)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHH
Confidence            569999999999999999999999999999999999999999985

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=99.05  E-value=6.3e-10  Score=107.73  Aligned_cols=77  Identities=35%  Similarity=0.531  Sum_probs=71.1

Q ss_pred             CChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHH
Q 020252          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK  289 (328)
Q Consensus       211 ~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~  289 (328)
                      .|.++ |+.+| +..|+||+++|..|+.+++.               |                         +..|++.
T Consensus        52 ~~~~~~y~~~~-~~~~~l~~~ee~~li~~~~~---------------G-------------------------d~~A~~~   90 (325)
T PRK05657         52 LDATQLYLNEI-GYSPLLTAEEEVYFARRALR---------------G-------------------------DFAARQR   90 (325)
T ss_pred             ccHHHHHHHHH-hcCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHH
Confidence            56778 99999 99999999999999988876               4                         4689999


Q ss_pred             HHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          290 MITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       290 LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      ||..|.++|.++|++|.+.+.+.+||+|||++||+++++
T Consensus        91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~  129 (325)
T PRK05657         91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVE  129 (325)
T ss_pred             HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999873

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=98.95  E-value=3e-09  Score=100.27  Aligned_cols=78  Identities=36%  Similarity=0.519  Sum_probs=72.0

Q ss_pred             CCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHH
Q 020252          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  288 (328)
Q Consensus       210 ~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are  288 (328)
                      ..|.+. ||.+| +..+.|+.++|.+|+..++.               |                         ...|++
T Consensus        11 ~~~~~~~~~~~~-~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~a~~   49 (285)
T TIGR02394        11 VADVTQLYLREI-GFKPLLTAEEEIAYARRALA---------------G-------------------------DFEARK   49 (285)
T ss_pred             cchHHHHHHHHH-hccCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHH
Confidence            467899 99999 99999999999999988876               4                         478999


Q ss_pred             HHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          289 KMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       289 ~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      .|+..|.++|..+|++|.+.+.+.+||+|||+|||++|++
T Consensus        50 ~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~   89 (285)
T TIGR02394        50 VMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVE   89 (285)
T ss_pred             HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999874

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).

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=98.89  E-value=4.8e-09  Score=97.25  Aligned_cols=68  Identities=26%  Similarity=0.453  Sum_probs=61.5

Q ss_pred             ccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHH
Q 020252          221 TSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS  300 (328)
Q Consensus       221 ~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvs  300 (328)
                      ++++|+|++++|.+|+..++.               |                         +..++++|+..|+++|.+
T Consensus        10 ~~~~~~l~~~~~~~li~~~~~---------------g-------------------------d~~a~~~L~~~~~~~v~~   49 (254)
T TIGR02850        10 TSKLPVLKNQEMRELFIRMQS---------------G-------------------------DTTAREKLINGNLRLVLS   49 (254)
T ss_pred             ccCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhHHHHHH
Confidence            468999999999999887765               4                         367999999999999999


Q ss_pred             HHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          301 IAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       301 IAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      +|++|.+.+.+.+||+|||++||+++++
T Consensus        50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~   77 (254)
T TIGR02850        50 VIQRFNNRGEYVDDLFQVGCIGLMKSID   77 (254)
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999874

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.

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=98.87  E-value=4.6e-09  Score=97.86  Aligned_cols=46  Identities=22%  Similarity=0.353  Sum_probs=42.3

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCC-CCChHHHHHHHHHHHHhhhC
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGA-GMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~-Gl~~~DLIQEG~iGLmrAve  328 (328)
                      ...++++||.+|++||.+||++|.++ |.+++||||+|+||||+|++
T Consensus        23 d~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~   69 (256)
T PRK07408         23 SIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIE   69 (256)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHH
Confidence            36899999999999999999999876 77899999999999999974

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

Probab=98.85  E-value=5.6e-09  Score=98.66  Aligned_cols=45  Identities=22%  Similarity=0.426  Sum_probs=42.3

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCC-ChHHHHHHHHHHHHhhhC
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGM-NLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl-~~~DLIQEG~iGLmrAve  328 (328)
                      ...++ +||+.|+|||.+||++|.++|. .++||||.||||||+||+
T Consensus        22 ~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aie   67 (247)
T COG1191          22 DEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIE   67 (247)
T ss_pred             CHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHH
Confidence            36788 9999999999999999999998 999999999999999985

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=98.82  E-value=1.1e-08  Score=94.79  Aligned_cols=67  Identities=27%  Similarity=0.475  Sum_probs=60.7

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHH
Q 020252          222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI  301 (328)
Q Consensus       222 ~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsI  301 (328)
                      .++|+|+++|+..|+..++.               |                         +..++++|+..|+++|..+
T Consensus        14 ~~~~~l~~~~~~~l~~~~~~---------------g-------------------------d~~a~~~l~~~~~~~v~~~   53 (258)
T PRK08215         14 SKLPVLKNEEMRELFERMQN---------------G-------------------------DKEAREKLINGNLRLVLSV   53 (258)
T ss_pred             CCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHHHHHHHHH
Confidence            56789999999998887764               3                         4689999999999999999


Q ss_pred             HhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          302 AKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       302 AkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      |++|.+.+.+.+||+|||++||++|++
T Consensus        54 a~~~~~~~~~aeDlvQe~~i~l~~a~~   80 (258)
T PRK08215         54 IQRFNNRGENVDDLFQVGCIGLMKAID   80 (258)
T ss_pred             HHHHhCCCCCHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999874

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=98.66  E-value=5.4e-08  Score=90.91  Aligned_cols=70  Identities=16%  Similarity=0.220  Sum_probs=60.9

Q ss_pred             hccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHH
Q 020252          220 TTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVI  299 (328)
Q Consensus       220 i~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVv  299 (328)
                      ++|++|+||.++|.+|+..++..              |                         +..+++.++..|++||.
T Consensus         5 ~~~~~~~~~~~~e~~l~~~~~~~--------------~-------------------------d~~a~~~l~~~y~~lv~   45 (268)
T PRK06288          5 MSGKIPKYAQQDETELWREYKKT--------------G-------------------------DPKIREYLILKYSPLVK   45 (268)
T ss_pred             ccCCCccccchHHHHHHHHHHHc--------------C-------------------------CHHHHHHHHHHHHHHHH
Confidence            35889999999999999887752              3                         46789999999999999


Q ss_pred             HHHhhcc-C--CCCChHHHHHHHHHHHHhhhC
Q 020252          300 SIAKNYQ-G--AGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       300 sIAkrY~-g--~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      .+|++|. +  .+.+.+||+|||++||++|++
T Consensus        46 ~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~   77 (268)
T PRK06288         46 YVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIE   77 (268)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Confidence            9999986 2  578899999999999999974

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=98.57  E-value=7e-08  Score=90.17  Aligned_cols=46  Identities=17%  Similarity=0.177  Sum_probs=41.2

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhcc---CCCCChHHHHHHHHHHHHhhhC
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQ---GAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~---g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      +..+|++||..|++||.+||++|.   ..+++++||+|+|+|||++|++
T Consensus        21 ~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~   69 (257)
T PRK05911         21 EIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVE   69 (257)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Confidence            467999999999999999999986   2456899999999999999985

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=98.56  E-value=2.9e-07  Score=84.09  Aligned_cols=74  Identities=23%  Similarity=0.432  Sum_probs=66.4

