Citrus Sinensis ID: 020126

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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
Protein Sequence
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPSFPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS
Secondary Structure (PSIPRED)
ccccccEEEcccccccccccccccccccccccccccccccccccccccHHHccccccccccccccccccHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHcccccccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHcccccccccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccccHHHEEcccccHHHcccccccccccccccccccccccccccccccEEEEEcccccccccccccHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccHHHccccHcccHHHHHHHHHccccccccccccccHHHHHHHHcccccccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHccHHHHHHHHHccccccccHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYIndlgsansqvgsTKNVVAAkkssnynpsfpssnrqtqpiKALKEhvdtnfastaepwaeppnsieeesseLDYSVEALLLLQKSMLEKQWNLSFertvltdspskkthkkvpvtcsgvsARQRRLNSKKKILSQNKSILQQNGSkqlrsmisPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIktglslddHKLRLkerlgcepSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIekfdsskgfkisTYVYWWIRQSIS
Flexible Loop (DISEMBL)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKssnynpsfpssnrqTQPIKALKEHVDTNFAstaepwaeppnSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERtvltdspskkthkkvpvtcsgvsarqrrlnskkkilsqnksilqqngskqlrsMISPELIQNRLKGYVKGVVSEELLTHAEVVRlskkiktglslddhKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGiekfdsskgfkistyvYWWIRQSIS
Low Complexity Region (SEG)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKssnynpsfpssnRQTQPIKALKEHVDTNFASTAEPWAEPPNsieeesseLDYSVEALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS
Disordered region (IsUnstruct)
*****AVIGLSAGKRLLSSSFYYSDISEKFSYINDL*********************************************************************YSVEALLLLQKSMLEKQWNLSFERTVL******************************************************ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGC**********LRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIR****
Disordered Region (DISOPRED)
***TAAVIGLSAGKRLLSSSFYYSDISEKFS*********************************************************************************LLQKSMLEKQWNLSF****************************************************************RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLK*********EQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS
Disordered Region (DISEMBL)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNY************PIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERTVL*****************GVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS
Disordered Region (DISPRO)
*MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYN*******************************************ELDYSVEALLLLQKSMLEKQWNLSFER*********************************************************ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPSFPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS
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	330	2.2.26 [Sep-21-2011]
O24629	502	RNA polymerase sigma fact	yes	no	0.945	0.621	0.645	1e-117
Q31ME3	320	RNA polymerase sigma fact	yes	no	0.430	0.443	0.390	2e-25
Q9LD95	547	RNA polymerase sigma fact	no	no	0.415	0.250	0.401	9e-24
O22056	572	RNA polymerase sigma fact	no	no	0.451	0.260	0.38	1e-23
P26683	390	RNA polymerase sigma fact	no	no	0.427	0.361	0.382	2e-21
Q03065	332	RNA polymerase sigma-B fa	no	no	0.409	0.406	0.348	3e-21
Q31QG5	320	RNA polymerase sigma fact	no	no	0.418	0.431	0.381	4e-21
P38023	399	RNA polymerase sigma fact	no	no	0.427	0.353	0.382	1e-19
P27785	317	RNA polymerase sigma fact	N/A	no	0.375	0.391	0.381	2e-19
Q03066	416	RNA polymerase sigma-C fa	no	no	0.306	0.242	0.390	7e-19

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

 Score =  422 bits (1086), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 220/341 (64%), Positives = 263/341 (77%), Gaps = 29/341 (8%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGL+ GKRLLSSSFY+SD++EKF  +ND  S+   + STK+ + AKK+SNY+PS
Sbjct: 1   MATAAVIGLNTGKRLLSSSFYHSDVTEKFLSVNDHCSSQYHIASTKSGITAKKASNYSPS 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSE--------LDYSVEALLL 113
           FPSSNR TQ  KALKE VD   AST +PW   PN  ++E  E        + +SVEA+LL
Sbjct: 61  FPSSNRHTQSAKALKESVDV--ASTEKPWL--PNGTDKELEEECYDDDDLISHSVEAILL 116

Query: 114 LQKSMLEKQWNLSFERTVLTDSPSKKT--HKKVPV-TCSGVSARQRRLNSKKKI-LSQNK 169
           LQKSMLEK WNLSFE+ V ++ P K T   KK+PV TCSG+SARQRR+ +KKK  ++  K
Sbjct: 117 LQKSMLEKSWNLSFEKAVSSEYPGKGTIRKKKIPVITCSGISARQRRIGAKKKTNMTHVK 176

Query: 170 SILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL 229
           ++   +  KQ+R             GYVKGV+SE++L+H EVVRLSKKIK+GL LDDHK 
Sbjct: 177 AVSDVSSGKQVR-------------GYVKGVISEDVLSHVEVVRLSKKIKSGLRLDDHKS 223

Query: 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGA 289
           RLK+RLGCEPS EQLA SL+ISR ELQ+ LMEC LAREKL MSNVRLVMSIAQRYDN+GA
Sbjct: 224 RLKDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGA 283

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQ +S
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVS 324

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)

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

 Score =  116 bits (291), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 57/146 (39%), Positives = 95/146 (65%), Gaps = 4/146 (2%)

Query: 185 SPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQL 244
           SP+L+    + Y++ +    LLT  E +   ++++  + L D +  L++RLG EPS E+ 
Sbjct: 9   SPDLV----RAYLQEIGRVRLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEW 64

Query: 245 AASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLR 304
           AA++ ++  +L   + +   A+ K++ +N+RLV+SIA++Y     +  DL+Q G +GL R
Sbjct: 65  AAAVDLNLEDLDRQIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLER 124

Query: 305 GIEKFDSSKGFKISTYVYWWIRQSIS 330
           G+EKFD SKG+K STY YWWIRQ+I+
Sbjct: 125 GVEKFDPSKGYKFSTYAYWWIRQAIT 150

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

 Score =  111 bits (277), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 55/137 (40%), Positives = 88/137 (64%)

Query: 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISR 252
           L+ ++ G  +++LLT  E   L   I+  L L+  K +L+ + GCEP++ + A ++ IS 
Sbjct: 235 LQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISS 294

Query: 253 PELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSS 312
           P L+S +     +REKL+ +N+RLV+ IA++Y N G +  DL+Q G +GL++ +EKF   
Sbjct: 295 PVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQ 354

Query: 313 KGFKISTYVYWWIRQSI 329
            G + +TY YWWIRQSI
Sbjct: 355 SGCRFATYAYWWIRQSI 371

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  110 bits (276), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 57/150 (38%), Positives = 93/150 (62%), Gaps = 1/150 (0%)

Query: 181 RSMISPELIQNRLKGYVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEP 239
           + +++ E+  N    Y++   S  +LLT  E   LS  I+  L L+  +  L ER G +P
Sbjct: 247 KRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSAGIQDLLKLERLQTELTERSGRQP 306

Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
           +  Q A++  + +  L+  +   +L ++K++ SN+RLV+SIA+ Y   G ++ DLVQ G 
Sbjct: 307 TFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGC 366

Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
            GL+RG EKFD++KGFK STY +WWI+Q++
Sbjct: 367 RGLVRGAEKFDATKGFKFSTYAHWWIKQAV 396

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  103 bits (257), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 54/141 (38%), Positives = 87/141 (61%)

Query: 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLR 249
           ++ ++ Y++ +    LL   E + L++KI   L L+  + RL E+L  +P   + A +++
Sbjct: 79  EDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRERLSEKLERDPRDSEWAEAVQ 138

Query: 250 ISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKF 309
           +  P  +  L     A++K+V SN+RLV+SIA++Y N G    DL+Q G +GL+R  EKF
Sbjct: 139 LPLPAFRYRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKF 198

Query: 310 DSSKGFKISTYVYWWIRQSIS 330
           D  KG+K STY  WWIRQ+I+
Sbjct: 199 DHEKGYKFSTYATWWIRQAIT 219

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

 Score =  102 bits (255), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 47/135 (34%), Positives = 85/135 (62%)

Query: 196 YVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPEL 255
           Y+  +    LL+H + +  +++++  + +   K  L E+L  EP++++ A  +++    L
Sbjct: 28  YLHKIGRVPLLSHEQEIFFAQQVQQMMVMFTAKEELAEKLQREPTLQEWADKMQLKEDVL 87

Query: 256 QSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGF 315
              L +  +A++K++ +N+RLV+SIA++Y     +  DL+Q G +GL RG+EKFD + G+
Sbjct: 88  LQQLSQGQIAKQKMIQANLRLVVSIAKKYQKRNLEFLDLIQEGALGLERGVEKFDPTLGY 147

Query: 316 KISTYVYWWIRQSIS 330
           K STY YWWIRQ I+
Sbjct: 148 KFSTYAYWWIRQGIT 162

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

 Score =  102 bits (254), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 53/139 (38%), Positives = 88/139 (63%), Gaps = 1/139 (0%)

Query: 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGC-EPSMEQLAASLRIS 251
           ++ Y++ +    LLTH E V L K+++  + L + +  L+   G  +PS  + AA+  +S
Sbjct: 12  VRTYLREIGRVPLLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWAAAAGLS 71

Query: 252 RPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDS 311
             EL+        A+ K++ +N+RLV+S+A++Y     D+ DL+Q G IG+ RG+EKFD 
Sbjct: 72  IEELRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQRGVEKFDP 131

Query: 312 SKGFKISTYVYWWIRQSIS 330
           +KG++ STY YWWIRQ+I+
Sbjct: 132 TKGYRFSTYAYWWIRQAIT 150

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

 Score = 97.4 bits (241), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 54/141 (38%), Positives = 86/141 (60%)

Query: 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLR 249
           ++ ++ Y++ +    LL   E + L+++I   L+L+  +  L E+L   PS  + AA++ 
Sbjct: 88  EDSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAVD 147

Query: 250 ISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKF 309
               E +  L     A++K+V SN+RLV+SIA++Y N G    DL+Q G +GL+R  EKF
Sbjct: 148 SPLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKF 207

Query: 310 DSSKGFKISTYVYWWIRQSIS 330
           D  KG+K STY  WWIRQ+I+
Sbjct: 208 DHEKGYKFSTYATWWIRQAIT 228

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|P27785|RPOD_STRAU RNA polymerase sigma factor RpoD OS=Streptomyces aureofaciens GN=rpoD PE=3 SV=1

 Score = 97.1 bits (240), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 53/139 (38%), Positives = 86/139 (61%), Gaps = 15/139 (10%)

Query: 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSME-QLAASLRIS 251
            + Y++ +    LLT AE V L+++++ GL  +       E+LG    ++ QLA      
Sbjct: 21  FRQYLREIGRIPLLTAAEEVDLARRVEAGLFAE-------EKLGGAADLDSQLAV----- 68

Query: 252 RPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDS 311
             +L  +++   +A+ +L+ SN+RLV+S+A+RY   G  M DLVQ G +GL+R +EKFD 
Sbjct: 69  --DLDRLVVMGRMAKRRLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDY 126

Query: 312 SKGFKISTYVYWWIRQSIS 330
           ++G+K STY  WWIRQ++S
Sbjct: 127 ARGYKFSTYATWWIRQAMS 145

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.

Streptomyces aureofaciens (taxid: 1894)

>sp|Q03066|RPSC_NOSS1 RNA polymerase sigma-C factor OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=sigC PE=3 SV=2

 Score = 95.1 bits (235), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 48/123 (39%), Positives = 72/123 (58%), Gaps = 22/123 (17%)

Query: 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECSL----------------------ARE 267
           RL   LG  PS+E+ AA+  I+  +L+ IL E                         ++E
Sbjct: 120 RLASELGHRPSLERWAATAGINLCDLKPILSEGKRRWAEIAKMTVEELEKMQSQGLQSKE 179

Query: 268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ 327
            ++ +N+RLV+S+A++Y N G ++ DLVQ G +GL R +EKFD +KG++ STY YWWIRQ
Sbjct: 180 HMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQ 239

Query: 328 SIS 330
            I+
Sbjct: 240 GIT 242

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)

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	330
255566078	508	RNA polymerase sigma factor rpoD, putati	0.996	0.647	0.763	1e-140
224146103	509	predicted protein [Populus trichocarpa]	1.0	0.648	0.734	1e-135
449468291	508	PREDICTED: RNA polymerase sigma factor s	0.996	0.647	0.716	1e-130
356543070	503	PREDICTED: RNA polymerase sigma factor r	0.975	0.640	0.704	1e-128
356531599	503	PREDICTED: RNA polymerase sigma factor r	0.975	0.640	0.701	1e-128
224124068	499	predicted protein [Populus trichocarpa]	0.969	0.641	0.697	1e-118
2565297	502	RNA polymerase sigma subunit 1 [Arabidop	0.945	0.621	0.648	1e-116
15217767	502	sigma factor A [Arabidopsis thaliana] gi	0.945	0.621	0.645	1e-116
334183639	498	sigma factor A [Arabidopsis thaliana] gi	0.945	0.626	0.645	1e-115
11762220	502	At1g64860 [Arabidopsis thaliana]	0.945	0.621	0.642	1e-115

>gi|255566078|ref|XP_002524027.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis] gi|223536754|gb|EEF38395.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]

 Score =  504 bits (1298), Expect = e-140,   Method: Compositional matrix adjust.
 Identities = 252/330 (76%), Positives = 285/330 (86%), Gaps = 1/330 (0%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGLSAGKRLLSS+FYYSD++EK S  N+ G  + Q+ STK ++ AKKSSNY PS
Sbjct: 1   MATAAVIGLSAGKRLLSSTFYYSDLTEKLSSANEHGLTHYQITSTKTLIVAKKSSNYGPS 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFA-STAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLE 120
           FPSSNR TQ IKALKEHVDT  A STA    +  N +EEESS+LDYSVEALLLLQKSMLE
Sbjct: 61  FPSSNRNTQSIKALKEHVDTASAPSTAATQFKTFNDMEEESSDLDYSVEALLLLQKSMLE 120

Query: 121 KQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQL 180
           KQWNLSFERT  +DSPS+K+ KK+PVTCSGVSARQRR+N ++K LSQ+K  +Q N  KQL
Sbjct: 121 KQWNLSFERTDSSDSPSRKSQKKIPVTCSGVSARQRRINIRRKNLSQSKFTVQANVFKQL 180

Query: 181 RSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPS 240
           +S +SPEL+QNRLKGYVKGVVSEELL+HAEVVRLS+ IK GLSL+DHK RLKERLGC+PS
Sbjct: 181 KSAVSPELLQNRLKGYVKGVVSEELLSHAEVVRLSRIIKAGLSLEDHKSRLKERLGCDPS 240

Query: 241 MEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLI 300
            EQ+A SL+ISR ELQS  + CSLAREKL MSNVRLVMSIAQRYDNMGA+MADLVQGGLI
Sbjct: 241 DEQVATSLKISRAELQSKSIACSLAREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLI 300

Query: 301 GLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
           GLLRGIEKFDSSKGF+ISTYVYWWIRQ +S
Sbjct: 301 GLLRGIEKFDSSKGFRISTYVYWWIRQGVS 330

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224146103|ref|XP_002325882.1| predicted protein [Populus trichocarpa] gi|222862757|gb|EEF00264.1| predicted protein [Populus trichocarpa]

 Score =  487 bits (1254), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 243/331 (73%), Positives = 279/331 (84%), Gaps = 1/331 (0%)

Query: 1   MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNP 60
           MMATAAVIGLS+GKRLLSSSFYYSD++EK S +ND G       +TKNV+ AKKSSNY P
Sbjct: 1   MMATAAVIGLSSGKRLLSSSFYYSDLTEKLSNVNDHGITYYPTATTKNVIVAKKSSNYGP 60

Query: 61  SFPSSNRQTQPIKALKEHVDTNFAST-AEPWAEPPNSIEEESSELDYSVEALLLLQKSML 119
           SFPSSNR +  IKALKEHVDT  AS+    W +  +  EEESS LDYSVEALLLLQKSML
Sbjct: 61  SFPSSNRNSHSIKALKEHVDTASASSNVATWFKTFDDFEEESSALDYSVEALLLLQKSML 120

Query: 120 EKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQ 179
           EKQWNLSFERT  +DS SKK +KK+PVTCSGVSARQRR+N+++K  +Q+K + Q +  K 
Sbjct: 121 EKQWNLSFERTNSSDSTSKKNNKKIPVTCSGVSARQRRVNNRRKNQNQSKFMSQSSDFKF 180

Query: 180 LRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEP 239
           LRS+ SP+L+QNRLKGYVKGVVS+E+L H EVVRLS+ I+ GLS +DHK RLKERLGCEP
Sbjct: 181 LRSVSSPDLLQNRLKGYVKGVVSDEVLPHTEVVRLSRIIRAGLSFEDHKSRLKERLGCEP 240

Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
           S EQ+A SLRISR +LQS L++CSLAREKL MSNVRLVMSIAQ+YDNMGA+MADLVQGGL
Sbjct: 241 SDEQIADSLRISRADLQSKLIQCSLAREKLAMSNVRLVMSIAQKYDNMGAEMADLVQGGL 300

Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
           IGLLRGIEKFDSSKGFKISTYVYWWIRQ +S
Sbjct: 301 IGLLRGIEKFDSSKGFKISTYVYWWIRQGVS 331

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449468291|ref|XP_004151855.1| PREDICTED: RNA polymerase sigma factor sigA-like [Cucumis sativus] gi|449514942|ref|XP_004164521.1| PREDICTED: RNA polymerase sigma factor sigA-like [Cucumis sativus]

 Score =  469 bits (1208), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 237/331 (71%), Positives = 278/331 (83%), Gaps = 2/331 (0%)

Query: 1   MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNP 60
           MMATAA+IGL A KRLL+SS YYSD +EK  Y ND     +QV S+K+VV AK S+N++P
Sbjct: 1   MMATAAIIGLGAAKRLLNSSSYYSDFTEKILYANDYRLGQTQVSSSKSVVIAKSSANFSP 60

Query: 61  SFPSSNRQTQP-IKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSML 119
            +PSSNR +Q  IKA+KEHV+T  +  AEPW     S E+E +EL Y+VEALLLLQKSML
Sbjct: 61  RYPSSNRHSQQCIKAVKEHVETPSSPIAEPWHNT-TSWEDEETELKYTVEALLLLQKSML 119

Query: 120 EKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQ 179
           EKQW+LSFE+TV TD+P +KT KKVPVTCSGVSARQRR++SK+KI S++  + Q   SKQ
Sbjct: 120 EKQWSLSFEQTVSTDTPKEKTLKKVPVTCSGVSARQRRMSSKRKIQSKHVFMAQPKISKQ 179

Query: 180 LRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEP 239
           LR  ISPEL+QNRLKGYVKG++SEELL+HAEVVRLSKKIK GL+L++ K RLK+RLGCEP
Sbjct: 180 LRPTISPELLQNRLKGYVKGLLSEELLSHAEVVRLSKKIKVGLTLEERKTRLKQRLGCEP 239

Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
           S +QLA SL+ISR EL+S +ME SLAREKL MSNVRLVMSIAQRYDNMGA+MADLVQGGL
Sbjct: 240 SEDQLAISLKISRAELRSRMMESSLAREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGL 299

Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
           IGLLRGIEKFDSSKGFKISTYVYWWIRQ +S
Sbjct: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQGVS 330

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356543070|ref|XP_003539986.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max]

 Score =  465 bits (1197), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 234/332 (70%), Positives = 281/332 (84%), Gaps = 10/332 (3%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGLS GKRLLSSS++YSDI EK SY +D GS + Q+  TK+++ AKKSSNY P+
Sbjct: 1   MATAAVIGLSGGKRLLSSSYHYSDIIEKLSYGSDFGSTHYQIVPTKSLIVAKKSSNYTPT 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNS--IEEESSELDYSVEALLLLQKSML 119
           FP+SN+Q Q IKALKEHVD +  + A+PW +  NS  +E ESSE+ YSVEALLLLQKSML
Sbjct: 61  FPASNQQNQSIKALKEHVD-DAPTIADPWFQSYNSNDLEVESSEMGYSVEALLLLQKSML 119

Query: 120 EKQWNLSFERTVLTDSPSK-KTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSK 178
           EKQWNLSFER VLT++ SK K  +KV VTCSGVSARQRR+N+K+K      + ++  G+ 
Sbjct: 120 EKQWNLSFEREVLTENSSKGKKCRKVAVTCSGVSARQRRMNTKRK------TAIKTCGAM 173

Query: 179 QLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCE 238
           QL+S ISPEL+Q+RLKGYVKG+VSEELL+HAEVV LS+KIK GLSL++HK RLKE+LGCE
Sbjct: 174 QLKSKISPELLQHRLKGYVKGLVSEELLSHAEVVNLSEKIKVGLSLEEHKSRLKEKLGCE 233

Query: 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGG 298
           PS +Q+A SL+ISR EL++ ++ECSLAREKL MSNVRLVMSIAQ+YDN+GA+M DLVQGG
Sbjct: 234 PSDDQMATSLKISRTELRARMIECSLAREKLAMSNVRLVMSIAQKYDNLGAEMGDLVQGG 293

Query: 299 LIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
           LIGLLRGIEKFDSSKGFKISTYVYWWIRQ +S
Sbjct: 294 LIGLLRGIEKFDSSKGFKISTYVYWWIRQGVS 325

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356531599|ref|XP_003534364.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max]

 Score =  464 bits (1195), Expect = e-128,   Method: Compositional matrix adjust.
 Identities = 233/332 (70%), Positives = 280/332 (84%), Gaps = 10/332 (3%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGLS GKRLLSSS++YSD+ EK SY +D GS + Q+  TK+++AAKKSSNY P+
Sbjct: 1   MATAAVIGLSGGKRLLSSSYHYSDVIEKLSYGSDFGSTHYQIVPTKSLIAAKKSSNYTPT 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNS--IEEESSELDYSVEALLLLQKSML 119
           FP+SN+Q Q IKALKEHVD +  + A+ W +  NS  +E ESSE+ YSVEALLLLQKSML
Sbjct: 61  FPASNQQNQSIKALKEHVD-DAPTIADSWFQSCNSNDLEVESSEMGYSVEALLLLQKSML 119

Query: 120 EKQWNLSFERTVLTDSPSK-KTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSK 178
           EKQWNLSFER VLT+  SK K  KKV VTCSGVSARQRR+N+K+K      + ++  G+ 
Sbjct: 120 EKQWNLSFEREVLTEHSSKGKKCKKVAVTCSGVSARQRRMNTKRK------TAIKTCGAM 173

Query: 179 QLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCE 238
           QL+S ISPEL+Q+RLKGYVKG+VSEELL+HAEVV LS++IK GLSL++HK RLKERLGCE
Sbjct: 174 QLKSKISPELLQHRLKGYVKGIVSEELLSHAEVVNLSERIKVGLSLEEHKSRLKERLGCE 233

Query: 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGG 298
           PS +Q+A SL+ISR EL++ ++EC+LAREKL MSNVRLVMSIAQ+YDN+GA+M DLVQGG
Sbjct: 234 PSDDQMAISLKISRTELRARMIECTLAREKLAMSNVRLVMSIAQKYDNLGAEMGDLVQGG 293

Query: 299 LIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
           LIGLLRGIEKFDSSKGFKISTYVYWWIRQ +S
Sbjct: 294 LIGLLRGIEKFDSSKGFKISTYVYWWIRQGVS 325

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224124068|ref|XP_002319237.1| predicted protein [Populus trichocarpa] gi|222857613|gb|EEE95160.1| predicted protein [Populus trichocarpa]

 Score =  429 bits (1103), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 231/331 (69%), Positives = 265/331 (80%), Gaps = 11/331 (3%)

Query: 1   MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNP 60
           MMATA+ IGL+ GKRLLSSSFY+SD++EK S +ND G A+ Q+ +TK+V+ AKKSS Y P
Sbjct: 1   MMATASFIGLTTGKRLLSSSFYFSDLTEKLSNVNDHGVAHYQITTTKSVIVAKKSSKYGP 60

Query: 61  SFPSSNRQTQPIKALKEHVDTNFAS-TAEPWAEPPNSIEEESSELDYSVEALLLLQKSML 119
           SFPSS R     KALKE +DT  AS T   W +  +  EEESS LDYSVEAL+LLQKSML
Sbjct: 61  SFPSSYRNPHSNKALKELIDTASASSTVATWFKTLDDFEEESSVLDYSVEALILLQKSML 120

