Citrus Sinensis ID: 010521

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------51
Protein Sequence
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPSFPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLVKH
Secondary Structure (PSIPRED)
ccccHHHHHcccccccHHcccccccccHHHHccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHccccccccccHHHHHHHHccccccccHHHHHHHHHHHHccccHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHccHHHEEccccccccccHHHHHHHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHcccccccccHHHHHHHHcccHHHHHHHHHHHHHHHHcHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccHHHEEcccccHHHcccccccccccccccccccccccccccccccEEEEEcccccccccccccHHHHHHHHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHcHHHHHHccccccccccccccccHHHHHccccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHccHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccccEccHHHHHHHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHccccccccccccccccccccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHccHHHccEEEEEEccccccccHHHHHHHHcccHHHHHHHHHHHHHHcccccHHHHHHHHHHcc
Coil and Loop (DISEMBL)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYIndlgsansqvgsTKNVVAAkkssnynpsfpssnrqtqpiKALKEhvdtnfastaepwaeppnsieeesseLDYSVEALLLLQKSMLEKQWNLSFertvltdspskkthkkvpvtcsgvsARQRRLNSKKKILSQNKSILQQNGSkqlrsmisPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIktglslddHKLRLkerlgcepSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIekfdsskgfkisTYVYWWIRQGVSRALvensrtlrlpnhlhERLGLIRNAKLrleekgvtpsvDRIAEYLNMSQKKVRNATEAIGKVFsldreafpslnglpgethhsyiadnrvennpwhgvddwaLKDEVNKLIIVTLGEREREIIRLYYGldkecltweDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLVKH
Flexible Loop (DISEMBL)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKssnynpsfpssnrqTQPIKALKEHVDTNFAstaepwaeppnSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERtvltdspskkthkkvpvtcsgvsarqrrlnskkkilsqnksilqqngskqlrsMISPELIQNRLKGYVKGVVSEELLTHAEVVRlskkiktglslddhKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGiekfdsskgfkisTYVYWWIRQGVSRALVENSrtlrlpnhlherlglirnaklrleekgvtpsvdrIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIvtlgererEIIRLYygldkecltwEDISkriglsrervrqVGLVALEKLKHAARKKKmeamlvkh
Low Complexity Region (SEG)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKssnynpsfpssnRQTQPIKALKEHVDTNFASTAEPWAEPPNsieeesseLDYSVEALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLVKH
Disordered region (IsUnstruct)
*****AVIGLSAGKRLLSSSFYYSDISEKFSYINDL*********************************************************************YSVEALLLLQKSMLEKQWNLSFERTVL******************************************************ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGC**********LRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL****************
Disordered Region (DISOPRED)
****AAV*GLSAGKRLLSSSFYYSDISEK*****************************************************************************************************************************************************************NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL***GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLVK*
Disordered Region (DISEMBL)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNY************PIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERTVL*****************GVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLVKH
Disordered Region (DISPRO)
*MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPS*****************************AE********SSELDYSVEALLLLQKSMLEKQWNLSF************************************************************LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML*KH
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPSFPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLVKH
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	508	2.2.26 [Sep-21-2011]
O24629	502	RNA polymerase sigma fact	yes	no	0.964	0.976	0.728	0.0
O22056	572	RNA polymerase sigma fact	no	no	0.647	0.575	0.331	1e-41
P26683	390	RNA polymerase sigma fact	no	no	0.584	0.761	0.353	2e-41
Q31ME3	320	RNA polymerase sigma fact	yes	no	0.594	0.943	0.320	1e-40
Q03065	332	RNA polymerase sigma-B fa	no	no	0.553	0.846	0.335	2e-40
P38023	399	RNA polymerase sigma fact	no	no	0.578	0.736	0.350	6e-40
O33662	371	RNA polymerase sigma fact	yes	no	0.448	0.614	0.376	1e-39
P0A4J0	369	RNA polymerase sigma fact	yes	no	0.448	0.617	0.376	5e-39
P0A4I9	369	RNA polymerase sigma fact	yes	no	0.448	0.617	0.376	5e-39
P27785	317	RNA polymerase sigma fact	N/A	no	0.572	0.917	0.339	5e-39

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

 Score =  752 bits (1942), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/519 (72%), Positives = 434/519 (83%), Gaps = 29/519 (5%)

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 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQGVSRALV+NSRTLRLP HLHER
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHER 343

Query: 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPG 409
           LGLIRNAKLRL+EKG+TPS+DRIAE LNMSQKKVRNATEA+ KVFSLDR+AFPSLNGLPG
Sbjct: 344 LGLIRNAKLRLQEKGITPSIDRIAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPG 403

Query: 410 ETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWED 469
           ETHHSYIAD R+ENNPWHG DD ALK+EV+KLI  TLGERE+EIIRLYYGLDKECLTWED
Sbjct: 404 ETHHSYIADTRLENNPWHGYDDLALKEEVSKLISATLGEREKEIIRLYYGLDKECLTWED 463

Query: 470 ISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLVKH 508
           ISKRIGLSRERVRQVGLVALEKLKHAARK+KMEAM++K+
Sbjct: 464 ISKRIGLSRERVRQVGLVALEKLKHAARKRKMEAMILKN 502

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

 Score =  171 bits (433), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 112/338 (33%), Positives = 192/338 (56%), Gaps = 9/338 (2%)

Query: 172 LQQNGSKQLRSMISPELIQNRLKGYVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLR 230
           ++   S + + +++ E+  N    Y++   S  +LLT  E   LS  I+  L L+  +  
Sbjct: 238 VKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSAGIQDLLKLERLQTE 297

Query: 231 LKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGAD 290
           L ER G +P+  Q A++  + +  L+  +   +L ++K++ SN+RLV+SIA+ Y   G +
Sbjct: 298 LTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMN 357

Query: 291 MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL 350
           + DLVQ G  GL+RG EKFD++KGFK STY +WWI+Q V ++L + SR +RLP H+ E  
Sbjct: 358 LQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEAT 417

Query: 351 GLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPG 409
             ++ A+ +L  E G  P  + IAE   +S K++     +     SLD++   + N  P 
Sbjct: 418 YRVKEARKQLYSETGKHPKNEEIAEATGLSMKRLMAVLLSPKPPRSLDQKIGMNQNLKPS 477

Query: 410 ETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWE 468
           E     IAD     +    + ++ ++ +++K ++ +LG RE+++IR  +G+ D    T +
Sbjct: 478 EV----IADPEAVTSEDILIKEF-MRQDLDK-VLDSLGTREKQVIRWRFGMEDGRMKTLQ 531

Query: 469 DISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 506
           +I + +G+SRERVRQ+   A  KLK+  R   ++  LV
Sbjct: 532 EIGEMMGVSRERVRQIESSAFRKLKNKKRNNHLQQYLV 569

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 =  170 bits (431), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 111/314 (35%), Positives = 180/314 (57%), Gaps = 17/314 (5%)

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 DSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLI-RNAKLRLEEKGVTPS 368
           D  KG+K STY  WWIRQ ++RA+ + SRT+RLP HL+E +  I +  KL  +E G  P+
Sbjct: 199 DHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPT 258

Query: 369 VDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFP-SLNGLPGETHHSYIADNRVENN--- 424
            + IA  + M+ +K+R         F       P SL    G+   S + D  +E++   
Sbjct: 259 EEEIATRMEMTIEKLR---------FIAKSAQLPISLETPIGKEEDSRLGDF-IESDGET 308

Query: 425 PWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECL-TWEDISKRIGLSRERVRQ 483
           P   V    L++++ K ++ +L  RER+++RL YGLD   + T E+I +   ++RER+RQ
Sbjct: 309 PEDQVSKNLLREDLEK-VLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQ 367

Query: 484 VGLVALEKLKHAAR 497
           +   AL KL+H  R
Sbjct: 368 IEAKALRKLRHPNR 381

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

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

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

 Score =  167 bits (424), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 101/315 (32%), Positives = 188/315 (59%), Gaps = 13/315 (4%)

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 GIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK- 363
           G+EKFD SKG+K STY YWWIRQ ++RA+ + SRT+RLP H+ E+L  ++  +  L ++ 
Sbjct: 125 GVEKFDPSKGYKFSTYAYWWIRQAITRAIAQQSRTIRLPIHITEKLNKLKKTQRELSQQL 184

Query: 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN 423
           G + +   +AE L +  ++VR   +   +  SLD +      G   +T    + ++  ++
Sbjct: 185 GRSATASELAEVLELPLEQVREYIQMNRQPVSLDVKV-----GDSQDTELQELLEDE-QS 238

Query: 424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVR 482
           +P   V+  +L+ ++  L +  L  +++ +I L YGLD+ + L+   + +R+ +SRERVR
Sbjct: 239 SPSDYVEQESLRRDLRNL-MAELTPQQQAVIALRYGLDEGDSLSLAKVGERLNISRERVR 297

Query: 483 QVGLVALEKLKHAAR 497
           ++   A++ L+  +R
Sbjct: 298 KLERQAMDHLRRRSR 312

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

 Score =  167 bits (422), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 98/292 (33%), Positives = 171/292 (58%), Gaps = 11/292 (3%)

Query: 205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSL 264
           LL+H + +  +++++  + +   K  L E+L  EP++++ A  +++    L   L +  +
Sbjct: 37  LLSHEQEIFFAQQVQQMMVMFTAKEELAEKLQREPTLQEWADKMQLKEDVLLQQLSQGQI 96

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A++K++ +N+RLV+SIA++Y     +  DL+Q G +GL RG+EKFD + G+K STY YWW
Sbjct: 97  AKQKMIQANLRLVVSIAKKYQKRNLEFLDLIQEGALGLERGVEKFDPTLGYKFSTYAYWW 156

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKV 383
           IRQG++RA+ + SRT+RLP H+ ++L  I+  +  L +K G    V  IA+ LN+   ++
Sbjct: 157 IRQGITRAIAQQSRTIRLPIHMADKLNKIKCVQRELSQKLGYIAGVTEIAQALNLEPSQI 216

Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETH-HSYIADNRVENNPWHGVDDWALKDEVNKLI 442
           R   + + +  SLD        G   +T     + D+ +  +P    +   L  +++ L 
Sbjct: 217 REYLQLVRQPVSLDMRI-----GFEQDTQLQDLLKDDGM--SPERYAERELLYQDIHNL- 268

Query: 443 IVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLK 493
           +  L  +++E++ L +GL   C LT   IS+R+G+SRERVRQV   AL  L+
Sbjct: 269 LAKLTPQQKEVLILRFGLAGGCELTLVQISQRMGISRERVRQVEKQALTLLR 320

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

 Score =  165 bits (418), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 111/317 (35%), Positives = 175/317 (55%), Gaps = 23/317 (7%)

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 DSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLI-RNAKLRLEEKGVTPS 368
           D  KG+K STY  WWIRQ ++RA+ + SRT+RLP HL+E +  I +  KL  +E G  P+
Sbjct: 208 DHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPT 267

Query: 369 VDRIAEYLNMSQKKVRNATEAIGKVFSLD----REAFPSLNGL---PGETHHSYIADNRV 421
            + IA  + M+ +K+R   ++     SL+    +E    L       GET    +A N +
Sbjct: 268 EEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPEDEVAKNLL 327

Query: 422 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECL-TWEDISKRIGLSRER 480
             +   GV             + TL  RER+++RL YGLD   + T E+I +   ++RER
Sbjct: 328 RED-LEGV-------------LSTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRER 373

Query: 481 VRQVGLVALEKLKHAAR 497
           +RQ+   AL KL+H  R
Sbjct: 374 IRQIEAKALRKLRHPNR 390

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|O33662|RPOD_STRMU RNA polymerase sigma factor RpoD OS=Streptococcus mutans serotype c (strain ATCC 700610 / UA159) GN=rpoD PE=3 SV=1

 Score =  164 bits (416), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 91/242 (37%), Positives = 151/242 (62%), Gaps = 14/242 (5%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+++L  +N+RLV+SIA+RY   G    DL+Q G +GL++ ++KFD SKGFK STY  WW
Sbjct: 133 AKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWW 192

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++RA+ + +RT+R+P H+ E +  L+R  +  L+E G  P+ ++IAE ++M+  KV
Sbjct: 193 IRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKV 252

Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIAD---NRVENNPWHGVDDWALKDEVNK 440
           R       ++  + +E   SL    GE   S++ D   + V  NP        L++++++
Sbjct: 253 R-------EILKIAQEPV-SLETPIGEEDDSHLGDFIEDEVIENPVDYTTRVVLREQLDE 304

Query: 441 LIIVTLGEREREIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499
            ++ TL +RE  ++RL +GLD   + T ED+ K   ++RER+RQ+   AL KL+H +R K
Sbjct: 305 -VLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFDVTRERIRQIEAKALRKLRHPSRSK 363

Query: 500 KM 501
           ++
Sbjct: 364 QL 365

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.

Streptococcus mutans (taxid: 1309)

>sp|P0A4J0|RPOD_STRR6 RNA polymerase sigma factor RpoD OS=Streptococcus pneumoniae (strain ATCC BAA-255 / R6) GN=rpoD PE=3 SV=1

 Score =  162 bits (411), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 91/242 (37%), Positives = 149/242 (61%), Gaps = 14/242 (5%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+++L  +N+RLV+SIA+RY   G    DL+Q G +GL++ ++KFD SKGFK STY  WW
Sbjct: 131 AKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWW 190

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++RA+ + +RT+R+P H+ E +  L+R  +  L+E G  P+ ++IAE ++M+  KV
Sbjct: 191 IRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKV 250

Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIAD---NRVENNPWHGVDDWALKDEVNK 440
           R       ++  + +E   SL    GE   S++ D   + V  NP        L++++++
Sbjct: 251 R-------EILKIAQEPV-SLETPIGEEDDSHLGDFIEDEVIENPVDYTTRIVLREQLDE 302

Query: 441 LIIVTLGEREREIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499
            I+ TL +RE  ++RL +GLD   + T ED+ K   ++RER+RQ+   AL KL+  +R K
Sbjct: 303 -ILDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSK 361

Query: 500 KM 501
            +
Sbjct: 362 PL 363

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.

Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (taxid: 171101)

>sp|P0A4I9|RPOD_STRPN RNA polymerase sigma factor RpoD OS=Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) GN=rpoD PE=3 SV=1

 Score =  162 bits (411), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 91/242 (37%), Positives = 149/242 (61%), Gaps = 14/242 (5%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A+++L  +N+RLV+SIA+RY   G    DL+Q G +GL++ ++KFD SKGFK STY  WW
Sbjct: 131 AKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWW 190

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++RA+ + +RT+R+P H+ E +  L+R  +  L+E G  P+ ++IAE ++M+  KV
Sbjct: 191 IRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKV 250

Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIAD---NRVENNPWHGVDDWALKDEVNK 440
           R       ++  + +E   SL    GE   S++ D   + V  NP        L++++++
Sbjct: 251 R-------EILKIAQEPV-SLETPIGEEDDSHLGDFIEDEVIENPVDYTTRIVLREQLDE 302

Query: 441 LIIVTLGEREREIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499
            I+ TL +RE  ++RL +GLD   + T ED+ K   ++RER+RQ+   AL KL+  +R K
Sbjct: 303 -ILDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSK 361

Query: 500 KM 501
            +
Sbjct: 362 PL 363

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.

Streptococcus pneumoniae (taxid: 1313)

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

 Score =  162 bits (411), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 108/318 (33%), Positives = 183/318 (57%), Gaps = 27/318 (8%)

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 SKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVD 370
           ++G+K STY  WWIRQ +SRAL + +RT+R+P H+ E +  ++R  +  L+E+G  P+ +
Sbjct: 127 ARGYKFSTYATWWIRQAMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTAE 186

Query: 371 RIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD 430
            +A +L ++ ++V        +V  L +E   SL+   GE     + D   + +    V+
Sbjct: 187 EVAVHLELTPERVL-------EVLRLAQEPV-SLHAPVGEEDDVALGDLIEDGDAASPVE 238

Query: 431 DWA--LKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLV 487
             A  L+ E  + ++ TLGERER++++L YGL D    T E+I +  G++RER+RQ+   
Sbjct: 239 SAAFFLRCEHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESK 298

Query: 488 ALEKLKHAARKKKMEAML 505
            L KL+  A   ++   L
Sbjct: 299 TLNKLRDHAFADQLRGYL 316

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)

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	508
255566078	508	RNA polymerase sigma factor rpoD, putati	0.998	0.998	0.820	0.0
224146103	509	predicted protein [Populus trichocarpa]	1.0	0.998	0.793	0.0
356543070	503	PREDICTED: RNA polymerase sigma factor r	0.984	0.994	0.768	0.0
449468291	508	PREDICTED: RNA polymerase sigma factor s	0.998	0.998	0.764	0.0
356531599	503	PREDICTED: RNA polymerase sigma factor r	0.984	0.994	0.764	0.0
224124068	499	predicted protein [Populus trichocarpa]	0.980	0.997	0.774	0.0
2565297	502	RNA polymerase sigma subunit 1 [Arabidop	0.964	0.976	0.730	0.0
15217767	502	sigma factor A [Arabidopsis thaliana] gi	0.964	0.976	0.728	0.0
11762220	502	At1g64860 [Arabidopsis thaliana]	0.964	0.976	0.726	0.0
2398851	502	plastid RNA polymerase sigma-subunit [Ar	0.964	0.976	0.726	0.0

>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 =  846 bits (2185), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 417/508 (82%), Positives = 457/508 (89%), Gaps = 1/508 (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 GLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL 360
           GLLRGIEKFDSSKGF+ISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAK+RL
Sbjct: 301 GLLRGIEKFDSSKGFRISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKIRL 360

Query: 361 EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNR 420
           EEKGVTPS+DRIAE LN+SQKKVRNATEA+ KVFSLDREAFPSLNGLPGETHHSYIADN 
Sbjct: 361 EEKGVTPSIDRIAESLNISQKKVRNATEAVSKVFSLDREAFPSLNGLPGETHHSYIADNC 420

Query: 421 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRER 480
           +ENNPWHGVDDWALKDEVNKLI +TL ERE+EIIRLYYGLD E LTWEDISKRIGLSRER
Sbjct: 421 LENNPWHGVDDWALKDEVNKLINLTLQEREQEIIRLYYGLDNESLTWEDISKRIGLSRER 480

Query: 481 VRQVGLVALEKLKHAARKKKMEAMLVKH 508
           VRQVGLVALEKLKHAARKKK+EAMLVKH
Sbjct: 481 VRQVGLVALEKLKHAARKKKLEAMLVKH 508

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 =  823 bits (2126), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 404/509 (79%), Positives = 450/509 (88%), Gaps = 1/509 (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 IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLR 359
           IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALV+NSRTLRLPNHLHERLGLIRNAK+R
Sbjct: 301 IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVDNSRTLRLPNHLHERLGLIRNAKIR 360

Query: 360 LEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADN 419
           LEEKGVTPS+DRIAE LNMSQ+KVRNATEAI KVFSLDREAFPSLNGLPGETHHSYIADN
Sbjct: 361 LEEKGVTPSIDRIAESLNMSQRKVRNATEAISKVFSLDREAFPSLNGLPGETHHSYIADN 420

Query: 420 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRE 479
           R ENNPWHGVD+WALK+EVNKLI  TL ERE+EIIRLY+GLD+ECLTWEDISKR+GLSRE
Sbjct: 421 RPENNPWHGVDEWALKEEVNKLIDSTLQEREKEIIRLYHGLDQECLTWEDISKRMGLSRE 480

Query: 480 RVRQVGLVALEKLKHAARKKKMEAMLVKH 508
           RVRQVGLVALEKLKHAARK+  EAMLVKH
Sbjct: 481 RVRQVGLVALEKLKHAARKRNTEAMLVKH 509

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  794 bits (2051), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 392/510 (76%), Positives = 451/510 (88%), Gaps = 10/510 (1%)

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 LIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKL 358
           LIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP HLHERL LIRNAK 
Sbjct: 294 LIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPAHLHERLSLIRNAKF 353

Query: 359 RLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIAD 418
           RLEE+G+TP++DRIA+YLNMSQKKVRNATEAI K+ SLDREAFPSLNGL GETHHSYIAD
Sbjct: 354 RLEERGITPTIDRIAKYLNMSQKKVRNATEAISKIISLDREAFPSLNGLQGETHHSYIAD 413

Query: 419 NRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSR 478
           NRVEN PW+GVD+WALKDEVN+LI VTL EREREIIRLYYGL+KECLTWEDISKRIGLSR
Sbjct: 414 NRVENIPWNGVDEWALKDEVNRLINVTLVEREREIIRLYYGLEKECLTWEDISKRIGLSR 473

Query: 479 ERVRQVGLVALEKLKHAARKKKMEAMLVKH 508
           ERVRQVGLVALEKLKHAARK++MEAML+KH
Sbjct: 474 ERVRQVGLVALEKLKHAARKRQMEAMLLKH 503

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  788 bits (2034), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 389/509 (76%), Positives = 445/509 (87%), Gaps = 2/509 (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 IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLR 359
           IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP HLHERLGLIRNAK++
Sbjct: 300 IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPTHLHERLGLIRNAKVK 359

Query: 360 LEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADN 419
           L+EKG+TPS+DRIAE LNMS+KKV+NATEAI KVFSLDREAFPSLNGLPGETHHSYIADN
Sbjct: 360 LQEKGITPSLDRIAESLNMSKKKVQNATEAISKVFSLDREAFPSLNGLPGETHHSYIADN 419

Query: 420 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRE 479
            +ENNPWHG D W LK EVN+LI +TLG+REREIIRLY+GLD ECLTWE+ISKRIGLSRE
Sbjct: 420 CLENNPWHGTDTWILKVEVNQLINMTLGDREREIIRLYHGLDNECLTWEEISKRIGLSRE 479

Query: 480 RVRQVGLVALEKLKHAARKKKMEAMLVKH 508
           RVRQVGLVALEKLK AA+ +KMEAML+KH
Sbjct: 480 RVRQVGLVALEKLKKAAKTRKMEAMLLKH 508

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  787 bits (2032), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 390/510 (76%), Positives = 448/510 (87%), Gaps = 10/510 (1%)

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 LIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKL 358
           LIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP HLHERL LIRNAK 
Sbjct: 294 LIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPAHLHERLSLIRNAKF 353

Query: 359 RLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIAD 418
           RLEE+G+TP++DRIA+YLNMSQKKVRNATEAI K  SLDREAFPSLNG+ GETHHSYIAD
Sbjct: 354 RLEERGITPTIDRIAKYLNMSQKKVRNATEAISKTISLDREAFPSLNGIQGETHHSYIAD 413

Query: 419 NRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSR 478
           +RVEN PW+GVD+WALKDEVNKLI VTL EREREIIRLYYGLDKE LTWEDISKRIGLSR
Sbjct: 414 DRVENIPWNGVDEWALKDEVNKLINVTLVEREREIIRLYYGLDKEGLTWEDISKRIGLSR 473

Query: 479 ERVRQVGLVALEKLKHAARKKKMEAMLVKH 508
           ERVRQVGLVALEKLKHAARK++MEAML+KH
Sbjct: 474 ERVRQVGLVALEKLKHAARKRQMEAMLLKH 503

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 =  767 bits (1980), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 394/509 (77%), Positives = 436/509 (85%), Gaps = 11/509 (2%)

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 IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLR 359
           IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVEN RTLRLPNHLHERLGLIRNAK+R
Sbjct: 291 IGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENPRTLRLPNHLHERLGLIRNAKIR 350

Query: 360 LEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADN 419
           LEEKGVTPS+DRIAE LNMSQ+KVRNATEAI KVFSLDREAFPSLNGLPGETHHSYIADN
Sbjct: 351 LEEKGVTPSIDRIAESLNMSQRKVRNATEAISKVFSLDREAFPSLNGLPGETHHSYIADN 410

Query: 420 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRE 479
           R+ENNPWHGVD+WALK+EVNKLI   L EREREIIRLY+GLDKECLTWEDISKR+GLSRE
Sbjct: 411 RLENNPWHGVDEWALKEEVNKLIDSALQEREREIIRLYHGLDKECLTWEDISKRMGLSRE 470

Query: 480 RVRQVGLVALEKLKHAARKKKMEAMLVKH 508
           RVRQVGLVALEKLKHAARK K+EAMLVKH
Sbjct: 471 RVRQVGLVALEKLKHAARKGKLEAMLVKH 499

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 =  754 bits (1946), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 379/519 (73%), Positives = 434/519 (83%), Gaps = 29/519 (5%)

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 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQGVSRALV+NSRTLRLP HLHER
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHER 343

Query: 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPG 409
           LGLIRNAKLRL+EKG+TPS+DRIAE LNMSQKKVRNATEA+ KVFSLDR+AFPSLNGLPG
Sbjct: 344 LGLIRNAKLRLQEKGITPSIDRIAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPG 403

Query: 410 ETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWED 469
           ETHHSYIAD R+ENNPWHG DD ALK+EV+KLI  TLGERE+EIIRLYYGLDKECLTWED
Sbjct: 404 ETHHSYIADTRLENNPWHGYDDLALKEEVSKLISATLGEREKEIIRLYYGLDKECLTWED 463

Query: 470 ISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLVKH 508
           ISKRIGLSRERVRQVGLVALEKLKHAARK+KMEAM++K+
Sbjct: 464 ISKRIGLSRERVRQVGLVALEKLKHAARKRKMEAMILKN 502

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 =  752 bits (1942), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 378/519 (72%), Positives = 434/519 (83%), Gaps = 29/519 (5%)

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 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQGVSRALV+NSRTLRLP HLHER
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHER 343

Query: 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPG 409
           LGLIRNAKLRL+EKG+TPS+DRIAE LNMSQKKVRNATEA+ KVFSLDR+AFPSLNGLPG
Sbjct: 344 LGLIRNAKLRLQEKGITPSIDRIAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPG 403

Query: 410 ETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWED 469
           ETHHSYIAD R+ENNPWHG DD ALK+EV+KLI  TLGERE+EIIRLYYGLDKECLTWED
Sbjct: 404 ETHHSYIADTRLENNPWHGYDDLALKEEVSKLISATLGEREKEIIRLYYGLDKECLTWED 463

Query: 470 ISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLVKH 508
           ISKRIGLSRERVRQVGLVALEKLKHAARK+KMEAM++K+
Sbjct: 464 ISKRIGLSRERVRQVGLVALEKLKHAARKRKMEAMILKN 502

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 =  750 bits (1937), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/519 (72%), Positives = 434/519 (83%), Gaps = 29/519 (5%)

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 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQGVSRALV+NSRTLRLP HLHER
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHER 343

Query: 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPG 409
           LGLIRNAKLRL+EKG+TPS+DRIAE LNMSQKKVRNATEA+ KVFSLDR+AFPSLNGLPG
Sbjct: 344 LGLIRNAKLRLQEKGITPSIDRIAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPG 403

Query: 410 ETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWED 469
           ETHHSYIAD R+ENNPWHG DD ALK+EV+KLI  TLGERE+EIIRLYYGLDKECLTWED
Sbjct: 404 ETHHSYIADTRLENNPWHGYDDLALKEEVSKLISATLGEREKEIIRLYYGLDKECLTWED 463

Query: 470 ISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLVKH 508
           ISKRIGLSRERVRQVGLVALEKLKHAARK+KMEAM++K+
Sbjct: 464 ISKRIGLSRERVRQVGLVALEKLKHAARKRKMEAMILKN 502

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2398851|dbj|BAA22214.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana]

 Score =  749 bits (1934), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/519 (72%), Positives = 433/519 (83%), Gaps = 29/519 (5%)

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+SAR RR+ +KKK  ++  K
Sbjct: 117 LQKSMLEKSWNLSFEKAVSSEYPGKGTIRKKKIPVITCSGISARPRRIGAKKKTNMTHVK 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 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER 349
           +M+DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQGVSRALV+NSRTLRLP HLHER
Sbjct: 284 EMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHER 343

Query: 350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPG 409
           LGLIRNAKLRL+EKG+TPS+DRIAE LNMSQKKVRNATEA+ KVFSLDR+AFPSLNGLPG
Sbjct: 344 LGLIRNAKLRLQEKGITPSIDRIAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPG 403

Query: 410 ETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWED 469
           ETHHSYIAD R+ENNPWHG DD ALK+EV+KLI  TLGERE+EIIRLYYGLDKECLTWED
Sbjct: 404 ETHHSYIADTRLENNPWHGYDDLALKEEVSKLISATLGEREKEIIRLYYGLDKECLTWED 463

Query: 470 ISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLVKH 508
           ISKRIGLSRERVRQVGLVALEKLKHAARK+KMEAM++K+
Sbjct: 464 ISKRIGLSRERVRQVGLVALEKLKHAARKRKMEAMILKN 502

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	508
TAIR|locus:2010871	502	SIGA "AT1G64860" [Arabidopsis	0.968	0.980	0.705	1.8e-183
UNIPROTKB|O48655	519	rsigA "Plastid RNA polymerase	0.976	0.955	0.529	1e-130
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.681	0.604	0.331	8.1e-44
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.580	0.511	0.331	2.5e-41
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.746	0.662	0.294	1.5e-39
UNIPROTKB|P0A602	528	rpoD "RNA polymerase sigma fac	0.580	0.558	0.327	1.5e-39
TIGR_CMR|DET_0551	520	DET_0551 "RNA polymerase sigma	0.498	0.486	0.344	1.9e-39
TIGR_CMR|CBU_1596	698	CBU_1596 "RNA polymerase sigma	0.456	0.332	0.329	5e-39
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.580	0.539	0.330	6.1e-39
TIGR_CMR|CHY_0455	370	CHY_0455 "RNA polymerase sigma	0.555	0.762	0.336	2.1e-38

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

 Score = 1780 (631.7 bits), Expect = 1.8e-183, P = 1.8e-183
 Identities = 365/517 (70%), Positives = 417/517 (80%)

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 ADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG 351
             +DLVQGGLIGLLRGIEKFDSSKGF+ISTYVYWWIRQGVSRALV+NSRTLRLP HLHERLG
Sbjct:   286 SDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVSRALVDNSRTLRLPTHLHERLG 345

Query:   352 LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGET 411
             LIRNAKLRL+EKG+TPS+DRIAE LNMSQKKVRNATEA+ KVFSLDR+AFPSLNGLPGET
Sbjct:   346 LIRNAKLRLQEKGITPSIDRIAESLNMSQKKVRNATEAVSKVFSLDRDAFPSLNGLPGET 405

Query:   412 HHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDIS 471
             HHSYIAD R+ENNPWHG DD ALK+EV+KLI  TLGERE+EIIRLYYGLDKECLTWEDIS
Sbjct:   406 HHSYIADTRLENNPWHGYDDLALKEEVSKLISATLGEREKEIIRLYYGLDKECLTWEDIS 465

Query:   472 KRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLVKH 508
             KRIGLSRERVRQVGLVALEKLKHAARK+KMEAM++K+
Sbjct:   466 KRIGLSRERVRQVGLVALEKLKHAARKRKMEAMILKN 502

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 = 1282 (456.3 bits), Expect = 1.0e-130, P = 1.0e-130
 Identities = 278/525 (52%), Positives = 357/525 (68%)

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 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL 340
             AQ+YDN+G ++ADL+QGGLIGLLRGIEKFD+S+GF+ISTYVYWWIRQGVSRAL ENS+T 
Sbjct:   292 AQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTYVYWWIRQGVSRALAENSKTF 351

Query:   341 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREA 400
             RLP +LHERL  IR AK  LE++G+ P+++ IA  LN+S+KKV NATEA+ KV SLD++A
Sbjct:   352 RLPTYLHERLIAIRGAKYELEDQGIAPTIENIAGSLNISEKKVLNATEAVNKVLSLDQQA 411

Query:   401 FPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGL 460
             FPSLNGLPGET HSYI D  V N+PWHG ++W LK+EVNKL+  TL ERER+IIRLY+G+
Sbjct:   412 FPSLNGLPGETLHSYIEDQNVANDPWHGFEEWYLKEEVNKLLNSTLNERERDIIRLYHGI 471

Query:   461 DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML 505
              K+C TWEDIS++ GLSRERVRQVGL+A+EKLKHAAR+K +EA+L
Sbjct:   472 GKQCHTWEDISRQFGLSRERVRQVGLIAMEKLKHAARRKNLEALL 516

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

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

 Score = 462 (167.7 bits), Expect = 8.1e-44, P = 8.1e-44
 Identities = 118/356 (33%), Positives = 199/356 (55%)

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 NVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRA 332
             N+RLV+SIA+ Y   G ++ DLVQ G  GL+RG EKFD++KGFK STY +WWI+Q V ++
Sbjct:   340 NIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKS 399

Query:   333 LVENSRTLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIG 391
             L + SR +RLP H+ E    ++ A+ +L  E G  P  + IAE   +S K++     +  
Sbjct:   400 LSDQSRMIRLPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEATGLSMKRLMAVLLSPK 459

Query:   392 KVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGERER 451
                SLD++   + N  P E     IAD     +    + ++ ++ +++K ++ +LG RE+
Sbjct:   460 PPRSLDQKIGMNQNLKPSEV----IADPEAVTSEDILIKEF-MRQDLDK-VLDSLGTREK 513

Query:   452 EIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV 506
             ++IR  +G+ D    T ++I + +G+SRERVRQ+   A  KLK+  R   ++  LV
Sbjct:   514 QVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRNNHLQQYLV 569

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

TIGR_CMR|GSU_3089 GSU_3089 "RNA polymerase sigma factor RpoD" [Geobacter sulfurreducens PCA (taxid:243231)]

 Score = 415 (151.1 bits), Expect = 2.5e-41, Sum P(2) = 2.5e-41
 Identities = 106/320 (33%), Positives = 179/320 (55%)

Query:   199 GVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI 258
             GV ++ L   A    + K IK  LSL+D +   K+    E  ++++         EL   
Sbjct:   269 GVSADTLKEIAASEAVGKGIK--LSLEDAQKHEKKVRSAEKKLKKVEEESGFKARELSDA 326

Query:   259 LM-------ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDS 311
             L        +  LA+ +LV +N+RLV+SIA++Y N G    DL+Q G IGL++ ++KF+ 
Sbjct:   327 LRAIDRGEAKSKLAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 386

Query:   312 SKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVD 370
              +G+K STY  WWIRQ ++RA+ + +RT+R+P H+ E +  LIR ++  ++E G  PS +
Sbjct:   387 QRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREPSPE 446

Query:   371 RIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN----NPW 426
              IAE +N+   KVR       KV  + +E   SL    GE   S++ D  +E+    +P 
Sbjct:   447 EIAERMNLPLDKVR-------KVLKIAKEPI-SLETPIGEEEDSHLGDF-IEDKGVVSPL 497

Query:   427 HGVDDWALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVG 485
               V    L ++  + ++ TL  RE +++R+ +G+ +K   T E++ +   ++RER+RQ+ 
Sbjct:   498 EAVIKANLSEQTAR-VLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIE 556

Query:   486 LVALEKLKHAARKKKMEAML 505
               AL KL+H +R KK+ + +
Sbjct:   557 AKALRKLRHPSRAKKLRSFV 576

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 398 (145.2 bits), Expect = 1.5e-39, Sum P(2) = 1.5e-39
 Identities = 116/394 (29%), Positives = 195/394 (49%)

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 YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP 343
             Y+  G D+ DLVQ G  GL++  EKF+ SKG +  TY YWWIRQ + +++ +NSR +RLP
Sbjct:   352 YEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQSIKKSIFKNSRLIRLP 411

Query:   344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPS 403
               ++  L  +  A++    +G  P+   +A    ++ +K+        K  S+    +  
Sbjct:   412 ESVYALLRKVGKARMECIMEGEQPTNANVARRAGITIEKLAKLRAKTRKPRSMQDHVWSD 471

Query:   404 LNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGL-DK 462
                  G T      D  VE  P   VD   ++ +V   + + L  RE+EII   +G+ D 
Sbjct:   472 ----EGVTFQEITEDPNVEP-PDLSVDRMMMRQQVRDFLGI-LSPREKEIIEHRFGIHDG 525

Query:   463 ECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496
             E  T   I    GLS+ER+RQ+   ALEKLK +A
Sbjct:   526 EPKTLHVIGDMFGLSKERIRQLQNRALEKLKRSA 559

GO:0009536 "plastid" evidence=RCA

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

 Score = 394 (143.8 bits), Expect = 1.5e-39, Sum P(2) = 1.5e-39
 Identities = 104/318 (32%), Positives = 179/318 (56%)

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 KGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE---RLGLIRNAKLRLEEKGVTPSV 369
             KG+K STY  WWIRQ ++RA+ + +RT+R+P H+ E   +LG I+  +L L++ G  P+ 
Sbjct:   339 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLGRIQR-EL-LQDLGREPTP 396

Query:   370 DRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETH-HSYIADNRVENNPWHG 428
             + +A+ ++++ +KV    +   +  SLD+       G  G++    +I D+         
Sbjct:   397 EELAKEMDITPEKVLEIQQYAREPISLDQTI-----GDEGDSQLGDFIEDSEAVVAV-DA 450

Query:   429 VDDWALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLV 487
             V    L+D++   ++ TL ERE  ++RL +GL D +  T ++I +  G++RER+RQ+   
Sbjct:   451 VSFTLLQDQLQS-VLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESK 509

Query:   488 ALEKLKHAARKKKMEAML 505
              + KL+H +R + +   L
Sbjct:   510 TMSKLRHPSRSQVLRDYL 527

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

TIGR_CMR|DET_0551 DET_0551 "RNA polymerase sigma factor RpoD" [Dehalococcoides ethenogenes 195 (taxid:243164)]

 Score = 395 (144.1 bits), Expect = 1.9e-39, Sum P(2) = 1.9e-39
 Identities = 93/270 (34%), Positives = 156/270 (57%)

Query:   241 MEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLI 300
             +E+  ASL+     L ++ ++   A   L+ +N+RLV+S+A+++   G  + DL+Q G I
Sbjct:   262 LERHEASLKYY---LDNLEIDAKRAERHLIQANLRLVVSVAKKHIGRGMPLLDLIQEGNI 318

Query:   301 GLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL 360
             GL+R +EKFD  +GFK STY  WWIRQ ++RA+ + +RT+R+P H+ E +  + +   +L
Sbjct:   319 GLIRAVEKFDFHRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLLSISRQL 378

Query:   361 EEK-GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADN 419
              +K G  P+ D IA  +++  +KVR     I KV  L      SL    GE   S++ D 
Sbjct:   379 SQKLGREPTPDEIAVEMDLPPEKVRE----IAKVSQLP----VSLESPIGEEEDSHLGDF 430

Query:   420 RVENN---PWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIG 475
               + N   P        LK++++  ++ +L  RER +++L +GL D    T E++ K   
Sbjct:   431 IEDQNALAPPDAASRQLLKEQIDT-VLGSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFN 489

Query:   476 LSRERVRQVGLVALEKLKHAARKKKMEAML 505
             ++RER+RQ+   AL KL+H +R +K++  L
Sbjct:   490 VTRERIRQIEAKALRKLRHPSRSRKLKDYL 519

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|CBU_1596 CBU_1596 "RNA polymerase sigma factor RpoD" [Coxiella burnetii RSA 493 (taxid:227377)]

 Score = 374 (136.7 bits), Expect = 5.0e-39, Sum P(3) = 5.0e-39
 Identities = 81/246 (32%), Positives = 148/246 (60%)

Query:   265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
             A+++++ +N+RLV+SIA++Y N G    DL+Q G IGL++ ++KF+  +G+K STY  WW
Sbjct:   458 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 517

Query:   325 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
             IRQ ++R++ + +RT+R+P H+ E +  L R ++  L+E G+  + + +   ++M ++KV
Sbjct:   518 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGIEATPEELGRRMDMPEEKV 577

Query:   384 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKD---EVNK 440
             R       KV  + +E   S+    GE   S + D  +E+       D+A      E  +
Sbjct:   578 R-------KVLKIAKEPI-SMETPIGEDEDSNLGDF-IEDINMESPVDFATSAGLMEATR 628

Query:   441 LIIVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499
              I+ TL  RE +++R+ +G+D     T E++ K+  ++RER+RQ+   AL KL+H +R +
Sbjct:   629 EILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAE 688

Query:   500 KMEAML 505
             K+ + +
Sbjct:   689 KLHSFI 694

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 416 (151.5 bits), Expect = 6.1e-39, P = 6.1e-39
 Identities = 100/303 (33%), Positives = 173/303 (57%)

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 KGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNA-KLRLEEKGVTPSVDR 371
              G + +TY YWWIRQ + +++ +NSRT+RLP +++  LG +  A K  ++E    PS + 
Sbjct:   355 SGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEE 414

Query:   372 IAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDD 431
             +A ++ +S +K+           S+ +  +   +     T      D+ +E  P   V  
Sbjct:   415 LAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQD----TTFQEITPDSGIET-PTMSVGK 469

Query:   432 WALKDEVNKLIIVTLGEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALE 490
               +++ V  L+ V L  +ER II+L +G+D  +  +  +I +  GLS+ERVRQ+   AL 
Sbjct:   470 QLMRNHVRNLLNV-LSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALY 528

Query:   491 KLK 493
             +LK
Sbjct:   529 RLK 531

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

TIGR_CMR|CHY_0455 CHY_0455 "RNA polymerase sigma factor RpoD" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 411 (149.7 bits), Expect = 2.1e-38, P = 2.1e-38
 Identities = 100/297 (33%), Positives = 172/297 (57%)

Query:   212 VRLSKKIKTGLSLDDH-KLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV 270
             V L   I  G+++DD  ++ LKE +G  P +      + +++ + +        A+ KL 
Sbjct:    85 VDLDLTIPEGIAIDDPVRMYLKE-IGRVPLLTP-EEEIELAKRKEEGD----EEAKRKLA 138

Query:   271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVS 330
              +N+RLV+SIA+RY   G    DL+Q G +GLL+ +EKFD  KG+K STY  WWIRQ ++
Sbjct:   139 EANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAIT 198

Query:   331 RALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEA 389
             RA+ + +RT+R+P H+ E +  LIR ++  L+E G  P+ + IA+ + +S+ KVR   + 
Sbjct:   199 RAIADQARTIRIPVHMVETINKLIRVSRNLLQELGREPTPEEIAKEMGISEDKVREIMKI 258

Query:   390 IGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGER 449
               +  SL+        G   ++H     ++     P        L++++++ ++ TL ER
Sbjct:   259 AQEPVSLETPI-----GEEEDSHLGDFVEDPDAKAPVEEASYTLLREQLDE-VLKTLTER 312

Query:   450 EREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML 505
             E++++RL +GLD     T E++ +  G++RER+RQ+   AL KL+H +R KK++  L
Sbjct:   313 EQKVLRLRFGLDDGRARTLEEVGQIFGVTRERIRQIEAKALRKLRHPSRSKKLKDFL 369

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	0.7283	0.9645	0.9760	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	grail3.0065010301	hypothetical protein (510 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.XIV.2894.1	hypothetical protein (684 aa)			•						0.431
	fgenesh4_pg.C_LG_XVII000398	hypothetical protein (677 aa)			•						0.430
	eugene3.17410001	annotation not avaliable (472 aa)			•						0.429
	estExt_fgenesh4_pg.C_3210002	hypothetical protein (472 aa)			•						0.426
	gw1.321.23.1	annotation not avaliable (657 aa)			•						0.420
	eugene3.00001972	hypothetical protein (485 aa)			•						0.411

---

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	508
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	4e-75
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	3e-56
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	8e-56
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	2e-54
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	3e-52
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	6e-49
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	5e-48
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	1e-47
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	3e-45
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	1e-42
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	2e-41
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	4e-41
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	6e-28
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	4e-26
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	5e-26
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	1e-21
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	5e-21
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	5e-21
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	6e-21
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	3e-19
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	3e-19
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	2e-18
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	6e-18
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	8e-18
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	2e-15
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	2e-12
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	7e-12
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	2e-11
PRK05911	257	PRK05911, PRK05911, RNA polymerase sigma factor si	5e-11
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	2e-10
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	2e-10
PRK07122	264	PRK07122, PRK07122, RNA polymerase sigma factor Si	3e-10
PRK07670	251	PRK07670, PRK07670, RNA polymerase sigma factor Si	4e-10
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	2e-09
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	1e-08
pfam04545	50	pfam04545, Sigma70_r4, Sigma-70, region 4	2e-08
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	3e-08
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	5e-08
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	6e-07
cd06171	55	cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers	6e-07
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	2e-04
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	0.001

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

 Score =  238 bits (610), Expect = 4e-75
 Identities = 113/292 (38%), Positives = 181/292 (61%), Gaps = 11/292 (3%)

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 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKV 383
           IRQG++RA+   SRT+RLP H+ E+L  I+  +  L ++ G TPS   IAE L +  ++V
Sbjct: 135 IRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQV 194

Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHS-YIADNRVENNPWHGVDDWALKDEVNKLI 442
           R   +   +  SLD        G   +T     + D+    +P   V+  +L+ ++  L+
Sbjct: 195 RELLQRARQPVSLDAPV-----GDEEDTELGDLLEDD--GESPEEQVERESLRQDLESLL 247

Query: 443 IVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLK 493
              L  RER+++RL +GLD    LT  +I +R+ LSRERVRQ+   AL KL+
Sbjct: 248 A-ELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298

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

 Score =  187 bits (476), Expect = 3e-56
 Identities = 90/245 (36%), Positives = 151/245 (61%), Gaps = 10/245 (4%)

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 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++RA+ + +RT+R+P H+ E +  LI+  +   +E G  P+ + +AE + M  +KV
Sbjct: 61  IRQAITRAIADQARTIRIPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKV 120

Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHS-YIADNRVENNPWHGVDDWALKDEVNKLI 442
           R   +   +  SL+        G   ++    +I D  +E +P        L++++++++
Sbjct: 121 REIKKIAQEPISLETPI-----GEEEDSFLGDFIEDTSIE-SPDDYAAKELLREQLDEVL 174

Query: 443 IVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM 501
             TL ERE +++R+ YGL D +  T E++ K   ++RER+RQ+   AL KL+H +R KK+
Sbjct: 175 E-TLTEREEKVLRMRYGLLDGQPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKL 233

Query: 502 EAMLV 506
           ++ L 
Sbjct: 234 KSFLD 238

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

 Score =  188 bits (480), Expect = 8e-56
 Identities = 109/302 (36%), Positives = 181/302 (59%), Gaps = 21/302 (6%)

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 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++RA+ E SRT+RLP H+ E+L  I+ A+ +L ++ G   ++  +AE L ++ K+V
Sbjct: 142 IRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQV 201

Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWA----LKDEVN 439
           R   E   +  SLD           G+   + + +  +  +     +D+A    L+ ++ 
Sbjct: 202 REYLERARQPLSLDLRV--------GDNQDTELGE--LLEDTGASPEDFATQSSLQLDLE 251

Query: 440 KLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498
           +L +  L  +++E+I L +GL D + LT   I +R+ +SRERVRQ+   AL KL    RK
Sbjct: 252 RL-MEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKL----RK 306

Query: 499 KK 500
           +K
Sbjct: 307 RK 308

Length = 317

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

 Score =  187 bits (476), Expect = 2e-54
 Identities = 110/298 (36%), Positives = 172/298 (57%), Gaps = 15/298 (5%)

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 IRQGVSRALVENSRTLRLPNHLHERLGLIRNA-KLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++RA+ + SRT+RLP HL+E +  I+   K+  +E G  P+ + IAE + M+ +K+
Sbjct: 197 IRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKL 256

Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE---NNPWHGVDDWALKDEVNK 440
           R   ++     SL+           G+   S + D  +E     P   V    L++++  
Sbjct: 257 RFIAKSAQLPISLETPI--------GKEEDSRLGD-FIEADGETPEDDVAKNLLREDLEG 307

Query: 441 LIIVTLGEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497
           + + TL  RER+++RL YGLD     T E+I +   ++RER+RQ+   AL KL+H  R
Sbjct: 308 V-LATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNR 364

Length = 373

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

 Score =  180 bits (458), Expect = 3e-52
 Identities = 113/340 (33%), Positives = 181/340 (53%), Gaps = 27/340 (7%)

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 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345
             G    DL+Q G IGL++ +EKFD  KGFK STY  WWIRQ ++RA+ + +RT+R+P H
Sbjct: 124 GRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 183

Query: 346 LHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSL 404
             E +  +R  K  L  E G  P+ + IAE L +S  KVR   +   +  SLD       
Sbjct: 184 QVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDDE 243

Query: 405 NGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDK-E 463
           +   G+    ++ D++   +P   V+  +LK+++N+++   L ERER +IRL +GLD  E
Sbjct: 244 DSELGD----FLEDDKSV-SPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGE 298

Query: 464 CLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEA 503
             T E++ +  G+SRERVRQ+   AL KL+    +  +  
Sbjct: 299 PKTLEELGEEFGISRERVRQIEAKALRKLRRHPERSALLR 338

Length = 342

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

 Score =  173 bits (440), Expect = 6e-49
 Identities = 107/323 (33%), Positives = 180/323 (55%), Gaps = 35/323 (10%)

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 LRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL-E 361
            R +EKFD +KG++ STY YWWIRQG++RA+   SRT+RLP H+ E+L  I+ A+ ++ +
Sbjct: 214 ERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQ 273

Query: 362 EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIAD--N 419
           EKG TP+++ IA+ L M+  +VR     + +  SL+ +         G+   + + D   
Sbjct: 274 EKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKV--------GKDKDTELGDLLE 325

Query: 420 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSR 478
             + +P   +   +L+ ++  L +  L  RER++IR+ +GL D    +  +I + + LSR
Sbjct: 326 TDDISPEEMLMRESLQRDLQHL-LADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSR 384

Query: 479 ERVRQVGLVALEKLKHAARKKKM 501
           ERVRQ+   AL+KL+   R+ ++
Sbjct: 385 ERVRQIESKALQKLRQPKRRNRI 407

Length = 415

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

 Score =  168 bits (427), Expect = 5e-48
 Identities = 103/314 (32%), Positives = 171/314 (54%), Gaps = 29/314 (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 KISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAE 374
           K STY  WWIRQ ++R + + SRT+RLP HL E++  +   K  L ++ G   + + +AE
Sbjct: 138 KFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAE 197

Query: 375 YLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHS----YIADNRVENNPWHGVD 430
              + ++K       I  +    R+   SL+   G    +    +I D+   +   + V 
Sbjct: 198 ESGIPEEK-------IADLLEHSRDPV-SLDMPVGSDEEAPLGDFIEDSEATSAE-NAVI 248

Query: 431 DWALKDEVNKLIIVTLGEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVAL 489
              L  ++   ++ TL ERE+++IRL +GLD  +  T + I K  GLSRERVRQ+    +
Sbjct: 249 AGLLHTDIRS-VLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVM 307

Query: 490 EKLKHAARKKKMEA 503
            KL++  R  ++ +
Sbjct: 308 SKLRNGERADRLRS 321

Length = 324

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

 Score =  167 bits (424), Expect = 1e-47
 Identities = 101/304 (33%), Positives = 177/304 (58%), Gaps = 11/304 (3%)

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 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKV 383
           IRQ ++RA+ + +RT+RLP H+ E+L  I+  +  L +K G + +   IA+ L +   ++
Sbjct: 152 IRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQI 211

Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLII 443
           R       +  SLD        G   +T  S + ++    +P   +    L+ ++N L +
Sbjct: 212 REYLSMARQPISLDVRV-----GDNQDTELSELLEDE-GPSPDQYITQELLRQDLNNL-L 264

Query: 444 VTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKME 502
             L  ++RE++ L +GL D + L+   + +R+ LSRERVRQ+   AL  L+   R+  ++
Sbjct: 265 AELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR--RRANVK 322

Query: 503 AMLV 506
             L 
Sbjct: 323 EYLA 326

Length = 327

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

 Score =  159 bits (405), Expect = 3e-45
 Identities = 97/286 (33%), Positives = 157/286 (54%), Gaps = 20/286 (6%)

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

Query: 271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVS 330
            SN+RLV+SIA+ Y N G  + DL++ G +GL+  +EKFD  +GF+ STY  WWIRQ + 
Sbjct: 53  ESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIE 112

Query: 331 RALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKVRNATEA 389
           RA++  +RT+RLP H+ + L +   A  +LE+K G  PSV+ IAE L+   + V      
Sbjct: 113 RAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLAL 172

Query: 390 IGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGER 449
             ++ SLD      L+    ++    IAD +   +P   V +  LK  +    +  L ER
Sbjct: 173 NERITSLDA----PLDDDSSKSLLDTIADEQ-SIDPESLVQNDDLKQLIEAW-LAELNER 226

Query: 450 EREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494
           +RE++   +GL   E  T E+++  +GL+RERVRQ+ + AL+KL+ 
Sbjct: 227 QREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRR 272

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|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional

 Score =  158 bits (401), Expect = 1e-42
 Identities = 104/311 (33%), Positives = 171/311 (54%), Gaps = 37/311 (11%)

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 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++RA+ + +RT+R+P H+ E +  L R  +  L+E G  P+ + +A+ +  + +KV
Sbjct: 332 IRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKV 391

Query: 384 RN----ATEAIGKVFSLDREAFPSLNGLPGETHHS----YIADNRVENNPWHGVDDWALK 435
           R       E I    SLD+          G+   S    +I D+    +P   V    L+
Sbjct: 392 REIQKYNREPI----SLDKTI--------GKEGDSQFGDFIEDSEAV-SPVDAVSFTLLQ 438

Query: 436 DEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494
           D++ +++  TL ERE  +IR+ +GL D +  T ++I +  G++RER+RQ+    L KL+H
Sbjct: 439 DQLQEVLE-TLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRH 497

Query: 495 AARKKKMEAML 505
            +R + +   L
Sbjct: 498 PSRSQVLRDFL 508

Length = 509

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

 Score =  150 bits (382), Expect = 2e-41
 Identities = 88/234 (37%), Positives = 138/234 (58%), Gaps = 14/234 (5%)

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 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKV 383
           IRQ + RA++  +RT+RLP H+ + L +   A   LE K    PS + IAE L+     V
Sbjct: 147 IRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDV 206

Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLI- 442
                   ++ SLD      L G P ++    +AD + EN P    +D    D++ + I 
Sbjct: 207 SRMLALNERITSLD----TPLGGDPEKSLLDILADEQ-ENGP----EDTTQDDDMKQSIV 257

Query: 443 --IVTLGEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALEKLK 493
             +  L +++RE++   +GL   E  T ED+++ IGL+RERVRQ+ + AL +L+
Sbjct: 258 KWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311

Length = 325

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

 Score =  151 bits (383), Expect = 4e-41
 Identities = 94/249 (37%), Positives = 147/249 (59%), Gaps = 28/249 (11%)

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 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++RA+ + +RT+R+P H+ E +  LIR  +  L+E G  P+ + IAE ++M  +KV
Sbjct: 190 IRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKV 249

Query: 384 RN----ATEAIGKVFSLDREAFPSLNGLPGETHHSYIAD---NRVENNPWHGVDDWA--- 433
           R     A E +            SL    GE   S++ D   ++   +P    D  A   
Sbjct: 250 REILKIAQEPV------------SLETPIGEEDDSHLGDFIEDQDATSP---ADHAAYEL 294

Query: 434 LKDEVNKLIIVTLGEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALEKL 492
           LK+++   ++ TL +RE  ++RL +GLD     T E++ K  G++RER+RQ+   AL KL
Sbjct: 295 LKEQLED-VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 353

Query: 493 KHAARKKKM 501
           +H +R K++
Sbjct: 354 RHPSRSKQL 362

Length = 367

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

 Score =  117 bits (295), Expect = 6e-28
 Identities = 88/252 (34%), Positives = 148/252 (58%), Gaps = 34/252 (13%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           A++++V +N+RLV+SIA++Y N G    DL+Q G IGL++ ++KF+  +G+K STY  WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++R++ + +RT+R+P H+ E +  L R ++  L+E G  P+ + +AE L M + KV
Sbjct: 441 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKV 500

Query: 384 RNATEAIGKVFSLDREAFP-SLNGLPGET--------HHS-YIADNRVENNPWHGVDDWA 433
           R       KV  + +E  P SL     ET        H   +I D   E  P     D A
Sbjct: 501 R-------KVLKIAKE--PISL-----ETPIGDDEDSHLGDFIEDKNAE-LPI----DAA 541

Query: 434 LKD---EVNKLIIVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVAL 489
           +++   E    ++ +L  RE +++R+ +G+D     T E++ K+  ++RER+RQ+   AL
Sbjct: 542 IQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 601

Query: 490 EKLKHAARKKKM 501
            KL+H +R +K+
Sbjct: 602 RKLRHPSRSRKL 613

Length = 619

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

 Score =  106 bits (266), Expect = 4e-26
 Identities = 70/233 (30%), Positives = 118/233 (50%), Gaps = 15/233 (6%)

Query: 268 KLVMSNVRLVMSIAQRYDN-MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIR 326
           +L+   + LV SIA++++N   ++  DL+Q G+IGL++ IE++D SKG K STY    IR
Sbjct: 27  RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIR 86

Query: 327 QGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRN 385
             +   L +N  ++++P  L E    I  A   LE E G  P+ + IAE L + +++   
Sbjct: 87  GEILDYLRKND-SVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIE 145

Query: 386 ATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVT 445
           A  AI        +       +  +             NP  GV+   L + + + I   
Sbjct: 146 ALLAING-----SQLLSLDEDVLKDDDDDVDD---QIENPDDGVEKEELLEILKEAIEP- 196

Query: 446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498
           L ERE+ ++ L Y   KE LT ++I++ +G+S  RV ++   A++KL+    K
Sbjct: 197 LPEREKLVLVLRY---KEELTQKEIAEVLGISESRVSRLHKKAIKKLRKELNK 246

Length = 247

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

 Score =  105 bits (264), Expect = 5e-26
 Identities = 77/240 (32%), Positives = 120/240 (50%), Gaps = 23/240 (9%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           AREKLV  N+ LV SIA+R+ N G    DLVQ G IGL++ I++FD S G K ST+    
Sbjct: 4   AREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPT 63

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKV 383
           I   + R   +++  +R+P  L E    I  A   L ++ G +P++  IAE L +S+++V
Sbjct: 64  IMGEIKRFFRDDTWAVRVPRRLKELGVKINKATEELTQRLGRSPTIAEIAERLGVSEEEV 123

Query: 384 RNATEAIG--KVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDW----ALKDE 437
             A EA    +  SLD                  + D   + +    ++      ALK  
Sbjct: 124 VEALEAGNAYQALSLDASIEDDDGDPI------ALLDTLGDEDD--ALETVEDRLALKP- 174

Query: 438 VNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497
               ++  L ERER I+ L +  DK   T  +I++R+G+S+  V ++   AL+KL+    
Sbjct: 175 ----LLAALPERERRILLLRFFEDK---TQSEIAERLGISQMHVSRLLRRALKKLREQLL 227

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|233844 TIGR02392, rpoH_proteo, alternative sigma factor RpoH

 Score = 94.3 bits (235), Expect = 1e-21
 Identities = 69/241 (28%), Positives = 132/241 (54%), Gaps = 19/241 (7%)

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 IRQGVSRALVENSRTLRLPNHLHERLGL---IRNAKLRLEEKGVTPS-VDRIAEYLNMSQ 380
           I+  +   ++ N R +++     +R  L   +R  K RL +  + P  V+ IAE L +S+
Sbjct: 96  IKAEIHEYILRNWRLVKVATTKAQR-KLFFNLRKMKKRL-QGWLNPEEVEAIAEELGVSE 153

Query: 381 KKVRNATEAI-GKVFSLDREAFPSLNGLPGETHH--SYIADNRVENNPWHGVDDWALKDE 437
           ++VR     + G+  SL+     S++    +     +Y+ D R  ++P   +++   ++ 
Sbjct: 154 REVREMESRLSGQDMSLN----ASIDDDEDDGGAPIAYLVDKR--SDPEDTLEEEQWEEL 207

Query: 438 VNKLI---IVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494
             + +   + +L  R R II   + LD + LT ++++   G+S ER+RQ+   A++KLK 
Sbjct: 208 QRQALANALGSLDARSRRIIEARW-LDDDKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266

Query: 495 A 495
           A
Sbjct: 267 A 267

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|180137 PRK05572, PRK05572, sporulation sigma factor SigF; Validated

 Score = 92.0 bits (229), Expect = 5e-21
 Identities = 84/240 (35%), Positives = 125/240 (52%), Gaps = 21/240 (8%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           AR+ LV  N+RLV S+ QR+ N G +  DL Q G IGLL+ ++KFD S   K STY    
Sbjct: 33  ARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPM 92

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKV 383
           I   + R L ++  T+++   L E    IR  K  L ++ G  P+++ +AEYL ++ ++V
Sbjct: 93  IIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEV 151

Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLII 443
             A EA     S+      + +G P  T    IAD   E+  W   D  ALK+ + +   
Sbjct: 152 VLAQEASRSPQSIHETVHEN-DGDP-ITLLDQIADQSEED--W--FDKIALKEAIRE--- 202

Query: 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEA 503
             L ERER I+ L Y  DK   T  +++KR+G+S     QV +  LEK      K+K++ 
Sbjct: 203 --LDERERLIVYLRYFKDK---TQSEVAKRLGIS-----QVQVSRLEKKILKQMKEKLDE 252

Length = 252

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

 Score = 92.5 bits (231), Expect = 5e-21
 Identities = 71/262 (27%), Positives = 119/262 (45%), Gaps = 62/262 (23%)

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 IR---------------------QGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK 363
           I+                     Q   R L  N R  +      +RLG +       EE 
Sbjct: 109 IKAEIHEYILRNWRIVKVATTKAQ---RKLFFNLRKAK------KRLGWLNP-----EE- 153

Query: 364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHS------YIA 417
                V+ +AE L +S+++VR   E   ++   D     SL+    +          Y+ 
Sbjct: 154 -----VEMVAEELGVSEEEVR---EMESRLSGQD----ASLDAPIDDDDEESGAPQDYLE 201

Query: 418 DNRVENNPWHGV--DDWALKDEVNKLI--IVTLGEREREIIRLYYGLDKECLTWEDISKR 473
           D    ++P   +  D+W        L   +  L ER R+II   + LD +  T ++++  
Sbjct: 202 DKS--SDPADVLEEDNW-EDQRRALLADALEGLDERSRDIIEARW-LDDDKSTLQELAAE 257

Query: 474 IGLSRERVRQVGLVALEKLKHA 495
            G+S ERVRQ+   A++KLK A
Sbjct: 258 YGVSAERVRQIEKNAMKKLKAA 279

Length = 284

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

 Score = 91.3 bits (227), Expect = 6e-21
 Identities = 77/230 (33%), Positives = 124/230 (53%), Gaps = 14/230 (6%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           AR+KL+  N+RLV SI +R+ N G +  DL Q G IGL++ I+KFD S   K STY    
Sbjct: 12  ARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPM 71

Query: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKV 383
           I   + R L ++   +++   L E    IR  K  L ++ G  P+++ +AE L +S +++
Sbjct: 72  IMGEIKRFLRDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEI 130

Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLII 443
             A E+     SL  +     +G P       IAD   E++ W  ++  ALK+ ++K   
Sbjct: 131 VMALESARSPQSL-YDTVHQDDGDP-IYLLDQIADKGSEDSDW--LEKIALKEAISK--- 183

Query: 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493
             L ERER+II L Y  DK   T  +++  +G+S+ +V ++    L+K+K
Sbjct: 184 --LDERERQIIMLRYFKDK---TQTEVANMLGISQVQVSRLEKKVLKKMK 228

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|181296 PRK08215, PRK08215, sporulation sigma factor SigG; Reviewed

 Score = 87.3 bits (217), Expect = 3e-19
 Identities = 79/243 (32%), Positives = 127/243 (52%), Gaps = 41/243 (16%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           AREKL+  N+RLV+S+ QR++N G ++ DL Q G IGL++ I+ FD S+  K STY    
Sbjct: 38  AREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPM 97

Query: 325 IRQGVSRALVEN-----SRTLRLPNH--LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLN 377
           I   + R L +N     SR+LR   +  L  R  LI        E    P+V+ IA+ L 
Sbjct: 98  IIGEIRRYLRDNNPIRVSRSLRDIAYKALQVREKLIN-------ENSKEPTVEEIAKELE 150

Query: 378 MSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHH--SYIADNRVENNPWHGVDDWALK 435
           + +++V  A +AI    SL    F  +    G+  +    I+D + ++  W  +++ ALK
Sbjct: 151 VPREEVVFALDAIQDPVSL----FEPIYHDGGDPIYVMDQISDEKNKDENW--LEEIALK 204

Query: 436 DEVNKLIIVTLGEREREII--RLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEK-- 491
           + + K     L +RE+ I+  R + G      T  ++++ IG+S+ +V +     LEK  
Sbjct: 205 EAMKK-----LNDREKLILNLRFFQG-----KTQMEVAEEIGISQAQVSR-----LEKAA 249

Query: 492 LKH 494
           LKH
Sbjct: 250 LKH 252

Length = 258

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

 Score = 87.8 bits (218), Expect = 3e-19
 Identities = 73/268 (27%), Positives = 108/268 (40%), Gaps = 69/268 (25%)

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

Query: 325 I---------------RQGVS---RALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVT 366
           I               R G S   +AL  N R LR              A+L    +   
Sbjct: 101 IRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLR--------------ARL---AQADE 143

Query: 367 PSVD-----RIAEYLNMSQKKVR-------------NATEAIGKVFSLDR-EAFPSLNGL 407
                     IA  L +S   V              NA ++       +R +     + L
Sbjct: 144 ELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSPL 203

Query: 408 PGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTW 467
           P E   S I   R           W L   +      TL ERE  IIR    L ++  T 
Sbjct: 204 PDEQVESSIDGERRR--------RW-LTQALQ-----TLNERELRIIR-ERRLREDGATL 248

Query: 468 EDISKRIGLSRERVRQVGLVALEKLKHA 495
           E + + +G+S+ERVRQ+   ALEKL+ A
Sbjct: 249 EALGEELGISKERVRQIEARALEKLRRA 276

Length = 289

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

 Score = 84.9 bits (210), Expect = 2e-18
 Identities = 76/239 (31%), Positives = 127/239 (53%), Gaps = 32/239 (13%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 324
           AREKL+  N+RLV+S+ QR++N G  + DL Q G IGL++ I+ FD S+  K STY    
Sbjct: 35  AREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPM 94

Query: 325 IRQGVSRALVEN-----SRTLRLPNH--LHERLGLI-RNAKLRLEEKGVTPSVDRIAEYL 376
           I   + R L +N     SR+LR   +  L  R  LI  N+K         P+V  IA+ L
Sbjct: 95  IIGEIRRYLRDNNPIRVSRSLRDIAYKALQVRDKLISENSK--------EPTVSEIAKEL 146

Query: 377 NMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHH--SYIADNRVENNPWHGVDDWAL 434
            + Q++V  A +AI    SL    F  +    G+  +    I+D + +++ W  ++  AL
Sbjct: 147 KVPQEEVVFALDAIQDPVSL----FEPIYNDGGDPIYVMDQISDEKNKDSQW--LEGIAL 200

Query: 435 KDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493
           K+ + +     L ERE+ I+ + +   K   T  ++++ IG+S+ +V ++   AL+ ++
Sbjct: 201 KEAMKR-----LNEREKMILNMRFFEGK---TQMEVAEEIGISQAQVSRLEKAALKHMR 251

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|218138 pfam04542, Sigma70_r2, Sigma-70 region 2

 Score = 77.6 bits (192), Expect = 6e-18
 Identities = 33/71 (46%), Positives = 44/71 (61%)

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

Query: 329 VSRALVENSRT 339
           +  AL +  RT
Sbjct: 61  IIDALRKQRRT 71

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

 Score = 81.9 bits (203), Expect = 8e-18
 Identities = 67/210 (31%), Positives = 102/210 (48%), Gaps = 20/210 (9%)

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGV---SRALVENSRTLRLPNHL 346
           ++ DL+Q G+ GLL  IE++D S+G K  TY    IR  +    R L    R+LR     
Sbjct: 25  ELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQKARK 84

Query: 347 HERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPS 403
            ER      A   LE + G  P+ + IAE L M  K+ R A   I    + SLD      
Sbjct: 85  LER------AIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLE-- 136

Query: 404 LNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKE 463
            +G  G +    I D     +P   ++   L++ + +  I +L ERE+ ++ LYY    E
Sbjct: 137 -SGDDGGSLIDRIED-DKSEDPEEELEREELREALAE-AIESLSEREQLVLSLYY---YE 190

Query: 464 CLTWEDISKRIGLSRERVRQVGLVALEKLK 493
            L  ++I + +GL+  RV Q+   AL+KL+
Sbjct: 191 ELNLKEIGEVLGLTESRVSQIHSQALKKLR 220

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|131987 TIGR02941, Sigma_B, RNA polymerase sigma-B factor

 Score = 76.1 bits (187), Expect = 2e-15
 Identities = 66/241 (27%), Positives = 111/241 (46%), Gaps = 14/241 (5%)

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

Query: 321 VYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMS 379
               I   + R L + + ++ +P  + E    I+ A   L +    +P +  IA++L +S
Sbjct: 86  AIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLS 145

Query: 380 QKKVRNATEAIG--KVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDE 437
           +++V    E     +  S+D       +G       S +A          G D    +  
Sbjct: 146 EEEVLEIMEMGQSYRALSVDDVIEADSDG-------STVARLDSVGEVEDGYDQ-TERRM 197

Query: 438 VNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497
           V + I+  L ERE+ II   +   +E L+ ++  +R+G+S+  V ++   A+ KLK AA 
Sbjct: 198 VLEKILPILSEREKSIIHCTF---EENLSQKETGERLGISQMHVSRLQRQAISKLKEAAF 254

Query: 498 K 498
            
Sbjct: 255 L 255

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

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

 Score = 66.6 bits (163), Expect = 2e-12
 Identities = 65/254 (25%), Positives = 114/254 (44%), Gaps = 40/254 (15%)

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

Query: 321 VYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMS 379
               I   + R L + + ++ +P  + E    I+ A   L  E   +P +  IA+ L +S
Sbjct: 86  AVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVS 145

Query: 380 QKKVRNATEAIGK---VFSLDR--EAFP-----SLNGLPGETHHSYIADNRVENNPWHGV 429
           +++V  A E  GK     S+D   EA       +L  + G+    Y              
Sbjct: 146 EEEVLEAMEM-GKSYQALSVDHSIEADSDGSTVTLLDIVGQQEDGY-------------- 190

Query: 430 DDWALKDEVNKLIIV-----TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQV 484
                 +   + +I+      L +RE+ II+  +    E L+ ++  +R+G+S+  V ++
Sbjct: 191 ------ELTEQRMILEKILPVLSDREKSIIQCTF---IENLSQKETGERLGISQMHVSRL 241

Query: 485 GLVALEKLKHAARK 498
              A++KL+ AA  
Sbjct: 242 QRQAIKKLREAAFL 255

Length = 257

>gnl|CDD|235901 PRK06986, fliA, flagellar biosynthesis sigma factor; Validated

 Score = 64.9 bits (159), Expect = 7e-12
 Identities = 57/217 (26%), Positives = 104/217 (47%), Gaps = 37/217 (17%)

Query: 290 DMADLVQGGLIGLLRGIEKFDSSKGFKISTY----VYW----WIRQG--VSRALVENSRT 339
           D+ DL+Q G+IGLL    ++D  +G    TY    +       +R    V R++  N+R 
Sbjct: 37  DLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLDWVPRSVRRNAR- 95

Query: 340 LRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSL 396
                        +  A  +LE E G  P+   +AE L +S ++ R       I ++FS+
Sbjct: 96  ------------EVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSI 143

Query: 397 DREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRL 456
           D      L G  G+     + ++  + +P   ++D  L++ + +  I +L ERE+ ++ L
Sbjct: 144 D-----ELRGEHGD--SILVTEDHQDEDPLQQLEDEELREALVE-AIESLPEREQLVLSL 195

Query: 457 YYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493
           YY   +E L  ++I   +G+S  RV Q+   A+++L+
Sbjct: 196 YY---QEELNLKEIGAVLGVSESRVSQIHSQAIKRLR 229

Length = 236

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

 Score = 63.4 bits (155), Expect = 2e-11
 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|235644 PRK05911, PRK05911, RNA polymerase sigma factor sigma-28; Reviewed

 Score = 62.7 bits (152), Expect = 5e-11
 Identities = 69/240 (28%), Positives = 117/240 (48%), Gaps = 22/240 (9%)

Query: 266 REKLVMSNVRLVMSIAQRY-DNMGA--DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVY 322
           R+ L+   + LV ++A R    M +     DL   G+ GL+R +E+FD  K  +   Y  
Sbjct: 25  RDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYAL 84

Query: 323 WWIRQGVSRALVENSRTLR-LPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQ 380
           + I+     A++++ R    +P  +H++   + +A   L +  G  P+   + EYLN+SQ
Sbjct: 85  FLIKA----AIIDDLRKQDWVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQ 140

Query: 381 KKVRN--ATEAIGKVFSLDREAFPSL-NGLPGETHHSYIADNRVENNPWHGVDDWALKDE 437
           +++    ++     + SL+ E FP   +   G      IAD R E     G D    K+ 
Sbjct: 141 QELSGWFSSARPALILSLNEE-FPCQSDDEAGLALEERIADERAET----GYDVVDKKEF 195

Query: 438 VNKLI--IVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA 495
            + L   I+ L E+ER+++ LYY    E L  ++I K +G+S  RV Q+   AL KL+  
Sbjct: 196 SSILAEAILALEEKERKVMALYY---YEELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252

Length = 257

>gnl|CDD|146934 pfam04539, Sigma70_r3, Sigma-70 region 3

 Score = 56.8 bits (138), Expect = 2e-10
 Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 1/76 (1%)

Query: 348 ERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNG 406
           E L  I+ A+  LE E G  P+ + IAE L +S++KVR   EA  +  SLD       +G
Sbjct: 1   ELLNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDG 60

Query: 407 LPGETHHSYIADNRVE 422
             G+      A++  +
Sbjct: 61  ELGDLLEDDDAESPED 76

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 as 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. Length = 78

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

 Score = 60.5 bits (147), Expect = 2e-10
 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|168831 PRK07122, PRK07122, RNA polymerase sigma factor SigF; Reviewed

 Score = 60.6 bits (147), Expect = 3e-10
 Identities = 55/217 (25%), Positives = 99/217 (45%), Gaps = 11/217 (5%)

Query: 266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWI 325
           R+++V   + L   IA+R+D  G    DLVQ   +GL+  + +FD   G    ++    I
Sbjct: 42  RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTI 101

Query: 326 RQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKVR 384
              V R   +NS ++++P  L E    +  A   L ++ G  P+   +A  L M +++V 
Sbjct: 102 MGEVRRHFRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVV 161

Query: 385 NATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIV 444
               A G  ++         +G         IAD   + +   G+D    ++ +  L + 
Sbjct: 162 EGLVA-GSAYNTLSIDSGGGSGDDDARA---IADTLGDVDA--GLDQIENREALRPL-LA 214

Query: 445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERV 481
            L ERER ++ L +    E +T   I++R+G+S+  V
Sbjct: 215 ALPERERTVLVLRF---FESMTQTQIAERVGISQMHV 248

Length = 264

>gnl|CDD|181075 PRK07670, PRK07670, RNA polymerase sigma factor SigD; Validated

 Score = 60.1 bits (146), Expect = 4e-10
 Identities = 57/209 (27%), Positives = 96/209 (45%), Gaps = 14/209 (6%)

Query: 293 DLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGL 352
           DL   G++GL   +EKFD S+  K  TY  + IR  +   L +      LP  + E+   
Sbjct: 54  DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED---WLPRSMREKTKK 110

Query: 353 IRNAKLRLEEK-GVTPSVDRIAEYLNMSQKKVRNA-TEA-IGKVFSLDREAFPSLNGLPG 409
           +  A  +LE++     +   +A  L M++++V     E     + S+D +     +   G
Sbjct: 111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDD---G 167

Query: 410 ETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWED 469
           E     I D++        + +  L +E+ +  I  L E+E+ +I L+Y   KE LT  +
Sbjct: 168 ENVSVTIRDDKTPTPEEKLLKE-ELIEELAEK-IKQLSEKEQLVISLFY---KEELTLTE 222

Query: 470 ISKRIGLSRERVRQVGLVALEKLKHAARK 498
           I + + LS  R+ Q+   AL KLK    K
Sbjct: 223 IGQVLNLSTSRISQIHSKALFKLKKLLEK 251

Length = 251

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

 Score = 58.2 bits (141), Expect = 2e-09
 Identities = 70/245 (28%), Positives = 114/245 (46%), Gaps = 37/245 (15%)

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

Query: 323 WWIRQGVSRALVENSRTL-RLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYLNMSQ 380
             IR     A+ +  R++  +P  + ++   I  A   LE + G TPS + IA+ L +S 
Sbjct: 93  TRIRG----AIFDELRSIDWIPRSVRQKARQIERAIAMLEARLGRTPSDEEIADELGISL 148

Query: 381 KKVRNATEAIGKV---------FSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDD 431
           ++  +    +            F  D     SL     +T  S  A N  E         
Sbjct: 149 EEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSL----MDTLESPAALNPDE--------- 195

Query: 432 WALKDEVNKLI---IVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA 488
            A ++E+ ++I   I TL ERE++++ LYY    E LT ++I K +G++  R+ Q+   A
Sbjct: 196 IAEREEIKRVIVEAIKTLPEREKKVLILYY---YEDLTLKEIGKVLGVTESRISQLHTKA 252

Query: 489 LEKLK 493
           + +L+
Sbjct: 253 VLQLR 257

Length = 268

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

 Score = 53.9 bits (130), Expect = 1e-08
 Identities = 35/148 (23%), Positives = 56/148 (37%), Gaps = 31/148 (20%)

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

Query: 325 IRQGVSRAL----------------VENSRTLRLPNHLHERLGLIRNAKLRLEEK----- 363
            R  +   L                +++  +        E    +R A  +L E+     
Sbjct: 60  ARNLILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVL 119