Q ss_pred             hhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHH
Q 020252          213 PLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI  291 (328)
Q Consensus       213 ~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI  291 (328)
                      .+. |+.++ ++.++||+++|..|...++.               |                         +..+.+.|+
T Consensus        17 ~~~~~~~~~-~~~~~~~~~~e~~l~~~~~~---------------g-------------------------d~~a~~~l~   55 (233)
T PRK05803         17 FLVSYVKNN-SFPQPLSEEEERKYLELMKE---------------G-------------------------DEEARNILI   55 (233)
T ss_pred             HHHHHHHHh-cccCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHH
Confidence            345 99999 99999999999988777654               3                         467899999


Q ss_pred             HHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          292 TSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       292 ~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ..+.++|.+++.+|.+.+.+.+||+|||.|||++++
T Consensus        56 ~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~   91 (233)
T PRK05803         56 ERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAI   91 (233)
T ss_pred             HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999986

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=98.50  E-value=3.2e-07  Score=84.74  Aligned_cols=66  Identities=29%  Similarity=0.295  Sum_probs=58.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHHHh
Q 020252          224 SRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAK  303 (328)
Q Consensus       224 ~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsIAk  303 (328)
                      .+.||+++|.+|...++..              |                         +..|.++|+..|.++|..+|+
T Consensus         7 ~~~l~~~~~~~li~~~~~~--------------g-------------------------d~~a~~~l~~~y~~~v~~~a~   47 (255)
T TIGR02941         7 PTNLTKEDVIQWIAEFQQN--------------Q-------------------------NGEAQEKLVDHYQNLVYSIAY   47 (255)
T ss_pred             CCCCCHHHHHHHHHHHHHC--------------C-------------------------CHHHHHHHHHHhHHHHHHHHH
Confidence            3678999998888877752              2                         367999999999999999999


Q ss_pred             hccCCCCChHHHHHHHHHHHHhhhC
Q 020252          304 NYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       304 rY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      +|.+.+.+.+||+|||++||+++++
T Consensus        48 ~~~~~~~~aeDlvQe~~i~l~~a~~   72 (255)
T TIGR02941        48 KYSKGGPMHEDLVQVGMLGLLGAIR   72 (255)
T ss_pred             HHhcCCCCHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999874

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

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=98.39  E-value=9.9e-07  Score=81.63  Aligned_cols=67  Identities=24%  Similarity=0.237  Sum_probs=58.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHHH
Q 020252          223 SSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA  302 (328)
Q Consensus       223 ~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsIA  302 (328)
                      ..+.|++++|.+|..+++..              |                         ...|.+.|+..|.++|..+|
T Consensus         6 ~~~~l~~~e~~~li~~~~~~--------------g-------------------------d~~a~~~l~~~~~~~v~~~a   46 (257)
T PRK08583          6 QPTKLTKEEVNKWIAEYQEN--------------Q-------------------------DEEAQEKLVKHYKNLVESLA   46 (257)
T ss_pred             cCCcCChHHHHHHHHHHHHc--------------C-------------------------CHHHHHHHHHHHHHHHHHHH
Confidence            34789999999888777641              3                         36799999999999999999


Q ss_pred             hhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          303 KNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       303 krY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      ++|.+.+.+.+||+|||++||+++++
T Consensus        47 ~~~~~~~~~aeDlvQe~~l~l~~~~~   72 (257)
T PRK08583         47 YKYSKGQSHHEDLVQVGMVGLLGAIR   72 (257)
T ss_pred             HHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999863

>PRK05572 sporulation sigma factor SigF; Validated

Probab=98.07  E-value=1.3e-05  Score=74.28  Aligned_cols=67  Identities=25%  Similarity=0.414  Sum_probs=58.6

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHH
Q 020252          222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI  301 (328)
Q Consensus       222 ~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsI  301 (328)
                      ...|.||.+++.+|...++.               |                         ...+.++|+..|.++|..+
T Consensus         9 ~~~~~l~~~~~~~li~~~~~---------------g-------------------------d~~a~~~L~~~y~~~v~~~   48 (252)
T PRK05572          9 KKKPQLKDEENKELIKKSQD---------------G-------------------------DQEARDTLVEKNLRLVWSV   48 (252)
T ss_pred             cCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhHHHHHHH
Confidence            45789999998888766554               3                         3678999999999999999


Q ss_pred             HhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          302 AKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       302 AkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      |++|.+.+.+.+||+|||.++|+++++
T Consensus        49 a~~~~~~~~~aeDl~Qe~~l~l~~~~~   75 (252)
T PRK05572         49 VQRFLNRGYEPDDLFQIGCIGLLKAVD   75 (252)
T ss_pred             HHHHccCCCCHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999863

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=98.03  E-value=1.9e-06  Score=59.38  Aligned_cols=33  Identities=42%  Similarity=0.554  Sum_probs=29.2

Q ss_pred             CChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHH
Q 020252          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK  244 (328)
Q Consensus       211 ~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~  244 (328)
                      +|+++ ||++| +++||||++||++|+++|+.+..
T Consensus         1 ~D~l~~Yl~ei-~~~~LLt~eeE~~LA~~i~~g~~   34 (37)
T PF00140_consen    1 SDSLRLYLKEI-GRYPLLTAEEEIELARRIRKGDE   34 (37)
T ss_dssp             HHHHHHHHHHH-HHS-EETTHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHhHH
Confidence            37899 99999 99999999999999999998754

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 ....

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=97.88  E-value=3.2e-05  Score=71.61  Aligned_cols=46  Identities=17%  Similarity=0.146  Sum_probs=42.0

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccC---CCCChHHHHHHHHHHHHhhhC
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQG---AGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g---~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      ...|.++|+..|.++|.++|.+|.+   .+.+.+||+|||++||+++++
T Consensus        20 d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~   68 (251)
T PRK07670         20 DPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALE   68 (251)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHH
Confidence            4789999999999999999999965   688999999999999999874

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=97.79  E-value=0.00013  Score=66.68  Aligned_cols=72  Identities=22%  Similarity=0.446  Sum_probs=62.2

Q ss_pred             HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhH
Q 020252          216 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI  295 (328)
Q Consensus       216 YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNL  295 (328)
                      |.-.-.++.+.|++.+|.+|...++.               |                         +..+.+.|+..|.
T Consensus        19 ~~~~~~~~~~~~~~~~~~~li~~~~~---------------g-------------------------d~~af~~l~~~y~   58 (227)
T TIGR02846        19 YVTNNGSFPQPLSEEEEKKYLDRLKE---------------G-------------------------DEEARNVLIERNL   58 (227)
T ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHc---------------C-------------------------CHHHHHHHHHHhH
Confidence            65443367888999999999877765               4                         3678999999999


Q ss_pred             HHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          296 RLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       296 RLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ++|.+++.+|.+.+.+.+||+||+.+++++++
T Consensus        59 ~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~   90 (227)
T TIGR02846        59 RLVAHIVKKFSNTGEDVDDLISIGTIGLIKAI   90 (227)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999886

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=97.67  E-value=0.00018  Score=65.58  Aligned_cols=76  Identities=24%  Similarity=0.486  Sum_probs=60.5