Query: 120 EKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQ 179
           EKQWNLSFE    +DS  KK++KK+PVTCSGVSARQRRLN+K+K          QN SK 
Sbjct: 121 EKQWNLSFESINSSDSKIKKSNKKIPVTCSGVSARQRRLNNKRK---------NQNQSKF 171

Query: 180 LRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEP 239
           + S ISP L+ NRLKGYVKGVVS+E+L H EVVRLS+ I+ GLSL+DHK  LKERLGCEP
Sbjct: 172 M-SDISPGLLLNRLKGYVKGVVSDEVLPHTEVVRLSRIIRAGLSLEDHKSSLKERLGCEP 230

Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGL 299
           S EQLA SLRISR +LQS L++CSLAREKL MSNVRLVMSIAQ+ DNMGA+MADLVQ GL
Sbjct: 231 SDEQLADSLRISRADLQSQLIQCSLAREKLAMSNVRLVMSIAQKNDNMGAEMADLVQAGL 290

Query: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
           IGLLRGIEKFDSSKGFKISTYVYWWIRQ +S
Sbjct: 291 IGLLRGIEKFDSSKGFKISTYVYWWIRQGVS 321

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2565297|gb|AAB81958.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana]

 Score =  424 bits (1090), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 221/341 (64%), Positives = 263/341 (77%), Gaps = 29/341 (8%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGL+ GKRLLSSSFY+SD++EKF  +ND  S+   + STK+ + AKK+SNY PS
Sbjct: 1   MATAAVIGLNTGKRLLSSSFYHSDVTEKFLSVNDHCSSQYHIASTKSGITAKKASNYRPS 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSE--------LDYSVEALLL 113
           FPSSNR TQ  KALKE VD   AST +PW   PN  ++E  E        + +SVEA+LL
Sbjct: 61  FPSSNRHTQSAKALKESVDV--ASTEKPWL--PNGTDKELEEECYDDDDLISHSVEAILL 116

Query: 114 LQKSMLEKQWNLSFERTVLTDSPSKKT--HKKVPV-TCSGVSARQRRLNSKKKI-LSQNK 169
           LQKSMLEK WNLSFE+ V ++ P K T   KK+PV TCSG+SARQRR+ +KKK  ++  K
Sbjct: 117 LQKSMLEKSWNLSFEKAVSSEYPGKGTIRKKKIPVITCSGISARQRRIGAKKKTNMTHVK 176

Query: 170 SILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL 229
           ++   +  KQ+R             GYVKGV+SE++L+HAEVVRLSKKIK+GL LDDHK 
Sbjct: 177 AVSDVSSGKQVR-------------GYVKGVISEDVLSHAEVVRLSKKIKSGLRLDDHKS 223

Query: 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGA 289
           RLK+RLGCEPS EQLA SL+ISR ELQ+ LMEC LAREKL MSNVRLVMSIAQRYDN+GA
Sbjct: 224 RLKDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGA 283

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQ +S
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVS 324

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15217767|ref|NP_176666.1| sigma factor A [Arabidopsis thaliana] gi|75098242|sp|O24629.1|SIGA_ARATH RecName: Full=RNA polymerase sigma factor sigA; Short=Sigma factor A; Short=Sigma-A; 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 sigB; Short=Sigma factor B; Short=Sigma-B; Flags: Precursor gi|5042421|gb|AAD38260.1|AC006193_16 RNA polymerase sigma subunit 1 [Arabidopsis thaliana] gi|2353171|gb|AAB69384.1| sigma factor 1 [Arabidopsis thaliana] gi|2443408|dbj|BAA22421.1| SigA [Arabidopsis thaliana] gi|2558514|emb|CAA74640.1| plastid RNA polymerase sigma factor [Arabidopsis thaliana] gi|5478439|dbj|BAA82448.1| sigma factor SigA [Arabidopsis thaliana] gi|17064900|gb|AAL32604.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana] gi|20259916|gb|AAM13305.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana] gi|222423019|dbj|BAH19492.1| AT1G64860 [Arabidopsis thaliana] gi|332196177|gb|AEE34298.1| sigma factor A [Arabidopsis thaliana]

 Score =  422 bits (1086), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 220/341 (64%), Positives = 263/341 (77%), Gaps = 29/341 (8%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGL+ GKRLLSSSFY+SD++EKF  +ND  S+   + STK+ + AKK+SNY+PS
Sbjct: 1   MATAAVIGLNTGKRLLSSSFYHSDVTEKFLSVNDHCSSQYHIASTKSGITAKKASNYSPS 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSE--------LDYSVEALLL 113
           FPSSNR TQ  KALKE VD   AST +PW   PN  ++E  E        + +SVEA+LL
Sbjct: 61  FPSSNRHTQSAKALKESVDV--ASTEKPWL--PNGTDKELEEECYDDDDLISHSVEAILL 116

Query: 114 LQKSMLEKQWNLSFERTVLTDSPSKKT--HKKVPV-TCSGVSARQRRLNSKKKI-LSQNK 169
           LQKSMLEK WNLSFE+ V ++ P K T   KK+PV TCSG+SARQRR+ +KKK  ++  K
Sbjct: 117 LQKSMLEKSWNLSFEKAVSSEYPGKGTIRKKKIPVITCSGISARQRRIGAKKKTNMTHVK 176

Query: 170 SILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL 229
           ++   +  KQ+R             GYVKGV+SE++L+H EVVRLSKKIK+GL LDDHK 
Sbjct: 177 AVSDVSSGKQVR-------------GYVKGVISEDVLSHVEVVRLSKKIKSGLRLDDHKS 223

Query: 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGA 289
           RLK+RLGCEPS EQLA SL+ISR ELQ+ LMEC LAREKL MSNVRLVMSIAQRYDN+GA
Sbjct: 224 RLKDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGA 283

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQ +S
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVS 324

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|334183639|ref|NP_001185314.1| sigma factor A [Arabidopsis thaliana] gi|332196178|gb|AEE34299.1| sigma factor A [Arabidopsis thaliana]

 Score =  422 bits (1085), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 220/341 (64%), Positives = 263/341 (77%), Gaps = 29/341 (8%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGL+ GKRLLSSSFY+SD++EKF  +ND  S+   + STK+ + AKK+SNY+PS
Sbjct: 1   MATAAVIGLNTGKRLLSSSFYHSDVTEKFLSVNDHCSSQYHIASTKSGITAKKASNYSPS 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSE--------LDYSVEALLL 113
           FPSSNR TQ  KALKE VD   AST +PW   PN  ++E  E        + +SVEA+LL
Sbjct: 61  FPSSNRHTQSAKALKESVD--VASTEKPWL--PNGTDKELEEECYDDDDLISHSVEAILL 116

Query: 114 LQKSMLEKQWNLSFERTVLTDSPSKKT--HKKVPV-TCSGVSARQRRLNSKKKI-LSQNK 169
           LQKSMLEK WNLSFE+ V ++ P K T   KK+PV TCSG+SARQRR+ +KKK  ++  K
Sbjct: 117 LQKSMLEKSWNLSFEKAVSSEYPGKGTIRKKKIPVITCSGISARQRRIGAKKKTNMTHVK 176

Query: 170 SILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL 229
           ++   +  KQ+R             GYVKGV+SE++L+H EVVRLSKKIK+GL LDDHK 
Sbjct: 177 AVSDVSSGKQVR-------------GYVKGVISEDVLSHVEVVRLSKKIKSGLRLDDHKS 223

Query: 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGA 289
           RLK+RLGCEPS EQLA SL+ISR ELQ+ LMEC LAREKL MSNVRLVMSIAQRYDN+GA
Sbjct: 224 RLKDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGA 283

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQ +S
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVS 324

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|11762220|gb|AAG40388.1|AF325036_1 At1g64860 [Arabidopsis thaliana]

 Score =  420 bits (1080), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 219/341 (64%), Positives = 263/341 (77%), Gaps = 29/341 (8%)

Query: 2   MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS 61
           MATAAVIGL+ GKRLLSSSFY+SD++EKF  +ND  S+   + STK+ + AKK+SNY+PS
Sbjct: 1   MATAAVIGLNTGKRLLSSSFYHSDVTEKFLSVNDHCSSQYHIASTKSGITAKKASNYSPS 60

Query: 62  FPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSE--------LDYSVEALLL 113
           FPSSNR TQ  KALKE VD   AST +PW   PN  ++E  E        + +SVEA+LL
Sbjct: 61  FPSSNRHTQSAKALKESVDV--ASTEKPWL--PNGTDKELEEECYDDDDLISHSVEAILL 116

Query: 114 LQKSMLEKQWNLSFERTVLTDSPSKKT--HKKVPV-TCSGVSARQRRLNSKKKI-LSQNK 169
           LQKSMLEK WNLSFE+ V ++ P K T   KK+PV TCSG+SARQRR+ +KKK  ++  K
Sbjct: 117 LQKSMLEKSWNLSFEKAVSSEYPGKGTIRKKKIPVITCSGISARQRRIGAKKKTNMTHVK 176

Query: 170 SILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL 229
           ++   +  KQ+R             GYVKGV+SE++L+H EVVRLSKKIK+GL LDDHK 
Sbjct: 177 AVSDVSSGKQVR-------------GYVKGVISEDVLSHVEVVRLSKKIKSGLRLDDHKS 223

Query: 230 RLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGA 289
           RLK+RLGCEPS EQLA SL+ISR ELQ+ LMEC LAREKL MSNVRLVMSIAQRY+N+GA
Sbjct: 224 RLKDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYNNLGA 283

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQ +S
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVS 324

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	330
TAIR|locus:2010871	502	SIGA "AT1G64860" [Arabidopsis	0.951	0.625	0.610	4.7e-96
UNIPROTKB|O48655	519	rsigA "Plastid RNA polymerase	0.972	0.618	0.454	4.2e-63
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.530	0.305	0.361	5.5e-24
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.660	0.381	0.309	3e-23
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.415	0.250	0.401	1.3e-22
UNIPROTKB|P0A602	528	rpoD "RNA polymerase sigma fac	0.390	0.244	0.391	1.2e-20
UNIPROTKB|Q59563	323	mysB "RNA polymerase sigma fac	0.369	0.377	0.422	2.7e-20
TAIR|locus:2173249	419	SIG4 "AT5G13730" [Arabidopsis	0.393	0.310	0.390	6.1e-16
TIGR_CMR|SO_3432	326	SO_3432 "RNA polymerase sigma	0.333	0.337	0.389	1.3e-15
TIGR_CMR|APH_0576	627	APH_0576 "RNA polymerase sigma	0.484	0.255	0.315	1.1e-14

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

 Score = 955 (341.2 bits), Expect = 4.7e-96, P = 4.7e-96
 Identities = 207/339 (61%), Positives = 246/339 (72%)

Query:     2 MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKXXXXXXX 61
             MATAAVIGL+ GKRLLSSSFY+SD++EKF  +ND  S+   + STK+ + AKK       
Sbjct:     1 MATAAVIGLNTGKRLLSSSFYHSDVTEKFLSVNDHCSSQYHIASTKSGITAKKASNYSPS 60

Query:    62 XXXXXRQTQPIKALKEHVDTNFASTAEPWA------EPPNXXXXXXXXLDYSVEALLLLQ 115
                  R TQ  KALKE VD   AST +PW       E           + +SVEA+LLLQ
Sbjct:    61 FPSSNRHTQSAKALKESVDV--ASTEKPWLPNGTDKELEEECYDDDDLISHSVEAILLLQ 118

Query:   116 KSMLEKQWNLSFERTVLTDSPSKKT--HKKVPV-TCSGVSARQRRLNSKKKI-LSQNKSI 171
             KSMLEK WNLSFE+ V ++ P K T   KK+PV TCSG+SARQRR+ +KKK  ++  K++
Sbjct:   119 KSMLEKSWNLSFEKAVSSEYPGKGTIRKKKIPVITCSGISARQRRIGAKKKTNMTHVKAV 178

Query:   172 LQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRL 231
                +  KQ+R             GYVKGV+SE++L+H EVVRLSKKIK+GL LDDHK RL
Sbjct:   179 SDVSSGKQVR-------------GYVKGVISEDVLSHVEVVRLSKKIKSGLRLDDHKSRL 225

Query:   232 KERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADM 291
             K+RLGCEPS EQLA SL+ISR ELQ+ LMEC LAREKL MSNVRLVMSIAQRYDN+GA+M
Sbjct:   226 KDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGAEM 285

Query:   292 ADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
             +DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQ +S
Sbjct:   286 SDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVS 324

GO:0003677 "DNA binding" evidence=ISS

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

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

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

GO:0009507 "chloroplast" evidence=IDA

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

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

GO:0005515 "protein binding" evidence=IPI

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

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

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

GO:0080005 "photosystem stoichiometry adjustment" evidence=IDA

GO:0006833 "water transport" evidence=RCA

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

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 644 (231.8 bits), Expect = 4.2e-63, P = 4.2e-63
 Identities = 159/350 (45%), Positives = 210/350 (60%)

Query:     1 MMATAAVIGLSAGKRLLSSSFYYSDIS-EKFSYI---NDLGSANSQVGSTKNVVAAKKXX 56
             M AT AVIGLSAG RLLS+SF  +D+  +K S        G      G   +  AA    
Sbjct:     1 MTATPAVIGLSAGNRLLSASFGPTDLMPDKVSLGVGGGGGGGGGGGGGDAMSFAAAPATP 60

Query:    57 XXXXXXXXXXR-----QTQPIKALKEHVDTNFASTAEPWAEPPNX-----XXXXXXXLDY 106
                       +     + Q ++AL+ H     A    P   PP              L+ 
Sbjct:    61 KLTAVAAHRLKLSPHGRAQVMRALRHHSSAAAALAPPPPPPPPPTPSPASRAAHAHDLES 120

Query:   107 SVEALLLLQKSMLEKQWNLSFE------RTVLTDSPSKKTHKKVPVTCSGVSARQRRLNS 160
             S+EA++LLQ+SMLEKQW L F+         L +     +   V V  S VSARQRR++ 
Sbjct:   121 SLEAIVLLQRSMLEKQWELPFDDDNHAMAIGLAEDDDDTSKATVVVARSSVSARQRRMSG 180

Query:   161 KKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKT 220
             +++   + K     NG+      +SPELIQ+R + Y++G VS+ELLTH +VV LS KIK 
Sbjct:   181 RRR--GRTK-----NGAAHFA--VSPELIQSRNRIYLRGTVSKELLTHKQVVHLSHKIKD 231

Query:   221 GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI 280
             G+ L   + +LKE+LG EPS +QLA SL+IS PEL+S + E  LARE L MSN+RLV+SI
Sbjct:   232 GIWLQQQRSKLKEKLGNEPSYKQLAHSLKISPPELRSRMHESFLAREMLTMSNLRLVISI 291

Query:   281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
             AQ+YDN+G ++ADL+QGGLIGLLRGIEKFD+S+GF+ISTYVYWWIRQ +S
Sbjct:   292 AQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTYVYWWIRQGVS 341

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

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

 Score = 282 (104.3 bits), Expect = 5.5e-24, P = 5.5e-24
 Identities = 64/177 (36%), Positives = 104/177 (58%)

Query:   154 RQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSE-ELLTHAEVV 212
             + RR    +K  S   S+   +  K+ R +++ E+  N    Y++   S  +LLT  E  
Sbjct:   221 KARRAKGLEKTASGIPSVKTGSSPKKKR-LVAQEVDHNDPLRYLRMTTSSSKLLTVREEH 279

Query:   213 RLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMS 272
              LS  I+  L L+  +  L ER G +P+  Q A++  + +  L+  +   +L ++K++ S
Sbjct:   280 ELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKS 339

Query:   273 NVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
             N+RLV+SIA+ Y   G ++ DLVQ G  GL+RG EKFD++KGFK STY +WWI+Q++
Sbjct:   340 NIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAV 396

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 = 258 (95.9 bits), Expect = 3.0e-23, Sum P(2) = 3.0e-23
 Identities = 70/226 (30%), Positives = 117/226 (51%)

Query:   110 ALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQ-- 167
             ALL  +  +L  Q   S   +V +   +++   K  V        +RR  SK++   +  
Sbjct:   174 ALLAEETDILATQLKASQLYSVDSSKSNEELQSKGQVFVRSTRLLERR--SKRRYAPRAS 231

Query:   168 --NKSILQQNGSKQLRSMISPELIQ--NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS 223
               + S    N  K+ +S     +++     K +++   + E LT  E   L  KI+  + 
Sbjct:   232 IADVSCSADNSKKKEKSKKYGRVLEPDEPFKLFLRDRETTEFLTAKEERHLFSKIQILMK 291

Query:   224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR 283
             +++   +L+ + G EP++ + A ++ +S  ELQS +      REK+  SN RLV+ +A++
Sbjct:   292 IEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRRCREKMARSNFRLVIHVARK 351

Query:   284 YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
             Y+  G D+ DLVQ G  GL++  EKF+ SKG +  TY YWWIRQSI
Sbjct:   352 YEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSI 397

GO:0009536 "plastid" evidence=RCA

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

 Score = 269 (99.8 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 55/137 (40%), Positives = 88/137 (64%)

Query:   193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISR 252
             L+ ++ G  +++LLT  E   L   I+  L L+  K +L+ + GCEP++ + A ++ IS 
Sbjct:   235 LQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISS 294

Query:   253 PELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSS 312
             P L+S +     +REKL+ +N+RLV+ IA++Y N G +  DL+Q G +GL++ +EKF   
Sbjct:   295 PVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQ 354

Query:   313 KGFKISTYVYWWIRQSI 329
              G + +TY YWWIRQSI
Sbjct:   355 SGCRFATYAYWWIRQSI 371

GO:0003677 "DNA binding" evidence=ISS

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009507 "chloroplast" evidence=IDA

GO:0009536 "plastid" evidence=IDA

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

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

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

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

GO:0090351 "seedling development" evidence=IMP

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

GO:0005515 "protein binding" evidence=IPI

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

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

GO:0030154 "cell differentiation" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

UNIPROTKB|P0A602 rpoD "RNA polymerase sigma factor RpoD" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 229 (85.7 bits), Expect = 1.2e-20, Sum P(2) = 1.2e-20
 Identities = 54/138 (39%), Positives = 81/138 (58%)

Query:   193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISR 252
             ++ Y+K +    LL   E V L+K+I+ GL        L ER G     E+L A+    R
Sbjct:   228 VRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSER-G-----EKLPAA---QR 278

Query:   253 PELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSS 312
              ++  I  +   A+  L+ +N+RLV+S+A+RY   G    DL+Q G +GL+R +EKFD +
Sbjct:   279 RDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYT 338

Query:   313 KGFKISTYVYWWIRQSIS 330
             KG+K STY  WWIRQ+I+
Sbjct:   339 KGYKFSTYATWWIRQAIT 356

GO:0003677 "DNA binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005618 "cell wall" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009405 "pathogenesis" evidence=IMP

GO:0009415 "response to water stimulus" evidence=IEP

GO:0016987 "sigma factor activity" evidence=IDA

GO:0040007 "growth" evidence=IMP

GO:0052572 "response to host immune response" evidence=IEP

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

 Score = 240 (89.5 bits), Expect = 2.7e-20, P = 2.7e-20
 Identities = 57/135 (42%), Positives = 81/135 (60%)

Query:   196 YVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPEL 255
             Y+ G+    LL  A  V L+K+I+ GL  + H L  ++RLG E     LAA +R      
Sbjct:    30 YLNGIGKTALLNAAGEVELAKRIEAGLYAE-HLLETRKRLG-ENRKRDLAAVVR------ 81

Query:   256 QSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGF 315
                  +   AR  L+ +N+RLV+S+A+RY   G  + DL+Q G +GL+R +EKFD +KGF
Sbjct:    82 -----DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGF 136

Query:   316 KISTYVYWWIRQSIS 330
             K STY  WWIRQ+I+
Sbjct:   137 KFSTYATWWIRQAIT 151

GO:0001666 "response to hypoxia" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009408 "response to heat" evidence=IEP

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

GO:0016987 "sigma factor activity" evidence=IGI

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

GO:0040007 "growth" evidence=IMP

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

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

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

TAIR|locus:2173249 SIG4 "AT5G13730" [Arabidopsis thaliana (taxid:3702)]

 Score = 216 (81.1 bits), Expect = 6.1e-16, P = 6.1e-16
 Identities = 52/133 (39%), Positives = 72/133 (54%)

Query:   197 VKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQ 256
             V G      L+  E V+L   +K G  L++    ++E    E     LA+     +    
Sbjct:   114 VVGASRSGFLSRLEEVQLCLYLKEGAKLENLGTSVEEN---EMVSVLLASGRGKKKRSAN 170

Query:   257 SILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFK 316
              IL     AREK+     RLV+SIA  Y   G ++ DL+Q G IGLLRG E+FD  +G+K
Sbjct:   171 EILCRRKEAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYK 230

Query:   317 ISTYVYWWIRQSI 329
             +STYVYWWI+Q+I
Sbjct:   231 LSTYVYWWIKQAI 243

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

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

GO:0016987 "sigma factor activity" evidence=ISS

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:0000023 "maltose metabolic process" evidence=RCA

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

GO:0016556 "mRNA modification" evidence=RCA

GO:0019252 "starch biosynthetic process" evidence=RCA

TIGR_CMR|SO_3432 SO_3432 "RNA polymerase sigma factor RpoS" [Shewanella oneidensis MR-1 (taxid:211586)]

 Score = 210 (79.0 bits), Expect = 1.3e-15, P = 1.3e-15
 Identities = 46/118 (38%), Positives = 73/118 (61%)

Query:   214 LSKKIKTGL--SLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM 271
             L ++++  L  +LD  +L L E +G  P +      +  SR  L+     C  +R +++ 
Sbjct:    39 LEQQVQDDLQKNLDATQLYLGE-IGFSPLLSA-EEEVYFSRKALKG----CEKSRNRMIE 92

Query:   272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
             SN+RLV+ IA+RY+N G  + DL++ G +GL+R +EKFD  +GF+ STY  WWIRQ+I
Sbjct:    93 SNLRLVVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 150

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

GO:0006950 "response to stress" evidence=ISS

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|APH_0576 APH_0576 "RNA polymerase sigma factor RpoD" [Anaplasma phagocytophilum HZ (taxid:212042)]

 Score = 210 (79.0 bits), Expect = 1.1e-14, P = 1.1e-14
 Identities = 54/171 (31%), Positives = 93/171 (54%)

Query:   162 KKILSQNKSILQQNGSKQLRSMISPELIQNR--LKGYVKGVVSEELLTHAEVVRLSKKIK 219
             ++I + +KSI  +  S  L S+     +  +  L  Y    ++E+  T  E   L  K  
Sbjct:   294 QQIYALSKSIAAEESS--LISLAESYGVDRKSFLDAYNNNTIAEQAKTSFEWQNLLDKEG 351

Query:   220 TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMS 279
               L    ++++L     C  S + L A  +I + E  +     + A+++++ +N+RLV+S
Sbjct:   352 DTLLEMQNRVKLLSGEDCPGSFKALVA--KIQKHERTA-----NRAKQEMIKANLRLVVS 404

Query:   280 IAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
             IA++Y N G    DLVQ G IGL++ ++KFD  +G+K STY  WW+RQ+I+
Sbjct:   405 IAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWWVRQAIT 455

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

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)
O24629	SIGA_ARATH	No assigned EC number	0.6451	0.9454	0.6215	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

Fail to connect to STRING server

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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	330
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	9e-42
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	2e-34
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	8e-31
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	1e-30
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	1e-27
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	4e-26
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	4e-25
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	1e-24
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	4e-24
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	6e-21
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	8e-21
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	2e-19
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	2e-18
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	2e-17
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	7e-16
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	5e-14
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	2e-13
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	3e-13
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	5e-13
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	6e-12
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	7e-12
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	9e-12
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	9e-12
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	5e-11
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	3e-09
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	8e-09
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	3e-08
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	2e-07
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	1e-05
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	2e-05
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	4e-05
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	1e-04
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	2e-04
PRK07122	264	PRK07122, PRK07122, RNA polymerase sigma factor Si	0.001
PRK08295	208	PRK08295, PRK08295, RNA polymerase factor sigma-70	0.004

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

 Score =  146 bits (371), Expect = 9e-42
 Identities = 55/125 (44%), Positives = 89/125 (71%)

