Citrus Sinensis ID: 022167

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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-
Protein Sequence
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPSFPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFYF
Secondary Structure (PSIPRED)
ccccccEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccHHcccccHHHHHHHHHHHHHHHccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHcccccHHHHccccHHHHHcHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHccccccccccHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccHHHEEcccccHHHccccccccHHHHHccccccccccccccccccEEEEcccccccccccccccccHHHHHHHHccccccccccccccccccccccccHHHcHHHHHHHHHHHHHHHHHcccccccccccccccccccEEEEEEcccHHHHHHHHHHHHHHHccccccccccccccccccccccHcccHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHcc
Coil and Loop (DISEMBL)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYIndlgsansqvgsTKNVVAAkkssnynpsfpssnrqtqpiKALKEhvdtnfastaepwaeppnsieeesseLDYSVEALLLLQKSMLEKQWNLSFertvltdspskkthkkvpvtcsgvsARQRRLNSKKKILSQNKSILQQNGSkqlrsmisPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIktglslddHKLRLkerlgcepSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFYF
Flexible Loop (DISEMBL)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKssnynpsfpssnrqTQPIKALKEHVDTNFAstaepwaeppnSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERtvltdspskkthkkvpvtcsgvsarqrrlnskkkilsqnksilqqngskqlrsMISPELIQNRLKGYVKGVVSEELLTHAEVVRlskkiktglslddhKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFYF
Low Complexity Region (SEG)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKssnynpsfpssnRQTQPIKALKEHVDTNFASTAEPWAEPPNsieeesseLDYSVEALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFYF
Disordered region (IsUnstruct)
*****AVIGLSAGKRLLSSSFYYSDISEKFSYINDL*********************************************************************YSVEALLLLQKSMLEKQWNLSFERTVL******************************************************ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGC**********LRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY*
Disordered Region (DISOPRED)
***TAAV*GLSAGKRLLSSSFYYSDIS*********************************************************************************************************************************************************************LKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLK***G*EPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFYF
Disordered Region (DISEMBL)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNY************PIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERTVL*****************GVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFYF
Disordered Region (DISPRO)
*MATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKS*************************************PP****EESSELDYSVEALLLLQKSMLEKQWNLSFERT*L******KTHKKVPVTCSGVS**********************************ELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFYF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMATAAVIGLSAGKRLLSSSFYYSDISEKFSYINDLGSANSQVGSTKNVVAAKKSSNYNPSFPSSNRQTQPIKALKEHVDTNFASTAEPWAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERTVLTDSPSKKTHKKVPVTCSGVSARQRRLNSKKKILSQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFYF
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	301	2.2.26 [Sep-21-2011]
O24629	502	RNA polymerase sigma fact	yes	no	0.923	0.553	0.615	6e-97
Q9LD95	547	RNA polymerase sigma fact	no	no	0.345	0.190	0.365	5e-11
O22056	572	RNA polymerase sigma fact	no	no	0.385	0.202	0.316	2e-08
Q31ME3	320	RNA polymerase sigma fact	yes	no	0.358	0.337	0.303	3e-08
P26683	390	RNA polymerase sigma fact	no	no	0.355	0.274	0.317	6e-07
Q03065	332	RNA polymerase sigma-B fa	no	no	0.335	0.304	0.257	1e-05
P27785	317	RNA polymerase sigma fact	N/A	no	0.299	0.283	0.323	3e-05
P38023	399	RNA polymerase sigma fact	no	no	0.355	0.268	0.317	7e-05
Q31QG5	320	RNA polymerase sigma fact	no	no	0.345	0.325	0.304	0.0002

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

 Score =  353 bits (907), Expect = 6e-97,   Method: Compositional matrix adjust.
 Identities = 189/307 (61%), Positives = 230/307 (74%), Gaps = 29/307 (9%)

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 DMADLVQ 296
           +M+DLVQ
Sbjct: 284 EMSDLVQ 290

Essential protein. Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released. Controls the transcription of the psaA gene and thus modulates photosystem stoichiometry. Thereby maintains an harmonious electron flow and photosynthetic efficiency.
Arabidopsis thaliana (taxid: 3702)

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

 Score = 68.9 bits (167), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 38/104 (36%), Positives = 65/104 (62%)

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

Query: 253 PELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           P L+S +     +REKL+ +N+RLV+ IA++Y N G +  DL+Q
Sbjct: 295 PVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQ 338

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 59.7 bits (143), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 37/117 (31%), Positives = 66/117 (56%), Gaps = 1/117 (0%)

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

Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           +  Q A++  + +  L+  +   +L ++K++ SN+RLV+SIA+ Y   G ++ DLVQ
Sbjct: 307 TFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQ 363

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 59.7 bits (143), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 34/112 (30%), Positives = 67/112 (59%), Gaps = 4/112 (3%)

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

Query: 245 AASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           AA++ ++  +L   + +   A+ K++ +N+RLV+SIA++Y     +  DL+Q
Sbjct: 65  AAAVDLNLEDLDRQIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQ 116

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

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

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

 Score = 55.1 bits (131), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 34/107 (31%), Positives = 62/107 (57%)

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

Query: 250 ISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           +  P  +  L     A++K+V SN+RLV+SIA++Y N G    DL+Q
Sbjct: 139 LPLPAFRYRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQ 185

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

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

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

 Score = 51.2 bits (121), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/101 (25%), Positives = 59/101 (58%)

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

Query: 256 QSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
              L +  +A++K++ +N+RLV+SIA++Y     +  DL+Q
Sbjct: 88  LQQLSQGQIAKQKMIQANLRLVVSIAKKYQKRNLEFLDLIQ 128

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

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

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

 Score = 49.7 bits (117), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 34/105 (32%), Positives = 59/105 (56%), Gaps = 15/105 (14%)

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

Query: 252 RPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
             +L  +++   +A+ +L+ SN+RLV+S+A+RY   G  M DLVQ
Sbjct: 69  --DLDRLVVMGRMAKRRLIESNLRLVVSVAKRYVGRGLTMLDLVQ 111

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

Streptomyces aureofaciens (taxid: 1894)

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

 Score = 48.1 bits (113), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 34/107 (31%), Positives = 61/107 (57%)

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

Query: 250 ISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
               E +  L     A++K+V SN+RLV+SIA++Y N G    DL+Q
Sbjct: 148 SPLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQ 194

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

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

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

 Score = 47.0 bits (110), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/105 (30%), Positives = 60/105 (57%), Gaps = 1/105 (0%)

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

Query: 252 RPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
             EL+        A+ K++ +N+RLV+S+A++Y     D+ DL+Q
Sbjct: 72  IEELRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQ 116

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

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

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	301
255566078	508	RNA polymerase sigma factor rpoD, putati	0.980	0.580	0.746	1e-119
224146103	509	predicted protein [Populus trichocarpa]	0.983	0.581	0.710	1e-114
449468291	508	PREDICTED: RNA polymerase sigma factor s	0.980	0.580	0.690	1e-108
356543070	503	PREDICTED: RNA polymerase sigma factor r	0.956	0.572	0.677	1e-107
356531599	503	PREDICTED: RNA polymerase sigma factor r	0.956	0.572	0.674	1e-107
224124068	499	predicted protein [Populus trichocarpa]	0.950	0.573	0.673	3e-97
2565297	502	RNA polymerase sigma subunit 1 [Arabidop	0.923	0.553	0.618	1e-95
15217767	502	sigma factor A [Arabidopsis thaliana] gi	0.923	0.553	0.615	4e-95
334183639	498	sigma factor A [Arabidopsis thaliana] gi	0.923	0.558	0.615	7e-95
11762220	502	At1g64860 [Arabidopsis thaliana]	0.923	0.553	0.612	2e-94

>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 =  434 bits (1115), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 221/296 (74%), Positives = 252/296 (85%), Gaps = 1/296 (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 MEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
            EQ+A SL+ISR ELQS  + CSLAREKL MSNVRLVMSIAQRYDNMGA+MADLVQ
Sbjct: 241 DEQVATSLKISRAELQSKSIACSLAREKLAMSNVRLVMSIAQRYDNMGAEMADLVQ 296

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 =  416 bits (1068), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 211/297 (71%), Positives = 246/297 (82%), Gaps = 1/297 (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 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           S EQ+A SLRISR +LQS L++CSLAREKL MSNVRLVMSIAQ+YDNMGA+MADLVQ
Sbjct: 241 SDEQIADSLRISRADLQSKLIQCSLAREKLAMSNVRLVMSIAQKYDNMGAEMADLVQ 297