Q ss_pred             ChhHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHH
Q 020252          212 DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI  291 (328)
Q Consensus       212 d~l~YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI  291 (328)
                      |.+-|+.+...-.+.++..++.+|...++.               |                         +..+.+.|+
T Consensus        19 ~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~---------------g-------------------------d~~af~~l~   58 (234)
T PRK08301         19 DEIYYIGGSEALPPPLSKEEEEYLLNKLPK---------------G-------------------------DEAVRSLLI   58 (234)
T ss_pred             HHHHHhccccccCCcCCHHHHHHHHHHHHc---------------c-------------------------CHHHHHHHH
Confidence            344477766334556777777777665554               3                         367899999


Q ss_pred             HHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          292 TSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       292 ~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ..+.++|..+|.+|.+.+.+.+||+||+.+++++++
T Consensus        59 ~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~   94 (234)
T PRK08301         59 ERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAV   94 (234)
T ss_pred             HHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999875

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=97.41  E-value=0.00059  Score=62.64  Aligned_cols=45  Identities=27%  Similarity=0.572  Sum_probs=42.6

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      +..+.+.++..+.+.|..++++|.+.+.+-+||+||+.+++++++
T Consensus        50 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~   94 (234)
T TIGR02835        50 DESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAV   94 (234)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHH
Confidence            468999999999999999999999999999999999999999875

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.

>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=97.20  E-value=0.00045  Score=50.55  Aligned_cols=38  Identities=21%  Similarity=0.306  Sum_probs=36.1

Q ss_pred             HHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          290 MITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       290 LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      |++.+.++|..++.+|.+.+.+.+|++||+.++|++++
T Consensus         1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~   38 (71)
T PF04542_consen    1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAI   38 (71)
T ss_dssp             HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhh
Confidence            68899999999999999999999999999999999875

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 ....

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=97.01  E-value=0.0017  Score=59.41  Aligned_cols=66  Identities=20%  Similarity=0.204  Sum_probs=57.5

Q ss_pred             cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHH
Q 020252          222 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI  301 (328)
Q Consensus       222 ~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsI  301 (328)
                      .+.|+|+...+..|...++.               |                         +..+.+.|+..|.++|..+
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            46788888888887776654               3                         4678899999999999999


Q ss_pred             HhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          302 AKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       302 AkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      +++|.+.+-+-+||+||+.++|++.+
T Consensus        47 a~~~~~~~~~AEDlvQE~fi~l~~~~   72 (231)
T PRK11922         47 ARAILRNDAEAEDVVQEAYLRAFRAL   72 (231)
T ss_pred             HHHHhCChhhHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999875

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=96.78  E-value=0.0027  Score=55.46  Aligned_cols=54  Identities=19%  Similarity=0.214  Sum_probs=46.1

Q ss_pred             HHHHHhhh-hhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          274 RELRRRLN-YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       274 ~~L~~~L~-~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ..|-..+. .+..+.+.|+..|.++|..+|.+|.+.+.+.+|++||+.++|++.+
T Consensus         8 ~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~   62 (186)
T PRK05602          8 EELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQA   62 (186)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHh
Confidence            34433333 3478999999999999999999999999999999999999999875

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=96.71  E-value=0.0045  Score=65.17  Aligned_cols=33  Identities=33%  Similarity=0.537  Sum_probs=31.2

Q ss_pred             CCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHH
Q 020252          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLL  243 (328)
Q Consensus       210 ~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~  243 (328)
                      .+||++ ||++| |..||||+++|++++++|..+.
T Consensus       102 t~DPVRMYLREM-G~V~LLTREgEIeIAKRIE~G~  135 (619)
T PRK05658        102 TDDPVRMYLREM-GTVELLTREGEIEIAKRIEAGE  135 (619)
T ss_pred             CCChHHHHHHHh-ccCcCCCcHHHHHHHHHHHHHH
Confidence            599999 99999 9999999999999999999873

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=96.70  E-value=0.0039  Score=57.64  Aligned_cols=21  Identities=14%  Similarity=0.273  Sum_probs=18.8

Q ss_pred             CCCChHHHHHHHHHHHHhhhC
Q 020252          308 AGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       308 ~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      .+++.+||||+|+|||++|++
T Consensus        41 ~~~~~eDLvQeg~igL~~a~~   61 (231)
T PRK12427         41 SVIDREDMEQIALMGLLEALR   61 (231)
T ss_pred             CCCCHHHHHHHHHHHHHHHHH
Confidence            457999999999999999974

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=96.67  E-value=0.0033  Score=54.36  Aligned_cols=45  Identities=9%  Similarity=0.003  Sum_probs=42.1

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ...+.+.++..+.++|..+|.+|.+.+.+.+|++||+.++|+++.
T Consensus        16 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~   60 (187)
T PRK09641         16 DQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNI   60 (187)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            377899999999999999999999999999999999999999875

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=96.66  E-value=0.005  Score=54.33  Aligned_cols=45  Identities=18%  Similarity=0.177  Sum_probs=42.4

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ...+.+.|+..+.++|..+|.+|.+.+.+.+||+||+.++|++++
T Consensus        22 d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~   66 (208)
T PRK08295         22 DKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAI   66 (208)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHH
Confidence            477999999999999999999999999999999999999999875

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=96.52  E-value=0.0073  Score=52.80  Aligned_cols=55  Identities=16%  Similarity=0.209  Sum_probs=46.8

Q ss_pred             HHHHHHhhhhh-HHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          273 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       273 ~~~L~~~L~~G-~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ...|-..+..| ..+.+.|+..+.+.|..+|.+|.+...+.+||+||+.+.+++.+
T Consensus         6 ~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~   61 (198)
T TIGR02859         6 DEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAI   61 (198)
T ss_pred             hHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHH
Confidence            34444444444 67999999999999999999999999999999999999999875

Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.

>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=96.50  E-value=0.0053  Score=46.96  Aligned_cols=40  Identities=30%  Similarity=0.381  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhh
Q 020252          243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY  282 (328)
Q Consensus       243 ~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~  282 (328)
                      .++.+.+.+|..++||+||.+|.|+.+|++.+.++..+..
T Consensus         4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~   43 (78)
T PF04539_consen    4 RKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQA   43 (78)
T ss_dssp             HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHh
Confidence            4566788999999999999999999999999988876653

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 ....

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=96.45  E-value=0.007  Score=56.89  Aligned_cols=54  Identities=7%  Similarity=0.214  Sum_probs=45.1

Q ss_pred             HHHHhhhhh-HHHHHHHHHHhHHHHHHHHhhccCCCC--ChHHHHHHHHHHHHhhhC
Q 020252          275 ELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGM--NLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       275 ~L~~~L~~G-~~Are~LI~sNLRLVvsIAkrY~g~Gl--~~~DLIQEG~iGLmrAve  328 (328)
                      .|-..+..| ..|.+.|+..+.++|..+|.+|.++..  ..+|++|+|.++++++++
T Consensus         7 ~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~   63 (237)
T PRK08311          7 DILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAID   63 (237)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHH
Confidence            334444444 679999999999999999999998876  489999999999999874

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=96.35  E-value=0.0056  Score=52.90  Aligned_cols=45  Identities=9%  Similarity=0.017  Sum_probs=42.2

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ...+..+|+..+.++|..+|.+|.+.+.+.+|++||+.++|++..
T Consensus        16 d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~   60 (187)
T TIGR02948        16 DENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNI   60 (187)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhH
Confidence            477899999999999999999999999999999999999999875

This sigma factor is restricted to certain lineages of the order Bacillales.