Query: 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264
           LLT  E + L+++++  + L++ +  L+E+LG EPS E+ AA+  +S  EL+  L +   
Sbjct: 15  LLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQR 74

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+EK++ +N+RLV+S+A++Y N G ++ DL+Q G +GL R +EKFD ++G+K STY YWW
Sbjct: 75  AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWW 134

Query: 325 IRQSI 329
           IRQ I
Sbjct: 135 IRQGI 139

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|180963 PRK07405, PRK07405, RNA polymerase sigma factor SigD; Validated

 Score =  127 bits (322), Expect = 2e-34
 Identities = 54/126 (42%), Positives = 86/126 (68%)

Query: 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264
           LLTH E +   K+++  ++L + +  L E LG EP+  + A + ++S  EL+S + E   
Sbjct: 22  LLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEA 81

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+ K+V +N+RLV+S+A++Y     D+ DL+Q G IG+ RG+EKFD +KG++ STY YWW
Sbjct: 82  AKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWW 141

Query: 325 IRQSIS 330
           IRQ+I+
Sbjct: 142 IRQAIT 147

Length = 317

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

 Score =  119 bits (299), Expect = 8e-31
 Identities = 55/126 (43%), Positives = 81/126 (64%)

Query: 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264
           LL   E + L++KI   L L++ + + +  LG EPS ++ A  + +  P+ +  LM    
Sbjct: 77  LLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRR 136

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+EK+V SN+RLV+SIA++Y N G    DL+Q G +GL+R  EKFD  KG+K STY  WW
Sbjct: 137 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 196

Query: 325 IRQSIS 330
           IRQ+I+
Sbjct: 197 IRQAIT 202

Length = 373

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

 Score =  118 bits (296), Expect = 1e-30
 Identities = 52/126 (41%), Positives = 87/126 (69%)

Query: 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264
           LLTH + +   K+++  +SL + K  L ++LG EPS+ + A ++ +S  EL+  L +   
Sbjct: 32  LLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKR 91

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A++K++ +N+RLV++IA++Y     +  DL+Q G +GL RG+EKFD ++G+K STY YWW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWW 151

Query: 325 IRQSIS 330
           IRQ+I+
Sbjct: 152 IRQAIT 157

Length = 327

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

 Score =  109 bits (274), Expect = 1e-27
 Identities = 53/135 (39%), Positives = 82/135 (60%), Gaps = 13/135 (9%)

Query: 196 YVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPEL 255
           Y+ G+    LLT A+ V L+K+I+ GL   +H L  ++RL                + +L
Sbjct: 31  YLNGIGKTALLTAADEVELAKRIEAGL-YAEHLLETRKRLS------------EARKRDL 77

Query: 256 QSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGF 315
            +++ +   AR  L+ +N+RLV+S+A+RY   G  + DL+Q G +GL+R +EKFD +KGF
Sbjct: 78  AAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGF 137

Query: 316 KISTYVYWWIRQSIS 330
           K STY  WWIRQ+I+
Sbjct: 138 KFSTYATWWIRQAIT 152

Length = 324

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

 Score =  105 bits (265), Expect = 4e-26
 Identities = 56/164 (34%), Positives = 86/164 (52%), Gaps = 20/164 (12%)

Query: 186 PELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKE-RLGCEPSMEQL 244
             L  + ++ Y+  +    LL     V L+K+++    L +    L + +LG EPS    
Sbjct: 4   VRLSADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERAR 63

Query: 245 AASLRISR--PELQSILM-----ECSL------------AREKLVMSNVRLVMSIAQRYD 285
             + R+S     +++  +     E +L            A++KLV SN+RLV+SIA++Y 
Sbjct: 64  RPAGRLSFYIRAIEAAPLLTPEEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYT 123

Query: 286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
             G    DL+Q G IGL++ +EKFD  KGFK STY  WWIRQ+I
Sbjct: 124 GRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAI 167

Length = 342

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

 Score =  105 bits (263), Expect = 4e-25
 Identities = 50/125 (40%), Positives = 74/125 (59%), Gaps = 13/125 (10%)

Query: 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264
           LL   E V L+K+I+ GL  ++    L E    +P +          R +LQ I  +   
Sbjct: 225 LLNAEEEVELAKRIEAGLYAEE---LLAEGEKLDPEL----------RRDLQWIGRDGKR 271

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+  L+ +N+RLV+S+A+RY N G    DL+Q G +GL++ +EKFD +KG+K STY  WW
Sbjct: 272 AKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWW 331

Query: 325 IRQSI 329
           IRQ+I
Sbjct: 332 IRQAI 336

Length = 509

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

 Score = 99.7 bits (249), Expect = 1e-24
 Identities = 37/66 (56%), Positives = 51/66 (77%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+++LV SN+RLV+SIA++Y N G    DL+Q G IGL++ +EKFD  KG+K STY  WW
Sbjct: 1   AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWW 60

Query: 325 IRQSIS 330
           IRQ+I+
Sbjct: 61  IRQAIT 66

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|236067 PRK07598, PRK07598, RNA polymerase sigma factor SigC; Validated

 Score =  101 bits (253), Expect = 4e-24
 Identities = 53/148 (35%), Positives = 81/148 (54%), Gaps = 22/148 (14%)

Query: 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRIS----RP------- 253
           ++         + IK  L L + + RL   LG  PS+E+ A +  IS    +P       
Sbjct: 94  IVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADISLADLKPTLAEGKR 153

Query: 254 -----------ELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGL 302
                      EL+ I  +   A+E ++ +N+RLV+S+A++Y N G ++ DLVQ G +GL
Sbjct: 154 RWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGL 213

Query: 303 LRGIEKFDSSKGFKISTYVYWWIRQSIS 330
            R +EKFD +KG++ STY YWWIRQ I+
Sbjct: 214 ERAVEKFDPTKGYRFSTYAYWWIRQGIT 241

Length = 415

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

 Score = 91.2 bits (227), Expect = 6e-21
 Identities = 34/65 (52%), Positives = 50/65 (76%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           AR++++ SN+RLV+ IA+RY N G  + DL++ G +GL+R +EKFD  +GF+ STY  WW
Sbjct: 87  ARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 146

Query: 325 IRQSI 329
           IRQ+I
Sbjct: 147 IRQTI 151

Length = 325

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

 Score = 90.2 bits (224), Expect = 8e-21
 Identities = 43/119 (36%), Positives = 68/119 (57%), Gaps = 12/119 (10%)

Query: 214 LSKKIKTGLSLDDHKLRLKERLGCEPSM---EQLAASLRISRPELQSILMECSLAREKLV 270
             K        D  +L L+E +G +P +   E++A + R    + +        AR+ ++
Sbjct: 2   FKKAETETRVADVTQLYLRE-IGFKPLLTAEEEIAYARRALAGDFE--------ARKVMI 52

Query: 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
            SN+RLV+SIA+ Y N G  + DL++ G +GL+  +EKFD  +GF+ STY  WWIRQ+I
Sbjct: 53  ESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTI 111

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

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

 Score = 87.3 bits (217), Expect = 2e-19
 Identities = 35/66 (53%), Positives = 49/66 (74%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+++L  +N+RLV+SIA+RY   G    DL+Q G +GL++ +EKFD  KGFK STY  WW
Sbjct: 130 AKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWW 189

Query: 325 IRQSIS 330
           IRQ+I+
Sbjct: 190 IRQAIT 195

Length = 367

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

 Score = 78.0 bits (193), Expect = 2e-18
 Identities = 30/61 (49%), Positives = 40/61 (65%)

Query: 269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS 328
           LV   + LV S+A+RY   GAD  DLVQ G +GLLR +E+FD  +G   ST++Y  IR +
Sbjct: 1   LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNA 60

Query: 329 I 329
           I
Sbjct: 61  I 61

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

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

 Score = 82.1 bits (204), Expect = 2e-17
 Identities = 44/147 (29%), Positives = 79/147 (53%), Gaps = 30/147 (20%)

Query: 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIK-----TGLSLDDHKLRLKERLGCEPSMEQ 243
                K + + +V        E+ +L ++++     TGL++++    LKE         Q
Sbjct: 325 EIASGKPWSEFLVRVY----DEIKKLQQELEAIEEETGLTIEE----LKEIN------RQ 370

Query: 244 LAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLL 303
           ++     +R            A++++V +N+RLV+SIA++Y N G    DL+Q G IGL+
Sbjct: 371 ISKGEAKAR-----------RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 419

Query: 304 RGIEKFDSSKGFKISTYVYWWIRQSIS 330
           + ++KF+  +G+K STY  WWIRQ+I+
Sbjct: 420 KAVDKFEYRRGYKFSTYATWWIRQAIT 446

Length = 619

>gnl|CDD|236033 PRK07500, rpoH2, RNA polymerase factor sigma-32; Reviewed

 Score = 76.2 bits (188), Expect = 7e-16
 Identities = 25/65 (38%), Positives = 41/65 (63%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A  +++ +++RLV+S+A ++   G  M DL+Q G +GLL    +F+  +  + STY  WW
Sbjct: 41  ALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWW 100

Query: 325 IRQSI 329
           IR SI
Sbjct: 101 IRASI 105

Length = 289

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

 Score = 70.8 bits (174), Expect = 5e-14
 Identities = 25/65 (38%), Positives = 43/65 (66%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A +KLV+S++R V+ IA+ Y   G   ADL+Q G IGL++ +++FD  +G ++ ++   W
Sbjct: 36  AAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHW 95

Query: 325 IRQSI 329
           I+  I
Sbjct: 96  IKAEI 100

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

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

 Score = 68.0 bits (167), Expect = 2e-13
 Identities = 31/56 (55%), Positives = 39/56 (69%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
           AREKLV  N+ LV SIA+R+ N G    DLVQ G IGL++ I++FD S G K ST+
Sbjct: 4   AREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTF 59

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

>gnl|CDD|235838 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed

 Score = 68.7 bits (169), Expect = 3e-13
 Identities = 24/65 (36%), Positives = 42/65 (64%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A ++LV+S++R V+ IA+ Y   G   ADL+Q G IGL++ +++FD   G ++ ++   W
Sbjct: 49  AAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHW 108

Query: 325 IRQSI 329
           I+  I
Sbjct: 109 IKAEI 113

Length = 284

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

 Score = 67.7 bits (166), Expect = 5e-13
 Identities = 29/56 (51%), Positives = 41/56 (73%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
           AREKL+  N+RLV+S+ QR++N G ++ DL Q G IGL++ I+ FD S+  K STY
Sbjct: 38  AREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTY 93

Length = 258

>gnl|CDD|131931 TIGR02885, spore_sigF, RNA polymerase sigma-F factor

 Score = 64.0 bits (156), Expect = 6e-12
 Identities = 29/56 (51%), Positives = 38/56 (67%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
           AR+KL+  N+RLV SI +R+ N G +  DL Q G IGL++ I+KFD S   K STY
Sbjct: 12  ARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTY 67

Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 231

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

 Score = 63.8 bits (156), Expect = 7e-12
 Identities = 26/59 (44%), Positives = 39/59 (66%)

Query: 262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
              AR  L+  N+RLV  I ++++N G D+ DL+  G IGL++ IE FD+ KG K++TY
Sbjct: 47  DEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATY 105

Length = 233

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

 Score = 64.1 bits (156), Expect = 9e-12
 Identities = 29/56 (51%), Positives = 40/56 (71%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
           AREKL+  N+RLV+S+ QR++N G  + DL Q G IGL++ I+ FD S+  K STY
Sbjct: 35  AREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTY 90

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

>gnl|CDD|180137 PRK05572, PRK05572, sporulation sigma factor SigF; Validated

 Score = 63.8 bits (156), Expect = 9e-12
 Identities = 29/56 (51%), Positives = 37/56 (66%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
           AR+ LV  N+RLV S+ QR+ N G +  DL Q G IGLL+ ++KFD S   K STY
Sbjct: 33  ARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTY 88

Length = 252

>gnl|CDD|131893 TIGR02846, spore_sigmaK, RNA polymerase sigma-K factor

 Score = 61.3 bits (149), Expect = 5e-11
 Identities = 24/57 (42%), Positives = 37/57 (64%)

Query: 264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
            AR  L+  N+RLV  I +++ N G D+ DL+  G IGL++ I+ FD  KG +++TY
Sbjct: 48  EARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATY 104

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 [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 227

>gnl|CDD|224112 COG1191, FliA, DNA-directed RNA polymerase specialized sigma subunit [Transcription]

 Score = 56.2 bits (136), Expect = 3e-09
 Identities = 24/54 (44%), Positives = 39/54 (72%), Gaps = 1/54 (1%)

Query: 268 KLVMSNVRLVMSIAQRYDN-MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
           +L+   + LV SIA++++N   ++  DL+Q G+IGL++ IE++D SKG K STY
Sbjct: 27  RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTY 80

Length = 247

>gnl|CDD|234065 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70 family

 Score = 53.5 bits (129), Expect = 8e-09
 Identities = 22/65 (33%), Positives = 32/65 (49%), Gaps = 2/65 (3%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A E+L    + LV   A+RY    AD  DLVQ   + LL  +++FD    FK   +++  
Sbjct: 2   AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFK--AWLFRI 59

Query: 325 IRQSI 329
            R  I
Sbjct: 60  ARNLI 64

This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs. Length = 158

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

 Score = 53.3 bits (128), Expect = 3e-08
 Identities = 25/65 (38%), Positives = 40/65 (61%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+  L+  N+RLV+ IA++++N G  + DLV  G IGL++ +  F+ SK  K++TY    
Sbjct: 53  AKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRC 112

Query: 325 IRQSI 329
           I   I
Sbjct: 113 IENEI 117

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

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

 Score = 51.0 bits (123), Expect = 2e-07
 Identities = 21/56 (37%), Positives = 37/56 (66%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
            R  L+  N+RLV+ IA++++N G ++ DL+  G IGL++ +  F+  K  K++TY
Sbjct: 53  VRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATY 108

Length = 234

>gnl|CDD|180965 PRK07408, PRK07408, RNA polymerase sigma factor SigF; Reviewed

 Score = 45.7 bits (109), Expect = 1e-05
 Identities = 28/65 (43%), Positives = 39/65 (60%), Gaps = 1/65 (1%)

Query: 266 REKLVMSNVRLVMSIAQRYDNMGAD-MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           R +LV  N+ LV   A R+ N  ++   DLVQ G +GL+R IE+FD SKG   S++   +
Sbjct: 27  RNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPY 86

Query: 325 IRQSI 329
           IR  I
Sbjct: 87  IRGEI 91

Length = 256

>gnl|CDD|131987 TIGR02941, Sigma_B, RNA polymerase sigma-B factor

 Score = 45.3 bits (107), Expect = 2e-05
 Identities = 24/60 (40%), Positives = 32/60 (53%)

Query: 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
           +   A+EKLV     LV SIA +Y   G    DLVQ G++GLL  I ++D S G     +
Sbjct: 26  QNGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPF 85

This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus , Listeria and Bacillus. Length = 255

>gnl|CDD|233885 TIGR02479, FliA_WhiG, RNA polymerase sigma factor, FliA/WhiG family

 Score = 43.8 bits (104), Expect = 4e-05
 Identities = 17/40 (42%), Positives = 26/40 (65%)

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
           ++ DL+Q G+ GLL  IE++D S+G K  TY    IR ++
Sbjct: 25  ELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAM 64

Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium. Length = 224

>gnl|CDD|236306 PRK08583, PRK08583, RNA polymerase sigma factor SigB; Validated

 Score = 42.4 bits (100), Expect = 1e-04
 Identities = 22/54 (40%), Positives = 31/54 (57%)

Query: 261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKG 314
           +   A+EKLV     LV S+A +Y    +   DLVQ G++GLL  I ++D S G
Sbjct: 26  QDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFG 79

Length = 257

>gnl|CDD|235770 PRK06288, PRK06288, RNA polymerase sigma factor WhiG; Reviewed

 Score = 42.0 bits (99), Expect = 2e-04
 Identities = 25/67 (37%), Positives = 34/67 (50%), Gaps = 3/67 (4%)

Query: 266 REKLVMSNVRLVMSIAQRYD-NMGADM--ADLVQGGLIGLLRGIEKFDSSKGFKISTYVY 322
           RE L++    LV  +A R    M  ++   DLV  G+ GL+  IEKFD  +  K  TY  
Sbjct: 33  REYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAV 92

Query: 323 WWIRQSI 329
             IR +I
Sbjct: 93  TRIRGAI 99

Length = 268

>gnl|CDD|168831 PRK07122, PRK07122, RNA polymerase sigma factor SigF; Reviewed

 Score = 39.4 bits (92), Expect = 0.001
 Identities = 17/49 (34%), Positives = 27/49 (55%)

Query: 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKG 314
           R+++V   + L   IA+R+D  G    DLVQ   +GL+  + +FD   G
Sbjct: 42  RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETG 90

Length = 264

>gnl|CDD|181361 PRK08295, PRK08295, RNA polymerase factor sigma-70; Validated

 Score = 37.6 bits (88), Expect = 0.004
 Identities = 16/38 (42%), Positives = 23/38 (60%)

Query: 276 LVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSK 313
            V + A+ Y  +GAD  D+VQ G+IGL + I  +D  K
Sbjct: 36  FVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDK 73

Length = 208

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	330
PRK07598	415	RNA polymerase sigma factor SigC; Validated	100.0
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	100.0
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	99.98
PRK05949	327	RNA polymerase sigma factor; Validated	99.97
PRK07405	317	RNA polymerase sigma factor SigD; Validated	99.97
PRK05901	509	RNA polymerase sigma factor; Provisional	99.96
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	99.95
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	99.94
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	99.9
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	99.9
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	99.89
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	99.89
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	99.85
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	99.84
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	99.8
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	99.79
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	99.76
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	99.76
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	99.73
PRK08215	258	sporulation sigma factor SigG; Reviewed	99.69
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	99.69
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	99.68
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	99.61
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	99.57
PRK05803	233	sporulation sigma factor SigK; Reviewed	99.54
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	99.52
PRK08583	257	RNA polymerase sigma factor SigB; Validated	99.5
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.49
PRK05572	252	sporulation sigma factor SigF; Validated	99.47
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	99.47
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	99.46
PRK07670	251	RNA polymerase sigma factor SigD; Validated	99.4
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	99.36
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	99.29
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.2
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.13
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.01
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.0
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	98.93
PRK08295	208	RNA polymerase factor sigma-70; Validated	98.85
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	98.76
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	98.76
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	98.59
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	98.58
PRK11922	231	RNA polymerase sigma factor; Provisional	98.52
PRK05602	186	RNA polymerase sigma factor; Reviewed	98.49
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	98.49
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	98.44
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	98.43
PRK12513	194	RNA polymerase sigma factor; Provisional	98.37
PRK06759	154	RNA polymerase factor sigma-70; Validated	98.37
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	98.31
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	98.31
PRK13919	186	putative RNA polymerase sigma E protein; Provision	98.29
PRK12519	194	RNA polymerase sigma factor; Provisional	98.27
PRK06811	189	RNA polymerase factor sigma-70; Validated	98.25
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	98.2
PRK12524	196	RNA polymerase sigma factor; Provisional	98.16
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	98.14
PRK12526	206	RNA polymerase sigma factor; Provisional	98.13
PRK11924	179	RNA polymerase sigma factor; Provisional	98.13
PRK12514	179	RNA polymerase sigma factor; Provisional	98.12
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	98.11
PRK12534	187	RNA polymerase sigma factor; Provisional	98.11
PRK12531	194	RNA polymerase sigma factor; Provisional	98.04
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	98.0
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	98.0
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	97.95
PRK12536	181	RNA polymerase sigma factor; Provisional	97.93
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	97.93
PRK12538	233	RNA polymerase sigma factor; Provisional	97.9
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	97.88
PRK12512	184	RNA polymerase sigma factor; Provisional	97.83
PRK12515	189	RNA polymerase sigma factor; Provisional	97.79
PRK12522	173	RNA polymerase sigma factor; Provisional	97.75
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	97.71
PRK12543	179	RNA polymerase sigma factor; Provisional	97.65
PRK12539	184	RNA polymerase sigma factor; Provisional	97.64
PRK12537	182	RNA polymerase sigma factor; Provisional	97.62
PRK12518	175	RNA polymerase sigma factor; Provisional	97.55
PRK09415	179	RNA polymerase factor sigma C; Reviewed	97.5
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	97.39
PRK12542	185	RNA polymerase sigma factor; Provisional	97.36
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	97.35
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	97.29
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	97.21
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	97.19
PRK12547	164	RNA polymerase sigma factor; Provisional	97.11
PRK08241	339	RNA polymerase factor sigma-70; Validated	96.99
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	96.98
PRK12541	161	RNA polymerase sigma factor; Provisional	96.96
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	96.85
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	96.79
PRK12528	161	RNA polymerase sigma factor; Provisional	96.76
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	96.74
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	96.69
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	96.69
PRK12520	191	RNA polymerase sigma factor; Provisional	96.55
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	96.53
PRK12535	196	RNA polymerase sigma factor; Provisional	96.52
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	96.5
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	96.46
PRK12533	216	RNA polymerase sigma factor; Provisional	96.44
PRK12532	195	RNA polymerase sigma factor; Provisional	96.42
PRK12517	188	RNA polymerase sigma factor; Provisional	96.34
PRK12516	187	RNA polymerase sigma factor; Provisional	96.32
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	96.24
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	96.12
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	96.11
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	95.96
PRK12540	182	RNA polymerase sigma factor; Provisional	95.9
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	95.87
PRK12529	178	RNA polymerase sigma factor; Provisional	95.69
PRK12546	188	RNA polymerase sigma factor; Provisional	95.65
PRK12523	172	RNA polymerase sigma factor; Reviewed	95.59
PRK12544	206	RNA polymerase sigma factor; Provisional	95.5
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	95.36
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	95.34
PRK12545	201	RNA polymerase sigma factor; Provisional	95.02
PRK09191	261	two-component response regulator; Provisional	94.94
PRK12530	189	RNA polymerase sigma factor; Provisional	94.32
PRK12511	182	RNA polymerase sigma factor; Provisional	94.27
PRK12525	168	RNA polymerase sigma factor; Provisional	93.53
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	93.24
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	93.13
PRK12527	159	RNA polymerase sigma factor; Reviewed	93.06
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	92.19
PRK06704	228	RNA polymerase factor sigma-70; Validated	90.21
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	88.42
PF07638	185	Sigma70_ECF: ECF sigma factor	88.28
PHA02547	179	55 RNA polymerase sigma factor; Provisional	88.11
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	87.43
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	87.32
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	86.35
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	86.07
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	85.81
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	84.18
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	83.94
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	82.52
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	82.4
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	81.38
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	80.28

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=6.9e-34  Score=282.09  Aligned_cols=140  Identities=39%  Similarity=0.678  Sum_probs=130.5

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCcc--------------------chhHHHHHHHhhCCCCchHHHHHHhcC
Q 020126          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS--------------------LDDHKLRLKERLGCEPSMEQLAASLRI  250 (330)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~--------------------Le~~~~~l~~~lg~ePt~~e~A~a~~~  250 (330)
                      |.++.||++|++.|+||++||++|+++|+.+..                    |++.+.+|++.+|++||.++||.++|+
T Consensus        60 d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa~~~~~  139 (415)
T PRK07598         60 DLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWAKTADI  139 (415)
T ss_pred             ChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHHHHhCC
Confidence            589999999999999999999999999999999                    888999999999999999999966554


Q ss_pred             ----------------------ChHHHHHHHhhhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhh
Q 020126          251 ----------------------SRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK  308 (330)
Q Consensus       251 ----------------------s~~eL~~~l~~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIek  308 (330)
                                            +.++|...+..|..|+++||..|+++|+++|++|.++|++++||||||+|||++|+++
T Consensus       140 ~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~ravek  219 (415)
T PRK07598        140 SLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEK  219 (415)
T ss_pred             cHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHH
Confidence                                  5555556667888999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCcchhHHHHHhhcccC
Q 020126          309 FDSSKGFKISTYVYWWIRQSIS  330 (330)
Q Consensus       309 FDpsrG~rFsTYA~~wIR~aIS  330 (330)
                      |||++|++|+|||+||||++|+
T Consensus       220 FDp~rG~rFSTYa~wwIRqaI~  241 (415)
T PRK07598        220 FDPTKGYRFSTYAYWWIRQGIT  241 (415)
T ss_pred             cCcccCCCHHHHHHHHHHHHHH
Confidence            9999999999999999999984