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  399 bits (1024), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 205/297 (69%), Positives = 245/297 (82%), Gaps = 2/297 (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 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           S +QLA SL+ISR EL+S +ME SLAREKL MSNVRLVMSIAQRYDNMGA+MADLVQ
Sbjct: 240 SEDQLAISLKISRAELRSRMMESSLAREKLAMSNVRLVMSIAQRYDNMGAEMADLVQ 296

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  395 bits (1014), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 202/298 (67%), Positives = 248/298 (83%), Gaps = 10/298 (3%)

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

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

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

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

Query: 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           PS +Q+A SL+ISR EL++ ++ECSLAREKL MSNVRLVMSIAQ+YDN+GA+M DLVQ
Sbjct: 234 PSDDQMATSLKISRTELRARMIECSLAREKLAMSNVRLVMSIAQKYDNLGAEMGDLVQ 291

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  394 bits (1012), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 201/298 (67%), Positives = 247/298 (82%), Gaps = 10/298 (3%)

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

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

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

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

Query: 239 PSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           PS +Q+A SL+ISR EL++ ++EC+LAREKL MSNVRLVMSIAQ+YDN+GA+M DLVQ
Sbjct: 234 PSDDQMAISLKISRTELRARMIECTLAREKLAMSNVRLVMSIAQKYDNLGAEMGDLVQ 291

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 =  361 bits (926), Expect = 3e-97,   Method: Compositional matrix adjust.
 Identities = 200/297 (67%), Positives = 233/297 (78%), Gaps = 11/297 (3%)

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

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

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

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

Query: 240 SMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           S EQLA SLRISR +LQS L++CSLAREKL MSNVRLVMSIAQ+ DNMGA+MADLVQ
Sbjct: 231 SDEQLADSLRISRADLQSQLIQCSLAREKLAMSNVRLVMSIAQKNDNMGAEMADLVQ 287

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 =  355 bits (911), Expect = 1e-95,   Method: Compositional matrix adjust.
 Identities = 190/307 (61%), Positives = 230/307 (74%), Gaps = 29/307 (9%)

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 DMADLVQ 296
           +M+DLVQ
Sbjct: 284 EMSDLVQ 290

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 =  353 bits (907), Expect = 4e-95,   Method: Compositional matrix adjust.
 Identities = 189/307 (61%), Positives = 230/307 (74%), Gaps = 29/307 (9%)

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 DMADLVQ 296
           +M+DLVQ
Sbjct: 284 EMSDLVQ 290

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  353 bits (905), Expect = 7e-95,   Method: Compositional matrix adjust.
 Identities = 189/307 (61%), Positives = 230/307 (74%), Gaps = 29/307 (9%)

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

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

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

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

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

Query: 290 DMADLVQ 296
           +M+DLVQ
Sbjct: 284 EMSDLVQ 290

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 =  351 bits (901), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 188/307 (61%), Positives = 230/307 (74%), Gaps = 29/307 (9%)

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 DMADLVQ 296
           +M+DLVQ
Sbjct: 284 EMSDLVQ 290

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	301
TAIR|locus:2010871	502	SIGA "AT1G64860" [Arabidopsis	0.930	0.557	0.577	7.9e-78
UNIPROTKB|O48655	519	rsigA "Plastid RNA polymerase	0.953	0.552	0.411	1.6e-45
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.345	0.190	0.365	1.3e-09
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.471	0.248	0.305	5.6e-09
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.614	0.323	0.264	5e-08
UNIPROTKB|Q59563	323	mysB "RNA polymerase sigma fac	0.292	0.272	0.356	8e-05
UNIPROTKB|P0A602	528	rpoD "RNA polymerase sigma fac	0.315	0.179	0.326	0.00092

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

 Score = 783 (280.7 bits), Expect = 7.9e-78, P = 7.9e-78
 Identities = 176/305 (57%), Positives = 213/305 (69%)

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 ADLVQ 296
             +DLVQ
Sbjct:   286 SDLVQ 290

GO:0003677 "DNA binding" evidence=ISS

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

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

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

GO:0009507 "chloroplast" evidence=IDA

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

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

GO:0005515 "protein binding" evidence=IPI

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

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

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

GO:0080005 "photosystem stoichiometry adjustment" evidence=IDA

GO:0006833 "water transport" evidence=RCA

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

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 478 (173.3 bits), Expect = 1.6e-45, P = 1.6e-45
 Identities = 130/316 (41%), Positives = 177/316 (56%)

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 AQRYDNMGADMADLVQ 296
             AQ+YDN+G ++ADL+Q
Sbjct:   292 AQKYDNLGVELADLIQ 307

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

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

 Score = 165 (63.1 bits), Expect = 1.3e-09, P = 1.3e-09
 Identities = 38/104 (36%), Positives = 65/104 (62%)

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

Query:   253 PELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
             P L+S +     +REKL+ +N+RLV+ IA++Y N G +  DL+Q
Sbjct:   295 PVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQ 338

GO:0003677 "DNA binding" evidence=ISS

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009507 "chloroplast" evidence=IDA

GO:0009536 "plastid" evidence=IDA

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

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

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

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

GO:0090351 "seedling development" evidence=IMP

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

GO:0005515 "protein binding" evidence=IPI

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

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

GO:0030154 "cell differentiation" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

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

 Score = 160 (61.4 bits), Expect = 5.6e-09, P = 5.6e-09
 Identities = 44/144 (30%), Positives = 77/144 (53%)

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 NVRLVMSIAQRYDNMGADMADLVQ 296
             N+RLV+SIA+ Y   G ++ DLVQ
Sbjct:   340 NIRLVISIAKNYQGAGMNLQDLVQ 363

GO:0003677 "DNA binding" evidence=ISS

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

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

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

GO:0009507 "chloroplast" evidence=ISM;IDA

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

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

GO:0009658 "chloroplast organization" evidence=IMP

GO:0006399 "tRNA metabolic process" evidence=IMP

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

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

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

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

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

GO:0006364 "rRNA processing" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

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

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

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

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 151 (58.2 bits), Expect = 5.0e-08, Sum P(2) = 5.0e-08
 Identities = 51/193 (26%), Positives = 94/193 (48%)

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 YDNMGADMADLVQ 296
             Y+  G D+ DLVQ
Sbjct:   352 YEGYGLDIQDLVQ 364

GO:0009536 "plastid" evidence=RCA

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

 Score = 120 (47.3 bits), Expect = 8.0e-05, P = 8.0e-05
 Identities = 36/101 (35%), Positives = 54/101 (53%)

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

Query:   256 QSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
                  +   AR  L+ +N+RLV+S+A+RY   G  + DL+Q
Sbjct:    82 -----DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQ 117

GO:0001666 "response to hypoxia" evidence=IEP

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009408 "response to heat" evidence=IEP

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

GO:0016987 "sigma factor activity" evidence=IGI

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

GO:0040007 "growth" evidence=IMP

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

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

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

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

 Score = 110 (43.8 bits), Expect = 0.00092, Sum P(2) = 0.00092
 Identities = 34/104 (32%), Positives = 54/104 (51%)

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 PELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
              ++  I  +   A+  L+ +N+RLV+S+A+RY   G    DL+Q
Sbjct:   279 RDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQ 322

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	301
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	1e-19
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	1e-14
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	2e-13
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	9e-12
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	1e-08
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	3e-07
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	4e-07
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	7e-07
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	9e-06
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	2e-05
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	2e-05
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	1e-04
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	3e-04
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	8e-04
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	0.001
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	0.001
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	0.002
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	0.002

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

 Score = 86.5 bits (215), Expect = 1e-19
 Identities = 35/92 (38%), Positives = 64/92 (69%)

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

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           A+EK++ +N+RLV+S+A++Y N G ++ DL+Q
Sbjct: 75  AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQ 106

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

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

 Score = 72.9 bits (179), Expect = 1e-14
 Identities = 33/92 (35%), Positives = 58/92 (63%)

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

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           A+ K+V +N+RLV+S+A++Y     D+ DL+Q
Sbjct: 82  AKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQ 113

Length = 317

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

 Score = 69.4 bits (170), Expect = 2e-13
 Identities = 35/92 (38%), Positives = 56/92 (60%)

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

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           A+EK+V SN+RLV+SIA++Y N G    DL+Q
Sbjct: 137 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQ 168

