Citrus Sinensis ID: 016077

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-----
Protein Sequence
MIDVAAAGLGKETQISTSSFNKNMSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGRMSRPC
Secondary Structure (PSIPRED)
cHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEccccccccccccccccccccccccccccccHHHHcccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHccccHHHHHccccccccccccccccccccccHHHHHHHHHHHHccHHHccHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEHcccccccEEEccccccccHccccccccccccEEEEcccccccccccccccccccccEEEEEEEEEccccccHHHHHccccHHHcccccccccccccccccccccEcccccccccccHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccHHcHHHHHHHHHHHHHHHHHccHHHccccccccccccccccccccccHHHHHHcccccccEEEEccHHHHHHHHHHHHHHHHcccccccccccccHcccccccccccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccc
Coil and Loop (DISEMBL)
MIDVAAaglgketqistssfnknmscllpqfkcqpdtfsIHFRtlhnhqhhsshpskskepicfrthcvlsttspststamtTVLDveklrlpsleahSNAVAAnrqwtyfgavgpsteenlgtslatetltSDEAVIAAASAEAVALARAAVKVAKDAALMVnhhnsakpkskpaisssadtnTSMWAQLTERERAsiigdsviveaapeeeyseqqplnksadleptHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSvksgstsrrkrpsvqevdysdplrylrattsssrlltANEEMQLSAGIQDLLKLEGLREVlsercggsptFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNyqgagrmsrpc
Flexible Loop (DISEMBL)
midvaaaglgketqistSSFNKNMSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVlsttspststamTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVnhhnsakpkskpaisssadtNTSMWAQLTERERASIIGDSVIVEAAPeeeyseqqplnkSADLEPTHEELKLLEeqvsqsiavrsrrqterkARRTRaaekaaanvmsvksgstsrrkrpsvqevdysdplrylRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAaaagvdqrelRRRLNYGilckdkmitsnIRLVISIAknyqgagrmsrpc
Low Complexity Region (SEG)
MIDVAAAGLGKETQISTSSFNKNMSCLLPQFKCQPDTFSIHFRTLhnhqhhsshpsksKEPICFRTHCVLsttspststamttVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTsdeaviaaasaeavalaraavkvakdaalMVNHHNsakpkskpaisssaDTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSrrqterkarrtraaekaaaNVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGRMSRPC
Disordered region (IsUnstruct)
**********************NMSCLLPQFKCQPDTFSIHFRTLH***************ICFRTHCVLST*******AMTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGP*********LATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMV************************************I******************************************************************************************************************LSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNY**********
Disordered Region (DISOPRED)
********************NKNMSCLLPQFKCQPDTFSIH************************THCVLSTTSP***TAMTTVLDVEKLRL**********************************************************************************************************************************************************************************************************RYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSE**GGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGRMSRP*
Disordered Region (DISEMBL)
********LGKETQISTSSFNKNMSCLLPQFKCQPDTFSIHFRTL**************EPICFRTHCVLSTTSPSTSTAMTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHH******************TSMWAQLTERERASIIGDSVIVEAAP***********KSADLEPTHEELKLLEEQVSQS********************************************VDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNY**********
Disordered Region (DISPRO)
MIDVAAAGLGKETQISTSSFNKNMSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTS*STSTAMTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNS******PAISSSADTNTSMWAQLTERERASIIGDSVIVEAA**********************ELKLLEEQVSQSIAVRSRR*TERKARRT*****************************DYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGRMS**C
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MIDVAAAGLGKETQISTSSFNKNMSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGRMSRPC
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	395	2.2.26 [Sep-21-2011]
O22056	572	RNA polymerase sigma fact	yes	no	0.875	0.604	0.553	1e-86
Q9LD95	547	RNA polymerase sigma fact	no	no	0.362	0.261	0.375	4e-17
P26683	390	RNA polymerase sigma fact	yes	no	0.296	0.3	0.420	1e-14
P38023	399	RNA polymerase sigma fact	yes	no	0.248	0.245	0.459	6e-11
O24621	571	RNA polymerase sigma fact	no	no	0.197	0.136	0.371	4e-10
Q31QG5	320	RNA polymerase sigma fact	no	no	0.237	0.293	0.443	4e-10
Q31ME3	320	RNA polymerase sigma fact	no	no	0.207	0.256	0.426	6e-10
P52322	416	RNA polymerase sigma fact	no	no	0.248	0.235	0.306	5e-07
Q03065	332	RNA polymerase sigma-B fa	no	no	0.205	0.243	0.345	7e-07
O24629	502	RNA polymerase sigma fact	no	no	0.311	0.245	0.296	8e-05

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

 Score =  320 bits (820), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 206/372 (55%), Positives = 257/372 (69%), Gaps = 26/372 (6%)

Query: 25  SCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTTV 84
           SCLLPQFKC PD+FSIHFRT          P  +K  + F+  C +ST SP+    +T++
Sbjct: 3   SCLLPQFKCPPDSFSIHFRT------SFCAPKHNKGSVFFQPQCAVST-SPAL---LTSM 52

Query: 85  LDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAASA 143
           LDV KLRLPS +  S+++ ++RQWTY    GPSTE     +LA+ETL TSDEAV+ AA+A
Sbjct: 53  LDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVVAAAA 112

Query: 144 EAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIG-- 201
           EAVALARAAVKVAKDA L  N +N+        ++SS     S W Q TE+ERA I+G  
Sbjct: 113 EAVALARAAVKVAKDATLFKNSNNTN------LLTSSTADKRSKWDQFTEKERAGILGHL 166

Query: 202 ---DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQV-SQSIAVRSRRQTERKAR 257
              D+ IV        S ++ +    DLE   +E   L E+  S S+AVRS RQTERKAR
Sbjct: 167 AVSDNGIVSDKITASASNKESI---GDLESEKQEEVELLEEQPSVSLAVRSTRQTERKAR 223

Query: 258 RTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSA 317
           R +  EK A+ + SVK+GS+ ++KR   QEVD++DPLRYLR TTSSS+LLT  EE +LSA
Sbjct: 224 RAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSA 283

Query: 318 GIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRL 377
           GIQDLLKLE L+  L+ER G  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI SNIRL
Sbjct: 284 GIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRL 343

Query: 378 VISIAKNYQGAG 389
           VISIAKNYQGAG
Sbjct: 344 VISIAKNYQGAG 355

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 = 89.4 bits (220), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 54/144 (37%), Positives = 80/144 (55%), Gaps = 1/144 (0%)

Query: 246 VRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSR 305
           VRS+RQ ER+A+  RA +    +        TS +K+   Q  D  D L+       + +
Sbjct: 188 VRSKRQLERRAKNRRAPKSNDVDDEGYVPQKTSAKKKYK-QGADNDDALQLFLWGPETKQ 246

Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
           LLTA EE +L + IQ LLKLE ++  L  + G  PT  +WA A G+    L+  ++ G  
Sbjct: 247 LLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRS 306

Query: 366 CKDKMITSNIRLVISIAKNYQGAG 389
            ++K+IT+N+RLV+ IAK YQ  G
Sbjct: 307 SREKLITANLRLVVHIAKQYQNRG 330

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 = 80.9 bits (198), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 50/119 (42%), Positives = 69/119 (57%), Gaps = 2/119 (1%)

Query: 273 KSG--STSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE 330
           KSG  + SRR+  S ++    D +R         RLL A+EE++L+  I DLL+LE +RE
Sbjct: 59  KSGKAAKSRRRTQSKKKHYTEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRE 118

Query: 331 VLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
            LSE+    P  ++WA A  +     R RL+ G   KDKM+ SN+RLV+SIAK Y   G
Sbjct: 119 RLSEKLERDPRDSEWAEAVQLPLPAFRYRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRG 177

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 = 68.9 bits (167), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 45/98 (45%), Positives = 58/98 (59%)

Query: 292 DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGV 351
           D +R         RLL A+EE++L+  I DLL LE +R+ L E+    P+ A+WAAA   
Sbjct: 89  DSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAVDS 148

Query: 352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
              E RRRL  G   KDKM+ SN+RLV+SIAK Y   G
Sbjct: 149 PLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRG 186

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|O24621|SIGC_ARATH RNA polymerase sigma factor sigC OS=Arabidopsis thaliana GN=SIGC PE=2 SV=1

 Score = 66.2 bits (160), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 29/78 (37%), Positives = 51/78 (65%)

Query: 312 EMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI 371
           E ++S G++ +  +E +R  L E  G   + + WAAAAG++++ L R L+YG  C+D+++
Sbjct: 278 ETEMSTGVKIVADMERIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELV 337

Query: 372 TSNIRLVISIAKNYQGAG 389
            S   LV+ +A+NY+G G
Sbjct: 338 KSTRSLVLFLARNYRGLG 355

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

 Score = 66.2 bits (160), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 43/97 (44%), Positives = 59/97 (60%), Gaps = 3/97 (3%)

Query: 291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVL-SERCGGSPTFAQWAAA 348
           SD +R YLR       LLT  EE+ L   +Q  +KL+ LR+ L SE     P+  +WAAA
Sbjct: 9   SDLVRTYLREIGRVP-LLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWAAA 67

Query: 349 AGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNY 385
           AG+   ELR++ + G   K KMI +N+RLV+S+AK Y
Sbjct: 68  AGLSIEELRQQQHLGEQAKRKMIEANLRLVVSVAKKY 104

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 = 65.9 bits (159), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 35/82 (42%), Positives = 50/82 (60%)

Query: 305 RLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGI 364
           RLLTA EE+     +Q L+ L   +  L +R G  P+  +WAAA  ++  +L R++  G 
Sbjct: 24  RLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEWAAAVDLNLEDLDRQIEQGQ 83

Query: 365 LCKDKMITSNIRLVISIAKNYQ 386
             K KMI +N+RLV+SIAK YQ
Sbjct: 84  RAKRKMIEANLRLVVSIAKKYQ 105

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

 Score = 55.8 bits (133), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 42/137 (30%), Positives = 56/137 (40%), Gaps = 39/137 (28%)

Query: 292 DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE--------------VLSERCG 337
           D +R         RLL A EE++L+  I DLLKLE +RE               L ER  
Sbjct: 67  DSIRIYLQEIGRIRLLRAEEEIELARKIADLLKLERIREDFCLYSDAEWGKQVFLFERIE 126

Query: 338 G-------------------------SPTFAQWAAAAGVDQRELRRRLNYGILCKDKMIT 372
                                     +P   +W A +       +RRL +G   K+KM+ 
Sbjct: 127 KIIVEKSEKEPKLSDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQ 186

Query: 373 SNIRLVISIAKNYQGAG 389
           SN+RLV+SIAK Y   G
Sbjct: 187 SNLRLVVSIAKKYMNRG 203

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 = 55.5 bits (132), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 28/81 (34%), Positives = 49/81 (60%)

Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
           LL+  +E+  +  +Q ++ +   +E L+E+    PT  +WA    + +  L ++L+ G +
Sbjct: 37  LLSHEQEIFFAQQVQQMMVMFTAKEELAEKLQREPTLQEWADKMQLKEDVLLQQLSQGQI 96

Query: 366 CKDKMITSNIRLVISIAKNYQ 386
            K KMI +N+RLV+SIAK YQ
Sbjct: 97  AKQKMIQANLRLVVSIAKKYQ 117

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 = 48.5 bits (114), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 40/135 (29%), Positives = 67/135 (49%), Gaps = 12/135 (8%)

Query: 256 ARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLR-YLRATTSSSRLLTANEEMQ 314
           AR+ R   K   N+  VK+          V +V     +R Y++   S   +L+  E ++
Sbjct: 159 ARQRRIGAKKKTNMTHVKA----------VSDVSSGKQVRGYVKGVISED-VLSHVEVVR 207