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

Probab=100.00  E-value=6.1e-33  Score=261.28  Aligned_cols=138  Identities=41%  Similarity=0.728  Sum_probs=134.8

Q ss_pred             hHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHH
Q 020126          192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM  271 (330)
Q Consensus       192 ~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~  271 (330)
                      .+..||++|.++|+||++||.+|+++++.|..+++.+..|++.+|++|+..+||+++|++..+|...+..|..|+++||.
T Consensus         2 ~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~   81 (298)
T TIGR02997         2 LVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIK   81 (298)
T ss_pred             cHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHH
Confidence            46679999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       272 ~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      .|+++|+++|++|.++|.+.+||||||++||++|+++|||++|++|+|||+||||++|
T Consensus        82 ~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I  139 (298)
T TIGR02997        82 ANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGI  139 (298)
T ss_pred             HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999876

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=99.98  E-value=5.5e-32  Score=265.16  Aligned_cols=139  Identities=40%  Similarity=0.677  Sum_probs=136.5

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHH
Q 020126          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (330)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI  270 (330)
                      +.+..||++|+++|+||++||++|++++++|..+++.+..+.+.+|++|+.++||.++|++..+|+..+..|..|+++||
T Consensus        63 d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Li  142 (373)
T PRK07406         63 DSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMV  142 (373)
T ss_pred             CHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHHH
Confidence            57888999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      ..|+|+|+++|++|.++|++++||+|||+|||++|+++|||++|++|+|||+||||++|
T Consensus       143 ~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI  201 (373)
T PRK07406        143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI  201 (373)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999998

>PRK05949 RNA polymerase sigma factor; Validated

Probab=99.97  E-value=7.3e-31  Score=252.34  Aligned_cols=140  Identities=38%  Similarity=0.714  Sum_probs=136.6

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHH
Q 020126          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (330)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI  270 (330)
                      +.+..||++|+++|+||++||++|+++++.|..+++.+..|+..+|++|+..+||.+++++..+|...+..|..|++.||
T Consensus        18 d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~Li   97 (327)
T PRK05949         18 DMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMI   97 (327)
T ss_pred             CHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHHHH
Confidence            57888999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcccC
Q 020126          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS  330 (330)
Q Consensus       271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aIS  330 (330)
                      ..|+++|+++|++|.+.+.+.+||+|||+|||++|+++|||++|++|+|||+||||++|.
T Consensus        98 ~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~  157 (327)
T PRK05949         98 EANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAIT  157 (327)
T ss_pred             HHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999883

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=99.97  E-value=4.2e-30  Score=245.53  Aligned_cols=139  Identities=40%  Similarity=0.716  Sum_probs=136.0

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHH
Q 020126          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (330)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI  270 (330)
                      +.+..||++|+++|+||++||++|++++++|..++..+..|++.+|++|+..+||.+++++..+|...+..|..|+++|+
T Consensus         8 ~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~~L~   87 (317)
T PRK07405          8 DLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMV   87 (317)
T ss_pred             cHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHHHHH
Confidence            57788999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      ..|+++|.++|++|.+.+.+.+||+|||++||++|+++|||++|++|+|||+||||++|
T Consensus        88 ~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I  146 (317)
T PRK07405         88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAI  146 (317)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999987

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=99.96  E-value=7.6e-30  Score=258.69  Aligned_cols=127  Identities=41%  Similarity=0.678  Sum_probs=112.8

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHH
Q 020126          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (330)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI  270 (330)
                      +.++.||++|+++|+||++||++|+++++.|+.+++..   .       ...+|+.   ....+|+.+++.|..|+++||
T Consensus       211 d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~~---~-------~~~~~~~---~~~~~l~~~~~~g~~Ar~~LI  277 (509)
T PRK05901        211 DPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEELL---A-------EGEKLDP---ELRRDLQWIGRDGKRAKNHLL  277 (509)
T ss_pred             cHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhhh---h-------hcccchh---hhhhhhhhhccchHHHHHHHH
Confidence            68899999999999999999999999999998754422   1       1123332   246788999999999999999


Q ss_pred             HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcccC
Q 020126          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS  330 (330)
Q Consensus       271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aIS  330 (330)
                      ..|+|||++||++|.++|++++||||||+||||+||++|||++|++|+|||+||||++|.
T Consensus       278 ~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~  337 (509)
T PRK05901        278 EANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAIT  337 (509)
T ss_pred             HHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999983

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

Probab=99.95  E-value=7.4e-28  Score=234.17  Aligned_cols=140  Identities=39%  Similarity=0.618  Sum_probs=122.1

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHH-hhCCCCchH---------------HHHHHhcCCh-H
Q 020126          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKE-RLGCEPSME---------------QLAASLRISR-P  253 (330)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~-~lg~ePt~~---------------e~A~a~~~s~-~  253 (330)
                      +.+..|+.+++..++++.++|..+.+.++....+......+.. .++..|+..               +|+..+..+. .
T Consensus         9 d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee~   88 (342)
T COG0568           9 DAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEEK   88 (342)
T ss_pred             hHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHHH
Confidence            4888999999999999999999999999988777667777777 677888875               4444444433 5


Q ss_pred             HHHHHHhhhH---HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcccC
Q 020126          254 ELQSILMECS---LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS  330 (330)
Q Consensus       254 eL~~~l~~g~---~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aIS  330 (330)
                      +|...+..|.   .|+.+||.+|++||++||++|.++|+.+.||||||+||||+||++|||++|++|+|||+||||++|+
T Consensus        89 ~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI~  168 (342)
T COG0568          89 ALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAIT  168 (342)
T ss_pred             HHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHHH
Confidence            6777777775   4999999999999999999999999999999999999999999999999999999999999999985

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=99.94  E-value=3.8e-27  Score=226.76  Aligned_cols=126  Identities=40%  Similarity=0.722  Sum_probs=110.7

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHH
Q 020126          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (330)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI  270 (330)
                      +.+..||++|+++|+||++||.+|+++++.|..++..          +|..++++..   ...++...++.|..|+++||
T Consensus        26 ~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~----------~~~~~~~~~~---~~~~l~~~~~~~~~A~~~Lv   92 (324)
T PRK07921         26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL----------LETRKRLSEA---RKRDLAAVVRDGEAARRHLL   92 (324)
T ss_pred             ChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh----------hccccccchh---HHHHHHHHHhcCHHHHHHHH
Confidence            5788899999999999999999999999998765443          1111111111   45688999999999999999


Q ss_pred             HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      ..|+|+|+++|++|.+.|++.+||+|||+|||++|+++|||++|++|+|||+||||++|
T Consensus        93 ~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI  151 (324)
T PRK07921         93 EANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAI  151 (324)
T ss_pred             HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999997

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=99.90  E-value=3.8e-24  Score=220.31  Aligned_cols=102  Identities=38%  Similarity=0.738  Sum_probs=94.3

Q ss_pred             hHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHH
Q 020126          192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM  271 (330)
Q Consensus       192 ~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~  271 (330)
                      .++.||+++...+.|+++++.+++++++.|+.                                     ....|+++||.
T Consensus       345 ~lq~~L~~ie~~~~Ls~eElk~l~~~i~~g~~-------------------------------------~~~~a~~~Li~  387 (619)
T PRK05658        345 KLQQELEAIEEETGLTIEELKEINRQISKGEA-------------------------------------KARRAKKEMVE  387 (619)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHhccch-------------------------------------hhhHHHHHHHH
Confidence            56788999999999999999999999998864                                     12378999999


Q ss_pred             HhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcccC
Q 020126          272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS  330 (330)
Q Consensus       272 ~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aIS  330 (330)
                      .|+|||++||++|.++|++++||||||+||||+||++|||++|++|+|||+||||++|+
T Consensus       388 ~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~  446 (619)
T PRK05658        388 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT  446 (619)
T ss_pred             HHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999984

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=99.90  E-value=1.5e-23  Score=204.10  Aligned_cols=100  Identities=45%  Similarity=0.761  Sum_probs=96.6

Q ss_pred             hhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHH
Q 020126          190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL  269 (330)
Q Consensus       190 q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekL  269 (330)
                      .+.++.||++|++.|+||++||.+|+++++.|+.                                        .|+++|
T Consensus        95 ~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~Gd~----------------------------------------~A~~~L  134 (367)
T PRK09210         95 NDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDE----------------------------------------EAKQRL  134 (367)
T ss_pred             CcHHHHHHHHhhccCCCCHHHHHHHHHHHHhhHH----------------------------------------HHHHHH
Confidence            4789999999999999999999999999999865                                        799999


Q ss_pred             HHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       270 I~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      |..|+|+|+++|++|.++|.+++||+|||+|||++|+++|||++|++|+|||+||||++|
T Consensus       135 i~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI  194 (367)
T PRK09210        135 AEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAI  194 (367)
T ss_pred             HHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999987

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=99.89  E-value=2.9e-23  Score=193.01  Aligned_cols=98  Identities=35%  Similarity=0.639  Sum_probs=92.8

Q ss_pred             hHHHHHHhcCCCCCCCHHHHHHHHHH-HHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHH
Q 020126          192 RLKGYVKGVVSEELLTHAEVVRLSKK-IKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (330)
Q Consensus       192 ~l~~YL~~i~~~~lLT~eEE~eL~rk-Ik~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI  270 (330)
                      .+..||++|+++|+|++++|.+|+++ .+.|+.                                        .|++.||
T Consensus         2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~~~~gd~----------------------------------------~a~~~Lv   41 (270)
T TIGR02392         2 SLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDL----------------------------------------DAAKKLV   41 (270)
T ss_pred             hHHHHHHHHhcCCCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHHH
Confidence            46789999999999999999999998 457765                                        7899999


Q ss_pred             HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      ..|+|+|.++|++|.+.+.+.+||+|+|+|||++|+++|||++|++|+|||.||||++|
T Consensus        42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i  100 (270)
T TIGR02392        42 LSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEI  100 (270)
T ss_pred             HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999987

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.

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=99.89  E-value=4.2e-23  Score=194.19  Aligned_cols=103  Identities=35%  Similarity=0.651  Sum_probs=97.5

Q ss_pred             CChhhhhhhHHHHHHhcCCCCCCCHHHHHHHHHHH-HcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhh
Q 020126          184 ISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC  262 (330)
Q Consensus       184 ~~pEl~q~~l~~YL~~i~~~~lLT~eEE~eL~rkI-k~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g  262 (330)
                      ++|+   +.+..|++++.+.|+|+.++|.+|+.++ +.|+.                                       
T Consensus        10 ~~~~---~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~~Gd~---------------------------------------   47 (284)
T PRK06596         10 LSPE---GNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDL---------------------------------------   47 (284)
T ss_pred             CCCc---cHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCCH---------------------------------------
Confidence            6787   7889999999999999999999999985 57765                                       


Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                       .++++||..|+|+|.++|++|.+.+++.+||+|+|++||++|+++|||++|++|+|||+||||++|
T Consensus        48 -~a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i  113 (284)
T PRK06596         48 -EAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEI  113 (284)
T ss_pred             -HHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHH
Confidence             789999999999999999999999999999999999999999999999999999999999999987

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=99.85  E-value=3.3e-21  Score=181.97  Aligned_cols=99  Identities=29%  Similarity=0.572  Sum_probs=93.2

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHH-cCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHH
Q 020126          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL  269 (330)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk-~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekL  269 (330)
                      +.+..||++|.++|+||+++|.+|+++++ .|+.                                        .|+++|
T Consensus         6 ~~~~~y~~~~~~~~~l~~~~e~~L~~~~~~~gd~----------------------------------------~A~~~L   45 (289)
T PRK07500          6 SADRSMIRSAMKAPYLEREEEHALAYRWKDHRDE----------------------------------------DALHRI   45 (289)
T ss_pred             hHHHHHHHHHhcCCCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHH
Confidence            35567999999999999999999999975 6765                                        889999


Q ss_pred             HHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       270 I~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      |..|+|+|.++|.+|.+.+.+.+||+|+|++||++|+++|||.+|.+|+|||+||||++|
T Consensus        46 v~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I  105 (289)
T PRK07500         46 ISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASI  105 (289)
T ss_pred             HHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999987

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=99.84  E-value=2e-21  Score=181.22  Aligned_cols=66  Identities=27%  Similarity=0.445  Sum_probs=64.8

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      .++++||..|+|||+++|++|.++|++++||||+|+||||+|+++|||++|++|+|||+||||++|
T Consensus        40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I  105 (264)
T PRK07122         40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEV  105 (264)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999999999999999999999999999999987

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=99.80  E-value=1.9e-19  Score=173.15  Aligned_cols=101  Identities=41%  Similarity=0.730  Sum_probs=96.5

Q ss_pred             hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHH
Q 020126          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK  268 (330)
Q Consensus       189 ~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~Arek  268 (330)
                      +-+.++.||++|+..|+||+++|..|+++++.|+.                                        .|++.
T Consensus        51 ~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~Gd~----------------------------------------~A~~~   90 (325)
T PRK05657         51 VLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDF----------------------------------------AARQR   90 (325)
T ss_pred             cccHHHHHHHHHhcCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHH
Confidence            33688899999999999999999999999999986                                        89999


Q ss_pred             HHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       269 LI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      ||..|.|+|.++|.+|.+.+.+.+||+|+|+|||++++++||+++|++|+|||+||||++|
T Consensus        91 Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai  151 (325)
T PRK05657         91 MIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI  151 (325)
T ss_pred             HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999876

>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain

Probab=99.79  E-value=1.5e-19  Score=164.73  Aligned_cols=65  Identities=57%  Similarity=1.003  Sum_probs=63.4

Q ss_pred             HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      |+++||..|+|+|.++|++|.+.|++++||+|+|+|||++|+++|||++|++|+|||+||||++|
T Consensus         1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I   65 (238)
T TIGR02393         1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAI   65 (238)
T ss_pred             CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHH
Confidence            57899999999999999999999999999999999999999999999999999999999999987

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.

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=99.76  E-value=2.7e-18  Score=160.69  Aligned_cols=102  Identities=38%  Similarity=0.683  Sum_probs=97.3

Q ss_pred             hhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHH
Q 020126          188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLARE  267 (330)
Q Consensus       188 l~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~Are  267 (330)
                      ...++++.||++|..+|.|+.++|.+|+++++.|+.                                        .|++
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~a~~   49 (285)
T TIGR02394        10 RVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDF----------------------------------------EARK   49 (285)
T ss_pred             CcchHHHHHHHHHhccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHH
Confidence            455799999999999999999999999999999976                                        8999


Q ss_pred             HHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       268 kLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      .|+..|.++|..+|.+|.+.+.+.+||+|+|+|||++|+++||+.+|++|+|||.|||+.+|
T Consensus        50 ~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ai  111 (285)
T TIGR02394        50 VMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTI  111 (285)
T ss_pred             HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999775

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).

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

Probab=99.76  E-value=1.5e-18  Score=162.95  Aligned_cols=85  Identities=40%  Similarity=0.606  Sum_probs=77.3

Q ss_pred             CCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHHHHH
Q 020126          204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR  283 (330)
Q Consensus       204 ~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sIAkr  283 (330)
                      +.++.++...+....++|+.                                        .++ .||+.|+|||.++|++
T Consensus         4 ~~~~~~e~~~~~~~~~~g~~----------------------------------------~~~-~Li~~ylpLV~~ia~k   42 (247)
T COG1191           4 QPLSKEEEEKLLEYYAEGDE----------------------------------------EAR-RLIERYLPLVKSIARK   42 (247)
T ss_pred             cccchHHHHHHHHHHHhcCH----------------------------------------HHH-HHHHHHHHHHHHHHHH
Confidence            45667777777777777654                                        788 9999999999999999


Q ss_pred             cccCCC-ChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          284 YDNMGA-DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       284 Y~~~Gv-d~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      |.+++. ++|||+|.|+|||++||++|||++|.+|+|||.++|+|+|
T Consensus        43 ~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei   89 (247)
T COG1191          43 FENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEI   89 (247)
T ss_pred             HHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHH
Confidence            999988 9999999999999999999999999999999999999987

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=99.73  E-value=1.3e-17  Score=154.38  Aligned_cols=66  Identities=42%  Similarity=0.619  Sum_probs=63.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccC-CCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNM-GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~-Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      .|+++||..|+|+|.++|++|.++ +.+.+||+|+|+|||++|+++|||++|++|+|||++|||++|
T Consensus        25 ~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i   91 (256)
T PRK07408         25 ALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEI   91 (256)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHH
Confidence            799999999999999999999875 677999999999999999999999999999999999999987

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=99.69  E-value=1e-16  Score=147.77  Aligned_cols=93  Identities=40%  Similarity=0.595  Sum_probs=85.8

Q ss_pred             HHhcC--CCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhH
Q 020126          197 VKGVV--SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV  274 (330)
Q Consensus       197 L~~i~--~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nL  274 (330)
                      +++++  ++|+|+++|+..|+.+++.|+.                                        .++++|+..|.
T Consensus         8 ~~~~~~~~~~~l~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~   47 (258)
T PRK08215          8 ICGVNTSKLPVLKNEEMRELFERMQNGDK----------------------------------------EAREKLINGNL   47 (258)
T ss_pred             eecccCCCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHH
Confidence            34444  4579999999999999998875                                        78999999999


Q ss_pred             HHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          275 RLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       275 pLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      |+|..+|++|.+.+.+.+||+|+|++||++|+++|||++|.+|.||+++||+++|
T Consensus        48 ~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i  102 (258)
T PRK08215         48 RLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEI  102 (258)
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999986

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=99.69  E-value=1.1e-16  Score=147.51  Aligned_cols=89  Identities=39%  Similarity=0.570  Sum_probs=84.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHH
Q 020126          201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI  280 (330)
Q Consensus       201 ~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sI  280 (330)
                      .++|+||++||.+|+.+++.|+.                                        .++++|+..|.|+|.++
T Consensus        11 ~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~~~~~v~~~   50 (254)
T TIGR02850        11 SKLPVLKNQEMRELFIRMQSGDT----------------------------------------TAREKLINGNLRLVLSV   50 (254)
T ss_pred             cCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHHH
Confidence            46799999999999999998875                                        78999999999999999


Q ss_pred             HHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       281 AkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      |.+|.+.+.+.+||+|+|++||++|+++|||.+|.+|+||+++||+++|
T Consensus        51 a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~   99 (254)
T TIGR02850        51 IQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEI   99 (254)
T ss_pred             HHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999876

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.

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=99.68  E-value=5.7e-17  Score=150.45  Aligned_cols=68  Identities=28%  Similarity=0.436  Sum_probs=63.3

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHccc---CCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~---~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      +..|+++||..|+|+|.++|++|..   .+++++||+|+|+|||++|+++|||++|++|+|||.||||++|
T Consensus        21 ~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i   91 (257)
T PRK05911         21 EIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAI   91 (257)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHH
Confidence            3479999999999999999999863   3578999999999999999999999999999999999999987

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=99.61  E-value=2.4e-15  Score=139.58  Aligned_cols=90  Identities=30%  Similarity=0.393  Sum_probs=81.5

Q ss_pred             cCCCCCCCHHHHHHHHHHHHc-CccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHH
Q 020126          200 VVSEELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVM  278 (330)
Q Consensus       200 i~~~~lLT~eEE~eL~rkIk~-G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~  278 (330)
                      -+.+|+||.++|.+|+++++. |+.                                        .+.+.|+..|.|+|.
T Consensus         6 ~~~~~~~~~~~e~~l~~~~~~~~d~----------------------------------------~a~~~l~~~y~~lv~   45 (268)
T PRK06288          6 SGKIPKYAQQDETELWREYKKTGDP----------------------------------------KIREYLILKYSPLVK   45 (268)
T ss_pred             cCCCccccchHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHH
Confidence            467899999999999999774 443                                        788999999999999


Q ss_pred             HHHHHccc---CCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          279 SIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       279 sIAkrY~~---~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      .+|++|..   .+.+.+||+|+|++||++|+++||+.+|.+|.||+.+|||+.|
T Consensus        46 ~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i   99 (268)
T PRK06288         46 YVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAI   99 (268)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHH
Confidence            99999863   5678999999999999999999999999999999999999876

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=99.57  E-value=1.1e-14  Score=133.54  Aligned_cols=86  Identities=34%  Similarity=0.406  Sum_probs=80.9

Q ss_pred             CCCCHHHHHHHHHHHHc-CccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHHHH
Q 020126          204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ  282 (330)
Q Consensus       204 ~lLT~eEE~eL~rkIk~-G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sIAk  282 (330)
                      |.||+++|.+|+.+++. |+.                                        .|.++|+..|.|+|..+|.
T Consensus         8 ~~l~~~~~~~li~~~~~~gd~----------------------------------------~a~~~l~~~y~~~v~~~a~   47 (255)
T TIGR02941         8 TNLTKEDVIQWIAEFQQNQNG----------------------------------------EAQEKLVDHYQNLVYSIAY   47 (255)
T ss_pred             CCCCHHHHHHHHHHHHHCCCH----------------------------------------HHHHHHHHHhHHHHHHHHH
Confidence            67999999999999987 454                                        7899999999999999999


Q ss_pred             HcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       283 rY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      +|.+.+.+.+||+|+|++||++|+++||+++|.+|.||+.+||++.|
T Consensus        48 ~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~   94 (255)
T TIGR02941        48 KYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEI   94 (255)
T ss_pred             HHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999875

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

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.54  E-value=4.6e-14  Score=128.18  Aligned_cols=98  Identities=37%  Similarity=0.550  Sum_probs=92.7

Q ss_pred             hHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHH
Q 020126          192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM  271 (330)
Q Consensus       192 ~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~  271 (330)
                      ++..|+.++...|+||+++|..|+..++.|+.                                        .+.+.|+.
T Consensus        17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~gd~----------------------------------------~a~~~l~~   56 (233)
T PRK05803         17 FLVSYVKNNSFPQPLSEEEERKYLELMKEGDE----------------------------------------EARNILIE   56 (233)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHH
Confidence            67899999999999999999999999998865                                        78999999


Q ss_pred             HhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       272 ~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      .|.|+|..++.+|.+.+.+.+|++|+|+|+|++++++||+++|.+|.+|+.+|||+.+
T Consensus        57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~  114 (233)
T PRK05803         57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEI  114 (233)
T ss_pred             HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999998754

>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily

Probab=99.52  E-value=2.5e-14  Score=128.58  Aligned_cols=67  Identities=49%  Similarity=0.627  Sum_probs=64.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      ..|+++|+..|.|+|.++|.+|.+.+.+.+||+|+|++||++|+++||+++|.+|+||+++||+++|
T Consensus         2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~   68 (227)
T TIGR02980         2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEI   68 (227)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHH
Confidence            4789999999999999999999999999999999999999999999999999999999999999876

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

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=99.50  E-value=9.7e-14  Score=127.56  Aligned_cols=86  Identities=33%  Similarity=0.374  Sum_probs=80.8

Q ss_pred             CCCCHHHHHHHHHHHHc-CccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHHHH
Q 020126          204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ  282 (330)
Q Consensus       204 ~lLT~eEE~eL~rkIk~-G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sIAk  282 (330)
                      |.|+++||.+|+.+++. |+.                                        .|.+.|+..|.|+|..+|.
T Consensus         8 ~~l~~~e~~~li~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~~a~   47 (257)
T PRK08583          8 TKLTKEEVNKWIAEYQENQDE----------------------------------------EAQEKLVKHYKNLVESLAY   47 (257)
T ss_pred             CcCChHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHH
Confidence            77999999999999885 665                                        7999999999999999999


Q ss_pred             HcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       283 rY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      +|.+.+.+.+||+|+|+++|++++++||+++|.+|.||+.+||++.|
T Consensus        48 ~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~   94 (257)
T PRK08583         48 KYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEI   94 (257)
T ss_pred             HHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999875

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.49  E-value=4.8e-14  Score=130.03  Aligned_cols=70  Identities=21%  Similarity=0.275  Sum_probs=64.1

Q ss_pred             hhhHHHHHHHHHHhHHHHHHHHHHcccCC--CChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          260 MECSLAREKLVMSNVRLVMSIAQRYDNMG--ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       260 ~~g~~ArekLI~~nLpLV~sIAkrY~~~G--vd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      ..|...+++||..|.|+|.++|.+|.+++  .+.|||+|+|+|||++||++|||++|.+|.+||.+|||++|
T Consensus         5 ~~gd~~~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i   76 (218)
T TIGR02895         5 QPGNEEREELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRL   76 (218)
T ss_pred             hcCChHHHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH
Confidence            44545599999999999999999998775  58999999999999999999999999999999999999876

Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).