Length = 373

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

 Score = 64.1 bits (156), Expect = 9e-12
 Identities = 31/92 (33%), Positives = 59/92 (64%)

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

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           A++K++ +N+RLV++IA++Y     +  DL+Q
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQ 123

Length = 327

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

 Score = 55.1 bits (133), Expect = 1e-08
 Identities = 32/101 (31%), Positives = 55/101 (54%), Gaps = 13/101 (12%)

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 QSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
            +++ +   AR  L+ +N+RLV+S+A+RY   G  + DL+Q
Sbjct: 78  AAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQ 118

Length = 324

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

 Score = 50.4 bits (121), Expect = 3e-07
 Identities = 35/131 (26%), Positives = 61/131 (46%), Gaps = 20/131 (15%)

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 NMGADMADLVQ 296
             G    DL+Q
Sbjct: 124 GRGLPFLDLIQ 134

Length = 342

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

 Score = 50.6 bits (121), Expect = 4e-07
 Identities = 33/114 (28%), Positives = 55/114 (48%), Gaps = 22/114 (19%)

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

Query: 254 -----------ELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
                      EL+ I  +   A+E ++ +N+RLV+S+A++Y N G ++ DLVQ
Sbjct: 154 RWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQ 207

Length = 415

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

 Score = 50.0 bits (120), Expect = 7e-07
 Identities = 31/92 (33%), Positives = 48/92 (52%), Gaps = 13/92 (14%)

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 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           A+  L+ +N+RLV+S+A+RY N G    DL+Q
Sbjct: 272 AKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQ 303

Length = 509

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

 Score = 45.7 bits (109), Expect = 9e-06
 Identities = 20/33 (60%), Positives = 23/33 (69%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQV 297
           AREKLV  N+ LV SIA+R+ N G    DLVQV
Sbjct: 4   AREKLVELNLPLVRSIARRFRNRGEPHEDLVQV 36

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

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

 Score = 45.0 bits (107), Expect = 2e-05
 Identities = 17/32 (53%), Positives = 25/32 (78%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           A+++LV SN+RLV+SIA++Y N G    DL+Q
Sbjct: 1   AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQ 32

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

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

 Score = 44.9 bits (107), Expect = 2e-05
 Identities = 18/33 (54%), Positives = 26/33 (78%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQV 297
           AREKL+  N+RLV+S+ QR++N G ++ DL QV
Sbjct: 38  AREKLINGNLRLVLSVIQRFNNRGENVDDLFQV 70

Length = 258

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

 Score = 42.5 bits (100), Expect = 1e-04
 Identities = 18/33 (54%), Positives = 25/33 (75%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQV 297
           AREKL+  N+RLV+S+ QR++N G  + DL QV
Sbjct: 35  AREKLINGNLRLVLSVIQRFNNRGEYVDDLFQV 67

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

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

 Score = 38.3 bits (90), Expect = 3e-04
 Identities = 16/31 (51%), Positives = 19/31 (61%)

Query: 269 LVMSNVRLVMSIAQRYDNMGADMADLVQVIF 299
           LV   + LV S+A+RY   GAD  DLVQ  F
Sbjct: 1   LVERYLPLVYSLARRYLGDGADAEDLVQEGF 31

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

 Score = 40.0 bits (94), Expect = 8e-04
 Identities = 11/32 (34%), Positives = 22/32 (68%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           A  +++ +++RLV+S+A ++   G  M DL+Q
Sbjct: 41  ALHRIISAHMRLVISMAGKFRRFGLPMNDLIQ 72

Length = 289

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

 Score = 39.7 bits (93), Expect = 0.001
 Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 12/86 (13%)

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

Query: 271 MSNVRLVMSIAQRYDNMGADMADLVQ 296
            SN+RLV+SIA+ Y N G  + DL++
Sbjct: 53  ESNLRLVVSIAKHYVNRGLPLLDLIE 78

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

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

 Score = 39.3 bits (92), Expect = 0.001
 Identities = 16/33 (48%), Positives = 23/33 (69%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQV 297
           AR+KL+  N+RLV SI +R+ N G +  DL Q+
Sbjct: 12  ARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQI 44

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|233844 TIGR02392, rpoH_proteo, alternative sigma factor RpoH

 Score = 38.4 bits (90), Expect = 0.002
 Identities = 15/32 (46%), Positives = 22/32 (68%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
           A +KLV+S++R V+ IA+ Y   G   ADL+Q
Sbjct: 36  AAKKLVLSHLRFVVKIARGYRGYGLPQADLIQ 67

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

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

 Score = 38.4 bits (90), Expect = 0.002
 Identities = 16/33 (48%), Positives = 22/33 (66%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQV 297
           AR+ LV  N+RLV S+ QR+ N G +  DL Q+
Sbjct: 33  ARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQI 65

Length = 252

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	301
PRK07598	415	RNA polymerase sigma factor SigC; Validated	99.91
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	99.89
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	99.85
PRK05949	327	RNA polymerase sigma factor; Validated	99.84
PRK07405	317	RNA polymerase sigma factor SigD; Validated	99.83
PRK05901	509	RNA polymerase sigma factor; Provisional	99.76
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	99.71
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	99.57
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	99.34
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	99.32
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	99.17
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	99.09
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	99.07
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	98.94
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	98.76
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	98.7
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	98.54
PRK08215	258	sporulation sigma factor SigG; Reviewed	98.44
PRK05803	233	sporulation sigma factor SigK; Reviewed	98.25
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	98.16
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	98.16
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	98.15
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	98.13
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	98.02
PRK08583	257	RNA polymerase sigma factor SigB; Validated	97.88
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	97.76
PRK05572	252	sporulation sigma factor SigF; Validated	97.7
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	97.46
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	97.1
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	97.0
PRK08301	234	sporulation sigma factor SigE; Reviewed	96.91
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	96.31
PRK11922	231	RNA polymerase sigma factor; Provisional	95.63
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	94.9
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	94.25
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	93.63
PRK12513	194	RNA polymerase sigma factor; Provisional	93.02
PRK08295	208	RNA polymerase factor sigma-70; Validated	92.82
PRK12519	194	RNA polymerase sigma factor; Provisional	92.26
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	92.03
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	91.3
PRK12534	187	RNA polymerase sigma factor; Provisional	90.94
PRK13919	186	putative RNA polymerase sigma E protein; Provision	90.88
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	88.85
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	87.75
PRK12531	194	RNA polymerase sigma factor; Provisional	87.42
PRK12524	196	RNA polymerase sigma factor; Provisional	87.01
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	86.58
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	86.25
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	86.19
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	85.85
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	84.38
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	83.23
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	81.32
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	80.42
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	80.4

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=99.91  E-value=1.1e-24  Score=213.63  Aligned_cols=110  Identities=30%  Similarity=0.435  Sum_probs=101.9

Q ss_pred             chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCc--------------------HHHHHHHHHHHhCCCCCHHHHHHHhcc
Q 022167          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS--------------------LDDHKLRLKERLGCEPSMEQLAASLRI  250 (301)
Q Consensus       191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~--------------------Le~~r~eLee~LGrePt~eEwA~a~g~  250 (301)
                      |+++.||++|+++||||++||++|+++||.++.                    |++++.+|++.+|++||.+|||.++|+
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            899999999999999999999999999999988                    899999999999999999999977776


Q ss_pred             ChHHHHHH----------------------hhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          251 SRPELQSI----------------------LMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       251 S~~eLrr~----------------------L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      ++.+|+..                      +..|+.|+++||++|+|||++||++|.++|++++||||||+|
T Consensus       140 ~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~i  211 (415)
T PRK07598        140 SLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTL  211 (415)
T ss_pred             cHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHH
Confidence            65555555                      567889999999999999999999999999999999999986

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

Probab=99.89  E-value=5.6e-23  Score=190.67  Aligned_cols=110  Identities=33%  Similarity=0.511  Sum_probs=107.0

Q ss_pred             chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHH
Q 022167          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (301)
Q Consensus       191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV  270 (301)
                      |.+..|++++++.|+||++||++|+++++.|..+++.+.+|++++|++|+..+||+++|++..+|...+..|..|+++||
T Consensus         1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv   80 (298)
T TIGR02997         1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI   80 (298)
T ss_pred             CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence            35688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          271 MSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       271 ~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      .+|+|||++||++|.|+|++++||||||++
T Consensus        81 ~~~lrlV~~iA~~y~~~~~~~eDLiQEg~i  110 (298)
T TIGR02997        81 KANLRLVVSVAKKYQNRGLELLDLIQEGSL  110 (298)
T ss_pred             HHhHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            999999999999999999999999999986