Query: 315 LSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSN 374
           LS  I+  L+L+  +  L +R G  P+  Q A +  + + EL+  L    L ++K+  SN
Sbjct: 208 LSKKIKSGLRLDDHKSRLKDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSN 267

Query: 375 IRLVISIAKNYQGAG 389
           +RLV+SIA+ Y   G
Sbjct: 268 VRLVMSIAQRYDNLG 282

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	395
255565968	569	RNA polymerase sigma factor rpoD1, putat	0.891	0.618	0.673	1e-112
449454538	580	PREDICTED: RNA polymerase sigma factor s	0.906	0.617	0.595	1e-105
224126061	567	predicted protein [Populus trichocarpa]	0.886	0.617	0.654	1e-102
296090195	575	unnamed protein product [Vitis vinifera]	0.906	0.622	0.679	7e-98
225436223	578	PREDICTED: RNA polymerase sigma factor r	0.913	0.624	0.673	1e-97
224144900	564	predicted protein [Populus trichocarpa]	0.881	0.617	0.623	2e-97
7363218	575	sigma factor 2 [Sinapis alba]	0.875	0.601	0.551	7e-89
297843640	572	hypothetical protein ARALYDRAFT_470915 [	0.883	0.610	0.566	3e-86
15223259	572	RNApolymerase sigma subunit 2 [Arabidops	0.875	0.604	0.553	7e-85
356509511	558	PREDICTED: RNA polymerase sigma factor r	0.865	0.612	0.550	7e-85

>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 =  409 bits (1052), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 247/367 (67%), Positives = 293/367 (79%), Gaps = 15/367 (4%)

Query: 24  MSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTT 83
           MSCLLPQFKCQPDTFSIHFR  + H  + +  +KS+EPI +R  C+LSTTSPSTSTA   
Sbjct: 2   MSCLLPQFKCQPDTFSIHFRANYFHFSNVTQSTKSREPIYYRAQCILSTTSPSTSTA--- 58

Query: 84  VLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAAS 142
           VLD+EKLRLPS EA S+++A N  WTY            G++LATETL TSDEAVIAAA+
Sbjct: 59  VLDLEKLRLPSFEAPSDSIAPNSPWTY---------ATFGSTLATETLITSDEAVIAAAA 109

Query: 143 AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGD 202
           AEAVALARAAVKVAKDAAL+V +  SA+ +SK  ++S +  + S W Q TE ERA IIGD
Sbjct: 110 AEAVALARAAVKVAKDAALLVKNFPSAETESK--LTSPSTIDASRWPQFTETERARIIGD 167

Query: 203 SVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAA 262
           SV  E  P EE S Q  + +S  LE TH+EL+LL++Q+S+ IAVRSRRQTERKARR RA 
Sbjct: 168 SVATETGPREESSMQSSIKESDYLELTHKELELLQKQLSEGIAVRSRRQTERKARRARAV 227

Query: 263 EKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDL 322
           EKAA++V+SVK GSTS++KR S+QEVDYSDPLRYLR TTS+SRLLTA+EE++LSA IQDL
Sbjct: 228 EKAASSVVSVKPGSTSKKKRGSLQEVDYSDPLRYLRGTTSTSRLLTASEELELSAAIQDL 287

Query: 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 382
           LKLE L+E L+ER GG PTFAQWAAAAGVDQR LR+R+N+G +CKDKMI SNIRLVISIA
Sbjct: 288 LKLERLQEELAERYGGQPTFAQWAAAAGVDQRTLRKRINHGTICKDKMIKSNIRLVISIA 347

Query: 383 KNYQGAG 389
           KNYQGAG
Sbjct: 348 KNYQGAG 354

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

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 =  389 bits (1000), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 222/373 (59%), Positives = 274/373 (73%), Gaps = 15/373 (4%)

Query: 24  MSCLLPQFKCQPDTFSIHFRTLHNHQHHSSH-------PSKSKEPICFRTHCVLSTTSPS 76
           MSCLLPQFKC P+TFSI F+T  N+ HH S         +K ++P   RT C+LS  SP 
Sbjct: 1   MSCLLPQFKCHPETFSIQFKTAANYSHHHSFLPTAYSSYTKVRDPHSLRTQCILSAASPP 60

Query: 77  TSTAMTTVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTSDEA 136
           TST   T LDV++L+LP  + ++++V+  R  +Y GAV         +SLA+  LTS+EA
Sbjct: 61  TSTGTATTLDVDRLKLPPFDTNTDSVSVERLRSYLGAVE--------SSLASTLLTSEEA 112

Query: 137 VIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERER 196
            IAAA+AEAV LA+AAVKVA+DAAL+ N+ NS++  +K   S   D     WAQ  E ER
Sbjct: 113 SIAAAAAEAVTLAKAAVKVARDAALLANNINSSRAGTKSQSSPKPDALHFKWAQFMESER 172

Query: 197 ASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKA 256
           A IIG+ V V   P E  + +    +S D+EPT EEL+LL++++S+SI V+S+RQTERKA
Sbjct: 173 ADIIGEPVGVNKRPMEGDALEPSTTESDDMEPTSEELELLQDELSESITVKSKRQTERKA 232

Query: 257 RRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLS 316
           RRTRAAEK   +V+S KSGS+SR+KR SVQEVDYSDPLRYLRATT++SRLLTA EE++LS
Sbjct: 233 RRTRAAEKTVTSVLSFKSGSSSRKKRNSVQEVDYSDPLRYLRATTNTSRLLTATEELELS 292

Query: 317 AGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIR 376
            GIQDLLKLE L+E L ER G  PTFAQWAAAAGV+QR LR+RLNYG LCKDKMI SNIR
Sbjct: 293 EGIQDLLKLERLQEELGERYGNEPTFAQWAAAAGVNQRTLRKRLNYGTLCKDKMIKSNIR 352

Query: 377 LVISIAKNYQGAG 389
           LVISIAKNYQGAG
Sbjct: 353 LVISIAKNYQGAG 365

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  379 bits (972), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 241/368 (65%), Positives = 286/368 (77%), Gaps = 18/368 (4%)

Query: 24  MSCLLPQFKCQPDTFSIHFRTLHNH-QHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMT 82
           MSCLLPQFKCQPDTFS+HFR L +H  +H+  P            CVLS+ SPST+    
Sbjct: 1   MSCLLPQFKCQPDTFSVHFRNLQHHGTNHTQLP-----------QCVLSSASPSTA---- 45

Query: 83  TVLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTS-DEAVIAAA 141
            VLD+EKLRLPSLE HS++++ANR WTY G +GP  +   GTSLA ETL + DEAVIAAA
Sbjct: 46  -VLDLEKLRLPSLEPHSDSISANRPWTYIGGIGPQKKPPFGTSLAAETLIANDEAVIAAA 104

Query: 142 SAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIG 201
           +AEAVALARAAVKVAKDAA M  +++S K ++K  I+S+ D+ +SMW+ LTE+ERA IIG
Sbjct: 105 AAEAVALARAAVKVAKDAAEMAKNYSSMKKETKIPIASTTDSFSSMWSLLTEKERADIIG 164

Query: 202 DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRA 261
           DSV  E    EEYS Q P  +   LEPT EEL LL++Q+S+ IAVRS+RQTERKARR RA
Sbjct: 165 DSVSAETRLREEYSVQYPTEEYDCLEPTQEELALLQKQLSEGIAVRSKRQTERKARRARA 224

Query: 262 AEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQD 321
           AEKAAANV+SVKSGSTS++KR  +QEVD SDPLR+ R  +SSSRLL+A EE++LS GIQD
Sbjct: 225 AEKAAANVVSVKSGSTSKKKRVPLQEVDQSDPLRFFRGASSSSRLLSATEEVELSEGIQD 284

Query: 322 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 381
           LLKLE + E L ER GG P+FAQWAAAAGVDQ  LR+RLNYGILCKDKMI SN+RLVISI
Sbjct: 285 LLKLERIEEELKERFGGEPSFAQWAAAAGVDQLTLRKRLNYGILCKDKMIKSNVRLVISI 344

Query: 382 AKNYQGAG 389
           AKNYQG G
Sbjct: 345 AKNYQGTG 352

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 =  363 bits (932), Expect = 7e-98,   Method: Compositional matrix adjust.
 Identities = 250/368 (67%), Positives = 281/368 (76%), Gaps = 10/368 (2%)

Query: 24  MSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTT 83
           MSCLLPQFKC PDTFS H + LH         SK++E I FR  C LSTTSP  ST+ T 
Sbjct: 1   MSCLLPQFKCPPDTFSTHPK-LHIL-------SKNREAIYFRVQCALSTTSPPLSTSTTA 52

Query: 84  VLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAAS 142
           VLD+EKLRLPSLE+HSN+VAA+R WTY G VGP TE N   +LA ETL TS+EAVIAAA+
Sbjct: 53  VLDIEKLRLPSLESHSNSVAAHRPWTYIGVVGPPTEANFEATLARETLLTSEEAVIAAAA 112

Query: 143 AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPA-ISSSADTNTSMWAQLTERERASIIG 201
           AEAVALA+AAVKVAKDAA +V  +NSAK ++KPA   S  DT+     Q TE ER  I+G
Sbjct: 113 AEAVALAKAAVKVAKDAARLVGKNNSAKSETKPASFLSGDDTSQFRRIQFTETERIGILG 172

Query: 202 DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRA 261
           DSV  E    +  S Q     S DLEPT EEL+LLE + S+SI VRS RQ ERKARR RA
Sbjct: 173 DSVGAETGMVDYNSLQDVTEDSDDLEPTLEELELLEAEFSKSIVVRSNRQVERKARRARA 232

Query: 262 AEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQD 321
           AEKA+A V+SV+SGSTSRRKR S+QEVDYSDPLRYLR TTS+SRLLTA EE++LS GIQD
Sbjct: 233 AEKASAGVVSVRSGSTSRRKRVSLQEVDYSDPLRYLRGTTSTSRLLTATEELELSEGIQD 292

Query: 322 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 381
           LLKLE L+E L ER G  PTFAQWAAAAGVDQ+ LRRR NYGI CKDKMI SNIRLVISI
Sbjct: 293 LLKLEKLQEDLEERFGVKPTFAQWAAAAGVDQKTLRRRTNYGIRCKDKMIKSNIRLVISI 352

Query: 382 AKNYQGAG 389
           AKNYQGAG
Sbjct: 353 AKNYQGAG 360

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 =  363 bits (931), Expect = 1e-97,   Method: Compositional matrix adjust.
 Identities = 248/368 (67%), Positives = 279/368 (75%), Gaps = 7/368 (1%)

Query: 24  MSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTT 83
           MSCLLPQFKC PDTFS H +      H      K++E I FR  C LSTTSP  ST+ T 
Sbjct: 1   MSCLLPQFKCPPDTFSTHPKL-----HILCKSPKNREAIYFRVQCALSTTSPPLSTSTTA 55

Query: 84  VLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAAS 142
           VLD+EKLRLPSLE+HSN+VAA+R WTY G VGP TE N   +LA ETL TS+EAVIAAA+
Sbjct: 56  VLDIEKLRLPSLESHSNSVAAHRPWTYIGVVGPPTEANFEATLARETLLTSEEAVIAAAA 115

Query: 143 AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPA-ISSSADTNTSMWAQLTERERASIIG 201
           AEAVALA+AAVKVAKDAA +V  +NSAK ++KPA   S  DT+     Q TE ER  I+G
Sbjct: 116 AEAVALAKAAVKVAKDAARLVGKNNSAKSETKPASFLSGDDTSQFRRIQFTETERIGILG 175