Query: 364 ------GVTPSVDRIAEYLNMSQKKVRN 385
                 G+  S   IAE L +S   V+ 
Sbjct: 120 VLRYLEGL--SYKEIAEILGISVGTVKR 145

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|218139 pfam04545, Sigma70_r4, Sigma-70, region 4

 Score = 50.1 bits (121), Expect = 2e-08
 Identities = 25/52 (48%), Positives = 36/52 (69%), Gaps = 3/52 (5%)

Query: 443 IVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494
           + +L  RERE++ L +G   E LT E+I +R+G+SRERVRQ+   AL KL+ 
Sbjct: 2   LASLPPREREVLVLRFG---EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50

Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives. Length = 50

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

 Score = 54.4 bits (131), Expect = 3e-08
 Identities = 27/75 (36%), Positives = 45/75 (60%)

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

Query: 325 IRQGVSRALVENSRT 339
           I   +   L  N++T
Sbjct: 113 IENEILMYLRRNNKT 127

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|180965 PRK07408, PRK07408, RNA polymerase sigma factor SigF; Reviewed

 Score = 53.8 bits (130), Expect = 5e-08
 Identities = 46/122 (37%), Positives = 67/122 (54%), Gaps = 10/122 (8%)

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 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAK-----LRLEEKGVTPSVDRIAEYLNMS 379
           IR  +   L + S T+R+P    E   L R AK     LR +E G  P+   IA+ L++S
Sbjct: 87  IRGEIQHYLRDKSPTVRIPRRWQE---LQRQAKKVRQELR-QELGRQPTDQEIAQALDIS 142

Query: 380 QK 381
            +
Sbjct: 143 LE 144

Length = 256

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

 Score = 50.2 bits (121), Expect = 6e-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|100119 cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

 Score = 45.9 bits (110), Expect = 6e-07
 Identities = 23/52 (44%), Positives = 35/52 (67%), Gaps = 3/52 (5%)

Query: 442 IIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493
            +  L ERERE+I L +G   E L++E+I++ +G+SR  VRQ    AL+KL+
Sbjct: 7   ALDKLPEREREVILLRFG---EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP). Length = 55

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

 Score = 42.6 bits (101), Expect = 2e-04
 Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 3/64 (4%)

Query: 434 LKDEVNKLI--IVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALE 490
           LK EV KL   I  L ERE+E+I + YGL + +  T  +I+K +G+SR  V ++   AL+
Sbjct: 162 LKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALK 221

Query: 491 KLKH 494
           KL  
Sbjct: 222 KLFK 225

Length = 233

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

 Score = 39.6 bits (93), Expect = 0.001
 Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 6/72 (8%)

Query: 427 HGVDDWALKDEVNKLI---IVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQ 483
              ++   ++E  + +   +  L ERERE++ L Y    E L++++I++ +G+S   V++
Sbjct: 89  PSPEEELEQEEEREALREALEKLPEREREVLVLRYL---EGLSYKEIAEILGISVGTVKR 145

Query: 484 VGLVALEKLKHA 495
               A +KL+  
Sbjct: 146 RLKRARKKLREL 157

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	508
PRK07598	415	RNA polymerase sigma factor SigC; Validated	100.0
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05949	327	RNA polymerase sigma factor; Validated	100.0
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	100.0
PRK07405	317	RNA polymerase sigma factor SigD; Validated	100.0
PRK05901	509	RNA polymerase sigma factor; Provisional	100.0
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	100.0
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	100.0
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	100.0
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	100.0
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	100.0
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	100.0
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	100.0
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	100.0
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	100.0
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	100.0
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	100.0
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	100.0
PRK08215	258	sporulation sigma factor SigG; Reviewed	100.0
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	100.0
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	100.0
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	100.0
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	100.0
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	100.0
PRK07670	251	RNA polymerase sigma factor SigD; Validated	100.0
PRK08583	257	RNA polymerase sigma factor SigB; Validated	100.0
PRK05572	252	sporulation sigma factor SigF; Validated	100.0
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	100.0
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	100.0
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	100.0
PRK05803	233	sporulation sigma factor SigK; Reviewed	99.96
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.94
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.94
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.92
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.91
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.91
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.9
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.9
PRK12513	194	RNA polymerase sigma factor; Provisional	99.9
PRK11922	231	RNA polymerase sigma factor; Provisional	99.89
PRK12519	194	RNA polymerase sigma factor; Provisional	99.89
PRK12524	196	RNA polymerase sigma factor; Provisional	99.89
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.89
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.89
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.89
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.89
PRK12514	179	RNA polymerase sigma factor; Provisional	99.89
PRK12534	187	RNA polymerase sigma factor; Provisional	99.89
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.88
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.88
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.88
PRK12538	233	RNA polymerase sigma factor; Provisional	99.88
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.88
PRK12537	182	RNA polymerase sigma factor; Provisional	99.88
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.87
PRK12526	206	RNA polymerase sigma factor; Provisional	99.87
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.87
PRK12531	194	RNA polymerase sigma factor; Provisional	99.87
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.86
PRK11924	179	RNA polymerase sigma factor; Provisional	99.86
PRK12542	185	RNA polymerase sigma factor; Provisional	99.86
PRK12515	189	RNA polymerase sigma factor; Provisional	99.86
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.86
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.85
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.85
PRK12543	179	RNA polymerase sigma factor; Provisional	99.85
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.85
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.85
PRK12536	181	RNA polymerase sigma factor; Provisional	99.85
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.85
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.85
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.85
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.85
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.85
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.85
PRK12539	184	RNA polymerase sigma factor; Provisional	99.84
PRK12520	191	RNA polymerase sigma factor; Provisional	99.84
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.84
PRK12522	173	RNA polymerase sigma factor; Provisional	99.84
PRK12512	184	RNA polymerase sigma factor; Provisional	99.84
PRK12518	175	RNA polymerase sigma factor; Provisional	99.84
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.83
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.83
PRK12533	216	RNA polymerase sigma factor; Provisional	99.83
PRK12535	196	RNA polymerase sigma factor; Provisional	99.83
PRK12516	187	RNA polymerase sigma factor; Provisional	99.82
PRK12547	164	RNA polymerase sigma factor; Provisional	99.82
PRK12529	178	RNA polymerase sigma factor; Provisional	99.82
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.82
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.82
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.82
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.82
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.81
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.81
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.8
PRK12528	161	RNA polymerase sigma factor; Provisional	99.8
PRK12532	195	RNA polymerase sigma factor; Provisional	99.8
PRK12530	189	RNA polymerase sigma factor; Provisional	99.8
PRK12545	201	RNA polymerase sigma factor; Provisional	99.8
PRK12541	161	RNA polymerase sigma factor; Provisional	99.8
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.8
PRK12544	206	RNA polymerase sigma factor; Provisional	99.79
PRK12540	182	RNA polymerase sigma factor; Provisional	99.79
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.78
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.78
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.78
PRK12517	188	RNA polymerase sigma factor; Provisional	99.78
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.78
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.77
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.77
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.77
PRK12546	188	RNA polymerase sigma factor; Provisional	99.76
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.76
PRK12511	182	RNA polymerase sigma factor; Provisional	99.75
PRK12525	168	RNA polymerase sigma factor; Provisional	99.74
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.7
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.7
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.69
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.67
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.65
PRK09191	261	two-component response regulator; Provisional	99.56
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.54
PF07638	185	Sigma70_ECF: ECF sigma factor	99.51
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.5
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.27
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	99.19
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	98.91
PRK06930	170	positive control sigma-like factor; Validated	98.67
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	98.62
PRK00118	104	putative DNA-binding protein; Validated	98.5
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	98.33
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	98.23
PRK03975	141	tfx putative transcriptional regulator; Provisiona	98.21
PRK04217	110	hypothetical protein; Provisional	98.15
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	98.14
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	97.96
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	97.84
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	97.83
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	97.73
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	97.72
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	97.7
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	97.63
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	97.63
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	97.46
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	97.45
PRK15201	198	fimbriae regulatory protein FimW; Provisional	97.43
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	97.39
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	97.37
PRK10840	216	transcriptional regulator RcsB; Provisional	97.37
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	97.28
TIGR03020	247	EpsA transcriptional regulator EpsA. Proteins in t	97.26
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	97.26
COG4566	202	TtrR Response regulator [Signal transduction mecha	97.26
COG2197	211	CitB Response regulator containing a CheY-like rec	97.25
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	97.24
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	97.19
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	97.18
PRK13870	234	transcriptional regulator TraR; Provisional	97.18
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	97.02
PRK09483	217	response regulator; Provisional	97.0
PRK15369	211	two component system sensor kinase SsrB; Provision	96.84
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	96.81
COG3413	215	Predicted DNA binding protein [General function pr	96.75
COG4941	415	Predicted RNA polymerase sigma factor containing a	96.72
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	96.66
PRK10651	216	transcriptional regulator NarL; Provisional	96.59
PRK09390	202	fixJ response regulator FixJ; Provisional	96.52
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	96.52
COG1356	143	tfx Transcriptional regulator [DNA replication, re	96.49
PRK01381	99	Trp operon repressor; Provisional	96.45
COG1342	99	Predicted DNA-binding proteins [General function p	96.37
PRK15320	251	transcriptional activator SprB; Provisional	96.31
TIGR01637	132	phage_arpU phage transcriptional regulator, ArpU f	96.18
PRK10403	215	transcriptional regulator NarP; Provisional	95.98
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	95.83
PRK09935	210	transcriptional regulator FimZ; Provisional	95.82
PRK13558	665	bacterio-opsin activator; Provisional	95.72
PRK04841	903	transcriptional regulator MalT; Provisional	95.71
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	95.55
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	95.34
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	95.21
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	95.17
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	95.1
PRK15418	318	transcriptional regulator LsrR; Provisional	95.07
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	94.93
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	94.83
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	94.19
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	94.18
PF06530	125	Phage_antitermQ: Phage antitermination protein Q;	93.94
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	93.52
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	92.84
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	92.83
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	92.8
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	92.5
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	92.46
PF13518	52	HTH_28: Helix-turn-helix domain	92.43
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	92.42
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	92.39
PF10668	60	Phage_terminase: Phage terminase small subunit; In	92.23
smart00351	125	PAX Paired Box domain.	92.17
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	92.1
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	91.86
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	91.35
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	91.32
PHA00675	78	hypothetical protein	90.67
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	90.23
PF13730	55	HTH_36: Helix-turn-helix domain	90.05
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	90.01
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	89.79
cd00131	128	PAX Paired Box domain	89.76
PHA02591	83	hypothetical protein; Provisional	89.75
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	89.7
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	89.53
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	89.34
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	89.07
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	88.96
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	88.93
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	88.87
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	88.57
PF02650	85	HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IP	87.97
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	87.97
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	87.74
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	87.63
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	87.53
PRK05901	509	RNA polymerase sigma factor; Provisional	87.5
PHA02547	179	55 RNA polymerase sigma factor; Provisional	87.31
PRK11083	228	DNA-binding response regulator CreB; Provisional	87.1
COG3415	138	Transposase and inactivated derivatives [DNA repli	86.99
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	86.89
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	86.82
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	86.75
PRK09413	121	IS2 repressor TnpA; Reviewed	86.67
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	86.39
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	86.23
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	86.21
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	86.03
TIGR02395	429	rpoN_sigma RNA polymerase sigma-54 factor. A sigma	85.93
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	85.73
COG3355	126	Predicted transcriptional regulator [Transcription	85.61
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	85.61
COG2973	103	TrpR Trp operon repressor [Transcription]	85.34
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	85.27
PRK10046	225	dpiA two-component response regulator DpiA; Provis	85.05
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	84.69
PRK11169	164	leucine-responsive transcriptional regulator; Prov	84.61
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	84.5
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	84.04
PRK13413	200	mpi multiple promoter invertase; Provisional	84.02
PRK15479	221	transcriptional regulatory protein TctD; Provision	83.97
COG0856	203	Orotate phosphoribosyltransferase homologs [Nucleo	83.65
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	83.37
PF13551	112	HTH_29: Winged helix-turn helix	83.02
PF12728	51	HTH_17: Helix-turn-helix domain	82.77
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	82.72
PRK05949	327	RNA polymerase sigma factor; Validated	82.46
PF13551	112	HTH_29: Winged helix-turn helix	82.12
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	81.99
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	81.88
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	81.57
CHL00148	240	orf27 Ycf27; Reviewed	81.37
PRK12423	202	LexA repressor; Provisional	80.96
TIGR01764	49	excise DNA binding domain, excisionase family. An	80.94
PF08822	165	DUF1804: Protein of unknown function (DUF1804); In	80.91
PRK07598	415	RNA polymerase sigma factor SigC; Validated	80.72
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	80.43
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	80.14

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=1.1e-57  Score=479.67  Aligned_cols=309  Identities=34%  Similarity=0.596  Sum_probs=284.0

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCc--------------------cchhHHHHHHhhCCCCchHHHHHHhcc
Q 010521          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS--------------------LDDHKLRLKERLGCEPSMEQLAASLRI  250 (508)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~--------------------l~~~~~~l~~~~g~~p~~~~~a~~~~~  250 (508)
                      |.++.||++|+++|+||++||++|+++++.+-.                    |+..+.+|++.+|++|+..+||.++|+
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            799999999999999999999999999999988                    888999999999999999999966554


Q ss_pred             ----------------------ChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhc
Q 010521          251 ----------------------SRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK  308 (508)
Q Consensus       251 ----------------------s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiek  308 (508)
                                            +.++|.+.+..|..|+++||.+|+++|+++|++|.++|.+++||+|||++|||+|+++
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                                  5555555567788999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHH
Q 010521          309 FDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNAT  387 (508)
Q Consensus       309 FDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l  387 (508)
                      |||.+|++|+||++||||++|.+++.+++|+|++|.|+.+.+++++++.+.+. ++|+.|+..|||+.+|+++++|+.++
T Consensus       220 FDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l  299 (415)
T PRK07598        220 FDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVL  299 (415)
T ss_pred             cCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999884 78999999999999999999999999


Q ss_pred             HHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCC
Q 010521          388 EAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLT  466 (508)
Q Consensus       388 ~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~T  466 (508)
                      .....++|||.++    +++++..+.+++.++.  .+|++.+....+...|..+| ..|||+||.||.|+|||+ ++++|
T Consensus       300 ~~~~~~~SLd~~v----g~~~d~~l~d~l~~~~--~~pee~~~~~~l~~~L~~~L-~~L~~reR~VI~LRygl~d~~~~T  372 (415)
T PRK07598        300 LRVPRSVSLETKV----GKDKDTELGDLLETDD--ISPEEMLMRESLQRDLQHLL-ADLTSRERDVIRMRFGLADGHTYS  372 (415)
T ss_pred             HHccCCccccccc----CCCccccHHHhccCCC--CCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHhcCCCCCCC
Confidence            9999999999985    2333445677776543  47888888889999999999 899999999999999984 67899


Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521          467 WEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV  506 (508)
Q Consensus       467 leEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~  506 (508)
                      ++|||+.||+|++||++++++|++|||+.-....++.|+.
T Consensus       373 l~EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~~  412 (415)
T PRK07598        373 LAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE  412 (415)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHHH
Confidence            9999999999999999999999999999988999999985

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=9.5e-57  Score=468.97  Aligned_cols=308  Identities=35%  Similarity=0.583  Sum_probs=290.5

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHH
Q 010521          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (508)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LI  270 (508)
                      +++..||++|+++|+||++||++|++++++|..++..+.+|.+..|++|+..+||.++|++..+|++++..+..|++.||
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            67889999999999999999999999999999999999999999999999999999999999999999998999999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q 010521          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL  350 (508)
Q Consensus       271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l  350 (508)
                      .+|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|++++++||+|.|+.+.+
T Consensus       143 ~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~~~~~  222 (373)
T PRK07406        143 QSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI  222 (373)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchH
Q 010521          351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGV  429 (508)
Q Consensus       351 ~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~v  429 (508)
                      ++++++...+. ++|+.|+.+|||+.+|+++++|..++.....++|||.++    +++++.++.+++++..  .+|++.+
T Consensus       223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i----~~~~~~~l~d~l~d~~--~~pee~~  296 (373)
T PRK07406        223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI----GKEEDSRLGDFIEADG--ETPEDDV  296 (373)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCC----CCCCcccHHHhcCCCC--CCHHHHH
Confidence            99999999885 789999999999999999999999988888999999985    2333456778887753  4788888


Q ss_pred             HHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhh
Q 010521          430 DDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML  505 (508)
Q Consensus       430 e~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l  505 (508)
                      ....+...|..+| +.||++||.||.+||||+ ++++|++|||+.||||++||+|++.+|++|||+......+..|+
T Consensus       297 ~~~~~~~~L~~aL-~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~  372 (373)
T PRK07406        297 AKNLLREDLEGVL-ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI  372 (373)
T ss_pred             HHHHHHHHHHHHH-HcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHh
Confidence            8889999999999 899999999999999995 57899999999999999999999999999999999999998886

>PRK05949 RNA polymerase sigma factor; Validated

Probab=100.00  E-value=2e-55  Score=453.13  Aligned_cols=308  Identities=31%  Similarity=0.573  Sum_probs=286.8

Q ss_pred             hhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHH
Q 010521          190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL  269 (508)
Q Consensus       190 ~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~L  269 (508)
                      .|.+..||++|+++|+||++||++|+++++.|-.++..+..|++.+|++|+..+||.+++|+..+|...+..+..|++.|
T Consensus        17 ~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~~L   96 (327)
T PRK05949         17 ADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKM   96 (327)
T ss_pred             CCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHHHH
Confidence            36888999999999999999999999999999999999999999999999999999999999999999999998999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHH
Q 010521          270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER  349 (508)
Q Consensus       270 Ie~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~  349 (508)
                      |..|+++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+|||+||||++|.++|.+++++||+|.|+.+.
T Consensus        97 i~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~~~~~~  176 (327)
T PRK05949         97 IEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK  176 (327)
T ss_pred             HHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccch
Q 010521          350 LGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHG  428 (508)
Q Consensus       350 l~kir~a~~~l-~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~  428 (508)
                      +++++++.+.+ .++|++|+.+|||+.+|+++++|..++.....++|||.++    +++++.++.+.+++..  .+|++.
T Consensus       177 ~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~l~~~l~d~~--~~pe~~  250 (327)
T PRK05949        177 LNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRV----GDNQDTELSELLEDEG--PSPDQY  250 (327)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCc----CCCCCccHHhhcCCCC--CCHHHH
Confidence            99999999888 5789999999999999999999999999889999999974    2333445677777653  478888


Q ss_pred             HHHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521          429 VDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV  506 (508)
Q Consensus       429 ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~  506 (508)
                      +........|..+| +.||++||.||.+||||+ ++++|++|||+.||||+++|++++.+|++|||+.  ...+..|+.
T Consensus       251 ~~~~~~~~~L~~~L-~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~--~~~l~~~~~  326 (327)
T PRK05949        251 ITQELLRQDLNNLL-AELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR--RANVKEYLA  326 (327)
T ss_pred             HHHHHHHHHHHHHH-HhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence            88889999999999 899999999999999994 6899999999999999999999999999999994  456777764

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

Probab=100.00  E-value=4.2e-55  Score=445.53  Aligned_cols=295  Identities=38%  Similarity=0.648  Sum_probs=276.4

Q ss_pred             hHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHH
Q 010521          192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM  271 (508)
Q Consensus       192 ~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe  271 (508)
                      ++..||++|+++|+||++||.+|+++++.|-.+++.+.+|++..|++|+..+||.++|++..+|..++..+..|++.||.
T Consensus         2 ~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv~   81 (298)
T TIGR02997         2 LVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMIK   81 (298)
T ss_pred             cHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHHH
Confidence            56789999999999999999999999999999999999999999999999999999999999999999988999999999


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHH
Q 010521          272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG  351 (508)
Q Consensus       272 ~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~  351 (508)
                      .|+++|+++|++|.++|.+++||+||||+|||+|+++|||.+|++|+||++||||++|.+++.++++++|+|.+....++
T Consensus        82 ~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~~~~~  161 (298)
T TIGR02997        82 ANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLN  161 (298)
T ss_pred             HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHH-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHH
Q 010521          352 LIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD  430 (508)
Q Consensus       352 kir~a~~~l-~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve  430 (508)
                      +++++...+ ...|+.|+.+|||+.+|+++++|..++.....++|||.++    +++++.++.+.+++.  ..+|++.+.
T Consensus       162 ~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~~~~~~~~~--~~~pe~~~~  235 (298)
T TIGR02997       162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPV----GDEEDTELGDLLEDD--GESPEEQVE  235 (298)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCc----CCCCcchHHHhccCC--CCCHHHHHH
Confidence            999998888 4789999999999999999999999999889999999974    222334566666664  357888899


Q ss_pred             HHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          431 DWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..+....|..+| +.||++||.||.++|||+ ++++|++|||+.||||++||+|++++|++|||
T Consensus       236 ~~~~~~~L~~~L-~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr  298 (298)
T TIGR02997       236 RESLRQDLESLL-AELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR  298 (298)
T ss_pred             HHHHHHHHHHHH-HcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            999999999999 899999999999999994 68999999999999999999999999999996

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).

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=1.8e-54  Score=444.57  Aligned_cols=307  Identities=35%  Similarity=0.590  Sum_probs=286.0

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHH
Q 010521          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (508)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LI  270 (508)
                      +++..||++|+++|+||++||.+|++++++|-.++..+..|.+.+|++|+..+||.+++++..+|...+.++..|++.||
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            57889999999999999999999999999999999999999999999999999999999999999999999899999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q 010521          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL  350 (508)
Q Consensus       271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l  350 (508)
                      ..|+++|+++|++|.+++.+++||+||||+|||+++++|||.+|++|+|||+||||++|.++|.+++++||+|.++...+
T Consensus        88 ~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~~~~~~~  167 (317)
T PRK07405         88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKL  167 (317)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCChHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchH
Q 010521          351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGV  429 (508)
Q Consensus       351 ~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~v  429 (508)
                      ++++++...+. ..|+.|+.+|||+.+|+++++|..++.....+.|||.++    +++++.++.+.+++..  .+|++.+
T Consensus       168 ~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~l~~~~~d~~--~~pe~~~  241 (317)
T PRK07405        168 NKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRV----GDNQDTELGELLEDTG--ASPEDFA  241 (317)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCC----CCCCCccHHHhhcCCC--CCHHHHH
Confidence            99999998884 789999999999999999999999998888899999874    2333446777777653  4789889


Q ss_pred             HHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521          430 DDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV  506 (508)
Q Consensus       430 e~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~  506 (508)
                      ...++...|..+| +.||++||.||.++|||+ ++++|++|||+.||||++||+|++.+|++|||+.  ...+..|+.
T Consensus       242 ~~~~~~~~l~~al-~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~~  316 (317)
T PRK07405        242 TQSSLQLDLERLM-EDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYLA  316 (317)
T ss_pred             HHHHHHHHHHHHH-HcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHh
Confidence            9999999999999 899999999999999994 6899999999999999999999999999999996  456677663

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=5e-54  Score=461.75  Aligned_cols=298  Identities=34%  Similarity=0.564  Sum_probs=268.5

Q ss_pred             hhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHH
Q 010521          190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL  269 (508)
Q Consensus       190 ~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~L  269 (508)
                      .++++.||++|+++|+||++||++|+++++.|+.+++.   +.       ...+|+.   ....+|++++..+..|+++|
T Consensus       210 ~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~~---~~~~~l~~~~~~g~~Ar~~L  276 (509)
T PRK05901        210 ADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLDP---ELRRDLQWIGRDGKRAKNHL  276 (509)
T ss_pred             ccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccchh---hhhhhhhhhccchHHHHHHH
Confidence            46899999999999999999999999999999874332   11       1122332   24577899999999999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHH
Q 010521          270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER  349 (508)
Q Consensus       270 Ie~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~  349 (508)
                      |..|+|||++||++|.++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++|++++|+||+|+|+.+.
T Consensus       277 I~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP~~~~e~  356 (509)
T PRK05901        277 LEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVET  356 (509)
T ss_pred             HHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecCHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccch
Q 010521          350 LGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHG  428 (508)
Q Consensus       350 l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~  428 (508)
                      +++++++.+.+. .+|++|+.+|||+.||+++++|..++.....++|||.++    +++++..+.+++.|.. ...|++.
T Consensus       357 i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i----~~d~~~~l~d~l~D~~-~~~p~~~  431 (509)
T PRK05901        357 INKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTI----GKEGDSQFGDFIEDSE-AVSPVDA  431 (509)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCccccccc----ccCCcccHHHhccCCC-CCCHHHH
Confidence            999999998885 789999999999999999999999998888999999975    2333346788888875 3578888


Q ss_pred             HHHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521          429 VDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV  506 (508)
Q Consensus       429 ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~  506 (508)
                      +....+...|..+| ..|+++||.||.+||||+ ++++|++|||+.||||++||||++.+|+.|||+......++.||+
T Consensus       432 ~~~~~l~~~L~~aL-~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~~l~  509 (509)
T PRK05901        432 VSFTLLQDQLQEVL-ETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD  509 (509)
T ss_pred             HHHHHHHHHHHHHH-hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            88999999999999 899999999999999995 689999999999999999999999999999999999999999874

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

Probab=100.00  E-value=6.7e-53  Score=431.06  Aligned_cols=310  Identities=36%  Similarity=0.569  Sum_probs=276.8

Q ss_pred             hhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHH-hhCCCCchH---------------HHHHHhccCh-
Q 010521          190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKE-RLGCEPSME---------------QLAASLRISR-  252 (508)
Q Consensus       190 ~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~-~~g~~p~~~---------------~~a~~~~~s~-  252 (508)
                      .+.++.|+.+++..++++.+++..+.+.++....+......+.. ..|..|+..               +|+..+.... 
T Consensus         8 ~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ee   87 (342)
T COG0568           8 ADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPEEE   87 (342)
T ss_pred             hhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChHHH
Confidence            46889999999999999999999999999888877666667776 678888886               4444454444 


Q ss_pred             HHHHHhhhhh---HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHH
Q 010521          253 PELQSILMEC---SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGV  329 (508)
Q Consensus       253 ~~L~~~l~e~---~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I  329 (508)
                      .+|..++..+   ..|..+||++|+++|++||++|.++|+++.||||||+|||++|+++|||++|++|+|||+||||++|
T Consensus        88 ~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~wWIrqaI  167 (342)
T COG0568          88 KALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAI  167 (342)
T ss_pred             HHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHHHHHHHH
Confidence            5566777655   4599999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhcccccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCC
Q 010521          330 SRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLP  408 (508)
Q Consensus       330 ~~~Ird~~R~irip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~  408 (508)
                      .++|.+++|+||+|+|+.+.++++++..+.+. +.|++|+.+|||+.+|+++++|..++.....++|||.|+    ++++
T Consensus       168 ~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~i----g~de  243 (342)
T COG0568         168 TRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPI----GDDE  243 (342)
T ss_pred             HHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcC----CCCc
Confidence            99999999999999999999999999998885 579999999999999999999999999999999999985    3444


Q ss_pred             CCccccccccccCCCCccchHHHHHHHHHHHHHHHcc-CCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521          409 GETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVT-LGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGL  486 (508)
Q Consensus       409 ~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~-Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~  486 (508)
                      ++.+.++++|... .+|++.+....+.+.+...| .. |+|+|+.||++|||++ +++.|++|||+.+|||++|||||+.
T Consensus       244 d~~l~d~leD~~~-~~p~~~~~~~~~~~~~~~~L-~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~  321 (342)
T COG0568         244 DSELGDFLEDDKS-VSPEDAVERESLKEDLNEVL-AEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEA  321 (342)
T ss_pred             ccHHHHHhhcCCc-CCHHHHHHHHHHHHHHHHHH-HhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHH
Confidence            5578999999863 48999999999999999999 77 9999999999999995 6899999999999999999999999


Q ss_pred             HHHHHHHH-HHHHhhHHHhh
Q 010521          487 VALEKLKH-AARKKKMEAML  505 (508)
Q Consensus       487 rALkKLR~-~L~~~~l~~~l  505 (508)
                      +|++|||. .-....++.||
T Consensus       322 kAl~KLr~~~~~~~~~~~~l  341 (342)
T COG0568         322 KALRKLRRHPERSALLRSYL  341 (342)
T ss_pred             HHHHHHHHhhhhhhHHHHhh
Confidence            99999994 44445567776

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=3.6e-52  Score=428.31  Aligned_cols=296  Identities=33%  Similarity=0.552  Sum_probs=263.6

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHH
Q 010521          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (508)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LI  270 (508)
                      +++..||++|+++|+||++||.+|+++++.|..++..          +| ..+|....  ...+|+..+..|..|++.||
T Consensus        26 ~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~----------~~-~~~~~~~~--~~~~l~~~~~~~~~A~~~Lv   92 (324)
T PRK07921         26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL----------LE-TRKRLSEA--RKRDLAAVVRDGEAARRHLL   92 (324)
T ss_pred             ChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh----------hc-cccccchh--HHHHHHHHHhcCHHHHHHHH
Confidence            5788999999999999999999999999998764332          11 11221111  34578888899999999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q 010521          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL  350 (508)
Q Consensus       271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l  350 (508)
                      ..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+++++.|++|.++.+.+
T Consensus        93 ~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~~~~~~  172 (324)
T PRK07921         93 EANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQV  172 (324)
T ss_pred             HHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchH
Q 010521          351 GLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGV  429 (508)
Q Consensus       351 ~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~v  429 (508)
                      ++++++...+. ++|+.|+.+|||+.+|+++++|..++.....++|||.++    +++++.++.++++|.. ..+|++.+
T Consensus       173 ~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~l~d~l~d~~-~~~pe~~~  247 (324)
T PRK07921        173 NKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPV----GSDEEAPLGDFIEDSE-ATSAENAV  247 (324)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCC----CCCCCchHHHHhcCCC-CCCHHHHH
Confidence            99999999985 789999999999999999999999988888899999984    2333446788888764 35788888


Q ss_pred             HHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhh
Q 010521          430 DDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML  505 (508)
Q Consensus       430 e~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l  505 (508)
                      ...++...|..+| ..||++|+.||.+||||+ ++++|++|||+.||||+++|+|++.+|++|||.......+..|+
T Consensus       248 ~~~~~~~~l~~~L-~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~  323 (324)
T PRK07921        248 IAGLLHTDIRSVL-ATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA  323 (324)
T ss_pred             HHHHHHHHHHHHH-HhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence            8889999999999 899999999999999994 67899999999999999999999999999999999888888876

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=1.2e-50  Score=423.95  Aligned_cols=272  Identities=36%  Similarity=0.600  Sum_probs=254.1

Q ss_pred             hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHH
Q 010521          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK  268 (508)
Q Consensus       189 ~~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~  268 (508)
                      ..+.++.||++|++.|+||++++.+|+++++.||.                                        .|++.
T Consensus        94 ~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~~~Gd~----------------------------------------~A~~~  133 (367)
T PRK09210         94 INDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDE----------------------------------------EAKQR  133 (367)
T ss_pred             cCcHHHHHHHHhhccCCCCHHHHHHHHHHHHhhHH----------------------------------------HHHHH
Confidence            34799999999999999999999999999999998                                        89999


Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHH
Q 010521          269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE  348 (508)
Q Consensus       269 LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~  348 (508)
                      ||..|+++|+++|++|.+++.+++||+|||++|||+|+++|||.+|++|+|||+||||++|.++|++++|++++|.|+.+
T Consensus       134 Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~~~~~  213 (367)
T PRK09210        134 LAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE  213 (367)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccc
Q 010521          349 RLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH  427 (508)
Q Consensus       349 ~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~  427 (508)
                      .++++.++.+.+. ++|+.||.+|||+.+|+++++|++++.....++|||.++    +++++..+.++++|.. ..+|++
T Consensus       214 ~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~l~d~i~d~~-~~~p~~  288 (367)
T PRK09210        214 TINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPI----GEEDDSHLGDFIEDQD-ATSPAD  288 (367)
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCC----CCCCcchhhhhccCCC-CCCHHH
Confidence            9999999988884 789999999999999999999999999888899999974    2333456788888765 357999


Q ss_pred             hHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521          428 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV  506 (508)
Q Consensus       428 ~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~  506 (508)
                      .+....+...|..+| ..||++||.||.+||||+ ++++|++|||+.||||++||||++.+||+|||+.....+++.|+.
T Consensus       289 ~~~~~~~~~~l~~~l-~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~~  367 (367)
T PRK09210        289 HAAYELLKEQLEDVL-DTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFLE  367 (367)
T ss_pred             HHHHHHHHHHHHHHH-HhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhhC
Confidence            889999999999999 899999999999999994 688999999999999999999999999999999999999999873

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=3.2e-47  Score=422.01  Aligned_cols=272  Identities=31%  Similarity=0.584  Sum_probs=252.7

Q ss_pred             hHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHH
Q 010521          192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM  271 (508)
Q Consensus       192 ~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe  271 (508)
                      .++.||++|...+.|+++++..++++++.|+.                                     .+..|+++||.
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            66789999999999999999999999999985                                     12278999999


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHH
Q 010521          272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG  351 (508)
Q Consensus       272 ~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~  351 (508)
                      .|+|||++||++|.++|++++||+|||+|||++|+++|||.+|++|+|||+||||++|.++|++++|+||+|+|+.+.++
T Consensus       388 ~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~irip~~~~~~~~  467 (619)
T PRK05658        388 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETIN  467 (619)
T ss_pred             HHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCceecCHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHH-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHH
Q 010521          352 LIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD  430 (508)
Q Consensus       352 kir~a~~~l-~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve  430 (508)
                      +++++.+.+ +++|++|+.+|||+.||+++++|..++.....++|||.|+    +++++.++.++++|... .+|.+.+.
T Consensus       468 k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i----~~~~~~~l~d~i~d~~~-~~p~~~~~  542 (619)
T PRK05658        468 KLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPI----GDDEDSHLGDFIEDKNA-ELPIDAAI  542 (619)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCC----CCCCCCchhhhcCCCCC-CChHHHHH
Confidence            999998888 5789999999999999999999999999888999999975    23344578889888753 57988888


Q ss_pred             HHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521          431 DWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV  506 (508)
Q Consensus       431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~  506 (508)
                      ...+...|..+| ..||++|+.||++||||+ .+++|++|||+.||||+++|||++.+|++|||+......++.||.
T Consensus       543 ~~~~~~~l~~~l-~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~~~~  618 (619)
T PRK05658        543 QESLREATTDVL-ASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLD  618 (619)
T ss_pred             HHHHHHHHHHHH-HcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHHHhc
Confidence            889999999999 899999999999999996 578999999999999999999999999999999999999999985

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=100.00  E-value=1.3e-43  Score=365.29  Aligned_cols=270  Identities=34%  Similarity=0.576  Sum_probs=246.0

Q ss_pred             hHhhhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHH
Q 010521          187 ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAR  266 (508)
Q Consensus       187 ~~~~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~  266 (508)
                      +.+.+.+++||++|+..|+||++++..|+.+++.||.                                        .|+
T Consensus        49 ~~~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~Gd~----------------------------------------~A~   88 (325)
T PRK05657         49 QRVLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDF----------------------------------------AAR   88 (325)
T ss_pred             cccccHHHHHHHHHhcCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHH
Confidence            3445789999999999999999999999999999998                                        999


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccH
Q 010521          267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL  346 (508)
Q Consensus       267 e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~  346 (508)
                      +.||..|.++|+++|++|.+++.+++||+||||+|+|+++++||+.+|++|+||++||||++|.++++++.+.+++|.++
T Consensus        89 ~~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~~~  168 (325)
T PRK05657         89 QRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHV  168 (325)
T ss_pred             HHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCc
Q 010521          347 HERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP  425 (508)
Q Consensus       347 ~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~P  425 (508)
                      .+.++.+.++...+. +.|+.|+.+|||+.+|+++++|..++.....+.|||.+.    ++++..++.+.+.+.. ..+|
T Consensus       169 ~~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~----~~~~~~~l~d~l~d~~-~~~p  243 (325)
T PRK05657        169 VKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPL----GGDPEKSLLDILADEQ-ENGP  243 (325)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCC----CCCCCcchhhhccCCC-CCCH
Confidence            999888777777775 579999999999999999999999998888889999873    2333445667777654 2478


Q ss_pred             cchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHH
Q 010521          426 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKME  502 (508)
Q Consensus       426 e~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~  502 (508)
                      +..+...+....|..+| ..||+++|.||.++|||. ++++|++|||+.||||++||++++++|+++||+.|...++.
T Consensus       244 e~~~~~~e~~~~L~~aL-~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~  320 (325)
T PRK05657        244 EDTTQDDDMKQSIVKWL-FELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS  320 (325)
T ss_pred             HHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccc
Confidence            88888888889999999 899999999999999994 79999999999999999999999999999999999877654

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=4.6e-43  Score=355.12  Aligned_cols=265  Identities=29%  Similarity=0.443  Sum_probs=227.0

Q ss_pred             CchhHhhhhHHHHHHhhcccCCCCHHHHHHHHHHH-HcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhh
Q 010521          184 ISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC  262 (508)
Q Consensus       184 ~~~~~~~~~~~~yl~~i~~~~lLt~~EE~eL~~~i-k~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~  262 (508)
                      .+|+   +.+..|++++++.|+++.++|.+|+.+. +.||.                                       
T Consensus        10 ~~~~---~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~~Gd~---------------------------------------   47 (284)
T PRK06596         10 LSPE---GNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDL---------------------------------------   47 (284)
T ss_pred             CCCc---cHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCCH---------------------------------------
Confidence            4555   6888999999999999999999999995 68897                                       


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (508)
Q Consensus       263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri  342 (508)
                       .|++.||..|+|+|+++|++|.+++.+.+||+|||++||++|+++|||++|++|+|||+|||+++|.++|+++++.+++
T Consensus        48 -~a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~  126 (284)
T PRK06596         48 -EAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKV  126 (284)
T ss_pred             -HHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeec
Confidence             8999999999999999999999999999999999999999999999999999999999999999999999999888999


Q ss_pred             cccHHH--HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHh-CccccccccCCCCCCCCCCCccccccccc
Q 010521          343 PNHLHE--RLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAI-GKVFSLDREAFPSLNGLPGETHHSYIADN  419 (508)
Q Consensus       343 p~~~~~--~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~-~~~~SLD~~~~~~~~~~~~~~l~d~i~d~  419 (508)
                      |.+...  ...++++....+. .+++|+.+|||+.||+++++|.+++... ..++|||.+...  +++++.++.+.++|.
T Consensus       127 p~~~~~~~~~~~~~~~~~~l~-~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~--~~~~~~~l~~~l~d~  203 (284)
T PRK06596        127 ATTKAQRKLFFNLRKAKKRLG-WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDD--DDEESGAPQDYLEDK  203 (284)
T ss_pred             cchHHHHHHHHHHHHHHHHhc-cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCC--CCCCcchHHHHcCCC
Confidence            998653  2345566665554 4689999999999999999999987644 578999997421  111223466777776


Q ss_pred             cCCCCccchHHHHH----HHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521          420 RVENNPWHGVDDWA----LKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA  495 (508)
Q Consensus       420 ~~e~~Pe~~ve~~e----l~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~  495 (508)
                      .  .+|++.++..+    ....|..+| +.||++||.||.+|||.+ +++|++|||+.||||+++|+|++.+|++|||..
T Consensus       204 ~--~~p~~~~~~~~~~~~~~~~L~~al-~~L~~rEr~VL~lry~~~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~  279 (284)
T PRK06596        204 S--SDPADVLEEDNWEDQRRALLADAL-EGLDERSRDIIEARWLDD-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA  279 (284)
T ss_pred             C--CCchHHHHHHHHHHHHHHHHHHHH-hcCCHHHHHHHHHHhcCC-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            3  46777666543    577899999 899999999999999643 689999999999999999999999999999998


Q ss_pred             HHH
Q 010521          496 ARK  498 (508)
Q Consensus       496 L~~  498 (508)
                      +..
T Consensus       280 l~~  282 (284)
T PRK06596        280 IEA  282 (284)
T ss_pred             HHh
Confidence            864

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

Probab=100.00  E-value=1.6e-43  Score=349.10  Aligned_cols=236  Identities=37%  Similarity=0.632  Sum_probs=216.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q 010521          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN  344 (508)
Q Consensus       265 A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~  344 (508)
                      |+++||..|+++|+++|++|.+++.+++||+|||++||++|+++|||++|++|+|||+||||++|.++++++.+.+++|.
T Consensus         1 a~~~Li~~~~~lv~~ia~~~~~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vrip~   80 (238)
T TIGR02393         1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV   80 (238)
T ss_pred             CHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEEeCH
Confidence            57899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          345 HLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       345 ~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                      ++.+.++++.++...+. +.|++||.+|||+.+|++.++|..++.....++|||.++    +++++.++.+.++|+. ..
T Consensus        81 ~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~----~~~~~~~l~d~l~d~~-~~  155 (238)
T TIGR02393        81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPI----GEEEDSFLGDFIEDTS-IE  155 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCC----CCCCcccHHHHhcCCC-CC
Confidence            99999999999998885 789999999999999999999999988888899999974    2233346777787765 35


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKME  502 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~  502 (508)
                      +|++.+...+....|..+| ..||++||.||.++|||+ ++++|++|||+.||||+++|+|++.+|++|||+.+....++
T Consensus       156 ~p~~~~~~~~~~~~l~~~l-~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~  234 (238)
T TIGR02393       156 SPDDYAAKELLREQLDEVL-ETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLK  234 (238)
T ss_pred             ChHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHH
Confidence            7888888888999999999 899999999999999995 68999999999999999999999999999999999988888


Q ss_pred             Hhhh
Q 010521          503 AMLV  506 (508)
Q Consensus       503 ~~l~  506 (508)
                      .|+.
T Consensus       235 ~~~~  238 (238)
T TIGR02393       235 SFLD  238 (238)
T ss_pred             HhhC
Confidence            8863

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.

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=1.4e-42  Score=352.50  Aligned_cols=264  Identities=25%  Similarity=0.354  Sum_probs=225.0

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHH-HcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHH
Q 010521          191 NRLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL  269 (508)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~i-k~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~L  269 (508)
                      +..+.||++|.++|+||+++|.+|++++ +.||.                                        .|+++|
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            3556799999999999999999999997 47887                                        999999


Q ss_pred             HHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHH-
Q 010521          270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE-  348 (508)
Q Consensus       270 Ie~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~-  348 (508)
                      |..|.|+|+++|++|.+++.+++||+||||+|||+++++|||.+|.+|+|||+||||++|.++|+++++.+|+|.+..+ 
T Consensus        46 v~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~~~~~~  125 (289)
T PRK07500         46 ISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQK  125 (289)
T ss_pred             HHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCccHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999998765 


Q ss_pred             -HHHHHHHHHHHHH----HcCCCCCHHHHHHHhCCCHHHHHHHHHH-hCccccccccCCCCCCCCCCCccccccccccCC
Q 010521          349 -RLGLIRNAKLRLE----EKGVTPSVDRIAEYLNMSQKKVRNATEA-IGKVFSLDREAFPSLNGLPGETHHSYIADNRVE  422 (508)
Q Consensus       349 -~l~kir~a~~~l~----~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~-~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e  422 (508)
                       ...++++....+.    .+|+.|+.+|||+.||+++++|..+... ...++|||.++..  +++.+.++.+.+++..  
T Consensus       126 ~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~--~~~~~~~l~d~i~d~~--  201 (289)
T PRK07500        126 ALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSE--EDEGRSERMDFLVDDS--  201 (289)
T ss_pred             HHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCC--CCCCcccHHHhccCCC--
Confidence             3345566555553    4799999999999999999999887643 3578999987421  1122235677887764  


Q ss_pred             CCccchHHH----HHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          423 NNPWHGVDD----WALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       423 ~~Pe~~ve~----~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      .+|++.+..    .+....|..+| ..||++||.||.++|+ +.+++|++|||+.||||++||+|++++|++|||..+..
T Consensus       202 ~~pe~~~~~~~~~~~~~~~l~~al-~~L~~rer~vl~lr~~-~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~~  279 (289)
T PRK07500        202 PLPDEQVESSIDGERRRRWLTQAL-QTLNERELRIIRERRL-REDGATLEALGEELGISKERVRQIEARALEKLRRALLS  279 (289)
T ss_pred             CCchHHHHHHHHHHHHHHHHHHHH-hcCCHHHHHHHHHHhc-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            367766543    34556788999 8999999999999994 23899999999999999999999999999999999975


Q ss_pred             hh
Q 010521          499 KK  500 (508)
Q Consensus       499 ~~  500 (508)
                      ..
T Consensus       280 ~~  281 (289)
T PRK07500        280 QS  281 (289)
T ss_pred             cC
Confidence            54

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=100.00  E-value=2.5e-42  Score=347.12  Aligned_cols=259  Identities=28%  Similarity=0.459  Sum_probs=217.8

Q ss_pred             hHHHHHHhhcccCCCCHHHHHHHHHH-HHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHH
Q 010521          192 RLKGYVKGVVSEELLTHAEVVRLSKK-IKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (508)
Q Consensus       192 ~~~~yl~~i~~~~lLt~~EE~eL~~~-ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LI  270 (508)
                      ++..||++|+++|+|+++++.+|+.+ .+.||.                                        .|++.||
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            57789999999999999999999999 578987                                        8999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHH--
Q 010521          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHE--  348 (508)
Q Consensus       271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~--  348 (508)
                      ..|+++|+++|++|.+++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+++++.+++|.+...  
T Consensus        42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~~~  121 (270)
T TIGR02392        42 LSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRK  121 (270)
T ss_pred             HHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHHHH
Confidence            999999999999999999999999999999999999999999999999999999999999999999888999987642  


Q ss_pred             HHHHHHHHHHHHHHcCCCC-CHHHHHHHhCCCHHHHHHHHHHhC-ccccccccCCCCCCCCCCCccccccccccCCCCcc
Q 010521          349 RLGLIRNAKLRLEEKGVTP-SVDRIAEYLNMSQKKVRNATEAIG-KVFSLDREAFPSLNGLPGETHHSYIADNRVENNPW  426 (508)
Q Consensus       349 ~l~kir~a~~~l~~~Gr~P-t~eEIA~~Lgis~e~v~~~l~~~~-~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe  426 (508)
                      ...+++++...+. .++.| +.+|||+.||+++++|.++..... .+.|||.++..  +++....+.+.++|..  .+|+
T Consensus       122 ~~~~~~~~~~~~~-~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~--~~~~~~~~~~~l~d~~--~~pe  196 (270)
T TIGR02392       122 LFFNLRKMKKRLQ-GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDD--DEDDGGAPIAYLVDKT--SDPE  196 (270)
T ss_pred             HHHHHHHHHHHHh-cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCC--CCCccccHHHHhcCCC--CChH
Confidence            3345555555543 22566 599999999999999999876543 47899987421  1111124566777664  3677


Q ss_pred             chHHHHH----HHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          427 HGVDDWA----LKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       427 ~~ve~~e----l~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      +.+...+    +...|..+| ..||++||.||.++||. .+++|++|||+.||||+++|+|++.+|++|||+.+.
T Consensus       197 ~~~~~~~~~~~~~~~L~~al-~~L~~rer~vl~l~y~~-~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l~  269 (270)
T TIGR02392       197 DTLEEEQWEELQRQALANAL-GSLDARSRRIIEARWLD-DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAALA  269 (270)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHhcC-CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence            7665433    557899999 89999999999999952 358999999999999999999999999999998774

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.

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=100.00  E-value=1.9e-40  Score=335.70  Aligned_cols=269  Identities=33%  Similarity=0.542  Sum_probs=241.6

Q ss_pred             hHhhhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHH
Q 010521          187 ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAR  266 (508)
Q Consensus       187 ~~~~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~  266 (508)
                      -.+.+.+++||.+|..+|.|+.+++.+|+.+++.||.                                        .|+
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~a~   48 (285)
T TIGR02394         9 TRVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDF----------------------------------------EAR   48 (285)
T ss_pred             cCcchHHHHHHHHHhccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHH
Confidence            3466899999999999999999999999999999998                                        999


Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccH
Q 010521          267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL  346 (508)
Q Consensus       267 e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~  346 (508)
                      +.||..|.++|+++|++|.+++.+++||+|||++|||+++++||+..|++|+||+.|||+.++.+++.++.+.+++|.++
T Consensus        49 ~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~~  128 (285)
T TIGR02394        49 KVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHV  128 (285)
T ss_pred             HHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHH-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCc
Q 010521          347 HERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP  425 (508)
Q Consensus       347 ~~~l~kir~a~~~l-~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~P  425 (508)
                      .+..+.+.+..+.+ ...|+.|+..++|+.+|+++.++..++....+..|+|.+.    +++...++.+.+.+.. ..+|
T Consensus       129 ~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~----~~~~~~~~~~~~~~~~-~~~p  203 (285)
T TIGR02394       129 IKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPL----DDDSSKSLLDTIADEQ-SIDP  203 (285)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCC----CCCCCcchhhhhcCCC-CCCH
Confidence            99998877766665 4579999999999999999999999999888899998753    2222233444554443 2478


Q ss_pred             cchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhcc-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521          426 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM  501 (508)
Q Consensus       426 e~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGL-d~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l  501 (508)
                      ++.+...+....|..+| ..||+++|.||.++||| +++++|++|||+.||+|.+||++++++|+++||+.|...+.
T Consensus       204 e~~~~~~e~~~~L~~al-~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~~  279 (285)
T TIGR02394       204 ESLVQNDDLKQLIEAWL-AELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGV  279 (285)
T ss_pred             HHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            88888999999999999 89999999999999998 47999999999999999999999999999999999986543

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).

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=3.8e-40  Score=330.56  Aligned_cols=220  Identities=25%  Similarity=0.367  Sum_probs=196.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .++++||.+|+|||+++|++|.++|.+.+||+|||+|||++|+++|||++|++|+|||+||||++|.++++++.++|++|
T Consensus        40 ~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~ir~P  119 (264)
T PRK07122         40 RQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP  119 (264)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCccccC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHh--CccccccccCCCCCCCCCC-Cccccccccc
Q 010521          344 NHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPG-ETHHSYIADN  419 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~~~-~~l~d~i~d~  419 (508)
                      +++.+.+++++++...+. ++|+.|+.+|||+.||+++++|.+++...  ..+.|||.+...   ++++ ..+.+.+   
T Consensus       120 r~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~---~~~~~~~~~d~~---  193 (264)
T PRK07122        120 RRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGS---GDDDARAIADTL---  193 (264)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccC---CCCCcccchhcc---
Confidence            999999999999998885 78999999999999999999999988753  578999997421   1111 1233322   


Q ss_pred             cCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          420 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       420 ~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                         ++|+..++..+....|..+| +.||+++|.||.++|   ++++|++|||+.||+|+++|++++++|+++||..+
T Consensus       194 ---~~~~~~~e~~~~~~~l~~~l-~~L~~rer~vl~l~y---~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l  263 (264)
T PRK07122        194 ---GDVDAGLDQIENREALRPLL-AALPERERTVLVLRF---FESMTQTQIAERVGISQMHVSRLLAKTLARLRDQL  263 (264)
T ss_pred             ---CCcHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHh---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence               24555667777888899999 899999999999999   79999999999999999999999999999999876

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=1.5e-38  Score=317.47  Aligned_cols=226  Identities=27%  Similarity=0.373  Sum_probs=195.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCC-CCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNM-GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~-g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri  342 (508)
                      .|+++||..|+|+|+++|++|.+. +.+++||+|||+||||+|+++|||++|++|+|||++||+++|.++++++.+++++
T Consensus        25 ~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~~vr~  104 (256)
T PRK07408         25 ALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRI  104 (256)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHHcCCeeee
Confidence            899999999999999999999875 6679999999999999999999999999999999999999999999999999999


Q ss_pred             cccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHH--hCccccccccCCCCCCCCCCCccccccccc
Q 010521          343 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFPSLNGLPGETHHSYIADN  419 (508)
Q Consensus       343 p~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~--~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~  419 (508)
                      |+++.+.+++++++...+. ++|++|+.+|||+.||+++++|..++..  .....|||.+...  +++....+.+.++++
T Consensus       105 pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~--~~~~~~~l~d~~~d~  182 (256)
T PRK07408        105 PRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQ--DEDGSTSLGDLLPDP  182 (256)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCC--CCCCccccccccCCc
Confidence            9999999999999999885 7899999999999999999999998754  3568899987421  111122455555554


Q ss_pred             cCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          420 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       420 ~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                      ..  .+.  ....+....|..+| ..||+++|.||.++|   ++++|++|||+.||+|+++|++++.+|+++||+.+...
T Consensus       183 ~~--~~~--~~~~~~~~~l~~~l-~~L~~~~r~vl~l~y---~~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~~~  254 (256)
T PRK07408        183 RY--RSF--QLAQEDRIRLQQAL-AQLEERTREVLEFVF---LHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPE  254 (256)
T ss_pred             cc--chh--hhhHHHHHHHHHHH-HcCCHHHHHHHHHHH---HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcc
Confidence            31  121  12345567899999 899999999999999   79999999999999999999999999999999998654

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=100.00  E-value=4.7e-38  Score=313.25  Aligned_cols=244  Identities=29%  Similarity=0.407  Sum_probs=214.0

Q ss_pred             hcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHH
Q 010521          200 VVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMS  279 (508)
Q Consensus       200 i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~s  279 (508)
                      .+++|+||++++.+|+.+++.||.                                        .|++.||..|+++|++
T Consensus        10 ~~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~~~~~v~~   49 (254)
T TIGR02850        10 TSKLPVLKNQEMRELFIRMQSGDT----------------------------------------TAREKLINGNLRLVLS   49 (254)
T ss_pred             ccCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHH
Confidence            357899999999999999999997                                        8999999999999999


Q ss_pred             HHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHH
Q 010521          280 IAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLR  359 (508)
Q Consensus       280 IAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~  359 (508)
                      +|++|.+++.+++||+|||++|||+++++|||.+|.+|+||+++||++.|.++++++. .+++|++..+..+++.++...
T Consensus        50 ~a~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~-~ir~p~~~~~~~~~~~~~~~~  128 (254)
T TIGR02850        50 VIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVRDK  128 (254)
T ss_pred             HHHHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CccCchHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999975 789999999998998888877


Q ss_pred             H-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHH
Q 010521          360 L-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEV  438 (508)
Q Consensus       360 l-~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L  438 (508)
                      + .++|++|+.+|||+.+|+++++|..++.....+.|||.++..+  +++..++.+.+.+..   .+.   ........|
T Consensus       129 l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~--~~~~~~~~~~~~d~~---~~~---~~~~~~~~l  200 (254)
T TIGR02850       129 LISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYND--GGDPIYVMDQISDEK---NKD---SQWLEGIAL  200 (254)
T ss_pred             HHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCC--CCCcchhhhhcCCcc---ccH---HHHHhHHHH
Confidence            7 4789999999999999999999999999888889999875311  111224556665542   121   233445678


Q ss_pred             HHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          439 NKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       439 ~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      ..+| ..||+++|.||.++|   ++++|++|||+.||+|+++|++++.+|++|||+.+
T Consensus       201 ~~~l-~~L~~rer~vi~~~~---~~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~~  254 (254)
T TIGR02850       201 KEAM-KRLNEREKMILNMRF---FEGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYV  254 (254)
T ss_pred             HHHH-HcCCHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence            8889 899999999999999   78999999999999999999999999999999753

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=100.00  E-value=1.7e-37  Score=310.21  Aligned_cols=227  Identities=27%  Similarity=0.409  Sum_probs=199.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~---~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~i  340 (508)
                      .|+++||..|+|+|+.+|++|.   ..+.+.+||+|||+||||+|+++|||++|++|+|||+||||++|.+++++..+  
T Consensus        23 ~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~~~--  100 (257)
T PRK05911         23 EYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDW--  100 (257)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCC--
Confidence            8999999999999999999986   24568999999999999999999999999999999999999999999999865  


Q ss_pred             cccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhC--ccccccccCCCCCCCCCCCccccccc
Q 010521          341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPSLNGLPGETHHSYIA  417 (508)
Q Consensus       341 rip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~--~~~SLD~~~~~~~~~~~~~~l~d~i~  417 (508)
                       +|+++.+.++++..+...+. +.|++|+.+|||+.+|+++++|..++....  .++|||.+.....+++++.++.+.++
T Consensus       101 -~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~~l~  179 (257)
T PRK05911        101 -VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEERIA  179 (257)
T ss_pred             -CCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhhhcc
Confidence             89999999999999888885 689999999999999999999999887653  46899986433222223345677787


Q ss_pred             cccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          418 DNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       418 d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      |... ..|++.+...+....|..+| ..|||++|.||.++|   ++++|++|||+.||+|+++|++++++|+++||+.+.
T Consensus       180 d~~~-~~~~~~~~~~~~~~~l~~al-~~L~~~er~vi~l~y---~e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~  254 (257)
T PRK05911        180 DERA-ETGYDVVDKKEFSSILAEAI-LALEEKERKVMALYY---YEELVLKEIGKILGVSESRVSQIHSKALLKLRATLS  254 (257)
T ss_pred             CCCC-CCHHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            7653 46778888888889999999 899999999999999   799999999999999999999999999999999885


Q ss_pred             H
Q 010521          498 K  498 (508)
Q Consensus       498 ~  498 (508)
                      .
T Consensus       255 ~  255 (257)
T PRK05911        255 A  255 (257)
T ss_pred             h
Confidence            4

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=100.00  E-value=6.6e-37  Score=305.51  Aligned_cols=242  Identities=29%  Similarity=0.424  Sum_probs=211.8

Q ss_pred             ccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHH
Q 010521          202 SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIA  281 (508)
Q Consensus       202 ~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIA  281 (508)
                      ++|+|+++++..|+.+++.||.                                        .|+++||..|.++|+++|
T Consensus        15 ~~~~l~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~~a   54 (258)
T PRK08215         15 KLPVLKNEEMRELFERMQNGDK----------------------------------------EAREKLINGNLRLVLSVI   54 (258)
T ss_pred             CCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHH
Confidence            5689999999999999999998                                        899999999999999999


Q ss_pred             HHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH
Q 010521          282 QRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE  361 (508)
Q Consensus       282 krY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~  361 (508)
                      ++|.+++.+++||+|||++|||+++++|||.+|.+|.||+++||+++|.++++++. .+++|++......++.++...+.
T Consensus        55 ~~~~~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~-~vrip~~~~~~~~~~~~~~~~l~  133 (258)
T PRK08215         55 QRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAYKALQVREKLI  133 (258)
T ss_pred             HHHhCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-ceEecHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999985 88999999998888888877774


Q ss_pred             -HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHH
Q 010521          362 -EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNK  440 (508)
Q Consensus       362 -~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~  440 (508)
                       +.|+.|+..|||+.+|+++++|..++.....+.|||.++..+  +....++.+.+++..   .+   .+.......+..
T Consensus       134 ~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~--~~~~~~~~~~~~~~~---~~---~~~~~~~~~l~~  205 (258)
T PRK08215        134 NENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHD--GGDPIYVMDQISDEK---NK---DENWLEEIALKE  205 (258)
T ss_pred             HHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCC--CCcchhhhhhccCcc---cc---HHHHHhHHHHHH
Confidence             789999999999999999999999988888888999875321  111223445554432   11   233345567888


Q ss_pred             HHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          441 LIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       441 ~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      +| +.||++++.||.++|   ++++|++|||+.||+|+++|++++.+|+++||+.|
T Consensus       206 ~l-~~L~~~er~vi~~~~---~~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l  257 (258)
T PRK08215        206 AM-KKLNDREKLILNLRF---FQGKTQMEVAEEIGISQAQVSRLEKAALKHMRKYI  257 (258)
T ss_pred             HH-HcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            88 899999999999999   78999999999999999999999999999999876

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

Probab=100.00  E-value=3.9e-37  Score=304.36  Aligned_cols=240  Identities=34%  Similarity=0.484  Sum_probs=215.0

Q ss_pred             cCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Q 010521          203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ  282 (508)
Q Consensus       203 ~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAk  282 (508)
                      .+.++..+...+....+.|+.                                        .+. .||++|+|||.++|+
T Consensus         3 ~~~~~~~e~~~~~~~~~~g~~----------------------------------------~~~-~Li~~ylpLV~~ia~   41 (247)
T COG1191           3 PQPLSKEEEEKLLEYYAEGDE----------------------------------------EAR-RLIERYLPLVKSIAR   41 (247)
T ss_pred             CcccchHHHHHHHHHHHhcCH----------------------------------------HHH-HHHHHHHHHHHHHHH
Confidence            356778888889999999997                                        888 999999999999999


Q ss_pred             HhcCCCC-CHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH
Q 010521          283 RYDNMGA-DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE  361 (508)
Q Consensus       283 rY~~~g~-d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~  361 (508)
                      +|.+++. +.+||+|.|+|||++|+++|||++|.+|+|||..+|+++|.+++|++. .+++|+.+.+..+++..+...+.
T Consensus        42 k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~-~v~vpR~~~~~~~~i~~~~~~l~  120 (247)
T COG1191          42 KFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND-SVKVPRSLRELGRRIEEAIDELE  120 (247)
T ss_pred             HHHhcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC-CccCcHHHHHHHHHHHHHHHHHH
Confidence            9998877 999999999999999999999999999999999999999999999999 99999999999999999999995


Q ss_pred             -HcCCCCCHHHHHHHhCCCHHHHHHHHHHhC--ccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHH
Q 010521          362 -EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEV  438 (508)
Q Consensus       362 -~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~--~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L  438 (508)
                       ++|++|+.+|||+.||++.+++..++....  ..+|+|....   ..+++.     +.+.  ..+|.+.++..+....|
T Consensus       121 ~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~---~~~d~~-----~~~~--~~~~~~~~~~~~~~~~l  190 (247)
T COG1191         121 QELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVL---KDDDDD-----VDDQ--IENPDDGVEKEELLEIL  190 (247)
T ss_pred             HHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhc---cccccc-----hhhc--cccchhHHHHHHHHHHH
Confidence             799999999999999999999999998874  6788887532   111111     1111  24788889999999999


Q ss_pred             HHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          439 NKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       439 ~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      .+++ ..|++|||.|+.+||   ++++|++|||+.||||+++|+|++.+|++|||+.|..
T Consensus       191 ~~ai-~~L~EREk~Vl~l~y---~eelt~kEI~~~LgISes~VSql~kkai~kLr~~l~~  246 (247)
T COG1191         191 KEAI-EPLPEREKLVLVLRY---KEELTQKEIAEVLGISESRVSRLHKKAIKKLRKELNK  246 (247)
T ss_pred             HHHH-HccCHHHHHHHHHHH---HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHhcc
Confidence            9999 699999999999999   8999999999999999999999999999999998753

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=100.00  E-value=1.2e-35  Score=298.07  Aligned_cols=251  Identities=26%  Similarity=0.325  Sum_probs=218.4

Q ss_pred             hcccCCCCHHHHHHHHHHHHc-CCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHH
Q 010521          200 VVSEELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVM  278 (508)
Q Consensus       200 i~~~~lLt~~EE~eL~~~ik~-Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~  278 (508)
                      .|++|+||.+++.+|+.+++. ||.                                        .|++.|+..|.++|+
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            467999999999999999764 566                                        899999999999999


Q ss_pred             HHHHHhc-C--CCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHH
Q 010521          279 SIAQRYD-N--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRN  355 (508)
Q Consensus       279 sIAkrY~-~--~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~  355 (508)
                      .+|++|. +  .+.+++||+|||++|||+++++||+.+|.+|.||+++|||+.|.+++++.   .++|.+.....+++++
T Consensus        46 ~~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~~---~~~p~~~~~~~~~i~~  122 (268)
T PRK06288         46 YVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSI---DWIPRSVRQKARQIER  122 (268)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhc---CccCHHHHHHHHHHHH
Confidence            9999986 2  56789999999999999999999999888999999999999999999865   4589999888889999


Q ss_pred             HHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHh--CccccccccCCCCCCCCCCCccccccccccCCCCccchHHHH
Q 010521          356 AKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDW  432 (508)
Q Consensus       356 a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~  432 (508)
                      +...+. +.|++|+.+|||+.+|++.+++.+++...  ..+.|||.+...+ ++.+..++.+.++++. .++|++.++..
T Consensus       123 ~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~-~~~~~~~l~~~~~~~~-~~~pe~~~~~~  200 (268)
T PRK06288        123 AIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGG-DEGDEVSLMDTLESPA-ALNPDEIAERE  200 (268)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccC-CCcccchhhhhccCCC-CCCHHHHHHHH
Confidence            888885 68999999999999999999999998765  4678998864311 1222234556666544 35788888888


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          433 ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       433 el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                      +....|..+| ..||+++|.||.++|   ++++|++|||+.||+|.++|++++.+|+++||..+...
T Consensus       201 e~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~  263 (268)
T PRK06288        201 EIKRVIVEAI-KTLPEREKKVLILYY---YEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLAEI  263 (268)
T ss_pred             HHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            8899999999 899999999999999   79999999999999999999999999999999998754

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=100.00  E-value=2.1e-35  Score=293.87  Aligned_cols=242  Identities=27%  Similarity=0.342  Sum_probs=213.4

Q ss_pred             CCCCHHHHHHHHHHHHc-CCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Q 010521          204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ  282 (508)
Q Consensus       204 ~lLt~~EE~eL~~~ik~-Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAk  282 (508)
                      |.||++++.+|+.+++. ||.                                        .|+++||..|.++|+.+|+
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            67899999999999998 576                                        8999999999999999999


Q ss_pred             HhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH-
Q 010521          283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-  361 (508)
Q Consensus       283 rY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~-  361 (508)
                      +|.+++.+++||+||||++||+++++||++.|.+|.||+++||++.|.+++++..+.+++|.+..+..++++++...+. 
T Consensus        48 ~~~~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~iri~~~~~~~~~~~~~~~~~l~~  127 (255)
T TIGR02941        48 KYSKGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAIDELTD  127 (255)
T ss_pred             HHhcCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999988885 


Q ss_pred             HcCCCCCHHHHHHHhCCCHHHHHHHHHHh--CccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHH
Q 010521          362 EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVN  439 (508)
Q Consensus       362 ~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~  439 (508)
                      ..|+.|+.+|+|+.+|++.+++..++...  ....|||.++..+    ++...... .+.  ..+|++.+...+....+.
T Consensus       128 ~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~----~~~~~~~~-~~~--~~~~~~~~~~~e~~~~l~  200 (255)
T TIGR02941       128 HLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEAD----SDGSTVAR-LDS--VGEVEDGYDQTERRMVLE  200 (255)
T ss_pred             HhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCC----CCCccccc-ccc--cCCcchHHHHHHHHHHHH
Confidence            67999999999999999999999887764  4678998875321    11111111 111  124667777788888899


Q ss_pred             HHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          440 KLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       440 ~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      .+| +.||+++|.||.++|   ++|+|++|||+.||+|.++|++++++|+++||+.+
T Consensus       201 ~~l-~~L~~~~r~ii~l~~---~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~  253 (255)
T TIGR02941       201 KIL-PILSEREKSIIHCTF---EENLSQKETGERLGISQMHVSRLQRQAISKLKEAA  253 (255)
T ss_pred             HHH-HcCCHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            999 899999999999999   79999999999999999999999999999999875

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

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=100.00  E-value=1.1e-34  Score=284.27  Aligned_cols=220  Identities=33%  Similarity=0.403  Sum_probs=191.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.++|+++|++|.+++.+++||+|||++|||+++++|||..|.+|.||+++||++.|.++++++. .+++|
T Consensus        11 ~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~lr~~~-~i~~p   89 (231)
T TIGR02885        11 EARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-IIKVS   89 (231)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCC-CeECC
Confidence            89999999999999999999999999999999999999999999999999989999999999999999999986 78999


Q ss_pred             ccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521          344 NHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE  422 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e  422 (508)
                      +++.....+++++...+. ++|+.|+.+|||+.+|++++++..++.....+.|||.+...+  +.+..++.+.+.+..  
T Consensus        90 ~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~--~~~~~~~~d~~~~~~--  165 (231)
T TIGR02885        90 RSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQD--DGDPIYLLDQIADKG--  165 (231)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCC--CCCcchhhhhcCCCC--
Confidence            999999999999888885 689999999999999999999999988888889999874311  111223445554432  


Q ss_pred             CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                       +++   ........+.+++ +.||++++.||.++|   ++++|++|||+.||+|+++|++++++|+++||..|
T Consensus       166 -~~~---~~~~~~~~l~~~l-~~L~~~e~~i~~~~~---~~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~l  231 (231)
T TIGR02885       166 -SED---SDWLEKIALKEAI-SKLDERERQIIMLRY---FKDKTQTEVANMLGISQVQVSRLEKKVLKKMKEKL  231 (231)
T ss_pred             -ccH---HhHHHHHHHHHHH-HcCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHhC
Confidence             122   2233456788889 899999999999999   68999999999999999999999999999999754

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.

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

Probab=100.00  E-value=3e-34  Score=280.34  Aligned_cols=222  Identities=33%  Similarity=0.401  Sum_probs=194.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (508)
Q Consensus       263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri  342 (508)
                      ..|+++|+..|.|+|+++|++|.+++.+.+||+|||++|||+|+++||+.+|.+|+||+++||++.|.++++++.+.+++
T Consensus         2 ~~a~~~lv~~y~~~v~~~a~~~~~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~~~ri   81 (227)
T TIGR02980         2 KEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTWAVRV   81 (227)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCCceec
Confidence            37999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCc--cccccccCCCCCCCCCCCccccccccc
Q 010521          343 PNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGK--VFSLDREAFPSLNGLPGETHHSYIADN  419 (508)
Q Consensus       343 p~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~--~~SLD~~~~~~~~~~~~~~l~d~i~d~  419 (508)
                      |.+..+.+++++++...+. +.|+.|+.+|+|+.+|++++++..++.....  +.|||.++. + ++..+..+.+.+   
T Consensus        82 ~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~-~-~~~~~~~~~d~~---  156 (227)
T TIGR02980        82 PRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIE-D-DDGDPIALLDTL---  156 (227)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCC-C-CCCCCccccccc---
Confidence            9999999899999888885 6899999999999999999999998887654  889998742 0 111111222322   


Q ss_pred             cCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          420 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       420 ~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                         .+|++.++..+....|..+| ..||++|+.||.++|   ++|+|++|||+.||+|+++|++++++|+++||+.+
T Consensus       157 ---~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~y---~~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~l  226 (227)
T TIGR02980       157 ---GDEDDALETVEDRLALKPLL-AALPERERRILLLRF---FEDKTQSEIAERLGISQMHVSRLLRRALKKLREQL  226 (227)
T ss_pred             ---CCcchHHHhHHHHHHHHHHH-HcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence               24555566667788899999 899999999999999   78999999999999999999999999999999865

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.