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

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=99.85  E-value=1.8e-21  Score=188.51  Aligned_cols=111  Identities=32%  Similarity=0.474  Sum_probs=108.6

Q ss_pred             cchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHH
Q 022167          190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL  269 (301)
Q Consensus       190 ~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekL  269 (301)
                      .|.+..||++|+++|+||++||++|+++|+.+..+++.+.+|++.+|++|+.++||.++|++..+|++.+..|..|+++|
T Consensus        62 ~d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~L  141 (373)
T PRK07406         62 EDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKM  141 (373)
T ss_pred             CCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHHH
Confidence            37889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          270 VMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       270 V~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      |.+|++||++||++|.++|++++||||||+|
T Consensus       142 i~~~l~lV~~iA~ry~~~~~~~eDLiQEG~i  172 (373)
T PRK07406        142 VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSL  172 (373)
T ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            9999999999999999999999999999986

>PRK05949 RNA polymerase sigma factor; Validated

Probab=99.84  E-value=8.2e-21  Score=180.17  Aligned_cols=111  Identities=29%  Similarity=0.469  Sum_probs=108.6

Q ss_pred             cchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHH
Q 022167          190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL  269 (301)
Q Consensus       190 ~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekL  269 (301)
                      .|.+..||++|++.|+||++||++|+++|+.+..+++.+..|+..+|++|+..+||.+++++..+|...+..|..|+++|
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            48899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          270 VMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       270 V~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      |++|+|+|++||++|.+.|.+++||||||+|
T Consensus        97 i~~~~~~V~~iA~~y~~~~~~~eDLvQEg~i  127 (327)
T PRK05949         97 IEANLRLVVAIAKKYQKRNMEFLDLIQEGTL  127 (327)
T ss_pred             HHHHHHHHHHHHHHHccCCCCHHHHHHHHHH
Confidence            9999999999999999999999999999986

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=99.83  E-value=1.5e-20  Score=177.09  Aligned_cols=110  Identities=31%  Similarity=0.469  Sum_probs=107.9

Q ss_pred             chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHH
Q 022167          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (301)
Q Consensus       191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV  270 (301)
                      |++..||+++++.|+||++||++|+++|+.+..+++++.+|++++|++|+..+||.+++++..+|...+..|..|+++|+
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            78899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          271 MSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       271 ~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      .+|+++|+++|++|.+.|.+++||||||++
T Consensus        88 ~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i  117 (317)
T PRK07405         88 EANLRLVVSVAKKYLKRNVDLLDLIQEGTI  117 (317)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            999999999999999999999999999986

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=99.76  E-value=9.8e-19  Score=175.57  Aligned_cols=100  Identities=35%  Similarity=0.467  Sum_probs=85.3

Q ss_pred             hhcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHH
Q 022167          188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLARE  267 (301)
Q Consensus       188 l~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARe  267 (301)
                      ...|.++.||++|+++|+||++||++|+++|+.|..++..   +.+       ..+|+..   ...+|+.++..|..||+
T Consensus       208 ~~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~~-------~~~~~~~---~~~~l~~~~~~g~~Ar~  274 (509)
T PRK05901        208 ATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LAE-------GEKLDPE---LRRDLQWIGRDGKRAKN  274 (509)
T ss_pred             ccccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hhh-------cccchhh---hhhhhhhhccchHHHHH
Confidence            4458999999999999999999999999999999764442   211       1223322   46789999999999999


Q ss_pred             HHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       268 kLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      +||.+|||||++||++|.++|++|+||||||||
T Consensus       275 ~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnI  307 (509)
T PRK05901        275 HLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNL  307 (509)
T ss_pred             HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            999999999999999999999999999999997

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

Probab=99.71  E-value=1.5e-17  Score=160.29  Aligned_cols=113  Identities=31%  Similarity=0.382  Sum_probs=95.7

Q ss_pred             hhcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHH-HhCCCCCHH---------------HHHHHhccC
Q 022167          188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKE-RLGCEPSME---------------QLAASLRIS  251 (301)
Q Consensus       188 l~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee-~LGrePt~e---------------EwA~a~g~S  251 (301)
                      +..|.+..|+.+++..+++++++|.++...++....+......|.. .+++.|+..               +|+..+...
T Consensus         6 ~~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~   85 (342)
T COG0568           6 LSADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTPE   85 (342)
T ss_pred             cchhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccChH
Confidence            4568899999999999999999999999999888877777788887 678888876               333333332


Q ss_pred             h-HHHHHHhhhHHH---HHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          252 R-PELQSILMECSL---AREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       252 ~-~eLrr~L~eG~~---ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      . .+|...+..|..   |+.+||.+|||||+||||+|.|+|++|.||||||||
T Consensus        86 Ee~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGni  138 (342)
T COG0568          86 EEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNI  138 (342)
T ss_pred             HHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccH
Confidence            2 557777777765   999999999999999999999999999999999997

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=99.57  E-value=3.3e-15  Score=142.22  Aligned_cols=97  Identities=29%  Similarity=0.456  Sum_probs=82.2

Q ss_pred             chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHH
Q 022167          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (301)
Q Consensus       191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV  270 (301)
                      |.+..||++++++|+||++||++|+++|+.|..++..           |+..+|+...  ...+|+..+..|..|+++||
T Consensus        26 ~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~Lv   92 (324)
T PRK07921         26 DLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRHLL   92 (324)
T ss_pred             ChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHHHH
Confidence            7889999999999999999999999999988765443           1122222111  35689999999999999999


Q ss_pred             HHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          271 MSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       271 ~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      .+|+++|+++|++|.++|++++||||||+|
T Consensus        93 ~~~~~lV~~iA~r~~~~~~~~eDLvQEg~i  122 (324)
T PRK07921         93 EANLRLVVSLAKRYTGRGMPLLDLIQEGNL  122 (324)
T ss_pred             HHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            999999999999999999999999999986

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=99.34  E-value=1.1e-12  Score=126.34  Aligned_cols=72  Identities=36%  Similarity=0.486  Sum_probs=68.0

Q ss_pred             hcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHH
Q 022167          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREK  268 (301)
Q Consensus       189 ~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARek  268 (301)
                      +.|.++.||++|++.|+||++||.+|+++++.|..                                        .|+++
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            45899999999999999999999999999987754                                        79999


Q ss_pred             HHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          269 LVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       269 LV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      ||.+|+++|++||++|.++|++++||||||+|
T Consensus       134 Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~i  165 (367)
T PRK09210        134 LAEANLRLVVSIAKRYVGRGMLFLDLIQEGNM  165 (367)
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            99999999999999999999999999999986

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=99.32  E-value=1.6e-12  Score=132.57  Aligned_cols=72  Identities=31%  Similarity=0.463  Sum_probs=61.1

Q ss_pred             hHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHH
Q 022167          192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM  271 (301)
Q Consensus       192 ~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~  271 (301)
                      .+..|++++...+.|+++|+.++.++|+.|..                                     ....|+++||.
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            45677777777888888888888888877654                                     12379999999


Q ss_pred             HhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          272 SNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       272 aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      +|||||++||++|.++|++|+||||||||
T Consensus       388 ~nlrlV~~iA~ky~~~gl~~~DLiQeG~i  416 (619)
T PRK05658        388 ANLRLVISIAKKYTNRGLQFLDLIQEGNI  416 (619)
T ss_pred             HHHHHHHHHHHHHhhCCCCHHHHHHHHHH
Confidence            99999999999999999999999999997

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=99.17  E-value=5.5e-11  Score=110.60  Aligned_cols=74  Identities=35%  Similarity=0.492  Sum_probs=68.4

Q ss_pred             cCchhhcchHHHHHhhcCCCCCCCHHHHHHHHHHH-HcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhH
Q 022167          184 ISPELIQNRLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC  262 (301)
Q Consensus       184 v~pel~~D~l~~YLkei~~~~LLT~EEEveLs~kI-q~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG  262 (301)
                      ++|+   +.+..|++++++.|+||.++|.+|+..+ +.|+.                                       
T Consensus        10 ~~~~---~~~~~y~~~~~~~~~l~~~~e~~l~~~~~~~Gd~---------------------------------------   47 (284)
T PRK06596         10 LSPE---GNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDL---------------------------------------   47 (284)
T ss_pred             CCCc---cHHHHHHHHHhccCCCCHHHHHHHHHHHHHcCCH---------------------------------------
Confidence            6787   8899999999999999999999999985 46665                                       