Query: 202 DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRA 261
           DSV  E    +  S Q     S DLEPT EEL+LLE + S+SI VRS RQ ERKARR RA
Sbjct: 176 DSVGAETGMVDYNSLQDVTEDSDDLEPTLEELELLEAEFSKSIVVRSNRQVERKARRARA 235

Query: 262 AEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQD 321
           AEKA+A V+SV+SGSTSRRKR S+QEVDYSDPLRYLR TTS+SRLLTA EE++LS GIQD
Sbjct: 236 AEKASAGVVSVRSGSTSRRKRVSLQEVDYSDPLRYLRGTTSTSRLLTATEELELSEGIQD 295

Query: 322 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 381
           LLKLE L+E L ER G  PTFAQWAAAAGVDQ+ LRRR NYGI CKDKMI SNIRLVISI
Sbjct: 296 LLKLEKLQEDLEERFGVKPTFAQWAAAAGVDQKTLRRRTNYGIRCKDKMIKSNIRLVISI 355

Query: 382 AKNYQGAG 389
           AKNYQGAG
Sbjct: 356 AKNYQGAG 363

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  362 bits (929), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 229/367 (62%), Positives = 272/367 (74%), Gaps = 19/367 (5%)

Query: 24  MSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTT 83
           MSCLLPQFKCQPD+FSIH                + EP CFR  C LS+    + +  T 
Sbjct: 1   MSCLLPQFKCQPDSFSIH---------------SNGEPFCFRAQCALSSA---SPSTSTA 42

Query: 84  VLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLT-SDEAVIAAAS 142
           VL++EKLRLPSLE+HS+++AANR WTY G +GP  E   GTSLATETL  +DEAVIAAA+
Sbjct: 43  VLNLEKLRLPSLESHSDSIAANRPWTYIGGIGPPKEPLFGTSLATETLIINDEAVIAAAA 102

Query: 143 AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGD 202
           AEAVALARAAVKVAKDAA M  ++ S   ++K  I+S+AD+ +SMW+ LT +ERA IIG 
Sbjct: 103 AEAVALARAAVKVAKDAAEMAKNYCSVNTETKIPIASTADSFSSMWSLLTGKERADIIGV 162

Query: 203 SVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAA 262
           S   E    EE S Q P  +S    PTHEEL LLE+Q+S+SI VRS+RQT+RKA+R RAA
Sbjct: 163 SFSAETGLREECSTQYPTEESDCFGPTHEELALLEKQLSESIVVRSKRQTQRKAKRARAA 222

Query: 263 EKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDL 322
           EKAAAN + +KSGS  ++KR  VQEVD SDPLR+ R  ++SSRLL+A EE++LS GIQDL
Sbjct: 223 EKAAANFVFMKSGSACKKKRVPVQEVDQSDPLRFFRGASTSSRLLSATEEVELSEGIQDL 282

Query: 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 382
           LKLE + E L ER GG PTFAQWAAAA VDQ  LR+RLNY ILCKDKMI SNIRLVISIA
Sbjct: 283 LKLERIEEELKERFGGKPTFAQWAAAARVDQITLRKRLNYAILCKDKMIKSNIRLVISIA 342

Query: 383 KNYQGAG 389
           KNYQGAG
Sbjct: 343 KNYQGAG 349

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  333 bits (855), Expect = 7e-89,   Method: Compositional matrix adjust.
 Identities = 205/372 (55%), Positives = 259/372 (69%), Gaps = 26/372 (6%)

Query: 25  SCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTTV 84
           SCLLP FKCQPD+FS+HFRT ++   HS      K    F+  C +ST+ P     +T+ 
Sbjct: 3   SCLLPNFKCQPDSFSVHFRTSYSVSKHS------KGSAFFQPQCAVSTSPP----LLTST 52

Query: 85  LDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAASA 143
           LDV KLRLPS +  S++  ++R WTY   +GPSTE     +LA+ETL TSDEAV+AAA+A
Sbjct: 53  LDVAKLRLPSFDTDSDSRISDRPWTYTRTIGPSTEAKYLEALASETLLTSDEAVVAAAAA 112

Query: 144 EAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIG-- 201
           EAVALARAA+KVAKDA L  N HN+     K ++SS+AD   S W Q TE+ERA I+G  
Sbjct: 113 EAVALARAALKVAKDATLFGNSHNT-----KLSVSSAADKR-SKWDQFTEKERAGILGHL 166

Query: 202 ---DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARR 258
              D+ +V        S +     S DL P  ++     E++S S AVRS RQTERKARR
Sbjct: 167 AVSDTGVVSDRITAPGSLECNKEASDDLTPAEKQE---VEKLSVSSAVRSTRQTERKARR 223

Query: 259 TRAAEKAAANVMS-VKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSA 317
            +  EK A+ + S VK+GS+SR+KR + QE+D++DPLRYLR TTSSS+LLTA EE QLS 
Sbjct: 224 VKGLEKTASGMQSSVKTGSSSRKKRVASQEIDHNDPLRYLRMTTSSSKLLTAREEQQLSE 283

Query: 318 GIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRL 377
           GIQDLLKLE L+  L+ERCG  PTF+QWA+AAGVD++ LR+R+ +G  CKD+MI SNIRL
Sbjct: 284 GIQDLLKLERLQAELTERCGHQPTFSQWASAAGVDKKTLRKRITHGTQCKDRMIKSNIRL 343

Query: 378 VISIAKNYQGAG 389
           VISIAKNYQGAG
Sbjct: 344 VISIAKNYQGAG 355

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 =  325 bits (833), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 209/369 (56%), Positives = 256/369 (69%), Gaps = 20/369 (5%)

Query: 25  SCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTTV 84
           SCLLPQFKC PD+FSIHFRT    + H+      K  + F+  C +ST SP+    +T++
Sbjct: 3   SCLLPQFKCPPDSFSIHFRTSFCARKHN------KGSVFFQPQCAVST-SPAL---LTSM 52

Query: 85  LDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAASA 143
           LDV KLRLPS +  S++  ++RQWTY    GPSTE     +LA+ETL TSDEAV+ AA+A
Sbjct: 53  LDVAKLRLPSFDTDSDSRISDRQWTYTRTDGPSTEAKYLEALASETLLTSDEAVVVAAAA 112

Query: 144 EAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGDS 203
           EAVALARAAVKVAKDA L  N +N+        ISS+AD   S W Q TE+ERA I+G  
Sbjct: 113 EAVALARAAVKVAKDATLFKNSNNT-----NLLISSTADKR-SKWDQFTEKERAGILGHL 166

Query: 204 VIVEAAPEEEYSEQQPLNKS--ADLEPTHEELKLLEEQV-SQSIAVRSRRQTERKARRTR 260
            + +     +       NK    DLE   +E   L E+  S S+AVRS RQTERKARR +
Sbjct: 167 AVSDNGIVSDKITAPASNKESPGDLESEKQEEVELLEEQPSVSLAVRSTRQTERKARRAK 226

Query: 261 AAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQ 320
             EK A+ + SVK+GS  R+KR   QEVD++DPLRYLR TTSSS+LLT  EE +LSAGIQ
Sbjct: 227 GLEKTASGIPSVKTGSNPRKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSAGIQ 286

Query: 321 DLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVIS 380
           DLLKLE L+  L+ERCG  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI SNIRLVIS
Sbjct: 287 DLLKLERLQTELTERCGRQPTFAQWASAAGVDQKSLRKRIHHGTLCKDKMIKSNIRLVIS 346

Query: 381 IAKNYQGAG 389
           IAKNYQGAG
Sbjct: 347 IAKNYQGAG 355

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 =  320 bits (820), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 206/372 (55%), Positives = 257/372 (69%), Gaps = 26/372 (6%)

Query: 25  SCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTTV 84
           SCLLPQFKC PD+FSIHFRT          P  +K  + F+  C +ST SP+    +T++
Sbjct: 3   SCLLPQFKCPPDSFSIHFRT------SFCAPKHNKGSVFFQPQCAVST-SPAL---LTSM 52

Query: 85  LDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAASA 143
           LDV KLRLPS +  S+++ ++RQWTY    GPSTE     +LA+ETL TSDEAV+ AA+A
Sbjct: 53  LDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVVAAAA 112

Query: 144 EAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIG-- 201
           EAVALARAAVKVAKDA L  N +N+        ++SS     S W Q TE+ERA I+G  
Sbjct: 113 EAVALARAAVKVAKDATLFKNSNNTN------LLTSSTADKRSKWDQFTEKERAGILGHL 166

Query: 202 ---DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQV-SQSIAVRSRRQTERKAR 257
              D+ IV        S ++ +    DLE   +E   L E+  S S+AVRS RQTERKAR
Sbjct: 167 AVSDNGIVSDKITASASNKESI---GDLESEKQEEVELLEEQPSVSLAVRSTRQTERKAR 223

Query: 258 RTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSA 317
           R +  EK A+ + SVK+GS+ ++KR   QEVD++DPLRYLR TTSSS+LLT  EE +LSA
Sbjct: 224 RAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSA 283

Query: 318 GIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRL 377
           GIQDLLKLE L+  L+ER G  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI SNIRL
Sbjct: 284 GIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRL 343

Query: 378 VISIAKNYQGAG 389
           VISIAKNYQGAG
Sbjct: 344 VISIAKNYQGAG 355

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 =  320 bits (820), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 202/367 (55%), Positives = 251/367 (68%), Gaps = 25/367 (6%)

Query: 24  MSCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTT 83
           MSCLLP F C  DTF  H   L       +H SK++  +CF+  CVLS TSPST      
Sbjct: 1   MSCLLPHFNCHLDTFRTHPYAL------PTHLSKTRPNLCFQPQCVLSATSPST------ 48

Query: 84  VLDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAAS 142
           +L +EK +L +L+A S+    N  W Y  A       N  ++L+ E+L T++EAVI AA+
Sbjct: 49  LLSLEK-KL-ALDAPSDP---NTSWPYIAAA------NFKSTLSAESLLTNEEAVIVAAA 97

Query: 143 AEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIGD 202
           +EA+ALA+AA KVAKDAAL+V     A+ + K  +SS +D     W +  E E    + +
Sbjct: 98  SEALALAKAAAKVAKDAALLVKKKPPAEAEYKSHVSSKSDDLLLKWFKQME-EVEDGVAE 156

Query: 203 SVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAA 262
             +   A   E  +  P  + +DLEP+HEEL+ L+EQ+S SIAVRSRRQTERKA+R RA 
Sbjct: 157 ESMGAGAEIMEGVDVSPSEEESDLEPSHEELERLQEQLSDSIAVRSRRQTERKAKRVRAT 216

Query: 263 EKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDL 322
           EKA  N  S K GS+SRRKR S+QEVDYSDPLRYLR TTS+SRLLT  EE++LSAGIQDL
Sbjct: 217 EKATTNFTSFKPGSSSRRKRVSMQEVDYSDPLRYLRTTTSASRLLTPTEEIKLSAGIQDL 276

Query: 323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIA 382
           LKLE ++E L+ER G  PTFAQWAA AGVDQ+ LR+RLNYGI CKDKMI SNIRLVISIA
Sbjct: 277 LKLEKIQEDLAERFGSQPTFAQWAAVAGVDQKTLRKRLNYGIFCKDKMIKSNIRLVISIA 336