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=7.5e-34  Score=282.46  Aligned_cols=223  Identities=28%  Similarity=0.386  Sum_probs=193.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcC---CCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~---~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~i  340 (508)
                      .|++.||..|.++|+++|++|.+   ++.+.+||+||||+|||+++++|||++|.+|.||+++||+|.|.++++++.   
T Consensus        22 ~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~~~---   98 (251)
T PRK07670         22 DAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED---   98 (251)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC---
Confidence            99999999999999999999975   688999999999999999999999999999999999999999999999876   


Q ss_pred             cccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHH--hCccccccccCCCCCCCCCCCccccccc
Q 010521          341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEA--IGKVFSLDREAFPSLNGLPGETHHSYIA  417 (508)
Q Consensus       341 rip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~--~~~~~SLD~~~~~~~~~~~~~~l~d~i~  417 (508)
                      ++|.+..+.+++++.+...+. ..|+.|+..|||+.+|+++++|..++..  ...+.|||.++.   +++++..+.+.+.
T Consensus        99 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~---~~~~~~~~~~~~~  175 (251)
T PRK07670         99 WLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTH---DQDDGENVSVTIR  175 (251)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCcccc---CCCCcchhhhhhc
Confidence            589998888888888887774 6899999999999999999999998764  367899998742   1222222333333


Q ss_pred             cccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          418 DNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       418 d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      +.. ..+|++.+...+....|..+| ..||+++|.||.++|   ++++|++|||+.||+|.++|++++++|+++||..+.
T Consensus       176 ~~~-~~~~e~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~  250 (251)
T PRK07670        176 DDK-TPTPEEKLLKEELIEELAEKI-KQLSEKEQLVISLFY---KEELTLTEIGQVLNLSTSRISQIHSKALFKLKKLLE  250 (251)
T ss_pred             CcC-CCCHHHHHHHHHHHHHHHHHH-hcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence            332 246777777788888999999 899999999999999   899999999999999999999999999999999875

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=100.00  E-value=2.2e-33  Score=279.76  Aligned_cols=244  Identities=26%  Similarity=0.326  Sum_probs=212.3

Q ss_pred             CCCCHHHHHHHHHHHHc-CCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Q 010521          204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ  282 (508)
Q Consensus       204 ~lLt~~EE~eL~~~ik~-Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAk  282 (508)
                      |.|+++++.+|+.+++. ||.                                        .|++.||..|.++|+++|+
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            78999999999999986 787                                        9999999999999999999


Q ss_pred             HhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH-
Q 010521          283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-  361 (508)
Q Consensus       283 rY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~-  361 (508)
                      +|.+++.+++||+||||++||+++++||+..|.+|.||+++||+|.|.+++++..+.+++|++.....++++.+...+. 
T Consensus        48 ~~~~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~~~~~~i~r~~~~~~~~~~~~~~~~~~  127 (257)
T PRK08583         48 KYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTT  127 (257)
T ss_pred             HHhcCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999998889999999999999999999999999999999998888888887775 


Q ss_pred             HcCCCCCHHHHHHHhCCCHHHHHHHHHHh--CccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHH
Q 010521          362 EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVN  439 (508)
Q Consensus       362 ~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~  439 (508)
                      ..++.|+.+++|+.+|++.+++..+....  ..+.|+|.++..+     ++.....+.+.  ..+|++.+...+....+.
T Consensus       128 ~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~-----~~~~~~~~~~~--~~~~e~~~~~~~~~~~l~  200 (257)
T PRK08583        128 ELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEAD-----SDGSTVTLLDI--VGQQEDGYELTEQRMILE  200 (257)
T ss_pred             HhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCC-----CCCccchHhhh--cCCcchhHHHHHHHHHHH
Confidence            67899999999999999999998876654  3577888764211     11111111111  135777777788888899


Q ss_pred             HHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          440 KLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       440 ~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      .+| ..||+++|.||.++|   ++|+|++|||+.||||++||++++++|+++||..+..
T Consensus       201 ~~l-~~L~~~~r~vl~l~~---~~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~~  255 (257)
T PRK08583        201 KIL-PVLSDREKSIIQCTF---IENLSQKETGERLGISQMHVSRLQRQAIKKLREAAFL  255 (257)
T ss_pred             HHH-HhCCHHHHHHHHHHH---hCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcc
Confidence            999 899999999999999   7999999999999999999999999999999998854

>PRK05572 sporulation sigma factor SigF; Validated

Probab=100.00  E-value=2.4e-33  Score=278.99  Aligned_cols=245  Identities=34%  Similarity=0.424  Sum_probs=211.8

Q ss_pred             HhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHH
Q 010521          198 KGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLV  277 (508)
Q Consensus       198 ~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV  277 (508)
                      +.-...|.||.+++.+|+.+++.||.                                        .|++.||..|.++|
T Consensus         6 ~~~~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~y~~~v   45 (252)
T PRK05572          6 KNKKKKPQLKDEENKELIKKSQDGDQ----------------------------------------EARDTLVEKNLRLV   45 (252)
T ss_pred             ccCcCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHH
Confidence            34456899999999999999999998                                        99999999999999


Q ss_pred             HHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHH
Q 010521          278 MSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAK  357 (508)
Q Consensus       278 ~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~  357 (508)
                      +.+|++|.+++.+++||+|||++++|+++++|++.++.+|.||+++||++.|.+++++.. .+++|++......+++++.
T Consensus        46 ~~~a~~~~~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~-~~r~~~~~~~~~~~~~~~~  124 (252)
T PRK05572         46 WSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDK  124 (252)
T ss_pred             HHHHHHHccCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCC-CCCCCHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999988889999999999999999999884 7899999999999999998


Q ss_pred             HHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHH
Q 010521          358 LRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKD  436 (508)
Q Consensus       358 ~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e  436 (508)
                      ..+. +.|+.|+..|+|+.+|++++++..+......+.||+.+...  ++....++.+.+.+..    .    .......
T Consensus       125 ~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~--~~~~~~~~~d~~~~~~----~----~~~~~~~  194 (252)
T PRK05572        125 DELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHE--NDGDPITLLDQIADQS----E----EDWFDKI  194 (252)
T ss_pred             HHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCccc--CCCCcchhhhhcCCCc----h----hhHHHHH
Confidence            8875 67999999999999999999999998888888899876421  1111112233333221    1    1234466


Q ss_pred             HHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          437 EVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       437 ~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      .|..+| +.||++++.||.++|   ++++|++|||+.+|+|+++|++++.+|+++||..|.
T Consensus       195 ~l~~~l-~~L~~~~~~v~~l~~---~~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l~  251 (252)
T PRK05572        195 ALKEAI-RELDERERLIVYLRY---FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKLD  251 (252)
T ss_pred             HHHHHH-HcCCHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence            788899 899999999999999   799999999999999999999999999999998874

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

Probab=100.00  E-value=5.5e-33  Score=271.33  Aligned_cols=217  Identities=32%  Similarity=0.468  Sum_probs=190.2

Q ss_pred             HHHHHHHHHHHHHHHhcC---CCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q 010521          269 LVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH  345 (508)
Q Consensus       269 LIe~yl~LV~sIAkrY~~---~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~  345 (508)
                      |+..|.++|+++|++|.+   ++.+++||+|||++|||+++++|||++|.+|+||+++||++.+.+++++..   ++|.+
T Consensus         1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~~---~~p~~   77 (224)
T TIGR02479         1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLD---WVPRS   77 (224)
T ss_pred             CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHcC---ccCHH
Confidence            578999999999999986   789999999999999999999999999999999999999999999998765   58988


Q ss_pred             HHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHh--CccccccccCCCCCCCCCCCccccccccccCC
Q 010521          346 LHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSYIADNRVE  422 (508)
Q Consensus       346 ~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e  422 (508)
                      ..+.++++.++...+. +.|++|+.+|+|+.+|+++++|..++...  ..+.|+|....   ++.++..+.++++++. .
T Consensus        78 ~~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~---~~~~~~~~~~~~~~~~-~  153 (224)
T TIGR02479        78 LRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLE---SGDDGGSLIDRIEDDK-S  153 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCccc---CCCccchhhhhccccc-c
Confidence            8888999999988885 68999999999999999999999998754  45678887521   1122334555565443 3


Q ss_pred             CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      ++|++.+...+....|.++| ..||+++|.||.++|   ++++|++|||+.||+|.++|++++++|+++||+.+
T Consensus       154 ~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~il~l~y---~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l  223 (224)
T TIGR02479       154 EDPEEELEREELREALAEAI-ESLSEREQLVLSLYY---YEELNLKEIGEVLGLTESRVSQIHSQALKKLRAKL  223 (224)
T ss_pred             CCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHc
Confidence            57888888888999999999 899999999999999   89999999999999999999999999999999875

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=100.00  E-value=1.5e-31  Score=263.37  Aligned_cols=224  Identities=28%  Similarity=0.435  Sum_probs=190.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhc
Q 010521          261 ECSLAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS  337 (508)
Q Consensus       261 e~~~A~e~LIe~yl~LV~sIAkrY~---~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~  337 (508)
                      +|.-++++|+..|.++|+.+|++|.   +++.+++||+||||+|||+++++|||..|.+|.||+++||++.|.++++++.
T Consensus         5 ~~~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~   84 (236)
T PRK06986          5 EGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLD   84 (236)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcC
Confidence            4557899999999999999999997   6789999999999999999999999998889999999999999999999986


Q ss_pred             ccccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHh--CccccccccCCCCCCCCCCCcccc
Q 010521          338 RTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHS  414 (508)
Q Consensus       338 R~irip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~~~~~l~d  414 (508)
                      +   +|.+......++.++...+. ..|++|+.+|||+.+|++.++|..++...  ..+.|++.+.     +++++.+..
T Consensus        85 ~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~-----~~~~~~~~~  156 (236)
T PRK06986         85 W---VPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELR-----GEHGDSILV  156 (236)
T ss_pred             C---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccc-----cCCCccccc
Confidence            4   67777766666777766664 68999999999999999999999998865  4567787753     112222222


Q ss_pred             ccccccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          415 YIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       415 ~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ...+.  .++|++.+...+....|..+| +.||+++|.||.++|   ++|+|++|||+.||+|.++|++++++|+++||+
T Consensus       157 ~~~~~--~~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~  230 (236)
T PRK06986        157 TEDHQ--DEDPLQQLEDEELREALVEAI-ESLPEREQLVLSLYY---QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRA  230 (236)
T ss_pred             ccCCC--CCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHhHh---ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            22222  346778888888889999999 899999999999999   899999999999999999999999999999999


Q ss_pred             HHHH
Q 010521          495 AARK  498 (508)
Q Consensus       495 ~L~~  498 (508)
                      .+..
T Consensus       231 ~l~~  234 (236)
T PRK06986        231 RLGE  234 (236)
T ss_pred             HHhc
Confidence            8864

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=100.00  E-value=1.2e-31  Score=264.18  Aligned_cols=210  Identities=20%  Similarity=0.305  Sum_probs=175.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcC---CCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~---~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~i  340 (508)
                      .-...|+..|.|+|+.+|++|..   .+.+.+||+|||++|||+|+++|||..| +|+||+++||||+|.+++++..+  
T Consensus        15 ~~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~~--   91 (231)
T PRK12427         15 QEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELDW--   91 (231)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcCC--
Confidence            45568899999999999999874   4679999999999999999999998666 89999999999999999998643  


Q ss_pred             cccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHh--CccccccccCCCCCCCCCCCccccccc
Q 010521          341 RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDREAFPSLNGLPGETHHSYIA  417 (508)
Q Consensus       341 rip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~~~~~~~~~~~~~l~d~i~  417 (508)
                       .|+++....++++++...+. ++|++|+.+|||+.||+++++|.+++...  ..+.|||.++..    +++   .+.+.
T Consensus        92 -~~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~----~~~---~~~~~  163 (231)
T PRK12427         92 -RPRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLAL----EAH---NDILQ  163 (231)
T ss_pred             -CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccC----CCc---ccccC
Confidence             67888888888988888884 68999999999999999999999987643  578999997421    111   11121


Q ss_pred             cccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521          418 DNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA  495 (508)
Q Consensus       418 d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~  495 (508)
                      +    .+|+   +.......|..+| ..||+++|.||.++|   ++++|++|||+.||||+++|+|++.+|++|||..
T Consensus       164 ~----~~~~---~~~~~~~~l~~~l-~~L~~~er~vi~l~~---~~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~~  230 (231)
T PRK12427        164 S----RDLE---ENIIIEDNLKQAL-SQLDEREQLILHLYY---QHEMSLKEIALVLDLTEARICQLNKKIAQKIKSF  230 (231)
T ss_pred             C----CCHH---HHHHHHHHHHHHH-HcCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence            1    1233   2233566788899 899999999999999   7999999999999999999999999999999964

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.96  E-value=2.2e-28  Score=240.62  Aligned_cols=213  Identities=30%  Similarity=0.379  Sum_probs=174.3

Q ss_pred             hHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHH
Q 010521          192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM  271 (508)
Q Consensus       192 ~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe  271 (508)
                      ++..|+.++++.|+||++++..|+..++.||.                                        .|++.|+.
T Consensus        17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~gd~----------------------------------------~a~~~l~~   56 (233)
T PRK05803         17 FLVSYVKNNSFPQPLSEEEERKYLELMKEGDE----------------------------------------EARNILIE   56 (233)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHH
Confidence            78899999999999999999999999999997                                        99999999


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHH
Q 010521          272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG  351 (508)
Q Consensus       272 ~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~  351 (508)
                      .|.++|+++|.+|.+++.+++|++||+++++|+++++||++++.+|.+|+++|+++.+.+++++..+..           
T Consensus        57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~-----------  125 (233)
T PRK05803         57 RNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTK-----------  125 (233)
T ss_pred             HhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccc-----------
Confidence            999999999999999999999999999999999999999988889999999999999999998764210           


Q ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHH
Q 010521          352 LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDD  431 (508)
Q Consensus       352 kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~  431 (508)
                                                              ...+++.+.... ++....++.+.+.+.  .++|++.+..
T Consensus       126 ----------------------------------------~~~~~~~~~~~~-~~~~~~~~~~~~~~~--~~~~~~~~~~  162 (233)
T PRK05803        126 ----------------------------------------KEVSLQDPIGVD-KEGNEISLIDILGSE--EDDVIEQVEL  162 (233)
T ss_pred             ----------------------------------------cCCCccccccCC-CCcCcccHHHHccCC--CCCHHHHHHH
Confidence                                                    011111110000 000111222333322  1246677777


Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          432 WALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       432 ~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                      ....+.|..+| +.||+++|+||.++|+++ ++|+|++|||+.||+|.++|++++++|+++||+.+...
T Consensus       163 ~~~~~~l~~~l-~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~~  230 (233)
T PRK05803        163 KMEVEKLYKKI-DILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYRA  230 (233)
T ss_pred             HHHHHHHHHHH-HhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence            77778899999 899999999999999774 58999999999999999999999999999999998653

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.94  E-value=5.5e-25  Score=215.79  Aligned_cols=210  Identities=29%  Similarity=0.361  Sum_probs=164.3

Q ss_pred             hHHHHHHhhccc-CCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHH
Q 010521          192 RLKGYVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (508)
Q Consensus       192 ~~~~yl~~i~~~-~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LI  270 (508)
                      ++-+|+..-|+. +.|++.++..|+.+++.||.                                        .|++.|+
T Consensus        15 ~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~af~~l~   54 (227)
T TIGR02846        15 FLVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDE----------------------------------------EARNVLI   54 (227)
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHH
Confidence            456788776644 56899999999999999998                                        9999999


Q ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q 010521          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL  350 (508)
Q Consensus       271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l  350 (508)
                      ..|.+.|+++|.+|.++..+++|++||+|+++|+++++|+++.+.+|.||++++++|.+.+++++..+..+         
T Consensus        55 ~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~Rk~~r~~~---------  125 (227)
T TIGR02846        55 ERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLRALKKTKG---------  125 (227)
T ss_pred             HHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHHHHhcccc---------
Confidence            99999999999999999999999999999999999999999888889999999999999999987643100         


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHH
Q 010521          351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD  430 (508)
Q Consensus       351 ~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve  430 (508)
                                                                ..+++...... .+.....+.+.+.+.  .++|++.+.
T Consensus       126 ------------------------------------------~~~~~~~~~~~-~~~~~~~~~~~~~~~--~~~~~~~~~  160 (227)
T TIGR02846       126 ------------------------------------------EVSLQDPIGVD-KEGNEISLIDILGSD--GDSVIEQVE  160 (227)
T ss_pred             ------------------------------------------ceeccccccCC-cccCcccHHHHhcCC--CCChHHHHH
Confidence                                                      01111100000 000001111111111  235666666


Q ss_pred             HHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          431 DWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      ..+..+.|.++| +.||+++|+||.++|.++ ++++|++|||+.||+|+++|++++++|+++||+.|
T Consensus       161 ~~~~~~~l~~~i-~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~~  226 (227)
T TIGR02846       161 LNLEIKKLYKKL-SVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKEL  226 (227)
T ss_pred             HHHHHHHHHHHH-HhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            667778899999 999999999999999442 38999999999999999999999999999999875

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=99.94  E-value=5.9e-25  Score=215.94  Aligned_cols=208  Identities=24%  Similarity=0.385  Sum_probs=160.2

Q ss_pred             HHHHhhccc-CCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHH
Q 010521          195 GYVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSN  273 (508)
Q Consensus       195 ~yl~~i~~~-~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~y  273 (508)
                      -|+.++... |.+++..+..|+.+++.||.                                        .|++.|+..|
T Consensus        22 ~~~~~~~~~~~~~~~~~~~~L~~~~~~gd~----------------------------------------~af~~l~~~y   61 (234)
T PRK08301         22 YYIGGSEALPPPLSKEEEEYLLNKLPKGDE----------------------------------------AVRSLLIERN   61 (234)
T ss_pred             HHhccccccCCcCCHHHHHHHHHHHHccCH----------------------------------------HHHHHHHHHh
Confidence            367777555 44788889999999999998                                        9999999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHH
Q 010521          274 VRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLI  353 (508)
Q Consensus       274 l~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~ki  353 (508)
                      .++|+.+|++|.+++.+++|++||+|+++|+++++|++..+++|.||++.+++|.+.++++++.+...            
T Consensus        62 ~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lRk~~~~~~------------  129 (234)
T PRK08301         62 LRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRNNKVKA------------  129 (234)
T ss_pred             HHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHHHHhcccc------------
Confidence            99999999999999999999999999999999999999888889999999999999999987643100            


Q ss_pred             HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCC-CccccccccccCCCCccchHHHH
Q 010521          354 RNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPG-ETHHSYIADNRVENNPWHGVDDW  432 (508)
Q Consensus       354 r~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~-~~l~d~i~d~~~e~~Pe~~ve~~  432 (508)
                                                             ..+++.+..  ...++. ....+...+.  ...++..+...
T Consensus       130 ---------------------------------------~~~~~~~~~--~~~~~~~~~~~~~~~~~--~~~~~~~~~~~  166 (234)
T PRK08301        130 ---------------------------------------EVSFDEPLN--IDWDGNELLLSDVLGTD--NDIIYKDIEDE  166 (234)
T ss_pred             ---------------------------------------ccccccccc--cccCCCcccHHHhccCc--ccchHHHHHHH
Confidence                                                   011111100  000000 0011111111  11233334445


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          433 ALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       433 el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      .....|..+| +.||+++|.||.|+|+|. .+|+|++|||+.||+|.+||++++++|+++||+.+..
T Consensus       167 ~~~~~l~~al-~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~~  232 (234)
T PRK08301        167 VDRKLLKKAL-KKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEINK  232 (234)
T ss_pred             HHHHHHHHHH-HhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            5566799999 899999999999999763 5899999999999999999999999999999998753

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=99.92  E-value=1.6e-23  Score=206.39  Aligned_cols=201  Identities=24%  Similarity=0.359  Sum_probs=155.3

Q ss_pred             cCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Q 010521          203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ  282 (508)
Q Consensus       203 ~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAk  282 (508)
                      .|.|+++++..|+..++.||.                                        .|++.|+..|.+.|+++|.
T Consensus        31 ~~~~~~~~~~~l~~~~~~~d~----------------------------------------~a~~~l~~~y~~~l~~~~~   70 (234)
T TIGR02835        31 PPPLTGEEEEALLQKLTQGDE----------------------------------------SAKSTLIERNLRLVVYIAR   70 (234)
T ss_pred             CCcCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHHHHH
Confidence            467888999999999999998                                        9999999999999999999


Q ss_pred             HhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHH
Q 010521          283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEE  362 (508)
Q Consensus       283 rY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~  362 (508)
                      +|.+++.+++|++||+++++|+++++|++..+++|.||++.+++|.+.++++++.+...                     
T Consensus        71 ~~~~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d~~Rk~~r~~~---------------------  129 (234)
T TIGR02835        71 KFENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRNNKTRS---------------------  129 (234)
T ss_pred             HhccCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhccccC---------------------
Confidence            99999999999999999999999999998887789999999999999999987653100                     


Q ss_pred             cCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHH
Q 010521          363 KGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLI  442 (508)
Q Consensus       363 ~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L  442 (508)
                                                    ..+++.+.... ..++.....+.. +.. .+.+++.+........|..+|
T Consensus       130 ------------------------------~~~~~~~~~~~-~~~~~~~~~~~~-~~~-~~~~~~~~~~~~~~~~l~~ai  176 (234)
T TIGR02835       130 ------------------------------EVSFDEPLNVD-WDGNELLLSDVL-GTD-SDIVYKYLEEEVDRELLRKAL  176 (234)
T ss_pred             ------------------------------cccccccccCC-CCCCcchHHHhc-CCC-CCcHHHHHHHHHHHHHHHHHH
Confidence                                          01111110000 000000011111 111 112223344455567799999


Q ss_pred             HccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          443 IVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       443 ~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                       +.||+++|.||.++|.|. ++|+|++|||+.||+|.+||++++++|+++||+.+..
T Consensus       177 -~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~~  232 (234)
T TIGR02835       177 -AKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKEINR  232 (234)
T ss_pred             -HhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhhc
Confidence             899999999999999543 4899999999999999999999999999999998864

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.

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=99.91  E-value=4.6e-23  Score=197.78  Aligned_cols=182  Identities=21%  Similarity=0.313  Sum_probs=137.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.++|+.+|.+|.++..+++|++||+++++|+++++|+++++.+|.||++.++++.+.+++++..+..+.+
T Consensus        24 ~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~~~d~~r~~~r~~~~~  103 (208)
T PRK08295         24 EALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQIITAIKTANRQKHIP  103 (208)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHhhhhcccc
Confidence            99999999999999999999999999999999999999999999999987778999999999999988887654311111


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                      ..                                              ...|++.+.   .+++.+..+.+.+.+.. ..
T Consensus       104 ~~----------------------------------------------~~~s~~~~~---~~~~~~~~~~~~~~~~~-~~  133 (208)
T PRK08295        104 LN----------------------------------------------SYVSLDKPI---YDEESDRTLLDVISEAK-VT  133 (208)
T ss_pred             cc----------------------------------------------ceeecCCcc---cCCccchhHHHHhcCcc-cC
Confidence            00                                              011222210   00111112223333222 13


Q ss_pred             CccchHHHHHHHHHHH-HHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          424 NPWHGVDDWALKDEVN-KLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~-~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                      +|++.+...+....+. .++ ..||+++|.||.+ |   .+|+|++|||+.||+|.++|+..++||+++||+++....
T Consensus       134 ~~~~~~~~~~~~~~l~~~~~-~~L~~~~r~vl~l-~---~e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~~~  206 (208)
T PRK08295        134 DPEELIISKEELEDIEEKIE-ELLSELEKEVLEL-Y---LDGKSYQEIAEELNRHVKSIDNALQRVKRKLEKYLENRE  206 (208)
T ss_pred             CHHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHH-H---HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence            6766665555555664 456 8999999999999 7   699999999999999999999999999999999987653

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.91  E-value=7.9e-23  Score=193.92  Aligned_cols=179  Identities=20%  Similarity=0.207  Sum_probs=147.4

Q ss_pred             CCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHhc
Q 010521          206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYD  285 (508)
Q Consensus       206 Lt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkrY~  285 (508)
                      +|+++...|+..++.||.                                        .|+++|+..|.+.|+.+|.++.
T Consensus         6 ~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~l~~~~~~~~   45 (189)
T PRK09648          6 DTGEELDALVAEAVAGDR----------------------------------------RALREVLEIIRPLVVRYCRARL   45 (189)
T ss_pred             CCchHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHHHHh
Confidence            477888889999999997                                        9999999999999999999988


Q ss_pred             CC----CCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH
Q 010521          286 NM----GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE  361 (508)
Q Consensus       286 ~~----g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~  361 (508)
                      ++    +.+++|++||+|+++|+++.+|++. +.+|.+|++..+++.+.++++++.+....+                  
T Consensus        46 ~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~~~d~~r~~~r~~~~~------------------  106 (189)
T PRK09648         46 GGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHKVADAHRAAGRDKAVP------------------  106 (189)
T ss_pred             cccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHHHHHHHHHhCCCcccc------------------
Confidence            65    4689999999999999999999864 447999999999999999887764310000                  


Q ss_pred             HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHH
Q 010521          362 EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKL  441 (508)
Q Consensus       362 ~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~  441 (508)
                                                        .+.             ..+...+   ..+|++.+...+..+.|..+
T Consensus       107 ----------------------------------~~~-------------~~~~~~~---~~~~~~~~~~~e~~~~l~~~  136 (189)
T PRK09648        107 ----------------------------------TEE-------------VPERPSD---DAGPEERALRSESSNRMREL  136 (189)
T ss_pred             ----------------------------------ccc-------------ccccccc---CCCHHHHHHHHHHHHHHHHH
Confidence                                              000             0000001   13566666777777889999


Q ss_pred             HHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          442 IIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       442 L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      | ..||+++|+||.++|   ++|+|++|||+.||+|.+||++.++||+++||+.+.
T Consensus       137 l-~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~  188 (189)
T PRK09648        137 L-DTLPEKQREILILRV---VVGLSAEETAEAVGSTPGAVRVAQHRALARLRAEIE  188 (189)
T ss_pred             H-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence            9 899999999999999   799999999999999999999999999999999874

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.90  E-value=9.1e-23  Score=194.84  Aligned_cols=184  Identities=13%  Similarity=0.148  Sum_probs=147.4

Q ss_pred             cCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Q 010521          203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ  282 (508)
Q Consensus       203 ~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAk  282 (508)
                      .|+....++..|+..+++|+.                                        .|+++|+..|.++|+++|.
T Consensus         9 ~~~~~~~~~~~li~~~~~g~~----------------------------------------~a~~~l~~~y~~~l~~~~~   48 (194)
T PRK09646          9 GPPAESPDLDALLRRVARGDQ----------------------------------------DAFAELYDRTSSRVYGLVR   48 (194)
T ss_pred             CCCCCcccHHHHHHHHHccCH----------------------------------------HHHHHHHHHHHHHHHHHHH
Confidence            355556667788888888887                                        9999999999999999999


Q ss_pred             HhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHH
Q 010521          283 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEE  362 (508)
Q Consensus       283 rY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~  362 (508)
                      +|.++..+++|++||+|+++|+++++|++..| .|.+|++..++|.+.++++++.+..+.-                   
T Consensus        49 ~~~~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~r~~~~~~~~~-------------------  108 (194)
T PRK09646         49 RVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAVDRVRSEQAASQRE-------------------  108 (194)
T ss_pred             HHhCCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHHHHHHhhccccccc-------------------
Confidence            99999999999999999999999999998665 6999999999999998887764210000                   


Q ss_pred             cCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHH
Q 010521          363 KGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLI  442 (508)
Q Consensus       363 ~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L  442 (508)
                                                     .....              .+. ...  ..++++.+...+..+.+..+|
T Consensus       109 -------------------------------~~~~~--------------~~~-~~~--~~~~~~~~~~~~~~~~l~~~l  140 (194)
T PRK09646        109 -------------------------------VRYGA--------------RNV-DPA--FDQVAEEVEARLERERVRDCL  140 (194)
T ss_pred             -------------------------------ccccc--------------ccc-ccc--ccchHHHHHHHhHHHHHHHHH
Confidence                                           00000              000 000  113334444456667899999


Q ss_pred             HccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          443 IVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       443 ~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                       ..||+++|.||.|+|   .+|+|++|||+.||+|.++|+++++||+++||..+..
T Consensus       141 -~~L~~~~r~vl~l~~---~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~~  192 (194)
T PRK09646        141 -DALTDTQRESVTLAY---YGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCLGV  192 (194)
T ss_pred             -HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHhcc
Confidence             899999999999999   7999999999999999999999999999999998853

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.90  E-value=1.3e-22  Score=191.88  Aligned_cols=162  Identities=15%  Similarity=0.185  Sum_probs=134.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.++|+.+|.+|.+++.+++|++||+|+++|+++.+|++. +.+|.+|++..+++.+.++++++...    
T Consensus        20 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~~~d~~R~~~~~----   94 (186)
T PRK05602         20 AAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNLCYDRLRRRREV----   94 (186)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHHHHHHHHhcCCC----
Confidence            9999999999999999999999999999999999999999999999986 44799999999999888888765310    


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                         +.+.             ..+ ..+.  ..
T Consensus        95 ---------------------------------------------------~~~~-------------~~~-~~~~--~~  107 (186)
T PRK05602         95 ---------------------------------------------------PVED-------------APD-VPDP--AP  107 (186)
T ss_pred             ---------------------------------------------------Cccc-------------ccc-cCCC--CC
Confidence                                                               0000             000 0011  12


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM  501 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l  501 (508)
                      .|++.+...+....+..+| ..||+++|.||.++|   ++|+|++|||+.||+|.++|+++++||+++||+.+...+.
T Consensus       108 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~  181 (186)
T PRK05602        108 GPDAGLEARQRARRVEQAL-AALPERQREAIVLQY---YQGLSNIEAAAVMDISVDALESLLARGRRALRAQLADLPG  181 (186)
T ss_pred             CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHhhHHH---hcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhccc
Confidence            3555556666777899999 899999999999999   8999999999999999999999999999999999986543

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.90  E-value=1.1e-22  Score=193.70  Aligned_cols=167  Identities=20%  Similarity=0.226  Sum_probs=137.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.+.|+++|.++.++..+++|++||+|+++|+++.+|++..  .|.+|++..+++.+.+++++..+....+
T Consensus        26 ~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~~~~~~R~~~~~~~~~  103 (194)
T PRK12513         26 AAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNLLIDHWRRHGARQAPS  103 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence            99999999999999999999999999999999999999999999999643  6999999999999999988765311100


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                          .+.          +.... ...+.  ..
T Consensus       104 ----------------------------------------------------~~~----------~~~~~-~~~~~--~~  118 (194)
T PRK12513        104 ----------------------------------------------------LDA----------DEQLH-ALADD--GA  118 (194)
T ss_pred             ----------------------------------------------------ccc----------chhhh-hcCCC--CC
Confidence                                                                000          00000 00011  23


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM  501 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l  501 (508)
                      +|+..++..+....+..+| +.||+++|.||.++|   .+|+|++|||+.||+|+++|+++++||+++||..+...++
T Consensus       119 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~  192 (194)
T PRK12513        119 APEQQLSLFRDRRRLQAAL-ETLPDEQREVFLLRE---HGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAEEVA  192 (194)
T ss_pred             CHHHHHHHHHHHHHHHHHH-HhCCHhHhhheeeeh---ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            5666666777788899999 899999999999999   8999999999999999999999999999999999987664

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.89  E-value=4.6e-22  Score=195.48  Aligned_cols=193  Identities=19%  Similarity=0.217  Sum_probs=156.5

Q ss_pred             cccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHH
Q 010521          201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI  280 (508)
Q Consensus       201 ~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sI  280 (508)
                      ...|+|+...+..|+..++.||.                                        .|++.|+..|.+.|+++
T Consensus         7 ~~~~~~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~   46 (231)
T PRK11922          7 SRPPPLSAASDRELVARVLAGDE----------------------------------------AAFEALMRRHNRRLYRT   46 (231)
T ss_pred             CCCCCcCcccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence            35689999999999999999998                                        99999999999999999


Q ss_pred             HHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHH
Q 010521          281 AQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL  360 (508)
Q Consensus       281 AkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l  360 (508)
                      |.++.++..+++|++||+|+++|+++++|++.  ..|.+|++..+++.+.+++++..+...++..               
T Consensus        47 a~~~~~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk~~r~~~~~~~---------------  109 (231)
T PRK11922         47 ARAILRNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRRRRRLVNLAEM---------------  109 (231)
T ss_pred             HHHHhCChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHhhcccccchhc---------------
Confidence            99999999999999999999999999999975  3799999999999999988776531110000               


Q ss_pred             HHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHH
Q 010521          361 EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNK  440 (508)
Q Consensus       361 ~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~  440 (508)
                                                          ..     .+...++ ......+  ...+|++.+...+..+.|..
T Consensus       110 ------------------------------------~~-----~~~~~~~-~~~~~~~--~~~~~e~~~~~~e~~~~l~~  145 (231)
T PRK11922        110 ------------------------------------VM-----ASTIAGG-ERTPLAD--PAEDPERAAARREIRALLER  145 (231)
T ss_pred             ------------------------------------cc-----ccccccc-cccccCc--ccCChHHHHHHHHHHHHHHH
Confidence                                                00     0000000 0000111  12367777777888888999


Q ss_pred             HHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          441 LIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       441 ~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      +| ..||+++|+||.++|   .+|+|++|||+.||+|.++|++++++|+++||+.+..
T Consensus       146 ~l-~~L~~~~r~i~~l~~---~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~  199 (231)
T PRK11922        146 AI-DALPDAFRAVFVLRV---VEELSVEETAQALGLPEETVKTRLHRARRLLRESLAR  199 (231)
T ss_pred             HH-HhCCHHHhhhheeeh---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            99 899999999999998   7999999999999999999999999999999999875

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.89  E-value=4.6e-22  Score=189.25  Aligned_cols=180  Identities=23%  Similarity=0.310  Sum_probs=143.7

Q ss_pred             CCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHhc
Q 010521          206 LTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYD  285 (508)
Q Consensus       206 Lt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkrY~  285 (508)
                      ++...+.+|+.+++.||.                                        .|++.|+..|.+.|+.+|+++.
T Consensus        11 ~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~L~~~y~~~l~~~~~~~~   50 (194)
T PRK12519         11 LSSRSDAELFSALKAGQS----------------------------------------AALGVLYDRHAGLVYGLALKIL   50 (194)
T ss_pred             CCcccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHHHHc
Confidence            445566778888899987                                        9999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHcCC
Q 010521          286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGV  365 (508)
Q Consensus       286 ~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~~Gr  365 (508)
                      ++..+++|++||+|+++|+. ..|++..+ +|.||++.++++.+.++++++.+.....                      
T Consensus        51 ~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~d~~Rk~~~~~~~~----------------------  106 (194)
T PRK12519         51 GNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAIDRLRSRRSRQRLL----------------------  106 (194)
T ss_pred             CCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHHHHHHhcccccchh----------------------
Confidence            99999999999999999976 67887555 7999999999999999988764310000                      


Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHHHcc
Q 010521          366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVT  445 (508)
Q Consensus       366 ~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~  445 (508)
                                                     +.         ....+   ..+. ..+.|++.+...+....|..+| ..
T Consensus       107 -------------------------------~~---------~~~~~---~~~~-~~~~~~~~~~~~~~~~~l~~~l-~~  141 (194)
T PRK12519        107 -------------------------------ER---------WQQEL---LGEA-SEDTPLEQASLAERSQRVQTAL-AQ  141 (194)
T ss_pred             -------------------------------hh---------hhhhh---cccc-cCCCHHHHHHHHHHHHHHHHHH-Hh
Confidence                                           00         00000   0000 0124555555666667888999 89


Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      ||++++.||.++|   ++|+|++|||+.||+|.++|+++++||+++||+.+.
T Consensus       142 L~~~~~~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~  190 (194)
T PRK12519        142 LPESQRQVLELAY---YEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQ  190 (194)
T ss_pred             CCHHHhhhhhhhh---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999   899999999999999999999999999999999885

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.89  E-value=5e-22  Score=190.03  Aligned_cols=163  Identities=18%  Similarity=0.219  Sum_probs=133.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.+.|+.+|.++.++..+++|++||+++++|+.+.+|++.. ..|.+|++..+++.+.++++++.+.    
T Consensus        26 ~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~~~d~~Rk~~~~----  100 (196)
T PRK12524         26 AAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNLCTDRLRRRRRA----  100 (196)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHHHHHHHHhhcCC----
Confidence            99999999999999999999999999999999999999999999998533 3699999999999888888765320    


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                       ...++..        .     + ..+.  ..
T Consensus       101 -------------------------------------------------~~~~~~~--------~-----~-~~~~--~~  115 (196)
T PRK12524        101 -------------------------------------------------SVDLDDA--------P-----E-PADA--AP  115 (196)
T ss_pred             -------------------------------------------------CCCcccc--------c-----c-cccc--CC
Confidence                                                             0000000        0     0 0011  12


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                      +|++.+...+....|..+| +.||+++|.||.|+|   ++|++++|||+.||+|..||+++++||+++||..+...+
T Consensus       116 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~L~~---~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~  188 (196)
T PRK12524        116 GAEEALIEGDRMRALDAAL-AALPERQRQAVVLRH---IEGLSNPEIAEVMEIGVEAVESLTARGKRALAALLAGQR  188 (196)
T ss_pred             CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence            4555566667778899999 899999999999999   799999999999999999999999999999999987644

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.89  E-value=6.6e-22  Score=188.11  Aligned_cols=178  Identities=18%  Similarity=0.264  Sum_probs=133.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.||..|.+.|+.+|.++.++..+++|++||+|+++|+++.+|+++.+.+|.||++.+|++.+.++++...+..+.+
T Consensus        19 ~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~~~~~~r~~~~~~~~~   98 (198)
T TIGR02859        19 HALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQIITAIKTATRQKHIP   98 (198)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence            99999999999999999999999999999999999999999999999987778999999999998888876543210000


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                      .                                              ....|++.+..   ..+.+.++.+.+.+.. .+
T Consensus        99 ~----------------------------------------------~~~~~~~~~~~---~~~~~~~~~~~~~~~~-~~  128 (198)
T TIGR02859        99 L----------------------------------------------NSYVSLNKPIY---DEESDRTLLDVISGAK-VT  128 (198)
T ss_pred             h----------------------------------------------hhhcCcccccc---cccccchHHHHhhccc-cC
Confidence            0                                              00122222110   0111112222222211 23


Q ss_pred             CccchHHHHHHHHHHHHHHHccC-CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTL-GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~L-p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      +|++.....+....|.++| +.| ++.++.|+. +|   .+|+|++|||+.||+|.++|+..++||+++||..+
T Consensus       129 ~~e~~~~~~e~~~~l~~~l-~~Ll~~~~~~i~~-~~---~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~l  197 (198)
T TIGR02859       129 DPEELIISQEEYGDIESKM-NELLSDLEWKVLQ-SY---LDGKSYQEIACDLNRHVKSIDNALQRVKRKLEKYL  197 (198)
T ss_pred             CHHHHHHHHHHHHHHHHHH-HHhcCHHHHHHHH-HH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence            6777777777778899999 775 566666665 56   69999999999999999999999999999999875

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.

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.89  E-value=8.8e-22  Score=187.16  Aligned_cols=188  Identities=21%  Similarity=0.246  Sum_probs=148.9

Q ss_pred             CCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHh
Q 010521          205 LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRY  284 (508)
Q Consensus       205 lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkrY  284 (508)
                      +||+..+..|+..++.||.                                        .|++.|+..|.+.|+.+++++
T Consensus         1 ~~~~~~~~~ll~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~~~~~   40 (193)
T PRK11923          1 MLTQEEDQQLVERVQRGDK----------------------------------------RAFDLLVLKYQHKILGLIVRF   40 (193)
T ss_pred             CCccccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHHHH
Confidence            3566667788888999987                                        899999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHcC
Q 010521          285 DNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKG  364 (508)
Q Consensus       285 ~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~~G  364 (508)
                      .++..+++|++||+++++|+++.+|++..  .|.+|++..+++.+.++++++.+.....                     
T Consensus        41 ~~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~rk~~~~~~~~---------------------   97 (193)
T PRK11923         41 VHDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAKNHLVSRGRRPPDS---------------------   97 (193)
T ss_pred             hCCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHHHHHHHhcCCCccc---------------------
Confidence            99999999999999999999999999864  5999999999998888887654310000                     


Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHHHc
Q 010521          365 VTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIV  444 (508)
Q Consensus       365 r~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~  444 (508)
                                                  ...++...     ..++.   ..+.+   ..+|+..+...+..+.+..+| .
T Consensus        98 ----------------------------~~~~~~~~-----~~~~~---~~~~~---~~~~e~~~~~~~~~~~l~~~l-~  137 (193)
T PRK11923         98 ----------------------------DVSSEDAE-----FYDGD---HALKD---IESPERALLRDEIEGTVHRTI-Q  137 (193)
T ss_pred             ----------------------------cccccchh-----hhccc---ccccC---cCCHHHHHHHHHHHHHHHHHH-H
Confidence                                        00000000     00000   00111   135666666777788899999 8


Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      .||+++|.||.++|   .+|+|++|||+.||+|..+|++.++||+++||.++..
T Consensus       138 ~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~  188 (193)
T PRK11923        138 QLPEDLRTALTLRE---FDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQP  188 (193)
T ss_pred             hCCHHHhHHHhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999998   8999999999999999999999999999999998863

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

Probab=99.89  E-value=5.7e-22  Score=183.70  Aligned_cols=160  Identities=18%  Similarity=0.230  Sum_probs=132.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.+.+++++.++.++..+++|++||+|+++|+++++|+...+ .|.+|++..+++.+.++++.+.+.... 
T Consensus        11 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~~R~~~~~~~~-   88 (170)
T TIGR02952        11 DAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDYFRGSKRHPLF-   88 (170)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHHHHhcCCCCCC-
Confidence            999999999999999999999998899999999999999999999987555 799999999999999998876431100 


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                         +.+.             ..+....   ..
T Consensus        89 ---------------------------------------------------~~~~-------------~~~~~~~---~~  101 (170)
T TIGR02952        89 ---------------------------------------------------SLDV-------------FKELLSN---EP  101 (170)
T ss_pred             ---------------------------------------------------cHHH-------------HhhcCCC---CC
Confidence                                                               0000             0000000   12


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      +|++.+...+....+..+| ..|||++|.||.++|   ++|+|++|||+.||+|.++|++.++||+++||+.|
T Consensus       102 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~l  170 (170)
T TIGR02952       102 NPEEAILKEEANEKLLKAL-KILTPKQQHVIALRF---GQNLPIAEVARILGKTEGAVKILQFRAIKKLARQM  170 (170)
T ss_pred             CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence            5666666677778899999 899999999999999   79999999999999999999999999999999864

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.

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.89  E-value=7.3e-22  Score=185.95  Aligned_cols=168  Identities=25%  Similarity=0.275  Sum_probs=133.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|+.+|+..|.+.|+.+|.+|.+++.+++|++||+++++|+++.+|++..  +|.+|++..+++.+.+++++..+..   
T Consensus        18 ~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~~~~rk~~~~~---   92 (187)
T TIGR02948        18 NAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLTIDRLRKRKPDF---   92 (187)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHHHHHhhcccc---
Confidence            99999999999999999999999999999999999999999999999865  6999999999998888876543100   


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                         .++..    ..+.++....+...+.  .+
T Consensus        93 ---------------------------------------------------~~~~~----~~~~~~~~~~~~~~~~--~~  115 (187)
T TIGR02948        93 ---------------------------------------------------YLDDE----VQGTDGLTMESQLAAD--EA  115 (187)
T ss_pred             ---------------------------------------------------ccccc----ccCccccccccccccC--cC
Confidence                                                               00000    0000010111111111  23


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      +|++.+...+....+.++| ..|||++|.||.++|   .+|+|++|||+.||+|.++|++.++||+++||..+.
T Consensus       116 ~~~~~~~~~e~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~  185 (187)
T TIGR02948       116 PPEDQVISLELRDTIQQEI-QALPPKYRMVIVLKY---MEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLR  185 (187)
T ss_pred             CHHHHHHHHHHHHHHHHHH-HhCCHHHhHHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhh
Confidence            5666666667777899999 899999999999998   799999999999999999999999999999999875

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

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.89  E-value=7.3e-22  Score=185.58  Aligned_cols=160  Identities=16%  Similarity=0.164  Sum_probs=130.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|+..|+..|.+.|+.+|.++.++..+++|++||+|+++|+++++|++..+ .|.+|++..++|.+.+++++..+. .. 
T Consensus        19 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~R~~~~~-~~-   95 (179)
T PRK12514         19 DAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHAIDRLRARKAV-AV-   95 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHHHHHhcCCc-cc-
Confidence            999999999999999999999999999999999999999999999986544 699999999999988888765320 00 


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                         .++.             ..+ ..+.  ..
T Consensus        96 ---------------------------------------------------~~~~-------------~~~-~~~~--~~  108 (179)
T PRK12514         96 ---------------------------------------------------DIDE-------------AHD-LADP--SP  108 (179)
T ss_pred             ---------------------------------------------------cccc-------------chh-cccc--CC
Confidence                                                               0000             000 0010  12


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      +|++.+...+....|..+| ..||++++.||.++|   ++|+|++|||+.||+|.++|++.++||+++||+++.
T Consensus       109 ~~e~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~  178 (179)
T PRK12514        109 GPEAEVIAGDEGQRIDACL-EELEKDRAAAVRRAY---LEGLSYKELAERHDVPLNTMRTWLRRSLLKLRECLS  178 (179)
T ss_pred             CHHHHHHhHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHHhc
Confidence            4555555555556788999 899999999999999   899999999999999999999999999999999874

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.89  E-value=7.4e-22  Score=186.80  Aligned_cols=162  Identities=19%  Similarity=0.213  Sum_probs=131.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .+++.|+..|.++|+++|.++.++..++||++||+|+++|+++++|++.++ .|.+|++..+++.+.+++++..+...  
T Consensus        25 ~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d~~R~~~~~~~--  101 (187)
T PRK12534         25 HAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAIDHLRANAPQRR--  101 (187)
T ss_pred             HHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHHHhcccccc--
Confidence            999999999999999999999999999999999999999999999998654 58899999999998888876532000  


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                       ..+++.             ..+.. +.  ..
T Consensus       102 -------------------------------------------------~~~~~~-------------~~~~~-~~--~~  116 (187)
T PRK12534        102 -------------------------------------------------NVALDD-------------AGELR-AA--DA  116 (187)
T ss_pred             -------------------------------------------------cccccc-------------hhhhc-cc--cC
Confidence                                                             000000             00000 00  11


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      +|++.....+....+..+| ..||++++.||.++|   .+|+|++|||+.||+|.++|+++++||+++||..+.
T Consensus       117 ~~~~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~  186 (187)
T PRK12534        117 SPLERTERASTRRRIDHCL-AELEPPRSELIRTAF---FEGITYEELAARTDTPIGTVKSWIRRGLAKLKACLE  186 (187)
T ss_pred             ChhhHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHHHc
Confidence            3444555566778899999 899999999999999   899999999999999999999999999999999874

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.88  E-value=2e-21  Score=182.99  Aligned_cols=168  Identities=24%  Similarity=0.266  Sum_probs=134.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|+..|+..|.++|+++|+++.++..+++|++||++++||+++++|++..  .|.+|++..+++.+.+++++..+..   
T Consensus        18 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~d~~R~~~~~~---   92 (187)
T PRK09641         18 NAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTIDRLRKRKPDY---   92 (187)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHHHHHHhcCccc---
Confidence            99999999999999999999999999999999999999999999999753  6999999999999888887653210   


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                         +++...    .+++.....+.+.+.  ..
T Consensus        93 ---------------------------------------------------~~~~~~----~~~~~~~~~~~~~~~--~~  115 (187)
T PRK09641         93 ---------------------------------------------------YLDAEV----AGTEGLTMYSQLAAD--DA  115 (187)
T ss_pred             ---------------------------------------------------cccccc----cCCcchhhhcccccC--cC
Confidence                                                               000000    000111111111111  23


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      +|++.+...+....+..+| ..||++++.||.++|   .+|+|++|||+.||||.++|++.++||+++||+.+.
T Consensus       116 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~il~l~~---~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~  185 (187)
T PRK09641        116 LPEEQVVSLELQETIQEAI-LQLPEKYRTVIVLKY---IEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLR  185 (187)
T ss_pred             CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHhhhHH---hhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence            5666667777778899999 899999999999999   799999999999999999999999999999999875

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.88  E-value=1e-21  Score=179.65  Aligned_cols=150  Identities=20%  Similarity=0.212  Sum_probs=123.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|++.|.++|+.+++++ ++..++||++||+++++|+++++|++..+ +|.+|++..+++.+.++++++.+..   
T Consensus         4 ~af~~l~~~y~~~l~~~~~~~-~~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~~~---   78 (154)
T PRK06759          4 ATFTEAVVLYEGLIVNQIKKL-GIYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQ---   78 (154)
T ss_pred             ccHHHHHHHHHHHHHHHHHHh-CCcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHhhc---
Confidence            799999999999999999886 55679999999999999999999998666 7999999999999999988763100   


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                           +..      . .             .+
T Consensus        79 -----------------------------------------------------~~~------~-~-------------~~   85 (154)
T PRK06759         79 -----------------------------------------------------EKC------V-C-------------VG   85 (154)
T ss_pred             -----------------------------------------------------ccc------c-c-------------cC
Confidence                                                                 000      0 0             01


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA  495 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~  495 (508)
                      +|++.....+....|..+| ..||+++|.||.++|   ++|+|.+|||+.||+|.++|++++.||+++||+.
T Consensus        86 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~ii~l~~---~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~  153 (154)
T PRK06759         86 EYEDHFHFEDVEMKVKDFM-SVLDEKEKYIIFERF---FVGKTMGEIALETEMTYYQVRWIYRQALEKMRNS  153 (154)
T ss_pred             CCcccccHHHHHHHHHHHH-HhCCHHHHHHHHHHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence            1222233344567788999 899999999999999   8999999999999999999999999999999963

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.88  E-value=1.8e-21  Score=181.31  Aligned_cols=168  Identities=24%  Similarity=0.231  Sum_probs=134.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|+++|+..|.++|+.++++|.+++.+.+|++||++++||+++++|+  .+.+|.+|++..+++.+.+++++..+....+
T Consensus        10 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~r~~~~~~~~~   87 (182)
T PRK09652         10 AAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYLRKQGRRPPAS   87 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHHHcccCCCCcc
Confidence            89999999999999999999999999999999999999999999999  3458999999999999988887654311000


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                         +++.      ...++....+.+.+   ..
T Consensus        88 ---------------------------------------------------~~~~------~~~~~~~~~~~~~~---~~  107 (182)
T PRK09652         88 ---------------------------------------------------DVDA------EEAEDFDLADALRD---IS  107 (182)
T ss_pred             ---------------------------------------------------cccc------cccccccccccccc---cc
Confidence                                                               0000      00000001111111   23


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      +|++.+...+....+..+| ..|||+++.||.++|   .+|+|++|||+.||+|+.+|++.+++|+++||+.+.
T Consensus       108 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~  177 (182)
T PRK09652        108 TPENELLSAELEQRVRAAI-ESLPEELRTAITLRE---IEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ  177 (182)
T ss_pred             ChHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            5676777777788899999 899999999999998   799999999999999999999999999999999885

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=1.5e-21  Score=192.66  Aligned_cols=162  Identities=19%  Similarity=0.224  Sum_probs=132.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.+.|+.++.++.++..++||++||+|+.+|+.+++|++..+ .|.+|++..+++.+.+++++..+. .  
T Consensus        63 ~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~id~~Rk~~~~-~--  138 (233)
T PRK12538         63 AAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRCIDLRRKPRTE-N--  138 (233)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHHHHHHHhhccc-c--
Confidence            999999999999999999999999999999999999999999999986544 799999999999888887653210 0  


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                          ++.             ..+. .+.  ..
T Consensus       139 ----------------------------------------------------~~~-------------~~~~-~~~--~~  150 (233)
T PRK12538        139 ----------------------------------------------------VDA-------------VPEV-ADG--KP  150 (233)
T ss_pred             ----------------------------------------------------ccc-------------cccc-ccC--CC
Confidence                                                                000             0000 000  12


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM  501 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l  501 (508)
                      ++++.+...+....|..+| ..||+++|+||.|+|   ++|+|++|||+.||+|.++|+++++||+++||+.+...+.
T Consensus       151 ~~~~~~~~~e~~~~l~~~L-~~Lp~~~R~v~~L~~---~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~~~~~  224 (233)
T PRK12538        151 DAVSVIERNELSDLLEAAM-QRLPEQQRIAVILSY---HENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRRHER  224 (233)
T ss_pred             CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHhhhHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhhh
Confidence            3444455566667889999 899999999999999   8999999999999999999999999999999999976553

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.88  E-value=2.2e-21  Score=183.21  Aligned_cols=162  Identities=18%  Similarity=0.260  Sum_probs=127.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.+.|+.+|+++.+++.+++|++||+++++|+++++|++..+ .|.+|++..+++.+.+++++..+...  
T Consensus        23 ~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d~~rk~~~~~~--   99 (186)
T PRK13919         23 EALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAAVDHVRRRAARPQ--   99 (186)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHHHHHHHhhhcccc--
Confidence            999999999999999999999999999999999999999999999987543 69999999999999998876532000  


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                       .  ++..      . .....   . +.   .
T Consensus       100 -------------------------------------------------~--~~~~------~-~~~~~---~-~~---~  114 (186)
T PRK13919        100 -------------------------------------------------P--LEPD------E-REPEA---F-DL---P  114 (186)
T ss_pred             -------------------------------------------------c--cccc------c-ccccc---c-cC---C
Confidence                                                             0  0000      0 00000   0 00   0


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      +|.......+..+.|..+| +.||++++.||.++|   .+|+|++|||+.||+|.++|+.+++||+++||..+.
T Consensus       115 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l~  184 (186)
T PRK13919        115 GPGLDEEGHLDRTRLGRAL-KALSPEERRVIEVLY---YQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLR  184 (186)
T ss_pred             CccccHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence            1111122333456788999 899999999999999   899999999999999999999999999999999875

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.88  E-value=3.9e-21  Score=181.62  Aligned_cols=159  Identities=19%  Similarity=0.279  Sum_probs=129.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.+.++.++.++.++..+++|++||+|+.+|+.+++|++..+ .|.+|++..+++.+.+++++..+...  
T Consensus        23 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~~~d~~r~~~~~~~--   99 (182)
T PRK12537         23 RALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHLALNVLRDTRREVV--   99 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHHHHHhccccCc--
Confidence            999999999999999999999999999999999999999999999986443 69999999999999999887642100  


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                          .+..        ..    +...+   ..
T Consensus       100 ----------------------------------------------------~~~~--------~~----~~~~~---~~  112 (182)
T PRK12537        100 ----------------------------------------------------LDDD--------AE----ETAQT---LH  112 (182)
T ss_pred             ----------------------------------------------------cccc--------hh----hhccc---cc
Confidence                                                                0000        00    00000   11


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      ++++..+..+....+..+| +.||+++|.||.++|   .+|+|++|||+.||+|.++|+..++||+++||..+
T Consensus       113 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l  181 (182)
T PRK12537        113 EIIDDFDLWANSGKIHRCL-EQLEPARRNCILHAY---VDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRECM  181 (182)
T ss_pred             chHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHHh
Confidence            2333344445567788999 899999999999999   89999999999999999999999999999999876

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.87  E-value=6e-21  Score=180.20  Aligned_cols=168  Identities=21%  Similarity=0.228  Sum_probs=133.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.+.|+.+|+++.++..+++|++||+|+++|+.+++|++.  .+|.+|++..+++.+.+++++..+.....
T Consensus        20 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~~~~~r~~~r~~~~~   97 (190)
T TIGR02939        20 QAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTAKNHLVAQGRRPPTS   97 (190)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHHHHHHHHhccCCCcc
Confidence            8999999999999999999999999999999999999999999999975  36999999999998888887554311000


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                       ..+.+.          .....+ ........
T Consensus        98 -------------------------------------------------~~~~~~----------~~~~~~-~~~~~~~~  117 (190)
T TIGR02939        98 -------------------------------------------------DVEIED----------AEHFEG-ADRLREID  117 (190)
T ss_pred             -------------------------------------------------cccccc----------hhhhcc-cccccccC
Confidence                                                             000000          000000 00000013


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      +|++.+...+....+..+| ..||+++|.||.++|   .+|+|++|||+.||+|.++|++.++||+++||+.+.
T Consensus       118 ~~e~~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~  187 (190)
T TIGR02939       118 TPERLLLSRELEQTVMRAV-EALPEDLRTAITLRE---LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRLR  187 (190)
T ss_pred             ChHHHHHHHHHHHHHHHHH-HcCCHHHhhhhhhhh---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence            5666666777778899999 899999999999999   899999999999999999999999999999999885

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.

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=7.2e-21  Score=183.82  Aligned_cols=167  Identities=17%  Similarity=0.184  Sum_probs=130.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|+++|+..|.+.|+.++.++.++..+++|++||+|+.+|++++.|++..+ .|.+|++.++++.+.+++++..+.....
T Consensus        38 ~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d~~Rk~~~~~~~~  116 (206)
T PRK12526         38 QAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFDMLRKIKAKKEQN  116 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHHHHHHhccccccc
Confidence            999999999999999999999999899999999999999999999997665 5999999999999999988764311000


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                          ++.         +.....+.+.+.  ..
T Consensus       117 ----------------------------------------------------~~~---------~~~~~~~~~~~~--~~  133 (206)
T PRK12526        117 ----------------------------------------------------LGD---------DIWPIEQALAES--QS  133 (206)
T ss_pred             ----------------------------------------------------ccc---------ccchhhhhcccc--cC
Confidence                                                                000         000000001111  01


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                      .+. ..........|..+| ..||+++|.||.++|   ++|+|++|||+.||+|.++|+.++++|+++||..+...
T Consensus       134 ~~~-~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~  204 (206)
T PRK12526        134 ESE-EFSDHLMDKQILSYI-EKLPEAQQTVVKGVY---FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGEQ  204 (206)
T ss_pred             chH-HHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhc
Confidence            122 222333446788999 899999999999999   89999999999999999999999999999999998754

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.87  E-value=4.9e-21  Score=182.16  Aligned_cols=159  Identities=22%  Similarity=0.211  Sum_probs=130.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCC---CCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMG---ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g---~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~i  340 (508)
                      .|++.|+..|.+.|+.++.++.+++   .+++|++||+++++|+++++|+++.+ .|.+|++..++|.+.+++++..+..
T Consensus        18 ~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~iarn~~~d~~rk~~~~~   96 (189)
T PRK06811         18 KALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAISKYKAIDYKRKLTKNN   96 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHHHHHHHHHHHHhcccc
Confidence            9999999999999999999998753   57999999999999999999997554 7999999999999999988764310


Q ss_pred             cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccccccc
Q 010521          341 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNR  420 (508)
Q Consensus       341 rip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~  420 (508)
                      ..                                                   .+.+.                ...+. 
T Consensus        97 ~~---------------------------------------------------~~~~~----------------~~~~~-  108 (189)
T PRK06811         97 EI---------------------------------------------------DSIDE----------------FILIS-  108 (189)
T ss_pred             cc---------------------------------------------------ccchh----------------hhhcc-
Confidence            00                                                   00000                00000 


Q ss_pred             CCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          421 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       421 ~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                       .++|++.+...+....|.++| ..|||++|.||.|+|   .+|+|.+|||+.||+|..+|++.++||+++||+..
T Consensus       109 -~~~~~~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~  179 (189)
T PRK06811        109 -EESIENEIILKENKEEILKLI-NDLEKLDREIFIRRY---LLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK  179 (189)
T ss_pred             -cCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence             125666667777778899999 899999999999998   79999999999999999999999999999999753

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.87  E-value=6.7e-21  Score=181.96  Aligned_cols=187  Identities=19%  Similarity=0.199  Sum_probs=143.7

Q ss_pred             CCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 010521          204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR  283 (508)
Q Consensus       204 ~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkr  283 (508)
                      |+.+..+...|+.+++.||.                                        .|++.|+..|.+.|+.+|.+
T Consensus         7 ~~~~~~~~~~li~~~~~~d~----------------------------------------~af~~l~~~y~~~l~~~~~~   46 (194)
T PRK12531          7 HTFGRQEWLECMEKVKSRDK----------------------------------------QAFALVFSYYAPKLKQFAMK   46 (194)
T ss_pred             cccccHhHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHHHHH
Confidence            44566677778888888887                                        99999999999999999999


Q ss_pred             hcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHc
Q 010521          284 YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK  363 (508)
Q Consensus       284 Y~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~~  363 (508)
                      +.++..+++|++||+|+.+|+.+++|++..+ .|.+|++..++|.+.+++++..+.....                    
T Consensus        47 ~~~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld~~Rk~~~~~~~~--------------------  105 (194)
T PRK12531         47 HVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFDLLRKQKGKDLHI--------------------  105 (194)
T ss_pred             HhCCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHHHHHHhccccccc--------------------
Confidence            9999899999999999999999999987544 6999999999999999988764210000                    


Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHHH
Q 010521          364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLII  443 (508)
Q Consensus       364 Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~  443 (508)
                                                     ..+..       .........+.+   ...|+    .....+.+.++| 
T Consensus       106 -------------------------------~~~~~-------~~~~~~~~~~~~---~~~~e----~~~~~~~l~~~l-  139 (194)
T PRK12531        106 -------------------------------HADDI-------WPSDYYPPDLVD---HYSPE----QDMLKEQVMKFL-  139 (194)
T ss_pred             -------------------------------chhhc-------cccccccccccc---ccCHH----HHHHHHHHHHHH-
Confidence                                           00000       000000000000   01222    223345688888 


Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                      ..||+++|.||.|+|   .+|+|++|||+.||+|.++|+..+++|+++||..+....
T Consensus       140 ~~Lp~~~r~v~~l~~---~eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~~~~  193 (194)
T PRK12531        140 DRLPKAQRDVLQAVY---LEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDAES  193 (194)
T ss_pred             HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhhcc
Confidence            899999999999999   899999999999999999999999999999999987653

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.86  E-value=5.8e-21  Score=181.38  Aligned_cols=173  Identities=18%  Similarity=0.247  Sum_probs=136.4

Q ss_pred             cChHHHHHhhhh----hHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHH
Q 010521          250 ISRPELQSILME----CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWI  325 (508)
Q Consensus       250 ~s~~~L~~~l~e----~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wI  325 (508)
                      ++.++|...++.    ++.|++.|+..|.+.|+++|.+|.++..+++|++||+|+.+|+++++|++.  .+|.+|++.++
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            566677777763    789999999999999999999999999999999999999999999999863  37999999999


Q ss_pred             HHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCC
Q 010521          326 RQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLN  405 (508)
Q Consensus       326 R~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~  405 (508)
                      ++.+.+++++..+.....                                                    .+.       
T Consensus        86 ~n~~~d~~R~~~~~~~~~----------------------------------------------------~~~-------  106 (188)
T PRK09640         86 YNECITQYRKERRKRRLM----------------------------------------------------DAL-------  106 (188)
T ss_pred             HHHHHHHHHHhcccccCc----------------------------------------------------chh-------
Confidence            999999988653210000                                                    000       


Q ss_pred             CCCCCccccccccccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 010521          406 GLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVG  485 (508)
Q Consensus       406 ~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~  485 (508)
                           .. +...+.    .+ +.....+....|..+| ..||+++|.||.++|   .+|+|++|||+.||||.++|+..+
T Consensus       107 -----~~-~~~~~~----~~-~~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l  171 (188)
T PRK09640        107 -----SL-DPLEEA----SE-EKAPKPEERGGLDRWL-VHVNPIDREILVLRF---VAELEFQEIADIMHMGLSATKMRY  171 (188)
T ss_pred             -----hh-cccccc----cc-cccccHHHHHHHHHHH-HhcChhheeeeeeHH---hcCCCHHHHHHHHCCCHHHHHHHH
Confidence                 00 000000    00 1111234456788899 899999999999999   799999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 010521          486 LVALEKLKHAARK  498 (508)
Q Consensus       486 ~rALkKLR~~L~~  498 (508)
                      .||+++||..+..
T Consensus       172 ~Ra~~~Lr~~l~~  184 (188)
T PRK09640        172 KRALDKLREKFAG  184 (188)
T ss_pred             HHHHHHHHHHHHH
Confidence            9999999998853

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=1.8e-20  Score=174.15  Aligned_cols=165  Identities=17%  Similarity=0.136  Sum_probs=136.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (508)
Q Consensus       263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri  342 (508)
                      ..|++.|++.|.+.|+++|+++.++..+++|++||+++++|+++++|+  .+..|.+|++..+++.+.+++++..+....
T Consensus        12 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~~r~~~~~~~~   89 (179)
T PRK11924         12 KEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDLLRRRRREKAV   89 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHHHHhccccccc
Confidence            399999999999999999999999999999999999999999999998  344799999999999988888765431000


Q ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521          343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE  422 (508)
Q Consensus       343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e  422 (508)
                                                                         . .+.         ..    +...+. ..
T Consensus        90 ---------------------------------------------------~-~~~---------~~----~~~~~~-~~  103 (179)
T PRK11924         90 ---------------------------------------------------L-SDD---------AL----EPEFAE-TA  103 (179)
T ss_pred             ---------------------------------------------------C-ccc---------cc----ccccCC-cc
Confidence                                                               0 000         00    000000 13


Q ss_pred             CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                      ++|++.+...+....+..+| ..||++++.||.++|   .+|+|++|||+.||+|+.+|++++++|+++||+.+...
T Consensus       104 ~~~e~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~~  176 (179)
T PRK11924        104 ETPEAALLAKDDLARIDRCL-DALPVKQREVFLLRY---VEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEAQ  176 (179)
T ss_pred             CCHHHHHhhHHHHHHHHHHH-HhCCHHHHHHhhHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            46778888888889999999 899999999999999   79999999999999999999999999999999988754

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=4.5e-21  Score=181.50  Aligned_cols=174  Identities=18%  Similarity=0.163  Sum_probs=137.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccc
Q 010521          261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (508)
Q Consensus       261 e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~i  340 (508)
                      ++..|++.|+..|.+.++.+|.+++++..+++|++||+|+.+|+.+.+|++..+..|.||++..++|.+.+++++..+..
T Consensus         6 gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk~~~~~   85 (185)
T PRK12542          6 NDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRHE   85 (185)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence            34599999999999999999999999999999999999999999999998654447999999999999999887764200


Q ss_pred             cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccccccc
Q 010521          341 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNR  420 (508)
Q Consensus       341 rip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~  420 (508)
                      .                  .                                   .+..        ..    +..... 
T Consensus        86 ~------------------~-----------------------------------~~~~--------~~----~~~~~~-   99 (185)
T PRK12542         86 T------------------F-----------------------------------LEEY--------ER----ESIEAV-   99 (185)
T ss_pred             h------------------h-----------------------------------hhhc--------cc----cchhhh-
Confidence            0                  0                                   0000        00    000000 


Q ss_pred             CCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          421 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       421 ~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                       .++|++.....+....|..+| ..|||++|+||.|+|   ++|+|++|||+.||+|.+||++.++||+++||+.+....
T Consensus       100 -~~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~  174 (185)
T PRK12542        100 -DENIEEWEKRKMSEVQIDTLL-KELNESNRQVFKYKV---FYNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGIQ  174 (185)
T ss_pred             -hccHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcccc
Confidence             112333333344456788999 899999999999998   899999999999999999999999999999999998888


Q ss_pred             HHHhh
Q 010521          501 MEAML  505 (508)
Q Consensus       501 l~~~l  505 (508)
                      ...|+
T Consensus       175 ~~~~~  179 (185)
T PRK12542        175 HDEFK  179 (185)
T ss_pred             hHHHH
Confidence            77774

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=1.8e-20  Score=178.02  Aligned_cols=163  Identities=20%  Similarity=0.232  Sum_probs=133.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.+.++.++.++.++..+++|++||+|+.+|+++++|++.  ..|.+|++..+++.+.+++++..+.   +
T Consensus        22 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~r~~~~~---~   96 (189)
T PRK12515         22 TAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFKALSALRRRKHE---E   96 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHHHHHHHHccCCC---C
Confidence            9999999999999999999999999999999999999999999999964  3799999999999888888654210   0


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                          +..           +.. ..+.+.  .+
T Consensus        97 ----------------------------------------------------~~~-----------~~~-~~~~~~--~~  110 (189)
T PRK12515         97 ----------------------------------------------------IDD-----------EAA-AAIEDG--AD  110 (189)
T ss_pred             ----------------------------------------------------Ccc-----------ccc-cccCCC--CC
Confidence                                                                000           000 001111  12


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM  501 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l  501 (508)
                      +|+......+....+..+| +.||+++|.||.++|   .+|+|++|||+.||+|..+|+++++||+++||+.+...+.
T Consensus       111 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~  184 (189)
T PRK12515        111 TPEVALQKSDTSAALRACL-AKLSPAHREIIDLVY---YHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLKAAGV  184 (189)
T ss_pred             CHHHHHHhHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhcc
Confidence            4555555666677889999 899999999999999   8999999999999999999999999999999999987643

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.86  E-value=3.6e-20  Score=176.96  Aligned_cols=159  Identities=14%  Similarity=0.135  Sum_probs=131.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .+++.|+..|.+.|+++|.++.++..++||++||+|+.+|+.+++|++..  +|.+|++..+++.+.+++++..+...  
T Consensus        27 ~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~~~d~~Rk~~~~~~--  102 (192)
T PRK09643         27 YAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNACLDRLRRAKARPT--  102 (192)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHHHHHHHHccccCCC--
Confidence            99999999999999999999999999999999999999999999999653  69999999999999999887542100  


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                        .+++.          ..   + .     ..
T Consensus       103 --------------------------------------------------~~~~~----------~~---~-~-----~~  113 (192)
T PRK09643        103 --------------------------------------------------VPLDD----------VY---P-V-----AQ  113 (192)
T ss_pred             --------------------------------------------------CCccc----------cc---c-c-----cC
Confidence                                                              00000          00   0 0     01


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                      +|.+.+...+....+..+| +.||+++|.||.|+|   .+|+|++|||+.||+|..+|++.+.+|+++||+.+...
T Consensus       114 ~~~~~~~~~e~~~~l~~~l-~~Lp~~~r~i~~l~~---~~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~~~  185 (192)
T PRK09643        114 LERDPTARVETALAVQRAL-MRLPVEQRAALVAVD---MQGYSVADAARMLGVAEGTVKSRCARGRARLAELLGYL  185 (192)
T ss_pred             CcccHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence            2333344556677899999 899999999999999   89999999999999999999999999999999998753

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.85  E-value=2.3e-20  Score=174.51  Aligned_cols=158  Identities=15%  Similarity=0.123  Sum_probs=126.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.+.|+.+|.++.++..+++|++||+|+++|++++.|++.  .+|.+|++..+++.+.+++++..+.....
T Consensus        18 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~r~~~~~~~~~   95 (176)
T PRK09638         18 AALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRLYKDHLRKQKREKLRL   95 (176)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHHhccccchh
Confidence            9999999999999999999999999999999999999999999999864  37999999999999999988764210000


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                +                       ...+.                 ..+.    
T Consensus        96 --------------------------~-----------------------~~~~~-----------------~~~~----  105 (176)
T PRK09638         96 --------------------------Q-----------------------RAKEE-----------------TLRK----  105 (176)
T ss_pred             --------------------------h-----------------------hcccc-----------------cCCc----
Confidence                                      0                       00000                 0000    


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      ...+..........|..+| ..||+++|.||.++|   .+|+|++|||+.||+|..+|++.++||+++||+.+.
T Consensus       106 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~l~  175 (176)
T PRK09638        106 EKWEAAIKGAEWSEMLDAL-SKLDPEFRAPVILKH---YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEWG  175 (176)
T ss_pred             cchHHHHHhhhHHHHHHHH-HcCCHHHhheeeehh---hcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHHhc
Confidence            0001122334456688899 899999999999998   799999999999999999999999999999999773

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

Probab=99.85  E-value=3.2e-20  Score=174.84  Aligned_cols=179  Identities=18%  Similarity=0.140  Sum_probs=135.9

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHhc----CCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhc
Q 010521          262 CSLAREKLVMSNVRLVMSIAQRYD----NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS  337 (508)
Q Consensus       262 ~~~A~e~LIe~yl~LV~sIAkrY~----~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~  337 (508)
                      +..|++.|+..|.+.|+.+|++|.    ++..+++|++||+++.+|+++.+|++..+.+|.+|++..+++.+.+++++..
T Consensus         5 ~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~~~   84 (189)
T TIGR02984         5 DQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRRHL   84 (189)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHHHH
Confidence            349999999999999999999975    3567899999999999999999998765568999999999999998887652


Q ss_pred             c-cccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccc
Q 010521          338 R-TLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYI  416 (508)
Q Consensus       338 R-~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i  416 (508)
                      + ..+.+                                               ....+++...   ..++....+.+.+
T Consensus        85 ~~~~r~~-----------------------------------------------~~~~~~~~~~---~~~~~~~~~~~~~  114 (189)
T TIGR02984        85 GAQKRDI-----------------------------------------------RREQSLDAGG---RLDESSVRLAAQL  114 (189)
T ss_pred             HHHhhhc-----------------------------------------------ccccCCCccc---ccCCcchhHHHHc
Confidence            1 00000                                               0011122110   0001111222223


Q ss_pred             ccccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          417 ADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       417 ~d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      .+.  .++|++.+...+....|..+| ..|||++|.||.++|   .+|+|++|||+.||||+++|++.++||+++||+.+
T Consensus       115 ~~~--~~~~~~~~~~~e~~~~l~~~l-~~L~~~~r~vi~l~~---~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~l  188 (189)
T TIGR02984       115 AAD--GPSPSQVAARREAAVRLAQAL-AKLPEDYREVILLRH---LEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQIL  188 (189)
T ss_pred             cCC--CCCHHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            222  235677777777778899999 899999999999999   79999999999999999999999999999999876

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).

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.85  E-value=4.1e-20  Score=174.22  Aligned_cols=165  Identities=17%  Similarity=0.165  Sum_probs=132.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccc
Q 010521          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR  341 (508)
Q Consensus       262 ~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~ir  341 (508)
                      +..|++.|+..|.+.|+.++.+|.++..+++|++||+|+.+|+++.+|++..  .|.+|++..+++.+.++++...+..+
T Consensus         5 d~~af~~l~~~~~~~l~~~~~~~~~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~~~~~~   82 (179)
T PRK12543          5 DQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKRWRRFR   82 (179)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhhccccc
Confidence            4489999999999999999999999999999999999999999999999764  69999999999988777655431000


Q ss_pred             ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccC
Q 010521          342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV  421 (508)
Q Consensus       342 ip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~  421 (508)
                                                                           .++..        .  ...    +...
T Consensus        83 -----------------------------------------------------~~~~~--------~--~~~----~~~~   95 (179)
T PRK12543         83 -----------------------------------------------------IFEKA--------E--EQR----KPVS   95 (179)
T ss_pred             -----------------------------------------------------ccccc--------c--ccc----cccc
Confidence                                                                 00000        0  000    0000


Q ss_pred             CCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          422 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       422 e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                      ...|++ +...+....|..+| ..|||++|.||.|+|   .+|+|++|||+.||+|.++|+..+++|+++||+.+...+
T Consensus        96 ~~~~~~-~~~~~~~~~l~~~l-~~Lp~~~r~i~~l~~---~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~  169 (179)
T PRK12543         96 IDFSED-VLSKESNQELIELI-HKLPYKLRQVIILRY---LHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEE  169 (179)
T ss_pred             ccChHH-HHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            123444 56667778899999 899999999999998   899999999999999999999999999999999997554

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

Probab=99.85  E-value=4.6e-20  Score=183.44  Aligned_cols=168  Identities=16%  Similarity=0.159  Sum_probs=132.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHH-------hhhccCCCCCCcchhHHHHHHHHHHHHHHHHh
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLR-------GIEKFDSSKGFKISTYVYWWIRQGVSRALVEN  336 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLir-------AiekFDperG~rFsTYA~~wIR~~I~~~Ird~  336 (508)
                      .|++.|+..|.+.|+.++.++.++..++||++||+|+.+|.       .+.+|++..  .|.||++..++|.+.+++++.
T Consensus        39 ~Af~~L~~~y~~~l~~~~~~~~~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~~--~~~tWL~~Ia~N~~id~lRk~  116 (244)
T TIGR03001        39 AALAALERHVLSKVPARLAGLRPPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGRG--PLLSWVRIVATRIALELQAQE  116 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhccchhhhhhccCCCC--chHhHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999994       788898643  699999999999999998765


Q ss_pred             cccccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccc
Q 010521          337 SRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYI  416 (508)
Q Consensus       337 ~R~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i  416 (508)
                      .+...                                                      ++.          .....+. 
T Consensus       117 ~r~~~------------------------------------------------------~~~----------~~~~~~~-  131 (244)
T TIGR03001       117 RRHSP------------------------------------------------------VEE----------PTELAAL-  131 (244)
T ss_pred             cccCc------------------------------------------------------ccc----------ccccccc-
Confidence            32100                                                      000          0000000 


Q ss_pred             ccccCCCCccchHHH----HHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521          417 ADNRVENNPWHGVDD----WALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL  492 (508)
Q Consensus       417 ~d~~~e~~Pe~~ve~----~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKL  492 (508)
                      .+.  ..+|++.+..    .+..+.|.++| ++||+++|+||.|+|   .+|+|++|||+.||||.+||+..+++|+++|
T Consensus       132 ~~~--~~~~e~~~~~~e~~~e~~~~l~~aL-~~Lp~~~R~v~~L~~---~eg~S~~EIA~~Lgis~~TVk~rl~RAr~~L  205 (244)
T TIGR03001       132 PAP--GSDPELDLLRERYRQDFRQALREAL-AALSERERHLLRLHF---VDGLSMDRIGAMYQVHRSTVSRWVAQARERL  205 (244)
T ss_pred             cCC--CCCHHHHHHHHhhHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            011  1134433332    23556789999 899999999999999   8999999999999999999999999999999


Q ss_pred             HHHHHHhhHHHh
Q 010521          493 KHAARKKKMEAM  504 (508)
Q Consensus       493 R~~L~~~~l~~~  504 (508)
                      |+.+++...+.|
T Consensus       206 r~~l~~~~~~~~  217 (244)
T TIGR03001       206 LERTRRRLAERL  217 (244)
T ss_pred             HHHHHHHHHHhc
Confidence            999988766554

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.

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

Probab=99.85  E-value=4.8e-20  Score=171.70  Aligned_cols=153  Identities=20%  Similarity=0.190  Sum_probs=123.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.+.|+++|.++.++..+++|++||+++.+|+.+++|++..  +|.+|++..+++.+.+++++..+.    
T Consensus        16 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~----   89 (169)
T TIGR02954        16 PAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINECIDLLKKKKKV----   89 (169)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHHHHHHHHhcCCc----
Confidence            99999999999999999999999999999999999999999999999753  699999999999999888765320    


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                        .+++..          ...    .+.    
T Consensus        90 --------------------------------------------------~~~~~~----------~~~----~~~----  101 (169)
T TIGR02954        90 --------------------------------------------------IPFDPN----------TSI----EKG----  101 (169)
T ss_pred             --------------------------------------------------Cccccc----------ccc----ccc----
Confidence                                                              000000          000    000    


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      ++.  .+. +....+..+| ..||+++|+||.++|   ++|+|.+|||+.||+|.++|+..++||+++||+.+.
T Consensus       102 ~~~--~~~-~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l~  168 (169)
T TIGR02954       102 ECE--THA-DSRLDLYKAI-DTLNDKYQTAIILRY---YHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKRLE  168 (169)
T ss_pred             hhh--hch-HHHHHHHHHH-HhCCHHHhHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence            011  011 1123688888 899999999999999   899999999999999999999999999999999874

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=99.85  E-value=6e-20  Score=173.39  Aligned_cols=158  Identities=19%  Similarity=0.174  Sum_probs=124.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcC-CCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDN-MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~-~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri  342 (508)
                      .|++.|+..|.+.|+.++.++.+ +..+++|++||+|+++|+.++.|++..  +|.+|++..++|.+.+++++..+....
T Consensus        21 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~~~~~~~~~~--~~~~wl~~iarN~~~d~~Rk~~~~~~~   98 (181)
T PRK12536         21 AAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRADQ--PLTAWVHAIARYKLMDFLRSRARREAL   98 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHHHHHHHHHhccccc
Confidence            99999999999999999998764 578999999999999999999999743  699999999999999998876421000


Q ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521          343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE  422 (508)
Q Consensus       343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e  422 (508)
                                                                        ..+++.             ..+...+    
T Consensus        99 --------------------------------------------------~~~~~~-------------~~~~~~~----  111 (181)
T PRK12536         99 --------------------------------------------------HDPLDD-------------ESELFAT----  111 (181)
T ss_pred             --------------------------------------------------cCCccc-------------hhhhcCC----
Confidence                                                              000000             0000000    


Q ss_pred             CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      ..++    ..+....+.++| ..||++++.||.++|   .+|+|.+|||+.||+|+++|+..+++|+++||+.+..
T Consensus       112 ~~~~----~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l~~  179 (181)
T PRK12536        112 SDDE----AAEARRDLGKLL-EQLPDRQRLPIVHVK---LEGLSVAETAQLTGLSESAVKVGIHRGLKALAAKIRG  179 (181)
T ss_pred             CCcc----hHHHHHHHHHHH-HHCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence            0111    123445688999 899999999999999   8999999999999999999999999999999998864

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.85  E-value=4.1e-20  Score=175.54  Aligned_cols=177  Identities=18%  Similarity=0.132  Sum_probs=137.8

Q ss_pred             CCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 010521          204 ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQR  283 (508)
Q Consensus       204 ~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkr  283 (508)
                      |-.+.+++..|+.++++||.                                        .|++.||..|.+.++.++. 
T Consensus         4 ~~~~~~~~~~l~~~~~~gd~----------------------------------------~af~~l~~~~~~~l~~~~~-   42 (185)
T PRK09649          4 TASDDEAVTALALSAAKGNG----------------------------------------RALEAFIKATQQDVWRFVA-   42 (185)
T ss_pred             cccccHHHHHHHHHHHccCH----------------------------------------HHHHHHHHHHHHHHHHHHH-
Confidence            44556778889999999997                                        9999999999999999995 


Q ss_pred             hcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHc
Q 010521          284 YDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEK  363 (508)
Q Consensus       284 Y~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~~  363 (508)
                      +.++..+++|++||+|+.+|+.+++|++.  ..|.+|++..++|.+.+++++..+.....                    
T Consensus        43 ~~~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d~~Rk~~~~~~~~--------------------  100 (185)
T PRK09649         43 YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVADHIRHVRSRPRTT--------------------  100 (185)
T ss_pred             HhCCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHHHHHHhccccccc--------------------
Confidence            68888899999999999999999999864  36999999999999999988653210000                    


Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHHH
Q 010521          364 GVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLII  443 (508)
Q Consensus       364 Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~  443 (508)
                                                      .+.         .    .+.+.+      +.......+....+..+| 
T Consensus       101 --------------------------------~~~---------~----~~~~~~------~~~~~~~~e~~~~l~~~l-  128 (185)
T PRK09649        101 --------------------------------RGA---------R----PEHLID------GDRHARGFEDLVEVTTMI-  128 (185)
T ss_pred             --------------------------------ccc---------c----hhhccC------hhhhhhhHHHHHHHHHHH-
Confidence                                            000         0    000000      000011112234578889 


Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      ..||+++|.||.|+|   ++|+|++|||+.||+|.++|++.++||+++||+.+..
T Consensus       129 ~~Lp~~~r~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~~~  180 (185)
T PRK09649        129 ADLTTDQREALLLTQ---LLGLSYADAAAVCGCPVGTIRSRVARARDALLADAEP  180 (185)
T ss_pred             HhCCHHHhHHhhhHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCc
Confidence            899999999999999   8999999999999999999999999999999986543

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.85  E-value=6.1e-20  Score=171.43  Aligned_cols=164  Identities=15%  Similarity=0.084  Sum_probs=130.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccc
Q 010521          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR  341 (508)
Q Consensus       262 ~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~ir  341 (508)
                      ++.|++.|+..|.+.++.+|.+++++..++||++||+|+.+|+..++|++.. ..|.+|++..++|.+.+++++..+...
T Consensus         7 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~~~~~~   85 (173)
T PRK09645          7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSARARPV   85 (173)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhhccccc
Confidence            3489999999999999999999999989999999999999999999997533 369999999999999998876532100


Q ss_pred             ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccC
Q 010521          342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV  421 (508)
Q Consensus       342 ip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~  421 (508)
                                                                          ...+          +..   + .++   
T Consensus        86 ----------------------------------------------------~~~~----------~~~---~-~~~---   96 (173)
T PRK09645         86 ----------------------------------------------------EGGD----------DVL---G-VPE---   96 (173)
T ss_pred             ----------------------------------------------------cccc----------ccc---c-CCC---
Confidence                                                                0000          000   0 000   


Q ss_pred             CCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          422 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       422 e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                       ..+.+.+...+....|..+| +.||+++|+||.|+|   ++|+|++|||+.||+|.++|+.+++||+++||+.|...+
T Consensus        97 -~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~L~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~  170 (173)
T PRK09645         97 -QSAPDEVDRALDRLLVADAL-AQLSPEHRAVLVRSY---YRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQERG  170 (173)
T ss_pred             -CCCchHHHHHhHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhccc
Confidence             11222333444456788999 899999999999999   899999999999999999999999999999999987543

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.85  E-value=5e-20  Score=173.79  Aligned_cols=164  Identities=15%  Similarity=0.165  Sum_probs=133.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccc
Q 010521          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR  341 (508)
Q Consensus       262 ~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~ir  341 (508)
                      ++.|+++|+..|.+.|+++|.++.++..+++|++||+|+.+|+++.+|++..  .|.+|++..+++.+.+++++..+...
T Consensus        14 ~~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQd~fl~l~~~~~~~~~~~--~~~awl~~ia~n~~~d~~Rk~~~~~~   91 (179)
T PRK09415         14 KEDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKS--SLKTWLYRIAINHCKDYLKSWHNKKV   91 (179)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCCc--ccHHHHHHHHHHHHHHHHHhhccccc
Confidence            3489999999999999999999999999999999999999999999998643  69999999999999998877532100


Q ss_pred             ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccC
Q 010521          342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV  421 (508)
Q Consensus       342 ip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~  421 (508)
                      .+                                                    .+.            .......+   
T Consensus        92 ~~----------------------------------------------------~~~------------~~~~~~~~---  104 (179)
T PRK09415         92 IV----------------------------------------------------TED------------IFTYMESQ---  104 (179)
T ss_pred             cc----------------------------------------------------ccc------------cccccccc---
Confidence            00                                                    000            00000001   


Q ss_pred             CCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          422 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       422 e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      .++|++.+...+....|..+| ..||+++|+||.|+|   ++|+|++|||+.||+|.++|++++.||+++||..+..
T Consensus       105 ~~~~e~~~~~~e~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l~~  177 (179)
T PRK09415        105 KESVEEEVIQNAEDERLASAV-MSLPIKYREVIYLFY---YEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE  177 (179)
T ss_pred             ccCcHHHHHHHHHHHHHHHHH-HhCCHHHhhHhHhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            135666666777788899999 899999999999999   7999999999999999999999999999999998754

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

Probab=99.85  E-value=1.9e-20  Score=170.69  Aligned_cols=161  Identities=20%  Similarity=0.212  Sum_probs=129.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|+++|+..|.+.|+.+++++.++..+++|++||+++++|+.+.+|++..  +|.+|++.++|+.+.+++++..+...  
T Consensus         1 ~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~~~d~~r~~~~~~~--   76 (161)
T TIGR02985         1 KAFEQLYRRYYPKLCAFAYRYVKDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNRSLNYLRHKQVEEK--   76 (161)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHHHHHHHHHHHhHhH--
Confidence            37899999999999999999999989999999999999999999998643  79999999999999988876642000  


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                  ....                                    +..       . ..        .....+
T Consensus        77 ------------~~~~------------------------------------~~~-------~-~~--------~~~~~~   92 (161)
T TIGR02985        77 ------------YQEE------------------------------------ILE-------I-EV--------DELSEN   92 (161)
T ss_pred             ------------HHHH------------------------------------HHh-------h-cc--------cccCCC
Confidence                        0000                                    000       0 00        000012


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      +|++.+...+....|..++ ..||++++.||.++|   .+|+|..|||+.||+|+++|++++++|+++||+.|
T Consensus        93 ~~~~~~~~~e~~~~l~~~l-~~L~~~~r~il~l~~---~~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~l  161 (161)
T TIGR02985        93 DPEEELEAKELQLIIYKAI-EKLPEQCRKIFILSR---FEGKSYKEIAEELGISVKTVEYHISKALKELRKEL  161 (161)
T ss_pred             CcHHHHHHHHHHHHHHHHH-HHCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence            4555666677778899999 899999999999988   79999999999999999999999999999999754

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.