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=96.21  E-value=0.0084  Score=52.69  Aligned_cols=53  Identities=11%  Similarity=0.026  Sum_probs=45.3

Q ss_pred             HHHHhhhh-hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          275 ELRRRLNY-GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       275 ~L~~~L~~-G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      .|-..+.. ...+.+.|+..|.+.|..+|.+|.+...+.+|++||+.++|+++.
T Consensus        15 ~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~   68 (194)
T PRK12513         15 ALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRAR   68 (194)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            33333343 478999999999999999999999999999999999999999875

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=96.18  E-value=0.017  Score=50.49  Aligned_cols=45  Identities=16%  Similarity=0.199  Sum_probs=39.5

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCC----CCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGA----GMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~----Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ...+.++|+..+.+.|..+|.+|.+.    +.+.+|++||+.++|++.+
T Consensus        22 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~   70 (189)
T PRK09648         22 DRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITAL   70 (189)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHH
Confidence            37899999999999999999988643    4689999999999999864

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=96.07  E-value=0.013  Score=50.85  Aligned_cols=54  Identities=15%  Similarity=0.084  Sum_probs=45.6

Q ss_pred             HHHHHhhh-hhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          274 RELRRRLN-YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       274 ~~L~~~L~-~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      .+|-..+. ....+.+.++..|.+.|..++++|.+.+.+.+|++||+.+.|+++.
T Consensus        11 ~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~   65 (186)
T PRK13919         11 EALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKA   65 (186)
T ss_pred             HHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhh
Confidence            34444443 3477999999999999999999999999999999999999999875

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=95.98  E-value=0.017  Score=49.60  Aligned_cols=45  Identities=11%  Similarity=0.019  Sum_probs=42.1

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      +..+.+.|+..+.+.|..++.+|.+..-+-+|++||+.+.|+++.
T Consensus        16 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~   60 (176)
T PRK09638         16 DDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENL   60 (176)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHH
Confidence            477999999999999999999999999999999999999999875

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=95.97  E-value=0.02  Score=50.24  Aligned_cols=45  Identities=9%  Similarity=0.081  Sum_probs=41.6

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ...+.+.|+..|.+.|..++++|.+..-+.+|++||+.+.+++++
T Consensus        18 d~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~   62 (193)
T PRK11923         18 DKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRAL   62 (193)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhH
Confidence            367899999999999999999999988899999999999999875

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=95.94  E-value=0.019  Score=50.50  Aligned_cols=57  Identities=18%  Similarity=0.269  Sum_probs=48.8

Q ss_pred             CcHHHHHHhhhh----hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          271 VDQRELRRRLNY----GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       271 ~d~~~L~~~L~~----G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ++.+.|...+..    +..+.+.|+..|.+.|..++.+|.+..-+.+|++||+.+.|++.+
T Consensus         8 ~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~   68 (188)
T PRK09640          8 LNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGL   68 (188)
T ss_pred             CCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHH
Confidence            344555556653    488999999999999999999999999999999999999999865

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=95.78  E-value=0.021  Score=50.48  Aligned_cols=53  Identities=13%  Similarity=0.014  Sum_probs=45.6

Q ss_pred             HHHHhhhh-hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          275 ELRRRLNY-GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       275 ~L~~~L~~-G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      .|-..+.. ...+.++++..|.++|..++.+|.+..-+-+|++||+.+.+++.+
T Consensus        19 ~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~   72 (194)
T PRK09646         19 ALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTA   72 (194)
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhh
Confidence            34344443 478999999999999999999999999999999999999999875

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=95.44  E-value=0.044  Score=48.26  Aligned_cols=56  Identities=14%  Similarity=0.099  Sum_probs=45.2

Q ss_pred             cHHHHHHhhhhh-HHHHHHHHHHhHHHHHHHHhhccCCC---CChHHHHHHHHHHHHhhh
Q 020252          272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAG---MNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       272 d~~~L~~~L~~G-~~Are~LI~sNLRLVvsIAkrY~g~G---l~~~DLIQEG~iGLmrAv  327 (328)
                      +.+.|-..+..| ..+.+.|+..|.++|..++.+|.+.+   .+.+|++||+.++|++.+
T Consensus         4 ~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~   63 (189)
T PRK06811          4 NEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNI   63 (189)
T ss_pred             cHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhH
Confidence            334455555544 67999999999999999999998764   358999999999999875

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=95.35  E-value=0.036  Score=47.99  Aligned_cols=45  Identities=11%  Similarity=0.144  Sum_probs=41.7

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      +..+.+.|+..+.+.|..+|.++.+...+.+||+||+.++|++.+
T Consensus        18 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~   62 (190)
T TIGR02939        18 EKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRAL   62 (190)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhH
Confidence            467899999999999999999999999999999999999998764

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 RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=95.18  E-value=0.042  Score=48.15  Aligned_cols=53  Identities=21%  Similarity=0.140  Sum_probs=44.3

Q ss_pred             HHHHHhhhh-hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhh
Q 020252          274 RELRRRLNY-GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNM  326 (328)
Q Consensus       274 ~~L~~~L~~-G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrA  326 (328)
                      .+|-.++.. +..+.+.|+..+.++|..++++|.+...+-+|++|++.++|++.
T Consensus        17 ~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~   70 (194)
T PRK12519         17 AELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK   70 (194)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh
Confidence            334444443 47799999999999999999999999999999999999999863

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=95.16  E-value=0.038  Score=47.85  Aligned_cols=45  Identities=7%  Similarity=-0.039  Sum_probs=41.9

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      +..+...|+..+.+.|..+|.+|.+...+-+|++||+.+++++.+
T Consensus        17 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~   61 (179)
T PRK12514         17 DRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKA   61 (179)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhH
Confidence            467999999999999999999999999999999999999998765

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=95.00  E-value=0.044  Score=47.79  Aligned_cols=46  Identities=4%  Similarity=-0.081  Sum_probs=42.4

Q ss_pred             hhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       282 ~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ....+.+.++..+.++|..++.+|.+...+-+|++||..+.+++..
T Consensus        22 ~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~   67 (187)
T PRK12534         22 GDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKA   67 (187)
T ss_pred             CCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhcc
Confidence            3478999999999999999999999999999999999999999865

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=94.88  E-value=0.063  Score=47.56  Aligned_cols=55  Identities=16%  Similarity=0.154  Sum_probs=47.0

Q ss_pred             HHHHHHhhhhh-HHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          273 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       273 ~~~L~~~L~~G-~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ...|-..+..| ..+.+.|+..+.++|..+|.+|.+...+-+|++||+.+.|++..
T Consensus        13 ~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~   68 (196)
T PRK12524         13 DEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIA   68 (196)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhh
Confidence            34455555544 78999999999999999999999999999999999999998764

>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family

Probab=94.19  E-value=0.11  Score=44.54  Aligned_cols=45  Identities=11%  Similarity=0.035  Sum_probs=41.6

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      +..+.+.++..+.+.+..++.+|.+..-+.+|++||..+-+.+..
T Consensus        14 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~   58 (169)
T TIGR02954        14 NKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSI   58 (169)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999999999999999988753