Query: 383 KNYQGAG 389
           KNYQG+G
Sbjct: 337 KNYQGSG 343

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	395
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.886	0.611	0.437	4.4e-68
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.410	0.283	0.303	1.5e-13
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.283	0.204	0.389	1.8e-12
TAIR|locus:2084420	571	SIGC "AT3G53920" [Arabidopsis	0.205	0.141	0.358	1.7e-08
UNIPROTKB|O48655	519	rsigA "Plastid RNA polymerase	0.235	0.179	0.382	5.4e-08
TAIR|locus:2010871	502	SIGA "AT1G64860" [Arabidopsis	0.265	0.209	0.308	0.00045

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

 Score = 691 (248.3 bits), Expect = 4.4e-68, P = 4.4e-68
 Identities = 161/368 (43%), Positives = 202/368 (54%)

Query:    25 SCLLPQFKCQPDTFSIHFRTLXXXXXXXXXXXXXKEPICFRTHCVLXXXXXXXXXXXXXV 84
             SCLLPQFKC PD+FSIHFRT              K  + F+  C +             +
Sbjct:     3 SCLLPQFKCPPDSFSIHFRT------SFCAPKHNKGSVFFQPQCAVSTSPALLTS----M 52

Query:    85 LDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETLTXXXXXXXXXXXX 144
             LDV KLRLPS +  S+++ ++RQWTY    GPSTE     +LA+ETL             
Sbjct:    53 LDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVVAAAA 112

Query:   145 XXXXXXXXXXXXXXXXXMVNHHNXXXXXXXXXXXXXXDTNTSMWAQLTERERASIIGDSV 204
                              +  + N                  S W Q TE+ERA I+G   
Sbjct:   113 EAVALARAAVKVAKDATLFKNSNNTNLLTSSTAD-----KRSKWDQFTEKERAGILGHLA 167

Query:   205 IVEAAPEEEYSEQQPLNKSA--DLEPT-HEELKLLEEQVSQSIAVRSXXXXXXXXXXXXX 261
             + +     +       NK +  DLE    EE++LLEEQ S S+AVRS             
Sbjct:   168 VSDNGIVSDKITASASNKESIGDLESEKQEEVELLEEQPSVSLAVRSTRQTERKARRAKG 227

Query:   262 XXXXXXNVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQD 321
                    + SVK+GS+ ++KR   QEVD++DPLRYLR TTSSS+LLT  EE +LSAGIQD
Sbjct:   228 LEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSAGIQD 287

Query:   322 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI 381
             LLKLE L+  L+ER G  PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI SNIRLVISI
Sbjct:   288 LLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRLVISI 347

Query:   382 AKNYQGAG 389
             AKNYQGAG
Sbjct:   348 AKNYQGAG 355

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 = 200 (75.5 bits), Expect = 1.5e-13, P = 1.5e-13
 Identities = 51/168 (30%), Positives = 75/168 (44%)

Query:   223 SADLEPTHEELKLLEEQVSQSIAVRSXXXXXXXXXXXXXXXXXXXNVMSVKSGSTSRRKR 282
             S D   ++EEL     Q    + VRS                   +V      S  + K 
Sbjct:   194 SVDSSKSNEEL-----QSKGQVFVRSTRLLERRSKRRYAPRASIADVSCSADNSKKKEKS 248

Query:   283 PSVQEV-DYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPT 341
                  V +  +P +       ++  LTA EE  L + IQ L+K+E     L  +CG  PT
Sbjct:   249 KKYGRVLEPDEPFKLFLRDRETTEFLTAKEERHLFSKIQILMKIEEAHRKLEVQCGREPT 308

Query:   342 FAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
              A+WA A G+  +EL+  +  G  C++KM  SN RLVI +A+ Y+G G
Sbjct:   309 LAEWAEAVGMSSKELQSSIRTGRRCREKMARSNFRLVIHVARKYEGYG 356

GO:0009536 "plastid" evidence=RCA

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

 Score = 191 (72.3 bits), Expect = 1.8e-12, P = 1.8e-12
 Identities = 44/113 (38%), Positives = 65/113 (57%)

Query:   277 TSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERC 336
             TS +K+   Q  D  D L+       + +LLTA EE +L + IQ LLKLE ++  L  + 
Sbjct:   219 TSAKKKYK-QGADNDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQN 277

Query:   337 GGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
             G  PT  +WA A G+    L+  ++ G   ++K+IT+N+RLV+ IAK YQ  G
Sbjct:   278 GCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRG 330

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

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

 Score = 157 (60.3 bits), Expect = 1.7e-08, P = 1.7e-08
 Identities = 29/81 (35%), Positives = 52/81 (64%)

Query:   309 ANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD 368
             +  E ++S G++ +  +E +R  L E  G   + + WAAAAG++++ L R L+YG  C+D
Sbjct:   275 SRNETEMSTGVKIVADMERIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRD 334

Query:   369 KMITSNIRLVISIAKNYQGAG 389
             +++ S   LV+ +A+NY+G G
Sbjct:   335 ELVKSTRSLVLFLARNYRGLG 355

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

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

 Score = 152 (58.6 bits), Expect = 5.4e-08, P = 5.4e-08
 Identities = 36/94 (38%), Positives = 53/94 (56%)

Query:   296 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRE 355
             YLR T S   LLT  + + LS  I+D + L+  R  L E+ G  P++ Q A +  +   E
Sbjct:   207 YLRGTVSKE-LLTHKQVVHLSHKIKDGIWLQQQRSKLKEKLGNEPSYKQLAHSLKISPPE 265

Query:   356 LRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
             LR R++   L ++ +  SN+RLVISIA+ Y   G
Sbjct:   266 LRSRMHESFLAREMLTMSNLRLVISIAQKYDNLG 299

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

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

 Score = 117 (46.2 bits), Expect = 0.00045, P = 0.00045
 Identities = 33/107 (30%), Positives = 58/107 (54%)

Query:   284 SVQEVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTF 342
             +V +V     +R Y++   S   +L+  E ++LS  I+  L+L+  +  L +R G  P+ 
Sbjct:   177 AVSDVSSGKQVRGYVKGVISED-VLSHVEVVRLSKKIKSGLRLDDHKSRLKDRLGCEPSD 235

Query:   343 AQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
              Q A +  + + EL+  L    L ++K+  SN+RLV+SIA+ Y   G
Sbjct:   236 EQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLG 282


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        0.315   0.128   0.362    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      395       307    0.0010  115 3  11 23  0.42    34
                                                     33  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  6
  No. of states in DFA:  610 (65 KB)
  Total size of DFA:  208 KB (2117 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:  21.94u 0.14s 22.08t   Elapsed:  00:00:01
  Total cpu time:  21.94u 0.14s 22.08t   Elapsed:  00:00:01
  Start:  Fri May 10 07:16:13 2013   End:  Fri May 10 07:16:14 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O22056	SIGB_ARATH	No assigned EC number	0.5537	0.8759	0.6048	yes	no

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	395
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	1e-20
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	1e-19
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	1e-16
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	1e-12
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	5e-08
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	6e-08
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	4e-06
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	3e-04
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	7e-04

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

 Score = 90.8 bits (226), Expect = 1e-20
 Identities = 46/99 (46%), Positives = 65/99 (65%), Gaps = 2/99 (2%)

Query: 292 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAG 350
           D +R YL+       LLT  EE++L+  +Q ++ LE LRE L E+ G  P+  +WAAAAG
Sbjct: 1   DLVRLYLQ-EIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAG 59

Query: 351 VDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
           + + ELR+RL  G   K+KMI +N+RLV+S+AK YQ  G
Sbjct: 60  LSEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKYQNRG 98

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 = 89.1 bits (221), Expect = 1e-19
 Identities = 47/171 (27%), Positives = 69/171 (40%), Gaps = 11/171 (6%)

Query: 219 PLNKSADLEPTHEELKLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTS 278
                 +L    E+ +        S                + A+  A            
Sbjct: 1   TPELEDELLLLEEDRQPAATDDLDSDEDEESSSENADELSEKEAKAKA-----------L 49

Query: 279 RRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGG 338
            R +   ++V   D +R         RLL  +EE++L+  I DLL+LE LRE      G 
Sbjct: 50  ARIKIGPKKVYTEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGR 109

Query: 339 SPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
            P+  +WA    +   + RRRL  G   K+KM+ SN+RLV+SIAK Y   G
Sbjct: 110 EPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRG 160

Length = 373

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

 Score = 79.8 bits (197), Expect = 1e-16
 Identities = 40/96 (41%), Positives = 57/96 (59%), Gaps = 2/96 (2%)

Query: 291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAA 349
           +D +R YLR       LLT  EE+     +Q L+ L+ +RE L+E  G  PT A+WA AA
Sbjct: 7   TDLVRTYLREIGRVP-LLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAA 65

Query: 350 GVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNY 385
            + + ELR  +  G   K KM+ +N+RLV+S+AK Y
Sbjct: 66  KLSEEELRSAIAEGEAAKRKMVEANLRLVVSVAKKY 101

Length = 317

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

 Score = 67.6 bits (165), Expect = 1e-12
 Identities = 30/81 (37%), Positives = 49/81 (60%)

Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
           LLT  +E+     +Q ++ L   +E L+++ G  P+  +WA A  + + EL++ L  G  
Sbjct: 32  LLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKR 91

Query: 366 CKDKMITSNIRLVISIAKNYQ 386
            K KMI +N+RLV++IAK YQ
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQ 112

Length = 327

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

 Score = 54.2 bits (131), Expect = 5e-08
 Identities = 50/276 (18%), Positives = 96/276 (34%), Gaps = 50/276 (18%)

Query: 124 TSLATETLTSDEAVIAAASAEAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADT 183
           + +  +T  + E+ I     +  A A AA   AK         +S K + K A+    D 
Sbjct: 60  SGMVKDTDDATESDIPKKKTKTAAKAAAAKAPAKKKLK-DELDSSKKAEKKNALDKDDDL 118

Query: 184 NTSMWAQLTE--RERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVS 241
           N      +     +      D  + +   +++  ++       D +   E+ +  E +  
Sbjct: 119 NYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKEL 178

Query: 242 QSIAVRSRRQTE-------RKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPL 294
           + ++       +       R+AR+       A                         DP+
Sbjct: 179 EKLSDDDDFVWDEDDSEALRQARKDAKLTATA-------------------------DPV 213

Query: 295 R-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQ 353
           + YL+      +LL A EE++L+  I+      GL        G               +
Sbjct: 214 KAYLK-QIGKVKLLNAEEEVELAKRIE-----AGLYAEELLAEGEKLDPEL--------R 259

Query: 354 RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
           R+L+     G   K+ ++ +N+RLV+S+AK Y   G
Sbjct: 260 RDLQWIGRDGKRAKNHLLEANLRLVVSLAKRYTNRG 295

Length = 509

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

 Score = 54.1 bits (130), Expect = 6e-08
 Identities = 31/117 (26%), Positives = 51/117 (43%), Gaps = 28/117 (23%)

Query: 295 RYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQR 354
           RY++       ++ AN   +    I+  L+L  +RE L+   G  P+  +WA  A +   
Sbjct: 89  RYMKL------IVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADISLA 142

Query: 355 ELRRRLNY----------------------GILCKDKMITSNIRLVISIAKNYQGAG 389
           +L+  L                        G+  K+ MI +N+RLV+S+AK YQ  G
Sbjct: 143 DLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRG 199

Length = 415

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

 Score = 48.1 bits (115), Expect = 4e-06
 Identities = 31/105 (29%), Positives = 44/105 (41%), Gaps = 20/105 (19%)

Query: 305 RLLTANEEMQLSAGIQDLLKLEGLREVL-SERCGGSPTFAQWAAAAGVDQ---------- 353
            LL    E++L+  ++D   L  L E L   + G  P+      A  +            
Sbjct: 22  PLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPL 81