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

Probab=99.85  E-value=7.5e-20  Score=172.13  Aligned_cols=160  Identities=16%  Similarity=0.108  Sum_probs=119.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCC-----CHHHHHHHHHHHHHH-hhhccCCCCCCcchhHHHHHHHHHHHHHHHHhc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGA-----DMADLVQGGLIGLLR-GIEKFDSSKGFKISTYVYWWIRQGVSRALVENS  337 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~-----d~EDLiQEG~IgLir-AiekFDperG~rFsTYA~~wIR~~I~~~Ird~~  337 (508)
                      .|++.|+..|.+.++.+|.+|.++..     +++|++||+|+.+|+ ...+|++.  ..|.+|++.+++|.+.+++++..
T Consensus        17 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~   94 (183)
T TIGR02999        17 AARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAMRRILVDHARRRR   94 (183)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999877     899999999999998 78889754  26999999999999988887653


Q ss_pred             ccccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccc
Q 010521          338 RTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIA  417 (508)
Q Consensus       338 R~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~  417 (508)
                      +..+..                                                  ...+            ..+.+..+
T Consensus        95 ~~~~~~--------------------------------------------------~~~~------------~~~~~~~~  112 (183)
T TIGR02999        95 AQKRGG--------------------------------------------------GAVR------------VPLDEVLP  112 (183)
T ss_pred             HHhccC--------------------------------------------------Cccc------------cccccccC
Confidence            200000                                                  0000            00000000


Q ss_pred             cccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          418 DNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       418 d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                          ...++. .+.....+.+...| ..||+++|.||.|+|   ++|+|++|||+.||+|.+||+.+++||+++||+.|
T Consensus       113 ----~~~~~~-~~~~~~l~~~~~~l-~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l  182 (183)
T TIGR02999       113 ----DAEADL-DEELLDLDDALDKL-AQVDPRQAEVVELRF---FAGLTVEEIAELLGVSVRTVERDWRFARAWLADEL  182 (183)
T ss_pred             ----CCCccH-HHHHHHHHHHHHHh-hcCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence                001111 11112223344456 679999999999999   89999999999999999999999999999999876

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.

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

Probab=99.85  E-value=4.8e-20  Score=164.57  Aligned_cols=157  Identities=27%  Similarity=0.385  Sum_probs=130.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q 010521          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN  344 (508)
Q Consensus       265 A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~  344 (508)
                      |++.|+..|.++|+++++++..++.+.+|++||+++++|++++.|++.  .+|.+|++.++++.+.+++++..+   .+.
T Consensus         2 a~~~l~~~~~~~v~~~~~~~~~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~---~~~   76 (158)
T TIGR02937         2 AFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR---LRR   76 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc---CCc
Confidence            789999999999999999999999999999999999999999999997  589999999999999999987753   110


Q ss_pred             cHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCC
Q 010521          345 HLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENN  424 (508)
Q Consensus       345 ~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~  424 (508)
                      ..                                                  ...          .    .+.+  ..++
T Consensus        77 ~~--------------------------------------------------~~~----------~----~~~~--~~~~   90 (158)
T TIGR02937        77 EL--------------------------------------------------DLL----------E----ELLD--SDPS   90 (158)
T ss_pred             ch--------------------------------------------------hhh----------h----hccc--ccCC
Confidence            00                                                  000          0    0000  0224


Q ss_pred             ccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          425 PWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       425 Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      |++..........|..+| ..||+.++.||.++|   ..|+|..|||+.+|+|+.+|+++..+++++||+.+
T Consensus        91 ~~~~~~~~~~~~~l~~~l-~~L~~~~~~ii~~~~---~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~l  158 (158)
T TIGR02937        91 PEEELEQEEEREALREAL-EKLPEREREVLVLRY---LEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL  158 (158)
T ss_pred             HHHHHHHHHHHHHHHHHH-HhCCHHHHHHHhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence            555666677778899999 899999999999998   68999999999999999999999999999999753

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.

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=1.4e-19  Score=171.29  Aligned_cols=158  Identities=18%  Similarity=0.198  Sum_probs=124.8

Q ss_pred             HHHHHHHHHHHHHHHHHHH----HhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccc
Q 010521          264 LAREKLVMSNVRLVMSIAQ----RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT  339 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAk----rY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~  339 (508)
                      .|++.|+..|.+.|+.+|+    ++.++..+++|++||+++.+|+.++.|++..  .|.+|++..+++.+.+++++..+.
T Consensus        21 ~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n~~~d~~R~~~~~   98 (184)
T PRK12539         21 AAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIARYKLIDHLRRTRAS   98 (184)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHHHHHHHHHHHhcc
Confidence            9999999999999999987    4557889999999999999999999999753  699999999999999888765320


Q ss_pred             ccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccc
Q 010521          340 LRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADN  419 (508)
Q Consensus       340 irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~  419 (508)
                      . .                                                  ..+.+.             ....    
T Consensus        99 ~-~--------------------------------------------------~~~~~~-------------~~~~----  110 (184)
T PRK12539         99 L-A--------------------------------------------------DVPIDD-------------ADEL----  110 (184)
T ss_pred             c-c--------------------------------------------------ccChhh-------------hccc----
Confidence            0 0                                                  000000             0000    


Q ss_pred             cCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          420 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       420 ~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                          .+.+.....+....+..+| ..||+++|.||.|+|   ++|+|++|||+.||+|.++|++++++|+++||+.+...
T Consensus       111 ----~~~~~~~~~e~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~  182 (184)
T PRK12539        111 ----VAHDDHAAVESTLDLGRLL-ARLPEKMRLAIQAVK---LEGLSVAEAATRSGMSESAVKVSVHRGLKALAALIGRE  182 (184)
T ss_pred             ----cCCcHHhhHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHhhc
Confidence                0001112234456788999 899999999999999   79999999999999999999999999999999988653

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=5.1e-20  Score=175.14  Aligned_cols=182  Identities=14%  Similarity=0.110  Sum_probs=136.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      -+++.|+..|.+.|+.+|.+++++..++||++||+|+.+|+.+++|++..  +|.+|++..++|.+.+++++..+.....
T Consensus         2 ~~~~~l~~~~~~~l~~~a~~~~~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~Rk~~r~~~~~   79 (191)
T PRK12520          2 TIAPAQLEALRPHLLRFARLQLRDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKHKIIDAIRSGRREVRLS   79 (191)
T ss_pred             cchHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHHHHHHHHHhhcCcCccc
Confidence            37899999999999999999999999999999999999999999998543  6999999999999999988765421111


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                      .....                 .....++                       ++..     .. .+. .....++.  ..
T Consensus        80 ~~~~~-----------------~~~~~~~-----------------------~~~~-----~~-~~~-~~~~~~~~--~~  110 (191)
T PRK12520         80 LDDAD-----------------EQSDDDL-----------------------FDAL-----FA-ADG-HYREPPSD--WG  110 (191)
T ss_pred             ccccc-----------------cchhhhh-----------------------hhhh-----cc-ccc-ccccCccc--cC
Confidence            00000                 0000000                       0000     00 000 00001111  13


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                      +|++.+...+....|..+| ..||+++|.||.|+|   ++|+|++|||+.||+|.+||++.++||+++||+++...+
T Consensus       111 ~~~~~~~~~~~~~~l~~~l-~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~  183 (191)
T PRK12520        111 DPDAALSRREFFEVLQACV-DRLPPRTGRVFMMRE---WLELETEEICQELQITATNAWVLLYRARMRLRECLDLHW  183 (191)
T ss_pred             CHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5666666777778899999 899999999999999   899999999999999999999999999999999998776

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

Probab=99.84  E-value=4e-20  Score=169.71  Aligned_cols=159  Identities=15%  Similarity=0.158  Sum_probs=126.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      +|++.++..|.+.|+.+|+++.++..++||++||+++.+|+++++|++..  .|.+|++..+++.+.++++++.+... +
T Consensus         1 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~~-~   77 (159)
T TIGR02989         1 EAFAALLQRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDRL-V   77 (159)
T ss_pred             CHHHHHHHHhHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhccccc-c
Confidence            37899999999999999999999999999999999999999999999754  69999999999999999987653110 0


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                      ..                        ++                                        ..+.+.+.   .
T Consensus        78 ~~------------------------~~----------------------------------------~~~~~~~~---~   90 (159)
T TIGR02989        78 FD------------------------DE----------------------------------------LLEALAAE---A   90 (159)
T ss_pred             cC------------------------HH----------------------------------------HHHHHHhh---c
Confidence            00                        00                                        00000000   0


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      +|.+..........+..+| +.||++++.||.++|   .+|+|.+|||+.||+|+++|+..++||+++||..+
T Consensus        91 ~~~~~~~~~~~~~~l~~~i-~~L~~~~r~v~~l~~---~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~~  159 (159)
T TIGR02989        91 EATEADRSEDELQALEGCL-EKLPERQRELLQLRY---QRGVSLTALAEQLGRTVNAVYKALSRLRVRLRDCV  159 (159)
T ss_pred             ccchHhhHHHHHHHHHHHH-HHCCHHHHHHHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcC
Confidence            1222223344456788999 899999999999998   79999999999999999999999999999999753

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).

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=8.8e-20  Score=170.72  Aligned_cols=166  Identities=14%  Similarity=0.151  Sum_probs=131.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      ..+++|+..|.++|+.+|++|.++..+++|++||+++.+|+++++|++..  +|.+|++..++|.+.++++++.+....+
T Consensus         3 ~~~~~l~~~y~~~i~~~~~~~~~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~~~~   80 (173)
T PRK12522          3 EKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWKDRI   80 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhccccccc
Confidence            56999999999999999999999999999999999999999999999754  7999999999999999988765311000


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccc-cccccCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSY-IADNRVE  422 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~-i~d~~~e  422 (508)
                      ...                                                 .+.           ....+. ..+.  .
T Consensus        81 ~~~-------------------------------------------------~~~-----------~~~~~~~~~~~--~   98 (173)
T PRK12522         81 LDL-------------------------------------------------FHK-----------EDGGEIEFADD--V   98 (173)
T ss_pred             ccc-------------------------------------------------cch-----------hhhhhhccccC--C
Confidence            000                                                 000           000000 0010  1


Q ss_pred             CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      ..|+. ....+..+.+..+| ..||++++.||.|+|   .+|+|++|||+.||+|.++|+..++||+++||+.+..
T Consensus        99 ~~~~~-~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~  169 (173)
T PRK12522         99 NISEE-FIQKVEAEMIREVI-QLLNEKYKTVLVLYY---YEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG  169 (173)
T ss_pred             CChHH-HHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            12333 44556678899999 899999999999999   8999999999999999999999999999999998864

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=1.4e-19  Score=170.77  Aligned_cols=157  Identities=17%  Similarity=0.201  Sum_probs=124.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcC----CCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDN----MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT  339 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~----~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~  339 (508)
                      .|++.|+..|.+.|+.+|.++++    +..+++|++||+++.+|...++|++.  ..|.+|++..+|+.+.+++++..+.
T Consensus        22 ~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~~d~~Rr~~~~   99 (184)
T PRK12512         22 AAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKLIDALRRRGRR   99 (184)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHHHHHHHhhccc
Confidence            99999999999999999999875    34689999999999999999999864  3699999999999999888765321


Q ss_pred             ccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccc
Q 010521          340 LRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADN  419 (508)
Q Consensus       340 irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~  419 (508)
                      ...                                                    .++.             ..+.+++.
T Consensus       100 ~~~----------------------------------------------------~~~~-------------~~~~~~~~  114 (184)
T PRK12512        100 VFV----------------------------------------------------DIDD-------------FAETLPAE  114 (184)
T ss_pred             ccC----------------------------------------------------Cchh-------------cccccccc
Confidence            000                                                    0000             00001110


Q ss_pred             cCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          420 RVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       420 ~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                          .+.    .....+.+.++| ..||+++++||.++|   .+|+|++|||+.||+|..+|+..+++|+++||..+.+.
T Consensus       115 ----~~~----~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~~  182 (184)
T PRK12512        115 ----PAT----ETLPAGDVGRHL-ETLPPRQRDVVQSIS---VEGASIKETAAKLSMSEGAVRVALHRGLAALAAKFRSE  182 (184)
T ss_pred             ----chh----hHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhcC
Confidence                000    122345678888 899999999999999   79999999999999999999999999999999988753

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=7.6e-20  Score=170.86  Aligned_cols=162  Identities=15%  Similarity=0.134  Sum_probs=125.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.+.|+.+++++.+ ..+++|++||+|+.+|+.++.|++.  ..|.+|++..+++.+.+++++..+...  
T Consensus        11 ~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~~~~~--   85 (175)
T PRK12518         11 QSFRQLYRRYQQKVRSTLYQLCG-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDARRQFAQRPS--   85 (175)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcC-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHHHHHhhcccc--
Confidence            99999999999999999999875 4789999999999999999999974  369999999999988888775432000  


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                       .                                                  .+.       ......    ...    .
T Consensus        86 -~--------------------------------------------------~~~-------~~~~~~----~~~----~   99 (175)
T PRK12518         86 -R--------------------------------------------------IQD-------DSLNDQ----PSR----P   99 (175)
T ss_pred             -c--------------------------------------------------hhc-------cccccc----ccC----C
Confidence             0                                                  000       000000    000    0


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                      .+.......+....+.++| +.||+++|.||.|+|   ++|+|++|||+.||+|.++|++.++||+++||+.+.+.+
T Consensus       100 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~~~  172 (175)
T PRK12518        100 SDTPDLMQLHYQDLVQQGL-QTLSLEHRAVLVLHD---LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQQG  172 (175)
T ss_pred             CCcHHHHHHHHHHHHHHHH-HhCCHHHeeeeeehH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence            1111223334445688889 899999999999999   899999999999999999999999999999999997654

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.83  E-value=8.5e-20  Score=168.36  Aligned_cols=156  Identities=12%  Similarity=0.081  Sum_probs=125.5

Q ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q 010521          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL  350 (508)
Q Consensus       271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l  350 (508)
                      +.|.+.|+.+|.+++++..+++|++||+|+.+|+++++|++.   .|.+|++..++|.+.+++++..+....        
T Consensus         2 ~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~--------   70 (160)
T PRK09642          2 QTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEE--------   70 (160)
T ss_pred             chHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccc--------
Confidence            579999999999999999999999999999999999999863   499999999999999998776421000        


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHH
Q 010521          351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD  430 (508)
Q Consensus       351 ~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve  430 (508)
                                                                 ..+..         +   ..+.+..   ..+|++.+.
T Consensus        71 -------------------------------------------~~~~~---------~---~~~~~~~---~~~~~~~~~   92 (160)
T PRK09642         71 -------------------------------------------LSLCK---------E---TEENIKS---SHNIEDLLL   92 (160)
T ss_pred             -------------------------------------------cccch---------h---hhhhccC---CCChHHHHH
Confidence                                                       00000         0   0000000   124555666


Q ss_pred             HHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          431 DWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                      ..+....|..+| +.||+++|.||.|+|   .+|+|++|||+.||+|.++|+++++||+++||+.+...
T Consensus        93 ~~e~~~~l~~~l-~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~  157 (160)
T PRK09642         93 TKEQKLLIAQKL-RELPENYRDVVLAHY---LEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEE  157 (160)
T ss_pred             HHHHHHHHHHHH-HhCCHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence            667778899999 899999999999999   89999999999999999999999999999999999654

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

Probab=99.83  E-value=4.2e-19  Score=167.89  Aligned_cols=169  Identities=22%  Similarity=0.208  Sum_probs=135.4

Q ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhc
Q 010521          258 ILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS  337 (508)
Q Consensus       258 ~l~e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~  337 (508)
                      .+..+..++..++..|.+.++.+|.++.++..++|||+||+|+.+|+++..| .. +..|.||++.+++|.+++.+++..
T Consensus         9 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~   86 (182)
T COG1595           9 ALRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRK   86 (182)
T ss_pred             HHhcchHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHHHHHHhc
Confidence            3445568999999999999999999999988899999999999999999999 33 347999999999999999998775


Q ss_pred             ccccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccc
Q 010521          338 RTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIA  417 (508)
Q Consensus       338 R~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~  417 (508)
                      +....                                                     .+.           ....+...
T Consensus        87 r~~~~-----------------------------------------------------~~~-----------~~~~~~~~  102 (182)
T COG1595          87 RRRAR-----------------------------------------------------VEE-----------ADLLPEEA  102 (182)
T ss_pred             ccccc-----------------------------------------------------ccc-----------cccccccc
Confidence            42111                                                     000           00000000


Q ss_pred             cccCCCCcc-chHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          418 DNRVENNPW-HGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       418 d~~~e~~Pe-~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      +..   .+. +.+...+....|.++| ..||+++|.||.|+|   ++|+|++|||+.||||.+||+..+++|+++||..+
T Consensus       103 ~~~---~~~~~~~~~~~~~~~l~~al-~~Lp~~~R~~~~l~~---~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l  175 (182)
T COG1595         103 DPA---PDLAELLLAEEELERLRRAL-ARLPPRQREAFLLRY---LEGLSYEEIAEILGISVGTVKSRLHRARKKLREQL  175 (182)
T ss_pred             Ccc---cccchHHHHHHHHHHHHHHH-HhCCHHHhHHhhhHh---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            000   111 2456677788999999 899999999999999   89999999999999999999999999999999998


Q ss_pred             HHh
Q 010521          497 RKK  499 (508)
Q Consensus       497 ~~~  499 (508)
                      ...
T Consensus       176 ~~~  178 (182)
T COG1595         176 EEA  178 (182)
T ss_pred             hhc
Confidence            754

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=3.6e-19  Score=173.96  Aligned_cols=169  Identities=14%  Similarity=0.097  Sum_probs=134.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (508)
Q Consensus       263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri  342 (508)
                      ..++..|+..|.+.++.++.++.++..++||++||+|+.+|+.+++|++.   .|.+|++..++|.+.++++++.+....
T Consensus        17 ~~~f~~l~~~~~~~l~~~~~~~~~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~~~~~~~   93 (216)
T PRK12533         17 GERFRQLVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRRANAHEV   93 (216)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhhcccccc
Confidence            48999999999999999999999999999999999999999999999852   499999999999999988776421000


Q ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521          343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE  422 (508)
Q Consensus       343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e  422 (508)
                                                                         ...+.       ..+...... +.+.  .
T Consensus        94 ---------------------------------------------------~~~~~-------~~~~~~~~~-~~~~--~  112 (216)
T PRK12533         94 ---------------------------------------------------AAPDT-------LDDADSLDD-WQPA--G  112 (216)
T ss_pred             ---------------------------------------------------ccccc-------ccccccccc-cccC--C
Confidence                                                               00000       000000000 0111  2


Q ss_pred             CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                      .+|++.+...+....|..+| ..||+++|.||.|+|   ++++|++|||+.||||.++|+++++||+++||+.+...
T Consensus       113 ~~~e~~~~~~e~~~~l~~al-~~Lp~~~R~v~~L~y---~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~~  185 (216)
T PRK12533        113 EDPLALLLRAEDVRLVNAAL-AKLPVEYREVLVLRE---LEDMSYREIAAIADVPVGTVMSRLARARRRLAALLGGA  185 (216)
T ss_pred             CCHHHHHHHHHHHHHHHHHH-HcCCHHHHhHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence            35667777778888899999 899999999999999   89999999999999999999999999999999998644

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=4.8e-19  Score=170.18  Aligned_cols=164  Identities=16%  Similarity=0.104  Sum_probs=127.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.+.++.++. +.++..++||++||+|+.+|+..++|++..  .|.+|++..+++.+.+++++..+..+..
T Consensus        25 ~a~~~l~~~y~~~l~~~~~-~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Iarn~~id~~Rk~~~~~~~~  101 (196)
T PRK12535         25 AALTEFIRETQDDVWRLLA-HLGGHDIADDLTQETYLRVMSALPRFAARS--SARTWLLSLARRVWVDNIRHDMARPRKS  101 (196)
T ss_pred             HHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHHHHHHHHhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhccCCCcc
Confidence            9999999999999999975 678888999999999999999999998632  6999999999999999988764210000


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                          .+.          ....    .+.  ..
T Consensus       102 ----------------------------------------------------~~~----------~~~~----~~~--~~  113 (196)
T PRK12535        102 ----------------------------------------------------ATE----------YEDA----AAT--TA  113 (196)
T ss_pred             ----------------------------------------------------ccc----------cccc----ccc--cC
Confidence                                                                000          0000    000  01


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEA  503 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~  503 (508)
                      .|+... .......+..+| ..||+++|+||.|+|   ++|+|++|||+.||+|.++|++.++||+++||+.|....+.+
T Consensus       114 ~~~~~~-~~~~~~~l~~~l-~~Lp~~~r~v~~l~~---~~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~  188 (196)
T PRK12535        114 SNETTG-SWSEWIDVRTLI-DALPPERREALILTQ---VLGYTYEEAAKIADVRVGTIRSRVARARADLIAATATGQASA  188 (196)
T ss_pred             CcchhH-HHHHHHHHHHHH-HcCCHHHHHHhhhHH---HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccccchh
Confidence            122111 122235788899 899999999999999   899999999999999999999999999999999997665544

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=3.9e-19  Score=169.53  Aligned_cols=160  Identities=13%  Similarity=0.160  Sum_probs=127.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (508)
Q Consensus       263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri  342 (508)
                      ..++..|+..|.+.++.+|.+++++..++||++||+|+.+|+..++|+...  .|.+|++..++|.+.++++++.+... 
T Consensus         9 ~~~f~~l~~~~~~~L~~~a~~~~~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~~~~~-   85 (187)
T PRK12516          9 TPPFKRELLAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRGREVQ-   85 (187)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhcCCcc-
Confidence            389999999999999999999999999999999999999999999998643  69999999999999988876642100 


Q ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521          343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE  422 (508)
Q Consensus       343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e  422 (508)
                                                                          ..+.            .+.+...     
T Consensus        86 ----------------------------------------------------~~~~------------~~~~~~~-----   96 (187)
T PRK12516         86 ----------------------------------------------------DTDG------------MFTEQLA-----   96 (187)
T ss_pred             ----------------------------------------------------cccc------------ccccccC-----
Confidence                                                                0000            0000000     


Q ss_pred             CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                      ..|+.  ........|..+| ..||+++|+||.|+|   ++|+|++|||+.||+|.++|++++++|+++||+.+...+
T Consensus        97 ~~~~~--~~~~~~~~l~~~L-~~Lp~~~r~i~~L~~---~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~~~  168 (187)
T PRK12516         97 VHPSQ--YGTLDLQDFRAAL-DQLPDDQREAIILVG---ASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIEG  168 (187)
T ss_pred             CCcch--hhHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhc
Confidence            01111  1122235688999 899999999999999   899999999999999999999999999999999998654

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=4.9e-19  Score=164.64  Aligned_cols=161  Identities=16%  Similarity=0.193  Sum_probs=127.3

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccc
Q 010521          261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (508)
Q Consensus       261 e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~i  340 (508)
                      .++..|.+++..|.+.|+.+|+++.++..++||++||+|+.+|+...+|++..  .|.+|++..++|.+.+++++..+..
T Consensus         3 ~~~~~f~~~~~~~~~~l~~~a~~~~~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~~   80 (164)
T PRK12547          3 KCSKNFKQELLLALPALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGREV   80 (164)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhcccc
Confidence            35689999999999999999999999999999999999999999999998543  6999999999999999887654210


Q ss_pred             cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccccccc
Q 010521          341 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNR  420 (508)
Q Consensus       341 rip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~  420 (508)
                      .   .                                                  .+.           . ..   ... 
T Consensus        81 ~---~--------------------------------------------------~~~-----------~-~~---~~~-   91 (164)
T PRK12547         81 Q---D--------------------------------------------------SDG-----------V-FT---ARV-   91 (164)
T ss_pred             c---c--------------------------------------------------ccc-----------c-cc---ccC-
Confidence            0   0                                                  000           0 00   000 


Q ss_pred             CCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          421 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       421 ~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                       ..+++.  ........+..+| ..||+++|+||.|+|   .+|+|++|||+.||+|.++|++.++||+++||..+...
T Consensus        92 -~~~~~~--~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~  163 (164)
T PRK12547         92 -AVHPAQ--YGSLDLQDFKKAL-NLLSADQREAIILIG---ASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKVD  163 (164)
T ss_pred             -CCCchh--hhHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence             001111  1122345688899 899999999999999   89999999999999999999999999999999988643

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=2.6e-19  Score=168.98  Aligned_cols=164  Identities=11%  Similarity=-0.028  Sum_probs=127.8

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHhcC--CCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcc
Q 010521          261 ECSLAREKLVMSNVRLVMSIAQRYDN--MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR  338 (508)
Q Consensus       261 e~~~A~e~LIe~yl~LV~sIAkrY~~--~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R  338 (508)
                      ++..|++.|+..|.+.|+.++.++++  +..++||++||+|+.+|+..++|++.....|.||++..++|.+.+++++..+
T Consensus        10 ~d~~af~~ly~~~~~~l~~~~~~~~~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~Rk~~~   89 (178)
T PRK12529         10 ADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWRRRQSL   89 (178)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHHHHHHH
Confidence            44599999999999999998766665  4678999999999999999999975444579999999999988888765421


Q ss_pred             cccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccccc
Q 010521          339 TLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIAD  418 (508)
Q Consensus       339 ~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d  418 (508)
                      .                . ..                                    .+.             ..+....
T Consensus        90 ~----------------~-~~------------------------------------~~~-------------~~~~~~~  103 (178)
T PRK12529         90 E----------------L-AW------------------------------------LEA-------------LATLPEP  103 (178)
T ss_pred             H----------------h-hh------------------------------------hhH-------------hhhccCc
Confidence            0                0 00                                    000             0000000


Q ss_pred             ccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          419 NRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       419 ~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      .  .++|++.+...+....|..+| ..||+++|.||.|+|   .+|+|++|||+.||+|.+||+.++++|+.+++..+
T Consensus       104 ~--~~~~e~~~~~~~~~~~l~~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~  175 (178)
T PRK12529        104 L--HPSPEQQSVILETLHEIDALL-DTLRPRVKQAFLMAT---LDGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLM  175 (178)
T ss_pred             C--CCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence            0  124555566666677899999 899999999999999   89999999999999999999999999999998764

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.82  E-value=4.7e-19  Score=164.59  Aligned_cols=158  Identities=15%  Similarity=0.114  Sum_probs=130.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q 010521          266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH  345 (508)
Q Consensus       266 ~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~  345 (508)
                      ++.|+..|.+.|+.+|+++.++..+++|++||+|+.+|+.++.|++.   .|.+|++..+++.+.+++++..+.....  
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~~--   77 (165)
T PRK09644          3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFVG--   77 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhccccc--
Confidence            67899999999999999999999999999999999999999999863   5999999999999999988764310000  


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCc
Q 010521          346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP  425 (508)
Q Consensus       346 ~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~P  425 (508)
                                             ..                                        .. +.+.    ..+|
T Consensus        78 -----------------------~~----------------------------------------~~-~~~~----~~~~   89 (165)
T PRK09644         78 -----------------------TD----------------------------------------EI-EAIQ----AEST   89 (165)
T ss_pred             -----------------------hh----------------------------------------HH-hhhc----ccCh
Confidence                                   00                                        00 0000    1245


Q ss_pred             cchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          426 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       426 e~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                      ++.+...+....+..+| ..||+++|+||.|+|   .+|+|.+|||+.||+|.++|+++++||+++||+.+....
T Consensus        90 ~~~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~~  160 (165)
T PRK09644         90 EEYVVAKNSYEKLIQII-HTLPVIEAQAILLCD---VHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEEK  160 (165)
T ss_pred             HHHHHHHHHHHHHHHHH-HhCCHHHHHHHHhHH---HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhhh
Confidence            55566667778899999 899999999999998   799999999999999999999999999999999987553

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

Probab=99.82  E-value=4.4e-19  Score=163.74  Aligned_cols=156  Identities=18%  Similarity=0.181  Sum_probs=126.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccc
Q 010521          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR  341 (508)
Q Consensus       262 ~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~ir  341 (508)
                      +..+++.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+.+++|+.  ...|.+|++..+++.+.+++++..+. .
T Consensus         4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~~~~-~   80 (162)
T TIGR02983         4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRRRLL-E   80 (162)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhhccc-c
Confidence            44999999999999999999999999999999999999999999999964  33799999999999888887755310 0


Q ss_pred             ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccC
Q 010521          342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV  421 (508)
Q Consensus       342 ip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~  421 (508)
                                                                          .. +..                +++.  
T Consensus        81 ----------------------------------------------------~~-~~~----------------~~~~--   89 (162)
T TIGR02983        81 ----------------------------------------------------LP-TRE----------------LPDA--   89 (162)
T ss_pred             ----------------------------------------------------cc-ccc----------------cCcc--
Confidence                                                                00 000                0000  


Q ss_pred             CCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          422 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       422 e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                        .+.......+..+.|..+| ..||+++|.||.|+|   .+|+|.+|||+.||+|.++|++.+.||+++||+.+.
T Consensus        90 --~~~~~~~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~  159 (162)
T TIGR02983        90 --AAPDPAPDVALRAALARAL-RRLPARQRAVVVLRY---YEDLSEAQVAEALGISVGTVKSRLSRALARLRELLE  159 (162)
T ss_pred             --cCCccchhHHHHHHHHHHH-HhCCHHHHHHhhhHH---HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence              0111122344556788899 899999999999999   899999999999999999999999999999999875

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.

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

Probab=99.82  E-value=2.8e-19  Score=170.36  Aligned_cols=172  Identities=15%  Similarity=0.175  Sum_probs=130.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (508)
Q Consensus       263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri  342 (508)
                      ..+|+.|+..|.+.|+.+|.+++++..+++|++||+|+.+|+.+.+|++.  .+|.+|++..++|.+.++++++.+....
T Consensus        10 ~~~f~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~~~~~~~   87 (193)
T TIGR02947        10 AQRFERDALEYLDQLYGAALRMTRNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKAQRRPQQ   87 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHhcCCccc
Confidence            48999999999999999999999999999999999999999999999864  3699999999999999998876431100


Q ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521          343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE  422 (508)
Q Consensus       343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e  422 (508)
                      ..                        .+++.           .        ..+..        ....      .... .
T Consensus        88 ~~------------------------~~~~~-----------~--------~~~~~--------~~~~------~~~~-~  109 (193)
T TIGR02947        88 SD------------------------DDDIE-----------D--------WQLAK--------AASH------TSNG-L  109 (193)
T ss_pred             cc------------------------chhhh-----------h--------hhhcc--------cccc------cccc-c
Confidence            00                        00000           0        00000        0000      0000 0


Q ss_pred             CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      ..|+......+....|..+| ..||+++|.||.|+|   .+|+|++|||+.||+|.++|+.+++||+++||+.+..
T Consensus       110 ~~~e~~~~~~~~~~~l~~~l-~~Lp~~~r~i~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~  181 (193)
T TIGR02947       110 RSAELEALDGLPDQDIKDAL-QGLPEEFRQAVYLAD---VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD  181 (193)
T ss_pred             cchhHHHHhhhhHHHHHHHH-HhCCHHHhhheeehh---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            12333333344556788999 899999999999999   8999999999999999999999999999999999864

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.

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.82  E-value=7.9e-19  Score=169.75  Aligned_cols=168  Identities=20%  Similarity=0.248  Sum_probs=136.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccc
Q 010521          262 CSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR  341 (508)
Q Consensus       262 ~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~ir  341 (508)
                      +..+++.|+..|.+.++.++.++.++..+++|++||+|+.+|+...+|++  + .|.+|++..+|+.+.+++++..+ .+
T Consensus        26 d~~a~~~l~~~~~~~L~~~~~~~~~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~~~-~~  101 (203)
T PRK09647         26 TMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRRAR-IR  101 (203)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhccc-Cc
Confidence            34899999999999999999999999999999999999999999999985  3 69999999999999999886532 00


Q ss_pred             ccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccC
Q 010521          342 LPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV  421 (508)
Q Consensus       342 ip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~  421 (508)
                      .                                                   ..++.         +   . +.....  
T Consensus       102 ~---------------------------------------------------~~~~~---------~---~-~~~~~~--  115 (203)
T PRK09647        102 M---------------------------------------------------EALPE---------D---Y-DRVPGD--  115 (203)
T ss_pred             c---------------------------------------------------ccccc---------c---c-cccCCC--
Confidence            0                                                   00000         0   0 000111  


Q ss_pred             CCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521          422 ENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM  501 (508)
Q Consensus       422 e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l  501 (508)
                      .++|+..+...+....|..+| ..||++++.||.|+|   ++|++++|||+.||+|.++|++.+.||+++||+.+...+-
T Consensus       116 ~~~~~~~~~~~~~~~~l~~~L-~~L~~~~r~v~~L~~---~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~~~~  191 (203)
T PRK09647        116 EPNPEQIYHDARLDPDLQAAL-DSLPPEFRAAVVLCD---IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAAHAP  191 (203)
T ss_pred             CCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhch
Confidence            234555566677778899999 899999999999999   8999999999999999999999999999999999987655


Q ss_pred             HH
Q 010521          502 EA  503 (508)
Q Consensus       502 ~~  503 (508)
                      .+
T Consensus       192 ~~  193 (203)
T PRK09647        192 HA  193 (203)
T ss_pred             hc
Confidence            43

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.81  E-value=3.5e-19  Score=166.65  Aligned_cols=160  Identities=15%  Similarity=0.111  Sum_probs=126.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|+..|+..|.+.|+.+|.++.++..+++|++||+|+.+|+. ..|...  ..|.+|++..++|.+.+++++..+.    
T Consensus        10 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk~~~~----   82 (172)
T PRK12523         10 ELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRAALE----   82 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHHHHHH----
Confidence            899999999999999999999999999999999999999986 446543  3699999999999999998876320    


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                 .  ....                       .          +...        .        .+.  ..
T Consensus        83 -----------~--~~~~-----------------------~----------~~~~--------~--------~~~--~~   98 (172)
T PRK12523         83 -----------Q--AYLA-----------------------E----------LALV--------P--------EAE--QP   98 (172)
T ss_pred             -----------H--HHHH-----------------------H----------Hhhc--------c--------ccc--CC
Confidence                       0  0000                       0          0000        0        000  11


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      +|+......+....+..+| ..||+++|.||.|+|   .+|+|++|||+.||+|.++|++++++|+++||..|..
T Consensus        99 ~~~~~~~~~~~~~~l~~~l-~~Lp~~~r~v~~L~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~  169 (172)
T PRK12523         99 SPEEQHLILEDLKAIDRLL-GKLSSKARAAFLYNR---LDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG  169 (172)
T ss_pred             ChHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence            3444444445556799999 899999999999999   8999999999999999999999999999999998864

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.81  E-value=1.2e-18  Score=161.35  Aligned_cols=161  Identities=16%  Similarity=0.129  Sum_probs=129.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (508)
Q Consensus       263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri  342 (508)
                      +.|++.|+..|.+.++.+|.++.++..+++|++||+|+.+|++  .|+.  +..|.+|++..+++.+.+++++..+....
T Consensus         2 ~~~f~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~~~~   77 (166)
T PRK09639          2 DETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRRRAR   77 (166)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhcccccc
Confidence            3789999999999999999999999999999999999999999  6764  34799999999999999988776421100


Q ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521          343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE  422 (508)
Q Consensus       343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e  422 (508)
                      ..                                                    +.           ....+ + +.  .
T Consensus        78 ~~----------------------------------------------------~~-----------~~~~~-~-~~--~   90 (166)
T PRK09639         78 IL----------------------------------------------------GE-----------FQWQE-V-DN--E   90 (166)
T ss_pred             cc----------------------------------------------------ch-----------hhhhh-c-cC--C
Confidence            00                                                    00           00000 0 11  2


Q ss_pred             CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                      .+|++.....+....+..+| ..||+++|.||.++|    +|+|++|||+.||+|.++|++.+.+|+++||..+...
T Consensus        91 ~~~e~~~~~~~~~~~l~~~l-~~L~~~~r~il~l~~----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~~  162 (166)
T PRK09639         91 PSPEEIWIRKEEITKVQEVL-AKMTERDRTVLLLRF----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYEQM  162 (166)
T ss_pred             CChHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            35666666667777899999 899999999999998    7899999999999999999999999999999998754

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.80  E-value=2.3e-18  Score=178.01  Aligned_cols=174  Identities=19%  Similarity=0.154  Sum_probs=128.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|+++|+..|.+.|+.+|.+++++..++||++||+|+.+|+.+++|++.  ..|.+|++..++|.+.+++++..+... +
T Consensus        19 ~af~~l~~~y~~~l~~~~~~~~~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~-~   95 (339)
T PRK08241         19 DAFAALVEPHRRELLAHCYRMLGSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVCLDALEGRARRPL-P   95 (339)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHHHHHHHhhccccC-c
Confidence            9999999999999999999999999999999999999999999999853  369999999999999999887643100 0


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCC---CCCCccccccccc-
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNG---LPGETHHSYIADN-  419 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~---~~~~~l~d~i~d~-  419 (508)
                                                                        ..++.+.....++   .......+.+.+. 
T Consensus        96 --------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (339)
T PRK08241         96 --------------------------------------------------TDLGAPAADPVDELVERPEVPWLEPYPDAL  125 (339)
T ss_pred             --------------------------------------------------cccCCCcCcccccccccccccccCCCCccc
Confidence                                                              0000000000000   0000000111110 


Q ss_pred             --cCCCCccchHHHHH-HHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          420 --RVENNPWHGVDDWA-LKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       420 --~~e~~Pe~~ve~~e-l~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                        ....+|++.+...+ ....|..+| .+||+++|.||.|+|   ++|+|++|||+.||+|.++|+++++||+++||+
T Consensus       126 ~~~~~~~~e~~~~~~e~~~~~l~~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~  199 (339)
T PRK08241        126 LDPAAADPAARVVARESVRLAFVAAL-QHLPPRQRAVLILRD---VLGWSAAEVAELLDTSVAAVNSALQRARATLAE  199 (339)
T ss_pred             ccccCCChHHHHHHHHHHHHHHHHHH-HhCCHHHhhhhhhHH---hhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence              00135665555444 345688899 899999999999999   899999999999999999999999999999998

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=1.4e-18  Score=160.68  Aligned_cols=157  Identities=15%  Similarity=0.105  Sum_probs=123.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|+++|+..|.+.|+.+|.++.++..++||++||+|+.+|+..+.|++   ..|.+|++.++++.+.+++++..+.    
T Consensus         4 ~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~~----   76 (161)
T PRK12528          4 ATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDLE----   76 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHHH----
Confidence            799999999999999999999999999999999999999999988864   2599999999999999888765310    


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                 ..  ..         .                        .++.                 .++.. .+
T Consensus        77 -----------~~--~~---------~------------------------~~~~-----------------~~~~~-~~   92 (161)
T PRK12528         77 -----------RA--YL---------E------------------------ALAQ-----------------LPERV-AP   92 (161)
T ss_pred             -----------Hh--hH---------H------------------------Hhhc-----------------ccccc-CC
Confidence                       00  00         0                        0000                 00000 11


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA  495 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~  495 (508)
                      +++......+....|..+| ..||+++|.||.|+|   .+|+|++|||+.||+|.+||++.+.+|+++||..
T Consensus        93 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~v~~L~~---~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~  160 (161)
T PRK12528         93 SEEERAIILETLVELDQLL-DGLPPLVKRAFLLAQ---VDGLGYGEIATELGISLATVKRYLNKAAMRCYFA  160 (161)
T ss_pred             CHHHHHHHHHHHHHHHHHH-HHCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence            2333333344556788999 899999999999999   8999999999999999999999999999999975

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=1.9e-18  Score=164.93  Aligned_cols=181  Identities=15%  Similarity=0.169  Sum_probs=132.2

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCC-HHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q 010521          267 EKLVMSNVRLVMSIAQRYDNMGAD-MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH  345 (508)
Q Consensus       267 e~LIe~yl~LV~sIAkrY~~~g~d-~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~  345 (508)
                      ++.+..|.+.|+.+|.++.++..+ ++|++||+|+.+|+++++|++.  ..|.+|++..++|.+.++++++.+.......
T Consensus         8 ~~~~~~~~~~l~~~a~~~~~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~~~   85 (195)
T PRK12532          8 DAELIESRKLLLHFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGRQRKVFTL   85 (195)
T ss_pred             hhhHHHHHHHHHHHHHHHcCChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHHHHHHHHHHhccccccccc
Confidence            456778999999999999999888 9999999999999999999864  3799999999999999999876431110000


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCc
Q 010521          346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP  425 (508)
Q Consensus       346 ~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~P  425 (508)
                      ..                     .+.+           ...      ......        .++....+...+.  ..+|
T Consensus        86 ~~---------------------~~~~-----------~~~------~~~~~~--------~~~~~~~~~~~~~--~~~~  117 (195)
T PRK12532         86 LD---------------------DELL-----------DEA------FESHFS--------QNGHWTPEGQPQH--WNTP  117 (195)
T ss_pred             cc---------------------cccc-----------chh------hhhhhc--------cccccccccCccc--cCCH
Confidence            00                     0000           000      000000        0000000000011  1367


Q ss_pred             cchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521          426 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM  501 (508)
Q Consensus       426 e~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l  501 (508)
                      ++.+...+....+..+| ..||+++|.||.|+|   .+|+|++|||+.||+|.++|+++++||+++||+.+....+
T Consensus       118 e~~~~~~e~~~~l~~~l-~~L~~~~r~i~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~  189 (195)
T PRK12532        118 EKSLNNNEFQKILQSCL-YNLPENTARVFTLKE---ILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF  189 (195)
T ss_pred             HHHHHHHHHHHHHHHHH-HhCCHHHHHHhhhHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            77777777778899999 899999999999999   8999999999999999999999999999999999976543

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=2.4e-18  Score=164.01  Aligned_cols=176  Identities=11%  Similarity=0.038  Sum_probs=129.5

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH
Q 010521          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH  347 (508)
Q Consensus       268 ~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~  347 (508)
                      .-+..|.+.++.+|.+++++..+++|++||+|+.+|+.+++|++..  +|.+|++..++|.+.++++++.+..... ...
T Consensus        11 ~~~~~~~~~l~~~~~~~~~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~-~~~   87 (189)
T PRK12530         11 LEIEEIRLQMLKFATLQLKDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNES-ELI   87 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCcc-ccc
Confidence            4467899999999999999999999999999999999999998653  6999999999999999988764311100 000


Q ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccc
Q 010521          348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH  427 (508)
Q Consensus       348 ~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~  427 (508)
                                            .+          .         .......       ...........++.  ..+|++
T Consensus        88 ----------------------~~----------~---------~~~~~~~-------~~~~~~~~~~~~~~--~~~~~~  117 (189)
T PRK12530         88 ----------------------EE----------D---------SPNSFFD-------EKGHWKPEYYEPSE--WQEVEN  117 (189)
T ss_pred             ----------------------cc----------c---------cchhhhc-------ccccccccccCCcc--ccCHHH
Confidence                                  00          0         0000000       00000000000111  124556


Q ss_pred             hHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          428 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       428 ~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                      .+...+....+..+| +.||+++|+||.|+|   ++|+|++|||+.||+|.+||+.+++||+++||+++....
T Consensus       118 ~~~~~~~~~~l~~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~  186 (189)
T PRK12530        118 TVYKEEFWLIFEACL-NHLPAQQARVFMMRE---YLELSSEQICQECDISTSNLHVLLYRARLQLQACLSKNW  186 (189)
T ss_pred             HHHHHHHHHHHHHHH-HhCCHHHHHHHhHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            666677778899999 899999999999999   899999999999999999999999999999999987543

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=2.3e-18  Score=165.76  Aligned_cols=181  Identities=15%  Similarity=0.086  Sum_probs=129.4

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH
Q 010521          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH  347 (508)
Q Consensus       268 ~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~  347 (508)
                      .++..|.+.++.+|.+++++..+++|++||+|+.+|+.+++|++..  .|.+|++..++|.+.+++++..+...++... 
T Consensus        12 ~~~~~~~~~l~~~~~~~~~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~~-   88 (201)
T PRK12545         12 AYLAQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSALD-   88 (201)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhcccccccccc-
Confidence            3488999999999999999999999999999999999999999753  6999999999999999998765311110000 


Q ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccc
Q 010521          348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH  427 (508)
Q Consensus       348 ~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~  427 (508)
                                            .++..                  ...++...    ....+....+..++.  ..+|++
T Consensus        89 ----------------------~~~~~------------------~~~~~~~~----~~~~~~~~~~~~~~~--~~~~~~  122 (201)
T PRK12545         89 ----------------------AELDG------------------EALLDREL----FKDNGHWAAHAKPRP--WPKPET  122 (201)
T ss_pred             ----------------------cccch------------------hhhhhhhh----hcccccccccccCcC--CCCHHH
Confidence                                  00000                  00000000    000000000000011  124555


Q ss_pred             hHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521          428 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM  501 (508)
Q Consensus       428 ~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l  501 (508)
                      .....+....+..+| ..||+++|.||.|+|   ++|+|++|||+.||+|.++|+..++||+++||+.+...++
T Consensus       123 ~~~~~~~~~~l~~~L-~~Lp~~~r~v~~L~~---~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~  192 (201)
T PRK12545        123 ILQQQQFWTLFETCL-DHLPEQIGRVFMMRE---FLDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGL  192 (201)
T ss_pred             HHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            555555666788899 899999999999999   8999999999999999999999999999999999975543

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=2.8e-18  Score=158.55  Aligned_cols=156  Identities=12%  Similarity=0.080  Sum_probs=122.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (508)
Q Consensus       263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri  342 (508)
                      ..|+++++..|.+.|+.+|.++.++..+++|++||+++.+|+.+++|++.   .|.||++..++|.+.+++++..+....
T Consensus         4 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~~~~~~   80 (161)
T PRK12541          4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEKKYKTT   80 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhccccccc
Confidence            48999999999999999999999999999999999999999999999863   599999999999999998876431000


Q ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521          343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE  422 (508)
Q Consensus       343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e  422 (508)
                                                                          ..+.                ...+..  
T Consensus        81 ----------------------------------------------------~~~~----------------~~~~~~--   90 (161)
T PRK12541         81 ----------------------------------------------------TIEE----------------FHLPNV--   90 (161)
T ss_pred             ----------------------------------------------------chhh----------------hhccCC--
Confidence                                                                0000                000000  


Q ss_pred             CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521          423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA  495 (508)
Q Consensus       423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~  495 (508)
                      ++|++..........+..+| ..||+++|.||.|+|   .+|+|.+|||+.||+|.++|++.++||+++||+.
T Consensus        91 ~~~~~~~~~~~~~~~~~~~l-~~L~~~~r~v~~l~~---~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~  159 (161)
T PRK12541         91 PSTEHEYFIKHEIASWLDSL-SSLPLERRNVLLLRD---YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI  159 (161)
T ss_pred             CCcHHHHHHHhHHHHHHHHH-HHCCHHHHHHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            11222222222334556788 899999999999999   8999999999999999999999999999999974

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

Probab=99.80  E-value=2.3e-18  Score=164.10  Aligned_cols=176  Identities=12%  Similarity=0.086  Sum_probs=131.2

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH
Q 010521          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH  347 (508)
Q Consensus       268 ~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~  347 (508)
                      +.+..|.+.|+.+|.+++++..+++|++||+|+.+|+...+|++.  .+|.+|++..+++.+.+++++..+....+....
T Consensus         6 ~~~~~~~~~l~~~~~~~~~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~~~~~   83 (188)
T TIGR02943         6 QELEQLRRDLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVSDLDD   83 (188)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcccccc
Confidence            567889999999999999999999999999999999999999864  379999999999999999987653211110000


Q ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccc
Q 010521          348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH  427 (508)
Q Consensus       348 ~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~  427 (508)
                                        .+.                        .-.++..     ....+....+..++.  .++|+.
T Consensus        84 ------------------~~~------------------------~~~~~~~-----~~~~~~~~~~~~~~~--~~~~e~  114 (188)
T TIGR02943        84 ------------------ELD------------------------DEAFNAL-----FTQNGHWAQHGQPQH--WNTPEK  114 (188)
T ss_pred             ------------------ccc------------------------cchhhhh-----hccccchhccccccc--cCCHHH
Confidence                              000                        0000000     000000000111111  235666


Q ss_pred             hHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          428 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       428 ~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      .+...+..+.+.++| ..||+++|+||.++|   ++|+|++|||+.||+|.++|++++.||+++||+.+..
T Consensus       115 ~~~~~e~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~  181 (188)
T TIGR02943       115 QLENKEFWEVFEACL-YHLPEQTARVFMMRE---VLGFESDEICQELEISTSNCHVLLYRARLSLRACLSI  181 (188)
T ss_pred             HHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            777777778899999 899999999999999   8999999999999999999999999999999999974

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.

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.79  E-value=3.3e-18  Score=165.79  Aligned_cols=180  Identities=14%  Similarity=0.137  Sum_probs=132.6

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q 010521          266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH  345 (508)
Q Consensus       266 ~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~  345 (508)
                      -..|+..|.+.|+.+|++++++..+++|++||+|+.+|+.+.+|++.  .+|.+|++..++|.+.+++++..+....+..
T Consensus        20 ~~~~~~~~~~~l~~~~~~~~~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~~~~   97 (206)
T PRK12544         20 DPVFLEDLRKQMIKFATLQLSDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSASSL   97 (206)
T ss_pred             hHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhccccccccc
Confidence            35788999999999999999999999999999999999999999864  3699999999999999999876531111100


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCc
Q 010521          346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP  425 (508)
Q Consensus       346 ~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~P  425 (508)
                      ..                   +...         ...+....         +.         ..........+  ...+|
T Consensus        98 ~~-------------------~~~~---------~~~~~~~~---------~~---------~~~~~~~~~~~--~~~~~  129 (206)
T PRK12544         98 LR-------------------DEEE---------EEDFEELF---------DE---------SGHWQKDERPQ--AWGNP  129 (206)
T ss_pred             cc-------------------ccch---------hhHHHHhh---------cc---------ccccccccccc--ccCCH
Confidence            00                   0000         00000000         00         00000000011  12357


Q ss_pred             cchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          426 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       426 e~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                      ++.+...+....+..+| ..||+++|+||.|+|   ++|+|++|||+.||+|.++|++.++||+++||+.+...
T Consensus       130 e~~~~~~e~~~~l~~~L-~~L~~~~r~v~~L~~---~~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~  199 (206)
T PRK12544        130 EESLEQEQFWRIFEACL-DGLPAKYARVFMMRE---FIELETNEICHAVDLSVSNLNVLLYRARLRLRECLENK  199 (206)
T ss_pred             HHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            76677777777888999 899999999999999   89999999999999999999999999999999999753

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.79  E-value=6.1e-18  Score=160.62  Aligned_cols=160  Identities=16%  Similarity=0.179  Sum_probs=127.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .++..++..|++.|+++|.+++++..++||++||+|+.+|+..++|++..  .|.+|++..++|.+.++++++.+...  
T Consensus         5 ~~~~~~~~~~~~~l~~~~~~~~~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~~--   80 (182)
T PRK12540          5 DSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREVE--   80 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhcccccc--
Confidence            67889999999999999999999999999999999999999999998654  69999999999988888876542100  


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                        . .+.            ...+..     ..
T Consensus        81 --------------------------------------------------~-~~~------------~~~~~~-----~~   92 (182)
T PRK12540         81 --------------------------------------------------D-ADG------------SYAKTL-----KS   92 (182)
T ss_pred             --------------------------------------------------c-ccc------------cccccc-----cC
Confidence                                                              0 000            000000     01


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM  501 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l  501 (508)
                      .|+..  .......|..+| ..||+++|.||.|+|   .+|+|++|||+.||+|.++|++.++||+++||+.+...+.
T Consensus        93 ~~~~~--~~~~~~~l~~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~~  164 (182)
T PRK12540         93 QPGQN--AHLEFEEFRAAL-DKLPQDQREALILVG---ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDGA  164 (182)
T ss_pred             CCchH--HHHHHHHHHHHH-HhCCHHHHHHhhHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhccc
Confidence            12111  112235688999 899999999999999   8999999999999999999999999999999999987654

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.78  E-value=7.4e-18  Score=159.80  Aligned_cols=154  Identities=19%  Similarity=0.183  Sum_probs=126.1

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q 010521          266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH  345 (508)
Q Consensus       266 ~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~  345 (508)
                      ++.|++.|.+.|+.+|.++.++..+++|++||+++.+|+.+..|++.  .+|.+|++..+++.+.+++++..+...++  
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~~--   78 (181)
T PRK09637          3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEELP--   78 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCcc--
Confidence            67899999999999999999999999999999999999999999853  37999999999999999987664210000  


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCc
Q 010521          346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP  425 (508)
Q Consensus       346 ~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~P  425 (508)
                                                                          .         + .    ...     +.+
T Consensus        79 ----------------------------------------------------~---------~-~----~~~-----~~~   87 (181)
T PRK09637         79 ----------------------------------------------------D---------D-L----LFE-----DEE   87 (181)
T ss_pred             ----------------------------------------------------h---------h-h----hcc-----CCC
Confidence                                                                0         0 0    000     011


Q ss_pred             cchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          426 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       426 e~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      ++.....+....+..+| +.||+++|.||.++|   .+|++.+|||+.||+|..+|+.++.||+++||+.+..
T Consensus        88 ~~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  156 (181)
T PRK09637         88 REENAKKELAPCLRPFI-DALPEKYAEALRLTE---LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG  156 (181)
T ss_pred             hhHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            22233445667788889 899999999999999   8999999999999999999999999999999998864

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.78  E-value=1.3e-18  Score=158.86  Aligned_cols=153  Identities=15%  Similarity=0.160  Sum_probs=122.5

Q ss_pred             HHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHH
Q 010521          270 VMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHER  349 (508)
Q Consensus       270 Ie~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~  349 (508)
                      +..|.+.|+.++.++.++..+++|++||+++.+|+.+++|++   .+|.+|++..+++.+.+++++..+.....      
T Consensus         1 y~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~------   71 (154)
T TIGR02950         1 YREYMHDVFRYLYRLTKDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID------   71 (154)
T ss_pred             CchHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc------
Confidence            357999999999999999899999999999999999999997   37999999999999988887654210000      


Q ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchH
Q 010521          350 LGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGV  429 (508)
Q Consensus       350 l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~v  429 (508)
                                          .                                       +.+.+...+.  ..+|++.+
T Consensus        72 --------------------~---------------------------------------~~~~~~~~~~--~~~~~~~~   90 (154)
T TIGR02950        72 --------------------D---------------------------------------DAIGDLEQHP--VESPEHHL   90 (154)
T ss_pred             --------------------H---------------------------------------hhhhhccccc--cCChhHHH
Confidence                                0                                       0000000011  12455555


Q ss_pred             HHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          430 DDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       430 e~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      ...+....+.++| ..||++++.||.++|   .+|+|++|||+.||+|..+|++.++||+++||+.+
T Consensus        91 ~~~~~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~l  153 (154)
T TIGR02950        91 LIKIEQEEITHHL-SRLPENYRTVLILRE---FKEFSYKEIAELLNLSLAKVKSNLFRARKELKKLL  153 (154)
T ss_pred             HHHHHHHHHHHHH-HhCCHhheeeeeehh---hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            6666677899999 899999999999998   79999999999999999999999999999999876

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.

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.78  E-value=7.6e-18  Score=155.63  Aligned_cols=158  Identities=16%  Similarity=0.203  Sum_probs=124.5

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH
Q 010521          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH  347 (508)
Q Consensus       268 ~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~  347 (508)
                      .++..|.+.++.+|.++.++..+++|++||+++++|+....|++.   .|.+|++..+++.+.+++++..+...      
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~------   72 (163)
T PRK07037          2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENK------   72 (163)
T ss_pred             hHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccc------
Confidence            357789999999999999999999999999999999998877653   47899999999998888876642100      


Q ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccc
Q 010521          348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH  427 (508)
Q Consensus       348 ~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~  427 (508)
                                                                    ..          ..+.... . ..+.  ..+|++
T Consensus        73 ----------------------------------------------~~----------~~~~~~~-~-~~~~--~~~~~~   92 (163)
T PRK07037         73 ----------------------------------------------YH----------GDEEDGL-D-VPSP--EASPEA   92 (163)
T ss_pred             ----------------------------------------------cc----------ccccccc-c-cCCC--CCCHHH
Confidence                                                          00          0000000 0 0011  124666


Q ss_pred             hHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          428 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       428 ~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      .+...+..+.+..+| ..|||++|.||.++|   .+|+|.+|||+.||+|.++|++.+.+|+++||+.+..
T Consensus        93 ~~~~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~~  159 (163)
T PRK07037         93 ALINRDTLRHVADAL-SELPARTRYAFEMYR---LHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDA  159 (163)
T ss_pred             HHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            666667778889999 899999999999999   7999999999999999999999999999999998864

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=8.2e-18  Score=160.43  Aligned_cols=163  Identities=17%  Similarity=0.155  Sum_probs=125.6

Q ss_pred             hhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcc
Q 010521          259 LMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR  338 (508)
Q Consensus       259 l~e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R  338 (508)
                      +..+..+++.++..|.+.|+.+|.+++++..+++|++||+|+.+|+.++.|++.  ..|.+|++..+++.+.+..++..+
T Consensus        18 ~~~~~~~f~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~~~~   95 (188)
T PRK12517         18 MLSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFERKQF   95 (188)
T ss_pred             hhccHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHHhcc
Confidence            444669999999999999999999999999999999999999999999999864  369999999988865544332210


Q ss_pred             cccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccccc
Q 010521          339 TLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIAD  418 (508)
Q Consensus       339 ~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d  418 (508)
                      .                                                     ....+.           .    ...+
T Consensus        96 ~-----------------------------------------------------~~~~~~-----------~----~~~~  107 (188)
T PRK12517         96 D-----------------------------------------------------LVDIED-----------D----SIED  107 (188)
T ss_pred             C-----------------------------------------------------ccCccc-----------c----cccC
Confidence            0                                                     000000           0    0011


Q ss_pred             ccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          419 NRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       419 ~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      .. ..+|+.    ....+.|..+| ..||+++|.||.++|   .+|++++|||+.||+|.++|+.+++||+++||..+..
T Consensus       108 ~~-~~~~e~----~~~~~~l~~~l-~~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  178 (188)
T PRK12517        108 DA-SHSSEE----EMEQEWLRRQI-AKLDPEYREPLLLQV---IGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEK  178 (188)
T ss_pred             cc-ccChhH----HHHHHHHHHHH-HhCCHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            00 112322    22335688899 899999999999999   7999999999999999999999999999999999975


Q ss_pred             hh
Q 010521          499 KK  500 (508)
Q Consensus       499 ~~  500 (508)
                      ..
T Consensus       179 ~~  180 (188)
T PRK12517        179 PD  180 (188)
T ss_pred             HH
Confidence            43

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

Probab=99.78  E-value=5.4e-18  Score=173.77  Aligned_cols=186  Identities=17%  Similarity=0.121  Sum_probs=132.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (508)
Q Consensus       263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri  342 (508)
                      ..|++.|+..|.+.|+++|.+++++..++||++||+|+.+|+.+++|++.  ..|.+|++..++|.+.+++++..+....
T Consensus         4 ~~af~~l~~~~~~~l~~~a~~~~~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~~~~~~   81 (324)
T TIGR02960         4 GAAFTALAEPHRRELLAHCYRMLGSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQRRPRP   81 (324)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhccCCcCc
Confidence            38999999999999999999999999999999999999999999999864  3699999999999999998876431000


Q ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccc-cc-ccc
Q 010521          343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSY-IA-DNR  420 (508)
Q Consensus       343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~-i~-d~~  420 (508)
                      ....                 .  +                        ......... ..........+.+. +. ...
T Consensus        82 ~~~~-----------------~--~------------------------~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  117 (324)
T TIGR02960        82 VGLG-----------------A--P------------------------SADGTAAAS-EAAEVTWLEPLPDLTLDLDDP  117 (324)
T ss_pred             cccC-----------------C--C------------------------CCccccccc-ccccccccCCCCccccccccC
Confidence            0000                 0  0                        000000000 00000000000000 00 000


Q ss_pred             CCCCccchHHHHH-HHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          421 VENNPWHGVDDWA-LKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       421 ~e~~Pe~~ve~~e-l~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      ...+|++.+...+ +...+..+| ..||+++|.||.|+|   .+|+|++|||+.||+|.++|+++++||+++||+.+..
T Consensus       118 ~~~~~~~~~~~~e~~~~~l~~~l-~~Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  192 (324)
T TIGR02960       118 AAADPSVAAGSRESVRLAFVAAI-QYLPPRQRAVLLLRD---VLGWRAAETAELLGTSTASVNSALQRARATLDEVGPS  192 (324)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHH-HhCCHHHhhHhhhHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccc
Confidence            1135655555444 445688899 899999999999999   8999999999999999999999999999999998874

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.

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.77  E-value=1.2e-17  Score=156.58  Aligned_cols=162  Identities=15%  Similarity=0.160  Sum_probs=124.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (508)
Q Consensus       263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri  342 (508)
                      ..|++.++..|.+.++.++.++.++..++||++||+|+.+|+. ..|++..  +|.+|++..+++.+.+++++..+.   
T Consensus         9 ~~af~~l~~~~~~~l~~~~~~~~~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~~~---   82 (172)
T PRK09651          9 SLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNALE---   82 (172)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHHHH---
Confidence            4899999999999999999999999999999999999999998 3555332  588999999999888887754210   


Q ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521          343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE  422 (508)
Q Consensus       343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e  422 (508)
                                  .   ..                       ..         .++.                 +.+.. .
T Consensus        83 ------------~---~~-----------------------~~---------~~~~-----------------~~~~~-~   97 (172)
T PRK09651         83 ------------K---AY-----------------------LE---------MLAL-----------------MPEGG-A   97 (172)
T ss_pred             ------------h---hh-----------------------hh---------HHhh-----------------ccccC-C
Confidence                        0   00                       00         0000                 00000 1


Q ss_pred             CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                      ++|+......+....+..+| ..||+++|+||.|+|   ++|+|++|||+.||+|.++|+..++||+++|+...-..
T Consensus        98 ~~~~~~~~~~e~~~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~~~~  170 (172)
T PRK09651         98 PSPEERESQLETLQLLDSML-DGLNGKTREAFLLSQ---LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFRLEY  170 (172)
T ss_pred             CChHHHHHHHHHHHHHHHHH-HhCCHHHhHHhhhhh---ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHc
Confidence            23443444445567788999 899999999999999   89999999999999999999999999999999865443

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.77  E-value=3e-17  Score=160.73  Aligned_cols=175  Identities=19%  Similarity=0.234  Sum_probs=128.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCC--CCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhc---c
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMG--ADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS---R  338 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g--~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~---R  338 (508)
                      . +++||..|.|+|.++|.+|.++.  .+.+|++|+|++|||+|+++|||++|.+|.+||.++|++.|.+++++..   +
T Consensus        10 ~-~e~LI~~Y~plI~~~a~~~~~~~~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dylRk~~k~~~   88 (218)
T TIGR02895        10 E-REELIRQYKPFIAKIVSSVCGRYIDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYIRKNQKYQN   88 (218)
T ss_pred             H-HHHHHHHhHHHHHHHHHHHHccCCCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHhcccccC
Confidence            5 99999999999999999998764  5899999999999999999999999999999999999999999999987   5


Q ss_pred             cccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHH------hCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCc
Q 010521          339 TLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEY------LNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGET  411 (508)
Q Consensus       339 ~irip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~------Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~  411 (508)
                      .+++|....+....+..+...+. +.++.|+.+||+..      .|++.+++.+                          
T Consensus        89 ~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv~--------------------------  142 (218)
T TIGR02895        89 LLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELVK--------------------------  142 (218)
T ss_pred             eeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHhh--------------------------
Confidence            66888765554445555555553 67899999999865      3555544322                          


Q ss_pred             cccccccccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHH
Q 010521          412 HHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQV  484 (508)
Q Consensus       412 l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi  484 (508)
                                 ..|-+.- .....-.+-..+.  -++.   ++..-+.  ...+..+||+..++||+.|+.+.
T Consensus       143 -----------~sPkh~d-~r~~~i~ia~~~~--~~~~---l~~~l~~--kk~LP~k~l~~~~~v~rktier~  196 (218)
T TIGR02895       143 -----------VSPKHRD-TRKKAIKIAKVIV--ENEE---LLEYLIR--KKKLPIKEIEERVRISRKTIERY  196 (218)
T ss_pred             -----------cCCCCHH-HHHHHHHHHHHHh--cCHH---HHHHHHH--hCCCCHHHHHHHcCCCHHHHHHh
Confidence                       1343322 2233333434441  2222   2222110  24689999999999999998654

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).

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.77  E-value=1.1e-17  Score=154.24  Aligned_cols=155  Identities=13%  Similarity=0.075  Sum_probs=123.2

Q ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q 010521          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL  350 (508)
Q Consensus       271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l  350 (508)
                      ..|.+.++.++.+++++..+++|++||+|+.+|+..+.|++  + +|.+|++..+++.+.+++++..+...         
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~aeDi~Qevf~~l~~~~~~~~~--~-~~~~wL~~ia~n~~~d~~R~~~~~~~---------   69 (159)
T PRK12527          2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQI--E-HPRAFLYRTALNLVVDRHRRHRVRQA---------   69 (159)
T ss_pred             hhHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHhccccccc--c-chHHHHHHHHHHHHHHHHHHHhcccc---------
Confidence            57899999999999999899999999999999999999875  2 69999999999998888876531000         


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHH
Q 010521          351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD  430 (508)
Q Consensus       351 ~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve  430 (508)
                                                                 .+++.             +.+.  .....++|++.+.
T Consensus        70 -------------------------------------------~~~~~-------------~~~~--~~~~~~~~~~~~~   91 (159)
T PRK12527         70 -------------------------------------------EPLEV-------------LDEE--ERLHSPSPQTRLD   91 (159)
T ss_pred             -------------------------------------------cchhh-------------hhcc--ccccCCCHHHHHH
Confidence                                                       00000             0000  0000124566666


Q ss_pred             HHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          431 DWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                      ..+....|..+| ..||++++.||.|+|   ++|+|.+|||+.||+|.++|+..+.||+++||+.+...
T Consensus        92 ~~~~~~~l~~~l-~~L~~~~r~v~~l~~---~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~~  156 (159)
T PRK12527         92 LGQRLALLQRAL-AELPPACRDSFLLRK---LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQW  156 (159)
T ss_pred             HHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence            667777899999 899999999999999   89999999999999999999999999999999998754

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.76  E-value=2.4e-17  Score=157.49  Aligned_cols=156  Identities=17%  Similarity=0.233  Sum_probs=121.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      ++++.|+. |.+.|+++|.+++++..+++|++||+|+.+|+.+..|+..  ..|.+|++..++|.+.+++++..+...  
T Consensus         8 ~~~~~l~~-~~~~l~~~a~~~l~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r~~~--   82 (188)
T PRK12546          8 DPRDELVE-HLPALRAFAISLTRNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKREVP--   82 (188)
T ss_pred             hHHHHHHH-HHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhccccc--
Confidence            56777766 7799999999999999999999999999999999999863  369999999999998888776542100  


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                         ..+.            ...+..     ..
T Consensus        83 ---------------------------------------------------~~~~------------~~~~~~-----~~   94 (188)
T PRK12546         83 ---------------------------------------------------DPEG------------VHAASL-----AV   94 (188)
T ss_pred             ---------------------------------------------------Cccc------------cccccc-----cc
Confidence                                                               0000            000000     01


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      +|..  +.......+..+| ..||+++|.||.|+|   .+|+|.+|||+.||+|..+|+++++||+++||+.+..
T Consensus        95 ~~~~--~~~~~~~~l~~~L-~~Lp~~~r~v~~L~~---~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~  163 (188)
T PRK12546         95 KPAH--DGRLAMSDFRAAF-AQLPDEQREALILVG---ASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL  163 (188)
T ss_pred             CCcc--hhHHHHHHHHHHH-HhCCHHHhHHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            1111  1122335688899 899999999999999   8999999999999999999999999999999998864

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.76  E-value=2e-17  Score=154.93  Aligned_cols=149  Identities=21%  Similarity=0.256  Sum_probs=121.3

Q ss_pred             HHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHH
Q 010521          271 MSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERL  350 (508)
Q Consensus       271 e~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l  350 (508)
                      ..|.+.++.++.++.++..+++|++||+|+.+|+++++|++.  .+|.+|++..+++.+.+++++..+...++       
T Consensus         2 ~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~-------   72 (170)
T TIGR02959         2 DEFRSELKAFIKSRVSDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELP-------   72 (170)
T ss_pred             chHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccc-------
Confidence            468999999999999999999999999999999999999863  47999999999999999988764310000       


Q ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHH
Q 010521          351 GLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVD  430 (508)
Q Consensus       351 ~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve  430 (508)
                                                                    +.                .+..    ..|.+...
T Consensus        73 ----------------------------------------------~~----------------~~~~----~~~~~~~~   86 (170)
T TIGR02959        73 ----------------------------------------------ES----------------LLAA----DSAREETF   86 (170)
T ss_pred             ----------------------------------------------hh----------------hccc----CCccHHHH
Confidence                                                          00                0000    01222333


Q ss_pred             HHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          431 DWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      ..+....+..+| ..||+++|.||.++|   .+|+|++|||+.||+|..+|++.++||+++||..+..
T Consensus        87 ~~e~~~~l~~~l-~~L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  150 (170)
T TIGR02959        87 VKELSQCIPPMI-KELPDEYREAIRLTE---LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET  150 (170)
T ss_pred             HHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            455567788999 899999999999999   8999999999999999999999999999999998863

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).