>PRK05572 sporulation sigma factor SigF; Validated

Probab=99.47  E-value=2.3e-13  Score=125.16  Aligned_cols=93  Identities=42%  Similarity=0.487  Sum_probs=86.4

Q ss_pred             HHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHH
Q 020126          197 VKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRL  276 (330)
Q Consensus       197 L~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpL  276 (330)
                      ++.-...|.||++++.+|+.+++.|+.                                        .+.++|+..|.|+
T Consensus         5 ~~~~~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~y~~~   44 (252)
T PRK05572          5 VKNKKKKPQLKDEENKELIKKSQDGDQ----------------------------------------EARDTLVEKNLRL   44 (252)
T ss_pred             hccCcCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHH
Confidence            445567899999999999999888865                                        7899999999999


Q ss_pred             HHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          277 VMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       277 V~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      |..+|.+|.+.+.+.+||+|+|+++|++++++||+.+|.+|.||+++||+++|
T Consensus        45 v~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i   97 (252)
T PRK05572         45 VWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEI   97 (252)
T ss_pred             HHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999876

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=99.47  E-value=5.7e-14  Score=128.81  Aligned_cols=65  Identities=22%  Similarity=0.345  Sum_probs=59.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccC---CCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNM---GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~---Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      ..+..|+..|+|+|.++|++|..+   +++.+||+|+|+|||++|+++|||..| +|+|||.+|||++|
T Consensus        15 ~~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~i   82 (231)
T PRK12427         15 QEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAI   82 (231)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHH
Confidence            567789999999999999999753   679999999999999999999998666 89999999999986

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=99.46  E-value=1.3e-13  Score=124.39  Aligned_cols=68  Identities=46%  Similarity=0.570  Sum_probs=65.2

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      +..++++|+..|.|+|.++|.+|.+.+.+.+||+|+|++||++|+++|||.+|.+|.||+++||+++|
T Consensus         9 d~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i   76 (231)
T TIGR02885         9 DKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEI   76 (231)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHH
Confidence            45899999999999999999999999999999999999999999999999999999999999999976

Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=99.40  E-value=1e-12  Score=120.77  Aligned_cols=66  Identities=33%  Similarity=0.474  Sum_probs=62.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccc---CCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~---~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      .|.+.|+..|.|+|..+|.+|..   .+.+.+||+|+|++||++++++|||++|.+|.||+++|||+.|
T Consensus        22 ~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~   90 (251)
T PRK07670         22 DAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAI   90 (251)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHH
Confidence            89999999999999999999965   5789999999999999999999999999999999999999875

>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family

Probab=99.36  E-value=8e-13  Score=119.05  Aligned_cols=61  Identities=38%  Similarity=0.622  Sum_probs=57.8

Q ss_pred             HHHHhHHHHHHHHHHccc---CCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          269 LVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       269 LI~~nLpLV~sIAkrY~~---~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      |+..|.|+|..+|++|.+   .+.+.+||+|+|++||++|+++|||++|.+|+||+.+|||+.|
T Consensus         1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~   64 (224)
T TIGR02479         1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAM   64 (224)
T ss_pred             CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHH
Confidence            578999999999999986   6899999999999999999999999999999999999999875

Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=99.29  E-value=5.3e-12  Score=114.76  Aligned_cols=69  Identities=33%  Similarity=0.542  Sum_probs=64.7

Q ss_pred             hhHHHHHHHHHHhHHHHHHHHHHcc---cCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          261 ECSLAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       261 ~g~~ArekLI~~nLpLV~sIAkrY~---~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      +|.-++++|+..|.|+|..+|.+|.   +.+.+.+||+|+|++||++++++|||++|.+|.||+.+|||+.|
T Consensus         5 ~~~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~   76 (236)
T PRK06986          5 EGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAM   76 (236)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHH
Confidence            5678999999999999999999997   56889999999999999999999999999999999999999875

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.20  E-value=1.2e-10  Score=105.73  Aligned_cols=98  Identities=35%  Similarity=0.556  Sum_probs=87.1

Q ss_pred             hHHHHHHhcC-CCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHH
Q 020126          192 RLKGYVKGVV-SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (330)
Q Consensus       192 ~l~~YL~~i~-~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI  270 (330)
                      ++-+|+..-+ ..+.|++.+|.+|+.+++.|+.                                        .+.+.|+
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~af~~l~   54 (227)
T TIGR02846        15 FLVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDE----------------------------------------EARNVLI   54 (227)
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHH
Confidence            4456665444 4577999999999999999876                                        8899999


Q ss_pred             HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      ..|.|+|.+++.+|.+...+.+|++|++.+++++++++|+++.+.+|.||+.+++|+.+
T Consensus        55 ~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~  113 (227)
T TIGR02846        55 ERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEI  113 (227)
T ss_pred             HHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHH
Confidence            99999999999999988899999999999999999999999999899999999988753

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

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=99.13  E-value=3.3e-10  Score=102.62  Aligned_cols=94  Identities=32%  Similarity=0.543  Sum_probs=84.5

Q ss_pred             HHHhcCCC-CCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhH
Q 020126          196 YVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV  274 (330)
Q Consensus       196 YL~~i~~~-~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nL  274 (330)
                      |+++.... +.+++..+.+|+.+++.|+.                                        .+.+.|+..|.
T Consensus        23 ~~~~~~~~~~~~~~~~~~~L~~~~~~gd~----------------------------------------~af~~l~~~y~   62 (234)
T PRK08301         23 YIGGSEALPPPLSKEEEEYLLNKLPKGDE----------------------------------------AVRSLLIERNL   62 (234)
T ss_pred             HhccccccCCcCCHHHHHHHHHHHHccCH----------------------------------------HHHHHHHHHhH
Confidence            77777554 55888899999999998875                                        78999999999


Q ss_pred             HHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          275 RLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       275 pLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      ++|..+|.+|.+.+.+.+|++|++++++++++.+|++.++++|.||+..++|+.+
T Consensus        63 ~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~  117 (234)
T PRK08301         63 RLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEI  117 (234)
T ss_pred             HHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHH
Confidence            9999999999998999999999999999999999999988899999999988754

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

Probab=99.01  E-value=7e-10  Score=81.38  Aligned_cols=61  Identities=30%  Similarity=0.470  Sum_probs=57.8

Q ss_pred             HHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       269 LI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      |++.|.|+|..++.+|.+.+.+.+|++|++.++|++++++||++++..|.+|+...+++.+
T Consensus         1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~   61 (71)
T PF04542_consen    1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRI   61 (71)
T ss_dssp             HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHH
Confidence            6889999999999999999999999999999999999999999999899999999988754

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

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=99.00  E-value=2.5e-09  Score=97.51  Aligned_cols=94  Identities=35%  Similarity=0.551  Sum_probs=82.9

Q ss_pred             HHHhcC-CCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhH
Q 020126          196 YVKGVV-SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV  274 (330)
Q Consensus       196 YL~~i~-~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nL  274 (330)
                      |+.+-. ..+.|+++++.+|...++.|+.                                        .+.+.|+..|.
T Consensus        23 ~~~~~~~~~~~~~~~~~~~l~~~~~~~d~----------------------------------------~a~~~l~~~y~   62 (234)
T TIGR02835        23 YIGGSEALPPPLTGEEEEALLQKLTQGDE----------------------------------------SAKSTLIERNL   62 (234)
T ss_pred             HhcccccCCCcCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhH
Confidence            444433 3578899999999998888765                                        88999999999


Q ss_pred             HHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          275 RLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       275 pLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      +.|..++.+|.+.+.+-+|++|++++++++++++|++..+++|.+|+..++++.+
T Consensus        63 ~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~  117 (234)
T TIGR02835        63 RLVVYIARKFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEI  117 (234)
T ss_pred             HHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999888899999999988643

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

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=98.93  E-value=3.6e-09  Score=98.72  Aligned_cols=67  Identities=18%  Similarity=0.265  Sum_probs=62.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCC--ChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGA--DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gv--d~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      ..|++.|+..|.|+|.++|.+|.++..  +.+|++|+|.+++++|+++||+++|.+|.+|+..+|++.+
T Consensus        17 ~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~   85 (237)
T PRK08311         17 EELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRL   85 (237)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            478999999999999999999988765  5899999999999999999999999899999999998764

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=98.85  E-value=1.3e-08  Score=89.49  Aligned_cols=66  Identities=30%  Similarity=0.420  Sum_probs=62.1

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..+.+.|+..|.|+|..+|.+|.+...+.+|++|++++.|++++.+||+.++.+|.||++.+|++.
T Consensus        23 ~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~   88 (208)
T PRK08295         23 KEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQ   88 (208)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHH
Confidence            488999999999999999999999999999999999999999999999998889999999888764

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=98.76  E-value=3.9e-08  Score=85.59  Aligned_cols=65  Identities=28%  Similarity=0.412  Sum_probs=60.7

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..|.+.|+..|.|.|..+|.++.+...+.+|++|++.+.+++++.+|+++.+.+|.||++.+|++
T Consensus        18 ~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~   82 (198)
T TIGR02859        18 THALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTR   82 (198)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHH
Confidence            48999999999999999999999888999999999999999999999998888999999877765

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

>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family

Probab=98.76  E-value=1.4e-08  Score=81.45  Aligned_cols=63  Identities=30%  Similarity=0.443  Sum_probs=59.1

Q ss_pred             HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      +.+.|+..|.|+|.++++++...+.+.+|++|+|+++|+++++.|++.  .+|.+|+..+|++.+
T Consensus         2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~   64 (158)
T TIGR02937         2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLI   64 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHH
Confidence            678999999999999999999889999999999999999999999999  689999999998754

Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=98.59  E-value=8.9e-08  Score=81.09  Aligned_cols=65  Identities=28%  Similarity=0.284  Sum_probs=59.5

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      +..|.++|+..|.|+|..++.+|.+.+.+.+|++|+++++|++++++|+  .+.+|.+|+...+++.
T Consensus         8 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~   72 (182)
T PRK09652          8 DRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNT   72 (182)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHH
Confidence            4589999999999999999999998889999999999999999999999  4558999999988754

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=98.58  E-value=2.7e-07  Score=80.43  Aligned_cols=64  Identities=14%  Similarity=0.181  Sum_probs=55.9

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccC----CCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNM----GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~----Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      .+.++|+..|.|.|..+|.++.+.    +.+.+|++||++++|++++.+|++. +.+|.+|++.-+++.
T Consensus        24 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~   91 (189)
T PRK09648         24 RALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHK   91 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHH
Confidence            899999999999999999998653    4689999999999999999999864 458999998776653

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=98.52  E-value=3.6e-07  Score=83.14  Aligned_cols=86  Identities=20%  Similarity=0.211  Sum_probs=76.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHH
Q 020126          201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI  280 (330)
Q Consensus       201 ~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sI  280 (330)
                      ...|+|++..+..|+..++.|+.                                        .+.+.|+..|.++|..+
T Consensus         7 ~~~~~~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~   46 (231)
T PRK11922          7 SRPPPLSAASDRELVARVLAGDE----------------------------------------AAFEALMRRHNRRLYRT   46 (231)
T ss_pred             CCCCCcCcccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence            34688999999999999988875                                        88999999999999999


Q ss_pred             HHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       281 AkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      +.++.+...+-+|++|+++++|++.+++|++.  ..|.+|+...+++.
T Consensus        47 a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~   92 (231)
T PRK11922         47 ARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNE   92 (231)
T ss_pred             HHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHH
Confidence            99999888899999999999999999999986  37999988776653

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=98.49  E-value=4.1e-07  Score=79.16  Aligned_cols=64  Identities=14%  Similarity=0.196  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..+.+.|+..|.++|..+|.+|.+.+.+.+|++|+++++|++++.+|+++ +.+|.+|++..+++
T Consensus        19 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n   82 (186)
T PRK05602         19 PAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLN   82 (186)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHH
Confidence            48999999999999999999999988999999999999999999999986 45799999887665

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=98.49  E-value=4e-07  Score=80.22  Aligned_cols=64  Identities=14%  Similarity=0.133  Sum_probs=58.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..+.++|+..|.|+|..++.+|.+...+-+|++||+++.+++.+.+||+.+| .|.+|++..+++
T Consensus        29 ~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n   92 (194)
T PRK09646         29 QDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHR   92 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHH
Confidence            4899999999999999999999998899999999999999999999998766 689998776554

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=98.44  E-value=6e-07  Score=77.31  Aligned_cols=64  Identities=20%  Similarity=0.223  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..+.++|+..|.|+|..+|.+|.+.+.+.+|++|++++.+++++..||+..  +|.+|+...+++.
T Consensus        17 ~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~   80 (187)
T TIGR02948        17 ENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNL   80 (187)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHH
Confidence            488999999999999999999998888999999999999999999999875  6999998877653

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

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=98.43  E-value=7.3e-07  Score=76.75  Aligned_cols=64  Identities=20%  Similarity=0.217  Sum_probs=58.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..+.+.|+..|.|+|..+|.++.+...+.+|++|+++++|++++.+|++..  +|.+|+...+|+.
T Consensus        17 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~   80 (187)
T PRK09641         17 QNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNL   80 (187)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHH
Confidence            488999999999999999999998889999999999999999999999863  7999998877653

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=98.37  E-value=1.2e-06  Score=76.80  Aligned_cols=64  Identities=17%  Similarity=0.204  Sum_probs=58.5

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..+.+.|+..|.+.|..+|.++.+...+.+|++|++++++++++.+|++..  .|.+|+...+++.
T Consensus        25 ~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~   88 (194)
T PRK12513         25 AAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNL   88 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHH
Confidence            489999999999999999999998888999999999999999999999753  6999999888765

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=98.37  E-value=8.8e-07  Score=74.18  Aligned_cols=63  Identities=24%  Similarity=0.371  Sum_probs=56.1

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      .+.++|+..|.|+|..+++++. ...+.||++||+.+++++++.+|+++.| .|.+|+...+++.
T Consensus         4 ~af~~l~~~y~~~l~~~~~~~~-~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~   66 (154)
T PRK06759          4 ATFTEAVVLYEGLIVNQIKKLG-IYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGY   66 (154)
T ss_pred             ccHHHHHHHHHHHHHHHHHHhC-CcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHH
Confidence            5788999999999999999874 4568999999999999999999998777 7999998887764

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=98.31  E-value=2.2e-06  Score=74.86  Aligned_cols=61  Identities=20%  Similarity=0.303  Sum_probs=54.6

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhh
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIR  326 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR  326 (330)
                      .+.+.|+..|.|.|..++.++.+...+.+|++|++++.+++++.+|++..  .|.+|+..-.+
T Consensus        20 ~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~   80 (193)
T PRK11923         20 RAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAI   80 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHH
Confidence            78999999999999999999998888999999999999999999999874  48888765443

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=98.31  E-value=2.4e-06  Score=74.78  Aligned_cols=77  Identities=22%  Similarity=0.344  Sum_probs=66.0

Q ss_pred             CChHHHHHHHhh----hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHh
Q 020126          250 ISRPELQSILME----CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWI  325 (330)
Q Consensus       250 ~s~~eL~~~l~~----g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wI  325 (330)
                      ++.+++...+..    +..+.+.|+..|.|.|..++.+|.+...+.+|++|++++.|++.+.+|++.  .+|.+|+...+
T Consensus         8 ~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~ia   85 (188)
T PRK09640          8 LNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSIT   85 (188)
T ss_pred             CCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHHH
Confidence            345556555553    588999999999999999999999988999999999999999999999853  47999999988


Q ss_pred             hcc
Q 020126          326 RQS  328 (330)
Q Consensus       326 R~a  328 (330)
                      ++.
T Consensus        86 ~n~   88 (188)
T PRK09640         86 YNE   88 (188)
T ss_pred             HHH
Confidence            764

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=98.29  E-value=1.9e-06  Score=74.69  Aligned_cols=65  Identities=20%  Similarity=0.289  Sum_probs=58.1

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..+.+.|+..|.|.|..++.+|.+.+.+.+|++|++++.+++++.+|++..+ .|.+|+...+++.
T Consensus        22 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~   86 (186)
T PRK13919         22 EEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHA   86 (186)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHH
Confidence            4899999999999999999999888889999999999999999999997653 6899998877653

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=98.27  E-value=2.3e-06  Score=74.79  Aligned_cols=64  Identities=25%  Similarity=0.327  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..+.+.|+..|.+.|..++.++.+...+-+|++|++++.+++. ..|++..+ .|.||++..+++.
T Consensus        28 ~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~   91 (194)
T PRK12519         28 SAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSR   91 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHH
Confidence            3889999999999999999999888888999999999999975 67887665 7999998887764

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=98.25  E-value=4.1e-06  Score=73.52  Aligned_cols=65  Identities=20%  Similarity=0.225  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCC---CChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMG---ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~G---vd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..+.+.|+..|.|+|..++.++.+.+   .+.+|++|+++++|++++++|+++.+ +|.+|+..-+++.
T Consensus        17 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~iarn~   84 (189)
T PRK06811         17 EKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAISKYK   84 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHHHHH
Confidence            38999999999999999999997643   46899999999999999999997655 7999998766543

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=98.20  E-value=5.4e-06  Score=71.05  Aligned_cols=64  Identities=16%  Similarity=0.151  Sum_probs=57.9

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..+.+.|+..|.|.|..++.+|.+...+-+|++|++++.++++++.|++.  .+|.+|+...+++.
T Consensus        17 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~   80 (176)
T PRK09638         17 DAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRL   80 (176)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHH
Confidence            48999999999999999999999888889999999999999999999874  47999998877653

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=98.16  E-value=5.1e-06  Score=73.34  Aligned_cols=65  Identities=18%  Similarity=0.258  Sum_probs=57.7

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..+.+.|+..|.|.|..+|.++.+...+-+|++||+.+.+++.+.+|++.. ..|.+|+..-+++.
T Consensus        25 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~   89 (196)
T PRK12524         25 PAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNL   89 (196)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHH
Confidence            489999999999999999999998889999999999999999999998533 47999998866653

>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family

Probab=98.14  E-value=7.9e-06  Score=69.18  Aligned_cols=66  Identities=15%  Similarity=0.114  Sum_probs=59.2

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      +..+.+.|+..|.+.+...+.++.+...+.||++|++++.+++.+++|+...+ +|.+|+...+++.
T Consensus         9 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~   74 (170)
T TIGR02952         9 EEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNV   74 (170)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHH
Confidence            45899999999999999999888777789999999999999999999997655 8999999888764

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=98.13  E-value=1.1e-05  Score=72.17  Aligned_cols=64  Identities=20%  Similarity=0.229  Sum_probs=58.1

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      .+.++|+..|.|.|..++.++.+...+-+|++|++++.+++++.+|++.++ .|.+|+...+|+.
T Consensus        38 ~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~  101 (206)
T PRK12526         38 QAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNA  101 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHH
Confidence            889999999999999999999887788999999999999999999998766 5999998877764

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=98.13  E-value=8.1e-06  Score=68.95  Aligned_cols=65  Identities=18%  Similarity=0.088  Sum_probs=59.0

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      +..+.+.|+..|.|.|..++.++.+...+.+|++|++.+.|++++..|+  .+.+|.+|+...+++.
T Consensus        11 ~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~   75 (179)
T PRK11924         11 DKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNV   75 (179)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHH
Confidence            4689999999999999999999998889999999999999999999999  3458999999887764

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=98.12  E-value=9.3e-06  Score=70.10  Aligned_cols=64  Identities=14%  Similarity=0.080  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..+...|+..|.+.+..+|.+|.+...+-+|++|++++.+++.+.+|++..+ .|.+|...-.++
T Consensus        18 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n   81 (179)
T PRK12514         18 RDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARN   81 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHH
Confidence            4899999999999999999999988889999999999999999999997643 588888765554

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=98.11  E-value=1.2e-05  Score=69.44  Aligned_cols=63  Identities=19%  Similarity=0.291  Sum_probs=56.5

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..+.+.|+..|.|.|..+|.++.+...+.+|++|++.|.|++.+.+|++.  .+|.+|+..-.++
T Consensus        19 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn   81 (190)
T TIGR02939        19 KQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVN   81 (190)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHH
Confidence            47899999999999999999998888899999999999999999999975  3699998776553

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=98.11  E-value=8.7e-06  Score=70.75  Aligned_cols=64  Identities=17%  Similarity=0.169  Sum_probs=56.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..+.+.|+..|.|+|..++.+|.+...+-||++||.++.+++.+.+|++.++ +|.+|.+.-+++
T Consensus        24 ~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n   87 (187)
T PRK12534         24 RHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARN   87 (187)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHH
Confidence            3889999999999999999999888888999999999999999999998754 578888765443

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=98.04  E-value=1.6e-05  Score=70.14  Aligned_cols=64  Identities=19%  Similarity=0.180  Sum_probs=57.4

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..+.+.|+..|.|.|..+|.++.+...+-+|++|+.++.+++.+.+|++..+ .|.+|+..-+++
T Consensus        26 ~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn   89 (194)
T PRK12531         26 KQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRN   89 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHH
Confidence            4889999999999999999999887778999999999999999999997554 699999887665

>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1

Probab=98.00  E-value=1.1e-05  Score=66.77  Aligned_cols=62  Identities=19%  Similarity=0.295  Sum_probs=56.2

Q ss_pred             HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      |.++|+..|.|.|..++.++.+...+.||++|++++.+++.+.+|++..  +|.+|+...+|+.
T Consensus         2 a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~   63 (161)
T TIGR02985         2 AFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNR   63 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHH
Confidence            6789999999999999999988888899999999999999999998644  7999999988764

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.

>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1

Probab=98.00  E-value=2.1e-05  Score=67.65  Aligned_cols=67  Identities=16%  Similarity=0.117  Sum_probs=57.9

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHccc----CCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDN----MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~----~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ...+.+.|+..|.+.|..+|.+|..    ...+-||++|++++.+++++.+|++..+.+|.+|+...+++.
T Consensus         5 ~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~   75 (189)
T TIGR02984         5 DQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNV   75 (189)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHH
Confidence            3589999999999999999998743    457899999999999999999999876678999988776654

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).

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

Probab=97.95  E-value=3e-05  Score=66.32  Aligned_cols=64  Identities=19%  Similarity=0.184  Sum_probs=57.8

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..+.+.|+..|.|.+..++.++.+...+.+|++|+..+.+++...+|++..  +|.+|+..-+++.
T Consensus        15 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~   78 (169)
T TIGR02954        15 KPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINE   78 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHH
Confidence            489999999999999999999999889999999999999999999999753  6999998877653

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

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=97.93  E-value=5.3e-05  Score=65.96  Aligned_cols=65  Identities=14%  Similarity=0.142  Sum_probs=56.0

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHccc-CCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDN-MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~-~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      +..+.+.|+..|.+.|..++.++.. ...+.||++|++++.|++.+..|++.  .+|.+|+..-+++.
T Consensus        19 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~   84 (181)
T PRK12536         19 DAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYK   84 (181)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHH
Confidence            3489999999999999999988764 46799999999999999999999974  36999998776653

>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family

Probab=97.93  E-value=2.2e-05  Score=65.95  Aligned_cols=62  Identities=16%  Similarity=0.222  Sum_probs=56.1

Q ss_pred             HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      +.+.++..|.|.|..+|.++.+...+.||++|++.+.+++.+.+|++..  .|.+|+..-+++.
T Consensus         2 ~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~   63 (159)
T TIGR02989         2 AFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNK   63 (159)
T ss_pred             HHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHH
Confidence            5788999999999999999999899999999999999999999999764  6999998877653

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=97.90  E-value=3.3e-05  Score=71.31  Aligned_cols=63  Identities=24%  Similarity=0.313  Sum_probs=56.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      .+.+.|+..|.+.|..++.++.+...+-||++|+.++.+++.+.+|++..+ .|.+|...-+++
T Consensus        63 ~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN  125 (233)
T PRK12538         63 AAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSN  125 (233)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHH
Confidence            889999999999999999999888788999999999999999999987555 699998776554

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=97.88  E-value=3.5e-06  Score=58.24  Aligned_cols=33  Identities=30%  Similarity=0.483  Sum_probs=30.2

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCcc
Q 020126          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS  223 (330)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~  223 (330)
                      +.++.||++|+++|+||++||++|+++|+.|+.
T Consensus         2 D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~~   34 (37)
T PF00140_consen    2 DSLRLYLKEIGRYPLLTAEEEIELARRIRKGDE   34 (37)
T ss_dssp             HHHHHHHHHHHHS-EETTHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhHH
Confidence            688999999999999999999999999999875

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 ....