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=93.26  E-value=0.22  Score=44.06  Aligned_cols=45  Identities=11%  Similarity=-0.049  Sum_probs=41.2

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ...+.+.|+..|.+.|..+|.+|.+..-.-+|++||.++.+++..
T Consensus        25 d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~   69 (194)
T PRK12531         25 DKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKA   69 (194)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhH
Confidence            467899999999999999999999988889999999999998764

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=93.14  E-value=0.21  Score=43.84  Aligned_cols=56  Identities=14%  Similarity=0.038  Sum_probs=46.5

Q ss_pred             cHHHHHHhhhh-hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          272 DQRELRRRLNY-GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       272 d~~~L~~~L~~-G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      +...|...+.. +..+.+.|+..+.+.+..++.+|.+...+-+|++||..+.+++..
T Consensus         8 ~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~   64 (189)
T PRK12515          8 TDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQA   64 (189)
T ss_pred             CHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHH
Confidence            34445444444 467999999999999999999999999999999999999998764

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=93.00  E-value=0.2  Score=46.48  Aligned_cols=45  Identities=18%  Similarity=0.157  Sum_probs=41.3

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      +..+.+.|+..+.+.|..++.+|.|..-+-+|++||..+.+++..
T Consensus        61 d~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~  105 (233)
T PRK12538         61 DEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHR  105 (233)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
Confidence            367999999999999999999999988899999999999998754

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=92.25  E-value=0.36  Score=42.13  Aligned_cols=46  Identities=9%  Similarity=0.031  Sum_probs=42.3

Q ss_pred             hhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          282 YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       282 ~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ....+.+.|+..+.+.+..++.++.+...+-+|++||..+.+++..
T Consensus        20 ~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~   65 (182)
T PRK12537         20 GDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGA   65 (182)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhcc
Confidence            3578999999999999999999999999999999999999998764

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=92.06  E-value=0.35  Score=42.86  Aligned_cols=54  Identities=17%  Similarity=0.091  Sum_probs=45.6

Q ss_pred             HHHHHhhh-hhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          274 RELRRRLN-YGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       274 ~~L~~~L~-~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      +.+-..+. ....+.+.++..+.+.|.+++.++.+...+-+|++||..+-+++..
T Consensus        15 ~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~   69 (192)
T PRK09643         15 AELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAA   69 (192)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHH
Confidence            34444443 4477999999999999999999999999999999999999999864

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=91.90  E-value=0.55  Score=40.81  Aligned_cols=44  Identities=14%  Similarity=0.091  Sum_probs=38.4

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCC-C---CChHHHHHHHHHHHHhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGA-G---MNLQDLVQLQALRYLNM  326 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~-G---l~~~DLIQEG~iGLmrA  326 (328)
                      +..+.+.|+..+.+.|..+|.+|.+. |   .+.+|++||+.+.+++.
T Consensus        20 d~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~   67 (184)
T PRK12512         20 DAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLK   67 (184)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHh
Confidence            57899999999999999999988753 3   57999999999998764

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=91.28  E-value=0.41  Score=42.97  Aligned_cols=45  Identities=11%  Similarity=-0.012  Sum_probs=41.4

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ...+.++|+..+.++|..++.+|.+..-+-+|++||+.+.+++.+
T Consensus        36 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~   80 (206)
T PRK12526         36 DKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKA   80 (206)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhH
Confidence            477889999999999999999999888899999999999999865

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=91.26  E-value=0.58  Score=40.80  Aligned_cols=47  Identities=13%  Similarity=0.015  Sum_probs=40.4

Q ss_pred             hhhHHHHHHHHHHhHHHHHHHHhhcc-CCCCChHHHHHHHHHHHHhhh
Q 020252          281 NYGILCKDKMITSNIRLVISIAKNYQ-GAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       281 ~~G~~Are~LI~sNLRLVvsIAkrY~-g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ..+..+.++++..+.+.|..++.++. +.+.+.+||+||+.+.|++..
T Consensus        17 ~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~   64 (181)
T PRK12536         17 AGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNAR   64 (181)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhH
Confidence            34577899999999999999998865 457899999999999998764

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=90.86  E-value=0.86  Score=39.84  Aligned_cols=45  Identities=11%  Similarity=0.027  Sum_probs=39.1

Q ss_pred             hHHHHHHHHHHhHHHHHHHHh----hccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAK----NYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAk----rY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      +..+.+.|+..+.+.|..+++    +|.+...+-+|++||..+.|++..
T Consensus        19 d~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~   67 (184)
T PRK12539         19 DAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRR   67 (184)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHH
Confidence            367999999999999999876    566778899999999999998764

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

Probab=84.84  E-value=1.9  Score=41.34  Aligned_cols=41  Identities=24%  Similarity=0.263  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhh
Q 020252          243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYG  283 (328)
Q Consensus       243 ~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G  283 (328)
                      .++..+..+|..++|++||..|.|+.+|++.+++...+..+
T Consensus       110 ~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~  150 (247)
T COG1191         110 RRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAI  150 (247)
T ss_pred             HHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHh
Confidence            34455778899999999999999999999998887766554

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=83.95  E-value=1.7  Score=39.27  Aligned_cols=45  Identities=16%  Similarity=0.214  Sum_probs=41.4

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ...+.++|+..|.+.+..++.+|.+....-+|++||..+.+++..
T Consensus        26 d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~   70 (203)
T PRK09647         26 TMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSL   70 (203)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhH
Confidence            367889999999999999999999999999999999999998764

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=83.52  E-value=2.7  Score=40.34  Aligned_cols=45  Identities=16%  Similarity=0.071  Sum_probs=41.0

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ...+.++|+..|.+.|..++.+|.+...+-+|++||-.+-+++..
T Consensus        17 d~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~   61 (339)
T PRK08241         17 DRDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGY   61 (339)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhh
Confidence            467899999999999999999999988899999999999988754

>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family

Probab=81.98  E-value=4.6  Score=34.84  Aligned_cols=43  Identities=16%  Similarity=0.150  Sum_probs=38.7

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCC-----ChHHHHHHHHHHHHh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGM-----NLQDLVQLQALRYLN  325 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl-----~~~DLIQEG~iGLmr  325 (328)
                      +..+.+.|+..+.+.+..++.+|.+...     +-+|++||..+.+++
T Consensus        15 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~   62 (183)
T TIGR02999        15 DAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSD   62 (183)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhh
Confidence            3678999999999999999999987766     789999999999986

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	328
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		2e-06
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		1e-05
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		3e-05
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		3e-05
3les_A	179	2f5 Epitope Scaffold Es2 Length = 179		5e-04

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

Iteration: 1
 Score = 50.1 bits (118), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 38/122 (31%), Positives = 60/122 (49%), Gaps = 15/122 (12%)
Query: 211 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 258
           SDP+R          LLT  EE+ L+     G++ + KL        E +REV+  +  G
Sbjct: 2   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 61
Query: 259 SPTFAQWAAAAGVDQRELRRRLNY---GILCKDKMITSNIRLVISIAKNYQGAGMNLQDL 315
           +    +         +EL+R L+    G   +  +I +N+RLV+SIAK Y G G++  DL
Sbjct: 62  TARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDL 121
Query: 316 VQ 317
           +Q
Sbjct: 122 IQ 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 = 47.4 bits (111), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/140 (29%), Positives = 65/140 (46%), Gaps = 30/140 (21%)
Query: 208 VDYSDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSER 255
           V  SDP+R          LLT  EE+ L+     G++ + KL        E +REV+  +
Sbjct: 90  VSTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAK 149
Query: 256 CGGS------PTFAQWAAAAGVDQ---------RELRRRLNY---GILCKDKMITSNIRL 297
             G+      P   +      V++         +EL+R L+    G   +  +I +N+RL
Sbjct: 150 ILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRL 209
Query: 298 VISIAKNYQGAGMNLQDLVQ 317
           V+SIAK Y G G++  DL+Q
Sbjct: 210 VVSIAKKYTGRGLSFLDLIQ 229