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=4.3e-17  Score=154.90  Aligned_cols=158  Identities=16%  Similarity=0.150  Sum_probs=122.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q 010521          266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH  345 (508)
Q Consensus       266 ~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~  345 (508)
                      ....+..+++.|+.+|.++.++..+++|++||+|+.+|+....|++.  .+|.+|++..+++.+.++++++.+.....  
T Consensus         6 ~~~~~~~~~~~l~~~~~~~~~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~~--   81 (182)
T PRK12511          6 KRFDVLDQLVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARRA--   81 (182)
T ss_pred             hhhhHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhccccccc--
Confidence            44457789999999999999999999999999999999999999864  36999999999999999987764210000  


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCc
Q 010521          346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP  425 (508)
Q Consensus       346 ~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~P  425 (508)
                                                                         +.             +.+. .+.. .+.+
T Consensus        82 ---------------------------------------------------~~-------------~~~~-~~~~-~~~~   95 (182)
T PRK12511         82 ---------------------------------------------------DE-------------LAVL-ADAS-LPAA   95 (182)
T ss_pred             ---------------------------------------------------cc-------------hhhc-cccC-CCcc
Confidence                                                               00             0000 0000 0011


Q ss_pred             cchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          426 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       426 e~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                         .........|..+| ..||+++|+||.|+|   ++|+|++|||+.||+|.++|++.++||+++||+.+...+
T Consensus        96 ---~~~~~~~~~l~~~l-~~Lp~~~R~v~~L~~---~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~~~  163 (182)
T PRK12511         96 ---QEHAVRLAQIRDAF-FDLPEEQRAALHLVA---IEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEGTG  163 (182)
T ss_pred             ---hHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhcC
Confidence               11223446788899 899999999999999   899999999999999999999999999999999987544

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.74  E-value=6.2e-17  Score=151.08  Aligned_cols=159  Identities=14%  Similarity=0.105  Sum_probs=125.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .++.+++..|.+.++.+|.+++++..+++|++||+|+.+|+....++.   ..|.+|++..++|.+.+++++...     
T Consensus         9 ~~~~~~~~~~~~~l~~~~~~~~~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~-----   80 (168)
T PRK12525          9 TLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDL-----   80 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHH-----
Confidence            789999999999999999999999999999999999999986555542   269999999999988887765421     


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                ++.  ...                                 +++.                . +.. ..+
T Consensus        81 ----------~~~--~~~---------------------------------~~~~----------------~-~~~-~~~   97 (168)
T PRK12525         81 ----------ERA--YLQ---------------------------------SLAE----------------A-PEA-VQP   97 (168)
T ss_pred             ----------HHH--HHH---------------------------------HHhc----------------c-ccc-ccC
Confidence                      000  000                                 0000                0 000 012


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      +|++.....+....|..+| +.||+++|.||.|+|   .+|+|++|||+.||+|.+||+..+.+|++++|..+.
T Consensus        98 ~~~~~~~~~~~~~~l~~~l-~~L~~~~r~v~~L~~---~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~~  167 (168)
T PRK12525         98 SPEEQWMVIETLLAIDRLL-DGLSGKARAAFLMSQ---LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGFQ  167 (168)
T ss_pred             ChHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhhc
Confidence            5555555666678899999 899999999999998   899999999999999999999999999999998764

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=99.70  E-value=2.5e-16  Score=144.77  Aligned_cols=156  Identities=14%  Similarity=0.100  Sum_probs=111.6

Q ss_pred             CCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHcCC
Q 010521          286 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGV  365 (508)
Q Consensus       286 ~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~~Gr  365 (508)
                      ++..+++|++||+|+.+|+..+.+ +  +..|.+|++..++|.+.+++++..+.......                    
T Consensus         2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~--------------------   58 (161)
T PRK09047          2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSL--------------------   58 (161)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhccccccccc--------------------
Confidence            345679999999999999998873 3  34699999999999999998876421000000                    


Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccC-CCCccchHHHHHHHHHHHHHHHc
Q 010521          366 TPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRV-ENNPWHGVDDWALKDEVNKLIIV  444 (508)
Q Consensus       366 ~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~-e~~Pe~~ve~~el~e~L~~~L~~  444 (508)
                                                 ..++...     .+.++....+.+.+... ..+|++.+...+....|..+| .
T Consensus        59 ---------------------------~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l-~  105 (161)
T PRK09047         59 ---------------------------FSSFSDD-----DDDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAI-Q  105 (161)
T ss_pred             ---------------------------ccccccc-----cccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHH-H
Confidence                                       0000000     00001111111211110 135677777777888899999 8


Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                      .||+++|.||.|+|   ++|+|++|||+.||+|.++|+.+++||+++||+.+...+
T Consensus       106 ~Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~  158 (161)
T PRK09047        106 KLPARQREAFLLRY---WEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKG  158 (161)
T ss_pred             hCCHHHHHHHHHHH---HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence            99999999999999   899999999999999999999999999999999997654

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.70  E-value=2.7e-16  Score=159.84  Aligned_cols=160  Identities=14%  Similarity=0.083  Sum_probs=122.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      ..+.+++..|.+.++.+|++++++..++||++||+|+. |.....|++   ..|.+|++..++|.+.+++++..+...  
T Consensus         4 ~~~~~l~~~~~~~l~~~a~~~~~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~~--   77 (293)
T PRK09636          4 ADAAAEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRRE--   77 (293)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhcccc--
Confidence            45778999999999999999999999999999999999 666677752   369999999999999998876532000  


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                        ....            ..+.+...+.  ..
T Consensus        78 --------------------------------------------------~~~~------------~~~~e~~~~~--~~   93 (293)
T PRK09636         78 --------------------------------------------------TYVG------------PWLPEPVVEE--LD   93 (293)
T ss_pred             --------------------------------------------------cccC------------CcCCcCCCCC--CC
Confidence                                                              0000            0000000011  11


Q ss_pred             CccchHH-HHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVD-DWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       424 ~Pe~~ve-~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      +|++... ..+....+..+| +.|||+||.||.|+|   .+++|++|||+.||+|.++|+++++||+++||+.+.
T Consensus        94 ~~~~~~~~~~~~~~~l~~~l-~~L~~~~R~v~~L~~---~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~  164 (293)
T PRK09636         94 DPLEAVVAAEDLSLALMLAL-ERLSPLERAAFLLHD---VFGVPFDEIASTLGRSPAACRQLASRARKHVRAARP  164 (293)
T ss_pred             ChHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence            3443332 344456688889 899999999999999   799999999999999999999999999999999754

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.69  E-value=6.5e-16  Score=152.38  Aligned_cols=149  Identities=17%  Similarity=0.131  Sum_probs=116.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .+++.+++.| +.++++|.++.++..++||++||+|+.+|+.   |+.. + .|.+|++..++|.+.+.+++..+...  
T Consensus        18 ~~~~~l~~~y-~~L~r~~~~~~~d~~dAEDlvQE~flk~~~~---~~~~-~-~~~~WL~~IarN~~id~~Rk~k~~~~--   89 (228)
T PRK06704         18 SNINFLIEQY-GELKRYCTFLTKNKWDGEDLAQETVCKVLQK---YSNK-D-ICMTLVYKIARNRWLDQIKSKSVHEK--   89 (228)
T ss_pred             HHHHHHHHHH-HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH---cCcc-c-cHHHHHHHHHHHHHHHHHhccccccc--
Confidence            7888888888 7899999999999999999999999999986   5533 2 58999999999988888876532000  


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                          +..          ..      .    ..
T Consensus        90 ----------------------------------------------------~~~----------~~------~----~~   97 (228)
T PRK06704         90 ----------------------------------------------------IRD----------QI------T----FE   97 (228)
T ss_pred             ----------------------------------------------------ccc----------cc------c----cC
Confidence                                                                000          00      0    00


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                      +|.+..  .+..+.+..+| ..||+++|.||.|+|   .+++|++|||+.||+|.++|+++++||+++||+.+..
T Consensus        98 ~~~~~~--~~~~~~l~~~L-~~Lp~~~R~v~lL~~---~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~  166 (228)
T PRK06704         98 EPHEKI--ADLHEMVGKVL-SSLNVQQSAILLLKD---VFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE  166 (228)
T ss_pred             ChHHHH--HHHHHHHHHHH-HhCCHHHhhHhhhHH---hhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence            111111  22345678888 899999999999999   7999999999999999999999999999999998865

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

Probab=99.67  E-value=1.7e-15  Score=153.41  Aligned_cols=156  Identities=17%  Similarity=0.087  Sum_probs=117.7

Q ss_pred             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHH
Q 010521          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH  347 (508)
Q Consensus       268 ~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~  347 (508)
                      ++++.|.+.++.+|++++++..++||++||+++.+++.  .|+.  ...|.+|++..++|.+.+++++..+...      
T Consensus         1 ~l~~~~~~~l~~~a~r~lg~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~------   70 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRMLGSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARRE------   70 (281)
T ss_pred             ChHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhccc------
Confidence            36889999999999999999999999999999997775  4543  2369999999999999998876532000      


Q ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccc
Q 010521          348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWH  427 (508)
Q Consensus       348 ~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~  427 (508)
                                                                    ... .           ..+.+...+.  ..+|++
T Consensus        71 ----------------------------------------------~~~-~-----------~~~~e~~~~~--~~~~~~   90 (281)
T TIGR02957        71 ----------------------------------------------VYV-G-----------PWLPEPLLTT--SADPAE   90 (281)
T ss_pred             ----------------------------------------------ccC-C-----------CCCCcccCCC--CCChHH
Confidence                                                          000 0           0000000000  124554


Q ss_pred             hHHHH-HHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          428 GVDDW-ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       428 ~ve~~-el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      .++.. .+...+..+| ++|||+||.||.|+|   .+++|++|||+.||+|..+|+++++||+++||....
T Consensus        91 ~~~~~e~~~~~l~~~l-~~L~~~~R~v~~L~~---~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~  157 (281)
T TIGR02957        91 SVELAESLSMAYLLLL-ERLSPLERAVFVLRE---VFDYPYEEIASIVGKSEANCRQLVSRARRHLDARRP  157 (281)
T ss_pred             HHHHHHHHHHHHHHHH-hhCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence            44433 3445677888 899999999999999   799999999999999999999999999999998653

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.

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=99.65  E-value=3e-15  Score=152.61  Aligned_cols=161  Identities=15%  Similarity=0.045  Sum_probs=122.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      ..+..+++.|.+.++.+|++++++..++||++||+|+.+|++...+ .   ..|.+|++...+|.+.+++++..+.... 
T Consensus         5 ~~~~~l~~~~~~~L~~~a~r~lgs~~dAEDvvQE~flr~~~~~~~~-~---~~~~aWL~~Ia~n~~id~lRk~~~rr~~-   79 (290)
T PRK09635          5 DPVSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD-I---DDERGWLIVVTSRLCLDHIKSASTRRER-   79 (290)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhcCccc-c---ccHHHHHHHHHHHHHHHHHhhhhccCcC-
Confidence            6789999999999999999999999999999999999999987653 1   2589999999999999888764320000 


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                                       ....+.         ...  .+...+   ..
T Consensus        80 -------------------------------------------------~~~~~~---------~~~--~~~~~~---~~   96 (290)
T PRK09635         80 -------------------------------------------------PQDIAA---------WHD--GDASVS---SV   96 (290)
T ss_pred             -------------------------------------------------cccccc---------cCc--cccCCC---CC
Confidence                                                             000000         000  000001   12


Q ss_pred             Cccch-HHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHG-VDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       424 ~Pe~~-ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      +|++. ....+....+..+| ..|||+||.||.|+|   ..++|++|||+.||+|..+|+++++||+++||...
T Consensus        97 ~~~~~~~~~~e~~~al~~~L-~~L~p~~R~vf~L~~---~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~  166 (290)
T PRK09635         97 DPADRVTLDDEVRLALLIML-ERLGPAERVVFVLHE---IFGLPYQQIATTIGSQASTCRQLAHRARRKINESR  166 (290)
T ss_pred             CcHHHHHHHHHHHHHHHHHH-HhCCHHHHHHhhHHH---HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence            34332 33455667788899 899999999999999   79999999999999999999999999999999854

>PRK09191 two-component response regulator; Provisional

Probab=99.56  E-value=3.4e-14  Score=139.69  Aligned_cols=136  Identities=11%  Similarity=0.105  Sum_probs=110.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccc
Q 010521          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPN  344 (508)
Q Consensus       265 A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~  344 (508)
                      ++..|+..|.+.++++|.++.++..+++|++||+|+.+|+...+|++..  .|.+|++.++++..    ....       
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~~~~~~aeDi~qd~~~~~~~~~~~~~~~~--~~~~wl~~~~~~~~----~~~~-------   68 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALTGSQSSGDAYVAATLEALLADPSIFPEAS--SPRVGLYRLFHRLW----SSAG-------   68 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhcCChhhHHHHHHHHHHHHHHhHHhcCCCc--chhhHHHHHHHHHh----cccc-------
Confidence            5889999999999999999999999999999999999999999998643  58999987665421    0000       


Q ss_pred             cHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCC
Q 010521          345 HLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENN  424 (508)
Q Consensus       345 ~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~  424 (508)
                                                                           .         ...      .    ...
T Consensus        69 -----------------------------------------------------~---------~~~------~----~~~   76 (261)
T PRK09191         69 -----------------------------------------------------A---------NDP------E----PGS   76 (261)
T ss_pred             -----------------------------------------------------c---------cCC------C----CCC
Confidence                                                                 0         000      0    001


Q ss_pred             ccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          425 PWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       425 Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      +..        ..+.++| +.||+++|.||.|+|   ++++|++|||+.||+|.++|+.+..+|+++||..+.
T Consensus        77 ~~~--------~~l~~~l-~~L~~~~r~v~~l~~---~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~  137 (261)
T PRK09191         77 PFE--------ARAERRL-AGLTPLPRQAFLLTA---LEGFSVEEAAEILGVDPAEAEALLDDARAEIARQVA  137 (261)
T ss_pred             Cch--------HHHHHHH-HhCCHHHhHHHHHHH---HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence            111        1688889 899999999999999   899999999999999999999999999999997664

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.54  E-value=5.6e-14  Score=127.34  Aligned_cols=136  Identities=19%  Similarity=0.210  Sum_probs=99.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhc-----cCCCCCCcchhHHHHHHHHHHHHHHHHhcccc
Q 010521          266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEK-----FDSSKGFKISTYVYWWIRQGVSRALVENSRTL  340 (508)
Q Consensus       266 ~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiek-----FDperG~rFsTYA~~wIR~~I~~~Ird~~R~i  340 (508)
                      ++.|+..|.++++.+|++|...    +|+ ||.++.+|..+.+     |++.  ..|.||++..++|.+.+++++..+..
T Consensus         1 f~~~~~~y~~~l~~~~~~~~~~----~~~-qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~~~~   73 (142)
T TIGR03209         1 FEEIYMNFKNTIDIFTRKYNLY----YDY-NDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKNRDK   73 (142)
T ss_pred             ChHHHHHHHHHHHHHHHHhcch----hhH-HHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence            4689999999999999999652    344 9999999999865     5532  36999999999999999987653200


Q ss_pred             cccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccccccc
Q 010521          341 RLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNR  420 (508)
Q Consensus       341 rip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~  420 (508)
                      ..              . .                                    .+.             .    .+..
T Consensus        74 ~~--------------~-~------------------------------------~~~-------------~----~~~~   85 (142)
T TIGR03209        74 KI--------------I-Y------------------------------------NSE-------------I----TDIK   85 (142)
T ss_pred             hh--------------h-h------------------------------------hhh-------------h----hccc
Confidence            00              0 0                                    000             0    0000


Q ss_pred             CCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHH
Q 010521          421 VENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVR  482 (508)
Q Consensus       421 ~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVr  482 (508)
                        ..+.+.+...+....+.++| +.||+++|.||.|+|   ++|+|++|||+.||+|.+||+
T Consensus        86 --~~~~~~~~~~~~~~~l~~~l-~~Lp~~~r~v~~l~~---~~~~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209        86 --LSLINVYSSNDLEFEFNDLI-SILPNKQKKIIYMKF---FEDMKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             --cchhHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHhhc
Confidence              01112233344556788899 899999999999999   899999999999999999996

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.

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=99.51  E-value=1.1e-12  Score=125.15  Aligned_cols=163  Identities=22%  Similarity=0.257  Sum_probs=111.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCC---CCCHHH--HHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNM---GADMAD--LVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR  338 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~---g~d~ED--LiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R  338 (508)
                      .|++.|+..|++.++.+|+++...   +.+.+|  |++|+|+.++..-...+++....|..|+...+++.+.++++...+
T Consensus        17 ~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~rr~lid~~R~~~a   96 (185)
T PF07638_consen   17 AALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMRRKLIDHARRRQA   96 (185)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999987642   334444  577888877764333343333458888888888877777765542


Q ss_pred             cccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCcccccccc
Q 010521          339 TLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIAD  418 (508)
Q Consensus       339 ~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d  418 (508)
                      ..|-+..                                              ...+|+..                ..+
T Consensus        97 ~KRg~~~----------------------------------------------~~~~l~~~----------------~~~  114 (185)
T PF07638_consen   97 QKRGGDQ----------------------------------------------VRVELDER----------------ADS  114 (185)
T ss_pred             HhcCCCC----------------------------------------------cccchhhh----------------hcc
Confidence            1110000                                              00112211                000


Q ss_pred             ccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          419 NRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       419 ~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      .. .+.|+.   ..++.+.+..+. . |+|+++.||.++|   ++|+|.+|||+.||||+.||++....|..+|+..|.
T Consensus       115 ~~-~~~~~~---~~~l~e~l~~L~-~-l~~~~~~~v~l~~---~~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~~l~  184 (185)
T PF07638_consen  115 GD-EPSPEE---LLELEEALERLL-A-LDPRQRRVVELRF---FEGLSVEEIAERLGISERTVRRRLRRARAWLRRELR  184 (185)
T ss_pred             cc-CCCHHH---HHHHHHHHHHHH-c-cCHHHHHHHHHHH---HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence            00 123333   234556666655 4 9999999999998   899999999999999999999999999999998764

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.50  E-value=1.6e-12  Score=129.02  Aligned_cols=78  Identities=17%  Similarity=0.207  Sum_probs=72.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCC--CHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGA--DMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLR  341 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~--d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~ir  341 (508)
                      .|++.|+..|.|+|+++|.+++++..  +.+|++|||++++|+++++|++++|.+|.+|++.+|++.+.++++++.+...
T Consensus        18 ~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~iDylRk~~~~~~   97 (237)
T PRK08311         18 ELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRLIDYFRKESKHNL   97 (237)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHhhcccc
Confidence            89999999999999999999998765  5999999999999999999999888789999999999999999998876433

>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=99.27  E-value=1.4e-11  Score=97.82  Aligned_cols=70  Identities=27%  Similarity=0.418  Sum_probs=66.7

Q ss_pred             HHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcc
Q 010521          269 LVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR  338 (508)
Q Consensus       269 LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R  338 (508)
                      |++.|.++|+++|.+|.+++.+.+|++||++++||+++++||++.+..|.+|++..+++.+.+.++++.|
T Consensus         1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r~~~r   70 (71)
T PF04542_consen    1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLRKRRR   70 (71)
T ss_dssp             HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHHCSSS
T ss_pred             CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHHHhcC
Confidence            6899999999999999999999999999999999999999999999889999999999999999988754

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 ....

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 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=99.19  E-value=5.7e-11  Score=89.72  Aligned_cols=50  Identities=48%  Similarity=0.679  Sum_probs=45.9

Q ss_pred             HHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          441 LIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       441 ~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      +| +.|||+|+.||.++|   ++++|+.|||+.||+|+++|+++..+|++|||+
T Consensus         1 Al-~~L~~~er~vi~~~y---~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~   50 (50)
T PF04545_consen    1 AL-DQLPPREREVIRLRY---FEGLTLEEIAERLGISRSTVRRILKRALKKLRK   50 (50)
T ss_dssp             HH-CTS-HHHHHHHHHHH---TST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             Ch-hhCCHHHHHHHHHHh---cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence            46 899999999999999   899999999999999999999999999999995

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 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; 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: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 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=98.91  E-value=3.7e-09  Score=80.78  Aligned_cols=53  Identities=28%  Similarity=0.464  Sum_probs=45.4

Q ss_pred             HHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521          436 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL  492 (508)
Q Consensus       436 e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKL  492 (508)
                      +.|..+| ..|||++|.||.++|   .+|+|+.|||+.+|+|.++|++.+.+|+++|
T Consensus         2 ~~l~~~l-~~L~~~~r~i~~l~~---~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L   54 (54)
T PF08281_consen    2 EALQQAL-AQLPERQREIFLLRY---FQGMSYAEIAEILGISESTVKRRLRRARKKL   54 (54)
T ss_dssp             HHHHHHH-HCS-HHHHHHHHHHH---TS---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred             HHHHHHH-HCCCHHHHHHHHHHH---HHCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence            5678889 899999999999999   8999999999999999999999999999987

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 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; 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: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>PRK06930 positive control sigma-like factor; Validated

Probab=98.67  E-value=1e-07  Score=90.40  Aligned_cols=71  Identities=17%  Similarity=0.156  Sum_probs=62.9

Q ss_pred             ccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          425 PWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       425 Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                      |.+.....+....|..+| +.||+++|.||.++|   .+|+|++|||+.||+|.++|++++.+|+++|+..+...
T Consensus        95 ~~~~~~~~e~~~~l~~al-~~L~~rer~V~~L~~---~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~~  165 (170)
T PRK06930         95 EPESVISEWDKIRIEDAL-SVLTEREKEVYLMHR---GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINES  165 (170)
T ss_pred             ChhHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence            444445566778899999 899999999999998   79999999999999999999999999999999988743

>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=98.62  E-value=8.2e-08  Score=78.70  Aligned_cols=76  Identities=32%  Similarity=0.364  Sum_probs=58.2

Q ss_pred             HHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCcc
Q 010521          348 ERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPW  426 (508)
Q Consensus       348 ~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe  426 (508)
                      +++++++++++.|. ++||.|+.+|||+.||+++++|..++.....+.||+.+.+    .+++.++.+++.|... .+|+
T Consensus         1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~----~~~~~~l~~~i~d~~~-~~P~   75 (78)
T PF04539_consen    1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVG----DEDDSTLGDFIEDDDA-PSPE   75 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCS----SSSSEEGGGSSB-SSS---HH
T ss_pred             ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeec----CCCCCchhheecCCCC-CChh
Confidence            35788999999995 7899999999999999999999999999999999999753    3345678888888753 4676


Q ss_pred             ch
Q 010521          427 HG  428 (508)
Q Consensus       427 ~~  428 (508)
                      +.
T Consensus        76 e~   77 (78)
T PF04539_consen   76 EE   77 (78)
T ss_dssp             HH
T ss_pred             hc
Confidence            43

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 ....

>PRK00118 putative DNA-binding protein; Validated

Probab=98.50  E-value=5.4e-07  Score=78.71  Aligned_cols=55  Identities=22%  Similarity=0.310  Sum_probs=52.1

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM  501 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l  501 (508)
                      ..||++++.||.++|   .+++|..|||+.+|+|++||++++.+|+++||+++.+.++
T Consensus        16 ~~L~ekqRevl~L~y---~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~   70 (104)
T PRK00118         16 SLLTEKQRNYMELYY---LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHL   70 (104)
T ss_pred             ccCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence            799999999999999   7999999999999999999999999999999999987654

>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

Probab=98.33  E-value=1.7e-06  Score=64.01  Aligned_cols=54  Identities=41%  Similarity=0.605  Sum_probs=49.1

Q ss_pred             HHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          436 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       436 e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      +.+..++ ..||+.++.++.++|   .+++|..+||+.+|+|..+|++++.++..+||
T Consensus         2 ~~~~~~~-~~l~~~~~~~~~~~~---~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~   55 (55)
T cd06171           2 ERLEEAL-DKLPEREREVILLRF---GEGLSYEEIAEILGISRSTVRQRLHRALKKLR   55 (55)
T ss_pred             HHHHHHH-HhCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            3566777 899999999999999   78999999999999999999999999988874

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=98.23  E-value=3.8e-06  Score=76.89  Aligned_cols=58  Identities=21%  Similarity=0.326  Sum_probs=50.6

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhh
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAML  505 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l  505 (508)
                      ..||++|++||.+++    +|+|++|||+.||+|+++|++++++|+++|+.......+-.++
T Consensus         5 ~~Lte~qr~VL~Lr~----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~~   62 (137)
T TIGR00721         5 TFLTERQIKVLELRE----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKFI   62 (137)
T ss_pred             CCCCHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHHh
Confidence            469999999999975    8999999999999999999999999999999876655554443

Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=98.21  E-value=4.6e-06  Score=76.71  Aligned_cols=52  Identities=31%  Similarity=0.367  Sum_probs=48.0

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                      ..|||+|++||.+++    +|+|++|||+.||+|+++|++++++|+++||+...--
T Consensus         5 ~~Lt~rqreVL~lr~----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl   56 (141)
T PRK03975          5 SFLTERQIEVLRLRE----RGLTQQEIADILGTSRANVSSIEKRARENIEKARETL   56 (141)
T ss_pred             cCCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            579999999999965    8999999999999999999999999999999987653

>PRK04217 hypothetical protein; Provisional

Probab=98.15  E-value=3.6e-06  Score=74.31  Aligned_cols=56  Identities=29%  Similarity=0.258  Sum_probs=51.6

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKME  502 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~  502 (508)
                      ..|++.|++||.++|   .+++|++|||+.||||++||++++.+|+++|+..+......
T Consensus        41 ~~Lt~eereai~l~~---~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~~   96 (110)
T PRK04217         41 IFMTYEEFEALRLVD---YEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGREL   96 (110)
T ss_pred             ccCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccce
Confidence            679999999999998   89999999999999999999999999999999999765543

>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT)

Probab=98.14  E-value=1.3e-05  Score=69.65  Aligned_cols=56  Identities=34%  Similarity=0.481  Sum_probs=45.1

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKME  502 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~  502 (508)
                      .-|+++|+.++.++|   .+++|+.|||+.+|||+.+|...+.||.++|...-.+.++-
T Consensus        16 ~LLT~kQ~~~l~lyy---~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~yE~kL~l~   71 (101)
T PF04297_consen   16 ELLTEKQREILELYY---EEDLSLSEIAEELGISRQAVYDSIKRAEKKLEEYEEKLGLV   71 (101)
T ss_dssp             GGS-HHHHHHHHHHC---TS---HHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHH-HH
T ss_pred             HHCCHHHHHHHHHHH---ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhhH
Confidence            459999999999999   89999999999999999999999999999998766655543

Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=97.96  E-value=3e-06  Score=60.47  Aligned_cols=33  Identities=30%  Similarity=0.483  Sum_probs=30.9

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCc
Q 010521          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS  223 (508)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~  223 (508)
                      |+++.||++|+++|+||++||++|+++|+.|+.
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            689999999999999999999999999999996

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 ....

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=97.84  E-value=4.3e-05  Score=57.42  Aligned_cols=46  Identities=37%  Similarity=0.536  Sum_probs=41.7

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..|++.|+.|+.+.    ..|+|..|||+.+|+|+.+|+++..+++++|+
T Consensus         2 ~~l~~~e~~i~~~~----~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~   47 (58)
T smart00421        2 ASLTPREREVLRLL----AEGLTNKEIAERLGISEKTVKTHLSNIMRKLG   47 (58)
T ss_pred             CCCCHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence            46899999999774    48899999999999999999999999998886

lux regulon (activates the bioluminescence operon

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=97.83  E-value=7.9e-05  Score=67.93  Aligned_cols=62  Identities=18%  Similarity=0.238  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          433 ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       433 el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      ...+.|..+| +.|++.++.||.++|+ +...+|+.+||..||+|+.+|.++..+++.+|+..+
T Consensus        71 ~~~~~I~~~l-~~Ld~~er~II~~rY~-~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~l  132 (134)
T TIGR01636        71 RNRDAIENCL-NEADEQTRVIIQELYM-KKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEEL  132 (134)
T ss_pred             HHHHHHHHHH-HhCCHHHHHHHHHHHc-cCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            4556788888 8999999999999993 112359999999999999999999999999999765

This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=97.73  E-value=7e-05  Score=58.11  Aligned_cols=47  Identities=28%  Similarity=0.437  Sum_probs=41.4

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      +.|+++|.+|+.+..    .|+|..|||+.+|+|..||+....++++||.-
T Consensus         2 ~~LT~~E~~vl~~l~----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~   48 (58)
T PF00196_consen    2 PSLTERELEVLRLLA----QGMSNKEIAEELGISEKTVKSHRRRIMKKLGV   48 (58)
T ss_dssp             GSS-HHHHHHHHHHH----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred             CccCHHHHHHHHHHH----hcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence            479999999999986    89999999999999999999999999999863

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19

Probab=97.72  E-value=0.00013  Score=63.22  Aligned_cols=56  Identities=34%  Similarity=0.506  Sum_probs=49.6

Q ss_pred             HHHHHHHHHHHccCC-HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521          433 ALKDEVNKLIIVTLG-EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL  492 (508)
Q Consensus       433 el~e~L~~~L~~~Lp-~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKL  492 (508)
                      .....+..+| +.|+ +.+|.||.++|   .+++++.+||+.||+|+.++-.++.+|++.|
T Consensus        43 ~~k~ei~~~I-~~l~d~~~r~iL~~~Y---i~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L   99 (100)
T PF07374_consen   43 KEKLEIRRAI-NKLEDPDERLILRMRY---INKLTWEQIAEELNISRRTYYRIHKKALKEL   99 (100)
T ss_pred             HHHHHHHHHH-HHccChhHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence            3446678888 6775 78999999999   8999999999999999999999999999876

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=97.70  E-value=9.4e-05  Score=55.78  Aligned_cols=45  Identities=33%  Similarity=0.405  Sum_probs=40.9

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      |+++|+.|+.+.+    +++|.+|||+.+|+|+.+|+++..+++++|+.
T Consensus         1 l~~~e~~i~~~~~----~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~   45 (57)
T cd06170           1 LTPREREVLRLLA----EGKTNKEIADILGISEKTVKTHLRNIMRKLGV   45 (57)
T ss_pred             CCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            6899999998854    78999999999999999999999999888875

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=97.63  E-value=0.00018  Score=55.53  Aligned_cols=47  Identities=32%  Similarity=0.487  Sum_probs=41.7

Q ss_pred             CCHHHHHHHhHHhccCC----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDK----ECLTWEDISKRIGLSRERVRQVGLVALEKL  492 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~----eg~TleEIAe~LgIS~erVrqi~~rALkKL  492 (508)
                      |+++|++||..-|-+++    .+.|+.|||+.||||.+|+..++.+|.+||
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kl   51 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKL   51 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            78999999999776542    368999999999999999999999999886

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=97.63  E-value=0.00011  Score=60.28  Aligned_cols=47  Identities=13%  Similarity=0.075  Sum_probs=40.6

Q ss_pred             HHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          438 VNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       438 L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      +.+.| +.||++.+.++.|.+.  .+++|++|||+.||+|..+|++++.+
T Consensus         9 ~~~~l-~~l~~~~r~af~L~R~--~eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879         9 LAERL-TWVDSLAEAAAALARE--EAGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             HHHHH-hcCCHHHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            44556 8999999999999531  58999999999999999999999875

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=97.46  E-value=0.0002  Score=69.56  Aligned_cols=46  Identities=17%  Similarity=0.226  Sum_probs=43.6

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      .|++||++|+.+.-    +|+|.+|||++||+|..||+....+.++||.-
T Consensus       137 ~LT~RE~eVL~lla----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v  182 (207)
T PRK15411        137 SLSRTESSMLRMWM----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT  182 (207)
T ss_pred             cCCHHHHHHHHHHH----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence            49999999999985    99999999999999999999999999999973

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=97.45  E-value=0.00021  Score=61.35  Aligned_cols=50  Identities=18%  Similarity=0.278  Sum_probs=41.1

Q ss_pred             HHHHHHHHccCCHHHHHHHhHHhccCC----CCCCHHHHHHHHCCCHHHHHHHH
Q 010521          436 DEVNKLIIVTLGEREREIIRLYYGLDK----ECLTWEDISKRIGLSRERVRQVG  485 (508)
Q Consensus       436 e~L~~~L~~~Lp~rER~VI~LryGLd~----eg~TleEIAe~LgIS~erVrqi~  485 (508)
                      +.+...|..-|+|+|+.+|.+||||-.    .++|++|||+.+|||+.+|.+..
T Consensus        23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~s   76 (94)
T TIGR01321        23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGS   76 (94)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHH
Confidence            445555545699999999999999943    58999999999999999997543

This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=97.43  E-value=0.0003  Score=66.89  Aligned_cols=47  Identities=17%  Similarity=0.269  Sum_probs=44.3

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ..|+++|++|+.+.-    +|+|.+|||+.|++|..||+....++++||.-
T Consensus       132 ~~LSpRErEVLrLLA----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV  178 (198)
T PRK15201        132 RHFSVTERHLLKLIA----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHV  178 (198)
T ss_pred             CCCCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            579999999999985    99999999999999999999999999999974

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=97.39  E-value=0.0003  Score=68.66  Aligned_cols=46  Identities=22%  Similarity=0.322  Sum_probs=43.7

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..|++||++|+.+.-    +|+|.+|||+.|++|..||+....+.++||.
T Consensus       133 ~~LT~RE~eVL~ll~----~G~snkeIA~~L~iS~~TV~~h~~~I~~KLg  178 (207)
T PRK11475        133 RMLSPTEREILRFMS----RGYSMPQIAEQLERNIKTIRAHKFNVMSKLG  178 (207)
T ss_pred             CCCCHHHHHHHHHHH----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            579999999999986    8999999999999999999999999999994

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=97.37  E-value=0.00032  Score=68.78  Aligned_cols=50  Identities=10%  Similarity=0.068  Sum_probs=46.1

Q ss_pred             HHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          439 NKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       439 ~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      .+++ ..|+|+|++|+.+.-    +|+|.+|||+.|++|..||+....+.++||.
T Consensus       138 ~~~~-~~LS~RE~eVL~Lia----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg  187 (217)
T PRK13719        138 LEAK-NKVTKYQNDVFILYS----FGFSHEYIAQLLNITVGSSKNKISEILKFFG  187 (217)
T ss_pred             hhcc-CCCCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            4455 789999999999985    8999999999999999999999999999986

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=97.37  E-value=0.00032  Score=67.47  Aligned_cols=46  Identities=26%  Similarity=0.371  Sum_probs=43.4

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..|++||++|+.+.-    +|+|.+|||+.|++|..||+....+.++||.
T Consensus       149 ~~Lt~rE~evl~~~~----~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~  194 (216)
T PRK10840        149 KRLSPKESEVLRLFA----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLG  194 (216)
T ss_pred             ccCCHHHHHHHHHHH----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            469999999999985    8999999999999999999999999999994

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=97.28  E-value=0.00043  Score=68.53  Aligned_cols=47  Identities=30%  Similarity=0.239  Sum_probs=44.2

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ..|+++|++||.+..    +|+|..|||+.||+|..||+..+.++++||+.
T Consensus       170 ~~Lt~re~evl~~~a----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~  216 (232)
T TIGR03541       170 GVLSEREREVLAWTA----LGRRQADIAAILGISERTVENHLRSARRKLGV  216 (232)
T ss_pred             ccCCHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            479999999999975    99999999999999999999999999999984

Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.

>TIGR03020 EpsA transcriptional regulator EpsA

Probab=97.26  E-value=0.00046  Score=69.30  Aligned_cols=47  Identities=26%  Similarity=0.237  Sum_probs=44.2

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ..|+++|++|+.+..    +|+|..|||+.||||..||+..+.++++||..
T Consensus       189 ~~LT~RE~evl~l~a----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v  235 (247)
T TIGR03020       189 GLITAREAEILAWVR----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDV  235 (247)
T ss_pred             cCCCHHHHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            579999999999975    99999999999999999999999999999974

Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=97.26  E-value=0.00066  Score=59.58  Aligned_cols=53  Identities=32%  Similarity=0.338  Sum_probs=48.7

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                      .|+..|-+.|+|.+   .+++|++|.|+.||||+.|+..++..|.+|+-..|-...
T Consensus        41 ~L~~dElEAiRL~D---~egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv~Gk   93 (106)
T PF02001_consen   41 VLTVDELEAIRLVD---YEGLSQEEAAERMGVSRPTFQRILESARKKIADALVEGK   93 (106)
T ss_pred             EeeHHHHHHHHHHH---HcCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHCCC
Confidence            58889999999998   899999999999999999999999999999998886543

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=97.26  E-value=0.0012  Score=63.37  Aligned_cols=68  Identities=19%  Similarity=0.243  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHh
Q 010521          432 WALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAM  504 (508)
Q Consensus       432 ~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~  504 (508)
                      ......+...+ .+|+||||+|+....    .|+..++||..||||..||+....+.++||+..--..-++.|
T Consensus       130 ~~~~~~~~~~l-~tLT~RERqVl~~vV----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr~a  197 (202)
T COG4566         130 ADRQAAIRARL-ATLTPRERQVLDLVV----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVRMA  197 (202)
T ss_pred             HHHHHHHHHHH-HhcCHHHHHHHHHHH----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHHHH
Confidence            34456777788 899999999999885    899999999999999999999999999999875544444433

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=97.25  E-value=0.00047  Score=67.40  Aligned_cols=45  Identities=33%  Similarity=0.403  Sum_probs=42.9

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      .|++||++|+++--    +|+|.+|||+.|++|..||+....+.++||.
T Consensus       148 ~LT~RE~eVL~lla----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~  192 (211)
T COG2197         148 LLTPRELEVLRLLA----EGLSNKEIAEELNLSEKTVKTHVSNILRKLG  192 (211)
T ss_pred             CCCHHHHHHHHHHH----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence            59999999999974    9999999999999999999999999999996

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=97.24  E-value=0.00058  Score=67.08  Aligned_cols=47  Identities=19%  Similarity=0.214  Sum_probs=44.2

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ..|+++|++|+.+..    +|+|.+|||+.|++|..||+....++++||.-
T Consensus       154 ~~Lt~rE~~Vl~l~~----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v  200 (216)
T PRK10100        154 ALLTHREKEILNKLR----IGASNNEIARSLFISENTVKTHLYNLFKKIAV  200 (216)
T ss_pred             CCCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            469999999999997    79999999999999999999999999999974

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=97.19  E-value=0.00048  Score=50.88  Aligned_cols=41  Identities=27%  Similarity=0.320  Sum_probs=24.5

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .+|++.||..|...+   .+|+|..+||+.||++++||...+.|
T Consensus         3 ~~Lt~~eR~~I~~l~---~~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen    3 KHLTPEERNQIEALL---EQGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             ---------HHHHHH---CS---HHHHHHHTT--HHHHHHHHHH
T ss_pred             cchhhhHHHHHHHHH---HcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            478999999998887   78999999999999999999988776

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=97.18  E-value=0.00068  Score=67.63  Aligned_cols=46  Identities=22%  Similarity=0.243  Sum_probs=43.6

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      .|++||++||.+..    +|+|..|||++||||..||+..+.++++||-.
T Consensus       179 ~LT~rE~evl~~~a----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~  224 (240)
T PRK10188        179 NFSKREKEILKWTA----EGKTSAEIAMILSISENTVNFHQKNMQKKFNA  224 (240)
T ss_pred             CCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence            69999999999986    99999999999999999999999999999963

>PRK13870 transcriptional regulator TraR; Provisional

Probab=97.18  E-value=0.00065  Score=67.52  Aligned_cols=45  Identities=22%  Similarity=0.202  Sum_probs=42.8

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      .|++||++||.+-=    +|+|..|||.+||||..||+..+..|++||-
T Consensus       173 ~LT~RE~E~L~W~A----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLg  217 (234)
T PRK13870        173 WLDPKEATYLRWIA----VGKTMEEIADVEGVKYNSVRVKLREAMKRFD  217 (234)
T ss_pred             CCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            59999999999985    9999999999999999999999999999995

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=97.02  E-value=0.0021  Score=49.92  Aligned_cols=47  Identities=32%  Similarity=0.379  Sum_probs=43.1

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ..|+++|.+|+.+.-    +|+|..|||..+|+|..||+....++..||.-
T Consensus         3 ~~Lt~rE~~v~~l~~----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~   49 (65)
T COG2771           3 ADLTPREREILRLVA----QGKSNKEIARILGISEETVKTHLRNIYRKLGV   49 (65)
T ss_pred             ccCCHHHHHHHHHHH----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence            369999999998875    78999999999999999999999999999874

>PRK09483 response regulator; Provisional

Probab=97.00  E-value=0.0013  Score=62.04  Aligned_cols=46  Identities=26%  Similarity=0.351  Sum_probs=42.8

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..|+++|++|+.+..    +|+|.+|||+.|++|..||+...++.++||-
T Consensus       147 ~~Lt~rE~~vl~~~~----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~  192 (217)
T PRK09483        147 ASLSERELQIMLMIT----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLN  192 (217)
T ss_pred             cccCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            569999999998864    8999999999999999999999999999984

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=96.84  E-value=0.0025  Score=58.70  Aligned_cols=46  Identities=33%  Similarity=0.435  Sum_probs=42.8

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..|+++|++|+.+.    .+|+|.+|||+.+++|..||+....++++||.
T Consensus       148 ~~lt~~e~~vl~l~----~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~  193 (211)
T PRK15369        148 PLLTPRERQILKLI----TEGYTNRDIAEQLSISIKTVETHRLNMMRKLD  193 (211)
T ss_pred             cCCCHHHHHHHHHH----HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            46999999999985    48999999999999999999999999999996

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.81  E-value=0.0062  Score=52.70  Aligned_cols=50  Identities=18%  Similarity=0.312  Sum_probs=44.6

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      .-|+++|+..+.++|   .+++|+.|||+.++||+++|...+.|+-+.|-..=
T Consensus        16 sLLT~KQ~~Y~~lyy---~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~YE   65 (105)
T COG2739          16 SLLTKKQKNYLELYY---LDDLSLSEIAEEFNVSRQAIYDNIKRTEKILEDYE   65 (105)
T ss_pred             HHHhHHHHHHHHHHH---HhhccHHHHHHHhCccHHHHHHHHHHHHHHHHHHH
Confidence            348999999999999   88999999999999999999999999887776543

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=96.75  E-value=0.0031  Score=61.76  Aligned_cols=52  Identities=27%  Similarity=0.405  Sum_probs=45.0

Q ss_pred             cCCHHHHHHHhHHhccCC----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDK----ECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~----eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      .|+++|++||+.-|=.|+    ...+.+|||+.||||.+|+.+++.+|.+||=..+
T Consensus       155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~~  210 (215)
T COG3413         155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEAY  210 (215)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            599999999999886642    3589999999999999999999999999985443

>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]

Probab=96.72  E-value=0.036  Score=57.72  Aligned_cols=159  Identities=12%  Similarity=0.034  Sum_probs=96.4

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccH
Q 010521          267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL  346 (508)
Q Consensus       267 e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~  346 (508)
                      +..+..-.+.++.---+|.++=.-+||.+|++|+..++...+=-|-+  .-..|++.--|+.-++.+++..+.-..|.+.
T Consensus         8 e~~~r~~~~r~~a~L~r~~rd~dlAEEa~~dA~~~Ale~WPr~G~P~--~PaAWL~~v~R~~aiD~~Rr~~~~~~~~~el   85 (415)
T COG4941           8 EAAARIERPRAMAALARYLRDLDLAEEALQDAFAAALERWPRAGPPR--NPAAWLIAVGRNRAIDRVRRRARRDAAPPEL   85 (415)
T ss_pred             HHHHHHhhhHHHHHHHHHhcccchHHHHHHHHHHHHHHhCcccCCCC--ChHHHHHHHHhhhHHHHHHHHHHhccCChhh
Confidence            34444455555555566777656789999999987665554433323  2456777777776666666654322222110


Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCcc
Q 010521          347 HERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPW  426 (508)
Q Consensus       347 ~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe  426 (508)
                                                                    .++.+         +.+....+...|..   -+ 
T Consensus        86 ----------------------------------------------~~~~e---------~~e~~~a~~~~d~~---i~-  106 (415)
T COG4941          86 ----------------------------------------------LLSDE---------DEEMEEAEALDDEH---IR-  106 (415)
T ss_pred             ----------------------------------------------ccccc---------chhhhccccccccc---cc-
Confidence                                                          00000         00000111111111   11 


Q ss_pred             chHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          427 HGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       427 ~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                           .+....|.-+-.-.||+.+|--+.|+.   ..|+|..|||..|=|+..++-|++.||.++++.
T Consensus       107 -----Dd~LRLiFvccHPal~~~~riALtLR~---v~GLs~~eIArAFLv~e~am~QRivRAK~ri~~  166 (415)
T COG4941         107 -----DDRLRLIFVCCHPALPPEQRIALTLRL---VGGLSTAEIARAFLVPEAAMAQRIVRAKARIRE  166 (415)
T ss_pred             -----hhhHHhhhhhcCCCCChhhHHHHHHHH---HcCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHh
Confidence                 112222222222579999999999998   789999999999999999999999999999985

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=96.66  E-value=0.0021  Score=72.53  Aligned_cols=58  Identities=22%  Similarity=0.356  Sum_probs=47.1

Q ss_pred             hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHH
Q 010521          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK  268 (508)
Q Consensus       189 ~~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~  268 (508)
                      ..|+++|||++||++||||.++|+++|++|..|..                              .+.+.+.+++-+...
T Consensus       102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~------------------------------~v~~al~~~P~~i~~  151 (619)
T PRK05658        102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGEN------------------------------IMIAALCESPLTIDA  151 (619)
T ss_pred             CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHH------------------------------HHHHHHHhCcHHHHH
Confidence            35899999999999999999999999999999996                              455555566666666


Q ss_pred             HHHHHHHH
Q 010521          269 LVMSNVRL  276 (508)
Q Consensus       269 LIe~yl~L  276 (508)
                      ++.-|-.+
T Consensus       152 il~~~e~v  159 (619)
T PRK05658        152 ILEWYDRL  159 (619)
T ss_pred             HHHHHHHH
Confidence            66666554

>PRK10651 transcriptional regulator NarL; Provisional

Probab=96.59  E-value=0.004  Score=58.08  Aligned_cols=46  Identities=28%  Similarity=0.392  Sum_probs=43.0

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..|+++|++|+.+..    +|++.++||+.+++|..||+....++++||.
T Consensus       154 ~~Lt~rE~~vl~~l~----~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~  199 (216)
T PRK10651        154 NQLTPRERDILKLIA----QGLPNKMIARRLDITESTVKVHVKHMLKKMK  199 (216)
T ss_pred             ccCCHHHHHHHHHHH----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence            469999999999865    8999999999999999999999999999996

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=96.52  E-value=0.0067  Score=55.51  Aligned_cols=55  Identities=20%  Similarity=0.319  Sum_probs=47.6

Q ss_pred             HHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          437 EVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       437 ~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      .+...+ ..|+++|+.|+.+.+    .+++.++||+.+|+|..+|+....++++||+..-
T Consensus       134 ~~~~~~-~~l~~~e~~vl~~~~----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~  188 (202)
T PRK09390        134 DIRARI-ASLSERERQVMDGLV----AGLSNKVIARDLDISPRTVEVYRANVMTKMQAGS  188 (202)
T ss_pred             HHHHHH-HhhhhhHHHHHHHHH----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHcccc
Confidence            345556 789999999999754    7899999999999999999999999999997543

>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=96.52  E-value=0.0097  Score=47.78  Aligned_cols=47  Identities=26%  Similarity=0.208  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcC------CCCCHHHHHHHHHHHHHHhhhccC
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDN------MGADMADLVQGGLIGLLRGIEKFD  310 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~------~g~d~EDLiQEG~IgLirAiekFD  310 (508)
                      .|.++++.+|.|++.+.+.+-..      ++.--+|+-|+--..|++++.+|+
T Consensus        13 ~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~   65 (65)
T PF12645_consen   13 EAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE   65 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence            99999999999999999987221      244459999999999999999996

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

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=96.49  E-value=0.0024  Score=57.30  Aligned_cols=49  Identities=24%  Similarity=0.316  Sum_probs=45.1

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      .-|+++|-.|+.||-    .|.|++|||++||.|+..|+-++.+|+.++.+.-
T Consensus         7 tflte~qikvl~lRe----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekar   55 (143)
T COG1356           7 TFLTEQQIKVLVLRE----KGLTQSEIARILKTTRANVSAIEKRALENIEKAR   55 (143)
T ss_pred             ceeehhheeeeehhh----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHH
Confidence            358999999999995    8999999999999999999999999999998754

>PRK01381 Trp operon repressor; Provisional

Probab=96.45  E-value=0.0032  Score=54.50  Aligned_cols=48  Identities=19%  Similarity=0.254  Sum_probs=38.6

Q ss_pred             HHHHHHHHHccCCHHHHHHHhHHhccCC---C-CCCHHHHHHHHCCCHHHHH
Q 010521          435 KDEVNKLIIVTLGEREREIIRLYYGLDK---E-CLTWEDISKRIGLSRERVR  482 (508)
Q Consensus       435 ~e~L~~~L~~~Lp~rER~VI~LryGLd~---e-g~TleEIAe~LgIS~erVr  482 (508)
                      .+.+...|..-|+|.|+..|..|+++-.   + ++|++|||+.+|||..||.
T Consensus        22 ~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTIT   73 (99)
T PRK01381         22 EDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATIT   73 (99)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeeh
Confidence            3445555534499999999999999832   4 5999999999999999885

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=96.37  E-value=0.0079  Score=51.55  Aligned_cols=52  Identities=31%  Similarity=0.293  Sum_probs=47.4

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK  499 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~  499 (508)
                      .|+..|-+.|+|..   +++++++|-|.+||||+.|+-+.+..|++|+-.+|-..
T Consensus        33 ~lt~eElEAlRLvD---~~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLveG   84 (99)
T COG1342          33 ILTIEELEALRLVD---YEGLTQEEAALRMGISRQTFWRLLTSARKKVADALVEG   84 (99)
T ss_pred             eecHHHHHHHHHHh---HhhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHhcC
Confidence            47888999999998   89999999999999999999999999999999887654

>PRK15320 transcriptional activator SprB; Provisional

Probab=96.31  E-value=0.0072  Score=58.59  Aligned_cols=46  Identities=13%  Similarity=0.148  Sum_probs=43.2

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      -.|+++|.+|+.+--    +|+|.+|||+.|++|..||+....+.+.||.
T Consensus       163 ~~LSdREIEVL~LLA----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLg  208 (251)
T PRK15320        163 PGVTQAKYALLILLS----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLG  208 (251)
T ss_pred             CCCCHHHHHHHHHHH----cCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence            578999999999875    8999999999999999999999999999986

>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family

Probab=96.18  E-value=0.033  Score=50.26  Aligned_cols=61  Identities=20%  Similarity=0.190  Sum_probs=49.9

Q ss_pred             HHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          436 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       436 e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      ..+..++...|++.+|.||..+| |+.++++..+|+..||+|+.+...+..+|+.++-..+.
T Consensus        70 ~~i~~ai~~~l~~~~r~Il~~~Y-l~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l~  130 (132)
T TIGR01637        70 RAIVNAIVNQLDEISRQILYDKY-LEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLYG  130 (132)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHH-cCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHhC
Confidence            34444442589999999999999 22238999999999999999999999999999877653

This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.

>PRK10403 transcriptional regulator NarP; Provisional

Probab=95.98  E-value=0.012  Score=54.62  Aligned_cols=48  Identities=23%  Similarity=0.246  Sum_probs=43.5

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA  495 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~  495 (508)
                      ..|+++|.+|+.+..    +|+|.++||+.+++|..||+..+.+.++||.-.
T Consensus       152 ~~Lt~~e~~vl~~~~----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~  199 (215)
T PRK10403        152 SVLTERELDVLHELA----QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVR  199 (215)
T ss_pred             ccCCHHHHHHHHHHH----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence            359999999998875    889999999999999999999999999998643

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=95.83  E-value=0.02  Score=52.97  Aligned_cols=46  Identities=26%  Similarity=0.342  Sum_probs=42.8

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..|+++|++|+.+..    +|+|.++||+.+++|..||+....+.++||.
T Consensus       136 ~~Lt~~E~~il~~l~----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~  181 (196)
T PRK10360        136 DPLTKRERQVAEKLA----QGMAVKEIAAELGLSPKTVHVHRANLMEKLG  181 (196)
T ss_pred             cCCCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            469999999999975    7899999999999999999999999999986

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=95.82  E-value=0.018  Score=53.58  Aligned_cols=45  Identities=27%  Similarity=0.290  Sum_probs=41.0

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      .|+++|..|+.+..    +|+|.+|||+.|++|..||+....++++||.
T Consensus       149 ~lt~re~~vl~~l~----~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~  193 (210)
T PRK09935        149 VLSNREVTILRYLV----SGLSNKEIADQLLLSNKTVSAHKSNIYGKLG  193 (210)
T ss_pred             cCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            58999999987654    7899999999999999999999999999986

>PRK13558 bacterio-opsin activator; Provisional

Probab=95.72  E-value=0.016  Score=65.25  Aligned_cols=52  Identities=23%  Similarity=0.222  Sum_probs=44.2

Q ss_pred             ccCCHHHHHHHhHHhccCC----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDK----ECLTWEDISKRIGLSRERVRQVGLVALEKLKHA  495 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~----eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~  495 (508)
                      ..|+++|+++|..-|-.++    .+.|.+|||+.||||++|+.+++.+|.+||=..
T Consensus       606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~~  661 (665)
T PRK13558        606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVGA  661 (665)
T ss_pred             hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            5799999999999984331    234999999999999999999999999998543

>PRK04841 transcriptional regulator MalT; Provisional

Probab=95.71  E-value=0.016  Score=67.28  Aligned_cols=46  Identities=20%  Similarity=0.288  Sum_probs=43.3

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..|+++|++|+.+..    +|+|++|||+.|+||..||+..+.+...||.
T Consensus       837 ~~lt~~e~~v~~~~~----~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~  882 (903)
T PRK04841        837 SPLTQREWQVLGLIY----SGYSNEQIAGELDVAATTIKTHIRNLYQKLG  882 (903)
T ss_pred             CCCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            359999999999976    9999999999999999999999999999996

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=95.55  E-value=0.028  Score=52.41  Aligned_cols=46  Identities=22%  Similarity=0.294  Sum_probs=42.7

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..|+++|++|+.+..    .|.|.++||+.+++|..||+....+.++||.
T Consensus       142 ~~lt~~E~~vl~~l~----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~  187 (204)
T PRK09958        142 DSLSKQEISVMRYIL----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLE  187 (204)
T ss_pred             ccCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            469999999999876    7899999999999999999999999999984

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=95.34  E-value=0.016  Score=43.20  Aligned_cols=32  Identities=38%  Similarity=0.412  Sum_probs=23.4

Q ss_pred             HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      ||.++.    +|+|..+||+.||||+.||.++..+-
T Consensus        10 ii~l~~----~G~s~~~ia~~lgvs~~Tv~~w~kr~   41 (50)
T PF13384_consen   10 IIRLLR----EGWSIREIAKRLGVSRSTVYRWIKRY   41 (50)
T ss_dssp             HHHHHH----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred             HHHHHH----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence            666665    69999999999999999999987664

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=95.21  E-value=0.026  Score=39.11  Aligned_cols=27  Identities=41%  Similarity=0.598  Sum_probs=19.4

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          464 CLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       464 g~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ++|.+|||+.+|++++||+    |++++|++
T Consensus         2 ~mtr~diA~~lG~t~ETVS----R~l~~l~~   28 (32)
T PF00325_consen    2 PMTRQDIADYLGLTRETVS----RILKKLER   28 (32)
T ss_dssp             E--HHHHHHHHTS-HHHHH----HHHHHHHH
T ss_pred             CcCHHHHHHHhCCcHHHHH----HHHHHHHH
Confidence            3799999999999999997    55555553

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=95.17  E-value=0.046  Score=41.80  Aligned_cols=50  Identities=22%  Similarity=0.326  Sum_probs=41.9

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      +|+..++-++.+.|-  ..+.++++||..+|||++||+++.+..+.-|-..+
T Consensus         2 kLs~~d~lll~L~~L--R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l   51 (53)
T PF13613_consen    2 KLSLEDQLLLTLMYL--RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL   51 (53)
T ss_pred             CCCHHHHHHHHHHHH--HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence            578888888877662  46899999999999999999999999888776543

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=95.10  E-value=0.056  Score=40.02  Aligned_cols=42  Identities=21%  Similarity=0.343  Sum_probs=30.4

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL  489 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL  489 (508)
                      |++.++.||..-.-  ..++|..|||+.+|+|..+|++++.+-.
T Consensus         1 l~~~~~~Il~~l~~--~~~~t~~ela~~~~is~~tv~~~l~~L~   42 (48)
T PF13412_consen    1 LDETQRKILNYLRE--NPRITQKELAEKLGISRSTVNRYLKKLE   42 (48)
T ss_dssp             --HHHHHHHHHHHH--CTTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            57788888877651  3569999999999999999987766543

...

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=95.07  E-value=0.029  Score=58.43  Aligned_cols=36  Identities=31%  Similarity=0.510  Sum_probs=33.0

Q ss_pred             HHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521          452 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE  490 (508)
Q Consensus       452 ~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALk  490 (508)
                      .|-.|||   .+++|+.|||++||+||.+|++++.+|++
T Consensus        20 ~vA~lYY---~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~   55 (318)
T PRK15418         20 RIAWFYY---HDGLTQSEIGERLGLTRLKVSRLLEKGRQ   55 (318)
T ss_pred             HHHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            3667888   89999999999999999999999999976

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=94.93  E-value=0.09  Score=47.93  Aligned_cols=56  Identities=23%  Similarity=0.422  Sum_probs=44.5

Q ss_pred             HHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521          435 KDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL  492 (508)
Q Consensus       435 ~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKL  492 (508)
                      .+.+...+ +.|.+.++.||.+||+- ..++|+.+||..|+++..|++.+...-...+
T Consensus        72 k~~id~~~-~~l~de~k~Ii~lry~~-r~~~TW~~IA~~l~i~erta~r~~~~fK~~i  127 (130)
T PF05263_consen   72 KEAIDRWL-ETLIDEEKRIIKLRYDR-RSRRTWYQIAQKLHISERTARRWRDRFKNDI  127 (130)
T ss_pred             HHHHHHHH-HhhCHHHHHHHHHHHcc-cccchHHHHHHHhCccHHHHHHHHHHHHHHh
Confidence            34555666 89999999999999952 1469999999999999999988776654433

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=94.83  E-value=0.064  Score=45.67  Aligned_cols=39  Identities=21%  Similarity=0.345  Sum_probs=32.0

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      +.|++| ..|+.+.-    .|+|..+||+.+|||+.||.++ .++
T Consensus        35 ~~Ls~R-~~I~~ll~----~G~S~~eIA~~LgISrsTIyRi-~R~   73 (88)
T TIGR02531        35 QSLAQR-LQVAKMLK----QGKTYSDIEAETGASTATISRV-KRC   73 (88)
T ss_pred             HhhhHH-HHHHHHHH----CCCCHHHHHHHHCcCHHHHHHH-HHh
Confidence            467888 77777753    7899999999999999999984 444

This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=94.19  E-value=0.093  Score=34.51  Aligned_cols=37  Identities=22%  Similarity=0.292  Sum_probs=28.9

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQV  484 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi  484 (508)
                      .+++.++..+...+   ..+.|..+||+.+|+++.+|.++
T Consensus         5 ~~~~~~~~~i~~~~---~~~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569           5 KLTPEQIEEARRLL---AAGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             cCCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHh
Confidence            35566666665556   47789999999999999999875

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=94.18  E-value=0.076  Score=39.21  Aligned_cols=32  Identities=34%  Similarity=0.456  Sum_probs=24.0

Q ss_pred             HHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 010521          450 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVG  485 (508)
Q Consensus       450 ER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~  485 (508)
                      ...|+.|+-    +|+|..+||+.+|||+.||.+++
T Consensus        11 ~~~i~~l~~----~G~si~~IA~~~gvsr~TvyR~l   42 (45)
T PF02796_consen   11 IEEIKELYA----EGMSIAEIAKQFGVSRSTVYRYL   42 (45)
T ss_dssp             HHHHHHHHH----TT--HHHHHHHTTS-HHHHHHHH
T ss_pred             HHHHHHHHH----CCCCHHHHHHHHCcCHHHHHHHH
Confidence            455777764    78999999999999999998765

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ

Probab=93.94  E-value=0.35  Score=43.62  Aligned_cols=55  Identities=15%  Similarity=0.158  Sum_probs=49.2

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM  501 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l  501 (508)
                      .+-.|.+-.+|.+||   ..+.|...||..+++|...|++.+.+|-.-+...|...+.
T Consensus        61 ~~~~~~~~~ll~~~Y---v~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~l~~~~~  115 (125)
T PF06530_consen   61 KKRDPEEYDLLILYY---VYGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGCLSMLTI  115 (125)
T ss_pred             HccCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhhhHHhhh
Confidence            468899999999999   7899999999999999999999999999999988765443

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent

>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=93.52  E-value=0.091  Score=42.74  Aligned_cols=36  Identities=33%  Similarity=0.540  Sum_probs=28.0

Q ss_pred             chhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhh
Q 010521          225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM  260 (508)
Q Consensus       225 ~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~  260 (508)
                      ..++.+|...+||+|+.+++|..+||+.+++...+.
T Consensus         7 ~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~   42 (78)
T PF04539_consen    7 ERARRELEQELGREPTDEEIAEELGISVEEVRELLQ   42 (78)
T ss_dssp             HHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHH
Confidence            356778999999999999999999999998776654

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 ....

>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []

Probab=92.84  E-value=0.21  Score=39.21  Aligned_cols=32  Identities=19%  Similarity=0.251  Sum_probs=27.1

Q ss_pred             HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      ...|+.    +|++..|||+.||+++.||.....+-
T Consensus         6 A~~LY~----~G~~~~eIA~~Lg~~~~TV~~W~~r~   37 (58)
T PF06056_consen    6 ARSLYL----QGWSIKEIAEELGVPRSTVYSWKDRY   37 (58)
T ss_pred             HHHHHH----cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence            444554    89999999999999999999998764

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=92.83  E-value=0.12  Score=59.67  Aligned_cols=45  Identities=27%  Similarity=0.276  Sum_probs=42.8

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      |+.||++|+.+.|    .|+|.+|||+++.||-.||+..+.....||.-
T Consensus       832 Ls~RE~eVL~Lia----~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV  876 (894)
T COG2909         832 LSQRELEVLGLIA----QGLSNEEIAQELFISLTTVKTHIRNIYQKLGV  876 (894)
T ss_pred             ccHHHHHHHHHHH----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Confidence            8999999999998    99999999999999999999999999999863

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=92.80  E-value=0.2  Score=40.23  Aligned_cols=43  Identities=21%  Similarity=0.297  Sum_probs=27.5

Q ss_pred             ccCCHHHHHHHhHHhc-c--CCCCCCHHHHHHHHCCC-HHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYG-L--DKECLTWEDISKRIGLS-RERVRQVGL  486 (508)
Q Consensus       444 ~~Lp~rER~VI~LryG-L--d~eg~TleEIAe~LgIS-~erVrqi~~  486 (508)
                      ..|+++|++|+...-. +  ++-.-|.+|||+.||++ .++|.+.+.
T Consensus         2 ~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~   48 (65)
T PF01726_consen    2 KELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK   48 (65)
T ss_dssp             ----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence            5799999999876322 1  23467999999999996 999976654

The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=92.50  E-value=0.31  Score=43.39  Aligned_cols=48  Identities=27%  Similarity=0.342  Sum_probs=42.5

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ..|++.+..-|..+.   ...=+++|+++.||||..|||.++.+.+++|.-
T Consensus        32 ~~L~~E~~~Fi~~Fi---~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~   79 (113)
T PF09862_consen   32 ARLSPEQLEFIKLFI---KNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY   79 (113)
T ss_pred             hcCCHHHHHHHHHHH---HhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence            689999999887766   445699999999999999999999999999875

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=92.46  E-value=0.33  Score=35.54  Aligned_cols=40  Identities=28%  Similarity=0.427  Sum_probs=26.8

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      |++..+.||..--.  ....|+.+||+.+|+|..+|.+++.+
T Consensus         1 lD~~D~~Il~~Lq~--d~r~s~~~la~~lglS~~~v~~Ri~r   40 (42)
T PF13404_consen    1 LDELDRKILRLLQE--DGRRSYAELAEELGLSESTVRRRIRR   40 (42)
T ss_dssp             --HHHHHHHHHHHH---TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--cCCccHHHHHHHHCcCHHHHHHHHHH
Confidence            34556677766441  24589999999999999999877654

...

>PF13518 HTH_28: Helix-turn-helix domain

Probab=92.43  E-value=0.2  Score=37.17  Aligned_cols=34  Identities=26%  Similarity=0.343  Sum_probs=27.1

Q ss_pred             HHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521          452 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL  489 (508)
Q Consensus       452 ~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL  489 (508)
                      .||.++.    ++.|..+||+.+|||+.+|.+++.+-.
T Consensus         4 ~iv~~~~----~g~s~~~~a~~~gis~~tv~~w~~~y~   37 (52)
T PF13518_consen    4 QIVELYL----EGESVREIAREFGISRSTVYRWIKRYR   37 (52)
T ss_pred             HHHHHHH----cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence            3555544    677999999999999999998877653

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=92.42  E-value=0.22  Score=48.75  Aligned_cols=46  Identities=9%  Similarity=0.147  Sum_probs=36.0

Q ss_pred             cCCHHHHHHHhHHh-ccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYY-GLDKECLTWEDISKRIGLSRERVRQVGLVALE  490 (508)
Q Consensus       445 ~Lp~rER~VI~Lry-GLd~eg~TleEIAe~LgIS~erVrqi~~rALk  490 (508)
                      .|++++.+++.... +...+|+|.+|||+.||+|..||+....++..
T Consensus       158 ~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~  204 (239)
T PRK10430        158 GLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVN  204 (239)
T ss_pred             CCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHh
Confidence            58888877664432 22247899999999999999999999987744

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=92.39  E-value=0.17  Score=52.96  Aligned_cols=35  Identities=40%  Similarity=0.533  Sum_probs=31.2

Q ss_pred             HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521          453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE  490 (508)
Q Consensus       453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALk  490 (508)
                      +-.+||   .+|+|+.|||++||||+.+|++.+.+|.+
T Consensus        18 ~A~lYY---~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~   52 (321)
T COG2390          18 AAWLYY---VEGLTQSEIAERLGISRATVSRLLAKARE   52 (321)
T ss_pred             HHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            445777   79999999999999999999999998875

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=92.23  E-value=0.23  Score=39.36  Aligned_cols=35  Identities=17%  Similarity=0.354  Sum_probs=26.5

Q ss_pred             HHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          452 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       452 ~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..+.++... ...+++.+||+.||||..||+.+..+
T Consensus        11 kA~e~y~~~-~g~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   11 KAFEIYKES-NGKIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             HHHHHHHHh-CCCccHHHHHHHHCCCHHHHHHHhhh
Confidence            345554421 35799999999999999999988764

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>smart00351 PAX Paired Box domain

Probab=92.17  E-value=0.34  Score=43.61  Aligned_cols=41  Identities=22%  Similarity=0.135  Sum_probs=32.8

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL  489 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL  489 (508)
                      ++..+|.=|...|   .+|.|..+||+.||||+.||.+++.+..
T Consensus        18 ~s~~~R~riv~~~---~~G~s~~~iA~~~gvs~~tV~kwi~r~~   58 (125)
T smart00351       18 LPDEERQRIVELA---QNGVRPCDISRQLCVSHGCVSKILGRYY   58 (125)
T ss_pred             CCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            5555555444555   4789999999999999999999998864

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=92.10  E-value=0.16  Score=39.04  Aligned_cols=40  Identities=25%  Similarity=0.216  Sum_probs=27.5

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|+-.|+.=|.-++   ..|.+..+||+.|||+++||+.|...
T Consensus         6 ~LTl~eK~~iI~~~---e~g~s~~~ia~~fgv~~sTv~~I~K~   45 (53)
T PF04218_consen    6 SLTLEEKLEIIKRL---EEGESKRDIAREFGVSRSTVSTILKN   45 (53)
T ss_dssp             S--HHHHHHHHHHH---HCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred             cCCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence            46666666444445   57889999999999999999998765

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B

Probab=91.86  E-value=0.31  Score=37.48  Aligned_cols=44  Identities=18%  Similarity=0.225  Sum_probs=32.6

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .|++.|..||..-+.-+..++|..|||+.+++++.+|.+++.+-
T Consensus         2 glt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L   45 (62)
T PF12802_consen    2 GLTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRL   45 (62)
T ss_dssp             TSTHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            37788888887765422233899999999999999998776553

...

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

Probab=91.35  E-value=5.8  Score=40.07  Aligned_cols=63  Identities=22%  Similarity=0.403  Sum_probs=45.7

Q ss_pred             hhhhHHHHHHhhc--ccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhh
Q 010521          189 IQNRLKGYVKGVV--SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME  261 (508)
Q Consensus       189 ~~~~~~~yl~~i~--~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e  261 (508)
                      +-+.+.+||+...  ..|    --..++.++      ...+..+|...+|++|+++++|..+|++.++....+..
T Consensus        85 I~Gei~d~LR~~~~v~vp----R~~~~~~~~------i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~  149 (247)
T COG1191          85 IRGEILDYLRKNDSVKVP----RSLRELGRR------IEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLA  149 (247)
T ss_pred             HHHHHHHHHHhCCCccCc----HHHHHHHHH------HHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHH
Confidence            4467788999877  444    334444444      34566789999999999999999999999875555443

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

Probab=91.32  E-value=2.9  Score=44.10  Aligned_cols=32  Identities=31%  Similarity=0.509  Sum_probs=30.4

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHcCC
Q 010521          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGL  222 (508)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd  222 (508)
                      +.+..|+..+...|+|+++||..|+++++.|+
T Consensus        67 ~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~   98 (342)
T COG0568          67 GRLSFYIRAIEAAPLLTPEEEKALARRLKRGE   98 (342)
T ss_pred             hhHHHHHHHHhhhcccChHHHHHHHHHHHcCC
Confidence            58889999999999999999999999999997

>PHA00675 hypothetical protein

Probab=90.67  E-value=0.49  Score=39.20  Aligned_cols=41  Identities=17%  Similarity=0.238  Sum_probs=32.3

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL  486 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~  486 (508)
                      .+|++.|-+.|+..+-  .+|.|+.+||+.||||+++|.+|.+
T Consensus        21 AKLt~~qV~~IR~l~~--r~G~s~~~IA~~fGVsrstV~~I~~   61 (78)
T PHA00675         21 AKLTDAEVERIRELHE--VEGMSYAVLAEKFEQSKGAIAKICR   61 (78)
T ss_pred             cccCHHHHHHHHHHHH--hcCccHHHHHHHhCCCHHHHHHHHc
Confidence            5677777766655441  2788999999999999999998865

>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression

Probab=90.23  E-value=0.4  Score=40.77  Aligned_cols=46  Identities=15%  Similarity=0.187  Sum_probs=34.2

Q ss_pred             ccCCHHHHHHHhHHhccC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLD----KECLTWEDISKRIGLSRERVRQVGLVALE  490 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd----~eg~TleEIAe~LgIS~erVrqi~~rALk  490 (508)
                      +-|+|.|+.-+..|+-+-    .+|+|+.||++.+|+|..||.+ ..++|+
T Consensus        25 dL~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItR-vsr~Lk   74 (87)
T PF01371_consen   25 DLCTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITR-VSRCLK   74 (87)
T ss_dssp             HHSSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHH-HHHHHH
T ss_pred             HhCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH-HHHHHH
Confidence            447888887776665442    2789999999999999999863 344444

The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....

>PF13730 HTH_36: Helix-turn-helix domain

Probab=90.05  E-value=1  Score=34.08  Aligned_cols=45  Identities=22%  Similarity=0.355  Sum_probs=32.0

Q ss_pred             cCCHHHHHHHhHHhcc-CCCC---CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGL-DKEC---LTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGL-d~eg---~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      .|++.++.|+..-.-+ +.++   .|.+.||+.+|+|+.||.    ++++.|.
T Consensus         2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~----~~i~~L~   50 (55)
T PF13730_consen    2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQ----RAIKELE   50 (55)
T ss_pred             CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHH
Confidence            5888888877654433 2222   389999999999999996    4555554

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=90.01  E-value=2.2  Score=45.39  Aligned_cols=129  Identities=19%  Similarity=0.307  Sum_probs=68.4

Q ss_pred             hhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHh
Q 010521          226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRG  305 (508)
Q Consensus       226 ~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirA  305 (508)
                      .+..+|...+|++|+.+++|..+|++.++++..+....            -..++-..   -+.+ +|      ..+...
T Consensus       220 ~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~------------~~~SLd~~---~~~~-~~------~~l~d~  277 (367)
T PRK09210        220 RVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQ------------EPVSLETP---IGEE-DD------SHLGDF  277 (367)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhc------------CCCCcCCC---CCCC-Cc------chhhhh
Confidence            34567788899999999999999999988766543210            00000000   0111 11      011111


Q ss_pred             hhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHH
Q 010521          306 IEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVR  384 (508)
Q Consensus       306 iekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~  384 (508)
                      +.  |+....+........++..+..+|.      .+|..-...+.    .  .+. .-|.+-|.+|||+.+|+|.++|+
T Consensus       278 i~--d~~~~~p~~~~~~~~~~~~l~~~l~------~L~~rEr~Vl~----l--rygl~~~~~~tl~EIa~~lgvs~erVr  343 (367)
T PRK09210        278 IE--DQDATSPADHAAYELLKEQLEDVLD------TLTDREENVLR----L--RFGLDDGRTRTLEEVGKVFGVTRERIR  343 (367)
T ss_pred             cc--CCCCCCHHHHHHHHHHHHHHHHHHH------hCCHHHHHHHH----H--HhccCCCCCccHHHHHHHHCCCHHHHH
Confidence            21  1111223344445555555555542      23322211110    0  000 12356799999999999999999


Q ss_pred             HHHHHh
Q 010521          385 NATEAI  390 (508)
Q Consensus       385 ~~l~~~  390 (508)
                      ++...+
T Consensus       344 Qi~~~A  349 (367)
T PRK09210        344 QIEAKA  349 (367)
T ss_pred             HHHHHH
Confidence            986543

>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I

Probab=89.79  E-value=1.7  Score=40.13  Aligned_cols=64  Identities=17%  Similarity=0.201  Sum_probs=40.3

Q ss_pred             HHccCCHHHHHHHhHH-----hccCCCCCCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHhhHHHhh
Q 010521          442 IIVTLGEREREIIRLY-----YGLDKECLTWEDISKRIGLSRERVRQVGL--VALEKLKHAARKKKMEAML  505 (508)
Q Consensus       442 L~~~Lp~rER~VI~Lr-----yGLd~eg~TleEIAe~LgIS~erVrqi~~--rALkKLR~~L~~~~l~~~l  505 (508)
                      |..+|++.|+....+-     .+.+++..|+.|||+.+||+++|+-++.+  ++.....+.+....+..++
T Consensus         7 le~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~~~~~   77 (142)
T PF13022_consen    7 LEAKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFLSSHR   77 (142)
T ss_dssp             HHTTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHHHTTH
T ss_pred             HHHHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHhH
Confidence            3378999998843332     22223569999999999999999999884  4566666666666666554

>cd00131 PAX Paired Box domain

Probab=89.76  E-value=0.78  Score=41.54  Aligned_cols=41  Identities=20%  Similarity=0.101  Sum_probs=31.5

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL  489 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL  489 (508)
                      |+...|.-|.+.|   .+|+|..+||+.||||+.+|..++.+-.
T Consensus        18 lS~d~R~rIv~~~---~~G~s~~~iA~~~~Vs~~tV~r~i~r~~   58 (128)
T cd00131          18 LPDSIRQRIVELA---QSGIRPCDISRQLRVSHGCVSKILNRYY   58 (128)
T ss_pred             CCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4554444333445   5899999999999999999999988754

>PHA02591 hypothetical protein; Provisional

Probab=89.75  E-value=0.58  Score=38.90  Aligned_cols=25  Identities=28%  Similarity=0.357  Sum_probs=22.7

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521          462 KECLTWEDISKRIGLSRERVRQVGL  486 (508)
Q Consensus       462 ~eg~TleEIAe~LgIS~erVrqi~~  486 (508)
                      ..|+|.++||+.||+++++|++...
T Consensus        57 eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         57 RKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            4689999999999999999999875

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=89.70  E-value=0.55  Score=47.15  Aligned_cols=60  Identities=25%  Similarity=0.412  Sum_probs=40.1

Q ss_pred             hhhhHHHHHHhhc---ccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521          189 IQNRLKGYVKGVV---SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI  258 (508)
Q Consensus       189 ~~~~~~~yl~~i~---~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~  258 (508)
                      +.+.+..||+...   +.|    ......+.+++      .++.+|...+|++|+.+++|..+|++.+++...
T Consensus        87 Ir~~i~~~lr~~~~~vr~p----r~~~~~~~~~~------~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~  149 (256)
T PRK07408         87 IRGEIQHYLRDKSPTVRIP----RRWQELQRQAK------KVRQELRQELGRQPTDQEIAQALDISLEEWQEI  149 (256)
T ss_pred             HHHHHHHHHHHcCCeeeeC----HHHHHHHHHHH------HHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence            4456666776533   233    22233343332      356678889999999999999999998876554

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

Probab=89.53  E-value=2.9  Score=41.36  Aligned_cols=32  Identities=28%  Similarity=0.499  Sum_probs=26.9

Q ss_pred             hHHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521          227 HKLRLKERLGCEPSMEQLAASLRISRPELQSI  258 (508)
Q Consensus       227 ~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~  258 (508)
                      +..++...+|++|+.+++|..+|++.+++...
T Consensus        92 ~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~  123 (238)
T TIGR02393        92 AERQLTQELGREPTDEELAERMGMPAEKVREI  123 (238)
T ss_pred             HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            45567788999999999999999998876554

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.

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=89.34  E-value=4.7  Score=40.51  Aligned_cols=61  Identities=25%  Similarity=0.283  Sum_probs=40.5

Q ss_pred             hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhh
Q 010521          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL  259 (508)
Q Consensus       189 ~~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l  259 (508)
                      +.+.+..|++.....|    ....+.+.++.      .++..|...+|++|+.+++|..+|++.+++...+
T Consensus        87 Ir~~i~~~lr~~~~~p----r~~~~~~~~l~------~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~  147 (257)
T PRK05911         87 IKAAIIDDLRKQDWVP----RSVHQKANKLA------DAMDSLRQSLGKEPTDGELCEYLNISQQELSGWF  147 (257)
T ss_pred             HHHHHHHHHHhcCCCC----HHHHHHHHHHH------HHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHH
Confidence            4455566666655533    23333444443      2445678889999999999999999988765543

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=89.07  E-value=0.69  Score=36.39  Aligned_cols=41  Identities=27%  Similarity=0.419  Sum_probs=28.9

Q ss_pred             CCHHHHHHHhHHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGL  486 (508)
Q Consensus       446 Lp~rER~VI~LryGL--d~eg~TleEIAe~LgIS~erVrqi~~  486 (508)
                      |++....-|...|-|  +.+..+..+||+.||+|+.+|...+.
T Consensus         2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~   44 (60)
T PF01325_consen    2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLK   44 (60)
T ss_dssp             CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHH
Confidence            455555555555555  35679999999999999999975443

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=88.96  E-value=1.1  Score=33.23  Aligned_cols=37  Identities=22%  Similarity=0.275  Sum_probs=27.9

Q ss_pred             HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          448 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       448 ~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      |.-..|+.+-.   ..+++..||++.+|+|+++|++.+..
T Consensus         2 ~~R~~Il~~L~---~~~~~~~el~~~l~~s~~~vs~hL~~   38 (47)
T PF01022_consen    2 PTRLRILKLLS---EGPLTVSELAEELGLSQSTVSHHLKK   38 (47)
T ss_dssp             HHHHHHHHHHT---TSSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHH---hCCCchhhHHHhccccchHHHHHHHH
Confidence            44455666655   47899999999999999999877654

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=88.93  E-value=1.5  Score=34.07  Aligned_cols=43  Identities=19%  Similarity=0.244  Sum_probs=31.9

Q ss_pred             HHHHHHccCCHHHHHHHhHH-hccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521          438 VNKLIIVTLGEREREIIRLY-YGLDKECLTWEDISKRIGLSRERVRQVGL  486 (508)
Q Consensus       438 L~~~L~~~Lp~rER~VI~Lr-yGLd~eg~TleEIAe~LgIS~erVrqi~~  486 (508)
                      +.++|   .+|.-+.|+.+- -   .+++|..|||+.+|++.++|++.+.
T Consensus         3 i~~aL---~~p~R~~Il~~L~~---~~~~t~~ela~~l~~~~~t~s~hL~   46 (61)
T PF12840_consen    3 IFKAL---SDPTRLRILRLLAS---NGPMTVSELAEELGISQSTVSYHLK   46 (61)
T ss_dssp             HHHHH---TSHHHHHHHHHHHH---CSTBEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHh---CCHHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            44555   356666777665 3   6899999999999999999986654

...

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=88.87  E-value=0.69  Score=34.96  Aligned_cols=38  Identities=26%  Similarity=0.483  Sum_probs=26.3

Q ss_pred             HHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          449 REREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       449 rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      |++.|+.+-+- ..++.|.+|||+.||||+.||++.+..
T Consensus         1 R~~~il~~L~~-~~~~it~~eLa~~l~vS~rTi~~~i~~   38 (55)
T PF08279_consen    1 RQKQILKLLLE-SKEPITAKELAEELGVSRRTIRRDIKE   38 (55)
T ss_dssp             HHHHHHHHHHH-TTTSBEHHHHHHHCTS-HHHHHHHHHH
T ss_pred             CHHHHHHHHHH-cCCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence            45566655421 134599999999999999999866554

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress

Probab=88.57  E-value=0.99  Score=37.65  Aligned_cols=41  Identities=29%  Similarity=0.379  Sum_probs=33.6

Q ss_pred             CCHHHHHHHhHHhcc---CCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGL---DKECLTWEDISKRIGLSRERVRQVGL  486 (508)
Q Consensus       446 Lp~rER~VI~LryGL---d~eg~TleEIAe~LgIS~erVrqi~~  486 (508)
                      |+++|+.||..-.-+   ..++..-++||+.+++|..|||+...
T Consensus         2 Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~   45 (78)
T PF03444_consen    2 LTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMA   45 (78)
T ss_pred             CCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHH
Confidence            889999988764433   35688999999999999999998754

Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent

>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA

Probab=87.97  E-value=0.97  Score=38.28  Aligned_cols=43  Identities=16%  Similarity=0.139  Sum_probs=32.8

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHH--CCCHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRI--GLSRERVRQVGLVA  488 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~L--gIS~erVrqi~~rA  488 (508)
                      +.||+..+.+..+|.-  ..+.|+.|+|+.+  .||.++|..+..+.
T Consensus        36 ~~l~~~l~~~a~lRl~--~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl   80 (85)
T PF02650_consen   36 DKLPEKLREFAELRLE--NPDASLKELGELLEPPISKSGVNHRLRKL   80 (85)
T ss_dssp             GGS-HHHHHHHHHHHH---TTS-HHHHHHTT--T--HHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHH--CccccHHHHHHHHcCcCcHHHHHHHHHHH
Confidence            7899999999999872  4689999999999  99999998776554

It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.