Query: 354 ------RELRRRLNYGIL---CKDKMITSNIRLVISIAKNYQGAG 389
                 + L RRL  G      K K++ SN+RLV+SIAK Y G G
Sbjct: 82  LTPEEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRG 126

Length = 342

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

 Score = 41.5 bits (98), Expect = 3e-04
 Identities = 12/23 (52%), Positives = 17/23 (73%)

Query: 367 KDKMITSNIRLVISIAKNYQGAG 389
           K +++ SN+RLV+SIAK Y   G
Sbjct: 2   KKQLVESNLRLVVSIAKKYTNRG 24

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 = 41.3 bits (98), Expect = 7e-04
 Identities = 12/19 (63%), Positives = 16/19 (84%)

Query: 367 KDKMITSNIRLVISIAKNY 385
           K +M+ +N+RLVISIAK Y
Sbjct: 382 KKEMVEANLRLVISIAKKY 400

Length = 619

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	395
PRK07598	415	RNA polymerase sigma factor SigC; Validated	99.87
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	99.8
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	99.78
PRK05949	327	RNA polymerase sigma factor; Validated	99.74
PRK07405	317	RNA polymerase sigma factor SigD; Validated	99.73
PRK05901	509	RNA polymerase sigma factor; Provisional	99.52
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	99.42
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	99.29
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	98.72
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	98.49
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	98.25
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	98.19
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	98.13
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	98.11
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	97.75
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	97.38
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	97.21
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	97.2
PRK08215	258	sporulation sigma factor SigG; Reviewed	96.85
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	96.78
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	96.47
PRK05803	233	sporulation sigma factor SigK; Reviewed	96.4
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	96.04
PRK05572	252	sporulation sigma factor SigF; Validated	92.16
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	88.43
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	85.16
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	82.64
PRK08301	234	sporulation sigma factor SigE; Reviewed	82.43
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	80.26

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=99.87  E-value=7.4e-22  Score=201.12  Aligned_cols=106  Identities=34%  Similarity=0.558  Sum_probs=97.5

Q ss_pred             CCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHH--------------------HHHHHHHHHHHcCCCCChHHHHH
Q 016077          289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK--------------------LEGLREVLSERCGGSPTFAQWAA  347 (395)
Q Consensus       289 ~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~--------------------LE~ir~~L~e~lGrePT~~EWAe  347 (395)
                      ..+|+++ ||++| |+.+|||++||++|+++||++++                    |++++.+|++++|++||..|||+
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            4589999 99999 99999999999999999999999                    89999999999999999999997


Q ss_pred             HhcCcHHHHHHhh----------------------hhcHHHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          348 AAGVDQRELRRRL----------------------NYGILCKDKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       348 A~Gms~~eLr~~L----------------------~~G~~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      ++|+++.+|+.+|                      ..|+.|+++||++|+|||++||++|.|+|++++|+
T Consensus       136 ~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDL  205 (415)
T PRK07598        136 TADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDL  205 (415)
T ss_pred             HhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHH
Confidence            7776666666654                      67889999999999999999999999999999985

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

Probab=99.80  E-value=1.5e-19  Score=174.90  Aligned_cols=103  Identities=45%  Similarity=0.685  Sum_probs=100.0

Q ss_pred             ChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHH
Q 016077          292 DPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM  370 (395)
Q Consensus       292 D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerL  370 (395)
                      |++. ||+++ +++||||++||.+|+++|+.++.+++++.+|+++.|++||..+||+++|++..+|..++..|..|+++|
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             HHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          371 ITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       371 VkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      |++|+|||++||++|.|+|++++|+
T Consensus        80 v~~~lrlV~~iA~~y~~~~~~~eDL  104 (298)
T TIGR02997        80 IKANLRLVVSVAKKYQNRGLELLDL  104 (298)
T ss_pred             HHHhHHHHHHHHHHHhcCCCCHHHH
Confidence            9999999999999999999999885

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=99.78  E-value=8.6e-19  Score=176.50  Aligned_cols=105  Identities=40%  Similarity=0.619  Sum_probs=102.2

Q ss_pred             CCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHH
Q 016077          290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  368 (395)
Q Consensus       290 ~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARe  368 (395)
                      ..|+++ ||++| +++||||++||++|+++|++++.+++++.+|+++.|++|+..+||+++|++..+|++++..|..|++
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             HHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          369 KMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       369 rLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      +||.+|++||++||++|.|+|++++|+
T Consensus       140 ~Li~~~l~lV~~iA~ry~~~~~~~eDL  166 (373)
T PRK07406        140 KMVQSNLRLVVSIAKKYMNRGLSFQDL  166 (373)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            999999999999999999999999885

>PRK05949 RNA polymerase sigma factor; Validated

Probab=99.74  E-value=1.3e-17  Score=164.90  Aligned_cols=106  Identities=32%  Similarity=0.513  Sum_probs=102.5

Q ss_pred             CCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHH
Q 016077          289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK  367 (395)
Q Consensus       289 ~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~AR  367 (395)
                      ..+|++. ||++| +++||||++||++|+++||.++.+++.+..|++++|++|+..+||++++|+..+|...+..|..|+
T Consensus        15 ~~~d~~~~yl~~i-~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~   93 (327)
T PRK05949         15 FSADMVRTYLHEI-GRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAK   93 (327)
T ss_pred             CCCCHHHHHHHHc-CCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHH
Confidence            3578999 99999 999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          368 DKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       368 erLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      ++||++|+++|++||++|.+.|++++|+
T Consensus        94 ~~Li~~~~~~V~~iA~~y~~~~~~~eDL  121 (327)
T PRK05949         94 QKMIEANLRLVVAIAKKYQKRNMEFLDL  121 (327)
T ss_pred             HHHHHHHHHHHHHHHHHHccCCCCHHHH
Confidence            9999999999999999999999999885

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=99.73  E-value=1.6e-17  Score=163.13  Aligned_cols=104  Identities=38%  Similarity=0.547  Sum_probs=101.2

Q ss_pred             CChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHH
Q 016077          291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK  369 (395)
Q Consensus       291 ~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARer  369 (395)
                      +|++. ||++| +++||||++||++|+++|++++.+++++..|++++|++|+..+||++++|+..+|..++..|..|+++
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             HHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          370 MITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       370 LVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      ||.+|+++|++||++|.|.|.+++|+
T Consensus        86 L~~~~~~~V~~~a~~~~~~~~~~eDL  111 (317)
T PRK07405         86 MVEANLRLVVSVAKKYLKRNVDLLDL  111 (317)
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            99999999999999999999999884

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=99.52  E-value=9.7e-15  Score=152.53  Aligned_cols=95  Identities=28%  Similarity=0.383  Sum_probs=79.1

Q ss_pred             cCCCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHH
Q 016077          287 EVDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL  365 (395)
Q Consensus       287 ~~~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~  365 (395)
                      .....|+++ ||++| +++++||++||++|+++|+.+..++...   .       ...+|+..   +..+|+++++.|..
T Consensus       206 ~~~~~d~l~~YL~~i-~~~~lLt~eEE~~La~~i~~g~~~~~~~---~-------~~~~~~~~---~~~~l~~~~~~g~~  271 (509)
T PRK05901        206 LTATADPVKAYLKQI-GKVKLLNAEEEVELAKRIEAGLYAEELL---A-------EGEKLDPE---LRRDLQWIGRDGKR  271 (509)
T ss_pred             ccccccHHHHHHHHh-ccCCCCCHHHHHHHHHHHHhCCchhhhh---h-------hcccchhh---hhhhhhhhccchHH
Confidence            344578999 99999 9999999999999999999885544422   1       11234422   56889999999999


Q ss_pred             HHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          366 CKDKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       366 ARerLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      ||++||.+|||||++||++|.|+|++|+|+
T Consensus       272 Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDL  301 (509)
T PRK05901        272 AKNHLLEANLRLVVSLAKRYTNRGLSFLDL  301 (509)
T ss_pred             HHHHHHHHhHHHHHHHHHHHhcCCCCHHHH
Confidence            999999999999999999999999999985

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

Probab=99.42  E-value=2.3e-13  Score=136.36  Aligned_cols=104  Identities=34%  Similarity=0.469  Sum_probs=92.7

Q ss_pred             CChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-HcCCCCChH---------------HHHHHhcCcH
Q 016077          291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSE-RCGGSPTFA---------------QWAAAAGVDQ  353 (395)
Q Consensus       291 ~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e-~lGrePT~~---------------EWAeA~Gms~  353 (395)
                      .|.+. |+.++ +..++++.++|.++.+.++....+......|.. .++..|+..               +|+..+..++
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 899999999999999999998888888888877 778999987               7777777666


Q ss_pred             -HHHHHhhhhcHH---HHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          354 -RELRRRLNYGIL---CKDKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       354 -~eLr~~L~~G~~---ARerLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                       ..|..++..|..   |+.+||.+||||||||||+|.|+||+|.|+
T Consensus        87 e~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DL  132 (342)
T COG0568          87 EKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDL  132 (342)
T ss_pred             HHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHH
Confidence             778899988865   999999999999999999999999999995

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=99.29  E-value=6e-12  Score=124.80  Aligned_cols=92  Identities=30%  Similarity=0.421  Sum_probs=77.5

Q ss_pred             CCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHH
Q 016077          290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  368 (395)
Q Consensus       290 ~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARe  368 (395)
                      .+|++. ||+++ +++++||++||++|+++|+.+..++..           |+..+|....  ...+|+.+++.|..|++
T Consensus        24 ~~~~~~~Yl~~i-~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~   89 (324)
T PRK07921         24 AADLVRVYLNGI-GKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARR   89 (324)
T ss_pred             CCChHHHHHHHh-cccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHH
Confidence            468899 99999 999999999999999999998765554           2233332111  45789999999999999


Q ss_pred             HHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          369 KMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       369 rLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      +||.+|++||++||++|.|.|++++|+
T Consensus        90 ~Lv~~~~~lV~~iA~r~~~~~~~~eDL  116 (324)
T PRK07921         90 HLLEANLRLVVSLAKRYTGRGMPLLDL  116 (324)
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCCHHHH
Confidence            999999999999999999999999885

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=98.72  E-value=1.5e-08  Score=101.80  Aligned_cols=67  Identities=39%  Similarity=0.596  Sum_probs=61.7

Q ss_pred             CCCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHH
Q 016077          288 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILC  366 (395)
Q Consensus       288 ~~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~A  366 (395)
                      ...+|+++ ||++| +++|+||++||.+|+++++.|                                        +..|
T Consensus        92 ~~~~d~~~~yl~~i-~~~~~l~~~ee~~L~~~~~~G----------------------------------------d~~A  130 (367)
T PRK09210         92 VKINDPVRMYLKEI-GRVPLLTAEEEIELAKRIEEG----------------------------------------DEEA  130 (367)
T ss_pred             cccCcHHHHHHHHh-hccCCCCHHHHHHHHHHHHhh----------------------------------------HHHH
Confidence            34578999 99999 999999999999999999887                                        5789


Q ss_pred             HHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          367 KDKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       367 RerLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      +++||++|++||++||++|.|+|++++|+
T Consensus       131 ~~~Li~~~~~lV~~iA~~~~~~~~~~eDL  159 (367)
T PRK09210        131 KQRLAEANLRLVVSIAKRYVGRGMLFLDL  159 (367)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCCHHHH
Confidence            99999999999999999999999999884

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=98.49  E-value=8.7e-08  Score=102.29  Aligned_cols=32  Identities=41%  Similarity=0.504  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          364 ILCKDKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       364 ~~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      ..|+++||.+|||||++||++|.|+|++|+|+
T Consensus       379 ~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DL  410 (619)
T PRK05658        379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDL  410 (619)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHH
Confidence            47999999999999999999999999999985