>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 = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 40/137 (29%), Positives = 64/137 (46%), Gaps = 30/137 (21%)
Query: 211 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 258
           SDP+R          LLT  EE+ L+     G++ + KL        E +REV+  +  G
Sbjct: 6   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 65
Query: 259 S------PTFAQWAAAAGVDQ---------RELRRRLNY---GILCKDKMITSNIRLVIS 300
           +      P   +      V++         +EL+R L+    G   +  +I +N+RLV+S
Sbjct: 66  TARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVS 125
Query: 301 IAKNYQGAGMNLQDLVQ 317
           IAK Y G G++  DL+Q
Sbjct: 126 IAKKYTGRGLSFLDLIQ 142

>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 = 45.8 bits (107), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 40/137 (29%), Positives = 64/137 (46%), Gaps = 30/137 (21%)
Query: 211 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 258
           SDP+R          LLT  EE+ L+     G++ + KL        E +REV+  +  G
Sbjct: 2   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 61
Query: 259 S------PTFAQWAAAAGVDQ---------RELRRRLNY---GILCKDKMITSNIRLVIS 300
           +      P   +      V++         +EL+R L+    G   +  +I +N+RLV+S
Sbjct: 62  TARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVS 121
Query: 301 IAKNYQGAGMNLQDLVQ 317
           IAK Y G G++  DL+Q
Sbjct: 122 IAKKYTGRGLSFLDLIQ 138

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 31/47 (65%), Gaps = 3/47 (6%)
Query: 274 RELRRRLNY---GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
           +EL+R L+    G   +  +I +N+RLV+SIAK Y G G++  DL+Q
Sbjct: 91  KELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 137

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	328
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	4e-08
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	8e-08
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	9e-08
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	2e-06
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	5e-06
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	4e-04

>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 = 53.3 bits (128), Expect = 4e-08
 Identities = 34/199 (17%), Positives = 63/199 (31%), Gaps = 20/199 (10%)

Query: 120 IGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVR-SRRQTERKARR 178
             D  + +     E        +   L+   EE  L   ++S S  VR    +  +    
Sbjct: 35  EPDPDLEDPDLALEDDLLDLPEEGEGLDLEEEEEDLPIPKISTSDPVRQYLHEIGQVPLL 94

Query: 179 TRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAG 238
           T   E   A  +     +  +    +  + D                ++ A         
Sbjct: 95  TLEEEVELARKVEEGMEAIKKLSEITGLDPDLIR------------EVVRAKILGSARVR 142

Query: 239 IQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLV 298
               LK     + + E      +  +       + +        G   +  +I +N+RLV
Sbjct: 143 HIPGLKETLDPKTVEEIDQKLKSLPK-------EHKRYLHIAREGEAARQHLIEANLRLV 195

Query: 299 ISIAKNYQGAGMNLQDLVQ 317
           +SIAK Y G G++  DL+Q
Sbjct: 196 VSIAKKYTGRGLSFLDLIQ 214

>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 = 51.4 bits (123), Expect = 8e-08
 Identities = 16/46 (34%), Positives = 26/46 (56%)

Query: 272 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
           + +        G   +  +I +N+RLV+SIAK Y G G++  DL+Q
Sbjct: 97  ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 142

>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 = 52.3 bits (125), Expect = 9e-08
 Identities = 31/228 (13%), Positives = 69/228 (30%), Gaps = 4/228 (1%)

Query: 94  KPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEEL 153
           K + S                +    + +    E   +    + + L    +LE   + L
Sbjct: 2   KKSKSKKKAAKAQEVEVKEPVKEPEPLPELEAAEDLQDLPEPDPELLASEPELEDLADPL 61

Query: 154 KLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDP 213
            L     +  +      + E +         +      +             +       
Sbjct: 62  DLEGPLEADLLPEEGLLEEEEEELSLPKVSTSDPVRQYLHEIGQVPLLTLEEEIDLARKV 121

Query: 214 LRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQ 273
              + A    S     ++E+        +L    ++++   +    P   +         
Sbjct: 122 EEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSL 181

Query: 274 RELRRRLNY----GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
            +  +R  +    G   +  +I +N+RLV+SIAK Y G G++  DL+Q
Sbjct: 182 PKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 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 = 47.6 bits (113), Expect = 2e-06
 Identities = 16/31 (51%), Positives = 22/31 (70%)

Query: 287 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
           K +M+ +N+RLVISIAK Y   G+   DL+Q
Sbjct: 267 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 297

>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 = 46.0 bits (110), Expect = 5e-06
 Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 272 DQRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
           + +EL RR   G    +D++I  N+RLV S+ + +   G    DL Q
Sbjct: 14  EMKELIRRSQEGDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQ 60

>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 = 41.2 bits (96), Expect = 4e-04
 Identities = 19/50 (38%), Positives = 30/50 (60%), Gaps = 4/50 (8%)

Query: 272 DQRELRRRLNYG----ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
             +++ RR++ G       K +M+ +N+RLVISIAK Y   G+   DL+Q
Sbjct: 357 QVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 406

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	328
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	99.79
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	99.79
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	99.76
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	98.53
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	98.1
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	97.56
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	96.61
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	96.37
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	94.48
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	94.03
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	92.92

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

Probab=99.79  E-value=3.2e-19  Score=177.33  Aligned_cols=119  Identities=25%  Similarity=0.378  Sum_probs=100.1

Q ss_pred             CCCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHH------------------HHHhhcCCCCchHHHHHH-
Q 020252          209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE------------------VLSERCGGSPTFAQWAAA-  268 (328)
Q Consensus       209 ~~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~------------------~L~~~~GrePT~~eWA~a-  268 (328)
                      ...|+++ ||++| +++||||++||++|+++|+.+..++....                  +.....++.|+..+|+.. 
T Consensus        91 ~~~d~~~~Yl~ei-~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (438)
T 1l9z_H           91 STSDPVRQYLHEI-GQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPK  169 (438)
T ss_pred             CCCChHHHHHHHh-ccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccch
Confidence            4568999 99999 99999999999999999999865543321                  122345678888887532 


Q ss_pred             -----------hcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          269 -----------AGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       269 -----------~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                                 ++++..+|..++..|..|+++||.+|+|+|++||++|.|+|++++||||||+||||+|++
T Consensus       170 ~~~~~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~IgL~kAve  240 (438)
T 1l9z_H          170 TVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVE  240 (438)
T ss_pred             hhhhhhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence                       355667888888889999999999999999999999999999999999999999999974

>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=99.79  E-value=5.4e-19  Score=162.61  Aligned_cols=118  Identities=26%  Similarity=0.390  Sum_probs=98.7