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=97.83  E-value=9.6e-05  Score=64.08  Aligned_cols=64  Identities=16%  Similarity=0.173  Sum_probs=55.2

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcccC----CCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDNM----GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~~----Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      +..+.+.|+..|.+.|..+|.++.+.    ..+.+|++|++.+.+++...+|++.  ..|.+|+..-+|+
T Consensus        20 d~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn   87 (184)
T PRK12512         20 DAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARN   87 (184)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHH
Confidence            35899999999999999999988752    3589999999999999999999874  3699999876665

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=97.79  E-value=8.5e-05  Score=64.98  Aligned_cols=64  Identities=19%  Similarity=0.151  Sum_probs=57.3

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      +..+.+.|+..|.+.+..++.++.+...+-+|++|++++.+++...+|++.  ..|.+|+..-++.
T Consensus        20 d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n   83 (189)
T PRK12515         20 DRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARF   83 (189)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHH
Confidence            458999999999999999999998888899999999999999999999964  4799999876664

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=97.75  E-value=6.1e-05  Score=64.86  Aligned_cols=63  Identities=11%  Similarity=0.140  Sum_probs=56.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ...++|+..|.|+|..++.+|.+...+.+|++|+.++.|++.++.|++..  +|.+|+..-+++.
T Consensus         3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~   65 (173)
T PRK12522          3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRT   65 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHH
Confidence            45789999999999999999999889999999999999999999999854  7999987766543

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=97.71  E-value=0.00016  Score=63.86  Aligned_cols=64  Identities=19%  Similarity=0.254  Sum_probs=57.4

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      +..+.+.|+..|.|.|..++.++.+...+-||++||.++.+++.+++|++..  .|.+|+..-+++
T Consensus        25 d~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn   88 (192)
T PRK09643         25 DRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVN   88 (192)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHH
Confidence            3589999999999999999999988888999999999999999999999753  699999876654

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=97.65  E-value=9.8e-05  Score=64.19  Aligned_cols=63  Identities=16%  Similarity=0.155  Sum_probs=56.2

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhh
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIR  326 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR  326 (330)
                      +..+.+.|+..|.|.|..++.+|.+...+-+|++|+..+.|++++.+|++..  .|.+|+..-++
T Consensus         5 d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iar   67 (179)
T PRK12543          5 DQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVI   67 (179)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHH
Confidence            3578999999999999999999998889999999999999999999999875  68888866544

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=97.64  E-value=0.00033  Score=61.16  Aligned_cols=63  Identities=17%  Similarity=0.236  Sum_probs=53.4

Q ss_pred             HHHHHHHHHHhHHHHHHHHHH----cccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQR----YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkr----Y~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..+.+.|+..|.|.+...+.+    +.+...+-+|++|+.++.+++.+..|++..  .|.+|+..-+++
T Consensus        20 ~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n   86 (184)
T PRK12539         20 AAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIARY   86 (184)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHH
Confidence            489999999999999998864    445668899999999999999999999754  599998766554

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=97.62  E-value=0.00017  Score=62.88  Aligned_cols=73  Identities=19%  Similarity=0.251  Sum_probs=61.4

Q ss_pred             HHHHHHhh-hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          254 ELQSILME-CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       254 eL~~~l~~-g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ++...+.. +..+.+.|+..|.+.+..++.++.+...+-+|++|+.++.+++.+.+|++..+ .|.+|+..-+++
T Consensus        12 ~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn   85 (182)
T PRK12537         12 ACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRH   85 (182)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHH
Confidence            34444443 57899999999999999999999988889999999999999999999987544 699998876654

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=97.55  E-value=0.00024  Score=60.82  Aligned_cols=63  Identities=19%  Similarity=0.170  Sum_probs=54.2

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      +..+.+.|+..|.|.|..++.++.+. .+.+|++||.++.+++.++.|++.  ..|.+|+..-+++
T Consensus         9 d~~a~~~l~~~~~~~l~~~~~~~~~~-~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n   71 (175)
T PRK12518          9 DRQSFRQLYRRYQQKVRSTLYQLCGR-ELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWN   71 (175)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHcCH-hHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHH
Confidence            35889999999999999999998643 678999999999999999999975  3699999776543

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=97.50  E-value=0.00023  Score=62.04  Aligned_cols=64  Identities=11%  Similarity=0.162  Sum_probs=56.8

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ...|.++|+..|.|.|..++.++.+...+-+|++|++.+.|++++.+|++..  .|.+|+..-+++
T Consensus        14 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~~--~~~awl~~ia~n   77 (179)
T PRK09415         14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKS--SLKTWLYRIAIN   77 (179)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCCc--ccHHHHHHHHHH
Confidence            4588999999999999999999988888899999999999999999998743  699998776654

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

Probab=97.39  E-value=0.00043  Score=59.69  Aligned_cols=64  Identities=19%  Similarity=0.145  Sum_probs=53.8

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCC-----ChhHHHHHHHHHHHH-HHhhcCCCCCCcchhHHHHHhhcc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGA-----DMADLVQGGLIGLLR-GIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gv-----d~EDLIQEG~IGLik-AIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..+.+.|+..|.+.+..++.+|.....     +-+|++|+..+.+++ ...+|++.  ..|.+|+..++++.
T Consensus        16 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~~n~   85 (183)
T TIGR02999        16 AAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAMRRI   85 (183)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHHHHH
Confidence            378999999999999999999987655     899999999999998 77788754  36889887766643

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

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=97.36  E-value=0.00023  Score=62.03  Aligned_cols=66  Identities=21%  Similarity=0.149  Sum_probs=58.4

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      +..+.+.|+..|.+.+..+|.++.+...+-+|++|+..+.+++.+.+|++..+..|.+|...-+++
T Consensus         7 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn   72 (185)
T PRK12542          7 DYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKN   72 (185)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHH
Confidence            458899999999999999999998888889999999999999999999976555799998776554

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=97.35  E-value=0.00067  Score=59.64  Aligned_cols=61  Identities=18%  Similarity=0.206  Sum_probs=52.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      .+.+.|+..|.+.+..++. +.+...+-+|++|+.++.+++...+|++.  ..|.+|...-+|+
T Consensus        24 ~af~~l~~~~~~~l~~~~~-~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn   84 (185)
T PRK09649         24 RALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARH   84 (185)
T ss_pred             HHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHH
Confidence            8899999999999999995 55556789999999999999999999964  3699998776554

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=97.29  E-value=0.00045  Score=58.52  Aligned_cols=61  Identities=16%  Similarity=0.030  Sum_probs=53.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      .+.++|+..|.+.+..+|.++.+...+.+|++|++++.+++.  .|+.  +..|.+|+...+++.
T Consensus         3 ~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~   63 (166)
T PRK09639          3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNV   63 (166)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHH
Confidence            678999999999999999999988889999999999999998  5653  447999998877654

>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family

Probab=97.21  E-value=0.00087  Score=56.73  Aligned_cols=65  Identities=14%  Similarity=0.064  Sum_probs=57.0

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      +..+.+.|+..|.|.|..++.++.+...+-+|++|++++-+++..++|+.  ...|.+|+..-+++.
T Consensus         4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~   68 (162)
T TIGR02983         4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNL   68 (162)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHH
Confidence            45789999999999999999999988889999999999999999999964  347999988776653

This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.

>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]

Probab=97.19  E-value=0.0016  Score=56.90  Aligned_cols=70  Identities=24%  Similarity=0.252  Sum_probs=59.1

Q ss_pred             HHHHhhhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          256 QSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       256 ~~~l~~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      .........+.+.++..|.+.+...+.++.+...+-|||+||.++.+++++..| +. +..|.||...-+++
T Consensus         7 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n   76 (182)
T COG1595           7 AEALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARN   76 (182)
T ss_pred             HHHHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHH
Confidence            344455678899999999999999999999877799999999999999999999 44 34799999876554

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=97.11  E-value=0.0012  Score=56.59  Aligned_cols=65  Identities=15%  Similarity=0.282  Sum_probs=57.2

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      +.....+++..|.|.|..+|.++.+...+-||++|+..+.+++...+|+...  .|.+|+..-+++.
T Consensus         4 ~~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~   68 (164)
T PRK12547          4 CSKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNE   68 (164)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHH
Confidence            4578899999999999999999998889999999999999999999998543  5999988766553

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=96.99  E-value=0.0024  Score=61.02  Aligned_cols=63  Identities=24%  Similarity=0.283  Sum_probs=55.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..+.++|+..|.+.|..++.++.+...+-+|++|+..+-+++.+.+|++.  ..|.+|.+.-.++
T Consensus        18 ~~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n   80 (339)
T PRK08241         18 RDAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATN   80 (339)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHH
Confidence            48899999999999999999998887899999999999999999999853  3699998776554

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=96.98  E-value=0.0016  Score=55.72  Aligned_cols=59  Identities=14%  Similarity=0.147  Sum_probs=52.1

Q ss_pred             HHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       266 rekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      .+.|++.|.|.|..++.++.+...+-+|++|+..+.+++.+..|++.   +|.+|...-+++
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n   61 (165)
T PRK09644          3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYH   61 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHH
Confidence            46799999999999999999888899999999999999999999863   589988775553

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=96.96  E-value=0.002  Score=54.68  Aligned_cols=62  Identities=11%  Similarity=0.157  Sum_probs=54.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..+.+.++..|.+.|..++.++.+...+-+|++||+.+.+++..++|++.   .|.||+..-+++
T Consensus         4 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n   65 (161)
T PRK12541          4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYN   65 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHH
Confidence            36789999999999999999999888899999999999999999999863   599998765554

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=96.85  E-value=0.0028  Score=54.30  Aligned_cols=64  Identities=16%  Similarity=0.113  Sum_probs=55.7

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..+.+.|+..|.+.+..++.++.+...+-||++|+..+-+++...+|++.. ..|.+|+..-+++
T Consensus         8 ~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn   71 (173)
T PRK09645          8 AALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARN   71 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHH
Confidence            488999999999999999999987777899999999999999999998533 3699998776554

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=96.79  E-value=0.0034  Score=56.63  Aligned_cols=63  Identities=21%  Similarity=0.305  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..+.++|+..|.+.+..++.++.+...+-+|++|+..+.+++.+.+|++  + +|.+|+..-+|+.
T Consensus        27 ~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~   89 (203)
T PRK09647         27 MPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNL   89 (203)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHH
Confidence            5789999999999999999999988889999999999999999999985  3 6999988776643

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=96.76  E-value=0.0036  Score=53.15  Aligned_cols=62  Identities=15%  Similarity=0.092  Sum_probs=54.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      .+.++|+..|.+.|..++.++.+...+-||++|+.++-+++....|+++   .|.+|...++++.
T Consensus         4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~~---~~~~wl~~i~~n~   65 (161)
T PRK12528          4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRV   65 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhcccccccc---CHHHHHHHHHHHH
Confidence            6788999999999999999999887899999999999999988877642   5899998877653

>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1

Probab=96.74  E-value=0.0051  Score=57.47  Aligned_cols=63  Identities=14%  Similarity=0.035  Sum_probs=54.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHH-------HHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLL-------RGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLi-------kAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..+.+.|+..|.+.|..++.++.+...+-||++|+..+-++       +.+.+|++..  .|.||...-.++
T Consensus        38 ~~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~~--~~~tWL~~Ia~N  107 (244)
T TIGR03001        38 PAALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGRG--PLLSWVRIVATR  107 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCCC--chHhHHHHHHHH
Confidence            48999999999999999999998778899999999999998       4788899643  689988765543

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=96.69  E-value=0.0018  Score=54.06  Aligned_cols=55  Identities=15%  Similarity=0.175  Sum_probs=48.3

Q ss_pred             HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..|.|.|..++.++.+.-.+-+|++|+..+.+++.+.+|++   .+|.+|+...++..
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~   56 (154)
T TIGR02950         2 REYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNA   56 (154)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHH
Confidence            46889999999999877778999999999999999999997   47999998876653

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.

>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family

Probab=96.69  E-value=0.0035  Score=55.02  Aligned_cols=63  Identities=17%  Similarity=0.264  Sum_probs=55.9

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..+.++|+..|.+.|...+.++.+...+-+|++|+..+-+++.+.+|++.  .+|.+|...-+++
T Consensus        10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN   72 (193)
T TIGR02947        10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTN   72 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHH
Confidence            47889999999999999999998877889999999999999999999864  3699998876654

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=96.55  E-value=0.0044  Score=54.28  Aligned_cols=61  Identities=16%  Similarity=0.151  Sum_probs=53.5

Q ss_pred             HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      +.++|+..|.+.+...|.++.+...+-||++|+..+.+++.+.+|+...  +|.+|+..-+++
T Consensus         3 ~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n   63 (191)
T PRK12520          3 IAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKH   63 (191)
T ss_pred             chHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHH
Confidence            5688999999999999999988888999999999999999999998553  699998765554

>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=96.53  E-value=0.0044  Score=47.37  Aligned_cols=38  Identities=32%  Similarity=0.536  Sum_probs=29.6

Q ss_pred             chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126          224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME  261 (330)
Q Consensus       224 Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~  261 (330)
                      +.....+|...+||+||.+|+|+.+|++.++++.++..
T Consensus         6 i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~   43 (78)
T PF04539_consen    6 IERARRELEQELGREPTDEEIAEELGISVEEVRELLQA   43 (78)
T ss_dssp             HHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHh
Confidence            34567789999999999999999999999999777653

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 ....

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=96.52  E-value=0.011  Score=52.77  Aligned_cols=63  Identities=13%  Similarity=0.107  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..+.+.|+..|.+.+..++. +.+...+-||++|+-++.|++.+.+|++.  ..|.+|+..-+|..
T Consensus        24 ~~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~   86 (196)
T PRK12535         24 RAALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRV   86 (196)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHH
Confidence            47899999999999999975 45566789999999999999999999864  36999988777654

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=96.50  E-value=0.0073  Score=53.14  Aligned_cols=61  Identities=16%  Similarity=0.180  Sum_probs=53.9

Q ss_pred             HHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       266 rekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      .+.|+..|.+.|..++.++.+...+.+|++||..+.+++.+..|++.  .+|.+|+..-+++.
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~   63 (181)
T PRK09637          3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNT   63 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHH
Confidence            46789999999999999999888999999999999999999999853  37999998876653

>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family

Probab=96.46  E-value=0.0048  Score=54.51  Aligned_cols=59  Identities=15%  Similarity=0.138  Sum_probs=52.2

Q ss_pred             HHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       267 ekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      .+.|..|.+.|..++.++.+...+-+|++|+..+.+++...+|++.  .+|.+|++..+++
T Consensus         5 ~~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn   63 (188)
T TIGR02943         5 PQELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKN   63 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHH
Confidence            4678899999999999999888899999999999999999999965  4799999876654

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

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=96.44  E-value=0.011  Score=54.18  Aligned_cols=63  Identities=17%  Similarity=0.251  Sum_probs=55.1

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ...+.+.|+..|.+.+..++.++.+...+-||++|+.++-+++.+.+|++.   .|.+|+..-+++
T Consensus        16 ~~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN   78 (216)
T PRK12533         16 RGERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRH   78 (216)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHH
Confidence            457899999999999999999998888889999999999999999999853   489998765543

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=96.42  E-value=0.0056  Score=53.79  Aligned_cols=59  Identities=15%  Similarity=0.276  Sum_probs=50.1

Q ss_pred             HHHHHHhHHHHHHHHHHcccCCCC-hhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          267 EKLVMSNVRLVMSIAQRYDNMGAD-MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       267 ekLI~~nLpLV~sIAkrY~~~Gvd-~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      +..+..|.+.|..+|.++.+...+ -||++|+.++.+++...+|+..  .+|.+|+..-+++
T Consensus         8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n   67 (195)
T PRK12532          8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKN   67 (195)
T ss_pred             hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHH
Confidence            356678999999999999887777 9999999999999999999864  3799998776654

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=96.34  E-value=0.0097  Score=52.68  Aligned_cols=66  Identities=17%  Similarity=0.121  Sum_probs=58.3

Q ss_pred             hhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       261 ~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ....+.+.++..|.+.|..+|.++.+...+-+|++|+..+-+++.+..|++..  .|.+|+...+|+.
T Consensus        20 ~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~~--~~~~wL~~Iarn~   85 (188)
T PRK12517         20 SKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEK--AAKAWLITILRRE   85 (188)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCcc--chHHHHHHHHHHH
Confidence            35689999999999999999999988888899999999999999999999653  6899988777653

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=96.32  E-value=0.011  Score=52.41  Aligned_cols=63  Identities=11%  Similarity=0.210  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..+.++|+..|.+.+...|.++.+...+-||++|+..+-+++...+|+...  .|.+|+..-.++
T Consensus         9 ~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n   71 (187)
T PRK12516          9 TPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRN   71 (187)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHH
Confidence            478899999999999999999998878899999999999999999998643  599998765544

>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family

Probab=96.24  E-value=0.011  Score=55.71  Aligned_cols=63  Identities=21%  Similarity=0.254  Sum_probs=55.9

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..+.+.|+..|.+.+..+|.++.+...+-||++|+..+-+++.+.+|++.  ..|.+|+..-+++
T Consensus         4 ~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n   66 (324)
T TIGR02960         4 GAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATN   66 (324)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHH
Confidence            47899999999999999999998888889999999999999999999964  3699998776654

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

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=96.12  E-value=0.0089  Score=51.78  Aligned_cols=56  Identities=18%  Similarity=0.243  Sum_probs=48.3

Q ss_pred             HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..|.+.+...+.++.+...+-+|++|+..+.+++++.+|++.  .+|.+|+..-+++.
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~   57 (170)
T TIGR02959         2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNT   57 (170)
T ss_pred             chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHH
Confidence            357888889999998888899999999999999999999963  47999998876653

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).

>PF12645 HTH_16: Helix-turn-helix domain; InterPro: IPR024760 This domain appears to be a helix-turn-helix domain, suggesting a transcriptional regulatory protein

Probab=96.11  E-value=0.026  Score=43.51  Aligned_cols=48  Identities=25%  Similarity=0.227  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHc----cc--CCCChhHHHHHHHHHHHHHHhhcC
Q 020126          263 SLAREKLVMSNVRLVMSIAQRY----DN--MGADMADLVQGGLIGLLRGIEKFD  310 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY----~~--~Gvd~EDLIQEG~IGLikAIekFD  310 (330)
                      ..|.++++..|.|++.+.+.|-    .+  .+.--+||-|+=...||+||.+|+
T Consensus        12 ~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~   65 (65)
T PF12645_consen   12 PEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE   65 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence            3899999999999999998772    11  245569999999999999999996

Some proteins with this domain are annotated as conjugative transposon proteins.

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=95.96  E-value=0.0063  Score=51.51  Aligned_cols=54  Identities=7%  Similarity=0.121  Sum_probs=47.2

Q ss_pred             HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..|.+.+..++.++.+...+-+|++||..+.+++.+.+|++.   .|.+|+..-+++
T Consensus         2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n   55 (160)
T PRK09642          2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATN   55 (160)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHH
Confidence            568999999999998887899999999999999999999963   499998776554

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=95.90  E-value=0.022  Score=50.31  Aligned_cols=62  Identities=19%  Similarity=0.327  Sum_probs=54.1

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      .+...++..|.|.+...+.++.+...+-||++|+..+.+++..++|++..  .|.+|+..-+++
T Consensus         5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n   66 (182)
T PRK12540          5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRN   66 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHH
Confidence            45678899999999999999988888999999999999999999998664  589998776654

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=95.87  E-value=0.013  Score=61.54  Aligned_cols=33  Identities=24%  Similarity=0.481  Sum_probs=31.5

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCcc
Q 020126          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS  223 (330)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~  223 (330)
                      +.++.||+++++.||||.++|++++++|..|..
T Consensus       104 DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~  136 (619)
T PRK05658        104 DPVRMYLREMGTVELLTREGEIEIAKRIEAGEN  136 (619)
T ss_pred             ChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHH
Confidence            799999999999999999999999999999864

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=95.69  E-value=0.022  Score=49.63  Aligned_cols=66  Identities=9%  Similarity=-0.108  Sum_probs=53.1

Q ss_pred             hHHHHHHHHHHhHHHHHHHHHHccc--CCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          262 CSLAREKLVMSNVRLVMSIAQRYDN--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       262 g~~ArekLI~~nLpLV~sIAkrY~~--~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      +..+.+.|+..|.+.|...+.++.+  ...+-||++|+..+-+++...+|+......|.+|...-.++
T Consensus        11 d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n   78 (178)
T PRK12529         11 DRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANC   78 (178)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHH
Confidence            3578999999999999997555444  24679999999999999999999865455799998776554

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=95.65  E-value=0.034  Score=49.51  Aligned_cols=61  Identities=20%  Similarity=0.314  Sum_probs=51.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      +..+.|. .|.|.|...|.++.+...+-+|++|+..+.+++.+..|+..  ..|.+|+..-+++
T Consensus         8 ~~~~~l~-~~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n   68 (188)
T PRK12546          8 DPRDELV-EHLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRN   68 (188)
T ss_pred             hHHHHHH-HHHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHH
Confidence            4455554 47799999999999888999999999999999999999864  3699998776654

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=95.59  E-value=0.023  Score=49.02  Aligned_cols=63  Identities=13%  Similarity=0.065  Sum_probs=52.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ..+..+|+..|.+.|..++.++.+...+-+|++|+.++.+++. ..|+..  ..|.+|....+++.
T Consensus         9 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~   71 (172)
T PRK12523          9 SELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGL   71 (172)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHH
Confidence            3789999999999999999999888889999999999999986 445533  36899987766653

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=95.50  E-value=0.029  Score=50.70  Aligned_cols=59  Identities=19%  Similarity=0.210  Sum_probs=51.8

Q ss_pred             HHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       267 ekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..++..|.+.|...+.++.+...+-+|++|+.++.+++.+.+|+..  .+|.+|...-+++
T Consensus        21 ~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN   79 (206)
T PRK12544         21 PVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKN   79 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHH
Confidence            5678889999999999999888899999999999999999999854  3699999776654

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=95.36  E-value=0.046  Score=47.35  Aligned_cols=62  Identities=16%  Similarity=0.182  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       263 ~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..+.+.++..|.+.+..++.++.+...+-||++|+..+-+++. ..|++-.  .|.+|+..-++.
T Consensus         9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn   70 (172)
T PRK09651          9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKR   70 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHH
Confidence            4789999999999999999999888888999999999999987 3454433  578887665554

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=95.34  E-value=0.027  Score=47.64  Aligned_cols=57  Identities=18%  Similarity=0.321  Sum_probs=45.9

Q ss_pred             HHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       268 kLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      +++..|.+.+..+|.++.+...+-+|++|+..+.+++....|++.   .|.+|+..-+|+
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn   58 (163)
T PRK07037          2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRN   58 (163)
T ss_pred             hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHH
Confidence            357788899999999998887889999999999999888777653   467777655543

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=95.02  E-value=0.046  Score=48.76  Aligned_cols=58  Identities=16%  Similarity=0.139  Sum_probs=50.2

Q ss_pred             HHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       268 kLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      .++..|.+-+...+.++.+...+-+|++|+..+.+++.+.+|++..  .|.+|+..-+|+
T Consensus        12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN   69 (201)
T PRK12545         12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRN   69 (201)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHH
Confidence            4478899999999999998878999999999999999999999763  599998766554

>PRK09191 two-component response regulator; Provisional

Probab=94.94  E-value=0.074  Score=47.60  Aligned_cols=61  Identities=11%  Similarity=0.096  Sum_probs=53.2