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=98.25  E-value=1.5e-06  Score=84.51  Aligned_cols=67  Identities=25%  Similarity=0.430  Sum_probs=59.5

Q ss_pred             CCCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHH
Q 016077          288 VDYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQ-DLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL  365 (395)
Q Consensus       288 ~~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ-~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~  365 (395)
                      +.+.+++. |++++ ++.|+|+.++|.+|+.+++ .|                                        +..
T Consensus        10 ~~~~~~~~~y~~~~-~~~~~l~~~~e~~l~~~~~~~G----------------------------------------d~~   48 (284)
T PRK06596         10 LSPEGNLDAYIQAV-NKIPMLTAEEEYMLAKRLREHG----------------------------------------DLE   48 (284)
T ss_pred             CCCccHHHHHHHHH-hccCCCCHHHHHHHHHHHHHcC----------------------------------------CHH
Confidence            34567888 99999 9999999999999998854 44                                        678


Q ss_pred             HHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          366 CKDKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       366 ARerLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      |+++||..|++||.+||++|.+.|++++||
T Consensus        49 a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDL   78 (284)
T PRK06596         49 AAKQLVLSHLRFVVHIARGYRGYGLPQADL   78 (284)
T ss_pred             HHHHHHHHhHHHHHHHHHHhcCCCCCHHHH
Confidence            999999999999999999999999999885

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=98.19  E-value=2e-06  Score=82.59  Aligned_cols=62  Identities=31%  Similarity=0.504  Sum_probs=55.8

Q ss_pred             hhH-HHHHhcCCCCCCCHHHHHHHHHHH-HHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHH
Q 016077          293 PLR-YLRATTSSSRLLTANEEMQLSAGI-QDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKM  370 (395)
Q Consensus       293 ~lr-YLrei~g~~~LLTaeEEveLa~~I-Q~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerL  370 (395)
                      ++. ||+++ +++++|+.++|.+|+.++ +.+                                        +..|+++|
T Consensus         2 ~~~~yl~~~-~~~~~l~~~~e~~l~~~~~~~g----------------------------------------d~~a~~~L   40 (270)
T TIGR02392         2 SLDAYIRAV-NRIPMLTPEEEYQLAKRLREHG----------------------------------------DLDAAKKL   40 (270)
T ss_pred             hHHHHHHHH-hcCCCCCHHHHHHHHHHHHHCC----------------------------------------CHHHHHHH
Confidence            567 99999 999999999999999885 343                                        67899999


Q ss_pred             HHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          371 ITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       371 VkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      |..|++||.++|++|.+.|.+++|+
T Consensus        41 v~~~~~lV~~~a~~~~~~~~~~eDL   65 (270)
T TIGR02392        41 VLSHLRFVVKIARGYRGYGLPQADL   65 (270)
T ss_pred             HHHhHHHHHHHHHHHcCCCCCHHHH
Confidence            9999999999999999999999885

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.

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=98.13  E-value=7.7e-07  Score=62.92  Aligned_cols=34  Identities=41%  Similarity=0.526  Sum_probs=30.0

Q ss_pred             CChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHH
Q 016077          291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKL  325 (395)
Q Consensus       291 ~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~L  325 (395)
                      +|+++ ||++| ++++|||++||++|+++|+.|...
T Consensus         1 ~D~l~~Yl~ei-~~~~LLt~eeE~~LA~~i~~g~~~   35 (37)
T PF00140_consen    1 SDSLRLYLKEI-GRYPLLTAEEEIELARRIRKGDEA   35 (37)
T ss_dssp             HHHHHHHHHHH-HHS-EETTHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHhHHh
Confidence            37899 99999 999999999999999999998644

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 ....

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=98.11  E-value=3.8e-06  Score=82.00  Aligned_cols=64  Identities=22%  Similarity=0.277  Sum_probs=57.4

Q ss_pred             CChhH-HHHHhcCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHH
Q 016077          291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQ-DLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKD  368 (395)
Q Consensus       291 ~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ-~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARe  368 (395)
                      .+.++ ||+++ .++++||.++|.+|.++++ .+                                        +..|++
T Consensus         5 ~~~~~~y~~~~-~~~~~l~~~~e~~L~~~~~~~g----------------------------------------d~~A~~   43 (289)
T PRK07500          5 ASADRSMIRSA-MKAPYLEREEEHALAYRWKDHR----------------------------------------DEDALH   43 (289)
T ss_pred             hhHHHHHHHHH-hcCCCCCHHHHHHHHHHHHHCC----------------------------------------CHHHHH
Confidence            34566 99999 8999999999999999875 33                                        688999


Q ss_pred             HHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          369 KMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       369 rLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      +||..|+++|.+||++|.+.|.+++|+
T Consensus        44 ~Lv~~~~~lV~~~a~~~~~~~~~~eDL   70 (289)
T PRK07500         44 RIISAHMRLVISMAGKFRRFGLPMNDL   70 (289)
T ss_pred             HHHHHhHHHHHHHHHHHcCCCCCHHHH
Confidence            999999999999999999999998885

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=97.75  E-value=3.8e-05  Score=76.50  Aligned_cols=64  Identities=34%  Similarity=0.427  Sum_probs=58.8

Q ss_pred             CChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHH
Q 016077          291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDK  369 (395)
Q Consensus       291 ~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARer  369 (395)
                      .|.++ |+.+| +..|+||+++|.+|..+++.|                                        +..|.++
T Consensus        52 ~~~~~~y~~~~-~~~~~l~~~ee~~li~~~~~G----------------------------------------d~~A~~~   90 (325)
T PRK05657         52 LDATQLYLNEI-GYSPLLTAEEEVYFARRALRG----------------------------------------DFAARQR   90 (325)
T ss_pred             ccHHHHHHHHH-hcCCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHH
Confidence            56778 99999 999999999999999999887                                        6889999


Q ss_pred             HHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          370 MITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       370 LVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      ||..|+++|.++|++|.+.|.+.+|+
T Consensus        91 Li~~y~~~V~~~a~~~~~~~~~aeDL  116 (325)
T PRK05657         91 MIESNLRLVVKIAKRYLNRGLALLDL  116 (325)
T ss_pred             HHHHhHHHHHHHHHHHhcCCCCHHHH
Confidence            99999999999999999999888774

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=97.38  E-value=7.3e-05  Score=72.10  Aligned_cols=33  Identities=21%  Similarity=0.302  Sum_probs=30.5

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          363 GILCKDKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       363 G~~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      ...+|++||.+|||||++||++|.++|++++|+
T Consensus        38 ~~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DL   70 (264)
T PRK07122         38 FQRQRDRIVTRCLPLADHIARRFDGRGEPRDDL   70 (264)
T ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHH
Confidence            356999999999999999999999999999985

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=97.21  E-value=0.00043  Score=65.88  Aligned_cols=54  Identities=24%  Similarity=0.369  Sum_probs=48.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHH
Q 016077          302 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI  381 (395)
Q Consensus       302 g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSI  381 (395)
                      +++|+|+++||.+|...++.+                                        +..|+++|+..|+++|.++
T Consensus        11 ~~~~~l~~~~~~~li~~~~~g----------------------------------------d~~a~~~L~~~~~~~v~~~   50 (254)
T TIGR02850        11 SKLPVLKNQEMRELFIRMQSG----------------------------------------DTTAREKLINGNLRLVLSV   50 (254)
T ss_pred             cCCCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHHHHHHhHHHHHHH
Confidence            678999999999999888765                                        6789999999999999999


Q ss_pred             HHhccCCCCCCCCC
Q 016077          382 AKNYQGAGRMSRPC  395 (395)
Q Consensus       382 AKrY~GrGLsf~D~  395 (395)
                      |++|.+.+.+.+|+
T Consensus        51 a~~~~~~~~~aeDl   64 (254)
T TIGR02850        51 IQRFNNRGEYVDDL   64 (254)
T ss_pred             HHHHhCCCCCHHHH
Confidence            99999999888774

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.

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=97.20  E-value=0.00064  Score=65.88  Aligned_cols=66  Identities=35%  Similarity=0.397  Sum_probs=60.3

Q ss_pred             CCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHH
Q 016077          289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCK  367 (395)
Q Consensus       289 ~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~AR  367 (395)
                      -..|.++ ||.+| +.++.|+.++|.+|...++.+                                        +..|.
T Consensus        10 ~~~~~~~~~~~~~-~~~~~~~~~~~~~li~~~~~g----------------------------------------d~~a~   48 (285)
T TIGR02394        10 RVADVTQLYLREI-GFKPLLTAEEEIAYARRALAG----------------------------------------DFEAR   48 (285)
T ss_pred             CcchHHHHHHHHH-hccCCCCHHHHHHHHHHHHcC----------------------------------------CHHHH
Confidence            3478899 99999 999999999999999999887                                        68899


Q ss_pred             HHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          368 DKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       368 erLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      +.|+..+..+|.++|.+|.+.|.+.+|+
T Consensus        49 ~~L~~~y~~~v~~~a~~~~~~~~~aeDL   76 (285)
T TIGR02394        49 KVMIESNLRLVVSIAKHYVNRGLPLLDL   76 (285)
T ss_pred             HHHHHHhHHHHHHHHHHHhcCCCCHHHH
Confidence            9999999999999999999999988874

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).

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=96.85  E-value=0.0013  Score=62.58  Aligned_cols=54  Identities=24%  Similarity=0.355  Sum_probs=48.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHH
Q 016077          302 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI  381 (395)
Q Consensus       302 g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSI  381 (395)
                      .++|+|+++|+..|...++.+                                        +..++++|+..|+++|..|
T Consensus        14 ~~~~~l~~~~~~~l~~~~~~g----------------------------------------d~~a~~~l~~~~~~~v~~~   53 (258)
T PRK08215         14 SKLPVLKNEEMRELFERMQNG----------------------------------------DKEAREKLINGNLRLVLSV   53 (258)
T ss_pred             CCCCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHHHHHHHHHHHHHH
Confidence            457899999999999888765                                        6789999999999999999


Q ss_pred             HHhccCCCCCCCCC
Q 016077          382 AKNYQGAGRMSRPC  395 (395)
Q Consensus       382 AKrY~GrGLsf~D~  395 (395)
                      |++|.+.+.+.+|+
T Consensus        54 a~~~~~~~~~aeDl   67 (258)
T PRK08215         54 IQRFNNRGENVDDL   67 (258)
T ss_pred             HHHHhCCCCCHHHH
Confidence            99999999888774

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=96.78  E-value=0.0015  Score=70.36  Aligned_cols=34  Identities=32%  Similarity=0.529  Sum_probs=32.1

Q ss_pred             CCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHH
Q 016077          290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK  324 (395)
Q Consensus       290 ~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~  324 (395)
                      .+||++ ||++| |+.+|||.++|++++++|..|.+
T Consensus       102 t~DPVRMYLREM-G~V~LLTREgEIeIAKRIE~G~~  136 (619)
T PRK05658        102 TDDPVRMYLREM-GTVELLTREGEIEIAKRIEAGEN  136 (619)
T ss_pred             CCChHHHHHHHh-ccCcCCCcHHHHHHHHHHHHHHH
Confidence            599999 99999 99999999999999999998865

>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=96.47  E-value=0.0059  Score=47.89  Aligned_cols=41  Identities=32%  Similarity=0.404  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhh
Q 016077          322 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY  362 (395)
Q Consensus       322 ~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~  362 (395)
                      +.++.+.+.+|..++||+||..|.|+.+||+.++++..+..
T Consensus         3 l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~   43 (78)
T PF04539_consen    3 LRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQA   43 (78)
T ss_dssp             HHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHh
Confidence            34567889999999999999999999999999999887753

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 ....