Q ss_pred             CCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHH-HHHHHHH--h-----------------------hcCCCCch
Q 020252          210 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLE-GLREVLS--E-----------------------RCGGSPTF  262 (328)
Q Consensus       210 ~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le-~~r~~L~--~-----------------------~~GrePT~  262 (328)
                      .+||++ ||++| |+.||||++||++|+++|+.++... .+.....  .                       ..+.+|+.
T Consensus         5 ~~d~~~~yl~~i-~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~   83 (245)
T 3ugo_A            5 TSDPVRQYLHEI-GQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKT   83 (245)
T ss_dssp             CCHHHHHHHHHH-TTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHHH
T ss_pred             CCCcHHHHHHHc-ccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccchh
Confidence            589999 99999 9999999999999999999987633 2222110  0                       01468899


Q ss_pred             HHHHHHhcCcH----HHHHHhhhhhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          263 AQWAAAAGVDQ----RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       263 ~eWA~a~g~d~----~~L~~~L~~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      .+||.+.|++.    ..|.+....|..|+++||..|+++|.++|++|.+.+.+.+||+|||++||+++++
T Consensus        84 ~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~  153 (245)
T 3ugo_A           84 VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVE  153 (245)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHH
Confidence            99999999864    3455566788999999999999999999999999999999999999999999873

>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=99.76  E-value=5e-19  Score=174.17  Aligned_cols=119  Identities=26%  Similarity=0.397  Sum_probs=96.5

Q ss_pred             CCCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH------------------HhhcCCCCchHHHHH--
Q 020252          209 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVL------------------SERCGGSPTFAQWAA--  267 (328)
Q Consensus       209 ~~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L------------------~~~~GrePT~~eWA~--  267 (328)
                      ...|+++ ||++| ++.|+||++||++|+++|+.+..+.......                  ....++.|+..+|+.  
T Consensus        76 ~~~d~~~~Yl~ei-~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (423)
T 2a6h_F           76 STSDPVRQYLHEI-GQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPK  154 (423)
T ss_dssp             TTHHHHHHHHHHH-HHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTH
T ss_pred             CCCcHHHHHHHHh-cccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhh
Confidence            3467999 99999 9999999999999999999986544322111                  112345677555432  


Q ss_pred             ----------HhcCcHHHHHHhhhhhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          268 ----------AAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       268 ----------a~g~d~~~L~~~L~~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                                +++++..+|..++..|..|+++||.+|+|+|++||++|.|+|++++||||||+||||+|++
T Consensus       155 ~~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~kav~  225 (423)
T 2a6h_F          155 TVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVE  225 (423)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence                      2456777888888889999999999999999999999999999999999999999999973

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

Probab=98.53  E-value=1.4e-07  Score=89.07  Aligned_cols=54  Identities=35%  Similarity=0.634  Sum_probs=47.9

Q ss_pred             HHHHhhhhhH----HHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          275 ELRRRLNYGI----LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       275 ~L~~~L~~G~----~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      .|-.++..|.    .|++.|+..|+++|+++|++|.+.|.+++||+|||+|||+++++
T Consensus       251 ~l~~~~~~gd~~~~~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~  308 (339)
T 1sig_A          251 DINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD  308 (339)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccccchhhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHHHH
Confidence            3455566664    69999999999999999999999999999999999999999873

>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=98.10  E-value=1.3e-06  Score=89.36  Aligned_cols=56  Identities=34%  Similarity=0.625  Sum_probs=48.8

Q ss_pred             HHHHHHhhhhhHH-H---HHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          273 QRELRRRLNYGIL-C---KDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       273 ~~~L~~~L~~G~~-A---re~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      ...|-.++..|.. |   ++.|+..|+++|+++|++|.++|.+++||+|||+|||+++++
T Consensus       358 ~~~Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi~l~~a~~  417 (613)
T 3iyd_F          358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD  417 (613)
T ss_dssp             HHHHHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence            3456666676743 4   999999999999999999999999999999999999999974

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

Probab=97.56  E-value=1.1e-05  Score=69.46  Aligned_cols=45  Identities=27%  Similarity=0.479  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          284 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       284 ~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      ..+.+.|+..|.++|..+|++|.+.+.+.+||+|||.++|+++++
T Consensus        27 ~~a~~~l~~~~~~~v~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~   71 (243)
T 1l0o_C           27 QEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVD   71 (243)
T ss_dssp             ---------------------------------------------
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHH
Confidence            678899999999999999999999999999999999999998863

>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A

Probab=96.61  E-value=0.0028  Score=53.04  Aligned_cols=52  Identities=17%  Similarity=0.187  Sum_probs=45.0

Q ss_pred             HHHHhhhhh-HHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          275 ELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       275 ~L~~~L~~G-~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      +|-..+..| ..+.+.|+..+.+.|..++.+|.+ ..+.+|++||+.+.+++++
T Consensus        12 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~~   64 (194)
T 1or7_A           12 VLVERVQKGDQKAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRAL   64 (194)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHHG
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHhH
Confidence            344444444 779999999999999999999999 9999999999999999875

>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=94.48  E-value=0.01  Score=60.78  Aligned_cols=35  Identities=31%  Similarity=0.564  Sum_probs=13.9

Q ss_pred             CCCCChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHH
Q 020252          208 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLL  243 (328)
Q Consensus       208 ~~~~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~  243 (328)
                      ...+||++ ||++| |+.+|||+++|++|+++|..+.
T Consensus        92 ~~~~dpvrmyl~em-g~~~ll~~~~e~~~ak~ie~g~  127 (613)
T 3iyd_F           92 GRTTDPVRMYMREM-GTVELLTREGEIDIAKRIEDGI  127 (613)
T ss_dssp             -------------C---------CSSSTTTHHHHHHH
T ss_pred             cCCCCcHHHHHHHh-cccccCCchhHHHHHHHHHHhH
Confidence            34699999 99999 9999999999999999999874

>2o7g_A Probable RNA polymerase sigma-C factor; sigma factor, transcription regulation, -10 element recognit domain, transcription; 2.70A {Mycobacterium tuberculosis}

Probab=94.03  E-value=0.069  Score=41.50  Aligned_cols=44  Identities=16%  Similarity=0.051  Sum_probs=39.9

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ...+.+.|+..+.+.+..+|.+| +..-+-+|++||..+.+++..
T Consensus        22 d~~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl~~~~~~   65 (112)
T 2o7g_A           22 NGRALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAI   65 (112)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHHHHHHHG
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHHHH
Confidence            36789999999999999999999 888889999999999998764

>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1

Probab=92.92  E-value=0.084  Score=39.14  Aligned_cols=45  Identities=13%  Similarity=-0.029  Sum_probs=41.0

Q ss_pred             hHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhh
Q 020252          283 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMA  327 (328)
Q Consensus       283 G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAv  327 (328)
                      ...+.+.|+..+.+.+..++.+|.+...+-+|++||..+.+++..
T Consensus        10 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~   54 (87)
T 1h3l_A           10 RSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASF   54 (87)
T ss_dssp             HHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHG
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
Confidence            367889999999999999999999988999999999999998754

---

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	328
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	5e-06
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	1e-05
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	0.001

>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 = 45.3 bits (106), Expect = 5e-06
 Identities = 16/32 (50%), Positives = 22/32 (68%)

Query: 286 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQ 317
            K +M+ +N+RLVISIAK Y   G+   DL+Q
Sbjct: 263 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 294