Q ss_pred             HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                       .|++.||..|++||.+||++|.+.|++++||||||++
T Consensus        48 -~a~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~i   84 (284)
T PRK06596         48 -EAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNI   84 (284)
T ss_pred             -HHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence             8999999999999999999999999999999999986

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=99.09  E-value=1.7e-10  Score=106.05  Aligned_cols=69  Identities=35%  Similarity=0.468  Sum_probs=63.4

Q ss_pred             hHHHHHhhcCCCCCCCHHHHHHHHHHH-HcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHH
Q 022167          192 RLKGYVKGVVSEELLTHAEVVRLSKKI-KTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLV  270 (301)
Q Consensus       192 ~l~~YLkei~~~~LLT~EEEveLs~kI-q~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV  270 (301)
                      ++..|++++++.|+|++++|.+|+.++ +.|+.                                        .|+++||
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            467899999999999999999999985 45654                                        8999999


Q ss_pred             HHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          271 MSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       271 ~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      ..|++||.++|++|.+.|.+++||||||++
T Consensus        42 ~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i   71 (270)
T TIGR02392        42 LSHLRFVVKIARGYRGYGLPQADLIQEGNI   71 (270)
T ss_pred             HHhHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            999999999999999999999999999986

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

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=99.07  E-value=2.5e-10  Score=106.59  Aligned_cols=70  Identities=21%  Similarity=0.339  Sum_probs=64.6

Q ss_pred             chHHHHHhhcCCCCCCCHHHHHHHHHHHH-cCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHH
Q 022167          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIK-TGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKL  269 (301)
Q Consensus       191 D~l~~YLkei~~~~LLT~EEEveLs~kIq-~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekL  269 (301)
                      +.++.||+++.+.|+||+++|.+|+.+++ .|+.                                        .|+++|
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            55688999999999999999999999975 5654                                        899999


Q ss_pred             HHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          270 VMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       270 V~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      |..|+++|.++|++|.+.|.+++||||||++
T Consensus        46 v~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i   76 (289)
T PRK07500         46 ISAHMRLVISMAGKFRRFGLPMNDLIQEGYV   76 (289)
T ss_pred             HHHhHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            9999999999999999999999999999986

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=98.94  E-value=1.5e-09  Score=103.35  Aligned_cols=73  Identities=30%  Similarity=0.399  Sum_probs=68.7

Q ss_pred             hhcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHH
Q 022167          188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLARE  267 (301)
Q Consensus       188 l~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARe  267 (301)
                      +..|.+..|+++|+..|+||+++|.+|..+++.|..                                        .|.+
T Consensus        50 ~~~~~~~~y~~~~~~~~~l~~~ee~~li~~~~~Gd~----------------------------------------~A~~   89 (325)
T PRK05657         50 RVLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDF----------------------------------------AARQ   89 (325)
T ss_pred             ccccHHHHHHHHHhcCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHH
Confidence            344889999999999999999999999999998886                                        8899


Q ss_pred             HHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       268 kLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      .||..|+++|.++|.+|.+.+.+.+||+|||+|
T Consensus        90 ~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi  122 (325)
T PRK05657         90 RMIESNLRLVVKIAKRYLNRGLALLDLIEEGNL  122 (325)
T ss_pred             HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            999999999999999999999999999999986

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=98.76  E-value=4.7e-09  Score=96.83  Aligned_cols=38  Identities=34%  Similarity=0.452  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      ..+|++||.+|+|||++||++|.++|++++||||||+|
T Consensus        39 ~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~i   76 (264)
T PRK07122         39 QRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARV   76 (264)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            46999999999999999999999999999999999986

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=98.70  E-value=3.2e-08  Score=91.58  Aligned_cols=73  Identities=29%  Similarity=0.371  Sum_probs=68.9

Q ss_pred             hhcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHH
Q 022167          188 LIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLARE  267 (301)
Q Consensus       188 l~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARe  267 (301)
                      ...|.+..||.+|...|.|+.++|.+|...++.|..                                        .|.+
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~a~~   49 (285)
T TIGR02394        10 RVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDF----------------------------------------EARK   49 (285)
T ss_pred             CcchHHHHHHHHHhccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHH
Confidence            455889999999999999999999999999999876                                        8999


Q ss_pred             HHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          268 KLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       268 kLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      .|+..+.++|..+|.+|.+.+.+.+||+|||+|
T Consensus        50 ~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i   82 (285)
T TIGR02394        50 VMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNL   82 (285)
T ss_pred             HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            999999999999999999999999999999986

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

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=98.54  E-value=1.3e-07  Score=86.03  Aligned_cols=61  Identities=36%  Similarity=0.500  Sum_probs=56.2

Q ss_pred             cCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHH
Q 022167          200 VVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMS  279 (301)
Q Consensus       200 i~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVS  279 (301)
                      .++.|+||++||.+|+..++.|..                                        .|.++|+..|+++|.+
T Consensus        10 ~~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~~~~~v~~   49 (254)
T TIGR02850        10 TSKLPVLKNQEMRELFIRMQSGDT----------------------------------------TAREKLINGNLRLVLS   49 (254)
T ss_pred             ccCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHH
Confidence            367899999999999999987765                                        7899999999999999


Q ss_pred             HHhhccCCCCChhhHhhhccC
Q 022167          280 IAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       280 IAKRY~grGLsfeDLIQEGnI  300 (301)
                      +|++|.+.+.+.+||+|||++
T Consensus        50 ~a~~~~~~~~~aeDlvQe~~i   70 (254)
T TIGR02850        50 VIQRFNNRGEYVDDLFQVGCI   70 (254)
T ss_pred             HHHHHhCCCCCHHHHHHHHHH
Confidence            999999999999999999986

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

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=98.44  E-value=3.3e-07  Score=83.47  Aligned_cols=60  Identities=37%  Similarity=0.534  Sum_probs=55.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHH
Q 022167          201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI  280 (301)
Q Consensus       201 ~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSI  280 (301)
                      .+.|+|+++|+..|..+++.|..                                        .|.++|+..|+++|..+
T Consensus        14 ~~~~~l~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~~~~~v~~~   53 (258)
T PRK08215         14 SKLPVLKNEEMRELFERMQNGDK----------------------------------------EAREKLINGNLRLVLSV   53 (258)
T ss_pred             CCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence            34679999999999999987765                                        78999999999999999


Q ss_pred             HhhccCCCCChhhHhhhccC
Q 022167          281 AQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       281 AKRY~grGLsfeDLIQEGnI  300 (301)
                      |++|.+.+.+.+||+|||++
T Consensus        54 a~~~~~~~~~aeDlvQe~~i   73 (258)
T PRK08215         54 IQRFNNRGENVDDLFQVGCI   73 (258)
T ss_pred             HHHHhCCCCCHHHHHHHHHH
Confidence            99999999999999999986

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=98.25  E-value=2.5e-06  Score=76.44  Aligned_cols=69  Identities=30%  Similarity=0.413  Sum_probs=63.6

Q ss_pred             hHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHH
Q 022167          192 RLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM  271 (301)
Q Consensus       192 ~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~  271 (301)
                      .+..|+.++++.++||+++|..|...++.|..                                        .|.+.|+.
T Consensus        17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~~~gd~----------------------------------------~a~~~l~~   56 (233)
T PRK05803         17 FLVSYVKNNSFPQPLSEEEERKYLELMKEGDE----------------------------------------EARNILIE   56 (233)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHH
Confidence            56899999999999999999999998887765                                        78899999


Q ss_pred             HhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          272 SNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       272 aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      .+.++|.++|.+|.+.+.+.+||||||.|
T Consensus        57 ~y~~~l~~~a~~~~~~~~daeDlvQE~fi   85 (233)
T PRK05803         57 RNLRLVAHIVKKFENTGEDVDDLISIGTI   85 (233)
T ss_pred             HhHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            99999999999999999999999999875

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=98.16  E-value=2.8e-06  Score=77.89  Aligned_cols=37  Identities=38%  Similarity=0.378  Sum_probs=34.6

Q ss_pred             HHHHHHHHHhHHHHHHHHhhccCC-CCChhhHhhhccC
Q 022167          264 LAREKLVMSNVRLVMSIAQRYDNM-GADMADLVQVIFY  300 (301)
Q Consensus       264 ~ARekLV~aNLRLVVSIAKRY~gr-GLsfeDLIQEGnI  300 (301)
                      .|+++||.+|++||.+||++|.++ +.+++||||||+|
T Consensus        25 ~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~i   62 (256)
T PRK07408         25 ALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSL   62 (256)
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHH
Confidence            899999999999999999999876 7789999999986

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=98.16  E-value=3.2e-07  Score=62.67  Aligned_cols=33  Identities=30%  Similarity=0.483  Sum_probs=30.3

Q ss_pred             chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCc
Q 022167          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS  223 (301)
Q Consensus       191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~  223 (301)
                      |+++.||++|++.|+||++||++|+++|+.|..
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            889999999999999999999999999998765

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 ....