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=96.40  E-value=0.0055  Score=57.47  Aligned_cols=61  Identities=23%  Similarity=0.336  Sum_probs=54.0

Q ss_pred             hH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHH
Q 016077          294 LR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMIT  372 (395)
Q Consensus       294 lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVk  372 (395)
                      +. |+.++ ++.++||+++|.+|...++.+                                        +..|.+.|+.
T Consensus        18 ~~~~~~~~-~~~~~~~~~~e~~l~~~~~~g----------------------------------------d~~a~~~l~~   56 (233)
T PRK05803         18 LVSYVKNN-SFPQPLSEEEERKYLELMKEG----------------------------------------DEEARNILIE   56 (233)
T ss_pred             HHHHHHHh-cccCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHHHHH
Confidence            45 99999 889999999999888887765                                        6789999999


Q ss_pred             HhHHHHHHHHHhccCCCCCCCCC
Q 016077          373 SNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       373 SNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      .+.++|.++|.+|.|.+.+.+||
T Consensus        57 ~y~~~l~~~a~~~~~~~~daeDl   79 (233)
T PRK05803         57 RNLRLVAHIVKKFENTGEDVDDL   79 (233)
T ss_pred             HhHHHHHHHHHHHhcCCCCHHHH
Confidence            99999999999999998887775

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=96.04  E-value=0.006  Score=58.57  Aligned_cols=57  Identities=12%  Similarity=0.027  Sum_probs=46.6

Q ss_pred             hcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHH
Q 016077          300 TTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVI  379 (395)
Q Consensus       300 i~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNLRLVV  379 (395)
                      ++|++++||.++|.+|...++.+                                       .+..+.+.|+..|++||.
T Consensus         5 ~~~~~~~~~~~~e~~l~~~~~~~---------------------------------------~d~~a~~~l~~~y~~lv~   45 (268)
T PRK06288          5 MSGKIPKYAQQDETELWREYKKT---------------------------------------GDPKIREYLILKYSPLVK   45 (268)
T ss_pred             ccCCCccccchHHHHHHHHHHHc---------------------------------------CCHHHHHHHHHHHHHHHH
Confidence            34789999999999999987754                                       167799999999999999


Q ss_pred             HHHHhcc-C--CCCCCCCC
Q 016077          380 SIAKNYQ-G--AGRMSRPC  395 (395)
Q Consensus       380 SIAKrY~-G--rGLsf~D~  395 (395)
                      .||++|. |  .+.+.+|+
T Consensus        46 ~~a~~~~~~~~~~~~~eDl   64 (268)
T PRK06288         46 YVAGRIAVGMPQNVEFDDL   64 (268)
T ss_pred             HHHHHHHhcCCCCCCHHHH
Confidence            9999986 2  45556653

>PRK05572 sporulation sigma factor SigF; Validated

Probab=92.16  E-value=0.22  Score=47.45  Aligned_cols=54  Identities=22%  Similarity=0.289  Sum_probs=46.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHH
Q 016077          302 SSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISI  381 (395)
Q Consensus       302 g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSI  381 (395)
                      ...|.||.+++.+|...++.+                                        +..|.++|+..+.++|..+
T Consensus         9 ~~~~~l~~~~~~~li~~~~~g----------------------------------------d~~a~~~L~~~y~~~v~~~   48 (252)
T PRK05572          9 KKKPQLKDEENKELIKKSQDG----------------------------------------DQEARDTLVEKNLRLVWSV   48 (252)
T ss_pred             cCCCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHHHHHHhHHHHHHH
Confidence            347899999999888777655                                        5789999999999999999


Q ss_pred             HHhccCCCCCCCCC
Q 016077          382 AKNYQGAGRMSRPC  395 (395)
Q Consensus       382 AKrY~GrGLsf~D~  395 (395)
                      |++|.+.+.+.+|+
T Consensus        49 a~~~~~~~~~aeDl   62 (252)
T PRK05572         49 VQRFLNRGYEPDDL   62 (252)
T ss_pred             HHHHccCCCCHHHH
Confidence            99999998877763

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=88.43  E-value=0.95  Score=42.44  Aligned_cols=60  Identities=22%  Similarity=0.323  Sum_probs=48.9

Q ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhH
Q 016077          296 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI  375 (395)
Q Consensus       296 YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNL  375 (395)
                      |...-.+..+.|++.+|.+|...++.+                                        +..|.+.|+..+.
T Consensus        19 ~~~~~~~~~~~~~~~~~~~li~~~~~g----------------------------------------d~~af~~l~~~y~   58 (227)
T TIGR02846        19 YVTNNGSFPQPLSEEEEKKYLDRLKEG----------------------------------------DEEARNVLIERNL   58 (227)
T ss_pred             HHHHHHhCCCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHHHHHHhH
Confidence            666553456789999999998888776                                        6788999999999


Q ss_pred             HHHHHHHHhccCCCCCCCCC
Q 016077          376 RLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       376 RLVVSIAKrY~GrGLsf~D~  395 (395)
                      ++|.++|.+|.+...+.+||
T Consensus        59 ~~v~~~~~~~~~~~~dAEDl   78 (227)
T TIGR02846        59 RLVAHIVKKFSNTGEDVDDL   78 (227)
T ss_pred             HHHHHHHHHhcCCCCCHHHH
Confidence            99999999998877766664

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.

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

Probab=85.16  E-value=1.7  Score=42.69  Aligned_cols=40  Identities=25%  Similarity=0.307  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhh
Q 016077          323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY  362 (395)
Q Consensus       323 ~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~  362 (395)
                      .+++.+..+|+.++||+||+.|.|+..|++.+++...+..
T Consensus       110 ~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~  149 (247)
T COG1191         110 RRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLA  149 (247)
T ss_pred             HHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHH
Confidence            3455678899999999999999999999999988776643

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=82.64  E-value=3.1  Score=39.99  Aligned_cols=38  Identities=21%  Similarity=0.232  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077          323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL  360 (395)
Q Consensus       323 ~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L  360 (395)
                      .++.+.+.+|...+|++||..|.|+.+|+++++++..+
T Consensus       113 ~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~  150 (256)
T PRK07408        113 RQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIK  150 (256)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHH
Confidence            34566788899999999999999999999999887653

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=82.43  E-value=2.1  Score=40.04  Aligned_cols=59  Identities=22%  Similarity=0.327  Sum_probs=45.0

Q ss_pred             HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhcHHHHHHHHHHhH
Q 016077          296 YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNI  375 (395)
Q Consensus       296 YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G~~ARerLVkSNL  375 (395)
                      |+++.-.-.+.++..++.+|...++.+                                        +..|.+.|+..+.
T Consensus        23 ~~~~~~~~~~~~~~~~~~~L~~~~~~g----------------------------------------d~~af~~l~~~y~   62 (234)
T PRK08301         23 YIGGSEALPPPLSKEEEEYLLNKLPKG----------------------------------------DEAVRSLLIERNL   62 (234)
T ss_pred             HhccccccCCcCCHHHHHHHHHHHHcc----------------------------------------CHHHHHHHHHHhH
Confidence            777772235667777877777776655                                        5678888999999


Q ss_pred             HHHHHHHHhccCCCCCCCC
Q 016077          376 RLVISIAKNYQGAGRMSRP  394 (395)
Q Consensus       376 RLVVSIAKrY~GrGLsf~D  394 (395)
                      ++|..+|++|.+.+.+.+|
T Consensus        63 ~~l~~~a~~~~~~~~~AeD   81 (234)
T PRK08301         63 RLVVYIARKFENTGINIED   81 (234)
T ss_pred             HHHHHHHHHhhcCCCCHHH
Confidence            9999999999888776655

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=80.26  E-value=4.3  Score=38.76  Aligned_cols=37  Identities=27%  Similarity=0.241  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhh
Q 016077          324 KLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRL  360 (395)
Q Consensus       324 ~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L  360 (395)
                      ++.+.+.+|...+|++||..|.|+.+|++++.+...+
T Consensus       121 ~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~  157 (254)
T TIGR02850       121 KALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFAL  157 (254)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            3445667888889999999999999999998876654

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	395
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		4e-04

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 54/114 (47%), Gaps = 15/114 (13%)
Query: 291 SDPLRYLRATTSSSRLLTANEEMQLS----AGIQDLLKL--------EGLREVLSERCGG 338
           SDP+R          LLT  EE+ L+     G++ + KL        E +REV+  +  G
Sbjct: 2   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 61
Query: 339 SPTFAQWAAAAGVDQRELRRRLNY---GILCKDKMITSNIRLVISIAKNYQGAG 389
           +    +         +EL+R L+    G   +  +I +N+RLV+SIAK Y G G
Sbjct: 62  TARVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRG 115

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	395
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	2e-05
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	6e-05
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	1e-04
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	2e-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 = 45.3 bits (107), Expect = 2e-05
 Identities = 31/191 (16%), Positives = 57/191 (29%), Gaps = 20/191 (10%)

Query: 200 IGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQVSQSIAVR-SRRQTERKARR 258
             D  + +     E        +   L+   EE  L   ++S S  VR    +  +    
Sbjct: 35  EPDPDLEDPDLALEDDLLDLPEEGEGLDLEEEEEDLPIPKISTSDPVRQYLHEIGQVPLL 94

Query: 259 TRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAG 318
           T   E   A  +     +  +    +  + D                ++ A         
Sbjct: 95  TLEEEVELARKVEEGMEAIKKLSEITGLDPDLIR------------EVVRAKILGSARVR 142

Query: 319 IQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLV 378
               LK     + + E      +  +       + +        G   +  +I +N+RLV
Sbjct: 143 HIPGLKETLDPKTVEEIDQKLKSLPK-------EHKRYLHIAREGEAARQHLIEANLRLV 195

Query: 379 ISIAKNYQGAG 389
           +SIAK Y G G
Sbjct: 196 VSIAKKYTGRG 206

>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 = 43.8 bits (103), Expect = 6e-05
 Identities = 28/220 (12%), Positives = 63/220 (28%), Gaps = 4/220 (1%)

Query: 174 KPAISSSADTNTSMWAQLTERERASIIGDSVIVEAAPEEEYSEQQPLNKSADLEPTHEEL 233
           K + S                +    + +    E   +    + + L    +LE   + L
Sbjct: 2   KKSKSKKKAAKAQEVEVKEPVKEPEPLPELEAAEDLQDLPEPDPELLASEPELEDLADPL 61

Query: 234 KLLEEQVSQSIAVRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDP 293
            L     +  +      + E +         +      +             +       
Sbjct: 62  DLEGPLEADLLPEEGLLEEEEEELSLPKVSTSDPVRQYLHEIGQVPLLTLEEEIDLARKV 121

Query: 294 LRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQ 353
              + A    S     ++E+        +L    ++++   +    P   +         
Sbjct: 122 EEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSL 181

Query: 354 RELRRRLNY----GILCKDKMITSNIRLVISIAKNYQGAG 389
            +  +R  +    G   +  +I +N+RLV+SIAK Y G G
Sbjct: 182 PKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRG 221

>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 = 42.2 bits (99), Expect = 1e-04
 Identities = 13/38 (34%), Positives = 20/38 (52%)

Query: 352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
           + +        G   +  +I +N+RLV+SIAK Y G G
Sbjct: 97  ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRG 134

>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 = 42.2 bits (99), Expect = 2e-04
 Identities = 13/23 (56%), Positives = 17/23 (73%)