Q ss_pred             HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      +..+|+..|.+.+...+.++.+...+-+|++|+.++-+++....|++.  ..|.+|...++++
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~   62 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHR   62 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHH
Confidence            357899999999999999998877889999999999999999999875  3588988877654

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=94.32  E-value=0.076  Score=46.86  Aligned_cols=58  Identities=12%  Similarity=0.181  Sum_probs=49.3

Q ss_pred             HHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       268 kLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      .-|..|.+.+...|.++.+...+-+|++|+..+-+++.+..|++..  +|.+|+..-.++
T Consensus        11 ~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n   68 (189)
T PRK12530         11 LEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKN   68 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHH
Confidence            3467788999999999988778999999999999999999998653  699998775544

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=94.27  E-value=0.077  Score=46.93  Aligned_cols=61  Identities=18%  Similarity=0.228  Sum_probs=51.8

Q ss_pred             HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      .++..+..+.+-|...+.++.+...+-+|++|+..+-+++.+..|+..  .+|.+|...-+++
T Consensus         5 ~~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn   65 (182)
T PRK12511          5 SKRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHN   65 (182)
T ss_pred             chhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHH
Confidence            345567889999999999998887889999999999999999999864  3699999876654

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=93.53  E-value=0.21  Score=43.00  Aligned_cols=61  Identities=7%  Similarity=-0.045  Sum_probs=49.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      .+..+++..|.+.+...+.++.+...+-+|++|+..+-+++-...++   ...|.+|...-.++
T Consensus         9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~---~~~~~~wl~~Iarn   69 (168)
T PRK12525          9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPAS---IREPRALLTTIARR   69 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCccc---ccCHHHHHHHHHHH
Confidence            67788999999999999999998888999999999999997544443   23688887765544

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

Probab=93.24  E-value=0.33  Score=48.60  Aligned_cols=32  Identities=31%  Similarity=0.509  Sum_probs=30.1

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCc
Q 020126          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGL  222 (330)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~  222 (330)
                      ..+..|+..+...+.|+++||.+|+++++.|.
T Consensus        67 ~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~   98 (342)
T COG0568          67 GRLSFYIRAIEAAPLLTPEEEKALARRLKRGE   98 (342)
T ss_pred             hhHHHHHHHHhhhcccChHHHHHHHHHHHcCC
Confidence            57888999999999999999999999999996

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=93.13  E-value=0.14  Score=48.46  Aligned_cols=59  Identities=14%  Similarity=0.053  Sum_probs=47.8

Q ss_pred             HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ...+|+..|.+.+..+|.++.+...+-||++||..+.+. ....|+   ...|.+|.+.-+++
T Consensus         5 ~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~~~-~~~~~~---~~~~~~WL~~Ia~n   63 (293)
T PRK09636          5 DAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWN-NADRAQ---IRDPRAWLTRVVTR   63 (293)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH-hccccc---ccCHHHHHHHHHHH
Confidence            466889999999999999999888899999999999844 445665   34799998775554

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=93.06  E-value=0.13  Score=43.59  Aligned_cols=54  Identities=7%  Similarity=0.050  Sum_probs=42.7

Q ss_pred             HHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       271 ~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      ..|.+.+...+.++.+...+-+|++|+..+.|++....|++.   +|.+|...-+++
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n   55 (159)
T PRK12527          2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALN   55 (159)
T ss_pred             hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHH
Confidence            356677777777777777789999999999999999988753   688887765554

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

Probab=92.19  E-value=0.6  Score=44.69  Aligned_cols=66  Identities=23%  Similarity=0.383  Sum_probs=49.3

Q ss_pred             hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhh
Q 020126          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC  262 (330)
Q Consensus       189 ~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g  262 (330)
                      +.+.+..||+.-.  ..--|---.++.+++.      .....++..+|++||++|+|+.+|++.+|+..++..+
T Consensus        85 I~Gei~d~LR~~~--~v~vpR~~~~~~~~i~------~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~  150 (247)
T COG1191          85 IRGEILDYLRKND--SVKVPRSLRELGRRIE------EAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAI  150 (247)
T ss_pred             HHHHHHHHHHhCC--CccCcHHHHHHHHHHH------HHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHh
Confidence            4567778888887  2223334445555544      4667899999999999999999999999988777664

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=90.21  E-value=0.62  Score=43.61  Aligned_cols=67  Identities=18%  Similarity=0.102  Sum_probs=47.7

Q ss_pred             HHHHHhhhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhc
Q 020126          255 LQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       255 L~~~l~~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~  327 (330)
                      |.+.+.-...+.+.+++.| +.+...+.++.+...+-||++|+..+-+++   +|+...  .|.+|+..-.|+
T Consensus         9 ~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~---~~~~~~--~~~~WL~~IarN   75 (228)
T PRK06704          9 LKNHIDMNHSNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQ---KYSNKD--ICMTLVYKIARN   75 (228)
T ss_pred             HhcccCCCHHHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHH---HcCccc--cHHHHHHHHHHH
Confidence            3333444446677777766 788888888887778999999999988876   466432  488888765543

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=88.42  E-value=0.68  Score=44.46  Aligned_cols=59  Identities=14%  Similarity=-0.062  Sum_probs=47.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhh
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIR  326 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR  326 (330)
                      .....++..|.+.+..+|.++.+...+-||++||.++-++++...+    ...|.+|.+.-.+
T Consensus         5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~----~~~~~aWL~~Ia~   63 (290)
T PRK09635          5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD----IDDERGWLIVVTS   63 (290)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc----cccHHHHHHHHHH
Confidence            4567889999999999999999888899999999999888775432    2358888775443

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=88.28  E-value=2  Score=38.09  Aligned_cols=63  Identities=19%  Similarity=0.143  Sum_probs=42.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHccc---CCCChhHHHHHHHHHHHHHHh--hc-CCCCCCcchhHHHHHhhc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIE--KF-DSSKGFKISTYVYWWIRQ  327 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~---~Gvd~EDLIQEG~IGLikAIe--kF-DpsrG~rFsTYA~~wIR~  327 (330)
                      .|.++|+..|.+-++.+|+++..   ++.+.+|..+ ..-++++.+.  .| +.+....|-.|+..-+++
T Consensus        17 ~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~l-v~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~rr   85 (185)
T PF07638_consen   17 AALDQLFERYYPELRRLARRRLRRERRGHDLQDTAL-VHEAFLRLARRGRFVQFSDRRHFWALLARIMRR   85 (185)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHH-HHHHHHHHhccccccCCCCHHHHHHHHHHHHHH
Confidence            89999999999999999988653   2456666544 3445555554  22 444434677777776654

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=88.11  E-value=0.97  Score=41.67  Aligned_cols=60  Identities=15%  Similarity=0.303  Sum_probs=48.0

Q ss_pred             HHHHhHHHHHHHHHHcccCCCC---hhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          269 LVMSNVRLVMSIAQRYDNMGAD---MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       269 LI~~nLpLV~sIAkrY~~~Gvd---~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      |-.+.+.++..++++|.-+|+.   .+|+|.+|.-.+++.+..|||++...+-+|.+..+-++
T Consensus        42 ig~~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~A  104 (179)
T PHA02547         42 IGLAIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNA  104 (179)
T ss_pred             HHHHHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHH
Confidence            3345666666777777666766   89999999999999999999999988889988766443

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=87.43  E-value=3.1  Score=39.30  Aligned_cols=66  Identities=21%  Similarity=0.281  Sum_probs=45.6

Q ss_pred             hhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126          188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM  260 (330)
Q Consensus       188 l~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~  260 (330)
                      ++...+..||++....-.+ |---.++..+++.      ....+...+|++||.+++|+.+|++.+++...+.
T Consensus       100 ~Irg~I~~~lr~~~~~ir~-Pr~~~~~~~~i~~------~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~  165 (264)
T PRK07122        100 TIMGEVRRHFRDNSWSVKV-PRRLKELHLRLGR------ATAELSQRLGRAPTASELAAELGMDREEVVEGLV  165 (264)
T ss_pred             HHHHHHHHHHHHcCCcccc-CHHHHHHHHHHHH------HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4666777788775542222 2223345555543      4557888899999999999999999999877654

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=87.32  E-value=1.8  Score=40.61  Aligned_cols=64  Identities=25%  Similarity=0.300  Sum_probs=43.9

Q ss_pred             hhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126          188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME  261 (330)
Q Consensus       188 l~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~  261 (330)
                      .+.+.+..|++....   + |-.-.+...+++      .....+...+|++|+.+++|+.+|++.+++..++..
T Consensus        86 ~Ir~~i~~~lr~~~~---~-pr~~~~~~~~l~------~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~  149 (257)
T PRK05911         86 LIKAAIIDDLRKQDW---V-PRSVHQKANKLA------DAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSS  149 (257)
T ss_pred             HHHHHHHHHHHhcCC---C-CHHHHHHHHHHH------HHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHH
Confidence            345566667766654   2 223334444443      345568888999999999999999999998776543

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=86.35  E-value=3.5  Score=38.39  Aligned_cols=65  Identities=15%  Similarity=0.240  Sum_probs=42.6

Q ss_pred             hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME  261 (330)
Q Consensus       189 ~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~  261 (330)
                      +.+.+..|++...... + |..-.++..++..      ...++...+|++||.+++|+.+|++.+++...+..
T Consensus        95 irn~~~~~lr~~~~ir-~-p~~~~~~~~~~~~------~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~  159 (254)
T TIGR02850        95 IIGEIRRYLRDNNPIR-V-SRSLRDIAYKALQ------VRDKLISENSKEPTVSEIAKELKVPQEEVVFALDA  159 (254)
T ss_pred             HHHHHHHHHHhCCCcc-C-chHHHHHHHHHHH------HHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            4455566666643221 2 2223344444432      34567888999999999999999999998776554

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.

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=86.07  E-value=2.3  Score=39.39  Aligned_cols=62  Identities=23%  Similarity=0.379  Sum_probs=42.9

Q ss_pred             hhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM  260 (330)
Q Consensus       189 ~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~  260 (330)
                      +.+.+..||+.....|    -.......+++      .....+...+|++|+.+++|+.+|++.+++..++.
T Consensus        78 Ir~~il~~lr~~~~~~----r~vr~~~~~i~------~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~  139 (231)
T PRK12427         78 IRGAILDELRELDWRP----RRLRQKTHKTN------DAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLL  139 (231)
T ss_pred             HHHHHHHHHHhcCCCC----HHHHHHHHHHH------HHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4456666777654322    12233444443      34567888899999999999999999999877654

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=85.81  E-value=3.1  Score=38.96  Aligned_cols=65  Identities=23%  Similarity=0.382  Sum_probs=43.4

Q ss_pred             hhhhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHH
Q 020126          188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL  259 (330)
Q Consensus       188 l~q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l  259 (330)
                      .+.+.+..||+.....-.+. -.-.++.++++      .....+...+|++|+.+++|+.+|++.+++..+.
T Consensus        86 ~Ir~~i~~~lr~~~~~vr~p-r~~~~~~~~~~------~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~  150 (256)
T PRK07408         86 YIRGEIQHYLRDKSPTVRIP-RRWQELQRQAK------KVRQELRQELGRQPTDQEIAQALDISLEEWQEIK  150 (256)
T ss_pred             HHHHHHHHHHHHcCCeeeeC-HHHHHHHHHHH------HHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHH
Confidence            34556667777554322221 12223444443      3456788899999999999999999999987764

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=84.18  E-value=2.5  Score=35.18  Aligned_cols=56  Identities=14%  Similarity=0.134  Sum_probs=41.5

Q ss_pred             HHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCC---CCCcchhHHHHHhhc
Q 020126          267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSS---KGFKISTYVYWWIRQ  327 (330)
Q Consensus       267 ekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDps---rG~rFsTYA~~wIR~  327 (330)
                      +.|+..|.+++..++++|..     +|.+|+-.+.+++...+|+.+   ....|.||...-.|+
T Consensus         2 ~~~~~~y~~~l~~~~~~~~~-----~~~~qdvf~~~w~~~~~~~~~~~~~~~~~~~wL~~iarN   60 (142)
T TIGR03209         2 EEIYMNFKNTIDIFTRKYNL-----YYDYNDILYHLWIILKKIDLNKFNTENDLEKYISTSLKR   60 (142)
T ss_pred             hHHHHHHHHHHHHHHHHhcc-----hhhHHHHHHHHHHHHHHhhhhhcCchhHHHHHHHHHHHH
Confidence            57899999999999999965     233499999999988654311   124699998876554

Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=83.94  E-value=4.4  Score=39.85  Aligned_cols=35  Identities=29%  Similarity=0.379  Sum_probs=30.0

Q ss_pred             hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126          226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILM  260 (330)
Q Consensus       226 ~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~  260 (330)
                      .....|...+|++||.+|+|..+|++.+++...+.
T Consensus       177 ~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~  211 (324)
T PRK07921        177 RIKRELHQQLGREATDEELAEESGIPEEKIADLLE  211 (324)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence            45667888999999999999999999999877643

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=82.52  E-value=4.8  Score=38.60  Aligned_cols=69  Identities=16%  Similarity=0.140  Sum_probs=44.3

Q ss_pred             hhhhhhHHHHHHhcCCCCCC-CHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHH
Q 020126          187 ELIQNRLKGYVKGVVSEELL-THAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI  258 (330)
Q Consensus       187 El~q~~l~~YL~~i~~~~lL-T~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~  258 (330)
                      -++...+..||+.-.....+ +...+..+..+++.   ++.........+|++|+.+|+|+.+|++.+++...
T Consensus        99 ~~Ir~~I~~~lr~~~~~iR~p~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~  168 (289)
T PRK07500         99 WWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRR---LRARLAQADEELTKQEIHREIATALGVSLSDVEMM  168 (289)
T ss_pred             HHHHHHHHHHHHHCCCceecCccHHHHHHHHHHHH---HHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHH
Confidence            35667777888764433222 33444555555542   22223333346899999999999999999998654

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=82.40  E-value=5.3  Score=39.70  Aligned_cols=37  Identities=24%  Similarity=0.368  Sum_probs=31.3

Q ss_pred             hhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126          225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME  261 (330)
Q Consensus       225 e~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~  261 (330)
                      .....++...+|++||.+|+|..+|++.++++.++..
T Consensus       219 ~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~  255 (367)
T PRK09210        219 IRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI  255 (367)
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence            3456678889999999999999999999999876543

>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain

Probab=81.38  E-value=2.4  Score=38.92  Aligned_cols=35  Identities=26%  Similarity=0.428  Sum_probs=29.9

Q ss_pred             hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHh
Q 020126          226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILM  260 (330)
Q Consensus       226 ~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~  260 (330)
                      .....+...+|++||.+++|+.+|++.+++..++.
T Consensus        91 ~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~  125 (238)
T TIGR02393        91 KAERQLTQELGREPTDEELAERMGMPAEKVREIKK  125 (238)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            34567888999999999999999999999977654

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.

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=80.28  E-value=1.5  Score=41.48  Aligned_cols=41  Identities=22%  Similarity=0.153  Sum_probs=35.6

Q ss_pred             HHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcC
Q 020126          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFD  310 (330)
Q Consensus       268 kLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFD  310 (330)
                      +++..|.|.+..+|.++.+...|-||++||..+-+.+.  .|+
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~   41 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRA   41 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Ccc
Confidence            36889999999999999988889999999999997764  454

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	330
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		6e-16
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		9e-16
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		1e-15
1sig_A	339	Crystal Structure Of A Sigma70 Subunit Fragment Fro		1e-15
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		1e-15
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		2e-15
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		2e-15
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		2e-15
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		2e-15
3les_A	179	2f5 Epitope Scaffold Es2 Length = 179		2e-15
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		3e-15
1l0o_C	243	Crystal Structure Of The Bacillus Stearothermophilu		9e-09

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

Iteration: 1
 Score = 81.6 bits (200), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 50/153 (32%), Positives = 84/153 (54%), Gaps = 15/153 (9%)
Query: 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLS----------LDDHKLR--LKERLGCEPS 240
           ++ Y+  +    LLT  E + L++K++ G+           LD   +R  ++ ++     
Sbjct: 5   VRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTAR 64
Query: 241 MEQLAASLRISRPELQSILM---ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG 297
           +E++   L+    EL+  L    E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q 
Sbjct: 65  VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQE 124
Query: 298 GLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
           G  GL+R +EKF+  + FK STY  WWIRQ+I+
Sbjct: 125 GNQGLIRAVEKFEYKRRFKFSTYATWWIRQAIN 157

>pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-Dependent Transcription Initiation Complex Length = 613

Iteration: 1
 Score = 80.9 bits (198), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 32/66 (48%), Positives = 51/66 (77%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A++++V +N+RLV+SIA++Y N G    DL+Q G IGL++ ++KF+  +G+K STY  WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
Query: 325 IRQSIS 330
           IRQ+I+
Sbjct: 435 IRQAIT 440

>pdb|4IGC|X Chain X, X-ray Crystal Structure Of Escherichia Coli Sigma70 Holoenzyme Length = 613

Iteration: 1
 Score = 80.9 bits (198), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 32/66 (48%), Positives = 51/66 (77%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A++++V +N+RLV+SIA++Y N G    DL+Q G IGL++ ++KF+  +G+K STY  WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434
Query: 325 IRQSIS 330
           IRQ+I+
Sbjct: 435 IRQAIT 440

>pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From Escherichia Coli Rna Polymerase Length = 339

Iteration: 1
 Score = 80.9 bits (198), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 32/66 (48%), Positives = 51/66 (77%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A++++V +N+RLV+SIA++Y N G    DL+Q G IGL++ ++KF+  +G+K STY  WW
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 325
Query: 325 IRQSIS 330
           IRQ+I+
Sbjct: 326 IRQAIT 331

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

Iteration: 1
 Score = 80.1 bits (196), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 55/178 (30%), Positives = 90/178 (50%), Gaps = 34/178 (19%)
Query: 185 SPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGL----------SLDDHKLR---- 230
            P +  + ++ Y+  +    LLT  E + L++K++ G+           LD   +R    
Sbjct: 1   GPHMTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVR 60
Query: 231 --------------LKERLGCEP-SMEQLAASLRISRPELQ---SILMECSLAREKLVMS 272
                         LKE+   +P ++E++   L+    EL+    I  E   AR+ L+ +
Sbjct: 61  AKILGTARIQKIPGLKEK--PDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEA 118
Query: 273 NVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSIS 330
           N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  + FK STY  WWIRQ+I+
Sbjct: 119 NLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAIN 176

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

Iteration: 1
 Score = 80.1 bits (196), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 35/73 (47%), Positives = 49/73 (67%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
           I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  + FK 
Sbjct: 176 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 235
Query: 318 STYVYWWIRQSIS 330
           STY  WWIRQ+I+
Sbjct: 236 STYATWWIRQAIN 248

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

Iteration: 1
 Score = 80.1 bits (196), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 35/73 (47%), Positives = 49/73 (67%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
           I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  + FK 
Sbjct: 176 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 235
Query: 318 STYVYWWIRQSIS 330
           STY  WWIRQ+I+
Sbjct: 236 STYATWWIRQAIN 248

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

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 35/73 (47%), Positives = 49/73 (67%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
           I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  + FK 
Sbjct: 196 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 255
Query: 318 STYVYWWIRQSIS 330
           STY  WWIRQ+I+
Sbjct: 256 STYATWWIRQAIN 268

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

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 35/73 (47%), Positives = 49/73 (67%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
           I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  + FK 
Sbjct: 191 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 250
Query: 318 STYVYWWIRQSIS 330
           STY  WWIRQ+I+
Sbjct: 251 STYATWWIRQAIN 263

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

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 35/73 (47%), Positives = 49/73 (67%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
           I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  +GF  
Sbjct: 99  IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRGFAF 158
Query: 318 STYVYWWIRQSIS 330
           STY  WWIRQ+I+
Sbjct: 159 STYATWWIRQAIN 171

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

Iteration: 1
 Score = 79.0 bits (193), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 35/73 (47%), Positives = 49/73 (67%)
Query: 258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI 317
           I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  + FK 
Sbjct: 100 IAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF 159
Query: 318 STYVYWWIRQSIS 330
           STY  WWIRQ+I+
Sbjct: 160 STYATWWIRQAIN 172

>pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti- Sigma Factor Spoiiab With The Sporulation Sigma Factor Sigmaf Length = 243

Iteration: 1
 Score = 57.8 bits (138), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 27/56 (48%), Positives = 38/56 (67%)
Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
           AR++++  N+RLV S+ QR+ N G +  DL Q G IGLL+ ++KFD S   K STY
Sbjct: 29  ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTY 84

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	330
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	1e-23
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	2e-23
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	3e-23
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	3e-22
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	6e-20
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	3e-18
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	4e-18
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-11
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	6e-06

>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 = 96.9 bits (241), Expect = 1e-23
 Identities = 47/163 (28%), Positives = 82/163 (50%), Gaps = 5/163 (3%)

Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVKGV--VSEELLTHAEVVRLSKKIKTGLSLDDHKL 229
           L + G   L ++     +  +++  ++ +  +SE      E++R   + K   +    K+
Sbjct: 13  LHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKI 72

Query: 230 RLKERLGCEPSMEQLAASLRISRPE---LQSILMECSLAREKLVMSNVRLVMSIAQRYDN 286
              +      ++E++   L+    E      I  E   AR+ L+ +N+RLV+SIA++Y  
Sbjct: 73  PGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG 132

Query: 287 MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
            G    DL+Q G  GL+R +EKF+  + FK STY  WWIRQ+I
Sbjct: 133 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAI 175

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

 Score = 95.7 bits (239), Expect = 2e-23
 Identities = 29/65 (44%), Positives = 40/65 (61%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           AR++++  N+RLV S+ QR+ N G +  DL Q G IGLL+ ++KFD S   K STY    
Sbjct: 29  ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPM 88

Query: 325 IRQSI 329
           I   I
Sbjct: 89  IIGEI 93

>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 = 98.4 bits (245), Expect = 3e-23
 Identities = 45/164 (27%), Positives = 71/164 (43%), Gaps = 30/164 (18%)

Query: 196 YVKGVVSEELLTHAEVVRLSKKIKTGL---------SLDDHKLRLKERLGCEPSMEQLAA 246
           Y+  +    LLT  E V L++K++ G+         +  D  L  +          ++  
Sbjct: 84  YLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRH 143

Query: 247 SLRISRPELQSILMECSL---------------------AREKLVMSNVRLVMSIAQRYD 285
              +        + E                        AR+ L+ +N+RLV+SIA++Y 
Sbjct: 144 IPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT 203

Query: 286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
             G    DL+Q G  GL+R +EKF+  + FK STY  WWIRQ+I
Sbjct: 204 GRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAI 247

>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 = 95.4 bits (237), Expect = 3e-22
 Identities = 54/260 (20%), Positives = 87/260 (33%), Gaps = 17/260 (6%)

Query: 70  QPIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFER 129
           +P+K  +   +   A   +   EP   +     EL+   + L L      +         
Sbjct: 20  EPVKEPEPLPELEAAEDLQDLPEPDPELLASEPELEDLADPLDLEGPLEADLLPEEGLLE 79

Query: 130 TVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELI 189
               +    K     PV       RQ      +  L   +  +        R +      
Sbjct: 80  EEEEELSLPKVSTSDPV-------RQYLHEIGQVPLLTLEEEIDLA-----RKVEEGMEA 127

Query: 190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLR 249
             +L                  +  + +I+    L +                       
Sbjct: 128 IKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPK---- 183

Query: 250 ISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKF 309
                   I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF
Sbjct: 184 -ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKF 242

Query: 310 DSSKGFKISTYVYWWIRQSI 329
           +  + FK STY  WWIRQ+I
Sbjct: 243 EYKRRFKFSTYATWWIRQAI 262

>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 = 88.0 bits (218), Expect = 6e-20
 Identities = 32/77 (41%), Positives = 53/77 (68%)

Query: 254 ELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSK 313
            +     +   A++++V +N+RLV+SIA++Y N G    DL+Q G IGL++ ++KF+  +
Sbjct: 255 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 314

Query: 314 GFKISTYVYWWIRQSIS 330
           G+K STY  WWIRQ+I+
Sbjct: 315 GYKFSTYATWWIRQAIT 331

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

 Score = 84.7 bits (209), Expect = 3e-18
 Identities = 32/77 (41%), Positives = 53/77 (68%)