>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 = 43.3 bits (101), Expect = 1e-05
 Identities = 31/138 (22%), Positives = 55/138 (39%), Gaps = 32/138 (23%)

Query: 211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK------------------LEGLREV 251
           SDP+R YL        LLT  EE+ L+  +++ ++                  +   + +
Sbjct: 1   SDPVRQYLH-EIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKIL 59

Query: 252 LSERCGGSPTFAQWAAAAGVDQ------------RELRRRLNYGILCKDKMITSNIRLVI 299
            + R    P   +      V++            +        G   +  +I +N+RLV+
Sbjct: 60  GTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVV 119

Query: 300 SIAKNYQGAGMNLQDLVQ 317
           SIAK Y G G++  DL+Q
Sbjct: 120 SIAKKYTGRGLSFLDLIQ 137

>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 = 35.3 bits (81), Expect = 0.001
 Identities = 8/34 (23%), Positives = 20/34 (58%), Gaps = 3/34 (8%)

Query: 287 KDKMITSNIRLVISIAKNYQG---AGMNLQDLVQ 317
           ++++I   + LV +IA N +      ++++DL+ 
Sbjct: 12  REELILKYLPLVKAIATNIKKHLPEDVDIRDLIS 45

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	328
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.91
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.48
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.03
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	96.88
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	96.86
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	95.97
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	95.74
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	80.04

>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=99.91  E-value=2.2e-25  Score=192.19  Aligned_cols=117  Identities=26%  Similarity=0.390  Sum_probs=93.3

Q ss_pred             CChhH-HHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH------------------hhcCCCCchHHHHHH---
Q 020252          211 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLS------------------ERCGGSPTFAQWAAA---  268 (328)
Q Consensus       211 ~d~l~-YL~ei~~~~~LLT~eEE~eL~~~Iq~~~~Le~~r~~L~------------------~~~GrePT~~eWA~a---  268 (328)
                      +||++ ||++| |++||||++||++|+++|+.++.+.+...+..                  ...+..|...+|...   
T Consensus         1 tDpVr~YLrei-g~v~LLT~EEEieLAr~Ie~g~~~~~~~~e~~~~~~~l~~e~~~~~~~~~~~~~~~~~~~e~~~~~~~   79 (180)
T d1ku2a2           1 SDPVRQYLHEI-GQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTV   79 (180)
T ss_dssp             CHHHHHHHHHH-TTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCSSCCCTTSCCSSCTTTH
T ss_pred             CCcHHHHHHHh-cCcCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHhhhHHHHhcchhhHHHhhHHHH
Confidence            47999 99999 99999999999999999998876655433221                  123344444444332   


Q ss_pred             ------hcC---cHHHHHHhhhhhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          269 ------AGV---DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       269 ------~g~---d~~~L~~~L~~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                            ...   ..+.+.+.+..|..||++||.+|+|||++||++|.++|++|+||||||+||||+||+
T Consensus        80 ~~~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl~q~g~~gl~~a~~  148 (180)
T d1ku2a2          80 EEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVE  148 (180)
T ss_dssp             HHHHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHHHHH
Confidence                  222   235566778899999999999999999999999999999999999999999999984

>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=99.48  E-value=3.4e-14  Score=130.26  Aligned_cols=49  Identities=33%  Similarity=0.501  Sum_probs=45.6

Q ss_pred             hhhhHHHHHHHHHHhHHHHHHHHhhccCCCCChHHHHHHHHHHHHhhhC
Q 020252          280 LNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       280 L~~G~~Are~LI~sNLRLVvsIAkrY~g~Gl~~~DLIQEG~iGLmrAve  328 (328)
                      -..+..|+++||++|||||++||++|.++|++|+||||+|++|||+||+
T Consensus       257 e~~~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~  305 (334)
T d1siga_         257 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD  305 (334)
T ss_dssp             HHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHH
T ss_pred             HhhccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHH
Confidence            3455779999999999999999999999999999999999999999984

>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=99.03  E-value=9.4e-11  Score=91.03  Aligned_cols=45  Identities=18%  Similarity=0.377  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHhHHHHHHHHhhccCC---CCChHHHHHHHHHHHHhhhC
Q 020252          284 ILCKDKMITSNIRLVISIAKNYQGA---GMNLQDLVQLQALRYLNMAH  328 (328)
Q Consensus       284 ~~Are~LI~sNLRLVvsIAkrY~g~---Gl~~~DLIQEG~iGLmrAve  328 (328)
                      ...|++||..|++||.+||++|.++   |++++||+|+|++||++|++
T Consensus         9 ~~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A~~   56 (87)
T d1rp3a3           9 QIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVD   56 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHH
Confidence            4568999999999999999999765   89999999999999999974

>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=96.88  E-value=0.0011  Score=48.68  Aligned_cols=42  Identities=26%  Similarity=0.358  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhh
Q 020252          241 DLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY  282 (328)
Q Consensus       241 ~~~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~  282 (328)
                      ...++++...+|..++||+||.+|.|+.+||+.+++++.+..
T Consensus         8 ~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~   49 (77)
T d1rp3a1           8 KERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDK   49 (77)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            345678889999999999999999999999999998877654

>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=96.86  E-value=0.00075  Score=47.61  Aligned_cols=41  Identities=20%  Similarity=0.254  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhhhh
Q 020252          243 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYG  283 (328)
Q Consensus       243 ~~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~~G  283 (328)
                      .++.+...+|..++|++||.+|.|+++|++.+++...|..+
T Consensus        15 ~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~   55 (57)
T d1l0oc_          15 NKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAV   55 (57)
T ss_dssp             HHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHh
Confidence            34566788999999999999999999999999998877654

>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=95.74  E-value=0.011  Score=42.11  Aligned_cols=41  Identities=24%  Similarity=0.396  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHhhcCCCCchHHHHHHhcC--cHHHHHHhhhhh
Q 020252          243 LKLEGLREVLSERCGGSPTFAQWAAAAGV--DQRELRRRLNYG  283 (328)
Q Consensus       243 ~~Le~~r~~L~~~~GrePT~~eWA~a~g~--d~~~L~~~L~~G  283 (328)
                      -++.++..+|.+++|++||.+|.|+++|+  +.+.++..+..+
T Consensus        12 ~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~~~   54 (60)
T d1ku2a1          12 NKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIA   54 (60)
T ss_dssp             HHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGGGS
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHc
Confidence            34566788999999999999999999984  577777766543

>d1bl0a1 a.4.1.8 (A:9-62) MarA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: MarA
species: Escherichia coli [TaxId: 562]

Probab=80.04  E-value=1.2  Score=29.24  Aligned_cols=38  Identities=8%  Similarity=0.249  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHhhcCCCCchHHHHHHhcCcHHHHHHhhh
Q 020252          244 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN  281 (328)
Q Consensus       244 ~Le~~r~~L~~~~GrePT~~eWA~a~g~d~~~L~~~L~  281 (328)
                      .++++..=+++....++|.+++|+.+|++...|.+..+
T Consensus         4 ~i~~v~~yI~~~~~~~~tl~~lA~~~~~s~~~l~r~Fk   41 (54)
T d1bl0a1           4 TIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFK   41 (54)
T ss_dssp             HHHHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            35556666778889999999999999999888876554