Query: 367 KDKMITSNIRLVISIAKNYQGAG 389
           K +M+ +N+RLVISIAK Y   G
Sbjct: 267 KKEMVEANLRLVISIAKKYTNRG 289

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	395
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	99.5
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	99.48
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	99.4
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	95.73
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	94.87
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	93.53

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

Probab=99.50  E-value=2.6e-14  Score=145.28  Aligned_cols=106  Identities=25%  Similarity=0.346  Sum_probs=88.3

Q ss_pred             CCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHH------------------HHHHHcCCCCChHHHHH--
Q 016077          289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE------------------VLSERCGGSPTFAQWAA--  347 (395)
Q Consensus       289 ~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~------------------~L~e~lGrePT~~EWAe--  347 (395)
                      ...|+++ ||++| +++||||++||++|+++|+.++.++....                  +....+++.|+..+|+.  
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 99999999999999999999866543321                  22234678899888753  


Q ss_pred             ----------HhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          348 ----------AAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       348 ----------A~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                                +++++..+|.+++..|..|+++||.+|+|||++||++|.|+|++++|+
T Consensus       170 ~~~~~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDL  227 (438)
T 1l9z_H          170 TVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDL  227 (438)
T ss_pred             hhhhhhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHH
Confidence                      235667888888889999999999999999999999999999999885

>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=99.48  E-value=4e-14  Score=133.08  Aligned_cols=105  Identities=29%  Similarity=0.363  Sum_probs=85.5

Q ss_pred             CCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHH-HHHHH------H-HHH------------------cCCCCCh
Q 016077          290 YSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLE-GLREV------L-SER------------------CGGSPTF  342 (395)
Q Consensus       290 ~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE-~ir~~------L-~e~------------------lGrePT~  342 (395)
                      .+||++ ||++| |++||||++||++|+++|+.|+... .+...      + .+.                  .+.+|+.
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 22211      0 000                  1478999


Q ss_pred             HHHHHHhcCcH----HHHHHhhhhcHHHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          343 AQWAAAAGVDQ----RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       343 ~EWAeA~Gms~----~eLr~~L~~G~~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      .+||++.|++.    ..|.+....|..|+++|+..|+++|.+||++|.+.+.+++|+
T Consensus        84 ~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDL  140 (245)
T 3ugo_A           84 VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDL  140 (245)
T ss_dssp             HHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHH
T ss_pred             HHHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHH
Confidence            99999999865    344555678899999999999999999999999999988774

>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=99.40  E-value=5.4e-14  Score=141.47  Aligned_cols=106  Identities=26%  Similarity=0.343  Sum_probs=84.7

Q ss_pred             CCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH------------------HHHHcCCCCChHHHHH--
Q 016077          289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREV------------------LSERCGGSPTFAQWAA--  347 (395)
Q Consensus       289 ~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~------------------L~e~lGrePT~~EWAe--  347 (395)
                      ...|+++ ||++| +++||||++||++|+++|+.+..++.....                  .....++.|+..+|+.  
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            3468999 99999 999999999999999999998654432211                  1123356777665442  


Q ss_pred             ----------HhcCcHHHHHHhhhhcHHHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          348 ----------AAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       348 ----------A~Gms~~eLr~~L~~G~~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                                +++++..+|..++..|..|+++||.+|+|||++||++|.|+|++++|+
T Consensus       155 ~~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDL  212 (423)
T 2a6h_F          155 TVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDL  212 (423)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHH
T ss_pred             hhhhhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHH
Confidence                      346677888888888999999999999999999999999999998884

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

Probab=95.73  E-value=0.0041  Score=59.92  Aligned_cols=31  Identities=42%  Similarity=0.546  Sum_probs=29.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          365 LCKDKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       365 ~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      .|++.|+..|+++|+++|++|.+.|..++|+
T Consensus       265 ~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDl  295 (339)
T 1sig_A          265 RAKKEMVEANLRLVISIAKKYTNRGLQFLDL  295 (339)
T ss_dssp             HHHHHHHHHTHHHHHHHHTTSTTSSSCHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHhcCCCCHhHH
Confidence            6999999999999999999999999988774

>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=94.87  E-value=0.0025  Score=66.78  Aligned_cols=35  Identities=31%  Similarity=0.602  Sum_probs=14.7

Q ss_pred             CCCChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHH
Q 016077          289 DYSDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK  324 (395)
Q Consensus       289 ~~~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~  324 (395)
                      ..+||++ ||++| |+.+|||.++|++|+++|..|..
T Consensus        93 ~~~dpvrmyl~em-g~~~ll~~~~e~~~ak~ie~g~~  128 (613)
T 3iyd_F           93 RTTDPVRMYMREM-GTVELLTREGEIDIAKRIEDGIN  128 (613)
T ss_dssp             ------------C---------CSSSTTTHHHHHHHH
T ss_pred             CCCCcHHHHHHHh-cccccCCchhHHHHHHHHHHhHH
Confidence            4699999 99999 99999999999999999998864

>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=93.53  E-value=0.011  Score=62.07  Aligned_cols=42  Identities=38%  Similarity=0.608  Sum_probs=34.5

Q ss_pred             HHHHHhhhhcHH-H---HHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          354 RELRRRLNYGIL-C---KDKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       354 ~eLr~~L~~G~~-A---RerLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      ..|-.++..|.. |   ++.|+..|+++|++||++|.++|..+.||
T Consensus       359 ~~Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDl  404 (613)
T 3iyd_F          359 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL  404 (613)
T ss_dssp             HHHHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTT
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHH
Confidence            344455555543 4   99999999999999999999999999996

---

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	395
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	0.002

>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 = 36.3 bits (83), Expect = 0.002
 Identities = 28/130 (21%), Positives = 49/130 (37%), Gaps = 32/130 (24%)

Query: 291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLK------------------LEGLREV 331
           SDP+R YL        LLT  EE+ L+  +++ ++                  +   + +
Sbjct: 1   SDPVRQYLH-EIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKIL 59

Query: 332 LSERCGGSPTFAQWAAAAGVDQ------------RELRRRLNYGILCKDKMITSNIRLVI 379
            + R    P   +      V++            +        G   +  +I +N+RLV+
Sbjct: 60  GTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVV 119

Query: 380 SIAKNYQGAG 389
           SIAK Y G G
Sbjct: 120 SIAKKYTGRG 129

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	395
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.73
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	98.43
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	96.91
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	96.88
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	96.13
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	95.73
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	81.78

>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=99.73  E-value=7.6e-19  Score=154.22  Aligned_cols=104  Identities=27%  Similarity=0.373  Sum_probs=81.6

Q ss_pred             CChhH-HHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH------------------HHcCCCCChHHHHHHhcC
Q 016077          291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLS------------------ERCGGSPTFAQWAAAAGV  351 (395)
Q Consensus       291 ~D~lr-YLrei~g~~~LLTaeEEveLa~~IQ~~~~LE~ir~~L~------------------e~lGrePT~~EWAeA~Gm  351 (395)
                      .||++ ||++| |++||||++||++|+++|+.++.+.....+..                  ...+..|...+|......
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 99999999999999999999887655433221                  123455555555433222


Q ss_pred             ------------cHHHHHHhhhhcHHHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          352 ------------DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       352 ------------s~~eLr~~L~~G~~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                                  ..+.+.+.+..|..||++||++|||||++|||+|.|+|++|+|+
T Consensus        80 ~~~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl  135 (180)
T d1ku2a2          80 EEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDL  135 (180)
T ss_dssp             HHHHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHH
T ss_pred             HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHH
Confidence                        23556677789999999999999999999999999999999885

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

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

Probab=98.43  E-value=4.1e-08  Score=91.13  Aligned_cols=48  Identities=29%  Similarity=0.379  Sum_probs=39.8

Q ss_pred             HhcCcHHHHHHhh-------hhcHHHHHHHHHHhHHHHHHHHHhccCCCCCCCCC
Q 016077          348 AAGVDQRELRRRL-------NYGILCKDKMITSNIRLVISIAKNYQGAGRMSRPC  395 (395)
Q Consensus       348 A~Gms~~eLr~~L-------~~G~~ARerLVkSNLRLVVSIAKrY~GrGLsf~D~  395 (395)
                      .+|++..+|+..+       ..+..||++||++|||||++|||+|.|+|++|+|+
T Consensus       238 ~~gl~~~elk~i~~~i~~ge~~~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl  292 (334)
T d1siga_         238 ETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDL  292 (334)
T ss_dssp             HHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHH
T ss_pred             HhhhhHHHHHHHHHHHHHHHhhccchHHHHHHhHHHHHHHHHHhccCCCCCHHHH
Confidence            3577776665543       45667999999999999999999999999999884

>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=96.91  E-value=0.00088  Score=50.35  Aligned_cols=42  Identities=26%  Similarity=0.358  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhh
Q 016077          321 DLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNY  362 (395)
Q Consensus       321 ~~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~  362 (395)
                      ...++++...+|..++||+||.+|.|+.+||+.+++++.+..
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            345678899999999999999999999999999999887643

>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=96.88  E-value=0.00098  Score=48.19  Aligned_cols=42  Identities=19%  Similarity=0.213  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhhhc
Q 016077          322 LLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYG  363 (395)
Q Consensus       322 ~~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~~G  363 (395)
                      ..++.++..+|..++||+||.+|.|+++||+++++...|..+
T Consensus        14 ~~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~   55 (57)
T d1l0oc_          14 GNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAV   55 (57)
T ss_dssp             HHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHh
Confidence            345667789999999999999999999999999998877654

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

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

Probab=96.13  E-value=0.0066  Score=44.34  Aligned_cols=44  Identities=23%  Similarity=0.397  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHHHHHcCCCCChHHHHHHhc--CcHHHHHHhhhhc
Q 016077          320 QDLLKLEGLREVLSERCGGSPTFAQWAAAAG--VDQRELRRRLNYG  363 (395)
Q Consensus       320 Q~~~~LE~ir~~L~e~lGrePT~~EWAeA~G--ms~~eLr~~L~~G  363 (395)
                      ...-++.++..+|.+.+||+||.+|.|+++|  ++++.++..+...
T Consensus         9 e~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~~~   54 (60)
T d1ku2a1           9 ETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIA   54 (60)
T ss_dssp             HHHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGGGS
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHc
Confidence            3445667889999999999999999999997  5577788777654

>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=95.73  E-value=0.0013  Score=51.13  Aligned_cols=33  Identities=21%  Similarity=0.228  Sum_probs=28.2

Q ss_pred             cHHHHHHHHHHhHHHHHHHHHhccCC---CCCCCCC
Q 016077          363 GILCKDKMITSNIRLVISIAKNYQGA---GRMSRPC  395 (395)
Q Consensus       363 G~~ARerLVkSNLRLVVSIAKrY~Gr---GLsf~D~  395 (395)
                      ....|++||..|++||.+||++|.++   |++++|+
T Consensus         8 ~~~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL   43 (87)
T d1rp3a3           8 NQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDL   43 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHH
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHH
Confidence            45578999999999999999999876   7787774

>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=81.78  E-value=0.92  Score=30.71  Aligned_cols=39  Identities=8%  Similarity=0.267  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHHHcCCCCChHHHHHHhcCcHHHHHHhhh
Q 016077          323 LKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLN  361 (395)
Q Consensus       323 ~~LE~ir~~L~e~lGrePT~~EWAeA~Gms~~eLr~~L~  361 (395)
                      ..++++..-+++.+..++|.+++|+.+||+...|.+..+
T Consensus         3 ~~i~~v~~yI~~~~~~~~tl~~lA~~~~~s~~~l~r~Fk   41 (54)
T d1bl0a1           3 ITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFK   41 (54)
T ss_dssp             HHHHHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            346677788899999999999999999999988876553