Query: 254 ELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSK 313
            +     +   A++++V +N+RLV+SIA++Y N G    DL+Q G IGL++ ++KF+  +
Sbjct: 364 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 423

Query: 314 GFKISTYVYWWIRQSIS 330
           G+K STY  WWIRQ+I+
Sbjct: 424 GYKFSTYATWWIRQAIT 440

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

 Score = 81.1 bits (201), Expect = 4e-18
 Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 3/68 (4%)

Query: 265 AREKLVMSNVRLVMSIAQR---YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYV 321
            RE+L++  + LV +IA     +     D+ DL+  G+IGL++ ++   +    +   Y+
Sbjct: 13  EREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYI 72

Query: 322 YWWIRQSI 329
              I+ +I
Sbjct: 73  KLRIKGAI 80

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

 Score = 64.9 bits (157), Expect = 1e-11
 Identities = 59/339 (17%), Positives = 112/339 (33%), Gaps = 78/339 (23%)

Query: 44  GSTKNVVAAKKSSNYN--PSFP------------SSNRQTQPIKALKEHVDTNFASTAEP 89
           GS K  VA     +Y                   S     + ++ L   +D N+ S ++ 
Sbjct: 160 GSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDH 219

Query: 90  WAEPPNSIEEESSEL-------DYSVEALLLLQKSMLEKQWNLSFE---RTVLTDSPSKK 139
            +     I    +EL        Y    LL+L      K WN +F    + +LT      
Sbjct: 220 SSNIKLRIHSIQAELRRLLKSKPY-ENCLLVLLNVQNAKAWN-AFNLSCKILLT------ 271

Query: 140 T-HKKVPVTCSGVSARQRRLNSKKKILS--QNKSILQQ--------------NGSKQLRS 182
           T  K+V    S  +     L+     L+  + KS+L +                + +  S
Sbjct: 272 TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS 331

Query: 183 MISPELIQ---NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGL-SLDDHKLR-LKERLGC 237
           +I  E I+        +           H    +L+  I++ L  L+  + R + +RL  
Sbjct: 332 II-AESIRDGLATWDNW----------KHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSV 380

Query: 238 EPS----MEQLAASL--RISRPELQSILMEC---SLAREKLVMSNVRLVMSIAQRYDNMG 288
            P        L + +   + + ++  ++ +    SL  ++   S + +  SI        
Sbjct: 381 FPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISI-PSIYLELKVKL 439

Query: 289 ADMADLVQGGLIGLLRGIEKFDSSKGFK--ISTYVYWWI 325
            +   L +  ++      + FDS       +  Y Y  I
Sbjct: 440 ENEYALHR-SIVDHYNIPKTFDSDDLIPPYLDQYFYSHI 477

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp} Length = 164

 Score = 44.8 bits (106), Expect = 6e-06
 Identities = 16/42 (38%), Positives = 28/42 (66%), Gaps = 1/42 (2%)

Query: 288 GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
           GA+  DLVQ G++GLL+ I+ +D +K    S++ +  IR+ +
Sbjct: 1   GAEKEDLVQEGILGLLKAIKFYDETKS-SFSSFAFLCIRREM 41

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	330
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	99.93
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	99.93
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	99.92
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.57
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	99.44
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	99.24
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	99.15
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	98.6
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	98.57
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	98.11
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	97.87
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	96.16
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	94.53
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	93.94

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

Probab=99.93  E-value=4.2e-26  Score=226.19  Aligned_cols=139  Identities=34%  Similarity=0.551  Sum_probs=120.2

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHH------------------HHHHhhCCCCchHHHHH------
Q 020126          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL------------------RLKERLGCEPSMEQLAA------  246 (330)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~------------------~l~~~lg~ePt~~e~A~------  246 (330)
                      +.++.||++|+++|+||++||++|+++|+.|+.+++...                  +....+++.|+.++|+.      
T Consensus        94 d~~~~Yl~ei~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  173 (438)
T 1l9z_H           94 DPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEE  173 (438)
T ss_pred             ChHHHHHHHhccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccchhhhh
Confidence            578889999999999999999999999999966443221                  12234567788777632      


Q ss_pred             ------HhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhH
Q 020126          247 ------SLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY  320 (330)
Q Consensus       247 ------a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTY  320 (330)
                            +++.+..+|...+..|..|+++||..|+++|+++|++|.++|.+++||||||+|||++|+++|||++|++|+||
T Consensus       174 ~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~IgL~kAvekFDp~kG~rFsTY  253 (438)
T 1l9z_H          174 VDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTY  253 (438)
T ss_pred             hhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHH
Confidence                  23566788888888899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhccc
Q 020126          321 VYWWIRQSI  329 (330)
Q Consensus       321 A~~wIR~aI  329 (330)
                      |+||||++|
T Consensus       254 A~~wIR~~I  262 (438)
T 1l9z_H          254 ATWWIRQAI  262 (438)
T ss_pred             HHHHHHHHH
Confidence            999999976

>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=99.93  E-value=8.1e-26  Score=207.46  Aligned_cols=139  Identities=32%  Similarity=0.522  Sum_probs=119.9

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHH---HHh-----------------------hCCCCchHHH
Q 020126          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRL---KER-----------------------LGCEPSMEQL  244 (330)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l---~~~-----------------------lg~ePt~~e~  244 (330)
                      |.++.||++|+++|+||++||++|+++|+.|..+.......   +..                       .+.+|+..+|
T Consensus         7 d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~~~~   86 (245)
T 3ugo_A            7 DPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEE   86 (245)
T ss_dssp             HHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHHHHHH
T ss_pred             CcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccchhHHH
Confidence            68999999999999999999999999999997633221100   000                       1367889999


Q ss_pred             HHHhcCCh----HHHHHHHhhhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhH
Q 020126          245 AASLRISR----PELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY  320 (330)
Q Consensus       245 A~a~~~s~----~eL~~~l~~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTY  320 (330)
                      |.+.+++.    .+|.+.+..|..|+++|+..|.|+|.++|.+|.+.+.+.+||+|+|++||++|+++|||++|++|+||
T Consensus        87 ~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~~fd~~~g~~F~ty  166 (245)
T 3ugo_A           87 VDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTY  166 (245)
T ss_dssp             HHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHH
T ss_pred             HHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCcccCCcHHHH
Confidence            99988864    34556677889999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhccc
Q 020126          321 VYWWIRQSI  329 (330)
Q Consensus       321 A~~wIR~aI  329 (330)
                      ++||||++|
T Consensus       167 a~~~ir~~i  175 (245)
T 3ugo_A          167 ATWWIRQAI  175 (245)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999976

>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=99.92  E-value=3.4e-26  Score=224.40  Aligned_cols=139  Identities=35%  Similarity=0.578  Sum_probs=116.8

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHH------------------HHHhhCCCCchHH---------
Q 020126          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLR------------------LKERLGCEPSMEQ---------  243 (330)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~------------------l~~~lg~ePt~~e---------  243 (330)
                      +.++.||++|++.|+||++||++|+++++.|+.+.+....                  ....+++.|+.++         
T Consensus        79 d~~~~Yl~ei~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (423)
T 2a6h_F           79 DPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVEE  158 (423)
T ss_dssp             HHHHHHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTHHHHH
T ss_pred             cHHHHHHHHhcccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhhhhhh
Confidence            5888999999999999999999999999998653332111                  1122345565433         


Q ss_pred             HHH---HhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhH
Q 020126          244 LAA---SLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY  320 (330)
Q Consensus       244 ~A~---a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTY  320 (330)
                      |+.   +++.+..+|...+..|..|+++||..|+++|+++|++|.++|.+++||||||+|||++|+++|||++|++|+||
T Consensus       159 ~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~kav~kFd~~~g~~FstY  238 (423)
T 2a6h_F          159 IDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTY  238 (423)
T ss_dssp             HHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHHHHHCCTTSCCCHHHH
T ss_pred             hhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHH
Confidence            322   34567788888888899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhccc
Q 020126          321 VYWWIRQSI  329 (330)
Q Consensus       321 A~~wIR~aI  329 (330)
                      |+||||++|
T Consensus       239 a~~wIr~~i  247 (423)
T 2a6h_F          239 ATWWIRQAI  247 (423)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999999976

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

Probab=99.57  E-value=2.9e-15  Score=141.27  Aligned_cols=66  Identities=48%  Similarity=0.953  Sum_probs=64.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      .|++.|+..|+|+|.++|.+|.+.+.+.+||+|+|+|||++++.+||+.+|.+|+||++||||+.|
T Consensus       265 ~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~f~~~~g~~f~twl~~iirn~~  330 (339)
T 1sig_A          265 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI  330 (339)
T ss_dssp             HHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHH
Confidence            789999999999999999999999999999999999999999999999999999999999999876

>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=99.44  E-value=7e-15  Score=149.86  Aligned_cols=65  Identities=49%  Similarity=0.979  Sum_probs=63.1

Q ss_pred             HHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       265 ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      |++.|+..|.|+|.++|++|.+++.+.+||+|+|+|||++|+++||+.+|++|+||++||||++|
T Consensus       375 A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi~l~~a~~~fd~~~g~~Fstyl~~~irn~i  439 (613)
T 3iyd_F          375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI  439 (613)
T ss_dssp             HHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHHHHHHHTTSCCTTSSSCSTTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccccCcHHHHHHHHHHHHH
Confidence            39999999999999999999999999999999999999999999999999999999999999876

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

Probab=99.24  E-value=7.4e-13  Score=113.83  Aligned_cols=90  Identities=36%  Similarity=0.501  Sum_probs=0.0

Q ss_pred             cCCCCCCCHHHHHHHHHHHHcCccchhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhHHHHHHHHHHhHHHHHH
Q 020126          200 VVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMS  279 (330)
Q Consensus       200 i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~~ArekLI~~nLpLV~s  279 (330)
                      +...+.++++++.+|+.+++.|+.                                        .+.+.|+..|.++|..
T Consensus         4 ~~~~~~~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~   43 (243)
T 1l0o_C            4 MQGQSPIKDQEMKELIRRSQEGDQ----------------------------------------EARDEIIEKNMRLVWS   43 (243)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHH
Confidence            345567788888899988888865                                        7899999999999999


Q ss_pred             HHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          280 IAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       280 IAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      +|.+|.+...+.+||+|+|+++|++++++||+.+|.+|.+|+..+|++.+
T Consensus        44 ~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~i~~~~~   93 (243)
T 1l0o_C           44 VVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEI   93 (243)
T ss_dssp             --------------------------------------------------
T ss_pred             HHHHHhccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHH
Confidence            99999988899999999999999999999999999999999999998765

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

Probab=99.15  E-value=5.3e-11  Score=102.54  Aligned_cols=66  Identities=26%  Similarity=0.521  Sum_probs=62.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcc---cCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~---~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      .++++|+..|.|+|..+|.+|.   +.+.+.+||+|+|+++|++++++||+.+|.+|.||+.+||++.+
T Consensus        12 ~a~~~l~~~~~~~v~~~a~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~~~~~~~   80 (239)
T 1rp3_A           12 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAI   80 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHH
Confidence            5799999999999999999998   56889999999999999999999999999999999999998764

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

Probab=98.57  E-value=1.2e-07  Score=79.66  Aligned_cols=62  Identities=26%  Similarity=0.377  Sum_probs=58.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      .+.+.|+..|.|.|..++.+|.+ ..+.+|++|++.+.+++++.+|++..  .|.+|+...+++.
T Consensus        23 ~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~~~~~~~~~--~~~~~l~~i~~n~   84 (194)
T 1or7_A           23 KAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRALDSFRGDS--AFYTWLYRIAVNT   84 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHH
Confidence            89999999999999999999999 89999999999999999999999875  5999999988764

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

Probab=98.11  E-value=5.9e-06  Score=64.88  Aligned_cols=62  Identities=16%  Similarity=0.168  Sum_probs=55.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      .+.+.|+..|.+.+..+|.++ +...+-+|++|+..+.+++.+.+|++.  ..|.+|+...+++.
T Consensus        24 ~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~   85 (112)
T 2o7g_A           24 RALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHV   85 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHHHHHHHGGGCCCS--SCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHHHHHhcCCC--CCHHHHHHHHHHHH
Confidence            789999999999999999999 777789999999999999999999964  37999998877653

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

Probab=97.87  E-value=1.8e-05  Score=59.37  Aligned_cols=66  Identities=21%  Similarity=0.248  Sum_probs=58.7

Q ss_pred             hhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       261 ~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      .+..+.+.|+..|.+.+...+.++.+...+-||++|+..+.+++.+.+|++.  ..|.+|+...+++.
T Consensus         9 g~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~   74 (87)
T 1h3l_A            9 ERSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNT   74 (87)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHH
Confidence            3468899999999999999999998877889999999999999999999975  47999998877653

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=96.16  E-value=0.00017  Score=60.09  Aligned_cols=61  Identities=7%  Similarity=0.082  Sum_probs=52.8

Q ss_pred             HHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       266 rekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      .+.|+..|.+.|..+|.++.+...+-+|++|++.+.+++.+.+|++..  .|.+|+...+++.
T Consensus         3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~--~~~~wl~~ia~n~   63 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRDV--DPRLGLYRMFQGI   63 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCSS--CTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--cHHHHHHHHHHHH
Confidence            356788999999999999988778899999999999999999999764  6999998877653

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=94.53  E-value=0.013  Score=53.63  Aligned_cols=63  Identities=13%  Similarity=0.074  Sum_probs=56.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      .+.++|+..|.+.+...|.+|.+...+-||++|+..+-+++...+|++.  ..|.+|.+.-+++.
T Consensus        21 ~~f~~l~~~~~~~l~~~a~~~~~~~~~AeD~vQe~fl~~~~~~~~~~~~--~~~~~wL~~ia~n~   83 (286)
T 3n0r_A           21 MHLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDAN--LSPRVALYRVFHAI   83 (286)
T ss_dssp             CCHHHHHGGGHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTSSCCCSS--SCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHhCchhcCCC--cChHHHHHHHHHHH
Confidence            5788999999999999999998877889999999999999999999975  36999998877653

>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=93.94  E-value=0.0095  Score=60.83  Aligned_cols=34  Identities=24%  Similarity=0.507  Sum_probs=14.9

Q ss_pred             hhhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCcc
Q 020126          190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS  223 (330)
Q Consensus       190 q~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~  223 (330)
                      .+.++.||+++++.|+||.++|++|+++|..|..
T Consensus        95 ~dpvrmyl~emg~~~ll~~~~e~~~ak~ie~g~~  128 (613)
T 3iyd_F           95 TDPVRMYMREMGTVELLTREGEIDIAKRIEDGIN  128 (613)
T ss_dssp             ----------C--------CSSSTTTHHHHHHHH
T ss_pred             CCcHHHHHHHhcccccCCchhHHHHHHHHHHhHH
Confidence            3799999999999999999999999999999964

---

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	330
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	1e-23
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	1e-22
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	5e-16

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

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

 Score = 96.9 bits (240), Expect = 1e-23
 Identities = 47/262 (17%), Positives = 103/262 (39%)

Query: 69  TQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFE 128
           T     L +    +     E   +  ++ ++ S + + + E    L+   +  +  +  +
Sbjct: 67  THVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAK 126

Query: 129 RTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPEL 188
                 +  +            +  +Q         +  ++   Q+    +L        
Sbjct: 127 GRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMP 186

Query: 189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASL 248
            +N +  +     S+     A  +      K     ++    L++    E         +
Sbjct: 187 KKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQV 246

Query: 249 RISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK 308
           +     +     +   A++++V +N+RLV+SIA++Y N G    DL+Q G IGL++ ++K
Sbjct: 247 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 306

Query: 309 FDSSKGFKISTYVYWWIRQSIS 330
           F+  +G+K STY  WWIRQ+I+
Sbjct: 307 FEYRRGYKFSTYATWWIRQAIT 328

>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 = 91.0 bits (225), Expect = 1e-22
 Identities = 50/167 (29%), Positives = 80/167 (47%), Gaps = 30/167 (17%)

Query: 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDH------------------KLRLKER 234
           ++ Y+  +    LLT  E + L++K++ G+                       K+    R
Sbjct: 4   VRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTAR 63

Query: 235 LGCEPS---------MEQLAASLRISRPELQ---SILMECSLAREKLVMSNVRLVMSIAQ 282
           +   P          +E++   L+    EL+    I  E   AR+ L+ +N+RLV+SIA+
Sbjct: 64  IQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAK 123

Query: 283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI 329
           +Y   G    DL+Q G  GL+R +EKF+  + FK STY  WWIRQ+I
Sbjct: 124 KYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAI 170

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

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

 Score = 69.9 bits (171), Expect = 5e-16
 Identities = 17/69 (24%), Positives = 35/69 (50%), Gaps = 3/69 (4%)

Query: 264 LAREKLVMSNVRLVMSIAQRYDNM---GADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
           + RE+L++  + LV +IA           D+ DL+  G+IGL++ ++   +    +   Y
Sbjct: 10  IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAY 69

Query: 321 VYWWIRQSI 329
           +   I+ +I
Sbjct: 70  IKLRIKGAI 78

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	330
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	100.0
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.89
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.83
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	98.43
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	97.03
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	96.9
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	96.87
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	95.39

>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=100.00  E-value=3e-34  Score=247.35  Aligned_cols=140  Identities=34%  Similarity=0.574  Sum_probs=112.8

Q ss_pred             hhHHHHHHhcCCCCCCCHHHHHHHHHHHHcCccchhHHHHHH------------------HhhCCCCc---------hHH
Q 020126          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLK------------------ERLGCEPS---------MEQ  243 (330)
Q Consensus       191 ~~l~~YL~~i~~~~lLT~eEE~eL~rkIk~G~~Le~~~~~l~------------------~~lg~ePt---------~~e  243 (330)
                      |.++.||++|+++|+||++||++|+++|+.|..+........                  ...+..|.         ..+
T Consensus         2 DpVr~YLreig~v~LLT~EEEieLAr~Ie~g~~~~~~~~e~~~~~~~l~~e~~~~~~~~~~~~~~~~~~~e~~~~~~~~~   81 (180)
T d1ku2a2           2 DPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEE   81 (180)
T ss_dssp             HHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCSSCCCTTSCCSSCTTTHHH
T ss_pred             CcHHHHHHHhcCcCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHhhhHHHHhcchhhHHHhhHHHHHH
Confidence            588999999999999999999999999998876433221111                  01112222         233


Q ss_pred             HHHHhcCC---hHHHHHHHhhhHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhH
Q 020126          244 LAASLRIS---RPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY  320 (330)
Q Consensus       244 ~A~a~~~s---~~eL~~~l~~g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTY  320 (330)
                      +.......   ..++.+.+..|..|+++||+.|+|||.+||++|.++|++++||||+|+|||++||++|||++|++|+||
T Consensus        82 ~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl~q~g~~gl~~a~~~fd~~~g~~f~ty  161 (180)
T d1ku2a2          82 VDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTY  161 (180)
T ss_dssp             HHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHHHHHHHHHHHHHHHHCCGGGCSCHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHHHHHHcCCCCCCCHHHH
Confidence            33333333   344566777899999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhcccC
Q 020126          321 VYWWIRQSIS  330 (330)
Q Consensus       321 A~~wIR~aIS  330 (330)
                      |+||||++|.
T Consensus       162 a~~~i~~~i~  171 (180)
T d1ku2a2         162 ATWWIRQAIN  171 (180)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999999873

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

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

Probab=99.89  E-value=4e-24  Score=196.40  Aligned_cols=86  Identities=38%  Similarity=0.757  Sum_probs=77.0

Q ss_pred             HHHhcCChHHHHHHHhh-------hHHHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcc
Q 020126          245 AASLRISRPELQSILME-------CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI  317 (330)
Q Consensus       245 A~a~~~s~~eL~~~l~~-------g~~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rF  317 (330)
                      ....|++..++..+...       +..|+++||..|++||.+||++|.++|++++||||+|++|||+||++|||.+|++|
T Consensus       236 e~~~gl~~~elk~i~~~i~~ge~~~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~f  315 (334)
T d1siga_         236 EEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF  315 (334)
T ss_dssp             HHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCH
T ss_pred             HHHhhhhHHHHHHHHHHHHHHHhhccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHHhcCCCCCCch
Confidence            33457777776655443       57799999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHhhcccC
Q 020126          318 STYVYWWIRQSIS  330 (330)
Q Consensus       318 sTYA~~wIR~aIS  330 (330)
                      +|||+|||||+|+
T Consensus       316 ~~~~~~~~~~~~~  328 (334)
T d1siga_         316 STYATWWIRQAIT  328 (334)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HhhhHHHHHHHHH
Confidence            9999999999985

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

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

Probab=99.83  E-value=3.2e-21  Score=151.29  Aligned_cols=66  Identities=26%  Similarity=0.533  Sum_probs=62.6

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccC---CCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhccc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNM---GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQSI  329 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~---Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~aI  329 (330)
                      ..+++||..|+|||.++|++|..+   ++++|||+|+|++||++|+++|||++|++|+|||.+|||++|
T Consensus        10 ~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A~~~yd~~~g~~F~tYA~~~Irgai   78 (87)
T d1rp3a3          10 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAI   78 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHH
Confidence            468999999999999999999764   899999999999999999999999999999999999999987

>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=97.03  E-value=0.00044  Score=48.91  Aligned_cols=38  Identities=21%  Similarity=0.245  Sum_probs=33.7

Q ss_pred             hHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhhhH
Q 020126          226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECS  263 (330)
Q Consensus       226 ~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~g~  263 (330)
                      ....+|...+|++||.+|+|+.+|++.+++..+++.++
T Consensus        19 ~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~r   56 (57)
T d1l0oc_          19 KAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVR   56 (57)
T ss_dssp             HHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHhc
Confidence            46678999999999999999999999999998887653

>d1h3la_ a.177.1.1 (A:) Sigma factor SigR {Streptomyces coelicolor a3(2) [TaxId: 100226]}

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 SigR
species: Streptomyces coelicolor a3(2) [TaxId: 100226]

Probab=96.90  E-value=0.00074  Score=48.60  Aligned_cols=63  Identities=19%  Similarity=0.241  Sum_probs=56.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHhhcCCCCCCcchhHHHHHhhcc
Q 020126          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQS  328 (330)
Q Consensus       264 ~ArekLI~~nLpLV~sIAkrY~~~Gvd~EDLIQEG~IGLikAIekFDpsrG~rFsTYA~~wIR~a  328 (330)
                      ...++++..|.+.+..+|.++.+...+-||++|+..+-+++...+|++.  ..|.+|...-+++.
T Consensus         7 ~~f~~~~~~y~~~l~~~~~~~~~d~~~aeDivQd~f~~~~~~~~~~~~~--~~~~~wl~~i~~n~   69 (75)
T d1h3la_           7 ARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNT   69 (75)
T ss_dssp             HHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCCC--CCHHHHHHHHHHHH
Confidence            5689999999999999999999888899999999999999999999975  36999998877653

>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=96.87  E-value=0.00082  Score=49.27  Aligned_cols=38  Identities=39%  Similarity=0.512  Sum_probs=33.8

Q ss_pred             chhHHHHHHHhhCCCCchHHHHHHhcCChHHHHHHHhh
Q 020126          224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME  261 (330)
Q Consensus       224 Le~~~~~l~~~lg~ePt~~e~A~a~~~s~~eL~~~l~~  261 (330)
                      ++....+|+..+||+||.+|+|..+|++.+++.+++..
T Consensus        12 i~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~   49 (77)
T d1rp3a1          12 IKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDK   49 (77)
T ss_dssp             HHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45677889999999999999999999999999887754

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

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

Probab=95.39  E-value=0.0097  Score=42.38  Aligned_cols=37  Identities=24%  Similarity=0.375  Sum_probs=30.4

Q ss_pred             hhHHHHHHHhhCCCCchHHHHHHhcC--ChHHHHHHHhh
Q 020126          225 DDHKLRLKERLGCEPSMEQLAASLRI--SRPELQSILME  261 (330)
Q Consensus       225 e~~~~~l~~~lg~ePt~~e~A~a~~~--s~~eL~~~l~~  261 (330)
                      .....+|...+|++||.+|+|+++|+  +.+.++.++..
T Consensus        15 ~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~~   53 (60)
T d1ku2a1          15 SRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKI   53 (60)
T ss_dssp             HHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGGG
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHH
Confidence            34667899999999999999999975  57778777654