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

Probab=98.15  E-value=2.5e-06  Score=79.75  Aligned_cols=36  Identities=36%  Similarity=0.586  Sum_probs=34.5

Q ss_pred             HHHHHHHHHhHHHHHHHHhhccCCCC-ChhhHhhhccC
Q 022167          264 LAREKLVMSNVRLVMSIAQRYDNMGA-DMADLVQVIFY  300 (301)
Q Consensus       264 ~ARekLV~aNLRLVVSIAKRY~grGL-sfeDLIQEGnI  300 (301)
                      .++ +||+.|++||.+||+||.++|. .++||||.|+|
T Consensus        24 ~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~i   60 (247)
T COG1191          24 EAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMI   60 (247)
T ss_pred             HHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHH
Confidence            888 9999999999999999999998 99999999986

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=98.13  E-value=3.7e-06  Score=77.18  Aligned_cols=61  Identities=21%  Similarity=0.229  Sum_probs=53.2

Q ss_pred             cCCCCCCCHHHHHHHHHHHHc-CCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHH
Q 022167          200 VVSEELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVM  278 (301)
Q Consensus       200 i~~~~LLT~EEEveLs~kIq~-g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVV  278 (301)
                      .|..|+||.++|.+|+.+++. +..                                        .|.+.|+..|++||.
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            478899999999999999874 343                                        788999999999999


Q ss_pred             HHHhhcc-C--CCCChhhHhhhccC
Q 022167          279 SIAQRYD-N--MGADMADLVQVIFY  300 (301)
Q Consensus       279 SIAKRY~-g--rGLsfeDLIQEGnI  300 (301)
                      .+|++|. +  .+.+.+||+|||++
T Consensus        46 ~~a~~~~~~~~~~~~~eDl~Qeg~l   70 (268)
T PRK06288         46 YVAGRIAVGMPQNVEFDDLVSYGVF   70 (268)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHHH
Confidence            9999986 2  57889999999986

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=98.02  E-value=8.1e-06  Score=74.00  Aligned_cols=57  Identities=35%  Similarity=0.362  Sum_probs=51.8

Q ss_pred             CCCCHHHHHHHHHHHHc-CCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHh
Q 022167          204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ  282 (301)
Q Consensus       204 ~LLT~EEEveLs~kIq~-g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAK  282 (301)
                      +.||+++|.+|..+++. |+.                                        .|.++|+..|.++|..+|+
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            66899999999999876 344                                        7889999999999999999


Q ss_pred             hccCCCCChhhHhhhccC
Q 022167          283 RYDNMGADMADLVQVIFY  300 (301)
Q Consensus       283 RY~grGLsfeDLIQEGnI  300 (301)
                      +|.+.+.+.+||+|||+|
T Consensus        48 ~~~~~~~~aeDlvQe~~i   65 (255)
T TIGR02941        48 KYSKGGPMHEDLVQVGML   65 (255)
T ss_pred             HHhcCCCCHHHHHHHHHH
Confidence            999999999999999986

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

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=97.88  E-value=2e-05  Score=71.52  Aligned_cols=57  Identities=33%  Similarity=0.296  Sum_probs=52.0

Q ss_pred             CCCCHHHHHHHHHHHHc-CCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHh
Q 022167          204 ELLTHAEVVRLSKKIKT-GLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ  282 (301)
Q Consensus       204 ~LLT~EEEveLs~kIq~-g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAK  282 (301)
                      +.|+++||.+|..+++. |..                                        .|.+.|+..|.++|..+|+
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            77999999999998875 554                                        7899999999999999999


Q ss_pred             hccCCCCChhhHhhhccC
Q 022167          283 RYDNMGADMADLVQVIFY  300 (301)
Q Consensus       283 RY~grGLsfeDLIQEGnI  300 (301)
                      +|.+.+.+.+||+|||++
T Consensus        48 ~~~~~~~~aeDlvQe~~l   65 (257)
T PRK08583         48 KYSKGQSHHEDLVQVGMV   65 (257)
T ss_pred             HHhcCCCCHHHHHHHHHH
Confidence            999999999999999975

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=97.76  E-value=2e-05  Score=72.50  Aligned_cols=38  Identities=21%  Similarity=0.113  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHhHHHHHHHHhhccC---CCCChhhHhhhccC
Q 022167          263 SLAREKLVMSNVRLVMSIAQRYDN---MGADMADLVQVIFY  300 (301)
Q Consensus       263 ~~ARekLV~aNLRLVVSIAKRY~g---rGLsfeDLIQEGnI  300 (301)
                      ..||++||.+|++||.+||++|.+   .+++++||||||+|
T Consensus        22 ~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~i   62 (257)
T PRK05911         22 IEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVE   62 (257)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHH
Confidence            379999999999999999999862   35679999999986

>PRK05572 sporulation sigma factor SigF; Validated

Probab=97.70  E-value=7.4e-05  Score=67.95  Aligned_cols=64  Identities=38%  Similarity=0.401  Sum_probs=57.5

Q ss_pred             HhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHH
Q 022167          197 VKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRL  276 (301)
Q Consensus       197 Lkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRL  276 (301)
                      ++.-...|.||.+++.+|...++.|..                                        .|.++|+..+.++
T Consensus         5 ~~~~~~~~~l~~~~~~~li~~~~~gd~----------------------------------------~a~~~L~~~y~~~   44 (252)
T PRK05572          5 VKNKKKKPQLKDEENKELIKKSQDGDQ----------------------------------------EARDTLVEKNLRL   44 (252)
T ss_pred             hccCcCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHH
Confidence            456677899999999999988877665                                        7899999999999


Q ss_pred             HHHHHhhccCCCCChhhHhhhccC
Q 022167          277 VMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       277 VVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      |..+|.+|.+.+.+.+||+|||.+
T Consensus        45 v~~~a~~~~~~~~~aeDl~Qe~~l   68 (252)
T PRK05572         45 VWSVVQRFLNRGYEPDDLFQIGCI   68 (252)
T ss_pred             HHHHHHHHccCCCCHHHHHHHHHH
Confidence            999999999999999999999975

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=97.46  E-value=0.00015  Score=74.71  Aligned_cols=35  Identities=23%  Similarity=0.456  Sum_probs=32.8

Q ss_pred             hcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCc
Q 022167          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS  223 (301)
Q Consensus       189 ~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~  223 (301)
                      ++||+++||++||.+||||+|+|++|+++|..|..
T Consensus       102 t~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~  136 (619)
T PRK05658        102 TDDPVRMYLREMGTVELLTREGEIEIAKRIEAGEN  136 (619)
T ss_pred             CCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHHH
Confidence            56999999999999999999999999999988765

>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=97.10  E-value=0.00095  Score=50.29  Aligned_cols=38  Identities=32%  Similarity=0.536  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167          224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME  261 (301)
Q Consensus       224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e  261 (301)
                      +.+.+.+|++.+||+||.+|+|+.+|++.++++.++..
T Consensus         6 i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~   43 (78)
T PF04539_consen    6 IERARRELEQELGREPTDEEIAEELGISVEEVRELLQA   43 (78)
T ss_dssp             HHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHh
Confidence            56788899999999999999999999999998876643

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 ....