>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A

Probab=87.97  E-value=1.3  Score=36.64  Aligned_cols=39  Identities=23%  Similarity=0.365  Sum_probs=27.7

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHH-----HHHHHHHHHHHHhh
Q 010521          462 KECLTWEDISKRIGLSRERVRQVGL-----VALEKLKHAARKKK  500 (508)
Q Consensus       462 ~eg~TleEIAe~LgIS~erVrqi~~-----rALkKLR~~L~~~~  500 (508)
                      ..++|+.|+|+.+|+++++|+++++     -.+.+|.+.+...|
T Consensus        29 ~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG   72 (80)
T PF13744_consen   29 ERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALG   72 (80)
T ss_dssp             CCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcC
Confidence            5789999999999999999999984     24667776665543

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=87.74  E-value=1.3  Score=33.09  Aligned_cols=35  Identities=26%  Similarity=0.430  Sum_probs=27.1

Q ss_pred             HHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          450 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       450 ER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      ++.|+.+..    +..|.++||+.+|+|..||..+..+.
T Consensus        17 ~~~i~~~~~----~~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   17 EQYILKLLR----ESRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             HHHHHHHHh----hcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            334554443    44799999999999999999998764

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=87.63  E-value=2.4  Score=36.25  Aligned_cols=42  Identities=29%  Similarity=0.381  Sum_probs=32.6

Q ss_pred             ccCCHHHHHHHhHH----hccC--CCCCCHHHHHHHHCCCHHHHHHHH
Q 010521          444 VTLGEREREIIRLY----YGLD--KECLTWEDISKRIGLSRERVRQVG  485 (508)
Q Consensus       444 ~~Lp~rER~VI~Lr----yGLd--~eg~TleEIAe~LgIS~erVrqi~  485 (508)
                      ..+++++..||..-    ||..  ..++|..|||+.+|+++++|++.+
T Consensus        21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L   68 (95)
T TIGR01610        21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAI   68 (95)
T ss_pred             CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHH
Confidence            67899999977632    3432  367999999999999999996443

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=87.53  E-value=1.4  Score=35.41  Aligned_cols=24  Identities=25%  Similarity=0.322  Sum_probs=20.8

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          464 CLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       464 g~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ++|..|||+.+|++..+|++++.+
T Consensus        22 ~~ta~eLa~~lgl~~~~v~r~L~~   45 (68)
T smart00550       22 TSTALQLAKNLGLPKKEVNRVLYS   45 (68)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHH
Confidence            599999999999999999766554

Helix-turn-helix-containing domain. Also known as Zab.

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=87.50  E-value=11  Score=41.91  Aligned_cols=32  Identities=28%  Similarity=0.449  Sum_probs=27.0

Q ss_pred             hHHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521          227 HKLRLKERLGCEPSMEQLAASLRISRPELQSI  258 (508)
Q Consensus       227 ~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~  258 (508)
                      ++.+|...+|++|+.+++|..+|++.++++..
T Consensus       363 ~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~  394 (509)
T PRK05901        363 IERELLQELGREPTPEELAKEMGFTPEKVREI  394 (509)
T ss_pred             HHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            45677788999999999999999998876554

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=87.31  E-value=2.1  Score=40.68  Aligned_cols=65  Identities=14%  Similarity=0.282  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHHHhcCCCCC---HHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHh
Q 010521          272 SNVRLVMSIAQRYDNMGAD---MADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVEN  336 (508)
Q Consensus       272 ~yl~LV~sIAkrY~~~g~d---~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~  336 (508)
                      +.+..+..+.++|--++..   -+|.|.+|.-.+++.++.|||++..-+-.|++..+-++..+.|...
T Consensus        45 ~imkIa~glS~r~nF~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~kE  112 (179)
T PHA02547         45 AIMKIAEGLSRRPNFSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKE  112 (179)
T ss_pred             HHHHHHhccccCCccccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHHHH
Confidence            3455555666666545554   7899999999999999999999987777777776666665555443

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=87.10  E-value=0.87  Score=42.78  Aligned_cols=50  Identities=12%  Similarity=0.013  Sum_probs=41.7

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCC-----HHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLS-----RERVRQVGLVALEKLKH  494 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS-----~erVrqi~~rALkKLR~  494 (508)
                      .|+++|.+|+.+-.-=.+.++|.++|++.++.+     ..||+..+.+.++||+.
T Consensus       154 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~  208 (228)
T PRK11083        154 TLTRYEFLLLKTLLLSPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA  208 (228)
T ss_pred             ecCHHHHHHHHHHHhCCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence            699999999988762112469999999999986     78999999999999963

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=86.99  E-value=1.1  Score=41.39  Aligned_cols=34  Identities=21%  Similarity=0.165  Sum_probs=28.4

Q ss_pred             HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521          453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL  489 (508)
Q Consensus       453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL  489 (508)
                      ++..++   .+|+|.+|||+++|||.+||..++.+-.
T Consensus        13 ~~~~~~---~~G~S~re~Ak~~gvs~sTvy~wv~r~~   46 (138)
T COG3415          13 VVDAVV---GEGLSCREAAKRFGVSISTVYRWVRRYR   46 (138)
T ss_pred             HHHHHH---HcCccHHHHHHHhCccHHHHHHHHHHhc
Confidence            444554   4899999999999999999999888754

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=86.89  E-value=5.7  Score=41.62  Aligned_cols=32  Identities=28%  Similarity=0.397  Sum_probs=26.8

Q ss_pred             hHHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521          227 HKLRLKERLGCEPSMEQLAASLRISRPELQSI  258 (508)
Q Consensus       227 ~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~  258 (508)
                      ++.+|...+|++|+.+++|..+|++.+++...
T Consensus       178 ~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~  209 (324)
T PRK07921        178 IKRELHQQLGREATDEELAEESGIPEEKIADL  209 (324)
T ss_pred             HHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence            45677788999999999999999998876544

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=86.82  E-value=1.1  Score=34.15  Aligned_cols=42  Identities=21%  Similarity=0.382  Sum_probs=30.9

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL  489 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL  489 (508)
                      |+..|-.||..-+-  ..++|..+||+.+++++++|.++..+-.
T Consensus         1 lt~~q~~iL~~l~~--~~~~~~~~la~~~~~~~~~~t~~i~~L~   42 (59)
T PF01047_consen    1 LTPSQFRILRILYE--NGGITQSELAEKLGISRSTVTRIIKRLE   42 (59)
T ss_dssp             STHHHHHHHHHHHH--HSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence            45667777766552  4679999999999999999987766543

This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=86.75  E-value=1.4  Score=33.74  Aligned_cols=39  Identities=31%  Similarity=0.390  Sum_probs=26.4

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL  486 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~  486 (508)
                      .|++.||.-|...+   ..|+++.|||+.+|-|+..|+..+.
T Consensus         4 ~Lt~~Eqaqid~m~---qlG~s~~~isr~i~RSr~~Ir~yl~   42 (50)
T PF11427_consen    4 TLTDAEQAQIDVMH---QLGMSLREISRRIGRSRTCIRRYLK   42 (50)
T ss_dssp             ---HHHHHHHHHHH---HTT--HHHHHHHHT--HHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH---HhchhHHHHHHHhCccHHHHHHHhc
Confidence            57888888777766   5689999999999999999987653

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=86.67  E-value=3.2  Score=36.98  Aligned_cols=34  Identities=9%  Similarity=0.122  Sum_probs=28.5

Q ss_pred             HHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          452 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       452 ~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .++...+   ..|.|..+||+.+|||..++.++....
T Consensus        20 ~aV~~~~---~~g~sv~evA~e~gIs~~tl~~W~r~y   53 (121)
T PRK09413         20 AIVQQSF---EPGMTVSLVARQHGVAASQLFLWRKQY   53 (121)
T ss_pred             HHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3555555   578999999999999999999998764

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=86.39  E-value=26  Score=36.45  Aligned_cols=179  Identities=19%  Similarity=0.104  Sum_probs=93.7

Q ss_pred             HHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccH
Q 010521          267 EKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL  346 (508)
Q Consensus       267 e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~  346 (508)
                      ++-+...+..|..++.+.   ++.  +-+.|....+++.+.....-+|.+...++.-.|.-    +++.+          
T Consensus       119 er~l~~a~~~I~~~~~~L---~Lp--~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYi----ACR~~----------  179 (310)
T PRK00423        119 ERNLAFALSELDRIASQL---GLP--RSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYA----ACRRC----------  179 (310)
T ss_pred             hHHHHHHHHHHHHHHHHc---CCC--HHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHH----HHHHc----------
Confidence            344445556677777665   222  45666666777776655555776665554433333    33332          


Q ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC-CCc
Q 010521          347 HERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE-NNP  425 (508)
Q Consensus       347 ~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e-~~P  425 (508)
                                       |..-+..||++..+++..++......+.+.+.++.+.         ....+++..-... .-|
T Consensus       180 -----------------~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~---------~~p~~~i~r~~~~L~L~  233 (310)
T PRK00423        180 -----------------KVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPP---------TDPIDYVPRFASELGLS  233 (310)
T ss_pred             -----------------CCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCC---------CCHHHHHHHHHHHcCCC
Confidence                             3334677888888888888877766665544443321         0111222111000 012


Q ss_pred             cchHHHHHHHHHHHHHHHccC----CHH--HHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521          426 WHGVDDWALKDEVNKLIIVTL----GER--EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL  492 (508)
Q Consensus       426 e~~ve~~el~e~L~~~L~~~L----p~r--ER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKL  492 (508)
                      .+ +. ......+..+....|    +|.  -..+|.+-.-+.+.+.|++|||...||+..||++....-.+.|
T Consensus       234 ~~-v~-~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l  304 (310)
T PRK00423        234 GE-VQ-KKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKL  304 (310)
T ss_pred             HH-HH-HHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence            11 11 111222222221111    121  1222333221235679999999999999999998777666554

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=86.23  E-value=1.6  Score=37.41  Aligned_cols=41  Identities=22%  Similarity=0.319  Sum_probs=31.7

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      |++.++.|+..-.-  ....|+.+||+.+|+|+.+|++.+.+-
T Consensus         1 ld~~D~~il~~L~~--~~~~~~~~la~~l~~s~~tv~~~l~~L   41 (108)
T smart00344        1 LDEIDRKILEELQK--DARISLAELAKKVGLSPSTVHNRVKRL   41 (108)
T ss_pred             CCHHHHHHHHHHHH--hCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            46678888876541  246899999999999999998766554

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=86.21  E-value=0.75  Score=34.40  Aligned_cols=34  Identities=29%  Similarity=0.343  Sum_probs=25.8

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH-------HHHHHHHHHHHh
Q 010521          466 TWEDISKRIGLSRERVRQVGLV-------ALEKLKHAARKK  499 (508)
Q Consensus       466 TleEIAe~LgIS~erVrqi~~r-------ALkKLR~~L~~~  499 (508)
                      |++|||+..|+|..||+..++.       ..+++...++..
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~l   41 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEEL   41 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHH
Confidence            7899999999999999998864       445555544443

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=86.03  E-value=0.97  Score=42.26  Aligned_cols=49  Identities=18%  Similarity=0.131  Sum_probs=40.6

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~Lg-----IS~erVrqi~~rALkKLR  493 (508)
                      .|+++|.+|+.+..-=.+..+|.++|++.+.     ++..||+..+.+.++||.
T Consensus       149 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~  202 (219)
T PRK10336        149 TLKPKEFALLELLMRNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLG  202 (219)
T ss_pred             ecCHHHHHHHHHHHhCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcC
Confidence            5999999999876510123489999999996     999999999999999885

>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor

Probab=85.93  E-value=31  Score=37.63  Aligned_cols=25  Identities=16%  Similarity=0.286  Sum_probs=22.1

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521          462 KECLTWEDISKRIGLSRERVRQVGL  486 (508)
Q Consensus       462 ~eg~TleEIAe~LgIS~erVrqi~~  486 (508)
                      ..++|+++||+.+|++.+||++...
T Consensus       316 LkPLtlkdiA~~lglheSTVSRav~  340 (429)
T TIGR02395       316 LKPLTLREVAEELGLHESTISRAIN  340 (429)
T ss_pred             CcCCcHHHHHHHhCCCccchhhhhc
Confidence            3689999999999999999987654

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 sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=85.73  E-value=1.5  Score=40.58  Aligned_cols=42  Identities=12%  Similarity=0.219  Sum_probs=32.9

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .|++.++.||..---  ....|+.|||+.+|+|+.+|+.++.+-
T Consensus         6 ~lD~~D~~Il~~Lq~--d~R~s~~eiA~~lglS~~tV~~Ri~rL   47 (153)
T PRK11179          6 QIDNLDRGILEALME--NARTPYAELAKQFGVSPGTIHVRVEKM   47 (153)
T ss_pred             ccCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            578888888877541  235899999999999999998776553

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=85.61  E-value=2.9  Score=38.06  Aligned_cols=51  Identities=24%  Similarity=0.343  Sum_probs=38.5

Q ss_pred             HHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521          436 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL  492 (508)
Q Consensus       436 e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKL  492 (508)
                      +.+.+++ -.|++.+-+|+..-.- ...++|..|||+.+|++++||.    +|+++|
T Consensus        16 ~dvl~c~-~GLs~~Dv~v~~~LL~-~~~~~tvdelae~lnr~rStv~----rsl~~L   66 (126)
T COG3355          16 EDVLKCV-YGLSELDVEVYKALLE-ENGPLTVDELAEILNRSRSTVY----RSLQNL   66 (126)
T ss_pred             HHHHHHH-hCCcHHHHHHHHHHHh-hcCCcCHHHHHHHHCccHHHHH----HHHHHH
Confidence            3455666 5899999998866541 1368999999999999999995    555554

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=85.61  E-value=1.9  Score=35.30  Aligned_cols=52  Identities=10%  Similarity=0.199  Sum_probs=34.8

Q ss_pred             HHHHHHHHHccCCHHHHHHHhHHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          435 KDEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       435 ~e~L~~~L~~~Lp~rER~VI~LryGL--d~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .+.|.... ..|++.|+.|.....--  +...+|..|||+..|||+.+|-+...+
T Consensus         4 ~~~i~~~~-~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kk   57 (77)
T PF01418_consen    4 LEKIRSQY-NSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKK   57 (77)
T ss_dssp             HHHHHHHG-GGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHH
T ss_pred             HHHHHHHH-hhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHH
Confidence            44566666 89999999988664311  134699999999999999999765443

Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.

>COG2973 TrpR Trp operon repressor [Transcription]

Probab=85.34  E-value=1.9  Score=37.33  Aligned_cols=46  Identities=22%  Similarity=0.391  Sum_probs=35.7

Q ss_pred             HHHHHHHHHHccCCHHHHHHHhHHhcc-C---CCCCCHHHHHHHHCCCHHHHH
Q 010521          434 LKDEVNKLIIVTLGEREREIIRLYYGL-D---KECLTWEDISKRIGLSRERVR  482 (508)
Q Consensus       434 l~e~L~~~L~~~Lp~rER~VI~LryGL-d---~eg~TleEIAe~LgIS~erVr  482 (508)
                      ....|..++   |+|.||+-+..|+.+ .   ...+|++||+..||+|..+|-
T Consensus        29 ~~~~lL~ll---LTpdEReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtIT   78 (103)
T COG2973          29 LHQPLLTLL---LTPDEREALGTRVRIVEELLRGELSQREIAQKLGVSIATIT   78 (103)
T ss_pred             HHHHHHHHH---cCHhHHHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhc
Confidence            344555555   899999988888765 1   257999999999999998883

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=85.27  E-value=1.2  Score=42.30  Aligned_cols=49  Identities=10%  Similarity=0.077  Sum_probs=42.4

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~Lg-----IS~erVrqi~~rALkKLR  493 (508)
                      .|+++|+.|+.+...=.+++.|.++|++.+.     ++..||+..+.+.++||.
T Consensus       160 ~Lt~~e~~il~~l~~~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~  213 (240)
T PRK10710        160 DLTPAEFRLLKTLSHEPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLE  213 (240)
T ss_pred             ecCHHHHHHHHHHHhCCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhh
Confidence            5999999999987631234799999999998     999999999999999996

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=85.05  E-value=0.84  Score=44.23  Aligned_cols=40  Identities=18%  Similarity=0.118  Sum_probs=29.3

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL  486 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~  486 (508)
                      +.|+++  +|+.+.- -+..|+|.+|||+.||+|+.||+....
T Consensus       160 ~~Lt~r--~Vl~~~~-~g~~g~s~~eIa~~l~iS~~Tv~~~~~  199 (225)
T PRK10046        160 DPLTLN--AVRKLFK-EPGVQHTAETVAQALTISRTTARRYLE  199 (225)
T ss_pred             CHHHHH--HHHHHHH-cCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence            345554  5665542 112369999999999999999998875

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=84.69  E-value=10  Score=33.65  Aligned_cols=27  Identities=26%  Similarity=0.433  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          463 ECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       463 eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      .+.|+.|||+.||||.++|.    ++|++|.
T Consensus        70 pd~tl~Ela~~l~Vs~~ti~----~~Lkrlg   96 (119)
T PF01710_consen   70 PDATLRELAERLGVSPSTIW----RALKRLG   96 (119)
T ss_pred             CCcCHHHHHHHcCCCHHHHH----HHHHHcC
Confidence            67999999999999999996    4555544

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=84.61  E-value=1.5  Score=41.17  Aligned_cols=42  Identities=21%  Similarity=0.226  Sum_probs=32.0

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .|++.++.||..--  .....|+.|||+.+|+|+.+|++++.+-
T Consensus        11 ~lD~~D~~IL~~Lq--~d~R~s~~eiA~~lglS~~tv~~Ri~rL   52 (164)
T PRK11169         11 DLDRIDRNILNELQ--KDGRISNVELSKRVGLSPTPCLERVRRL   52 (164)
T ss_pred             hHHHHHHHHHHHhc--cCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            46677888886543  0235899999999999999998776653

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=84.50  E-value=1.8  Score=33.76  Aligned_cols=43  Identities=19%  Similarity=0.285  Sum_probs=27.2

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL  489 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL  489 (508)
                      |+..|..||..-. -...++|..+||+.++++..+|.+.+.+..
T Consensus         1 lt~~q~~vL~~l~-~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~   43 (68)
T PF13463_consen    1 LTRPQWQVLRALA-HSDGPMTQSDLAERLGISKSTVSRIIKKLE   43 (68)
T ss_dssp             --HHHHHHHHHHT---TS-BEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-ccCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4566777765543 125789999999999999999986655443

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=84.04  E-value=0.76  Score=43.02  Aligned_cols=49  Identities=12%  Similarity=0.192  Sum_probs=40.6

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHH-----HHHHCCCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDI-----SKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEI-----Ae~LgIS~erVrqi~~rALkKLR  493 (508)
                      .|+++|.+|+.+-..--+.++|.++|     |+.++++..||+..+.+.++||.
T Consensus       154 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~l~~Kl~  207 (226)
T TIGR02154       154 SLGPTEFRLLHFFMTHPERVYSREQLLDRVWGRDVYVEERTVDVHIRRLRKALN  207 (226)
T ss_pred             EcCHHHHHHHHHHHhCCCceEcHHHHHHHhcCCCCCCCCccHHHHHHHHHHhhc
Confidence            59999999998876211246788888     77899999999999999999986

PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=84.02  E-value=1.8  Score=41.61  Aligned_cols=37  Identities=19%  Similarity=0.348  Sum_probs=29.0

Q ss_pred             CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          447 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       447 p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ++.++.|+.++    .+|+|..+||+.||||++||.++...
T Consensus       159 ~~~~~~i~~~~----~~g~s~~~iak~lgis~~Tv~r~~k~  195 (200)
T PRK13413        159 TGKEEKIKKLL----DKGTSKSEIARKLGVSRTTLARFLKT  195 (200)
T ss_pred             chhHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            33445666664    37899999999999999999888753

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=83.97  E-value=1.7  Score=40.58  Aligned_cols=49  Identities=14%  Similarity=0.145  Sum_probs=40.3

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~Lg-----IS~erVrqi~~rALkKLR  493 (508)
                      .|+++|.+|+.+..-=.+...|.++|++.+.     +|..||+..+.+.++||.
T Consensus       148 ~Lt~~E~~il~~l~~~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~  201 (221)
T PRK15479        148 ALTPREQALLTVLMYRRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQ  201 (221)
T ss_pred             ecCHHHHHHHHHHHhCCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcC
Confidence            5999999999876510123479999999996     999999999999999985

>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]

Probab=83.65  E-value=1.3  Score=42.34  Aligned_cols=38  Identities=24%  Similarity=0.211  Sum_probs=31.7

Q ss_pred             HHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q 010521          451 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKL  492 (508)
Q Consensus       451 R~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKL  492 (508)
                      +..+.|+-    .|+|..|||++||+|++|++.+..|+.++.
T Consensus         9 ~kA~eLk~----~Glt~gEIAdELNvSreTa~WL~~r~~~~~   46 (203)
T COG0856           9 KKARELKS----KGLTTGEIADELNVSRETATWLLTRAFKKE   46 (203)
T ss_pred             HHHHHHHH----CCCcHHHhhhhhhhhHHHHHHHHhhhhhcc
Confidence            34555663    899999999999999999999999987654

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=83.37  E-value=17  Score=37.20  Aligned_cols=65  Identities=17%  Similarity=0.156  Sum_probs=37.1

Q ss_pred             HhhhhHHHHHHhhcccCCC-CHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHH
Q 010521          188 LIQNRLKGYVKGVVSEELL-THAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPEL  255 (508)
Q Consensus       188 ~~~~~~~~yl~~i~~~~lL-t~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L  255 (508)
                      ++.+.+..||+.-...+.+ +......+..+++.   ++....++...+|++|+.+++|..+|++.+++
T Consensus       100 ~Ir~~I~~~lr~~~~~iR~p~~~~~~~~~~~~~~---~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v  165 (289)
T PRK07500        100 WIRASIQDYILRNWSIVRGGTSSAQKALFFNLRR---LRARLAQADEELTKQEIHREIATALGVSLSDV  165 (289)
T ss_pred             HHHHHHHHHHHHCCCceecCccHHHHHHHHHHHH---HHHHHHhhhcccCCCCCHHHHHHHhCcCHHHH
Confidence            4556777777664333221 22233334333332   11122222236899999999999999998764

>PF13551 HTH_29: Winged helix-turn helix

Probab=83.02  E-value=12  Score=31.73  Aligned_cols=23  Identities=22%  Similarity=0.291  Sum_probs=21.4

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHh
Q 010521          368 SVDRIAEYLNMSQKKVRNATEAI  390 (508)
Q Consensus       368 t~eEIA~~Lgis~e~v~~~l~~~  390 (508)
                      +..+||+.+|++..+|.+.+...
T Consensus        14 ~~~~ia~~lg~s~~Tv~r~~~~~   36 (112)
T PF13551_consen   14 TIAEIARRLGISRRTVYRWLKRY   36 (112)
T ss_pred             cHHHHHHHHCcCHHHHHHHHHHH
Confidence            79999999999999999998875

>PF12728 HTH_17: Helix-turn-helix domain

Probab=82.77  E-value=1.4  Score=32.80  Aligned_cols=24  Identities=25%  Similarity=0.266  Sum_probs=21.5

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          465 LTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       465 ~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      +|.+|+|+.||||+.||.++..+.
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g   25 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQG   25 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcC
Confidence            689999999999999999988653

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=82.72  E-value=0.96  Score=35.85  Aligned_cols=41  Identities=24%  Similarity=0.272  Sum_probs=31.3

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|++.|..|+..-.  ...++|..|||+.+|+++.+|...+.+
T Consensus         5 gLs~~E~~vy~~Ll--~~~~~t~~eIa~~l~i~~~~v~~~L~~   45 (68)
T PF01978_consen    5 GLSENEAKVYLALL--KNGPATAEEIAEELGISRSTVYRALKS   45 (68)
T ss_dssp             CHHHHHHHHHHHHH--HHCHEEHHHHHHHHTSSHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            57788888775543  146799999999999999999755443

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>PRK05949 RNA polymerase sigma factor; Validated

Probab=82.46  E-value=8.4  Score=40.36  Aligned_cols=34  Identities=15%  Similarity=0.354  Sum_probs=26.9

Q ss_pred             chhHHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521          225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSI  258 (508)
Q Consensus       225 ~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~  258 (508)
                      ..++.++...+|++|+.+++|..+|++.+++...
T Consensus       181 ~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~  214 (327)
T PRK05949        181 KKTQRELSQKLGRSATPAEIAKELELEPSQIREY  214 (327)
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence            3345566778999999999999999998775553

>PF13551 HTH_29: Winged helix-turn helix

Probab=82.12  E-value=2.5  Score=35.98  Aligned_cols=33  Identities=30%  Similarity=0.370  Sum_probs=26.6

Q ss_pred             HHHhHHhccCCCCC-CHHHHHHHHCCCHHHHHHHHHHH
Q 010521          452 EIIRLYYGLDKECL-TWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       452 ~VI~LryGLd~eg~-TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .||.+..    +|. |..+||+.+|+|+.||.+++.+-
T Consensus         3 ~~l~l~~----~g~~~~~~ia~~lg~s~~Tv~r~~~~~   36 (112)
T PF13551_consen    3 QILLLLA----EGVSTIAEIARRLGISRRTVYRWLKRY   36 (112)
T ss_pred             HHHHHHH----cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence            3555543    778 59999999999999999888774

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=81.99  E-value=1.4  Score=31.45  Aligned_cols=25  Identities=20%  Similarity=0.205  Sum_probs=22.2

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521          465 LTWEDISKRIGLSRERVRQVGLVAL  489 (508)
Q Consensus       465 ~TleEIAe~LgIS~erVrqi~~rAL  489 (508)
                      +|..|+|+.+|||+.||+++...+.
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g~   25 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGK   25 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence            5889999999999999999987753

Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=81.88  E-value=1.9  Score=40.70  Aligned_cols=47  Identities=9%  Similarity=0.027  Sum_probs=40.3

Q ss_pred             cCCHHHHHHHhHHhccCCCC--CCHHHH--HHHHCCCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKEC--LTWEDI--SKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg--~TleEI--Ae~LgIS~erVrqi~~rALkKLR  493 (508)
                      .|+++|..|+.+..-  ..|  +|.++|  |..++++..||+..+.+.++||.
T Consensus       156 ~Lt~~E~~il~~l~~--~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~  206 (227)
T TIGR03787       156 DLTVTEFWMVHALAK--HPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQ  206 (227)
T ss_pred             cCCHHHHHHHHHHHh--CCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhc
Confidence            599999999988761  124  599999  88899999999999999999996

This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.

>PF00046 Homeobox: Homeobox domain not present here

Probab=81.57  E-value=4.1  Score=30.85  Aligned_cols=50  Identities=16%  Similarity=0.256  Sum_probs=39.9

Q ss_pred             cCCHHHHHHHhHHhccCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDK--ECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~--eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      .+++.+..+|...|..+.  .....++||..+||+...|..+...-..+.|+
T Consensus         6 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    6 RFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            578888899999885421  22458899999999999999999988777663

; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....

>CHL00148 orf27 Ycf27; Reviewed

Probab=81.37  E-value=1.9  Score=40.95  Aligned_cols=50  Identities=18%  Similarity=0.118  Sum_probs=41.8

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHH-------CCCHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRI-------GLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~L-------gIS~erVrqi~~rALkKLR~  494 (508)
                      .|+++|.+|+.+...-.++++|.++|++.+       +++..+|+.++.+.++||..
T Consensus       161 ~Lt~~E~~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~~~tv~~~i~~lr~KL~~  217 (240)
T CHL00148        161 RLTGMEFSLLELLISKSGEIFSRATILKEVWGYTPERHIDTRVVDVHISRLRAKLED  217 (240)
T ss_pred             EcCHHHHHHHHHHHHCCCEEEcHHHHHHHhcCCCcccCCCcccHHHHHHHHHHHhcc
Confidence            599999999988752123579999999999       48999999999999999963

>PRK12423 LexA repressor; Provisional

Probab=80.96  E-value=2.8  Score=40.64  Aligned_cols=47  Identities=19%  Similarity=0.290  Sum_probs=33.2

Q ss_pred             ccCCHHHHHHHhHHhc-cC--CCCCCHHHHHHHHC-CCHHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYG-LD--KECLTWEDISKRIG-LSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       444 ~~Lp~rER~VI~LryG-Ld--~eg~TleEIAe~Lg-IS~erVrqi~~rALkKLR~  494 (508)
                      ..|+++|++|+..--. +.  +-..|..|||+.|| +|+++|+.    ++++|++
T Consensus         2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~----~l~~L~~   52 (202)
T PRK12423          2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK----HVQALAE   52 (202)
T ss_pred             CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence            3589999998875331 11  12459999999999 59999984    5555554

>TIGR01764 excise DNA binding domain, excisionase family

Probab=80.94  E-value=1.9  Score=31.00  Aligned_cols=24  Identities=25%  Similarity=0.357  Sum_probs=21.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          465 LTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       465 ~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      +|.+|+|+.||||+.+|.++....
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g   25 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEG   25 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcC
Confidence            689999999999999999988654

An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).

>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24

Probab=80.91  E-value=3.2  Score=39.36  Aligned_cols=42  Identities=21%  Similarity=0.242  Sum_probs=34.0

Q ss_pred             CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521          447 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE  490 (508)
Q Consensus       447 p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALk  490 (508)
                      |+.-|.-++..|=  ++++|++.+|...|||..|++++..+|..
T Consensus         4 ~~e~R~~~R~~YV--~~~~sLe~aA~~~gVs~~TarrWK~~Ak~   45 (165)
T PF08822_consen    4 PQETRDAVRRAYV--FDRLSLEQAAAKCGVSYATARRWKREAKA   45 (165)
T ss_pred             cHHHHHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            3445566666661  37899999999999999999999999864

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=80.72  E-value=14  Score=40.26  Aligned_cols=38  Identities=16%  Similarity=0.495  Sum_probs=30.7

Q ss_pred             ccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhh
Q 010521          223 SLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM  260 (508)
Q Consensus       223 ~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~  260 (508)
                      .+..++.+|...+|++|+.+++|..+||+.+.++..+.
T Consensus       263 ~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~vr~~l~  300 (415)
T PRK07598        263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLL  300 (415)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            34445667778899999999999999999998776643

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=80.43  E-value=4.2  Score=39.79  Aligned_cols=31  Identities=35%  Similarity=0.536  Sum_probs=25.2

Q ss_pred             HHHHHHhhCCCCchHHHHHHhccChHHHHHh
Q 010521          228 KLRLKERLGCEPSMEQLAASLRISRPELQSI  258 (508)
Q Consensus       228 ~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~  258 (508)
                      ...+...+|++|+.+++|..+|++.+++...
T Consensus       103 ~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~  133 (231)
T TIGR02885       103 KEELSKELGREPTINELAEALGVSPEEIVMA  133 (231)
T ss_pred             HHHHHHHHCcCCCHHHHHHHHCcCHHHHHHH
Confidence            3456677899999999999999998876543

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.

>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)

Probab=80.14  E-value=1.9  Score=32.35  Aligned_cols=26  Identities=15%  Similarity=0.442  Sum_probs=21.5

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          462 KECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       462 ~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..++|+.|+|+.+|+|+.+|++++..
T Consensus         7 ~~gls~~~la~~~gis~~~i~~~~~g   32 (55)
T PF01381_consen    7 EKGLSQKELAEKLGISRSTISRIENG   32 (55)
T ss_dssp             HTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred             HcCCCHHHHHHHhCCCcchhHHHhcC
Confidence            35799999999999999999999875

; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	508
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		3e-34
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		5e-34
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		3e-31
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		7e-31
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		2e-30
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		2e-30
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		2e-30
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		2e-23
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		4e-23
1l0o_C	243	Crystal Structure Of The Bacillus Stearothermophilu		7e-18
1sig_A	339	Crystal Structure Of A Sigma70 Subunit Fragment Fro		6e-17
3les_A	179	2f5 Epitope Scaffold Es2 Length = 179		7e-17
4g6d_A	73	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		6e-07
1tty_A	87	Solution Structure Of Sigma A Region 4 From Thermot		5e-06
1rp3_A	239	Cocrystal Structure Of The Flagellar SigmaANTI-Sigm		6e-05
1tlh_B	81	T4 Asia Bound To Sigma70 Region 4 Length = 81		6e-05
2p7v_B	68	Crystal Structure Of The Escherichia Coli Regulator		1e-04
3t72_q	99	Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna		2e-04
4g94_A	62	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		2e-04

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

Iteration: 1
 Score =  143 bits (360), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 80/247 (32%), Positives = 147/247 (59%), Gaps = 16/247 (6%)
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 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++R++ + +RT+R+P H+ E +  L R ++  L+E G  P+ + +AE + M + K+
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKI 494
Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENN----PWHGVDDWALKDEVN 439
           R       KV  + +E   S+    G+   S++ D  +E+     P       +L+   +
Sbjct: 495 R-------KVLKIAKEPI-SMETPIGDDEDSHLGDF-IEDTTLELPLDSATTESLRAATH 545
Query: 440 KLIIVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498
             ++  L  RE +++R+ +G+D     T E++ K+  ++RER+RQ+   AL KL+H +R 
Sbjct: 546 D-VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 604
Query: 499 KKMEAML 505
           + + + L
Sbjct: 605 EVLRSFL 611

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

Iteration: 1
 Score =  142 bits (358), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 80/247 (32%), Positives = 147/247 (59%), Gaps = 16/247 (6%)
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 IRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKV 383
           IRQ ++R++ + +RT+R+P H+ E +  L R ++  L+E G  P+ + +AE + M + K+
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKI 494
Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENN----PWHGVDDWALKDEVN 439
           R       KV  + +E   S+    G+   S++ D  +E+     P       +L+   +
Sbjct: 495 R-------KVLKIAKEPI-SMETPIGDDEDSHLGDF-IEDTTLELPLDSATTESLRAATH 545
Query: 440 KLIIVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498
             ++  L  RE +++R+ +G+D     T E++ K+  ++RER+RQ+   AL KL+H +R 
Sbjct: 546 D-VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 604
Query: 499 KKMEAML 505
           + + + L
Sbjct: 605 EVLRSFL 611

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

Iteration: 1
 Score =  132 bits (333), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 104/334 (31%), Positives = 171/334 (51%), Gaps = 28/334 (8%)
Query: 193 LKGYVKGVVSEELLTHAEVVRLSKKIKTGL----------SLDDHKLR--LKERLGCEPS 240
           ++ Y+  +    LLT  E + L++K++ G+           LD   +R  ++ ++     
Sbjct: 5   VRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTAR 64
Query: 241 MEQLAASLRISRPELQ---SILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQG 297
           +E++   L+    EL+    I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q 
Sbjct: 65  VEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQE 124
Query: 298 GLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNA 356
           G  GL+R +EKF+  + FK STY  WWIRQ ++RA+ + +RT+R+P H+ E +  L R A
Sbjct: 125 GNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTA 184
Query: 357 KLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYI 416
           +   +E G  PS + IAE +       R     + +   + +E   SL    G+   S+ 
Sbjct: 185 RQLQQELGREPSYEEIAEAMGPGWDAKR-----VEETLKIAQEPV-SLETPIGDEKDSFY 238
Query: 417 ADNRVENN---PWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISK 472
            D   + N   P        L +E+ K  +  L ERE  +++L  GL D    T E++  
Sbjct: 239 GDFIPDENLPSPVEAAAQSLLSEELEK-ALSKLSEREAMVLKLRKGLIDGREHTLEEVGA 297
Query: 473 RIGLSRERVRQVGLVALEKLK-HAARKKKMEAML 505
             G++RER+RQ+   AL KLK H +R +K+   L
Sbjct: 298 YFGVTRERIRQIENKALRKLKYHESRTRKLRDFL 331

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

Iteration: 1
 Score =  131 bits (330), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 89/254 (35%), Positives = 136/254 (53%), Gaps = 13/254 (5%)
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 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 376
           STY  WWIRQ ++RA+ + +RT+R+P H+ E +  L R A+   +E G  PS + IAE +
Sbjct: 251 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAM 310
Query: 377 NMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENN---PWHGVDDWA 433
                  R     + +   + +E   SL    G+   S+  D   + N   P        
Sbjct: 311 GPGWDAKR-----VEETLKIAQEPV-SLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSL 364
Query: 434 LKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKL 492
           L +E+ K  +  L ERE  +++L  GL D    T E++    G++RER+RQ+   AL KL
Sbjct: 365 LSEELEK-ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKL 423
Query: 493 K-HAARKKKMEAML 505
           K H +R +K+   L
Sbjct: 424 KYHESRTRKLRDFL 437

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

Iteration: 1
 Score =  130 bits (327), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 87/253 (34%), Positives = 137/253 (54%), Gaps = 11/253 (4%)
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 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 376
           STY  WWIRQ ++RA+ + +RT+R+P H+ E +  L R A+   +E G  P+ + IAE +
Sbjct: 236 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAM 295
Query: 377 NM--SQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWAL 434
                 K+V    +   +  SL+       +   G+    +I D  +  +P        L
Sbjct: 296 GPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGD----FIPDEHL-PSPVDAATQSLL 350
Query: 435 KDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493
            +E+ K  +  L ERE  +++L  GL D    T E++    G++RER+RQ+   AL KLK
Sbjct: 351 SEELEK-ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK 409
Query: 494 -HAARKKKMEAML 505
            H +R +K+   L
Sbjct: 410 YHESRTRKLRDFL 422

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

Iteration: 1
 Score =  130 bits (327), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 87/253 (34%), Positives = 137/253 (54%), Gaps = 11/253 (4%)
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 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 376
           STY  WWIRQ ++RA+ + +RT+R+P H+ E +  L R A+   +E G  P+ + IAE +
Sbjct: 236 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAM 295
Query: 377 NM--SQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWAL 434
                 K+V    +   +  SL+       +   G+    +I D  +  +P        L
Sbjct: 296 GPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGD----FIPDEHL-PSPVDAATQSLL 350
Query: 435 KDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493
            +E+ K  +  L ERE  +++L  GL D    T E++    G++RER+RQ+   AL KLK
Sbjct: 351 SEELEK-ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK 409
Query: 494 -HAARKKKMEAML 505
            H +R +K+   L
Sbjct: 410 YHESRTRKLRDFL 422

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

Iteration: 1
 Score =  130 bits (326), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 87/253 (34%), Positives = 137/253 (54%), Gaps = 11/253 (4%)
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 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 376
           STY  WWIRQ ++RA+ + +RT+R+P H+ E +  L R A+   +E G  P+ + IAE +
Sbjct: 256 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAM 315
Query: 377 NM--SQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWAL 434
                 K+V    +   +  SL+       +   G+    +I D  +  +P        L
Sbjct: 316 GPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGD----FIPDEHL-PSPVDAATQSLL 370
Query: 435 KDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493
            +E+ K  +  L ERE  +++L  GL D    T E++    G++RER+RQ+   AL KLK
Sbjct: 371 SEELEK-ALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK 429
Query: 494 -HAARKKKMEAML 505
            H +R +K+   L
Sbjct: 430 YHESRTRKLRDFL 442

>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 =  107 bits (266), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 118/226 (52%), Gaps = 35/226 (15%)
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 NVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRA 332
           N+RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  + FK STY  WWIRQ ++RA
Sbjct: 119 NLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRA 178
Query: 333 LVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYLN 377
           + + +RT+R+P H+ E +  L R A+   +E G  PS + IAE + 
Sbjct: 179 IADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMG 224

>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 =  106 bits (264), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 52/121 (42%), Positives = 77/121 (63%), Gaps = 1/121 (0%)
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 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL 376
           STY  WWIRQ ++RA+ + +RT+R+P H+ E +  L R A+   +E G  PS + IAE +
Sbjct: 160 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAM 219
Query: 377 N 377
Sbjct: 220 G 220

>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 = 88.6 bits (218), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 81/233 (34%), Positives = 122/233 (52%), Gaps = 23/233 (9%)
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 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEE-KGVTPSVDRIAEYLNMSQKKV 383
           I   + R L ++  T+++   L E    IR AK  L + +G  P+V  IA++L +S + V
Sbjct: 89  IIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDV 147
Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLII 443
             A EA+    S+    + + +G P  T    IAD   +   W   D  ALK  + +   
Sbjct: 148 VLAQEAVRLPTSIHETVYEN-DGDPI-TLLDQIAD--ADEASW--FDKIALKKAIEE--- 198
Query: 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEK--LKH 494
             L ERER I+ L Y  D+   T  +++ R+G+S     QV +  LEK  L+H
Sbjct: 199 --LDERERLIVYLRYYKDQ---TQSEVASRLGIS-----QVQMSRLEKKILQH 241

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

Iteration: 1
 Score = 85.5 bits (210), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 33/74 (44%), Positives = 56/74 (75%)
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 IRQGVSRALVENSR 338
           IRQ ++R++ + +R
Sbjct: 326 IRQAITRSIADQAR 339

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

Iteration: 1
 Score = 85.5 bits (210), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 37/81 (45%), Positives = 54/81 (66%)
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 STYVYWWIRQGVSRALVENSR 338
           STY  WWIRQ ++RA+ + +R
Sbjct: 159 STYATWWIRQAINRAIADQAR 179

>pdb|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 73

Iteration: 1
 Score = 52.4 bits (124), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 43/65 (66%), Gaps = 1/65 (1%)
Query: 442 IIVTLGEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500
           ++ TL +RE  ++RL +GLD     T E++ K  G++RER+RQ+   AL KL+H +R K+
Sbjct: 8   VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKR 67
Query: 501 MEAML 505
           ++  +
Sbjct: 68  LKDFM 72

>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga Maritima Length = 87

Iteration: 1
 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 50/73 (68%), Gaps = 2/73 (2%)
Query: 434 LKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKL 492
           +++E+ K ++ TL  RE  ++R+ YGL D +  T E++ +   ++RER+RQ+ + AL KL
Sbjct: 8   MREELEK-VLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKL 66
Query: 493 KHAARKKKMEAML 505
           +H +R K ++++L
Sbjct: 67  RHPSRSKYLKSLL 79

>pdb|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma Complex, Sigma-28FLGM Length = 239

Iteration: 1
 Score = 45.8 bits (107), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 60/241 (24%), Positives = 116/241 (48%), Gaps = 29/241 (12%)
Query: 264 LAREKLVMSNVRLVMSIA---QRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
           + RE+L++  + LV +IA   +++     D+ DL+  G+IGL++ ++   +    +   Y
Sbjct: 12  IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAY 71
Query: 321 VYWWIRQGVS---RALVENSRTLRLPNHLHERLGLIRNAKLRLEEK-GVTPSVDRIAEYL 376
           +   I+  +    R+L   SR +R      E+   I+    +L+EK G  P+ + +A+ L
Sbjct: 72  IKLRIKGAIYDYLRSLDFGSRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKEL 125
Query: 377 NMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKD 436
            +S       TE + K  +LD+  F  +  L  E    +  D          V++  +K 
Sbjct: 126 GIS-------TEELFK--TLDKINFSYILSL-EEVFRDFARDYSELIPSSTNVEEEVIKR 175
Query: 437 EVNKLI---IVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493
           E+ + +   +  L ERE+ +I+L +    E L  ++++K +  S  RV Q+   ALE+L+
Sbjct: 176 ELTEKVKEAVSKLPEREKLVIQLIFY---EELPAKEVAKILETSVSRVSQLKAKALERLR 232
Query: 494 H 494
Sbjct: 233 E 233

>pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4 Length = 81

Iteration: 1
 Score = 45.4 bits (106), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 442 IIVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500
           ++  L  RE +++R+ +G+D     T E++ K+  ++RER+RQ+   AL KL+H +R + 
Sbjct: 15  VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 74
Query: 501 MEAML 505
           + + L
Sbjct: 75  LRSFL 79

>pdb|2P7V|B Chain B, Crystal Structure Of The Escherichia Coli Regulator Of Sigma 70, Rsd, In Complex With Sigma 70 Domain 4 Length = 68

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 442 IIVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500
           ++  L  RE +++R+ +G+D     T E++ K+  ++RER+RQ+   AL KL+H +R + 
Sbjct: 2   VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61
Query: 501 MEAML 505
           + + L
Sbjct: 62  LRSFL 66

>pdb|3T72|QQ Chain q, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna Transcription Activation Sub-Complex Length = 99

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/57 (35%), Positives = 37/57 (64%), Gaps = 1/57 (1%)
Query: 442 IIVTLGEREREIIRLYYGLDKEC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497
           ++  L  RE +++R+ +G+D     T E++ K+  ++RER+RQ+   AL KL+H +R
Sbjct: 16  VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 72

>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 62

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/54 (42%), Positives = 36/54 (66%), Gaps = 1/54 (1%)
Query: 442 IIVTLGEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494
           ++ TL +RE  ++RL +GLD     T E++ K  G++RER+RQ+   AL KL+H
Sbjct: 8   VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRH 61

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	508
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	4e-48
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	8e-45
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	2e-44
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	2e-43
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	7e-42
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	1e-32
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	5e-20
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-16
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	8e-12
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	1e-11
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	3e-11
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	8e-11
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	5e-09
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	6e-09

>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 =  165 bits (421), Expect = 4e-48
 Identities = 71/230 (30%), Positives = 116/230 (50%), Gaps = 16/230 (6%)

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 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKV 383
           I   + R L ++  T+++   L E    IR AK  L + +G  P+V  IA++L +S + V
Sbjct: 89  IIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDV 147

Query: 384 RNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLII 443
             A EA+    S+    +        +     + D   + +     D  ALK       I
Sbjct: 148 VLAQEAVRLPTSIHETVY------ENDGDPITLLDQIADADEASWFDKIALKK-----AI 196

Query: 444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK 493
             L ERER I+ L Y  D+   T  +++ R+G+S+ ++ ++    L+ +K
Sbjct: 197 EELDERERLIVYLRYYKDQ---TQSEVASRLGISQVQMSRLEKKILQHIK 243

>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 =  165 bits (419), Expect = 8e-45
 Identities = 80/258 (31%), Positives = 147/258 (56%), Gaps = 16/258 (6%)

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

Query: 314 GFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRI 372
           G+K STY  WWIRQ ++R++ + +RT+R+P H+ E +  L R ++  L+E G  P+ + +
Sbjct: 424 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEEL 483

Query: 373 AEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHS----YIADNRVENNPWHG 428
           AE + M + K+R       KV  + +E   S+    G+   S    +I D  +E  P   
Sbjct: 484 AERMLMPEDKIR-------KVLKIAKEPI-SMETPIGDDEDSHLGDFIEDTTLE-LPLDS 534

Query: 429 VDDWALKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLV 487
               +L+   +  ++  L  RE +++R+ +G+      T E++ K+  ++RER+RQ+   
Sbjct: 535 ATTESLRAATHD-VLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 593

Query: 488 ALEKLKHAARKKKMEAML 505
           AL KL+H +R + + + L
Sbjct: 594 ALRKLRHPSRSEVLRSFL 611

>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 =  161 bits (408), Expect = 2e-44
 Identities = 100/350 (28%), Positives = 162/350 (46%), Gaps = 51/350 (14%)

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 NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH 345
             G    DL+Q G  GL+R +EKF+  + FK STY  WWIRQ ++RA+ + +RT+R+P H
Sbjct: 204 GRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVH 263

Query: 346 LHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL--NMSQKKVRNATEAIGKVFSLDREAFP 402
           + E +  L R A+   +E G  P+ + IAE +      K+V        +   + +E  P
Sbjct: 264 MVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVE-------ETLKIAQE--P 314

Query: 403 -SLNGLPGETHHS----YIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLY 457
            SL    G+   S    +I D  +  +P        L +E+ K  +  L ERE  +++L 
Sbjct: 315 VSLETPIGDEKDSFYGDFIPDEHLP-SPVDAATQSLLSEELEK-ALSKLSEREAMVLKLR 372

Query: 458 YGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK-HAARKKKMEAML 505
            GL D    T E++    G++RER+RQ+   AL KLK H +R +K+   L
Sbjct: 373 KGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFL 422

>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 =  158 bits (400), Expect = 2e-43
 Identities = 96/300 (32%), Positives = 149/300 (49%), Gaps = 19/300 (6%)

Query: 215 SKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNV 274
           +K + T        L+ K        ++    SL         I  E   AR+ L+ +N+
Sbjct: 148 AKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANL 207

Query: 275 RLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALV 334
           RLV+SIA++Y   G    DL+Q G  GL+R +EKF+  + FK STY  WWIRQ ++RA+ 
Sbjct: 208 RLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIA 267

Query: 335 ENSRTLRLPNHLHERLG-LIRNAKLRLEEKGVTPSVDRIAEYL--NMSQKKVRNATEAIG 391
           + +RT+R+P H+ E +  L R A+   +E G  PS + IAE +      K+V        
Sbjct: 268 DQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVE------- 320

Query: 392 KVFSLDREAFPSLNGLPGETHHS----YIADNRVENNPWHGVDDWALKDEVNKLIIVTLG 447
           +   + +E   SL    G+   S    +I D  +  +P        L +E+ K  +  L 
Sbjct: 321 ETLKIAQEPV-SLETPIGDEKDSFYGDFIPDENLP-SPVEAAAQSLLSEELEK-ALSKLS 377

Query: 448 EREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK-HAARKKKMEAML 505
           ERE  +++L  GL D    T E++    G++RER+RQ+   AL KLK H +R +K+   L
Sbjct: 378 EREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFL 437

>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 =  148 bits (377), Expect = 7e-42
 Identities = 53/246 (21%), Positives = 109/246 (44%), Gaps = 24/246 (9%)

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

Query: 322 YWWIRQGVSRALVENSRTL-RLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMS 379
              I+  +   L    R+L      + E+   I+    +L+ + G  P+ + +A+ L +S
Sbjct: 73  KLRIKGAIYDYL----RSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGIS 128

Query: 380 QKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVN 439
            +++    + I   + L      SL  +  +    Y        N    V    L ++V 
Sbjct: 129 TEELFKTLDKINFSYIL------SLEEVFRDFARDYSELIPSSTNVEEEVIKRELTEKVK 182

Query: 440 KLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKK 499
           +  +  L ERE+ +I+L +  +   L  ++++K +  S  RV Q+   ALE+L     ++
Sbjct: 183 EA-VSKLPEREKLVIQLIFYEE---LPAKEVAKILETSVSRVSQLKAKALERL-----RE 233

Query: 500 KMEAML 505
            +   L
Sbjct: 234 MLSNPL 239

>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 =  123 bits (311), Expect = 1e-32
 Identities = 66/221 (29%), Positives = 114/221 (51%), Gaps = 8/221 (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 MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHL 346
            G    DL+Q G  GL+R +EKF+  + FK STY  WWIRQ ++RA+ + +RT+R+P H+
Sbjct: 133 RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHM 192

Query: 347 HERLG-LIRNAKLRLEEKGVTPSVDRIAEYL--NMSQKKVR 384
            E +  L R A+   +E G  PS + IAE +      K+V 
Sbjct: 193 VETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVE 233

>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 = 90.3 bits (224), Expect = 5e-20
 Identities = 33/85 (38%), Positives = 58/85 (68%)

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

Query: 314 GFKISTYVYWWIRQGVSRALVENSR 338
           G+K STY  WWIRQ ++R++ + +R
Sbjct: 315 GYKFSTYATWWIRQAITRSIADQAR 339

>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 = 79.9 bits (196), Expect = 8e-16
 Identities = 88/513 (17%), Positives = 162/513 (31%), Gaps = 142/513 (27%)

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--ISTYVYWWIRQGVSRALVENSRTLRLPNHL 346
            +   L +  ++      + FDS       +  Y Y  I                  +HL
Sbjct: 440 ENEYALHR-SIVDHYNIPKTFDSDDLIPPYLDQYFYSHI-----------------GHHL 481

Query: 347 HERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMS--QKKVRNATEAIGKVFSLDREAFPSL 404
                 I +     E   +   V     +L+    ++K+R+ + A     S+      +L
Sbjct: 482 KN----IEHP----ERMTLFRMV-----FLDFRFLEQKIRHDSTAWNASGSI----LNTL 524

Query: 405 NGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKEC 464
             L  + +  YI DN           +  +       I+  L + E  +I       K  
Sbjct: 525 QQL--KFYKPYICDN-------DPKYERLVNA-----ILDFLPKIEENLIC-----SKYT 565

Query: 465 LTWEDISKRIGLSRERVRQVGLVALEKLKHAAR 497
               D+  RI L  E       +  E  K   R
Sbjct: 566 ----DLL-RIALMAED----EAIFEEAHKQVQR 589

>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 = 67.2 bits (163), Expect = 8e-12
 Identities = 81/546 (14%), Positives = 158/546 (28%), Gaps = 167/546 (30%)

Query: 21  FYYSDISEKF--SYINDLGSANSQVGSTKNVVAAKKSSNYNPSFPSSNRQTQPI------ 72
           + Y DI   F  +++++    + Q    K+++        +    S +  +  +      
Sbjct: 16  YQYKDILSVFEDAFVDNFDCKDVQ-DMPKSIL---SKEEIDHIIMSKDAVSGTLRLFWTL 71

Query: 73  ---------KALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQW 123
                    K ++E +  N+     P                         Q SM+ + +
Sbjct: 72  LSKQEEMVQKFVEEVLRINYKFLMSPIKTEQR-------------------QPSMMTRMY 112

Query: 124 NLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSM 183
               +R    +    K +  V         R +     ++ L +    L+   +  +  +
Sbjct: 113 IEQRDRLYNDNQVFAKYN--VS--------RLQPYLKLRQALLE----LRPAKNVLIDGV 158

Query: 184 ISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQ 243
                      G  K       +   +V   S K++  +      L LK     E  +E 
Sbjct: 159 ----------LGSGKTW-----VA-LDVCL-SYKVQCKMDFKIFWLNLKNCNSPETVLEM 201

Query: 244 LAASLRISRPEL-------QSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           L   L    P          +I +     + +L     RL+ S  + Y+N       L  
Sbjct: 202 LQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAEL----RRLLKS--KPYENC------L-- 247

Query: 297 GGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNA 356
             L+  L  ++   +   F +S            + L+    T R    + + L      
Sbjct: 248 --LV--LLNVQNAKAWNAFNLS-----------CKILL----TTRFKQ-VTDFLSAATTT 287

Query: 357 KLRLEE--KGVTP--SVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETH 412
            + L+     +TP      + +YL+              +   L RE    L   P    
Sbjct: 288 HISLDHHSMTLTPDEVKSLLLKYLDC-------------RPQDLPREV---LTTNP--RR 329

Query: 413 HSYIADN-RVENNPWHGVDDWA--LKDEVNKLIIVTLGEREREIIRLYYG----LDKE-- 463
            S IA++ R     W   D+W     D++  +I  +L   E    R  +           
Sbjct: 330 LSIIAESIRDGLATW---DNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAH 386

Query: 464 ------CLTWEDISK-----------RIGL----SRERVRQVGLVALEKLKHAARKKKME 502
                  L W D+ K           +  L     +E    +  + LE       +  + 
Sbjct: 387 IPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALH 446

Query: 503 AMLVKH 508
             +V H
Sbjct: 447 RSIVDH 452

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2 Length = 87

 Score = 59.7 bits (145), Expect = 1e-11
 Identities = 26/73 (35%), Positives = 50/73 (68%), Gaps = 2/73 (2%)

Query: 434 LKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKL 492
           +++E+ K ++ TL  RE  ++R+ YGL D +  T E++ +   ++RER+RQ+ + AL KL
Sbjct: 8   MREELEK-VLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKL 66

Query: 493 KHAARKKKMEAML 505
           +H +R K ++++L
Sbjct: 67  RHPSRSKYLKSLL 79

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B Length = 99

 Score = 59.0 bits (143), Expect = 3e-11
 Identities = 20/73 (27%), Positives = 42/73 (57%), Gaps = 2/73 (2%)

Query: 434 LKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKL 492
           L+   +  ++  L  RE +++R+ +G+      T E++ K+  ++RER+RQ+   AL KL
Sbjct: 9   LRAATHD-VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKL 67

Query: 493 KHAARKKKMEAML 505
           +H +R + + +  
Sbjct: 68  RHPSRSEVLRSGS 80

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2 Length = 68

 Score = 56.9 bits (138), Expect = 8e-11
 Identities = 20/65 (30%), Positives = 40/65 (61%), Gaps = 1/65 (1%)

Query: 442 IIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500
           ++  L  RE +++R+ +G+      T E++ K+  ++RER+RQ+   AL KL+H +R + 
Sbjct: 2   VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61

Query: 501 MEAML 505
           + + L
Sbjct: 62  LRSFL 66

>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 = 54.5 bits (131), Expect = 5e-09
 Identities = 27/212 (12%), Positives = 68/212 (32%), Gaps = 57/212 (26%)

Query: 288 GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLH 347
           GA+  DLVQ G++GLL+ I+ +D +K    S++ +  IR+                    
Sbjct: 1   GAEKEDLVQEGILGLLKAIKFYDETKS-SFSSFAFLCIRR-------------------- 39

Query: 348 ERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGL 407
                                     E ++  +K        + +    +     S    
Sbjct: 40  --------------------------EMISAIRKANTQKHMVLNEALKTNAILEDSAYFD 73

Query: 408 PGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTW 467
               + +    +  E+NP          +E  K       + E+E++           ++
Sbjct: 74  DEGHNINNYKSS--ESNPEEAYLLKEEIEEFKKFSENNFSKFEKEVLTYLI----RGYSY 127

Query: 468 EDISKRIGLSRERVRQVGLVALEKLKHAARKK 499
            +I+  +  + + +       +++++  + + 
Sbjct: 128 REIATILSKNLKSIDN----TIQRIRKKSEEW 155

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A* Length = 73

 Score = 51.6 bits (124), Expect = 6e-09
 Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 2/66 (3%)

Query: 442 IIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLK-HAARKK 499
            +  L ERE  ++++  GL D    T E++    G++RER+RQ+   AL KLK H +R +
Sbjct: 7   ALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTR 66

Query: 500 KMEAML 505
           K+   L
Sbjct: 67  KLRDFL 72

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	508
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	100.0
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	100.0
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	100.0
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	100.0
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	99.97
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	99.96
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	99.9
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	99.89
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	99.85
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.73
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.66
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.6
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	99.44
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	99.31
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	99.16
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	99.12
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	99.11
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	99.04
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	99.0
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	98.95
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	98.84
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	98.7
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	98.65
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	98.51
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	98.51
3c57_A	95	Two component transcriptional regulatory protein;	98.49
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	98.46
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	98.36
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	98.18
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	98.08
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	97.96
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	97.96
2q0o_A	236	Probable transcriptional activator protein TRAR; h	97.54
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	97.52
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	97.38
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	97.26
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	97.11
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	96.88
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	96.6
1yio_A	208	Response regulatory protein; transcription regulat	96.5
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	96.36
3c3w_A	225	Two component transcriptional regulatory protein;	96.1
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	95.78
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	95.4
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	94.81
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	93.76
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	93.69
2gwr_A	238	DNA-binding response regulator MTRA; two-component	93.53
2oqr_A	230	Sensory transduction protein REGX3; response regul	93.26
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	93.13
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	92.81
1ys7_A	233	Transcriptional regulatory protein PRRA; response	92.53
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	92.04
1u78_A	141	TC3 transposase, transposable element TC3 transpos	91.99
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	91.88
2hqr_A	223	Putative transcriptional regulator; phosporylation	91.18
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	91.03
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	90.85
3q9s_A	249	DNA-binding response regulator; DNA binding protei	90.8
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	90.44
3frw_A	107	Putative Trp repressor protein; structural genomic	90.14
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	89.62
3r0j_A	250	Possible two component system response transcript	89.51
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	88.94
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	88.41
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	88.3
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	88.0
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	87.72
3r0a_A	123	Putative transcriptional regulator; structural gen	87.54
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	87.31
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	86.92
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	86.77
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	86.46
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	86.37
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	86.33
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	86.28
3nqo_A	189	MARR-family transcriptional regulator; structural	86.16
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	86.07
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	86.01
2w25_A	150	Probable transcriptional regulatory protein; trans	85.98
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	85.96
1sfx_A	109	Conserved hypothetical protein AF2008; structural	85.95
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	85.9
2k27_A	159	Paired box protein PAX-8; paired domain, solution	85.8
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	85.77
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	85.28
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	85.23
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	85.05
1u78_A	141	TC3 transposase, transposable element TC3 transpos	85.03
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	84.92
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	84.74
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	84.37
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	84.3
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	84.25
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	83.99
3jth_A	98	Transcription activator HLYU; transcription factor	83.7
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	83.66
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	83.57
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	82.81
2gxg_A	146	146AA long hypothetical transcriptional regulator;	82.75
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	82.7
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	82.61
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	82.45
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	82.44
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	82.42
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	82.1
1ku9_A	152	Hypothetical protein MJ223; putative transcription	82.1
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	82.06
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	81.67
3iwf_A	107	Transcription regulator RPIR family; transcription	81.3
2nnn_A	140	Probable transcriptional regulator; structural gen	81.23
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	81.1
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	81.06
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	80.82
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	80.58
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	80.55
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	80.41
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	80.34
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	80.28
2kko_A	108	Possible transcriptional regulatory protein (possi	80.27
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	80.21
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	80.18
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	80.11

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

Probab=100.00  E-value=3.3e-50  Score=426.60  Aligned_cols=310  Identities=31%  Similarity=0.495  Sum_probs=272.5

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHH------------------HHHHhhCCCCchHHHHH------
Q 010521          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL------------------RLKERLGCEPSMEQLAA------  246 (508)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~------------------~l~~~~g~~p~~~~~a~------  246 (508)
                      |.++.||++|+++|+||++||++|+++++.|..+++...                  +.....++.|+.++|+.      
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            688999999999999999999999999999975443221                  11234567888777642      


Q ss_pred             ------HhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhH
Q 010521          247 ------SLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY  320 (508)
Q Consensus       247 ------~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTY  320 (508)
                            .++++..+|...+.++..|+++||..|+++|++||++|.++|.+++||+||||||||+|+++|||++|++|+||
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                  23567788999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhC--CCHHHHHHHHHHhCcccccc
Q 010521          321 VYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLN--MSQKKVRNATEAIGKVFSLD  397 (508)
Q Consensus       321 A~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lg--is~e~v~~~l~~~~~~~SLD  397 (508)
                      |+||||+.|.++|++++|.+++|+|+.+.+++++++++.+. ..|+.|+.++||+.+|  +++++|..++.....++|+|
T Consensus       254 A~~wIR~~I~~~i~~~~R~irlp~~~~~~l~~lrr~~r~l~~~lgr~pt~eeiA~~l~~~v~~e~V~~~~~~~~~~~SLd  333 (438)
T 1l9z_H          254 ATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLE  333 (438)
T ss_pred             HHHHHHHHHHHHHHHhcchhccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhcccccccc
Confidence            99999999999999999999999999999999999988874 7899999999999999  99999999998888899999


Q ss_pred             ccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCC
Q 010521          398 REAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGL  476 (508)
Q Consensus       398 ~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgI  476 (508)
                      .++    +++++..+.+++++.. ..+|++.+...+....|..+| +.||++||.||.+||||+ ++++|++|||+.|||
T Consensus       334 ~~~----~~d~d~~l~d~l~d~~-~~~pee~~~~~~~~~~L~~aL-~~L~ereR~VI~LRygL~~~e~~TleEIAe~LgI  407 (438)
T 1l9z_H          334 TPI----GDEKDSFYGDFIPDEN-LPSPVEAAAQSLLSEELEKAL-SKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGV  407 (438)
T ss_pred             ccc----ccccchhhhhhhcccc-cCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHHhccCCCCCCHHHHHHHHCc
Confidence            874    2223345666776653 246888888888889999999 899999999999999984 579999999999999


Q ss_pred             CHHHHHHHHHHHHHHHH-HHHHHhhHHHhhh
Q 010521          477 SRERVRQVGLVALEKLK-HAARKKKMEAMLV  506 (508)
Q Consensus       477 S~erVrqi~~rALkKLR-~~L~~~~l~~~l~  506 (508)
                      |++||+|++++|++||| +.+....++.||.
T Consensus       408 S~erVRqi~~RAlkKLR~~~~~~~~l~~yl~  438 (438)
T 1l9z_H          408 TRERIRQIENKALRKLKYHESRTRKLRDFLE  438 (438)
T ss_pred             CHHHHHHHHHHHHHHHHHhHhhHHHHHHhhC
Confidence            99999999999999999 8888888999873

>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=100.00  E-value=9.6e-50  Score=422.73  Aligned_cols=306  Identities=32%  Similarity=0.526  Sum_probs=264.0

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHh---------------------hCCCCchHH------
Q 010521          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKER---------------------LGCEPSMEQ------  243 (508)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~---------------------~g~~p~~~~------  243 (508)
                      +++++||++|+++|+||++||++|+++++.|+.+..   .|...                     .++.|+.++      
T Consensus        79 d~~~~Yl~ei~~~plLt~eEE~~La~ri~~g~~~~~---~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (423)
T 2a6h_F           79 DPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIK---KLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKT  155 (423)
T ss_dssp             HHHHHHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHH---HHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTHH
T ss_pred             cHHHHHHHHhcccCCCCHHHHHHHHHHHHhchhHHH---HHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhhh
Confidence            689999999999999999999999999999975332   22222                     345555333      


Q ss_pred             ---HH---HHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcc
Q 010521          244 ---LA---ASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKI  317 (508)
Q Consensus       244 ---~a---~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rF  317 (508)
                         |+   .+++++..+|...+.++..|+++||..|+++|++||++|.++|.+++||+||||+|||+|+++|||.+|++|
T Consensus       156 ~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~kav~kFd~~~g~~F  235 (423)
T 2a6h_F          156 VEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKF  235 (423)
T ss_dssp             HHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHHHHHCCTTSCCCH
T ss_pred             hhhhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCcccCCCH
Confidence               33   235678889999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhC--CCHHHHHHHHHHhCccc
Q 010521          318 STYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLN--MSQKKVRNATEAIGKVF  394 (508)
Q Consensus       318 sTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lg--is~e~v~~~l~~~~~~~  394 (508)
                      +|||+||||+.|.++|++++|++++|+|+.+.+++++++.+.+. ..|+.|+.++||+.+|  +++++|..++.....++
T Consensus       236 stYa~~wIr~~i~~~i~~~~r~ir~p~~~~~~~~~lrr~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~~~~~~~~~~~  315 (423)
T 2a6h_F          236 STYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPV  315 (423)
T ss_dssp             HHHHHHHHHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHHHHHHHHSCCE
T ss_pred             HHHHHHHHHHHHHHHHHHccceeeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhccCCc
Confidence            99999999999999999999999999999999999999988774 7899999999999999  99999999999889999


Q ss_pred             cccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHH
Q 010521          395 SLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKR  473 (508)
Q Consensus       395 SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~  473 (508)
                      |+|.++    +++++..+.+++++.. ..+|++.+...+....|..+| ..||++||.||.+||||+ ++++|++|||+.
T Consensus       316 Sld~~~----~~~~~~~l~d~l~d~~-~~~pe~~~~~~~~~~~L~~aL-~~L~~rer~Vl~lr~~L~~~e~~Tl~EIA~~  389 (423)
T 2a6h_F          316 SLETPI----GDEKDSFYGDFIPDEH-LPSPVDAATQSLLSEELEKAL-SKLSEREAMVLKLRKGLIDGREHTLEEVGAF  389 (423)
T ss_dssp             ESSCBC----SSSSSCBGGGSSCCSS-SCCHHHHHHHHHHHHHHHHHH-HSSCHHHHHHHHHHHHTTCC-----CHHHHS
T ss_pred             cccccc----CCCCccchhhhhcccc-CCCHHHHHHHHHHHHHHHHHH-HhCCHHHHHHHHHHhccCCCCCCCHHHHHHH
Confidence            999874    2223345777777654 247888888888889999999 899999999999999984 579999999999


Q ss_pred             HCCCHHHHHHHHHHHHHHHH-HHHHHhhHHHhh
Q 010521          474 IGLSRERVRQVGLVALEKLK-HAARKKKMEAML  505 (508)
Q Consensus       474 LgIS~erVrqi~~rALkKLR-~~L~~~~l~~~l  505 (508)
                      ||||++||+|++.+|++||| +.+....++.||
T Consensus       390 lgiS~erVrqi~~rAl~kLR~~~~~~~~l~~~l  422 (423)
T 2a6h_F          390 FGVTRERIRQIENKALRKLKYHESRTRKLRDFL  422 (423)
T ss_dssp             SSSCHHHHHHHHHHHHHHHHHHHHHTTSSSSCC
T ss_pred             HCcCHHHHHHHHHHHHHHHHhhhhhhHHHHHhh
Confidence            99999999999999999999 788877777776

>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=100.00  E-value=2.7e-40  Score=364.99  Aligned_cols=270  Identities=29%  Similarity=0.550  Sum_probs=235.7

Q ss_pred             HHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHH
Q 010521          194 KGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSN  273 (508)
Q Consensus       194 ~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~y  273 (508)
                      +.-|..|.....++..++.+|+.+++.||.                                     ....|++.||..|
T Consensus       341 q~kL~~ie~~~~~~~~~~~~Li~~~~~Gd~-------------------------------------~A~~A~~~L~~~y  383 (613)
T 3iyd_F          341 LQKLQQIEEETGLTIEQVKDINRRMSIGEA-------------------------------------KARRAKKEMVEAN  383 (613)
T ss_dssp             HHHHHHHHHHHTSCTTTHHHHHHTHHHHHH-------------------------------------HHHHHHTTTTTTT
T ss_pred             HHHHHHHHHHhCCChHHHHHHHHHHHHHhh-------------------------------------hhHHHHHHHHHHH
Confidence            444555666666666677777777777775                                     0012499999999


Q ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHH
Q 010521          274 VRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLI  353 (508)
Q Consensus       274 l~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~ki  353 (508)
                      +++|+++|++|++++.+++||+||||+|||+++++||+.+|++|+||++||||++|.++++++.|++++|.|+.+.++++
T Consensus       384 ~~~v~~ia~r~~~~~~~aeDlvQE~fi~l~~a~~~fd~~~g~~Fstyl~~~irn~i~~~lr~~~r~~rip~~~~~~~~k~  463 (613)
T 3iyd_F          384 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKL  463 (613)
T ss_dssp             THHHHHGGGSSSTTSSCSTTTTHHHHHHHHHHTTSCCTTSSSCSTTTHHHHHHHHHHHHTTTSCSSSCCCSHHHHTTTTT
T ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCccccCcHHHHHHHHHHHHHHHHHHhcCcceeCcHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHH-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHH
Q 010521          354 RNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDW  432 (508)
Q Consensus       354 r~a~~~l-~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~  432 (508)
                      +++...+ ++.|++|+++|||+.+|+++++++.++.....++|++.++    +++++..+.+++.+.. ..+|++.+...
T Consensus       464 ~r~~~~l~~~~gr~pt~eela~~l~~~~~~v~~~~~~~~~~~sld~~~----~~~~~~~l~d~i~d~~-~~~p~~~~~~~  538 (613)
T 3iyd_F          464 NRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPI----GDDEDSHLGDFIEDTT-LELPLDSATTE  538 (613)
T ss_dssp             TTTTTTTTTTTCSCCCTTTTTTTSSCCSSHHHHHHHHSCCCCCSSCCC----SSSSSCCGGGSCCCSS-SCCHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhccCCcccCCCC----CCCCCccHHHHhcCCC-CCCHHHHHHHH
Confidence            8887777 4789999999999999999999999999999999999874    2334446777777654 34788888888


Q ss_pred             HHHHHHHHHHHccCCHHHHHHHhHHhccCC-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521          433 ALKDEVNKLIIVTLGEREREIIRLYYGLDK-ECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV  506 (508)
Q Consensus       433 el~e~L~~~L~~~Lp~rER~VI~LryGLd~-eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~  506 (508)
                      ++...|..+| ..||+++|.||.|+||++. +++|++|||+.||||++||++++++|+++||+.+....++.||+
T Consensus       539 e~~~~l~~aL-~~Lp~~er~Vl~Lr~~~~~~e~~s~~EIA~~lgis~~tVk~~~~rAl~kLR~~~~~~~l~~~l~  612 (613)
T 3iyd_F          539 SLRAATHDVL-AGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD  612 (613)
T ss_dssp             TTSSSHHHHT-TSSCHHHHHHHHHHHTSSSCCCCSTTGGGTTTSSCSSHHHHHHHHHHTTTTSCSSSCSSTTCC-
T ss_pred             HHHHHHHHHH-HcCCHHHHHHHHHHhccCCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhhCcchhhHHHHHhc
Confidence            8888899999 9999999999999998764 89999999999999999999999999999999998888888875

>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=100.00  E-value=1e-33  Score=279.84  Aligned_cols=208  Identities=32%  Similarity=0.527  Sum_probs=131.2

Q ss_pred             hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHH-------H--HH-----------------hhCCCCchH
Q 010521          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLR-------L--KE-----------------RLGCEPSME  242 (508)
Q Consensus       189 ~~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~-------l--~~-----------------~~g~~p~~~  242 (508)
                      ..|++++||++|+++|+||++||++|+++|+.|....+....       +  +.                 ..+.+|+..
T Consensus         5 ~~d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~~~   84 (245)
T 3ugo_A            5 TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTV   84 (245)
T ss_dssp             CCHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHHHH
T ss_pred             CCCcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccchhH
Confidence            347999999999999999999999999999999863322111       0  00                 024788999


Q ss_pred             HHHHHhccChH----HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcch
Q 010521          243 QLAASLRISRP----ELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKIS  318 (508)
Q Consensus       243 ~~a~~~~~s~~----~L~~~l~e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFs  318 (508)
                      +||.+.+++..    +|.+.+.++..|+++||+.|.++|+++|++|.+++.+++||+||||+|||+++++|||++|++|+
T Consensus        85 ~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a~~~fd~~~g~~F~  164 (245)
T 3ugo_A           85 EEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS  164 (245)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHH
T ss_pred             HHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHHHHHcCcccCCcHH
Confidence            99999998754    45556778899999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhC--CCHHHHHHHHHHhCcccc
Q 010521          319 TYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLN--MSQKKVRNATEAIGKVFS  395 (508)
Q Consensus       319 TYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lg--is~e~v~~~l~~~~~~~S  395 (508)
                      ||++||||++|.++++++.+.+++|.++.+.++++..+.+.+. ..|+.|+.+|||+.||  +|+.+|...+......+|
T Consensus       165 tya~~~ir~~i~~~ir~~~r~~r~p~~l~e~i~~l~~~~~~L~~~~~~~ps~~EIAe~Lg~~is~~tVk~~l~~ar~~ls  244 (245)
T 3ugo_A          165 TYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVS  244 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHTC------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHHhhccC
Confidence            9999999999999999999999999999999999998888885 6799999999999999  999999999988877776


Q ss_pred             c
Q 010521          396 L  396 (508)
Q Consensus       396 L  396 (508)
                      |
T Consensus       245 l  245 (245)
T 3ugo_A          245 L  245 (245)
T ss_dssp             -
T ss_pred             C
Confidence            5

>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=99.97  E-value=1.7e-29  Score=242.26  Aligned_cols=221  Identities=22%  Similarity=0.338  Sum_probs=186.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccc
Q 010521          263 SLAREKLVMSNVRLVMSIAQRYD---NMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT  339 (508)
Q Consensus       263 ~~A~e~LIe~yl~LV~sIAkrY~---~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~  339 (508)
                      ..|++.|+..|.++|+++|++|.   +++.+++||+|||+++||+++++||+.+|.+|.||+++||++.+.+++++..  
T Consensus        11 ~~a~~~l~~~~~~~v~~~a~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~d~~r~~~--   88 (239)
T 1rp3_A           11 QIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLD--   88 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSS--
T ss_pred             chHHHHHHHHhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC--
Confidence            36999999999999999999998   6789999999999999999999999998889999999999999999999875  


Q ss_pred             ccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhC--ccccccccCCCCCCCCCCCcccccc
Q 010521          340 LRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIG--KVFSLDREAFPSLNGLPGETHHSYI  416 (508)
Q Consensus       340 irip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~--~~~SLD~~~~~~~~~~~~~~l~d~i  416 (508)
                       +.|.+......++.++...+. ..|+.|+.+++|+.+|++++++..++....  ...|++.+..    ++++.. .+. 
T Consensus        89 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~sl~~~~~----~~~~~~-~~~-  161 (239)
T 1rp3_A           89 -FGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFR----DFARDY-SEL-  161 (239)
T ss_dssp             -TTCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHH-TTT-
T ss_pred             -ccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccCCCcccccccc----CCCccc-ccc-
Confidence             466666777778888888885 679999999999999999999998877652  3456665310    000011 122 


Q ss_pred             ccccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          417 ADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       417 ~d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      ++.  ..+|++.+...+....|..+| ..||+++|.||.++|   ++|+|++|||+.||||+++|++++++|+++||+.+
T Consensus       162 ~~~--~~~~~~~~~~~e~~~~l~~~l-~~L~~~~r~vl~l~~---~~g~s~~EIA~~lgis~~~V~~~~~ra~~~Lr~~l  235 (239)
T 1rp3_A          162 IPS--STNVEEEVIKRELTEKVKEAV-SKLPEREKLVIQLIF---YEELPAKEVAKILETSVSRVSQLKAKALERLREML  235 (239)
T ss_dssp             GGG--SCHHHHHHHHHHHHHHHHHHH-TTSCHHHHHHHHHHH---TSCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCC--CCCHHHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence            222  236777788888889999999 999999999999999   79999999999999999999999999999999988