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=97.00  E-value=0.0015  Score=58.58  Aligned_cols=68  Identities=31%  Similarity=0.464  Sum_probs=58.1

Q ss_pred             HHHHHhhc-CCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHH
Q 022167          193 LKGYVKGV-VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVM  271 (301)
Q Consensus       193 l~~YLkei-~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~  271 (301)
                      +-.|+..- +..+.|++.+|.+|...++.|..                                        .|-+.|+.
T Consensus        16 ~~~~~~~~~~~~~~~~~~~~~~li~~~~~gd~----------------------------------------~af~~l~~   55 (227)
T TIGR02846        16 LVGYVTNNGSFPQPLSEEEEKKYLDRLKEGDE----------------------------------------EARNVLIE   55 (227)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHH
Confidence            34565444 45677999999999999988775                                        78889999


Q ss_pred             HhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          272 SNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       272 aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      .+.++|..+|.+|.+...+.+||+||+.+
T Consensus        56 ~y~~~v~~~~~~~~~~~~dAEDlvQevfi   84 (227)
T TIGR02846        56 RNLRLVAHIVKKFSNTGEDVDDLISIGTI   84 (227)
T ss_pred             HhHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence            99999999999999999999999999864

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=96.91  E-value=0.0021  Score=57.42  Aligned_cols=66  Identities=29%  Similarity=0.425  Sum_probs=56.4

Q ss_pred             HHHhhcCCC-CCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHh
Q 022167          195 GYVKGVVSE-ELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSN  273 (301)
Q Consensus       195 ~YLkei~~~-~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aN  273 (301)
                      -|+.+.... +.++..++.+|...++.|..                                        .|-+.|+..+
T Consensus        22 ~~~~~~~~~~~~~~~~~~~~L~~~~~~gd~----------------------------------------~af~~l~~~y   61 (234)
T PRK08301         22 YYIGGSEALPPPLSKEEEEYLLNKLPKGDE----------------------------------------AVRSLLIERN   61 (234)
T ss_pred             HHhccccccCCcCCHHHHHHHHHHHHccCH----------------------------------------HHHHHHHHHh
Confidence            467776553 55888899999888887765                                        7888999999


Q ss_pred             HHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          274 VRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       274 LRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      .++|..+|.+|.+.+.+.+||+||+.+
T Consensus        62 ~~~l~~~a~~~~~~~~~AeDlvQevfl   88 (234)
T PRK08301         62 LRLVVYIARKFENTGINIEDLISIGTI   88 (234)
T ss_pred             HHHHHHHHHHhhcCCCCHHHHHHHHHH
Confidence            999999999999999999999999865

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=96.31  E-value=0.0091  Score=53.81  Aligned_cols=58  Identities=33%  Similarity=0.443  Sum_probs=51.9

Q ss_pred             CCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHh
Q 022167          203 EELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQ  282 (301)
Q Consensus       203 ~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAK  282 (301)
                      .+.|++++|.+|...++.|..                                        .|.+.|+..+.++|..+|.
T Consensus        31 ~~~~~~~~~~~l~~~~~~~d~----------------------------------------~a~~~l~~~y~~~l~~~~~   70 (234)
T TIGR02835        31 PPPLTGEEEEALLQKLTQGDE----------------------------------------SAKSTLIERNLRLVVYIAR   70 (234)
T ss_pred             CCcCCHHHHHHHHHHHHcCCH----------------------------------------HHHHHHHHHhHHHHHHHHH
Confidence            578888999999888877664                                        7889999999999999999


Q ss_pred             hccCCCCChhhHhhhccC
Q 022167          283 RYDNMGADMADLVQVIFY  300 (301)
Q Consensus       283 RY~grGLsfeDLIQEGnI  300 (301)
                      +|.+.+.+-+||+||+.+
T Consensus        71 ~~~~~~~~AEDlvQE~fl   88 (234)
T TIGR02835        71 KFENTGIGIEDLVSIGTI   88 (234)
T ss_pred             HhccCCCCHHHHHHHHHH
Confidence            999999999999999864

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.

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=95.63  E-value=0.016  Score=52.11  Aligned_cols=60  Identities=22%  Similarity=0.176  Sum_probs=53.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHH
Q 022167          201 VSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMSI  280 (301)
Q Consensus       201 ~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSI  280 (301)
                      ...|+|+...+..|...++.|..                                        .|-+.|+..+.++|..+
T Consensus         7 ~~~~~~~~~~~~~l~~~~~~gd~----------------------------------------~a~~~l~~~y~~~l~~~   46 (231)
T PRK11922          7 SRPPPLSAASDRELVARVLAGDE----------------------------------------AAFEALMRRHNRRLYRT   46 (231)
T ss_pred             CCCCCcCcccHHHHHHHHHcCCH----------------------------------------HHHHHHHHHHHHHHHHH
Confidence            46789999999999888887765                                        77888999999999999


Q ss_pred             HhhccCCCCChhhHhhhccC
Q 022167          281 AQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       281 AKRY~grGLsfeDLIQEGnI  300 (301)
                      |.+|.+.+-+-+||+||+.+
T Consensus        47 a~~~~~~~~~AEDlvQE~fi   66 (231)
T PRK11922         47 ARAILRNDAEAEDVVQEAYL   66 (231)
T ss_pred             HHHHhCChhhHHHHHHHHHH
Confidence            99999999999999999864

>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=94.90  E-value=0.016  Score=41.43  Aligned_cols=32  Identities=34%  Similarity=0.382  Sum_probs=29.9

Q ss_pred             HHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          269 LVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       269 LV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      |++.+.++|..+|.+|.+.+.+.+|++||+.+
T Consensus         1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~   32 (71)
T PF04542_consen    1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFI   32 (71)
T ss_dssp             HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHH
Confidence            68899999999999999999999999999864

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 ....

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=94.25  E-value=0.082  Score=45.34  Aligned_cols=37  Identities=16%  Similarity=0.082  Sum_probs=32.3

Q ss_pred             HHHHHHHHHhHHHHHHHHhhccCC----CCChhhHhhhccC
Q 022167          264 LAREKLVMSNVRLVMSIAQRYDNM----GADMADLVQVIFY  300 (301)
Q Consensus       264 ~ARekLV~aNLRLVVSIAKRY~gr----GLsfeDLIQEGnI  300 (301)
                      .|-+.|+..+...|..+|.+|.+.    +.+.+|++||+.+
T Consensus        24 ~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi   64 (189)
T PRK09648         24 RALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCL   64 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHH
Confidence            889999999999999999998643    4689999999864

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

Probab=93.63  E-value=0.31  Score=48.17  Aligned_cols=32  Identities=31%  Similarity=0.509  Sum_probs=29.9

Q ss_pred             chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCC
Q 022167          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGL  222 (301)
Q Consensus       191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~  222 (301)
                      ..+..|+..+...++|+++||..|+..++.|.
T Consensus        67 ~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~   98 (342)
T COG0568          67 GRLSFYIRAIEAAPLLTPEEEKALARRLKRGE   98 (342)
T ss_pred             hhHHHHHHHHhhhcccChHHHHHHHHHHHcCC
Confidence            67789999999999999999999999999996

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=93.02  E-value=0.1  Score=44.95  Aligned_cols=38  Identities=18%  Similarity=0.075  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      ..|-+.|+..+.++|..+|.+|.+...+.+||+||+.+
T Consensus        25 ~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi   62 (194)
T PRK12513         25 AAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWL   62 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            48899999999999999999999998999999999865

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=92.82  E-value=0.18  Score=43.59  Aligned_cols=38  Identities=32%  Similarity=0.271  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      ..|-+.|+..+.++|..+|.+|.+.+.+-+||+||+.+
T Consensus        23 ~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l   60 (208)
T PRK08295         23 KEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMI   60 (208)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            47889999999999999999999999999999999865

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=92.26  E-value=0.15  Score=43.78  Aligned_cols=37  Identities=27%  Similarity=0.241  Sum_probs=34.2

Q ss_pred             HHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       264 ~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      .|-+.|+..+.++|..+|++|.+...+-+|++||+.+
T Consensus        29 ~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl   65 (194)
T PRK12519         29 AALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFL   65 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence            7888999999999999999999988899999999864

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

Probab=92.03  E-value=0.22  Score=47.00  Aligned_cols=62  Identities=21%  Similarity=0.333  Sum_probs=46.8

Q ss_pred             chHHHHHhhcC--CCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhH
Q 022167          191 NRLKGYVKGVV--SEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMEC  262 (301)
Q Consensus       191 D~l~~YLkei~--~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG  262 (301)
                      .-+..||+.-.  ..|.    --.      +.+..+..+.++|+..+||+||.+|+|+.+|++.+++..++..+
T Consensus        87 Gei~d~LR~~~~v~vpR----~~~------~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~  150 (247)
T COG1191          87 GEILDYLRKNDSVKVPR----SLR------ELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAI  150 (247)
T ss_pred             HHHHHHHHhCCCccCcH----HHH------HHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHh
Confidence            34678888877  2221    122      23556677889999999999999999999999999987776654