Q ss_pred             HH
Q 010521          497 RK  498 (508)
Q Consensus       497 ~~  498 (508)
                      ..
T Consensus       236 ~~  237 (239)
T 1rp3_A          236 SN  237 (239)
T ss_dssp             HC
T ss_pred             hc
Confidence            53

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

Probab=99.96  E-value=3.1e-31  Score=254.22  Aligned_cols=239  Identities=31%  Similarity=0.404  Sum_probs=49.3

Q ss_pred             hcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHHHHHHHHHH
Q 010521          200 VVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMS  279 (508)
Q Consensus       200 i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe~yl~LV~s  279 (508)
                      +...+.++++++.+|+.+++.||.                                        .|++.|+..|.++|++
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            455677888899999999999998                                        9999999999999999


Q ss_pred             HHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHH
Q 010521          280 IAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLR  359 (508)
Q Consensus       280 IAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~  359 (508)
                      +|++|.++..+++|++|||++++|+++++|++.+|.+|.||+++++++.+.++++++. .+++|.+......+++++...
T Consensus        44 ~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~i~~~~~~d~~r~~~-~~~~~~~~~~~~~~~~~~~~~  122 (243)
T 1l0o_C           44 VVQRFLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKEMGNKIRKAKDE  122 (243)
T ss_dssp             --------------------------------------------------------CC-CCTTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC-CccCcHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999998889999999999999999999987 788999999888888888888


Q ss_pred             HH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHH
Q 010521          360 LE-EKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEV  438 (508)
Q Consensus       360 l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L  438 (508)
                      +. +.++.|+..+++..+|++.+++...+.......|++.+...  ++.+..++.+.+        |++.+...+....|
T Consensus       123 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~--~~~~~~~~~~~~--------~~~~~~~~~~~~~l  192 (243)
T 1l0o_C          123 LSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYE--NDGDPITLLDQI--------ADADEASWFDKIAL  192 (243)
T ss_dssp             HHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHHC----------------------------------------------
T ss_pred             HHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHhccccCccccccc--cCCcccchhhcc--------CcchhHHHHHHHHH
Confidence            85 57899999999999999999999888777667777765210  011111222222        23334445666788


Q ss_pred             HHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          439 NKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       439 ~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..+| ..||+++|.||.++|   ++|+|++|||+.||||+++|++++++|+++||
T Consensus       193 ~~~l-~~L~~~~r~vl~l~~---~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr  243 (243)
T 1l0o_C          193 KKAI-EELDERERLIVYLRY---YKDQTQSEVASRLGISQVQMSRLEKKILQHIK  243 (243)
T ss_dssp             -------------------------------------------------------
T ss_pred             HHHH-HhCCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            8999 899999999999999   79999999999999999999999999999997

>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=99.90  E-value=8.6e-23  Score=190.42  Aligned_cols=167  Identities=22%  Similarity=0.239  Sum_probs=130.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLP  343 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip  343 (508)
                      .|++.|+..|.+.|+.+|.++.+ ..+++|++||+|+++|+++++|++..  .|.+|++.++++.+.+++++..+.... 
T Consensus        23 ~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~~~~~~~~~--~~~~~l~~i~~n~~~d~~R~~~~~~~~-   98 (194)
T 1or7_A           23 KAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRALDSFRGDS--AFYTWLYRIAVNTAKNYLVAQGRRPPS-   98 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHHHHHHHHHTTCCTH-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHHHHHHHHhccCcc-
Confidence            99999999999999999999999 99999999999999999999999865  599999999999999999876542110 


Q ss_pred             ccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCC
Q 010521          344 NHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVEN  423 (508)
Q Consensus       344 ~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~  423 (508)
                                                .++..           ..     ...++.+          .    .+.+.   +
T Consensus        99 --------------------------~~~~~-----------~~-----~~~~~~~----------~----~~~~~---~  119 (194)
T 1or7_A           99 --------------------------SDVDA-----------IE-----AENFESG----------G----ALKEI---S  119 (194)
T ss_dssp             --------------------------HHHHH-----------HH-----HHSCCSS----------C----C--------
T ss_pred             --------------------------ccccc-----------cc-----ccccccc----------c----cccCC---C
Confidence                                      00000           00     0001100          0    01111   2


Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      +|++.+...+....|..+| ..||+++|.||.|+|   .+|+|++|||+.||+|.++|++++++|+++||+.+.
T Consensus       120 ~~~~~~~~~e~~~~l~~~l-~~L~~~~r~vl~l~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~  189 (194)
T 1or7_A          120 NPENLMLSEELRQIVFRTI-ESLPEDLRMAITLRE---LDGLSYEEIAAIMDCPVGTVRSRIFRAREAIDNKVQ  189 (194)
T ss_dssp             ---CEEEHHHHHHHHHHHH-HHSCHHHHHHHHHHH---TTCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHC
T ss_pred             ChHHHHHHHHHHHHHHHHH-HhCCHHHHHHhHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            3444445566677888999 899999999999999   799999999999999999999999999999999875

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}

Probab=99.85  E-value=9.1e-21  Score=170.93  Aligned_cols=155  Identities=17%  Similarity=0.250  Sum_probs=108.7

Q ss_pred             CCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHHHHHHHHcCCCC
Q 010521          288 GADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTP  367 (508)
Q Consensus       288 g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~~Gr~P  367 (508)
                      |.+++|++||+++++|+++.+||+.+ .+|.+|++.++++.+.+++++..+..+.+...                     
T Consensus         1 g~daeDl~Qe~~~~l~~~~~~~~~~~-~~f~~~l~~i~~n~~~d~~r~~~~~~~~~~~~---------------------   58 (164)
T 3mzy_A            1 GAEKEDLVQEGILGLLKAIKFYDETK-SSFSSFAFLCIRREMISAIRKANTQKHMVLNE---------------------   58 (164)
T ss_dssp             ----CTTHHHHHHHHHHHHHHCCTTT-SCHHHHHHHHHHHHHHHHHHHHHHCC---------------------------
T ss_pred             CCcHHHHHHHHHHHHHHHHHHhCccC-CChHHHhHHHHHHHHHHHHHHhhcccchhhHH---------------------
Confidence            57899999999999999999999987 68999999999999999998875432222110                     


Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccc----cccccccCCCCccchHHHHHHHHHHHHHHH
Q 010521          368 SVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHH----SYIADNRVENNPWHGVDDWALKDEVNKLII  443 (508)
Q Consensus       368 t~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~----d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~  443 (508)
                                               .++.+.+.    +++....+.    +.+.+.  ..+|++.+...+....|..+| 
T Consensus        59 -------------------------~~~~~~~~----~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~e~~~~l~~~l-  106 (164)
T 3mzy_A           59 -------------------------ALKTNAIL----EDSAYFDDEGHNINNYKSS--ESNPEEAYLLKEEIEEFKKFS-  106 (164)
T ss_dssp             --------------------------------------------------------------CHHHHHHHHHHHHHHHH-
T ss_pred             -------------------------Hhhhhhhh----ccCCCCCcccchhhhhccc--CCCHHHHHHHHHHHHHHHHHH-
Confidence                                     01111100    000000110    111222  247888888888899999999 


Q ss_pred             c-cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          444 V-TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       444 ~-~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                      . .||+++|.||. +|   .+|+|++|||+.||+|.++|++++++|+++||+.+...+
T Consensus       107 ~~~L~~~~r~v~~-~~---~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~~  160 (164)
T 3mzy_A          107 ENNFSKFEKEVLT-YL---IRGYSYREIATILSKNLKSIDNTIQRIRKKSEEWIKEEE  160 (164)
T ss_dssp             HHHSCHHHHHHHH-HH---TTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HhhCCHHHHHHHH-HH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHcC
Confidence            7 99999999999 67   699999999999999999999999999999999997653

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=99.73  E-value=4.3e-20  Score=169.04  Aligned_cols=141  Identities=11%  Similarity=0.109  Sum_probs=115.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhccccccccc
Q 010521          266 REKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRLPNH  345 (508)
Q Consensus       266 ~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~irip~~  345 (508)
                      |+.|+..|.+.|+.+|.+++++..+++|++||+|+++|+++++|++..  .|.+|++..++|.+.+++++...       
T Consensus         3 f~~l~~~~~~~l~~~~~~~~~~~~~AeDlvQe~fl~~~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~R~~~~-------   73 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALTGSQNQGDKYVRATLEAIVAAPDQFPRDV--DPRLGLYRMFQGIWASANADGEA-------   73 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTTSCHHHHHHHHHHHHHTTTTCGGGCCCSS--CTTHHHHHHHHHHHHHHTTTTSC-------
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhHHHcCCCC--cHHHHHHHHHHHHHHHHhhccCc-------
Confidence            567889999999999999999999999999999999999999999754  69999999999977777653210       


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCc
Q 010521          346 LHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNP  425 (508)
Q Consensus       346 ~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~P  425 (508)
                                                                         +.         ..  .     +.     .
T Consensus        74 ---------------------------------------------------~~---------~~--~-----e~-----~   81 (157)
T 2lfw_A           74 ---------------------------------------------------QT---------SQ--S-----DA-----E   81 (157)
T ss_dssp             ---------------------------------------------------CC---------CC--C-----SC-----S
T ss_pred             ---------------------------------------------------cc---------CC--c-----ch-----H
Confidence                                                               00         00  0     00     0


Q ss_pred             cchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q 010521          426 WHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK  498 (508)
Q Consensus       426 e~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~  498 (508)
                             +....|..+| ..||+++|.||.|+|   .+|+|++|||+.||+|.+||++.+.+|+++||+.+..
T Consensus        82 -------~~~~~l~~~l-~~Lp~~~r~vl~L~~---~~g~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~  143 (157)
T 2lfw_A           82 -------GTEAVARARL-ARMTPLSRQALLLTA---MEGFSPEDAAYLIEVDTSEVETLVTEALAEIEKQTRA  143 (157)
T ss_dssp             -------SSSSTTTTTT-TTSCTTHHHHHTTTS---SSCCCHHHHHHTTTSCHHHHHHHHHHHHHHHHTTSSC
T ss_pred             -------HHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence                   0112355677 899999999999999   8999999999999999999999999999999987753

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

Probab=99.66  E-value=1.9e-16  Score=162.54  Aligned_cols=109  Identities=35%  Similarity=0.698  Sum_probs=95.4

Q ss_pred             hHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHHHHH
Q 010521          192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM  271 (508)
Q Consensus       192 ~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~LIe  271 (508)
                      ..+..|.++.....|+..++..|+.+++.||.                                     ....|++.||.
T Consensus       230 ~~q~kl~~ie~~~~l~~~~~~~l~~~~~~gd~-------------------------------------~~~~A~~~L~~  272 (339)
T 1sig_A          230 RALQKLQQIEEETGLTIEQVKDINRRMSIGEA-------------------------------------KARRAKKEMVE  272 (339)
T ss_dssp             HHHHHHHHHHHHHTSCHHHHHHHHHHHHHHHH-------------------------------------HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCChHHHHHHHHHHHhccc-------------------------------------cchhhhHHHHH
Confidence            45566777777777788888888888888774                                     11279999999


Q ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhc
Q 010521          272 SNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS  337 (508)
Q Consensus       272 ~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~  337 (508)
                      .|+++|+++|++|++++.+++||+||||+|||+++++|++.+|.+|+||++|||+|.|.++++++.
T Consensus       273 ~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~~f~~~~g~~f~twl~~iirn~~~~~lr~~~  338 (339)
T 1sig_A          273 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQA  338 (339)
T ss_dssp             HTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHhc
Confidence            999999999999999999999999999999999999999998889999999999999999999875

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.60  E-value=5.1e-16  Score=155.70  Aligned_cols=140  Identities=11%  Similarity=0.020  Sum_probs=115.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcccccc
Q 010521          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRTLRL  342 (508)
Q Consensus       263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R~iri  342 (508)
                      ..+|+.|+..|.+.++.+|.+|+++..++||++||+|+.+|+...+|++..  .|.+|++..++|.+.++++...     
T Consensus        20 ~~~f~~l~~~~~~~l~~~a~~~~~~~~~AeD~vQe~fl~~~~~~~~~~~~~--~~~~wL~~ia~n~~~d~~r~~~-----   92 (286)
T 3n0r_A           20 EMHLLARLAPHLPYIRRYARALTGDQATGDHYVRVALEALAAGELVLDANL--SPRVALYRVFHAIWLSSGAQLE-----   92 (286)
T ss_dssp             CCCHHHHHGGGHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHTTSSCCCSSS--CHHHHHHHHHHHHHSCTTC--------
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHhCchhcCCCc--ChHHHHHHHHHHHHHhhccccc-----
Confidence            379999999999999999999999999999999999999999999999753  6999999998886555443110     


Q ss_pred             cccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCC
Q 010521          343 PNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVE  422 (508)
Q Consensus       343 p~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e  422 (508)
                                                                             .+      ...         +    
T Consensus        93 -------------------------------------------------------~~------~~~---------~----   98 (286)
T 3n0r_A           93 -------------------------------------------------------VG------HDQ---------G----   98 (286)
T ss_dssp             --------------------------------------------------------C------CCC---------C----
T ss_pred             -------------------------------------------------------cC------CCc---------c----
Confidence                                                                   00      000         0    


Q ss_pred             CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      ...         ...|.++| +.||+++|.||.|+|   .+|+|++|||+.+|++.++|+....+|+++|+..+
T Consensus        99 ~~~---------~~~l~~al-~~Lp~~~R~v~~L~~---~eg~s~~EIA~~lgis~~tVks~l~rA~~~Lr~~l  159 (286)
T 3n0r_A           99 LHA---------GDDAAQRL-MRIAPRSRQAFLLTA---LEGFTPTEAAQILDCDFGEVERLIGDAQAEIDAEL  159 (286)
T ss_dssp             CCT---------TSHHHHHH-HHHSCHHHHHHHHHH---TTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHTSC
T ss_pred             cch---------HHHHHHHH-HhCCHHHeeEEEEEe---eCCCCHHHHHHHhCcCHHHHHHHHHHHHhhhhccC
Confidence            000         12477888 899999999999999   89999999999999999999999999999998643

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B

Probab=99.44  E-value=4.8e-13  Score=114.49  Aligned_cols=79  Identities=27%  Similarity=0.498  Sum_probs=72.5

Q ss_pred             hHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521          428 GVDDWALKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV  506 (508)
Q Consensus       428 ~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~  506 (508)
                      .+...++...|..+| +.|||+||.||.++||++ .+++|++|||+.||+|++||++++.+|+++||..+....++.|+.
T Consensus         3 ~~~~~el~~~l~~aL-~~Lp~reR~Vi~Lry~l~~~e~~s~~EIA~~lgiS~~tVr~~~~rAlkkLR~~~~~~~l~~~~~   81 (99)
T 3t72_q            3 SATTESLRAATHDVL-AGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSGSS   81 (99)
T ss_pred             HHHHHHHHHHHHHHH-HcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            356677888999999 899999999999999885 479999999999999999999999999999999999999999885


Q ss_pred             c
Q 010521          507 K  507 (508)
Q Consensus       507 ~  507 (508)
                      .
T Consensus        82 ~   82 (99)
T 3t72_q           82 G   82 (99)
T ss_pred             h
Confidence            3

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=99.31  E-value=9.1e-12  Score=104.09  Aligned_cols=74  Identities=14%  Similarity=0.150  Sum_probs=69.6

Q ss_pred             CCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Q 010521          423 NNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK  500 (508)
Q Consensus       423 ~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~  500 (508)
                      .+|++.++..+....|..+| ..||+++|.||.|+|   ++|+|++|||+.||||.+||++++++|+++||+.+...+
T Consensus        16 ~~~~~~~~~~~~~~~l~~~l-~~L~~~~r~vl~l~~---~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~   89 (92)
T 3hug_A           16 QSTPDEVNAALDRLLIADAL-AQLSAEHRAVIQRSY---YRGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQELG   89 (92)
T ss_dssp             CCHHHHHHHHHHHHHHHHHH-HTSCHHHHHHHHHHH---TSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCchHHHHHHHHHHHHHHHH-HcCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhC
Confidence            47888899999999999999 899999999999999   899999999999999999999999999999999997654

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=99.16  E-value=7.2e-12  Score=98.92  Aligned_cols=63  Identities=33%  Similarity=0.625  Sum_probs=58.0

Q ss_pred             ccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521          444 VTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV  506 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~  506 (508)
                      +.|||+|+.||.++||++ ++|+|++|||+.||+|++||++++.+|+++||..+....+..|+.
T Consensus         4 ~~L~~~er~il~l~~~l~~~~g~s~~eIA~~lgis~~tV~~~~~ra~~kLr~~~~~~~~~~~~~   67 (68)
T 2p7v_B            4 AGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD   67 (68)
T ss_dssp             CCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCCGGGGGSCTTC
T ss_pred             HcCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            689999999999999884 589999999999999999999999999999999988887777764

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=99.12  E-value=6.5e-11  Score=98.12  Aligned_cols=71  Identities=35%  Similarity=0.605  Sum_probs=63.7

Q ss_pred             HHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhhc
Q 010521          436 DEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLVK  507 (508)
Q Consensus       436 e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~~  507 (508)
                      ..|..+| +.||+++|.||.++|+|+ .+++|++|||+.||+|++||++++.+|+++||..+....+..|+..
T Consensus        10 ~~l~~~l-~~L~~~er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~kLr~~l~~~~~~~~~~~   81 (87)
T 1tty_A           10 EELEKVL-KTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLKSLLSL   81 (87)
T ss_dssp             SHHHHHH-TTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTBSSHHHHHHHHH
T ss_pred             HHHHHHH-HhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence            4577888 899999999999999763 3799999999999999999999999999999999988888887754

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

Probab=99.11  E-value=1.6e-10  Score=99.00  Aligned_cols=72  Identities=15%  Similarity=0.157  Sum_probs=63.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhcc
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSR  338 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~R  338 (508)
                      .|++.|+..|.+.++.+|.++ ++..+++|++||+|+.+|+.+.+|++..  .|.+|++..++|.+.+++++..+
T Consensus        24 ~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl~~~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~   95 (112)
T 2o7g_A           24 RALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAIPRFSARS--SARTWLLAIARHVVADHIRHVRS   95 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHHHHHHHGGGCCCSS--CHHHHHHHHHHHHHHHHTC----
T ss_pred             HHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHHHHHhcCCCC--CHHHHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999999999 8888999999999999999999999643  69999999999999888876643

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=99.04  E-value=5.8e-11  Score=94.95  Aligned_cols=67  Identities=36%  Similarity=0.567  Sum_probs=52.4

Q ss_pred             HHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH-HHHHHhhHHHhh
Q 010521          438 VNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLK-HAARKKKMEAML  505 (508)
Q Consensus       438 L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR-~~L~~~~l~~~l  505 (508)
                      |..+| +.||++|+.||.++|+|+ .+|+|++|||+.||+|++||++++.+|+++|| ..+....++.|+
T Consensus         4 l~~~l-~~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~~~~~~~~~~~~   72 (73)
T 1ku3_A            4 LEKAL-SKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFL   72 (73)
T ss_dssp             CSSST-TTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTC---------
T ss_pred             HHHHH-HhCCHHHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHhhHHHHHHhh
Confidence            34456 899999999999999764 37999999999999999999999999999999 888777777765

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=99.00  E-value=6.1e-10  Score=87.27  Aligned_cols=65  Identities=22%  Similarity=0.175  Sum_probs=54.2

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521          433 ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM  501 (508)
Q Consensus       433 el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l  501 (508)
                      +....+..+| +.||++++.||.++|   .+|+|++|||+.||+|+.+|++++++|+++||..+....+
T Consensus         4 e~~~~l~~~l-~~L~~~~r~il~l~~---~~g~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~l~~~~~   68 (70)
T 2o8x_A            4 EDLVEVTTMI-ADLTTDQREALLLTQ---LLGLSYADAAAVCGCPVGTIRSRVARARDALLADAEPDDL   68 (70)
T ss_dssp             HHHHHHHTTT-TSSCHHHHHHHHHHH---TSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHC-------
T ss_pred             HHHHHHHHHH-HhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhcccC
Confidence            4456788888 899999999999999   7999999999999999999999999999999998876543

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

Probab=98.95  E-value=9.9e-10  Score=89.82  Aligned_cols=75  Identities=19%  Similarity=0.207  Sum_probs=66.2

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHhc
Q 010521          261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENS  337 (508)
Q Consensus       261 e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~~  337 (508)
                      +++.|++.|+..|.+.++.+|.++.++..++||++||+|+.+|+.+++|++.  ..|.+|++..+++.+.+++++..
T Consensus         9 g~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R~~~   83 (87)
T 1h3l_A            9 ERSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYRKKQ   83 (87)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC---
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHHHHHHHHHhc
Confidence            4568999999999999999999999999999999999999999999999975  36999999999998888776543

>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3

Probab=98.84  E-value=1.4e-08  Score=88.50  Aligned_cols=72  Identities=14%  Similarity=0.156  Sum_probs=62.2

Q ss_pred             HHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHH
Q 010521          429 VDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEA  503 (508)
Q Consensus       429 ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~  503 (508)
                      ++..+....+..+|...||+++|.||.++|   .+|+|++|||+.||+|++||++++++|+++||..+...++..
T Consensus         9 ~e~~~~~~~l~~~l~~~L~~~~r~vl~l~~---~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~~~~   80 (113)
T 1xsv_A            9 LVKTLRMNYLFDFYQSLLTNKQRNYLELFY---LEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLELYQ   80 (113)
T ss_dssp             HHHHHHHHHHHHHHGGGSCHHHHHHHHHHH---TSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHCHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhHHh
Confidence            445556667777774689999999999999   799999999999999999999999999999999987765543

>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3

Probab=98.70  E-value=3e-08  Score=86.45  Aligned_cols=65  Identities=20%  Similarity=0.265  Sum_probs=56.8

Q ss_pred             HHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHH
Q 010521          435 KDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKME  502 (508)
Q Consensus       435 ~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~  502 (508)
                      ...+..++...|||+++.||.++|   .+|+|++|||+.+|+|++||++++++|+++||..+...++.
T Consensus        12 ~~~l~~~l~~~L~~~~r~vl~l~y---~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~~~   76 (113)
T 1s7o_A           12 MNALFEFYAALLTDKQMNYIELYY---ADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHMY   76 (113)
T ss_dssp             HHHHHHHHGGGSCHHHHHHHHHHH---HTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHCHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhhHH
Confidence            345555553689999999999998   79999999999999999999999999999999998776553

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=98.65  E-value=4.4e-11  Score=117.84  Aligned_cols=153  Identities=13%  Similarity=0.056  Sum_probs=107.4

Q ss_pred             HHHhhh-hhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHH----HHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHH
Q 010521          255 LQSILM-ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLV----QGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGV  329 (508)
Q Consensus       255 L~~~l~-e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLi----QEG~IgLirAiekFDperG~rFsTYA~~wIR~~I  329 (508)
                      |..++. ++..+.+.+...|.++++.+............|+.    ||.++.+|+.+..|++..  .|.+|++..+++.+
T Consensus        87 ll~~i~p~D~~~~~~~~~~~~~fi~~l~~~~~~~~~~~~dl~~~~~qe~fl~~~~~~~~~~~~~--~~~~WL~~ia~n~~  164 (258)
T 3clo_A           87 IYRRIHPEDLVEKRLMEYKFFQKTFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNTP--AGNVWLIFCLYSLS  164 (258)
T ss_dssp             HHTTBCHHHHHHHHHHHHHHHHHHTTSCHHHHTTEEEEEEEEEECTTSCEEEEEEEEEEEEECT--TSCEEEEEEEEEEC
T ss_pred             HHHhCChHHHHHHHHHHHHHHHHHHhcCHHhccCCeeeEEeecCCcCHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHH
Confidence            444443 45678999999999999999988877777788886    999999999999998644  58888865444421


Q ss_pred             HHHHHHhcccccccccHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCC
Q 010521          330 SRALVENSRTLRLPNHLHERLGLIRNAKLRLEEKGVTPSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPG  409 (508)
Q Consensus       330 ~~~Ird~~R~irip~~~~~~l~kir~a~~~l~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~  409 (508)
                      .++    .+..                                                      .+.            
T Consensus       165 ~d~----~r~~------------------------------------------------------~~~------------  174 (258)
T 3clo_A          165 ADQ----RPEQ------------------------------------------------------GIY------------  174 (258)
T ss_dssp             SCC----CCCS------------------------------------------------------SCC------------
T ss_pred             cch----hhhh------------------------------------------------------HHH------------
Confidence            111    0000                                                      000            


Q ss_pred             CccccccccccCCCCccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521          410 ETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL  489 (508)
Q Consensus       410 ~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL  489 (508)
                      ..+.+.......  .+.          .+..++ ..||++||+||.|++    +|+|.+|||+.||+|.+||+.+++||+
T Consensus       175 ~~~~~~~~~~~~--~~~----------~~~~~~-~~L~~~erevl~L~~----~G~s~~EIA~~L~iS~~TVk~~l~ra~  237 (258)
T 3clo_A          175 ATITQMERGEVE--TLS----------LSEEHR-NILSEREKEILRCIR----KGLSSKEIAATLYISVNTVNRHRQNIL  237 (258)
T ss_dssp             CEEEETTTTEEE--ECC----------CHHHHT-TSSCHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHhhcccccc--cch----------hhHHHH-ccCCHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            000000000000  000          134566 899999999999976    899999999999999999999999999


Q ss_pred             HHHHHHH
Q 010521          490 EKLKHAA  496 (508)
Q Consensus       490 kKLR~~L  496 (508)
                      +|||..-
T Consensus       238 ~kL~~~~  244 (258)
T 3clo_A          238 EKLSVGN  244 (258)
T ss_dssp             HHTTCSS
T ss_pred             HHHcCCC
Confidence            9998643

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=98.51  E-value=4.4e-08  Score=81.44  Aligned_cols=59  Identities=22%  Similarity=0.168  Sum_probs=47.2

Q ss_pred             HHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          431 DWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      .......+..++ ..||++|+.||.+++    +|+|.+|||+.||+|..||+.++.++++||+.
T Consensus        16 ~~~~~~~l~~~l-~~Lt~~e~~vl~l~~----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~   74 (91)
T 2rnj_A           16 RGSHMKKRAELY-EMLTEREMEILLLIA----KGYSNQEIASASHITIKTVKTHVSNILSKLEV   74 (91)
T ss_dssp             ---------CTG-GGCCSHHHHHHHHHH----TTCCTTHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             cHHHHHHHHHHH-hcCCHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            344456677888 899999999999954    89999999999999999999999999999985

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=98.51  E-value=7.7e-08  Score=82.33  Aligned_cols=68  Identities=13%  Similarity=0.125  Sum_probs=55.8

Q ss_pred             HHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCC---CC-CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          429 VDDWALKDEVNKLIIVTLGEREREIIRLYYGLDK---EC-LTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       429 ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~---eg-~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      +......+.+..++.+.|+++|+.+|.+||||..   +| +|++|||+.+|+|+.||+++ .++|++|...+.
T Consensus        19 i~~~~~~~~l~~~l~~lLT~~Er~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L~~l~~~~k   90 (101)
T 1jhg_A           19 LKNAYQNDLHLPLLNLMLTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSLKAAPVELR   90 (101)
T ss_dssp             HHHHHHTTCHHHHHHHHSCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHHHHSCHHHH
T ss_pred             HHhcCCHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHHHHccHHHH
Confidence            3344444556666645799999999999999942   45 99999999999999999999 899999987664

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=98.49  E-value=1.6e-07  Score=78.92  Aligned_cols=57  Identities=25%  Similarity=0.281  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          433 ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       433 el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      +....|..+| ..||++|++||.+++    +|+|.+|||+.||+|..||+.++.++++||+.
T Consensus        16 ~~~~~l~~~l-~~Lt~~e~~vl~l~~----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~   72 (95)
T 3c57_A           16 PRGSHMQDPL-SGLTDQERTLLGLLS----EGLTNKQIADRMFLAEKTVKNYVSRLLAKLGM   72 (95)
T ss_dssp             ------------CCCHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHH-hcCCHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            3455677888 899999999999975    89999999999999999999999999999985

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=98.46  E-value=1.9e-07  Score=74.75  Aligned_cols=54  Identities=22%  Similarity=0.318  Sum_probs=49.1

Q ss_pred             HHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          436 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       436 e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ..+..++ ..||++|+.||.++    .+|+|.+|||+.||+|..+|+++..++++||+.
T Consensus         8 ~~l~~~l-~~L~~~e~~vl~l~----~~g~s~~eIA~~l~is~~tV~~~~~r~~~kl~~   61 (79)
T 1x3u_A            8 NDIRARL-QTLSERERQVLSAV----VAGLPNKSIAYDLDISPRTVEVHRANVMAKMKA   61 (79)
T ss_dssp             HHHHHHH-HHHCHHHHHHHHHH----TTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHH-HhCCHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcC
Confidence            4566777 89999999999994    489999999999999999999999999999985

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=98.36  E-value=2.8e-07  Score=75.32  Aligned_cols=56  Identities=25%  Similarity=0.369  Sum_probs=48.0

Q ss_pred             HHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          437 EVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       437 ~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      .+..++ ..|+++|++||.++    .+|+|.+|||+.||+|..||+..+.++++||+....
T Consensus        14 ~~~~~~-~~Lt~~e~~vl~l~----~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~   69 (82)
T 1je8_A           14 TTERDV-NQLTPRERDILKLI----AQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSR   69 (82)
T ss_dssp             ---CCG-GGSCHHHHHHHHHH----TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSSH
T ss_pred             HHHHHH-ccCCHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCH
Confidence            345566 89999999999995    489999999999999999999999999999986543

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=98.18  E-value=1.7e-06  Score=68.10  Aligned_cols=51  Identities=27%  Similarity=0.258  Sum_probs=45.6

Q ss_pred             HHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521          440 KLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHA  495 (508)
Q Consensus       440 ~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~  495 (508)
                      ..+ ..|+++|+.||.++    .+|+|.+|||+.||+|..+|++.+.+++++|+..
T Consensus         7 ~~~-~~L~~~e~~il~~~----~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~   57 (74)
T 1fse_A            7 QSK-PLLTKREREVFELL----VQDKTTKEIASELFISEKTVRNHISNAMQKLGVK   57 (74)
T ss_dssp             -CC-CCCCHHHHHHHHHH----TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCS
T ss_pred             CCC-CCCCHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence            345 78999999999994    4899999999999999999999999999999854

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=98.08  E-value=4.9e-06  Score=69.40  Aligned_cols=47  Identities=21%  Similarity=0.191  Sum_probs=43.8

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ..|+++|++||.+.+    +|+|.+|||+.||||..||+..+.++++||.-
T Consensus        28 ~~Lt~rE~~Vl~l~~----~G~s~~eIA~~L~iS~~TV~~~~~~i~~Klgv   74 (90)
T 3ulq_B           28 DVLTPRECLILQEVE----KGFTNQEIADALHLSKRSIEYSLTSIFNKLNV   74 (90)
T ss_dssp             -CCCHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             cCCCHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            689999999999987    89999999999999999999999999999863

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=97.96  E-value=9.9e-06  Score=68.84  Aligned_cols=47  Identities=26%  Similarity=0.349  Sum_probs=43.8

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ..||++|++||.+.+    +|+|.+|||+.||||..||+..+.++++||.-
T Consensus        33 ~~Lt~re~~Vl~l~~----~G~s~~EIA~~L~iS~~TV~~~l~ri~~KLgv   79 (99)
T 1p4w_A           33 KRLSPKESEVLRLFA----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV   79 (99)
T ss_dssp             SSCCHHHHHHHHHHH----HTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            579999999999965    89999999999999999999999999999963

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=97.96  E-value=5.7e-06  Score=62.89  Aligned_cols=43  Identities=28%  Similarity=0.397  Sum_probs=39.9

Q ss_pred             HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          448 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       448 ~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      |+|++|+.+ +   .+|+|.+|||+.||+|..||+....++++||+.
T Consensus         1 ~re~~vl~l-~---~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~   43 (61)
T 2jpc_A            1 LRERQVLKL-I---DEGYTNHGISEKLHISIKTVETHRMNMMRKLQV   43 (61)
T ss_dssp             CHHHHHHHH-H---HTSCCSHHHHHHTCSCHHHHHHHHHHHHHHHTC
T ss_pred             CHHHHHHHH-H---HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHCC
Confidence            579999999 5   589999999999999999999999999999985

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=97.54  E-value=0.00011  Score=70.67  Aligned_cols=46  Identities=20%  Similarity=0.044  Sum_probs=43.3

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      .|+++|++|+.+..    +|+|.+|||+.||||..||+..+.++++||.-
T Consensus       175 ~Lt~~e~~vl~~~~----~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~  220 (236)
T 2q0o_A          175 MLSPREMLCLVWAS----KGKTASVTANLTGINARTVQHYLDKARAKLDA  220 (236)
T ss_dssp             SCCHHHHHHHHHHH----TTCCHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            69999999999965    89999999999999999999999999999963

>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A*

Probab=97.52  E-value=0.00012  Score=70.40  Aligned_cols=45  Identities=22%  Similarity=0.202  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      .|+++|++|+.+..    +|+|.+|||+.||+|..||+..+.++++||.
T Consensus       173 ~Lt~~e~~vl~~~~----~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~  217 (234)
T 1l3l_A          173 WLDPKEATYLRWIA----VGKTMEEIADVEGVKYNSVRVKLREAMKRFD  217 (234)
T ss_dssp             CCCHHHHHHHHHHT----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhC
Confidence            59999999999964    8999999999999999999999999999996

>3szt_A QCSR, quorum-sensing control repressor; quorum sensing acyl-homoserine lactone, helix-turn-helix, transcription factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas aeruginosa}

Probab=97.38  E-value=0.00019  Score=69.39  Aligned_cols=46  Identities=24%  Similarity=0.304  Sum_probs=43.4

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..|+++|++|+.+..    +|+|.+|||+.||||..||+..+.++++||.
T Consensus       174 ~~Lt~re~~vl~~~~----~G~s~~eIa~~l~is~~tV~~~~~~~~~kl~  219 (237)
T 3szt_A          174 VRLTARETEMLKWTA----VGKTYGEIGLILSIDQRTVKFHIVNAMRKLN  219 (237)
T ss_dssp             CCCCHHHHHHHHHHH----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence            479999999999975    8999999999999999999999999999986

>3qp6_A CVIR transcriptional regulator; quorum sensing, agonist, antagonist, LUXR, acylated homoseri lactone, transcription factor; HET: HL6; 2.00A {Chromobacterium violaceum} PDB: 3qp5_A*

Probab=97.26  E-value=0.00031  Score=69.32  Aligned_cols=46  Identities=22%  Similarity=0.210  Sum_probs=43.6

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      .|+++|++|+.+..    +|+|.+|||+.||||..||+..+.++++||..
T Consensus       197 ~Lt~re~~vl~~~~----~G~s~~eIA~~l~is~~TV~~~~~~~~~kl~~  242 (265)
T 3qp6_A          197 PLSQREYDIFHWMS----RGKTNWEIATILNISERTVKFHVANVIRKLNA  242 (265)
T ss_dssp             CCCHHHHHHHHHHH----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence            69999999999986    89999999999999999999999999999863

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=97.11  E-value=0.00058  Score=48.40  Aligned_cols=40  Identities=20%  Similarity=0.236  Sum_probs=33.3

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|++.++..|...+   .+|+|..|||+.||||+.||..++.+
T Consensus         5 ~l~~~~~~~i~~~~---~~g~s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            5 ALSDTERAQLDVMK---LLNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CCCHHHHHHHHHHH---HTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            57888886555556   58899999999999999999988754

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=96.88  E-value=0.0021  Score=54.80  Aligned_cols=46  Identities=20%  Similarity=0.223  Sum_probs=42.3

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      .+++.-..|-.++|   .+|+|+.|||+.||+|+.+|++.+.+|...+.
T Consensus        18 ~~~~~~~~~A~lyY---v~g~tQ~eIA~~lGiSR~~VsrlL~~Ar~~~~   63 (101)
T 2w7n_A           18 EVGQQTIEIARGVL---VDGKPQATFATSLGLTRGAVSQAVHRVWAAFE   63 (101)
T ss_dssp             CCCHHHHHHHHHHH---TTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            68888889999999   89999999999999999999999999987753

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=96.60  E-value=0.0012  Score=48.86  Aligned_cols=39  Identities=21%  Similarity=0.153  Sum_probs=30.7

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      +++..+.|+.+ +   .+|+|..|||+.||+|+.||++++.+|
T Consensus        17 ~~~~~~~i~~l-~---~~g~s~~eIA~~lgis~~TV~~~l~~a   55 (55)
T 2x48_A           17 EDDLVSVAHEL-A---KMGYTVQQIANALGVSERKVRRYLESC   55 (55)
T ss_dssp             HHHHHHHHHHH-H---HTTCCHHHHHHHHTSCHHHHHHHHTC-
T ss_pred             CHHHHHHHHHH-H---HcCCCHHHHHHHHCcCHHHHHHHHHhC
Confidence            34555667666 4   488999999999999999999987654

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A

Probab=96.50  E-value=0.0071  Score=55.49  Aligned_cols=50  Identities=22%  Similarity=0.373  Sum_probs=44.6

Q ss_pred             HHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          439 NKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       439 ~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ...+ ..|+++|++|+.+..    +|+|.++||+.+|+|..||+....++++||.
T Consensus       137 ~~~~-~~Lt~rE~~vl~~l~----~g~s~~~Ia~~l~is~~TV~~~~~~i~~Kl~  186 (208)
T 1yio_A          137 EQLF-SSLTGREQQVLQLTI----RGLMNKQIAGELGIAEVTVKVHRHNIMQKLN  186 (208)
T ss_dssp             HHHH-HTSCHHHHHHHHHHT----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             HHHH-HhcCHHHHHHHHHHH----cCCcHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence            3344 579999999998864    7899999999999999999999999999996

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A

Probab=96.36  E-value=0.0057  Score=56.55  Aligned_cols=46  Identities=28%  Similarity=0.392  Sum_probs=42.9

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..|+++|++|+.+..    +|+|.+|||+.+++|..||+..+.+.++||.
T Consensus       153 ~~Lt~rE~~vl~~l~----~g~s~~~Ia~~l~is~~TV~~hi~~i~~Kl~  198 (215)
T 1a04_A          153 NQLTPRERDILKLIA----QGLPNKMIARRLDITESTVKVHVKHMLKKMK  198 (215)
T ss_dssp             GGSCHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            469999999998875    8899999999999999999999999999995

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=96.10  E-value=0.0075  Score=56.63  Aligned_cols=46  Identities=30%  Similarity=0.348  Sum_probs=42.6

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..|+++|++|+.+-.    +|+|.+|||+.+++|..||+..+.+.++||.
T Consensus       148 ~~LT~rE~~vL~~l~----~g~s~~eIa~~l~is~~TV~~hi~~l~~KL~  193 (225)
T 3c3w_A          148 SGLTDQERTLLGLLS----EGLTNKQIADRMFLAEKTVKNYVSRLLAKLG  193 (225)
T ss_dssp             TTSCHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            469999999998875    7899999999999999999999999999985

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

Probab=95.78  E-value=0.0013  Score=72.36  Aligned_cols=59  Identities=22%  Similarity=0.341  Sum_probs=35.0

Q ss_pred             hhhhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhhHHHHHH
Q 010521          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK  268 (508)
Q Consensus       189 ~~~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~~~A~e~  268 (508)
                      +.|+++|||++||++||||.++|++|+++|..|+.                              .+...+.+++-+.+.
T Consensus        94 ~~dpvrmyl~emg~~~ll~~~~e~~~ak~ie~g~~------------------------------~~~~~~~~~P~ti~~  143 (613)
T 3iyd_F           94 TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGIN------------------------------QVQCSVAEYPEAITY  143 (613)
T ss_dssp             -----------C--------CSSSTTTHHHHHHHH------------------------------HHHHHHHSCHHHHHH
T ss_pred             CCCcHHHHHHHhcccccCCchhHHHHHHHHHHhHH------------------------------HHHHHHccCHHHHHH
Confidence            45899999999999999999999999999999996                              567777888899999


Q ss_pred             HHHHHHHHH
Q 010521          269 LVMSNVRLV  277 (508)
Q Consensus       269 LIe~yl~LV  277 (508)
                      |+..|-.+.
T Consensus       144 il~~~~~l~  152 (613)
T 3iyd_F          144 LLEQYNRVE  152 (613)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            998888765

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=95.40  E-value=0.011  Score=55.33  Aligned_cols=46  Identities=22%  Similarity=0.278  Sum_probs=42.3

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..|+++|++|+.+..    +|+|.++||+.+++|..||+..+.+.++||.
T Consensus       158 ~~Lt~rE~~vL~~l~----~g~s~~~Ia~~l~~s~~Tv~~~i~~l~~KL~  203 (225)
T 3klo_A          158 AKLTKREQQIIKLLG----SGASNIEIADKLFVSENTVKTHLHNVFKKIN  203 (225)
T ss_dssp             HTSCHHHHHHHHHHT----TTCCHHHHHHHTTCCHHHHHHHHHHHTTTSC
T ss_pred             ccCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence            469999999998864    7899999999999999999999999999984

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=94.81  E-value=0.072  Score=50.23  Aligned_cols=57  Identities=26%  Similarity=0.399  Sum_probs=49.6

Q ss_pred             HHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          433 ALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       433 el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      .........+ ..|+++++.|+.+..    .+++..+||..||+|..+|+....++++||.-
T Consensus       187 ~~~~~~~~~l-~~L~~r~~~i~~~~~----~g~~~~eia~~l~~s~~tv~~~l~~i~~kl~~  243 (258)
T 3p7n_A          187 ARRERAAEML-KTLSPRQLEVTTLVA----SGLRNKEVAARLGLSEKTVKMHRGLVMEKLNL  243 (258)
T ss_dssp             HHHHHHHHHH-TTSCHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHH-hhcCHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            3445666777 899999999999875    78999999999999999999999999999863

>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nns_A*

Probab=93.76  E-value=0.055  Score=49.98  Aligned_cols=49  Identities=18%  Similarity=0.118  Sum_probs=41.1

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHC---CCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIG---LSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~Lg---IS~erVrqi~~rALkKLR  493 (508)
                      .|+++|++|+.+-.-=.++.+|.+|||+.++   +|..||+..+.+.++||.
T Consensus       145 ~Lt~rE~~vl~~l~~~~~~~~s~~~Ia~~l~~~~~s~~tv~~~i~~l~~Kl~  196 (220)
T 1p2f_A          145 HLPKKEFEILLFLAENAGKVVTREKLLETFWEDPVSPRVVDTVIKRIRKAIE  196 (220)
T ss_dssp             CCCHHHHHHHHHHHHTTTSCEEHHHHHHHHCSSCCCTHHHHHHHHHHHHHHC
T ss_pred             ecCHHHHHHHHHHHHCCCceEcHHHHHHHHhCCCCCcchHHHHHHHHHHHHh
Confidence            5999999999876410023499999999999   999999999999999985

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=93.69  E-value=0.051  Score=38.55  Aligned_cols=33  Identities=12%  Similarity=0.142  Sum_probs=26.3

Q ss_pred             HHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          451 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       451 R~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      +.|+.+ +   .++.|..+||+.+|||+.||.+++.+
T Consensus        12 ~~i~~l-~---~~g~s~~~ia~~lgvs~~Tv~r~l~~   44 (52)
T 1jko_C           12 EQISRL-L---EKGHPRQQLAIIFGIGVSTLYRYFPA   44 (52)
T ss_dssp             HHHHHH-H---HTTCCHHHHHHTTSCCHHHHHHHSCT
T ss_pred             HHHHHH-H---HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            445555 3   36799999999999999999887654

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=93.53  E-value=0.075  Score=49.94  Aligned_cols=49  Identities=10%  Similarity=0.047  Sum_probs=40.2

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRI-----GLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~L-----gIS~erVrqi~~rALkKLR  493 (508)
                      .|+++|.+|+.+-.-=-+..+|.+|||+.+     ++|..||+..+.+.++||.
T Consensus       153 ~LT~rE~~vL~~l~~~~~~~~s~~eIa~~lw~~~~~~s~~tV~~hi~~lr~KL~  206 (238)
T 2gwr_A          153 SLTPLEFDLLVALARKPRQVFTRDVLLEQVWGYRHPADTRLVNVHVQRLRAKVE  206 (238)
T ss_dssp             CCCHHHHHHHHHHHHSTTCCBCHHHHHHHHTCCC--CCTHHHHHHHHHHHHHHC
T ss_pred             ccCHHHHHHHHHHHHCCCceecHHHHHHHHcCCCCCCCcccHHHHHHHHHHHhc
Confidence            699999999987651001349999999999     9999999999999999985

>2oqr_A Sensory transduction protein REGX3; response regulator, winged-helix-turn-helix, DNA-binding, 3D swapping, two component system; 2.03A {Mycobacterium tuberculosis H37RV}

Probab=93.26  E-value=0.068  Score=49.61  Aligned_cols=49  Identities=14%  Similarity=0.084  Sum_probs=41.3

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRI-----GLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~L-----gIS~erVrqi~~rALkKLR  493 (508)
                      .|+++|.+|+.+-.-=.++.+|.+|||+.+     ++|..||+..+.+.++||.
T Consensus       156 ~Lt~rE~~vL~~l~~~~~~~~s~~~Ia~~lw~~~~~~s~~tv~~hi~~i~~Kl~  209 (230)
T 2oqr_A          156 TLPLKEFDLLEYLMRNSGRVLTRGQLIDRVWGADYVGDTKTLDVHVKRLRSKIE  209 (230)
T ss_dssp             CCCHHHHHHHHHHHHTTTSCEEHHHHHHHHTSSCCTTHHHHHHHHHHHHHHHHC
T ss_pred             ecCHHHHHHHHHHHhCCCceEcHHHHHHHhcCCCCCCCCcCHHHHHHHHHHHHh
Confidence            699999999987651012349999999999     9999999999999999985

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=93.13  E-value=0.22  Score=43.49  Aligned_cols=39  Identities=18%  Similarity=0.315  Sum_probs=28.7

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL  489 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL  489 (508)
                      .|+.| .+|+.+-.    +|+|+.|||+.+|+|..||.+ ..++|
T Consensus        61 aLs~R-~eV~klL~----~G~syreIA~~~g~S~aTIsR-v~r~L   99 (119)
T 3kor_A           61 SLSQR-LQVAKMIK----QGYTYATIEQESGASTATISR-VKRSL   99 (119)
T ss_dssp             HHHHH-HHHHHHHH----HTCCHHHHHHHHCCCHHHHHH-HHHHH
T ss_pred             HHHHH-HHHHHHHH----cCCCHHHHHHHHCCCHHHHHH-HHHHH
Confidence            34444 56666643    789999999999999999976 34444

>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein, ALPH-beta sandwich, winged-helix, helix helix, DNA binding protein; HET: DNA MSE; 1.50A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nnn_A*

Probab=92.81  E-value=0.082  Score=48.77  Aligned_cols=50  Identities=14%  Similarity=0.146  Sum_probs=41.2

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~Lg-----IS~erVrqi~~rALkKLR~  494 (508)
                      .|+++|.+|+.+-.-=.+..+|.+|||+.++     +|..||+..+.+.++||..
T Consensus       151 ~Lt~rE~~vL~~l~~~~~~~~s~~eIa~~l~~~~~~~s~~tv~~hi~~l~~Kl~~  205 (225)
T 1kgs_A          151 DLTKKEYQILEYLVMNKNRVVTKEELQEHLWSFDDEVFSDVLRSHIKNLRKKVDK  205 (225)
T ss_dssp             CCCHHHHHHHHHHHHTTTSCEEHHHHHHHCC-----CHHHHHHHHHHHHHHHHHT
T ss_pred             ecCHHHHHHHHHHHhCCCcccCHHHHHHHhcCCCCCCCcchHHHHHHHHHHHhhC
Confidence            6999999999876410012399999999998     9999999999999999863

>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA binding domain, phosphorylation; 1.58A {Mycobacterium tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A

Probab=92.53  E-value=0.078  Score=49.19  Aligned_cols=50  Identities=14%  Similarity=0.084  Sum_probs=40.4

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIG-----LSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~Lg-----IS~erVrqi~~rALkKLR~  494 (508)
                      .|+++|.+|+.+-.-=.+..+|.++||+.++     +|..||+..+.+.++||..
T Consensus       159 ~Lt~rE~~vL~~l~~g~~~~~s~~~Ia~~l~~~~~~~s~~tv~~hi~~l~~Kl~~  213 (233)
T 1ys7_A          159 DLTKREFDLLAVLAEHKTAVLSRAQLLELVWGYDFAADTNVVDVFIGYLRRKLEA  213 (233)
T ss_dssp             CCCHHHHHHHHHHHHTTTCCBCHHHHHHHHHCCCCC-CCCHHHHHHHHHHHHHHC
T ss_pred             ccCHHHHHHHHHHHhCCCCeEcHHHHHHHhcCcccCCCccCHHHHHHHHHHHhcc
Confidence            6999999999886510012299999999998     9999999999999999963

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=92.04  E-value=0.17  Score=47.83  Aligned_cols=36  Identities=22%  Similarity=0.353  Sum_probs=29.6

Q ss_pred             HHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521          450 EREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL  489 (508)
Q Consensus       450 ER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL  489 (508)
                      -..+..+ |   ..|+|++|||+.||||+.+|++++..|.
T Consensus        14 G~ria~~-y---~~g~tQ~eIA~~lGiSr~~VSR~L~~A~   49 (192)
T 1zx4_A           14 GLRLMRM-K---NDGMSQKDIAAKEGLSQAKVTRALQAAS   49 (192)
T ss_dssp             HHHHHHH-H---HTTCCHHHHHHHHTCCHHHHHHHHHHHT
T ss_pred             HHHHHHH-H---HcCCCHHHHHHHhCcCHHHHHHHHHHhc
Confidence            3345555 5   5889999999999999999999987764

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=91.99  E-value=0.16  Score=43.68  Aligned_cols=40  Identities=20%  Similarity=0.236  Sum_probs=33.1

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|++.++..|...+   .+|+|..+||+.||+|+.||..++.+
T Consensus         6 ~~s~~~r~~i~~~~---~~G~s~~~ia~~lgis~~Tv~r~~~~   45 (141)
T 1u78_A            6 ALSDTERAQLDVMK---LLNVSLHEMSRKISRSRHCIRVYLKD   45 (141)
T ss_dssp             CCCHHHHHHHHHHH---HTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             cCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHc
Confidence            57777777665555   57899999999999999999998865

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=91.88  E-value=0.23  Score=41.63  Aligned_cols=41  Identities=17%  Similarity=-0.001  Sum_probs=31.5

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .+++.++.-|...+   .+|+|..+||+.||||+.||++++.+.
T Consensus        17 ~~s~~~r~~i~~~~---~~g~s~~~ia~~lgis~~Tv~~w~~~~   57 (128)
T 1pdn_C           17 PLPNNIRLKIVEMA---ADGIRPCVISRQLRVSHGCVSKILNRY   57 (128)
T ss_dssp             CCCHHHHHHHHHHH---HTTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            45666555444444   478999999999999999999998764

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=91.18  E-value=0.069  Score=49.39  Aligned_cols=46  Identities=9%  Similarity=0.062  Sum_probs=41.3

Q ss_pred             cCCHHHHHHHhHHhccCCCC----CCHHHHHHHHC-----CCHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKEC----LTWEDISKRIG-----LSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg----~TleEIAe~Lg-----IS~erVrqi~~rALkKLR~  494 (508)
                      .|+++|++|+.+-.    ++    +|.+|||+.++     +|..||+..+.+.++||..
T Consensus       143 ~Lt~rE~~vL~~l~----~~~~~~~s~~~Ia~~l~~~~~~~s~~tv~~~i~~lr~KL~~  197 (223)
T 2hqr_A          143 EVKGKPFEVLTHLA----RHRDQIVSKEQLLDAIWEEPEMVTPNVIEVAINQIRQKMDK  197 (223)
T ss_dssp             CCCSTTTHHHHHHH----HTCSEEEEHHHHHHHHCCSSCSCGGGTHHHHHHHHHHHHHT
T ss_pred             ecCHHHHHHHHHHH----hCCCCcCCHHHHHHHhcCCccCCCCcCHHHHHHHHHHHHhc
Confidence            69999999998865    44    99999999999     9999999999999999863

>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=91.03  E-value=0.041  Score=53.64  Aligned_cols=51  Identities=20%  Similarity=0.279  Sum_probs=0.0

Q ss_pred             HHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHC--CCHHHHHHHHHHHHHHHH
Q 010521          438 VNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIG--LSRERVRQVGLVALEKLK  493 (508)
Q Consensus       438 L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~Lg--IS~erVrqi~~rALkKLR  493 (508)
                      +...+ ..|++.++.+. ..+   +.+.|.+|||+.||  ||.++|+.++.+|++.|.
T Consensus       192 l~e~i-~~l~~~~~~L~-~~~---~~~ps~~EIAe~Lg~~is~~tVk~~l~~ar~~ls  244 (245)
T 3ugo_A          192 MVETI-NKLSRTARQLQ-QEL---GREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVS  244 (245)
T ss_dssp             ----------------------------------------------------------
T ss_pred             HHHHH-HHHHHHHHHHH-HHh---CCCCCHHHHHHHHCCCCCHHHHHHHHHHHhhccC
Confidence            34445 67777777744 455   47789999999999  999999999999987763

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=90.85  E-value=0.26  Score=39.44  Aligned_cols=40  Identities=20%  Similarity=0.396  Sum_probs=27.8

Q ss_pred             HHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          448 EREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       448 ~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      +.++.||.+-.-.+ +++.|..|||+.||||+.+|++++++
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~   54 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYS   54 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            34566654433221 24689999999999999999766554

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=90.80  E-value=0.14  Score=48.83  Aligned_cols=49  Identities=18%  Similarity=0.183  Sum_probs=40.8

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHH-----HHCCCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISK-----RIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe-----~LgIS~erVrqi~~rALkKLR  493 (508)
                      .|+++|++|+.+..-=.+..+|.+|||+     .++++..||+..+.+.++||.
T Consensus       182 ~LT~rE~evL~ll~~g~~~~~s~~eIa~~l~~~~l~~s~~TV~~hi~~lr~KL~  235 (249)
T 3q9s_A          182 RLSPKEFDILALLIRQPGRVYSRQEIGQEIWQGRLPEGSNVVDVHMANLRAKLR  235 (249)
T ss_dssp             CCCHHHHHHHHHHHHSTTCCCCHHHHHHHHHTTCSCTTCSHHHHHHHHHHHHHC
T ss_pred             ecCHHHHHHHHHHHHCCCceEcHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhh
Confidence            6999999999987611123499999999     588899999999999999985

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=90.44  E-value=0.36  Score=42.42  Aligned_cols=41  Identities=20%  Similarity=0.080  Sum_probs=32.2

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .+++.++.-|...+   .+|+|..+||+.||||+.||++++.+.
T Consensus        32 ~~s~e~r~~iv~~~---~~G~s~~~iA~~lgis~~TV~rw~~~~   72 (149)
T 1k78_A           32 PLPDVVRQRIVELA---HQGVRPCDISRQLRVSHGCVSKILGRY   72 (149)
T ss_dssp             CCCHHHHHHHHHHH---HTTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            45666665444444   478999999999999999999998774

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=90.14  E-value=0.45  Score=40.77  Aligned_cols=40  Identities=18%  Similarity=0.179  Sum_probs=31.7

Q ss_pred             ccCCHHHHHHHhHHhccC---CCCCCHHHHHHHHCCCHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLD---KECLTWEDISKRIGLSRERVRQ  483 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd---~eg~TleEIAe~LgIS~erVrq  483 (508)
                      +-|++.|+.-+-.|+-+-   .+|+|+.||++.+|+|..||.+
T Consensus        35 dL~T~~E~~alaqR~~Ia~lL~~G~SyreIa~~tG~StaTIsR   77 (107)
T 3frw_A           35 DVCTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISR   77 (107)
T ss_dssp             HHSCHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHH
T ss_pred             HhCCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCccHHHHHH
Confidence            447888887776665441   3789999999999999999975

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=89.62  E-value=0.52  Score=38.06  Aligned_cols=26  Identities=12%  Similarity=0.166  Sum_probs=23.0

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          463 ECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       463 eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .+.|..+||+.+|||+.||.+++.+.
T Consensus        37 ~g~s~~~iA~~~gIs~sTl~rW~k~~   62 (87)
T 2elh_A           37 DGESKASVARDIGVPESTLRGWCKNE   62 (87)
T ss_dssp             HTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            56899999999999999999987544

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=89.51  E-value=0.49  Score=44.67  Aligned_cols=50  Identities=16%  Similarity=0.123  Sum_probs=42.4

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRI-----GLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~L-----gIS~erVrqi~~rALkKLR~  494 (508)
                      .|+++|.+|+.+..-=.++..|.++|++.+     +++..||+..+.+.++||..
T Consensus       176 ~LT~rE~~iL~~l~~~~~~~~s~~~i~~~lw~~~~~~~~~tv~~~i~~lr~KL~~  230 (250)
T 3r0j_A          176 SLSPTEFTLLRYFVINAGTVLSKPKILDHVWRYDFGGDVNVVESYVSYLRRKIDT  230 (250)
T ss_dssp             CCCHHHHHHHHHHHHTTTCCBCHHHHHHHHTTTSCCSCTHHHHHHHHHHHHHHCC
T ss_pred             ecCHHHHHHHHHHHHCCCceEcHHHHHHHHcCCCCCCCccCHHHHHHHHHHhhcC
Confidence            699999999988752124569999999999     78999999999999999863

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=88.94  E-value=0.4  Score=47.95  Aligned_cols=36  Identities=25%  Similarity=0.475  Sum_probs=31.0

Q ss_pred             HHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q 010521          452 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALE  490 (508)
Q Consensus       452 ~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALk  490 (508)
                      .|..++|   .+++|..|||+.||||+.|||+.+..+.+
T Consensus        12 ~ia~l~~---~~~~~~~ela~~l~vS~~tIrRdL~~l~~   47 (315)
T 2w48_A           12 KIAQLYY---EQDMTQAQIARELGIYRTTISRLLKRGRE   47 (315)
T ss_dssp             HHHHHHH---TSCCCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4667777   78899999999999999999988887654

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=88.41  E-value=0.37  Score=39.41  Aligned_cols=25  Identities=12%  Similarity=0.221  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          463 ECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       463 eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .+.|..|||+.||||+++|++++++
T Consensus        29 ~g~sa~eLAk~LgiSk~aVr~~L~~   53 (82)
T 1oyi_A           29 EGATAAQLTRQLNMEKREVNKALYD   53 (82)
T ss_dssp             STEEHHHHHHHSSSCHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4599999999999999999987765

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=88.30  E-value=0.55  Score=43.58  Aligned_cols=41  Identities=15%  Similarity=0.185  Sum_probs=32.2

Q ss_pred             cCCHHHHHHHhHHhcc---CCCCCCHHHHHHHHCCCHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGL---DKECLTWEDISKRIGLSRERVRQVG  485 (508)
Q Consensus       445 ~Lp~rER~VI~LryGL---d~eg~TleEIAe~LgIS~erVrqi~  485 (508)
                      .|+++|++|+..-...   .+.+.|.+|||+.||+|..+|++++
T Consensus         2 ~lt~~q~~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~l   45 (196)
T 3k2z_A            2 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHL   45 (196)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHHH
Confidence            5899999999875422   1346899999999999998876554

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=88.00  E-value=0.54  Score=38.09  Aligned_cols=38  Identities=21%  Similarity=0.380  Sum_probs=25.8

Q ss_pred             HHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          450 EREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       450 ER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ++.|+.+-...+ ++..|..|||+.||||+.+|++.+++
T Consensus        12 ~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~   50 (81)
T 1qbj_A           12 EQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYS   50 (81)
T ss_dssp             HHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            445554433211 24689999999999999998755443

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=87.72  E-value=0.6  Score=36.07  Aligned_cols=40  Identities=15%  Similarity=0.182  Sum_probs=26.4

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL  486 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~  486 (508)
                      +++..+.||.+--. +..++|..|||+.+|+|+.+|.+++.
T Consensus         8 m~~~~~~IL~~L~~-~~~~~s~~eLA~~lglsr~tv~~~l~   47 (67)
T 2heo_A            8 GDNLEQKILQVLSD-DGGPVAIFQLVKKCQVPKKTLNQVLY   47 (67)
T ss_dssp             -CHHHHHHHHHHHH-HCSCEEHHHHHHHHCSCHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHH-cCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            34444455554320 13568999999999999999975543

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=87.54  E-value=0.96  Score=38.87  Aligned_cols=42  Identities=12%  Similarity=0.229  Sum_probs=33.0

Q ss_pred             ccCCHHHHHHHhHHhccCCCC--CCHHHHHHHHCCCHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKEC--LTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg--~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      -.|++.+..|+..-..  ..+  +|..|||+.+|++++||.+.+.+
T Consensus        22 ~gLt~~e~~il~~L~~--~~~~~~t~~eLa~~l~~s~sTV~r~L~~   65 (123)
T 3r0a_A           22 LNLTKADLNVMKSFLN--EPDRWIDTDALSKSLKLDVSTVQRSVKK   65 (123)
T ss_dssp             HTCCHHHHHHHHHHHH--STTCCEEHHHHHHHHTSCHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHH--CCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            4799999999876542  233  89999999999999999655443

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=87.31  E-value=0.94  Score=39.71  Aligned_cols=41  Identities=20%  Similarity=0.208  Sum_probs=32.3

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|++.++.||.+-..  ....|..|||+.+|+|+.+|++++.+
T Consensus         2 ~ld~~d~~il~~L~~--~~~~s~~ela~~lg~s~~tv~~~l~~   42 (144)
T 2cfx_A            2 KLDQIDLNIIEELKK--DSRLSMRELGRKIKLSPPSVTERVRQ   42 (144)
T ss_dssp             CCCHHHHHHHHHHHH--CSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            378888888876431  35699999999999999999766544

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=86.92  E-value=0.71  Score=37.67  Aligned_cols=40  Identities=15%  Similarity=0.284  Sum_probs=30.3

Q ss_pred             CCHHHHH-HHhHHhccCCC-CCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          446 LGERERE-IIRLYYGLDKE-CLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       446 Lp~rER~-VI~LryGLd~e-g~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .++.++. |+.++.   .. +.|..+||+.+|||+.||.++..+.
T Consensus         6 ys~e~k~~~v~~~~---~~~g~s~~~ia~~~gIs~~tl~rW~~~~   47 (97)
T 2jn6_A            6 YSEEFKRDAVALYE---NSDGASLQQIANDLGINRVTLKNWIIKY   47 (97)
T ss_dssp             CCHHHHHHHHHHHT---TGGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---HcCCChHHHHHHHHCcCHHHHHHHHHHH
Confidence            4555554 555554   24 7999999999999999999998653

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=86.77  E-value=0.75  Score=34.29  Aligned_cols=47  Identities=6%  Similarity=0.088  Sum_probs=31.6

Q ss_pred             CCHHHHHHHhHHhccCCCCCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLT----WEDISKRIGLSRERVRQVGLVALEKLKHAA  496 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~T----leEIAe~LgIS~erVrqi~~rALkKLR~~L  496 (508)
                      .++..+.-+...+   ..+.|    ..+||..+||++++|+++... ...++..+
T Consensus         6 ys~efK~~~~~~~---~~g~s~~~~~~~vA~~~gIs~~tl~~W~~~-~~~~~~~~   56 (59)
T 2glo_A            6 FTPHFKLQVLESY---RNDNDCKGNQRATARKYNIHRRQIQKWLQC-ESNLRSSV   56 (59)
T ss_dssp             CCHHHHHHHHHHH---HHCTTTTTCHHHHHHHTTSCHHHHHHHHTT-HHHHHHHH
T ss_pred             CCHHHHHHHHHHH---HcCCCcchHHHHHHHHHCcCHHHHHHHHHH-HHHHHHHH
Confidence            3444444333333   35678    999999999999999999764 44444433

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=86.46  E-value=1.3  Score=39.06  Aligned_cols=41  Identities=22%  Similarity=0.293  Sum_probs=32.3

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|++.++.||.+-..  ....|+.|||+.+|+|+.+|++++.+
T Consensus         4 ~ld~~~~~il~~L~~--~~~~s~~ela~~lg~s~~tv~~~l~~   44 (151)
T 2cyy_A            4 PLDEIDKKIIKILQN--DGKAPLREISKITGLAESTIHERIRK   44 (151)
T ss_dssp             CCCHHHHHHHHHHHH--CTTCCHHHHHHHHCSCHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            478888888875431  34689999999999999999766544

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=86.37  E-value=2.2  Score=35.82  Aligned_cols=39  Identities=18%  Similarity=0.158  Sum_probs=31.5

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .++.+..||..-.   ..+.|..|||+.+|+|+.+|++.+.+
T Consensus        30 ~~~~~~~il~~L~---~~~~s~~ela~~l~is~stvsr~l~~   68 (119)
T 2lkp_A           30 ATPSRLMILTQLR---NGPLPVTDLAEAIGMEQSAVSHQLRV   68 (119)
T ss_dssp             CCHHHHHHHHHHH---HCCCCHHHHHHHHSSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH---HCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            5677888887765   35799999999999999999866554

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=86.33  E-value=1.2  Score=39.13  Aligned_cols=42  Identities=12%  Similarity=0.262  Sum_probs=32.5

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..|++.++.||.+--.  ....|..|||+.+|+|+.+|++++.+
T Consensus         5 ~~ld~~d~~il~~L~~--~~~~s~~ela~~lg~s~~tv~~~l~~   46 (151)
T 2dbb_A            5 RKLDRVDMQLVKILSE--NSRLTYRELADILNTTRQRIARRIDK   46 (151)
T ss_dssp             -CCCHHHHHHHHHHHH--CTTCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred             hhCCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3588889888875431  35699999999999999999766544

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=86.28  E-value=1.2  Score=38.03  Aligned_cols=40  Identities=23%  Similarity=0.345  Sum_probs=32.8

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|++.|..|+..-.   ..+.|..|||+.+|+++++|++++.+
T Consensus        35 ~lt~~~~~iL~~l~---~~~~t~~eLa~~l~~s~~tvs~~l~~   74 (146)
T 3tgn_A           35 ALTNTQEHILMLLS---EESLTNSELARRLNVSQAAVTKAIKS   74 (146)
T ss_dssp             CCCHHHHHHHHHHT---TCCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH---hCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            57888888887765   34499999999999999999876654

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=86.16  E-value=1.9  Score=39.28  Aligned_cols=54  Identities=20%  Similarity=0.241  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          434 LKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       434 l~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      +...+...+ ..|++.|..||..-+....++.|..+||+.+|+++++|.+++.+-
T Consensus        28 ~~~~~~~~~-~~lt~~q~~vL~~L~~~~~~~~t~~eLa~~l~is~~tvs~~l~~L   81 (189)
T 3nqo_A           28 IQIEGDKYF-GILTSRQYMTILSILHLPEEETTLNNIARKMGTSKQNINRLVANL   81 (189)
T ss_dssp             HHHHHHHHH-CSSCHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHH-ccCCHHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            344455555 679999999987765222357999999999999999998766543

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=86.07  E-value=1.2  Score=38.47  Aligned_cols=40  Identities=23%  Similarity=0.424  Sum_probs=30.7

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      |++.++.|+..-..  ....|..|||+.+|+|+.+|++.+.+
T Consensus         2 ld~~~~~il~~L~~--~~~~~~~ela~~lg~s~~tv~~~l~~   41 (141)
T 1i1g_A            2 IDERDKIILEILEK--DARTPFTEIAKKLGISETAVRKRVKA   41 (141)
T ss_dssp             CCSHHHHHHHHHHH--CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            67778888875431  35689999999999999999765543

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=86.01  E-value=1.3  Score=35.90  Aligned_cols=43  Identities=12%  Similarity=0.103  Sum_probs=33.2

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..|++.+..+|...+. ...+.|..|||+.+|+|+.+|++++.+
T Consensus        17 ~~l~~~~~~~l~~l~~-~~~~~t~~ela~~l~is~~tv~~~l~~   59 (109)
T 2d1h_A           17 YKITDTDVAVLLKMVE-IEKPITSEELADIFKLSKTTVENSLKK   59 (109)
T ss_dssp             HTCCHHHHHHHHHHHH-HCSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHH-cCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4789998888755441 135799999999999999999765543

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=85.98  E-value=1.1  Score=39.40  Aligned_cols=42  Identities=21%  Similarity=0.230  Sum_probs=32.8

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..|++.++.||.+-..  ....|..|||+.+|+|+.+|++++.+
T Consensus         3 ~~ld~~~~~iL~~L~~--~~~~s~~ela~~lg~s~~tv~~~l~~   44 (150)
T 2w25_A            3 EALDDIDRILVRELAA--DGRATLSELATRAGLSVSAVQSRVRR   44 (150)
T ss_dssp             -CCCHHHHHHHHHHHH--CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             cccCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3588889888876431  35699999999999999999766554

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=85.96  E-value=1.4  Score=38.86  Aligned_cols=41  Identities=17%  Similarity=0.319  Sum_probs=32.4

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|++.++.||.+-..  ....|..|||+.+|+|+.+|++++.+
T Consensus         5 ~ld~~d~~il~~L~~--~~~~s~~ela~~lg~s~~tv~~~l~~   45 (152)
T 2cg4_A            5 LIDNLDRGILEALMG--NARTAYAELAKQFGVSPETIHVRVEK   45 (152)
T ss_dssp             CCCHHHHHHHHHHHH--CTTSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            478888888876431  35689999999999999999876554

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=85.95  E-value=1.1  Score=36.24  Aligned_cols=41  Identities=20%  Similarity=0.243  Sum_probs=33.1

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|++.+..|+..-..  ..+.|..|||+.+|+++.+|.+.+.+
T Consensus        17 ~l~~~~~~il~~l~~--~~~~s~~ela~~l~is~~tv~~~l~~   57 (109)
T 1sfx_A           17 SFKPSDVRIYSLLLE--RGGMRVSEIARELDLSARFVRDRLKV   57 (109)
T ss_dssp             CCCHHHHHHHHHHHH--HCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            688999888876541  36799999999999999999766554

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=85.90  E-value=1.2  Score=37.00  Aligned_cols=38  Identities=24%  Similarity=0.163  Sum_probs=28.7

Q ss_pred             HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          448 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       448 ~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      +|...|+.+..   ..+.|..+||+.+|||..||+..+..-
T Consensus         7 ~R~~~I~~~l~---~~~~ti~dlA~~~gVS~~TVsR~L~~~   44 (93)
T 2l0k_A            7 ERTIKIGKYIV---ETKKTVRVIAKEFGVSKSTVHKDLTER   44 (93)
T ss_dssp             HHHHHHHHHHH---HHCCCHHHHHHHHTSCHHHHHHHHTTH
T ss_pred             HHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHcCC
Confidence            34455555443   345899999999999999999988753

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=85.80  E-value=0.39  Score=42.80  Aligned_cols=40  Identities=23%  Similarity=0.097  Sum_probs=30.5

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .++..++.-|...+   .+|+|..+||+.||||+.||++++.+
T Consensus        25 ~~s~e~r~~ii~l~---~~G~s~~~IA~~lgis~~TV~rwl~r   64 (159)
T 2k27_A           25 PLPEVVRQRIVDLA---HQGVRPCDISRQLRVSHGCVSKILGR   64 (159)
T ss_dssp             SSCHHHHHHHHHHH---HHTCCHHHHHHHHTCCSHHHHHHHCC
T ss_pred             CCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45555555444444   36899999999999999999998764

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=85.77  E-value=0.7  Score=35.73  Aligned_cols=24  Identities=21%  Similarity=0.249  Sum_probs=21.5

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          465 LTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       465 ~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      +|+.|||+.+|||+.||+++++.-
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLng~   24 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVINGK   24 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHTC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCC
Confidence            488999999999999999998743

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=85.28  E-value=1.3  Score=38.73  Aligned_cols=40  Identities=10%  Similarity=0.188  Sum_probs=30.6

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      |++.++.||.+--.  ....|..|||+.+|+|+++|++++.+
T Consensus         1 ld~~~~~il~~L~~--~~~~~~~ela~~lg~s~~tv~~~l~~   40 (150)
T 2pn6_A            1 MDEIDLRILKILQY--NAKYSLDEIAREIRIPKATLSYRIKK   40 (150)
T ss_dssp             CCHHHHHHHHHHTT--CTTSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CChHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            56777788765431  24689999999999999999766544

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=85.23  E-value=1.3  Score=39.53  Aligned_cols=41  Identities=22%  Similarity=0.218  Sum_probs=32.5

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|++.++.||.+-..  ....|..|||+.+|+|+.+|++++.+
T Consensus         7 ~ld~~~~~il~~L~~--~~~~s~~ela~~lg~s~~tv~~~l~~   47 (162)
T 2p5v_A            7 TLDKTDIKILQVLQE--NGRLTNVELSERVALSPSPCLRRLKQ   47 (162)
T ss_dssp             CCCHHHHHHHHHHHH--CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            478888888876431  34689999999999999999876554

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28

Probab=85.05  E-value=3.3  Score=34.95  Aligned_cols=44  Identities=9%  Similarity=0.041  Sum_probs=34.4

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .|++.|..|+..-+.-+..+.|..|||+.+|+++.+|.+.+.+-
T Consensus        31 ~lt~~~~~iL~~l~~~~~~~~~~~ela~~l~~~~~tvs~~l~~L   74 (141)
T 3bro_A           31 DLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRM   74 (141)
T ss_dssp             TCCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCcchHHHHHHHH
Confidence            68999999887765322237999999999999999998665543

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=85.03  E-value=4.1  Score=34.58  Aligned_cols=77  Identities=18%  Similarity=0.188  Sum_probs=48.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhCccccccccCCCCCCCCCCCccccccccccCCCCccchHHHHHHHHHHHHHHHccC
Q 010521          367 PSVDRIAEYLNMSQKKVRNATEAIGKVFSLDREAFPSLNGLPGETHHSYIADNRVENNPWHGVDDWALKDEVNKLIIVTL  446 (508)
Q Consensus       367 Pt~eEIA~~Lgis~e~v~~~l~~~~~~~SLD~~~~~~~~~~~~~~l~d~i~d~~~e~~Pe~~ve~~el~e~L~~~L~~~L  446 (508)
                      -+..+||+.+|++..+|..........            +...      .  .   .-|                  ..|
T Consensus        23 ~s~~~ia~~lgis~~Tv~r~~~~~~~~------------g~~~------~--~---gr~------------------~~l   61 (141)
T 1u78_A           23 VSLHEMSRKISRSRHCIRVYLKDPVSY------------GTSK------R--A---PRR------------------KAL   61 (141)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHSGGGT------------TCCC------C--C---CCC------------------CSS
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHccccc------------CCcC------C--C---CCC------------------CcC
Confidence            478999999999999999987654211            0000      0  0   011                  122


Q ss_pred             CHHHH-HHHhHHhccCCCCCCHHHHHHHHC--CCHHHHHHHHHH
Q 010521          447 GERER-EIIRLYYGLDKECLTWEDISKRIG--LSRERVRQVGLV  487 (508)
Q Consensus       447 p~rER-~VI~LryGLd~eg~TleEIAe~Lg--IS~erVrqi~~r  487 (508)
                      ++.+. .|+.+.-   ....|..+|+..||  +|.+||.+++.+
T Consensus        62 ~~~~~~~i~~~~~---~~~~s~~~i~~~lg~~~s~~tV~r~l~~  102 (141)
T 1u78_A           62 SVRDERNVIRAAS---NSCKTARDIRNELQLSASKRTILNVIKR  102 (141)
T ss_dssp             CHHHHHHHHHHHH---HCCCCHHHHHHHTTCCSCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHh---CCCCCHHHHHHHHCCCccHHHHHHHHHH
Confidence            33222 2332211   24589999999999  899999998875

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=84.92  E-value=2.4  Score=35.10  Aligned_cols=41  Identities=22%  Similarity=0.207  Sum_probs=30.2

Q ss_pred             ccCC-HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          444 VTLG-EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       444 ~~Lp-~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..|. +....||.+-.   ..++|..|||+.+|+|+++|++.+..
T Consensus        21 ~~l~~~~r~~IL~~L~---~~~~~~~ela~~l~is~stvs~~L~~   62 (106)
T 1r1u_A           21 KALGDYNRIRIMELLS---VSEASVGHISHQLNLSQSNVSHQLKL   62 (106)
T ss_dssp             HHTCSHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3444 55566776544   46789999999999999999866543

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=84.74  E-value=1.5  Score=39.41  Aligned_cols=41  Identities=22%  Similarity=0.345  Sum_probs=31.5

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      |++.++.||.+--.  ....|+.|||+.+|+|+.+|+.++.+-
T Consensus         1 lD~~d~~il~~L~~--~~~~s~~~la~~lg~s~~tv~~rl~~L   41 (162)
T 3i4p_A            1 MDRLDRKILRILQE--DSTLAVADLAKKVGLSTTPCWRRIQKM   41 (162)
T ss_dssp             CCHHHHHHHHHHTT--CSCSCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--CCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            56778888876531  246899999999999999998766553

>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A

Probab=84.37  E-value=2.3  Score=36.53  Aligned_cols=48  Identities=13%  Similarity=-0.018  Sum_probs=33.8

Q ss_pred             HHHHHHHHH-ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          435 KDEVNKLII-VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       435 ~e~L~~~L~-~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ...+...+. ..+++.+-.-++...     ++|++++|+.+|+|+.+|++++.-
T Consensus        59 ~~e~~r~~~~~~~~~~~l~~~R~~~-----glsq~~la~~~g~s~~~i~~~E~g  107 (133)
T 3o9x_A           59 VKAFRASVNAETVAPEFIVKVRKKL-----SLTQKEASEIFGGGVNAFSRYEKG  107 (133)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHT-----TCCHHHHHHHHCSCTTHHHHHHHT
T ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHCC
Confidence            334444442 335555544555444     699999999999999999999874

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=84.30  E-value=2.9  Score=35.44  Aligned_cols=53  Identities=13%  Similarity=0.197  Sum_probs=38.6

Q ss_pred             HHHHHHHH-ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          436 DEVNKLII-VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       436 e~L~~~L~-~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      ..+...+. ..|++.|..|+..-+.-+.++.|..|||+.+|+++++|.+++.+-
T Consensus        18 ~~~~~~~~~~~lt~~~~~vL~~l~~~~~~~~t~~ela~~l~~~~~tvs~~l~~L   71 (139)
T 3eco_A           18 QKADQKLEQFDITNEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNL   71 (139)
T ss_dssp             HHHHHHHGGGTCCHHHHHHHHHHHHSTTTCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHhcCCCCcCHHHHHHHhCCCcccHHHHHHHH
Confidence            34444441 268999999988765322248999999999999999998766553

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=84.25  E-value=2  Score=36.73  Aligned_cols=52  Identities=8%  Similarity=0.166  Sum_probs=36.5

Q ss_pred             HHHHHHHHH---ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          435 KDEVNKLII---VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       435 ~e~L~~~L~---~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      ...+...+.   ..|++.|..||..-+.  ..+.|..|||+.+|+++++|.+++.+-
T Consensus        21 ~~~~~~~l~~~~~~lt~~~~~vL~~l~~--~~~~t~~eLa~~l~~~~~tvs~~l~~L   75 (142)
T 3ech_A           21 RTRIQSELDCQRLDLTPPDVHVLKLIDE--QRGLNLQDLGRQMCRDKALITRKIREL   75 (142)
T ss_dssp             HHHHHHHHHHTTCCCCHHHHHHHHHHHH--TTTCCHHHHHHHHC---CHHHHHHHHH
T ss_pred             HHHHHHHHhhccCCCCHHHHHHHHHHHh--CCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence            344555552   2599999999887652  358999999999999999998776553

>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20

Probab=83.99  E-value=2.3  Score=36.06  Aligned_cols=61  Identities=15%  Similarity=0.070  Sum_probs=43.7

Q ss_pred             HHHHHHHHccCCHHHHHHHhHHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHH
Q 010521          436 DEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAAR  497 (508)
Q Consensus       436 e~L~~~L~~~Lp~rER~VI~LryGL--d~eg~TleEIAe~LgIS~erVrqi~~r----ALkKLR~~L~  497 (508)
                      ..|.... ..|++.|+.|......-  ....+|..|||+..|+|..||.+.-++    +...||..+.
T Consensus        10 ~~i~~~~-~~ls~~e~~ia~yil~~~~~~~~~si~elA~~~~vS~aTv~Rf~kklG~~gf~efk~~l~   76 (111)
T 2o3f_A           10 AIIQSMX-HXLPPSERKLADYILAHPHXAIESTVNEISALANSSDAAVIRLCXSLGLKGFQDLXMRVA   76 (111)
T ss_dssp             HHHHHHG-GGSCHHHHHHHHHHHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHHHTTCSSHHHHHHHHH
T ss_pred             HHHHHHh-ccCCHHHHHHHHHHHHChHHHHhcCHHHHHHHHCCCHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            4566666 79999999988765411  013699999999999999999766543    3445555543

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=83.70  E-value=2.2  Score=34.50  Aligned_cols=37  Identities=19%  Similarity=0.264  Sum_probs=28.0

Q ss_pred             CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521          447 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL  486 (508)
Q Consensus       447 p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~  486 (508)
                      ++....|+.+-.   ..++|..|||+.+|+|+.+|++.+.
T Consensus        22 ~~~r~~Il~~L~---~~~~~~~ela~~l~is~~tvs~~L~   58 (98)
T 3jth_A           22 NERRLQILCMLH---NQELSVGELCAKLQLSQSALSQHLA   58 (98)
T ss_dssp             SHHHHHHHHHTT---TSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHh---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            555556665543   4678999999999999999976554

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=83.66  E-value=3.1  Score=33.96  Aligned_cols=38  Identities=11%  Similarity=0.106  Sum_probs=28.2

Q ss_pred             CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          447 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       447 p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      +|.-..||.+-.   ..++|..|||+.+|+|+.+|++.+..
T Consensus        22 ~~~r~~Il~~L~---~~~~~~~ela~~l~is~~tvs~~L~~   59 (102)
T 3pqk_A           22 HPVRLMLVCTLV---EGEFSVGELEQQIGIGQPTLSQQLGV   59 (102)
T ss_dssp             SHHHHHHHHHHH---TCCBCHHHHHHHHTCCTTHHHHHHHH
T ss_pred             CHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            455555665544   45799999999999999999765543

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85

Probab=83.57  E-value=0.79  Score=37.88  Aligned_cols=44  Identities=7%  Similarity=0.066  Sum_probs=34.9

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..|++.|..|+..-+-.+.+|.+.+|||+.+|++..+|..++.+
T Consensus        16 ~~Lt~~q~~Vl~~I~~~g~~gi~qkeLa~~~~l~~~tvt~iLk~   59 (91)
T 2dk5_A           16 KGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKN   59 (91)
T ss_dssp             CCSCSSHHHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHcCCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            56888888888877633346899999999999999998755544

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=82.81  E-value=3.3  Score=34.95  Aligned_cols=42  Identities=12%  Similarity=0.113  Sum_probs=34.3

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .|++.+..|+..-+.  ..+.|..|||+.+|+++++|.+.+.+-
T Consensus        28 ~l~~~~~~iL~~l~~--~~~~~~~ela~~l~is~~~vs~~l~~L   69 (142)
T 3bdd_A           28 GISLTRYSILQTLLK--DAPLHQLALQERLQIDRAAVTRHLKLL   69 (142)
T ss_dssp             SSCHHHHHHHHHHHH--HCSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh--CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            699999998877652  357999999999999999998765543

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=82.75  E-value=1.9  Score=36.77  Aligned_cols=41  Identities=10%  Similarity=-0.039  Sum_probs=34.5

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .|++.|..|+..-+   ..+.|..|||+.+|+++++|.+.+.+-
T Consensus        34 ~l~~~~~~iL~~l~---~~~~~~~ela~~l~~s~~tvs~~l~~L   74 (146)
T 2gxg_A           34 NLSYLDFLVLRATS---DGPKTMAYLANRYFVTQSAITASVDKL   74 (146)
T ss_dssp             TCCHHHHHHHHHHT---TSCBCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHh---cCCcCHHHHHHHhCCCchhHHHHHHHH
Confidence            68999999887765   578999999999999999998765543

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=82.61  E-value=4.9  Score=34.88  Aligned_cols=42  Identities=12%  Similarity=0.075  Sum_probs=35.1

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .|++.|..||..-+.  ..+.|..|||+.+|+++.+|.+++.+-
T Consensus        46 ~lt~~~~~iL~~l~~--~~~~t~~ela~~l~is~~tvs~~l~~L   87 (162)
T 2fa5_A           46 GMAIPEWRVITILAL--YPGSSASEVSDRTAMDKVAVSRAVARL   87 (162)
T ss_dssp             CCCHHHHHHHHHHHH--STTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh--CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            699999998877652  368999999999999999998766554

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=82.45  E-value=1.8  Score=37.15  Aligned_cols=43  Identities=16%  Similarity=0.075  Sum_probs=31.9

Q ss_pred             cCCHHHHHHHhHHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGL--d~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|++.+..+|..-+-+  ...+.|..+||+.+|+++.+|++.+.+
T Consensus        10 ~lt~~~~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~~~l~~   54 (139)
T 2x4h_A           10 NLSRREFSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVFEEVSH   54 (139)
T ss_dssp             -CCHHHHHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHHHHHHH
Confidence            5777777776655433  235789999999999999999866554

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=82.44  E-value=2.7  Score=34.49  Aligned_cols=45  Identities=22%  Similarity=0.214  Sum_probs=32.7

Q ss_pred             HHHHHHHccCCHHHHHHHh-HHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          437 EVNKLIIVTLGEREREIIR-LYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       437 ~L~~~L~~~Lp~rER~VI~-LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .+.++|   -+|....|+. +.-   ..++|..|||+.+|+|+++|++.+..
T Consensus        19 ~~~~aL---~~~~Rl~IL~~l~~---~~~~~~~ela~~l~is~stvs~hL~~   64 (99)
T 2zkz_A           19 ELLKTM---AHPMRLKIVNELYK---HKALNVTQIIQILKLPQSTVSQHLCK   64 (99)
T ss_dssp             HHHHHH---CSHHHHHHHHHHHH---HSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHh---CCHHHHHHHHHHHH---CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            444555   3566667773 332   35799999999999999999877654

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=82.42  E-value=3.1  Score=33.16  Aligned_cols=39  Identities=13%  Similarity=0.059  Sum_probs=29.6

Q ss_pred             CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          447 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       447 p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ++.+..|+..-.  +..+.|..|||+.+|+|+++|++.+.+
T Consensus        23 ~~~~~~il~~l~--~~~~~s~~ela~~l~is~~tvs~~l~~   61 (99)
T 3cuo_A           23 HPKRLLILCMLS--GSPGTSAGELTRITGLSASATSQHLAR   61 (99)
T ss_dssp             SHHHHHHHHHHT--TCCSEEHHHHHHHHCCCHHHHHHHHHH
T ss_pred             ChHHHHHHHHHH--hCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            566777776543  134799999999999999999766543

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=82.10  E-value=1.9  Score=39.14  Aligned_cols=42  Identities=19%  Similarity=0.262  Sum_probs=32.3

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..|++.++.||.+--.  ....|..|||+.+|+|+.+|++++.+
T Consensus        13 ~~ld~~d~~IL~~L~~--~~~~s~~eLA~~lglS~~tv~~~l~~   54 (171)
T 2ia0_A           13 IHLDDLDRNILRLLKK--DARLTISELSEQLKKPESTIHFRIKK   54 (171)
T ss_dssp             -CCCHHHHHHHHHHHH--CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4678888888876431  34689999999999999999876554

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36

Probab=82.10  E-value=3.4  Score=35.07  Aligned_cols=42  Identities=21%  Similarity=0.260  Sum_probs=33.9

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|++.+..|+.+-+ +...++|..|||+.+|+++++|.+++.+
T Consensus        23 gl~~~~~~il~~L~-~~~~~~t~~ela~~l~~~~stvs~~l~~   64 (152)
T 1ku9_A           23 GLNKSVGAVYAILY-LSDKPLTISDIMEELKISKGNVSMSLKK   64 (152)
T ss_dssp             TCCHHHHHHHHHHH-HCSSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCChhHHHHHHHHH-HcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            68999998887653 2236799999999999999999766654

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=82.06  E-value=2.2  Score=36.04  Aligned_cols=41  Identities=2%  Similarity=0.024  Sum_probs=33.7

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|++.|..|+..-+.  ..+.|..|||+.+|+++++|.+.+.+
T Consensus        26 ~l~~~~~~iL~~l~~--~~~~~~~ela~~l~~s~~tvs~~l~~   66 (138)
T 3bpv_A           26 NLTDAQVACLLRIHR--EPGIKQDELATFFHVDKGTIARTLRR   66 (138)
T ss_dssp             TCCHHHHHHHHHHHH--STTCBHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            688988888877652  36799999999999999999876654

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=81.67  E-value=5  Score=34.30  Aligned_cols=46  Identities=17%  Similarity=0.208  Sum_probs=33.2

Q ss_pred             HHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          436 DEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       436 e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..+.++|   -++....||.+-.   ..+++..|||+.+|+|+++|++.+..
T Consensus        37 ~~~~kaL---~~~~rl~IL~~L~---~~~~s~~ela~~lgis~stvs~~L~~   82 (122)
T 1r1t_A           37 AEFFAVL---ADPNRLRLLSLLA---RSELCVGDLAQAIGVSESAVSHQLRS   82 (122)
T ss_dssp             HHHHHHH---CCHHHHHHHHHHT---TCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHh---CCHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3444444   3566667776654   35799999999999999999866543

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=81.30  E-value=3.1  Score=35.16  Aligned_cols=62  Identities=11%  Similarity=0.177  Sum_probs=45.2

Q ss_pred             HHHHHHHHHccCCHHHHHHHhHHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHH----HHHHHHHHHHH
Q 010521          435 KDEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGL----VALEKLKHAAR  497 (508)
Q Consensus       435 ~e~L~~~L~~~Lp~rER~VI~LryGL--d~eg~TleEIAe~LgIS~erVrqi~~----rALkKLR~~L~  497 (508)
                      ...|.... ..|++.|+.|.....--  ....+|..|||+..|+|..||-+.-+    .+..-||..+.
T Consensus         5 ~~~I~~~~-~~lt~~e~~ia~yil~~~~~~~~~si~elA~~~~vS~aTv~Rf~kkLGf~gf~efk~~l~   72 (107)
T 3iwf_A            5 LYKIDNQY-PYFTKNEKKIAQFILNYPHKVVNMTSQEIANQLETSSTSIIRLSKKVTPGGFNELKTRLS   72 (107)
T ss_dssp             HHHHHHHG-GGSCHHHHHHHHHHHHCHHHHTTCCHHHHHHHHTSCHHHHHHHHHHHSTTHHHHHHHHHH
T ss_pred             HHHHHHHH-HhcCHHHHHHHHHHHhCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            34566667 89999999998765421  12469999999999999999976544    35566665554

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=81.23  E-value=3  Score=35.13  Aligned_cols=41  Identities=5%  Similarity=-0.044  Sum_probs=33.8

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|++.|..|+..-+.  ..+.|..|||+.+|+++++|.+.+.+
T Consensus        35 ~l~~~~~~iL~~l~~--~~~~t~~ela~~l~~~~~tvs~~l~~   75 (140)
T 2nnn_A           35 GLTPTQWAALVRLGE--TGPCPQNQLGRLTAMDAATIKGVVER   75 (140)
T ss_dssp             CCCHHHHHHHHHHHH--HSSBCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            689999998877542  35799999999999999999876554

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=81.10  E-value=3.1  Score=35.53  Aligned_cols=51  Identities=10%  Similarity=0.042  Sum_probs=38.0

Q ss_pred             HHHHHHHH-ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          436 DEVNKLII-VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       436 e~L~~~L~-~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      ..+...+. ..|++.|..|+..-+.  .++.|..|||+.+|+++++|.+++.+-
T Consensus        23 ~~~~~~~~~~glt~~q~~vL~~l~~--~~~~t~~eLa~~l~~~~~tvs~~l~~L   74 (140)
T 3hsr_A           23 KKYTNYLKEYDLTYTGYIVLMAIEN--DEKLNIKKLGERVFLDSGTLTPLLKKL   74 (140)
T ss_dssp             HHHHHHHGGGTCCHHHHHHHHHSCT--TCEEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHH--cCCcCHHHHHHHHCCChhhHHHHHHHH
Confidence            33444441 3699999988877652  457999999999999999998766554

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=81.06  E-value=5.2  Score=34.53  Aligned_cols=42  Identities=10%  Similarity=0.105  Sum_probs=34.6

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .|++.|..||..-+.  ..+.|..+||+.+|+++.+|.+++.+-
T Consensus        40 ~lt~~~~~iL~~l~~--~~~~t~~ela~~l~i~~~tvs~~l~~L   81 (155)
T 3cdh_A           40 GLRVPEWRVLACLVD--NDAMMITRLAKLSLMEQSRMTRIVDQM   81 (155)
T ss_dssp             TCCHHHHHHHHHHSS--CSCBCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            699999999877652  357999999999999999998766543

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=80.82  E-value=1.2  Score=36.93  Aligned_cols=41  Identities=20%  Similarity=0.334  Sum_probs=29.7

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVG  485 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~  485 (508)
                      ..+.+....|+...+- .++.+|..|||+.+|+|+.+|++.+
T Consensus        14 ~~~~~~~l~Il~~l~~-~g~~~s~~eLa~~lgvs~~tV~~~L   54 (110)
T 1q1h_A           14 SLLGDDVIDVLRILLD-KGTEMTDEEIANQLNIKVNDVRKKL   54 (110)
T ss_dssp             TTSCSTTHHHHHHHHH-HCSCBCHHHHHHTTTSCHHHHHHHH
T ss_pred             HHcChHHHHHHHHHHH-cCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            4456666777765431 1346899999999999999997544

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=80.58  E-value=5.1  Score=34.51  Aligned_cols=43  Identities=9%  Similarity=0.091  Sum_probs=35.4

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      ..|++.|..||..-+.  .++.|..|||+.+|+++++|.+++.+-
T Consensus        37 ~~lt~~q~~iL~~l~~--~~~~~~~eLa~~l~~~~~~vs~~l~~L   79 (149)
T 4hbl_A           37 FGITYSQYLVMLTLWE--ENPQTLNSIGRHLDLSSNTLTPMLKRL   79 (149)
T ss_dssp             TTCCHHHHHHHHHHHH--SSSEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHH--CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3699999998877652  468999999999999999998766554

>2a6c_A Helix-turn-helix motif; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: CIT; 1.90A {Nitrosomonas europaea} SCOP: a.35.1.13

Probab=80.55  E-value=1.9  Score=34.02  Aligned_cols=26  Identities=19%  Similarity=0.181  Sum_probs=23.3

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          462 KECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       462 ~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..++|+.++|+.+|||+.+|+++++.
T Consensus        29 ~~glsq~elA~~~gis~~~is~~e~g   54 (83)
T 2a6c_A           29 NSGLTQFKAAELLGVTQPRVSDLMRG   54 (83)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            35799999999999999999999864

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=80.41  E-value=4.2  Score=35.00  Aligned_cols=42  Identities=14%  Similarity=0.155  Sum_probs=34.6

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .|++.|..|+..-+.  ..+.|..|||+.+|+++++|.+++.+-
T Consensus        38 ~lt~~~~~iL~~l~~--~~~~t~~eLa~~l~~~~~tvs~~l~~L   79 (154)
T 2qww_A           38 GLTIQQLAMINVIYS--TPGISVADLTKRLIITGSSAAANVDGL   79 (154)
T ss_dssp             TCCHHHHHHHHHHHH--STTEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            699999998877652  357999999999999999998766553

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=80.34  E-value=2.6  Score=36.12  Aligned_cols=42  Identities=21%  Similarity=0.236  Sum_probs=34.0

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .|++.|..|+..-+.  ..+.|..|||+.+|+++++|.+++.+-
T Consensus        37 ~l~~~~~~iL~~l~~--~~~~t~~ela~~l~~~~~tvs~~l~~L   78 (148)
T 3nrv_A           37 GIGMTEWRIISVLSS--ASDCSVQKISDILGLDKAAVSRTVKKL   78 (148)
T ss_dssp             TCCHHHHHHHHHHHH--SSSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHc--CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            588888888876542  358999999999999999998766554

>1uly_A Hypothetical protein PH1932; helix-turn-helix, structural genomics, DNA binding protein; 2.50A {Pyrococcus horikoshii} SCOP: a.4.5.58 PDB: 2cwe_A

Probab=80.28  E-value=2.5  Score=39.29  Aligned_cols=39  Identities=18%  Similarity=0.275  Sum_probs=32.4

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      +++.++.|+.+-.   ..++|..|||+.+|+|+++|++++.+
T Consensus        18 ~d~~~~~IL~~L~---~~~~s~~eLA~~lglS~stv~~~l~~   56 (192)
T 1uly_A           18 LEDTRRKILKLLR---NKEMTISQLSEILGKTPQTIYHHIEK   56 (192)
T ss_dssp             HSHHHHHHHHHHT---TCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            5788888887764   35799999999999999999876654

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=80.27  E-value=4.7  Score=33.51  Aligned_cols=37  Identities=16%  Similarity=0.113  Sum_probs=27.7

Q ss_pred             HHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          448 EREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       448 ~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      +....||.+-.   ..++|..|||+.+|+|+++|++.+..
T Consensus        25 ~~r~~IL~~L~---~~~~s~~eLa~~lgis~stvs~~L~~   61 (108)
T 2kko_A           25 GRRLQILDLLA---QGERAVEAIATATGMNLTTASANLQA   61 (108)
T ss_dssp             STTHHHHHHHT---TCCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            33455666543   46789999999999999999866543

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=80.21  E-value=1.7  Score=33.96  Aligned_cols=26  Identities=4%  Similarity=0.276  Sum_probs=23.7

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          462 KECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       462 ~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..++|++++|+.+|||+.+|++++..
T Consensus        21 ~~gltq~elA~~~gis~~~is~~E~G   46 (78)
T 3qq6_A           21 EKGYSLSELAEKAGVAKSYLSSIERN   46 (78)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            46799999999999999999999875

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=80.18  E-value=4.8  Score=33.85  Aligned_cols=52  Identities=8%  Similarity=0.106  Sum_probs=38.4

Q ss_pred             HHHHHHHHH-ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          435 KDEVNKLII-VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       435 ~e~L~~~L~-~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      ...+.+.+. ..|++.|..|+..-+.  ..+.|..+||+.+|+++++|.+++.+-
T Consensus        20 ~~~~~~~~~~~~lt~~~~~iL~~l~~--~~~~~~~~la~~l~~~~~tvs~~l~~L   72 (138)
T 1jgs_A           20 DRLLNEYLSPLDITAAQFKVLCSIRC--AACITPVELKKVLSVDLGALTRMLDRL   72 (138)
T ss_dssp             HHHHHHHHTTTTSCHHHHHHHHHHHH--HSSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHhhhcCCCHHHHHHHHHHHh--cCCCCHHHHHHHHCCChHHHHHHHHHH
Confidence            334444441 3689999998877652  357899999999999999998766553

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=80.11  E-value=3.9  Score=35.69  Aligned_cols=53  Identities=17%  Similarity=0.058  Sum_probs=38.3

Q ss_pred             HHHHHHHH-ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          436 DEVNKLII-VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       436 e~L~~~L~-~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      ..+...+. -.|+..|-.|+.+-+.-...++|..|||+.+++++++|.+++.+-
T Consensus        22 ~~~~~~l~~~gLt~~q~~vL~~L~~~~~~~~t~~eLa~~l~~~~~tvs~~v~~L   75 (147)
T 4b8x_A           22 GEVDAVVKPYGLTFARYEALVLLTFSKSGELPMSKIGERLMVHPTSVTNTVDRL   75 (147)
T ss_dssp             HHHHHHHGGGTCCHHHHHHHHHHHTSGGGEEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            34444441 259999999887655222346899999999999999998776653

---

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	508
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	3e-24
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	2e-22
d1ttya_	87	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga mar	1e-15
d2p7vb1	68	a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escheri	1e-14
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	2e-14
d1ku3a_	61	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquati	6e-13
d1rp3a2	71	a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA)	1e-06
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	6e-06
d1rp3a1	77	a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {	8e-04

>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 = 97.6 bits (242), Expect = 3e-24
 Identities = 53/177 (29%), Positives = 87/177 (49%), Gaps = 30/177 (16%)

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 RYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVENSRT 339
           +Y   G    DL+Q G  GL+R +EKF+  + FK STY  WWIRQ ++RA+ + +RT
Sbjct: 124 KYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQART 180

>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 = 96.1 bits (238), Expect = 2e-22
 Identities = 47/265 (17%), Positives = 105/265 (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 FDSSKGFKISTYVYWWIRQGVSRAL 333
           F+  +G+K STY  WWIRQ ++R++
Sbjct: 307 FEYRRGYKFSTYATWWIRQAITRSI 331

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]} Length = 87

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: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

 Score = 70.2 bits (172), Expect = 1e-15
 Identities = 26/73 (35%), Positives = 50/73 (68%), Gaps = 2/73 (2%)

Query: 434 LKDEVNKLIIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKL 492
           +++E+ K++  TL  RE  ++R+ YGL D +  T E++ +   ++RER+RQ+ + AL KL
Sbjct: 8   MREELEKVL-KTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKL 66

Query: 493 KHAARKKKMEAML 505
           +H +R K ++++L
Sbjct: 67  RHPSRSKYLKSLL 79

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]} Length = 68

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: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

 Score = 66.3 bits (162), Expect = 1e-14
 Identities = 20/65 (30%), Positives = 40/65 (61%), Gaps = 1/65 (1%)

Query: 442 IIVTLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKK 500
           ++  L  RE +++R+ +G+      T E++ K+  ++RER+RQ+   AL KL+H +R + 
Sbjct: 2   VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61

Query: 501 MEAML 505
           + + L
Sbjct: 62  LRSFL 66

>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 = 66.1 bits (161), Expect = 2e-14
 Identities = 17/73 (23%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 264 LAREKLVMSNVRLVMSIAQRYDNM---GADMADLVQGGLIGLLRGIEKFDSSKGFKISTY 320
           + RE+L++  + LV +IA           D+ DL+  G+IGL++ ++   +    +   Y
Sbjct: 10  IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAY 69

Query: 321 VYWWIRQGVSRAL 333
           +   I+  +   L
Sbjct: 70  IKLRIKGAIYDYL 82

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]} Length = 61

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: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

 Score = 61.2 bits (149), Expect = 6e-13
 Identities = 20/51 (39%), Positives = 31/51 (60%), Gaps = 1/51 (1%)

Query: 445 TLGEREREIIRLYYGL-DKECLTWEDISKRIGLSRERVRQVGLVALEKLKH 494
            L ERE  ++++  GL D    T E++    G++RER+RQ+   AL KLK+
Sbjct: 8   KLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKY 58

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 71

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: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 43.7 bits (103), Expect = 1e-06
 Identities = 20/70 (28%), Positives = 39/70 (55%), Gaps = 6/70 (8%)

Query: 429 VDDWALKDEVNKLI---IVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVG 485
           V++  +K E+ + +   +  L ERE+ +I+L +    E L  ++++K +  S  RV Q+ 
Sbjct: 2   VEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFY---EELPAKEVAKILETSVSRVSQLK 58

Query: 486 LVALEKLKHA 495
             ALE+L+  
Sbjct: 59  AKALERLREM 68

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]} Length = 57

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]

 Score = 41.2 bits (97), Expect = 6e-06
 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 338 RTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI 390
            T+++   L E    IR AK  L   +G  P+V  IA++L +S + V  A EA+
Sbjct: 2   GTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAV 55

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 77

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]

 Score = 35.9 bits (83), Expect = 8e-04
 Identities = 14/64 (21%), Positives = 31/64 (48%), Gaps = 9/64 (14%)

Query: 337 SRTLRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKV 393
           SR +R      E+   I+    +L+ + G  P+ + +A+ L +S +++    + I    +
Sbjct: 2   SRQVR------EKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYI 55

Query: 394 FSLD 397
            SL+
Sbjct: 56  LSLE 59

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	508
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.96
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.8
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.73
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	99.44
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	99.44
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.38
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	99.38
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.29
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.19
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	98.86
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	98.84
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	98.73
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	98.66
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.51
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	98.3
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	98.11
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.01
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	97.97
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	97.93
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	97.62
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	94.87
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	94.75
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	94.7
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	93.97
d1hlva1	66	DNA-binding domain of centromere binding protein B	92.18
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	92.08
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	91.82
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	91.46
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	91.45
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	90.3
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	89.93
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	89.2
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	89.18
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	88.56
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	87.61
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	87.42
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	86.81
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	86.75
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	85.63
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	85.56
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	85.36
d1zyba1	73	Probable transcription regulator BT4300, C-termina	84.97
d1nr3a_	122	DNA-binding protein Tfx {Archaeon Methanobacterium	84.94
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	84.88
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	84.68
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	84.55
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	84.52
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	84.51
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	84.48
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	84.45
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	84.27
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	84.21
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	84.0
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	83.96
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	83.9
d1jhga_	101	Trp repressor, TrpR {Escherichia coli [TaxId: 562]	83.41
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	83.02
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	82.87
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	82.39
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	82.27
d1y7ya1	69	Restriction-modification controller protein C.AhdI	82.09
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	82.02
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	82.0
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	81.88
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	81.47
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	81.28
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	81.2
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	81.06
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	80.37
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	80.24

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

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

Probab=99.96  E-value=1.1e-30  Score=243.76  Aligned_cols=149  Identities=34%  Similarity=0.585  Sum_probs=122.0

Q ss_pred             hhHHHHHHhhcccCCCCHHHHHHHHHHHHcCCccchhHHHHH------------------HhhCCCCc---------hHH
Q 010521          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLK------------------ERLGCEPS---------MEQ  243 (508)
Q Consensus       191 ~~~~~yl~~i~~~~lLt~~EE~eL~~~ik~Gd~l~~~~~~l~------------------~~~g~~p~---------~~~  243 (508)
                      |++++||++|+++|+||++||++|+++|+.|..+........                  ...++.|.         ..+
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            689999999999999999999999999999876433322211                  01222333         233


Q ss_pred             HHHHhccC---hHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhH
Q 010521          244 LAASLRIS---RPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTY  320 (508)
Q Consensus       244 ~a~~~~~s---~~~L~~~l~e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTY  320 (508)
                      +.......   ..++.+.+.++..|+++||++|++||++||++|.+.|.+++||+|||+|||++|+++|||++|++|+||
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   344566777889999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhccc
Q 010521          321 VYWWIRQGVSRALVENSRT  339 (508)
Q Consensus       321 A~~wIR~~I~~~Ird~~R~  339 (508)
                      |+||||++|.++|++++|+
T Consensus       162 a~~~i~~~i~~~~~~~~rt  180 (180)
T d1ku2a2         162 ATWWIRQAINRAIADQART  180 (180)
T ss_dssp             HHHHHHHHHHHHHTTSCCC
T ss_pred             HHHHHHHHHHHHHHHhCCC
Confidence            9999999999999999864

>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=99.80  E-value=3.1e-20  Score=186.84  Aligned_cols=76  Identities=42%  Similarity=0.888  Sum_probs=73.4

Q ss_pred             hhHHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHh
Q 010521          261 ECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVEN  336 (508)
Q Consensus       261 e~~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~  336 (508)
                      +...|.++|++.|++||++||++|.++|.+++||+|+|++||++|+++|||.+|++|+|||+||||++|.++|+++
T Consensus       259 ~~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~  334 (334)
T d1siga_         259 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ  334 (334)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHHHHHHC
T ss_pred             hccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHHHHhcCCCCCCchHhhhHHHHHHHHHHHHhCC
Confidence            4568999999999999999999999999999999999999999999999999999999999999999999999875

>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=99.73  E-value=5.2e-18  Score=140.11  Aligned_cols=73  Identities=23%  Similarity=0.449  Sum_probs=68.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhcC---CCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHHHHh
Q 010521          264 LAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRALVEN  336 (508)
Q Consensus       264 ~A~e~LIe~yl~LV~sIAkrY~~---~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~Ird~  336 (508)
                      ..+++||..|+|||.++|.+|.+   .+++.+||+|+|++||++|+++|||++|.+|+|||.+|||++|.++||+.
T Consensus        10 ~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A~~~yd~~~g~~F~tYA~~~Irgai~d~lRk~   85 (87)
T d1rp3a3          10 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSL   85 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHhC
Confidence            56799999999999999999875   47899999999999999999999999999999999999999999999875

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]}

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: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

Probab=99.44  E-value=2.4e-14  Score=117.73  Aligned_cols=72  Identities=35%  Similarity=0.632  Sum_probs=65.4

Q ss_pred             HHHHHHHHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhh
Q 010521          434 LKDEVNKLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLV  506 (508)
Q Consensus       434 l~e~L~~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~  506 (508)
                      +.+.|..+| +.|+|+|+.||.+||||+ ++++|+.|||+.||||+++|+|++.+|++|||.......++.||.
T Consensus         8 l~~~l~~~l-~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrERVRQie~~al~kLr~~~~~~~L~~~l~   80 (87)
T d1ttya_           8 MREELEKVL-KTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLKSLLS   80 (87)
T ss_dssp             CCSHHHHHH-TTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTBSSHHHHHHHH
T ss_pred             HHHHHHHHH-hcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcHHHHHHHHHHH
Confidence            345678888 899999999999999994 689999999999999999999999999999999888888888874

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]}

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: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

Probab=99.44  E-value=9.8e-15  Score=114.69  Aligned_cols=64  Identities=33%  Similarity=0.618  Sum_probs=59.6

Q ss_pred             ccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhHHHhhhc
Q 010521          444 VTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKMEAMLVK  507 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l~~~l~~  507 (508)
                      +.|+|+|+.||.+||||+ ++++|++|||+.||||+++|+|++.+|++|||+......++.||.+
T Consensus         4 ~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrerVrqie~~al~kLr~~~~~~~L~~yl~d   68 (68)
T d2p7vb1           4 AGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD   68 (68)
T ss_dssp             CCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCCGGGGGSCTTCC
T ss_pred             hcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHHHHHHHHHhcC
Confidence            789999999999999996 5789999999999999999999999999999999888888888753

>d1rp3a2 a.4.13.2 (A:164-234) 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: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.38  E-value=6e-13  Score=104.26  Aligned_cols=70  Identities=30%  Similarity=0.366  Sum_probs=65.9

Q ss_pred             CccchHHHHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          424 NPWHGVDDWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       424 ~Pe~~ve~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      ||++.+...+..+.|..+| +.|||++|.||.++|   ++|+|++|||+.||+|+++|++++++|+++||+.|.
T Consensus         1 d~e~~~~~~e~~~~l~~~l-~~L~~~~r~v~~l~~---~~~~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~~L~   70 (71)
T d1rp3a2           1 NVEEEVIKRELTEKVKEAV-SKLPEREKLVIQLIF---YEELPAKEVAKILETSVSRVSQLKAKALERLREMLS   70 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHH-TTSCHHHHHHHHHHH---TSCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHH-HCCCHHHHHHHHHHH---hHhCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHcc
Confidence            3667788889999999999 999999999999999   899999999999999999999999999999999875

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {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: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

Probab=99.38  E-value=1.3e-13  Score=105.91  Aligned_cols=55  Identities=36%  Similarity=0.497  Sum_probs=51.4

Q ss_pred             HHHHccCCHHHHHHHhHHhccC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521          440 KLIIVTLGEREREIIRLYYGLD-KECLTWEDISKRIGLSRERVRQVGLVALEKLKHA  495 (508)
Q Consensus       440 ~~L~~~Lp~rER~VI~LryGLd-~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~  495 (508)
                      ++| +.|+++|+.||.+||||+ ++++|++|||+.||||+++|+|++.+|++|||+.
T Consensus         4 ~~L-~~L~~rer~Ii~~ryGl~~~~~~tl~eIa~~lgiS~erVrqi~~~al~kLR~~   59 (61)
T d1ku3a_           4 KAL-SKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH   59 (61)
T ss_dssp             SST-TTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHT
T ss_pred             HHH-hcCCHHHHHHHHHHhCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhcC
Confidence            456 899999999999999995 7899999999999999999999999999999974

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

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: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=99.19  E-value=1.5e-11  Score=95.71  Aligned_cols=63  Identities=24%  Similarity=0.217  Sum_probs=59.1

Q ss_pred             HHHHHHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          431 DWALKDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       431 ~~el~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      ..+....|.++| +.||+++|.||.++|   ++|+|++|||+.||+|.+||++++++|+++||..++
T Consensus         5 ~~e~~~~l~~~l-~~Lp~~~r~v~~l~~---~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~   67 (68)
T d1or7a1           5 SEELRQIVFRTI-ESLPEDLRMAITLRE---LDGLSYEEIAAIMDCPVGTVRSRIFRAREAIDNKVQ   67 (68)
T ss_dssp             HHHHHHHHHHHH-HHSCHHHHHHHHHHH---TTCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHH-HcCCHHHHHHHHHHH---HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcC
Confidence            456778899999 899999999999999   899999999999999999999999999999999873

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=98.86  E-value=4.4e-09  Score=88.88  Aligned_cols=62  Identities=16%  Similarity=0.232  Sum_probs=53.5

Q ss_pred             HHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521          437 EVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM  501 (508)
Q Consensus       437 ~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l  501 (508)
                      .|......-|||+||.||.+||   ++++|+.|||+.||||+++|++.++||+++||....+.++
T Consensus        10 ~L~d~y~~LLpe~QR~vl~L~~---~e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~L~~ye~kL~l   71 (106)
T d1xsva_          10 YLFDFYQSLLTNKQRNYLELFY---LEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLEL   71 (106)
T ss_dssp             HHHHHHGGGSCHHHHHHHHHHH---TSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH---HhCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence            3333332349999999999999   8999999999999999999999999999999997766655

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=98.84  E-value=4.1e-09  Score=89.04  Aligned_cols=55  Identities=24%  Similarity=0.322  Sum_probs=50.9

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARKKKM  501 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~~~~l  501 (508)
                      +-|||+||.||.|+|   ++|+|+.|||+.||||+++|++.++||+++||....+.++
T Consensus        15 ~lLp~~qR~v~~L~y---~~~ls~~EIA~~lgiS~~aV~~~l~RA~~~L~~~e~kL~l   69 (106)
T d1s7oa_          15 ALLTDKQMNYIELYY---ADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMKLHM   69 (106)
T ss_dssp             GGSCHHHHHHHHHHH---HTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred             hhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHCh
Confidence            449999999999999   8999999999999999999999999999999997766655

>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=98.73  E-value=7.4e-09  Score=81.35  Aligned_cols=69  Identities=19%  Similarity=0.217  Sum_probs=62.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhhccCCCCCCcchhHHHHHHHHHHHHHH
Q 010521          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWWIRQGVSRAL  333 (508)
Q Consensus       263 ~~A~e~LIe~yl~LV~sIAkrY~~~g~d~EDLiQEG~IgLirAiekFDperG~rFsTYA~~wIR~~I~~~I  333 (508)
                      ..+|++++..|.+.++.+|.+++++..++||++||+++.+|+..++|++.  .+|.+|++..++|.+.+++
T Consensus         6 ~~~f~~~~~~y~~~l~~~~~~~~~d~~~aeDivQd~f~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~   74 (75)
T d1h3la_           6 SARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSY   74 (75)
T ss_dssp             HHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHhhhhcCCC--CCHHHHHHHHHHHHHHHHh
Confidence            37899999999999999999999999999999999999999999999864  3699999999999777654

>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=98.66  E-value=1.7e-08  Score=76.61  Aligned_cols=57  Identities=28%  Similarity=0.454  Sum_probs=51.9

Q ss_pred             ccccccHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhC--CCHHHHHHHHHHhCccccc
Q 010521          340 LRLPNHLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLN--MSQKKVRNATEAIGKVFSL  396 (508)
Q Consensus       340 irip~~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lg--is~e~v~~~l~~~~~~~SL  396 (508)
                      ||+|.|+.+.+++++++.+.+. +.||+||.+|||+.+|  +++++|..++.....++||
T Consensus         1 IRlPvH~~e~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~~~~~p~SL   60 (60)
T d1ku2a1           1 IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL   60 (60)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGGGSSSCCCC
T ss_pred             CccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHccCCCCC
Confidence            6899999999999999999994 7899999999999997  5588999999998888876

>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=98.51  E-value=7e-08  Score=72.40  Aligned_cols=53  Identities=36%  Similarity=0.463  Sum_probs=48.9

Q ss_pred             ccccccccHHHHHHHHHHHHHHH-HHcCCCCCHHHHHHHhCCCHHHHHHHHHHh
Q 010521          338 RTLRLPNHLHERLGLIRNAKLRL-EEKGVTPSVDRIAEYLNMSQKKVRNATEAI  390 (508)
Q Consensus       338 R~irip~~~~~~l~kir~a~~~l-~~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~  390 (508)
                      ++||+|+++.+.+++++++...| +++||+||.+|||+.||+++++|..++.+.
T Consensus         2 g~IrvPr~~~e~~~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~   55 (57)
T d1l0oc_           2 GTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAV   55 (57)
T ss_dssp             CCCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCEeCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHh
Confidence            47899999999999999999998 489999999999999999999999988754

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=98.30  E-value=8.8e-07  Score=68.77  Aligned_cols=54  Identities=22%  Similarity=0.406  Sum_probs=49.1

Q ss_pred             HHHHHHHHHccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          435 KDEVNKLIIVTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       435 ~e~L~~~L~~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      .+.+...+ +.|+|+|++|+.+..    +|+|..|||+.||+|..||+....++++||.
T Consensus         3 ~~~~~~~~-~~LT~rE~~vl~~l~----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klg   56 (70)
T d1yioa1           3 QDQLEQLF-SSLTGREQQVLQLTI----RGLMNKQIAGELGIAEVTVKVHRHNIMQKLN   56 (70)
T ss_dssp             HHHHHHHH-HTSCHHHHHHHHHHT----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHH-ccCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            45677777 799999999999975    8999999999999999999999999999985

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=98.11  E-value=2.5e-06  Score=65.53  Aligned_cols=46  Identities=28%  Similarity=0.392  Sum_probs=43.8

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      +.|+|+|++|+.+..    +|+|..|||+.||+|..||++...++++||.
T Consensus         5 ~~LT~rE~~vl~ll~----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klg   50 (67)
T d1a04a1           5 NQLTPRERDILKLIA----QGLPNKMIARRLDITESTVKVHVKHMLKKMK   50 (67)
T ss_dssp             GGSCHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             ccCCHHHHHHHHHHH----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence            689999999999986    8999999999999999999999999999986

>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=98.01  E-value=5.4e-07  Score=71.08  Aligned_cols=55  Identities=20%  Similarity=0.360  Sum_probs=47.1

Q ss_pred             cHHHHHHHHHHHHHHHH-HcCCCCCHHHHHHHhCCCHHHHHHHHHHh--Ccccccccc
Q 010521          345 HLHERLGLIRNAKLRLE-EKGVTPSVDRIAEYLNMSQKKVRNATEAI--GKVFSLDRE  399 (508)
Q Consensus       345 ~~~~~l~kir~a~~~l~-~~Gr~Pt~eEIA~~Lgis~e~v~~~l~~~--~~~~SLD~~  399 (508)
                      .+.++.+++.++...|. ++||+|+.+|||+.||+++++|..++...  ..++|||.+
T Consensus         4 s~r~~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~~~~~~~~SLD~~   61 (77)
T d1rp3a1           4 QVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEV   61 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHHhcCCceecccC
Confidence            34467788999998885 78999999999999999999999998765  467899985

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.97  E-value=6.6e-06  Score=62.64  Aligned_cols=46  Identities=22%  Similarity=0.198  Sum_probs=43.1

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..|+++|++|+.+.-    +|+|.+|||+.||+|..||+....++++||.
T Consensus         3 ~~Lt~rE~~vl~l~~----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klg   48 (65)
T d1l3la1           3 AWLDPKEATYLRWIA----VGKTMEEIADVEGVKYNSVRVKLREAMKRFD   48 (65)
T ss_dssp             CCCCHHHHHHHHHHT----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             cccCHHHHHHHHHHH----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            369999999998874    8999999999999999999999999999986

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=97.93  E-value=8.7e-06  Score=62.26  Aligned_cols=45  Identities=31%  Similarity=0.347  Sum_probs=42.3

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      .|+++|++|+.+..    +|+|.+|||+.||+|..||+....++++||.
T Consensus         4 ~LT~rE~~vl~l~~----~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~   48 (67)
T d1fsea_           4 LLTKREREVFELLV----QDKTTKEIASELFISEKTVRNHISNAMQKLG   48 (67)
T ss_dssp             CCCHHHHHHHHHHT----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHH----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            59999999999874    9999999999999999999999999999985

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=97.62  E-value=3.8e-05  Score=61.70  Aligned_cols=46  Identities=26%  Similarity=0.371  Sum_probs=43.3

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLK  493 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rALkKLR  493 (508)
                      ..|+++|++|+.+..    .|++..|||+.|++|..||+....++++||.
T Consensus        21 ~~LT~rE~~vl~ll~----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~   66 (87)
T d1p4wa_          21 KRLSPKESEVLRLFA----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLG   66 (87)
T ss_dssp             SSCCHHHHHHHHHHH----HTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence            369999999999986    8999999999999999999999999999985

>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=94.87  E-value=0.014  Score=42.51  Aligned_cols=36  Identities=22%  Similarity=0.255  Sum_probs=31.7

Q ss_pred             hHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhhh
Q 010521          227 HKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC  262 (508)
Q Consensus       227 ~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e~  262 (508)
                      +..+|...+|++|+.+|+|..+||+.+++...|..+
T Consensus        20 ~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~   55 (57)
T d1l0oc_          20 AKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAV   55 (57)
T ss_dssp             HHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHh
Confidence            556788999999999999999999999998877643

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=94.75  E-value=0.017  Score=40.65  Aligned_cols=37  Identities=11%  Similarity=0.202  Sum_probs=31.3

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQV  484 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi  484 (508)
                      .|++.|.+-++-.+   ..|.|..+||+.||||+.||-+.
T Consensus         5 ~lt~~q~~~a~~l~---~~G~s~~~iA~~~gVSr~TiYry   41 (47)
T d1ijwc_           5 AINKHEQEQISRLL---EKGHPRQQLAIIFGIGVSTLYRY   41 (47)
T ss_dssp             SSCHHHHHHHHHHH---HTTCCHHHHHHHHTCCHHHHHHH
T ss_pred             cCCHHHHHHHHHHH---HCCCCHHHHHHHHCcCHHHHHhh
Confidence            57888877776666   58999999999999999999765

>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=94.70  E-value=0.017  Score=44.25  Aligned_cols=38  Identities=39%  Similarity=0.512  Sum_probs=33.0

Q ss_pred             cchhHHHHHHhhCCCCchHHHHHHhccChHHHHHhhhh
Q 010521          224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME  261 (508)
Q Consensus       224 l~~~~~~l~~~~g~~p~~~~~a~~~~~s~~~L~~~l~e  261 (508)
                      ++.+..+|...+|++|+.+|+|..+||+.+++.+.+..
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            44577889999999999999999999999998887653

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=93.97  E-value=0.036  Score=42.05  Aligned_cols=42  Identities=21%  Similarity=0.253  Sum_probs=33.1

Q ss_pred             cCCHHHHHHHhHHhcc---CCCCCCHHHHHHHHCC-CHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGL---DKECLTWEDISKRIGL-SRERVRQVGL  486 (508)
Q Consensus       445 ~Lp~rER~VI~LryGL---d~eg~TleEIAe~LgI-S~erVrqi~~  486 (508)
                      .|+++|+.|+...-..   ++-.-|++|||+.+|+ |.++|+..+.
T Consensus         2 ~LT~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~   47 (71)
T d1jhfa1           2 ALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLK   47 (71)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHH
Confidence            5899999998763222   2456899999999999 8999987754

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.18  E-value=0.075  Score=39.88  Aligned_cols=41  Identities=20%  Similarity=0.161  Sum_probs=31.5

Q ss_pred             cCCHHHHHHHhHHhccCCC--CCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKE--CLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~e--g~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .|+-.++.=|..+|   .+  .++..|||+.|||+++||+.|+..-
T Consensus         7 ~LT~~eK~~ii~~~---e~g~k~sq~eIA~~fGv~~STvs~IlKnK   49 (66)
T d1hlva1           7 QLTFREKSRIIQEV---EENPDLRKGEIARRFNIPPSTLSTILKNK   49 (66)
T ss_dssp             CCCHHHHHHHHHHH---HHCTTSCHHHHHHHHTCCHHHHHHHHHTH
T ss_pred             cCCHHHHHHHHHHH---HcCCcchHHHHHHHhCCChhHHHHHHHHH
Confidence            46777766444554   33  3789999999999999999998774

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=92.08  E-value=0.17  Score=37.02  Aligned_cols=41  Identities=17%  Similarity=0.324  Sum_probs=32.9

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      |++..+.||..--.  .-.+|+.|||+.+|+|..+|+.++.+-
T Consensus         3 lD~~D~~IL~~L~~--~~r~s~~eiA~~l~ls~~~v~~Ri~rL   43 (63)
T d2cg4a1           3 IDNLDRGILEALMG--NARTAYAELAKQFGVSPETIHVRVEKM   43 (63)
T ss_dssp             CCHHHHHHHHHHHH--CTTSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            67888888887651  246899999999999999998776553

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=91.82  E-value=0.16  Score=37.33  Aligned_cols=41  Identities=20%  Similarity=0.208  Sum_probs=32.8

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      +|++..+.||..--.  ....|+.|||+.+|+|+++|.+++.+
T Consensus         2 klD~~D~~IL~~L~~--n~r~s~~~iA~~lgis~~tv~~Ri~~   42 (63)
T d2cfxa1           2 KLDQIDLNIIEELKK--DSRLSMRELGRKIKLSPPSVTERVRQ   42 (63)
T ss_dssp             CCCHHHHHHHHHHHH--CSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            477888888877541  24589999999999999999877654

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=91.46  E-value=0.085  Score=36.19  Aligned_cols=31  Identities=23%  Similarity=0.331  Sum_probs=26.3

Q ss_pred             HHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521          452 EIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL  486 (508)
Q Consensus       452 ~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~  486 (508)
                      .|..|+-    +|+.-.+||+.|||++.+|-+++.
T Consensus        10 ~V~~L~~----~G~gat~IAk~lgI~R~SVYR~L~   40 (43)
T d1gdta1          10 AVLNMWQ----QGLGASHISKTMNIARSTVYKVIN   40 (43)
T ss_dssp             HHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHh
Confidence            4677764    999999999999999999976654

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=91.45  E-value=0.19  Score=36.44  Aligned_cols=40  Identities=23%  Similarity=0.424  Sum_probs=30.9

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      |++.++.||.+--.  ....|+.|||+.+|+|+++|.+++.+
T Consensus         1 lD~~D~kIl~~L~~--n~r~s~~~lA~~~gls~~~v~~Ri~~   40 (60)
T d1i1ga1           1 IDERDKIILEILEK--DARTPFTEIAKKLGISETAVRKRVKA   40 (60)
T ss_dssp             CCSHHHHHHHHHHH--CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            46677888876541  23589999999999999999876654

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=90.30  E-value=0.35  Score=34.87  Aligned_cols=41  Identities=22%  Similarity=0.283  Sum_probs=30.5

Q ss_pred             CCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          446 LGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       446 Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      |++..+.||..--.  .-..|+.|||+.+|+|+.+|..++.+-
T Consensus         1 lD~~D~~Il~~L~~--n~r~s~~eiA~~l~ls~~~v~~Ri~~L   41 (60)
T d2cyya1           1 LDEIDKKIIKILQN--DGKAPLREISKITGLAESTIHERIRKL   41 (60)
T ss_dssp             CCHHHHHHHHHHHH--CTTCCHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            45667777766441  235899999999999999998766543

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.93  E-value=0.22  Score=36.82  Aligned_cols=32  Identities=22%  Similarity=0.174  Sum_probs=27.0

Q ss_pred             HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      ||.+.    .+|+|..+||++|+||.++|.++..+-
T Consensus        23 iv~~~----~~G~s~r~aA~rf~VS~s~v~k~l~r~   54 (63)
T d1k78a1          23 IVELA----HQGVRPCDISRQLRVSHGCVSKILGRY   54 (63)
T ss_dssp             HHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            55554    389999999999999999999888764

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=89.20  E-value=0.25  Score=41.03  Aligned_cols=39  Identities=18%  Similarity=0.112  Sum_probs=30.3

Q ss_pred             CCHHHHH-HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          446 LGERERE-IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       446 Lp~rER~-VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      |+...|. ||.+ +   .+|++..+||+.||||+++|.+++.+=
T Consensus        17 Ls~dlR~rIv~~-~---~~G~s~r~iA~~~~VS~~tV~k~l~r~   56 (123)
T d1pdnc_          17 LPNNIRLKIVEM-A---ADGIRPCVISRQLRVSHGCVSKILNRY   56 (123)
T ss_dssp             CCHHHHHHHHHH-H---HTTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHH-H---HhcCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4555444 5555 4   489999999999999999999887763

>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=89.18  E-value=0.21  Score=36.54  Aligned_cols=35  Identities=26%  Similarity=0.416  Sum_probs=27.2

Q ss_pred             hhHHHHHHhhCCCCchHHHHHHhccC--hHHHHHhhh
Q 010521          226 DHKLRLKERLGCEPSMEQLAASLRIS--RPELQSILM  260 (508)
Q Consensus       226 ~~~~~l~~~~g~~p~~~~~a~~~~~s--~~~L~~~l~  260 (508)
                      .+..+|...+|++|+.+|+|.++|++  .+.+...+.
T Consensus        16 r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~   52 (60)
T d1ku2a1          16 RTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLK   52 (60)
T ss_dssp             HHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGG
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHH
Confidence            35667889999999999999999854  555655543

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=88.56  E-value=0.24  Score=38.59  Aligned_cols=36  Identities=17%  Similarity=0.387  Sum_probs=29.3

Q ss_pred             HHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          451 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       451 R~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      ..+|.++.  ..+|.|..+||+.|||+..+|++++...
T Consensus        12 ~~aV~l~~--~~~g~s~~~vA~~lGIs~~tl~~W~k~~   47 (89)
T d2jn6a1          12 RDAVALYE--NSDGASLQQIANDLGINRVTLKNWIIKY   47 (89)
T ss_dssp             HHHHHHHT--TGGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHH--HcCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            45777765  1247999999999999999999998765

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=87.61  E-value=0.24  Score=36.00  Aligned_cols=25  Identities=24%  Similarity=0.122  Sum_probs=23.0

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          463 ECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       463 eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      -|+|++|+|+.+|||+.+|++++..
T Consensus        11 ~gltQ~elA~~lGvs~~tvs~~E~G   35 (62)
T d2ppxa1          11 LKLTQEEFSARYHIPLGTLRDWEQG   35 (62)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHTT
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence            4699999999999999999999974

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=87.42  E-value=0.28  Score=37.17  Aligned_cols=27  Identities=37%  Similarity=0.437  Sum_probs=22.7

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          464 CLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       464 g~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ++|.+|||..+|+|+++|.    +++++|++
T Consensus        30 ~~t~~eiA~~lG~sretvs----r~l~~l~~   56 (80)
T d1ft9a1          30 DFTVEEIANLIGSSRQTTS----TALNSLIK   56 (80)
T ss_dssp             CCCHHHHHHHHCSCHHHHH----HHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            6899999999999999996    56666664

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=86.81  E-value=0.62  Score=33.92  Aligned_cols=38  Identities=18%  Similarity=0.250  Sum_probs=27.9

Q ss_pred             CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521          447 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGL  486 (508)
Q Consensus       447 p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~  486 (508)
                      ++....||.+--  +....|.+|+|+.||||+.||++.+.
T Consensus         4 ~~~~~~iL~~L~--~~~~~s~~eLa~~l~vS~~ti~r~i~   41 (63)
T d1biaa1           4 NTVPLKLIALLA--NGEFHSGEQLGETLGMSRAAINKHIQ   41 (63)
T ss_dssp             CHHHHHHHHHHT--TSSCBCHHHHHHHHTSCHHHHHHHHH
T ss_pred             cHHHHHHHHHHH--HCCcCCHHHHHHHHCcCHHHHHHHHH
Confidence            445555665532  24568999999999999999986654

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.75  E-value=0.73  Score=33.20  Aligned_cols=50  Identities=16%  Similarity=0.147  Sum_probs=42.5

Q ss_pred             cCCHHHHHHHhHHhccC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLD--KECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd--~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      .+++.|..+|...|..+  -......+||..+|++...|+.+...-..+.|+
T Consensus         7 ~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   58 (60)
T d1yz8p1           7 HFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK   58 (60)
T ss_dssp             CCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHh
Confidence            47888999999998664  245789999999999999999999998888775

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=85.63  E-value=0.64  Score=35.82  Aligned_cols=61  Identities=16%  Similarity=0.097  Sum_probs=43.8

Q ss_pred             HHHHHHHHccCCHHHHHHHhHHhcc--CCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHH
Q 010521          436 DEVNKLIIVTLGEREREIIRLYYGL--DKECLTWEDISKRIGLSRERVRQVGLV----ALEKLKHAAR  497 (508)
Q Consensus       436 e~L~~~L~~~Lp~rER~VI~LryGL--d~eg~TleEIAe~LgIS~erVrqi~~r----ALkKLR~~L~  497 (508)
                      ..|.... ..|++.|+.|.....--  ....+|.+|||+..|||..||-+.-++    ....||..+.
T Consensus         7 ~~i~~~~-~~Ls~~e~~ia~yil~~~~~~~~~si~~lA~~~~vS~sTi~Rf~kklG~~gf~e~k~~l~   73 (83)
T d2o3fa1           7 AIIQSMK-HKLPPSERKLADYILAHPHKAIESTVNEISALANSSDAAVIRLCKSLGLKGFQDLKMRVA   73 (83)
T ss_dssp             HHHHHHG-GGSCHHHHHHHHHHHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHHHTTCSSHHHHHHHHH
T ss_pred             HHHHHHH-hhCCHHHHHHHHHHHcCHHHHHHccHHHHHHHHCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence            4566666 89999999988664311  124699999999999999999766544    4555555544

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=85.56  E-value=0.41  Score=36.15  Aligned_cols=27  Identities=26%  Similarity=0.297  Sum_probs=22.7

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          464 CLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       464 g~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ++|.+|||..+|+|+++|.    +++++|++
T Consensus        30 ~lt~~elA~~~g~sretvs----r~l~~l~~   56 (80)
T d3e5ua1          30 PLSQKSIGEITGVHHVTVS----RVLASLKR   56 (80)
T ss_dssp             CCCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            5899999999999999996    56666664

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=85.36  E-value=0.44  Score=37.28  Aligned_cols=42  Identities=14%  Similarity=0.237  Sum_probs=32.5

Q ss_pred             cCCHHHHHHHhHHhc--c-CCCCCCHHHHHHHHC--CCHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYG--L-DKECLTWEDISKRIG--LSRERVRQVGL  486 (508)
Q Consensus       445 ~Lp~rER~VI~LryG--L-d~eg~TleEIAe~Lg--IS~erVrqi~~  486 (508)
                      +|++||+.||....-  + .+.+.+.++|++.+|  +|..|||..+.
T Consensus         1 ~Lt~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~   47 (87)
T d1stza1           1 KLNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMK   47 (87)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHH
Confidence            489999999875322  2 357899999999966  58999988764

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=84.97  E-value=0.38  Score=36.16  Aligned_cols=27  Identities=15%  Similarity=0.326  Sum_probs=22.5

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          464 CLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       464 g~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ++|.+|||..+|+|+++|.    |++++|++
T Consensus        27 ~lt~~elA~~lg~sr~tvs----r~l~~l~~   53 (73)
T d1zyba1          27 KVKMDDLARCLDDTRLNIS----KTLNELQD   53 (73)
T ss_dssp             ECCHHHHHHHHTSCHHHHH----HHHHHHHH
T ss_pred             ecCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            4799999999999999996    66666664

>d1nr3a_ d.236.1.1 (A:) DNA-binding protein Tfx {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a+b)
fold: DNA-binding protein Tfx
superfamily: DNA-binding protein Tfx
family: DNA-binding protein Tfx
domain: DNA-binding protein Tfx
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=84.94  E-value=0.0084  Score=50.46  Aligned_cols=33  Identities=15%  Similarity=0.323  Sum_probs=30.7

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          462 KECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       462 ~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ..|+|++|||+.||.|+..|+.++.+|++++++
T Consensus         3 ~kGltQ~eIA~~LgTSraNIs~IEk~A~eNIek   35 (122)
T d1nr3a_           3 ERGWSQKKIARELKTTRQNVSAIERKAMENIEK   35 (122)
T ss_dssp             CCSCSSCSTHHHHHHCCSSSCCHHHHHHTTCSS
T ss_pred             cccCCHHHHHHHHCccHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999999998875

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=84.88  E-value=0.8  Score=36.36  Aligned_cols=43  Identities=12%  Similarity=0.102  Sum_probs=33.9

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVA  488 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rA  488 (508)
                      .|++.+..||..-+- ...++|..|||+.+|+++++|++++.+-
T Consensus        18 gLs~~~~~iL~~L~~-~~~~~t~~eLa~~~~i~~~tvs~~l~~L   60 (109)
T d2d1ha1          18 KITDTDVAVLLKMVE-IEKPITSEELADIFKLSKTTVENSLKKL   60 (109)
T ss_dssp             TCCHHHHHHHHHHHH-HCSCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHH-cCCCCCHHHHHHHHCccHhHHHHHHHHH
Confidence            699999999864431 1346999999999999999998766543

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=84.68  E-value=1.7  Score=35.33  Aligned_cols=43  Identities=9%  Similarity=0.047  Sum_probs=34.1

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|++.|-.||..-+..++.+.|..|||+.++++.++|...+.+
T Consensus        26 glt~~q~~vL~~l~~~~~~~it~~ela~~~~~~~~~vs~~l~~   68 (135)
T d3broa1          26 DLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQR   68 (135)
T ss_dssp             TCCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCCCCHHHHHHHHCcCHhHHHHHHHH
Confidence            5899999998776533345699999999999999999755443

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=84.55  E-value=0.25  Score=34.99  Aligned_cols=47  Identities=13%  Similarity=0.233  Sum_probs=38.0

Q ss_pred             cCCHHHHHHHhHHhccCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDK--ECLTWEDISKRIGLSRERVRQVGLVALEK  491 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~--eg~TleEIAe~LgIS~erVrqi~~rALkK  491 (508)
                      .|+|.++.||.-.|..+-  .....++||..+|++...|+.+...-..|
T Consensus         3 ~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k   51 (53)
T d1le8a_           3 SISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR   51 (53)
T ss_dssp             CCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhc
Confidence            589999999999995431  23458899999999999999998776554

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=84.52  E-value=0.44  Score=35.89  Aligned_cols=27  Identities=11%  Similarity=0.170  Sum_probs=22.4

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          464 CLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       464 g~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ++|.+|||..+|+|+++|.    |++++|++
T Consensus        29 ~lt~~eLA~~~G~sretvs----r~L~~l~~   55 (81)
T d2gaua1          29 YLSREELATLSNMTVSNAI----RTLSTFVS   55 (81)
T ss_dssp             CCCHHHHHHHTTSCHHHHH----HHHHHHHH
T ss_pred             cCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            5899999999999999996    55666654

>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: HTH-motif protein NE1354
species: Nitrosomonas europaea [TaxId: 915]

Probab=84.51  E-value=0.52  Score=34.67  Aligned_cols=42  Identities=19%  Similarity=0.169  Sum_probs=31.6

Q ss_pred             HHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH-----HHHHHHHHHH
Q 010521          453 IIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV-----ALEKLKHAAR  497 (508)
Q Consensus       453 VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r-----ALkKLR~~L~  497 (508)
                      |-.++.   ..|+|++|+|+.+||++.+|+.+++.     .+..|.+.+.
T Consensus        11 i~~~r~---~~gltq~elA~~~gv~~~~is~ie~g~~~~~s~~~L~~ia~   57 (69)
T d2a6ca1          11 LQEHLR---NSGLTQFKAAELLGVTQPRVSDLMRGKIDLFSLESLIDMIT   57 (69)
T ss_dssp             HHHHHH---TTTCCHHHHHHHHTSCHHHHHHHHTTCGGGCCHHHHHHHHH
T ss_pred             HHHHHH---HcCCCHHHHHHHHHcCHhHHHHHHcccccchhHHHHHHHHH
Confidence            444555   67899999999999999999999962     2345555444

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=84.48  E-value=0.45  Score=35.47  Aligned_cols=26  Identities=19%  Similarity=0.302  Sum_probs=23.1

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          462 KECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       462 ~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..|+|+.|+|+.||||+.+|.+++.-
T Consensus        12 ~~gltQ~elA~~LGvs~~ti~~yE~G   37 (67)
T d2auwa1          12 RNNLSLTTAAEALGISRRMVSYYRTA   37 (67)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence            35799999999999999999998763

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=84.45  E-value=0.73  Score=33.76  Aligned_cols=25  Identities=20%  Similarity=0.060  Sum_probs=20.6

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521          462 KECLTWEDISKRIGLSRERVRQVGL  486 (508)
Q Consensus       462 ~eg~TleEIAe~LgIS~erVrqi~~  486 (508)
                      ....+..+||+.||||+.+|.+.+.
T Consensus        21 ~~~v~~~~iA~~L~vs~~SVt~mvk   45 (63)
T d2isya1          21 GVTPLRARIAERLDQSGPTVSQTVS   45 (63)
T ss_dssp             TCCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCcHHHHHHHhCCCchhHHHHHH
Confidence            3568999999999999999975443

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=84.27  E-value=0.4  Score=34.92  Aligned_cols=26  Identities=12%  Similarity=0.258  Sum_probs=23.6

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          462 KECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       462 ~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..++|++|+|+.+|||+++|+++++.
T Consensus        12 ~~g~tq~elA~~~gis~~~is~~e~g   37 (66)
T d1utxa_          12 KKKISQSELAALLEVSRQTINGIEKN   37 (66)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             HcCCCHHHHHHhcccCHHHHHHHHcC
Confidence            46899999999999999999999863

>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Fructose repressor (FruR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=84.21  E-value=0.4  Score=34.82  Aligned_cols=36  Identities=22%  Similarity=0.336  Sum_probs=27.8

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHH----------HHHHHHHHHHHHhh
Q 010521          465 LTWEDISKRIGLSRERVRQVGL----------VALEKLKHAARKKK  500 (508)
Q Consensus       465 ~TleEIAe~LgIS~erVrqi~~----------rALkKLR~~L~~~~  500 (508)
                      +|++|||+..|+|..||+..++          ...++++..++..+
T Consensus         1 vTl~diA~~agvS~sTVSrvLn~~~~~~~vs~~tr~rV~~~a~~lg   46 (59)
T d1uxda_           1 MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHN   46 (59)
T ss_dssp             CCHHHHHHHHTSCTTHHHHHHHTCGGGTTCTTTTHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCCCcCcCCHHHHHHHHHHHHHHC
Confidence            5899999999999999999886          24556666555443

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=84.00  E-value=1.1  Score=37.03  Aligned_cols=42  Identities=21%  Similarity=0.260  Sum_probs=35.0

Q ss_pred             cCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .|++.+-.|+.+-+ +..+++|..|||+.+|+|+++|++.+.+
T Consensus        23 Gl~~~~~~i~~~L~-~~~~plt~~ela~~l~vsk~~vs~~l~~   64 (151)
T d1ku9a_          23 GLNKSVGAVYAILY-LSDKPLTISDIMEELKISKGNVSMSLKK   64 (151)
T ss_dssp             TCCHHHHHHHHHHH-HCSSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH-hCCCCcCHHHHHHHhCCCcchHHHHHHH
Confidence            68999999997775 3346799999999999999999866654

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=83.96  E-value=0.37  Score=35.47  Aligned_cols=27  Identities=33%  Similarity=0.449  Sum_probs=21.8

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          464 CLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       464 g~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ++|.+|||..+|+|+++|.    |.+++|++
T Consensus        29 ~lt~~~lA~~~G~sRetvs----r~L~~l~~   55 (69)
T d1i5za1          29 KITRQEIGQIVGCSRETVG----RILKMLED   55 (69)
T ss_dssp             ECCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            4899999999999999996    45555543

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=83.90  E-value=0.69  Score=34.11  Aligned_cols=37  Identities=16%  Similarity=0.199  Sum_probs=28.5

Q ss_pred             HHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q 010521          451 REIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVAL  489 (508)
Q Consensus       451 R~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~rAL  489 (508)
                      ..|+.+-+-  ..+.|..|||+.+|+|+.||++++.+-.
T Consensus         9 ~~Il~~l~~--~g~~sr~eLa~~~glS~~Tv~~~l~~L~   45 (71)
T d1z05a1           9 GRVYKLIDQ--KGPISRIDLSKESELAPASITKITRELI   45 (71)
T ss_dssp             HHHHHHHHH--HCSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHH--cCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            345555441  3579999999999999999998876643

>d1jhga_ a.4.12.1 (A:) Trp repressor, TrpR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: Trp repressor, TrpR
domain: Trp repressor, TrpR
species: Escherichia coli [TaxId: 562]

Probab=83.41  E-value=0.6  Score=37.56  Aligned_cols=40  Identities=13%  Similarity=0.214  Sum_probs=31.4

Q ss_pred             ccCCHHHHHHHhHHhccC---CCC-CCHHHHHHHHCCCHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLD---KEC-LTWEDISKRIGLSRERVRQ  483 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd---~eg-~TleEIAe~LgIS~erVrq  483 (508)
                      +-|+|.|+.-|-.|+-+-   .+| +|+.||++.+|+|..||.+
T Consensus        34 dLlT~~E~~~la~R~~ia~~L~~G~~s~reI~~~~gvs~aTItR   77 (101)
T d1jhga_          34 LMLTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITR   77 (101)
T ss_dssp             HHSCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHH
T ss_pred             HhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCChHHHHH
Confidence            458899888777776541   255 8999999999999998853

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.02  E-value=0.65  Score=35.10  Aligned_cols=50  Identities=16%  Similarity=0.157  Sum_probs=41.6

Q ss_pred             cCCHHHHHHHhHHhccCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLDK--ECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd~--eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      .+++.|..||...|-.+-  .....++||..+|++...|+.+......++|+
T Consensus         9 r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~   60 (76)
T d2ecca1           9 RKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKH   60 (76)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHh
Confidence            578888889988885431  23568899999999999999999999999986

>d1vz0a1 a.4.14.1 (A:116-208) Putative partitioning protein ParB/Spo0J {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Putative partitioning protein ParB/Spo0J
species: Thermus thermophilus [TaxId: 274]

Probab=82.87  E-value=0.72  Score=36.38  Aligned_cols=24  Identities=29%  Similarity=0.444  Sum_probs=21.7

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          464 CLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       464 g~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ++|+++||+++|.|+++|.+++.-
T Consensus        19 g~t~~~iA~~~Gks~~~V~~~LrL   42 (93)
T d1vz0a1          19 GLTQEEVARRVGKARSTVANALRL   42 (93)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHG
T ss_pred             CCCHHHHHHHHccchHHHHHHHHH
Confidence            589999999999999999988754

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=82.39  E-value=0.57  Score=36.32  Aligned_cols=37  Identities=16%  Similarity=0.300  Sum_probs=29.5

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHH-----HHHHHHHHHHH
Q 010521          462 KECLTWEDISKRIGLSRERVRQVGLV-----ALEKLKHAARK  498 (508)
Q Consensus       462 ~eg~TleEIAe~LgIS~erVrqi~~r-----ALkKLR~~L~~  498 (508)
                      ..|+|++++|+.+|+|+.+|.++++-     .+.+|.+.+..
T Consensus        22 ~~gltq~~lA~~~gis~~~is~ie~G~~~~~~~~~L~~ia~~   63 (89)
T d2o38a1          22 RARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLNA   63 (89)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHHhhHhHHHHHHcCCCCCCcHHHHHHHHHH
Confidence            46899999999999999999999972     25566655543

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=82.27  E-value=0.83  Score=33.52  Aligned_cols=51  Identities=14%  Similarity=0.213  Sum_probs=42.0

Q ss_pred             cCCHHHHHHHhHHhccC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLD--KECLTWEDISKRIGLSRERVRQVGLVALEKLKHA  495 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd--~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~  495 (508)
                      .+++.|..+|...|-.+  -......+||..+|++...|+.+......|.|+.
T Consensus         8 ~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~   60 (65)
T d1fjla_           8 TFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ   60 (65)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhc
Confidence            46788889999988543  1235688999999999999999999999988863

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

Probab=82.09  E-value=0.64  Score=34.01  Aligned_cols=26  Identities=27%  Similarity=0.188  Sum_probs=23.5

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          462 KECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       462 ~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..++|++++|+.+|+|+++|++++..
T Consensus        20 ~~gltq~~lA~~~gis~~~i~~~E~g   45 (69)
T d1y7ya1          20 AKGLSQETLAFLSGLDRSYVGGVERG   45 (69)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHTT
T ss_pred             HcCCCHHHHHhHhCCCHHHHHHHHCC
Confidence            46899999999999999999999863

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=82.02  E-value=1  Score=32.71  Aligned_cols=40  Identities=23%  Similarity=0.284  Sum_probs=28.1

Q ss_pred             CHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          447 GEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       447 p~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      .+|...|+.+-.- .....|..|+|+.||||+.||++-+..
T Consensus         6 ~eR~~~Il~~L~~-~~~~vs~~~La~~l~VS~~TI~rdi~~   45 (65)
T d1j5ya1           6 QERLKSIVRILER-SKEPVSGAQLAEELSVSRQVIVQDIAY   45 (65)
T ss_dssp             HHHHHHHHHHHHH-CSSCBCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH-cCCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence            3455566654321 023579999999999999999877653

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=82.00  E-value=0.81  Score=32.72  Aligned_cols=50  Identities=10%  Similarity=0.030  Sum_probs=40.2

Q ss_pred             cCCHHHHHHHhHHhccC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLD--KECLTWEDISKRIGLSRERVRQVGLVALEKLKH  494 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd--~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~  494 (508)
                      ..++.|..+|...|--+  .....-++||..+|++...|..+...-..|+|+
T Consensus         6 ~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   57 (58)
T d1ig7a_           6 PFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR   57 (58)
T ss_dssp             CCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhcc
Confidence            36788888998888543  123568899999999999999999988888775

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

Probab=81.88  E-value=0.67  Score=33.18  Aligned_cols=26  Identities=12%  Similarity=0.298  Sum_probs=23.6

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          462 KECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       462 ~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..++|++|+|+.+|||+.+|++++..
T Consensus        12 ~~g~sq~elA~~~gvs~~~is~~E~g   37 (63)
T d1r69a_          12 QLGLNQAELAQKVGTTQQSIEQLENG   37 (63)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             HcCCcHHHHHHHhCcCHHHHHHHHCC
Confidence            46899999999999999999999863

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Transcriptional repressor protein KorB DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=81.47  E-value=0.87  Score=36.71  Aligned_cols=42  Identities=26%  Similarity=0.075  Sum_probs=33.1

Q ss_pred             ccCCHHHHHHHhHHhccCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLV  487 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGLd~eg~TleEIAe~LgIS~erVrqi~~r  487 (508)
                      ..|+|-|...-.-++ + ..|.|.++||+.+|+|+.+|++++.-
T Consensus        12 ~~L~p~e~A~a~~~l-~-~~g~s~~eiA~~~G~s~~~V~~~l~L   53 (114)
T d1r71a_          12 NELTPREIADFIGRE-L-AKGKKKGDIAKEIGKSPAFITQHVTL   53 (114)
T ss_dssp             TCCCHHHHHHHHHHH-H-HTTCCHHHHHHHHTCCHHHHHHHHGG
T ss_pred             cCCCHHHHHHHHHHH-H-HhCCCHHHHHHHHCCcHHHHHHHHHH
Confidence            468888777655544 2 25899999999999999999998763

>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro 434
species: Bacteriophage 434 [TaxId: 10712]

Probab=81.28  E-value=0.82  Score=32.99  Aligned_cols=25  Identities=8%  Similarity=0.278  Sum_probs=22.9

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHH
Q 010521          462 KECLTWEDISKRIGLSRERVRQVGL  486 (508)
Q Consensus       462 ~eg~TleEIAe~LgIS~erVrqi~~  486 (508)
                      ..++|++|+|+.+|||+++|.++++
T Consensus        14 ~~gltq~~lA~~~gvs~~ti~~~E~   38 (65)
T d2croa_          14 ALKMTQTELATKAGVKQQSIQLIEA   38 (65)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHhHHHHHHC
Confidence            3579999999999999999999986

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.20  E-value=1.7  Score=31.99  Aligned_cols=53  Identities=11%  Similarity=0.181  Sum_probs=43.4

Q ss_pred             cCCHHHHHHHhHHhccC-C-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLD-K-ECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd-~-eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      ..++.|..+|...|-.+ + ...+.++||..+|++...|..+......+.|+...
T Consensus         7 ~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~   61 (68)
T d2cuea1           7 SFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK   61 (68)
T ss_dssp             CSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhh
Confidence            46888999999999543 1 23568999999999999999999999988887543

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.06  E-value=0.84  Score=34.13  Aligned_cols=43  Identities=16%  Similarity=0.260  Sum_probs=35.9

Q ss_pred             ccCCHHHHHHHhHHhcc-CCCCCCHHHHHHHH-CCCHHHHHHHHH
Q 010521          444 VTLGEREREIIRLYYGL-DKECLTWEDISKRI-GLSRERVRQVGL  486 (508)
Q Consensus       444 ~~Lp~rER~VI~LryGL-d~eg~TleEIAe~L-gIS~erVrqi~~  486 (508)
                      +.|++.++.|+.+.-.- +.+|++..||+.+| |++...|++...
T Consensus         2 nGLs~~q~~V~~~i~s~~~~eGi~~~el~~~l~~~~~~~i~~aid   46 (69)
T d1dpua_           2 NGLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVD   46 (69)
T ss_dssp             CCSCHHHHHHHHHHHHCCCTTTEEHHHHHHHSTTSCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhCCCccCcCHHHHHHHccCCCHHHHHHHHH
Confidence            46899999999987665 35799999999999 899999876554

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=80.37  E-value=1.6  Score=32.09  Aligned_cols=53  Identities=11%  Similarity=0.045  Sum_probs=43.0

Q ss_pred             cCCHHHHHHHhHHhccC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q 010521          445 TLGEREREIIRLYYGLD--KECLTWEDISKRIGLSRERVRQVGLVALEKLKHAAR  497 (508)
Q Consensus       445 ~Lp~rER~VI~LryGLd--~eg~TleEIAe~LgIS~erVrqi~~rALkKLR~~L~  497 (508)
                      .+++.|..+|...|-.+  -......+||..|||+...|..+...-..+.|+...
T Consensus         7 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~   61 (67)
T d1zq3p1           7 TFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD   61 (67)
T ss_dssp             CCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhh
Confidence            46888999999998542  123568899999999999999999999988887553

>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Purine repressor (PurR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=80.24  E-value=0.66  Score=33.42  Aligned_cols=35  Identities=23%  Similarity=0.200  Sum_probs=27.0

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH-------HHHHHHHHHHHhh
Q 010521          466 TWEDISKRIGLSRERVRQVGLV-------ALEKLKHAARKKK  500 (508)
Q Consensus       466 TleEIAe~LgIS~erVrqi~~r-------ALkKLR~~L~~~~  500 (508)
                      |++|||+..|||..||++.++.       ..++++..++..+
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~~~~vs~~tr~rV~~~a~~lg   43 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELH   43 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCCCccCHHHHHHHHHHHHHHC
Confidence            8899999999999999988875       4555555555443