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=91.30  E-value=0.22  Score=43.16  Aligned_cols=38  Identities=13%  Similarity=0.032  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      ..|-++|+..+-++|..+|.+|.+...+-+|++||+.|
T Consensus        29 ~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi   66 (194)
T PRK09646         29 QDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYL   66 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            47889999999999999999999999999999999864

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=90.94  E-value=0.3  Score=41.74  Aligned_cols=38  Identities=18%  Similarity=0.182  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      ..+-+.|+..+.++|..+|.+|.+...+-+|++||..+
T Consensus        24 ~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl   61 (187)
T PRK12534         24 RHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFT   61 (187)
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            37788899999999999999999998999999999754

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=90.88  E-value=0.21  Score=42.53  Aligned_cols=38  Identities=26%  Similarity=0.297  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      ..|-+.|+..+.++|..+|.+|.+.+.+-+||+||+.+
T Consensus        22 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i   59 (186)
T PRK13919         22 EEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFI   59 (186)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence            37888899999999999999999999999999999864

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=88.85  E-value=0.87  Score=42.06  Aligned_cols=36  Identities=33%  Similarity=0.427  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167          225 DDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM  260 (301)
Q Consensus       225 e~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~  260 (301)
                      ......|.+.+|++|+.+|+|+.+|++.+++..++.
T Consensus       113 ~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~  148 (257)
T PRK05911        113 ADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFS  148 (257)
T ss_pred             HHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHH
Confidence            345567888999999999999999999998876654

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=87.75  E-value=0.87  Score=41.95  Aligned_cols=36  Identities=31%  Similarity=0.452  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHh
Q 022167          224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL  259 (301)
Q Consensus       224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L  259 (301)
                      +...+.+|.+.+|++|+.+|+|+.+|+++++++.++
T Consensus       115 ~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~  150 (256)
T PRK07408        115 AKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIK  150 (256)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHH
Confidence            445678899999999999999999999999887654

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=87.42  E-value=0.69  Score=40.12  Aligned_cols=38  Identities=11%  Similarity=-0.066  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      ..|-+.|++.+.+.|..+|.+|.+..-.-+||+||..+
T Consensus        26 ~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l   63 (194)
T PRK12531         26 KQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMS   63 (194)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            37788899999999999999999888889999999764

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=87.01  E-value=0.54  Score=40.86  Aligned_cols=38  Identities=18%  Similarity=0.174  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      ..|-+.|+..+-.+|..+|.+|.+...+-+|++||+.+
T Consensus        25 ~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l   62 (196)
T PRK12524         25 PAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAML   62 (196)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence            47889999999999999999999999999999999864

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

Probab=86.58  E-value=1.2  Score=40.24  Aligned_cols=37  Identities=27%  Similarity=0.407  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167          224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM  260 (301)
Q Consensus       224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~  260 (301)
                      +.+...++.+.+|++||.+|+|+.+|++.++++.++.
T Consensus        89 ~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~  125 (238)
T TIGR02393        89 LIKAERQLTQELGREPTDEELAERMGMPAEKVREIKK  125 (238)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4456778889999999999999999999988876543

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.

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=86.25  E-value=1.3  Score=40.53  Aligned_cols=35  Identities=20%  Similarity=0.298  Sum_probs=29.2

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167          226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILM  260 (301)
Q Consensus       226 ~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~  260 (301)
                      ....++...+|++|+.+|+|+.+|++.+++..++.
T Consensus       124 ~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~  158 (254)
T TIGR02850       124 QVRDKLISENSKEPTVSEIAKELKVPQEEVVFALD  158 (254)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            35667888999999999999999999888766543

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

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=86.19  E-value=1.3  Score=40.34  Aligned_cols=37  Identities=32%  Similarity=0.578  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167          224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM  260 (301)
Q Consensus       224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~  260 (301)
                      +.....++.+.+|++|+.+|+|+.+|++.+++...+.
T Consensus       103 i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~  139 (231)
T PRK12427        103 TNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLL  139 (231)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3456678889999999999999999999988876653

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=85.85  E-value=1.4  Score=40.94  Aligned_cols=63  Identities=22%  Similarity=0.305  Sum_probs=42.0

Q ss_pred             chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILM  260 (301)
Q Consensus       191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~  260 (301)
                      ..+..|+++....-.+... -.++..+      +.....+|.+.+|++||.+|+|+.+|++.+++..++.
T Consensus       103 g~I~~~lr~~~~~ir~Pr~-~~~~~~~------i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~  165 (264)
T PRK07122        103 GEVRRHFRDNSWSVKVPRR-LKELHLR------LGRATAELSQRLGRAPTASELAAELGMDREEVVEGLV  165 (264)
T ss_pred             HHHHHHHHHcCCccccCHH-HHHHHHH------HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3456677765543223221 2233333      3345678888999999999999999999988876553

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=84.38  E-value=1.7  Score=42.54  Aligned_cols=38  Identities=26%  Similarity=0.393  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167          224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME  261 (301)
Q Consensus       224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e  261 (301)
                      +.....+|.+.+||+||.+|+|..+|++.++++.++..
T Consensus       218 ~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~  255 (367)
T PRK09210        218 LIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKI  255 (367)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHH
Confidence            45567788899999999999999999999888876443

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=83.23  E-value=1.9  Score=41.72  Aligned_cols=36  Identities=31%  Similarity=0.422  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHh
Q 022167          224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSIL  259 (301)
Q Consensus       224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L  259 (301)
                      +...+.+|.+.+|++||.+|+|..+|++.+++...+
T Consensus       175 l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~  210 (324)
T PRK07921        175 LARIKRELHQQLGREATDEELAEESGIPEEKIADLL  210 (324)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence            456677888999999999999999999988876653

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=81.32  E-value=1.3  Score=38.21  Aligned_cols=38  Identities=24%  Similarity=0.339  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          263 SLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       263 ~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      ..|-+.|+..+.+.|..+|.+|.+...+-+|++||+.+
T Consensus        25 ~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~   62 (188)
T PRK09640         25 TRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVML   62 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHH
Confidence            47888999999999999999999999999999999864

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=80.42  E-value=3.1  Score=37.11  Aligned_cols=35  Identities=34%  Similarity=0.455  Sum_probs=29.3

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhh
Q 022167          226 DHKLRLKERLGCEPSMEQLAASLRISRPELQSILM  260 (301)
Q Consensus       226 ~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~  260 (301)
                      .....+...+|++||.+|+|+.+|++.+++...+.
T Consensus       101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~  135 (231)
T TIGR02885       101 YMKEELSKELGREPTINELAEALGVSPEEIVMALE  135 (231)
T ss_pred             HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45567888899999999999999999988776544

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.

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=80.40  E-value=4.1  Score=40.47  Aligned_cols=35  Identities=23%  Similarity=0.433  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHH
Q 022167          224 LDDHKLRLKERLGCEPSMEQLAASLRISRPELQSI  258 (301)
Q Consensus       224 Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~  258 (301)
                      +......|.+.+|++||.+|+|..+|++.++++..
T Consensus       225 i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~  259 (373)
T PRK07406        225 IKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFI  259 (373)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            44566788899999999999999999998887654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	301
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-06
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	1e-07
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	1e-05
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	1e-05
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	5e-05
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	4e-04

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

 Score = 61.0 bits (147), Expect = 2e-10
 Identities = 52/292 (17%), Positives = 87/292 (29%), Gaps = 106/292 (36%)

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

Query: 90  WAEPPNSIEEESSELDYSVEALLLLQKSMLEKQWNLSFERT--VLTDSPSKKTHKKVPVT 147
            +     I    +EL       LL  K          +E    VL +  + K      ++
Sbjct: 220 SSNIKLRIHSIQAELRR-----LLKSK---------PYENCLLVLLNVQNAKAWNAFNLS 265

Query: 148 CSGVSARQRRLNSKKKIL--SQNKSILQQNGSKQLRSMISPELIQNRLKGYVKGVVSEE- 204
           C              KIL  ++ K +                   + L       +S + 
Sbjct: 266 C--------------KILLTTRFKQVT------------------DFLSAATTTHISLDH 293

Query: 205 ---LLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEP---SMEQLAASLR--ISRPE-- 254
               LT  EV  L  K    L      L  +E L   P   S+  +A S+R  ++  +  
Sbjct: 294 HSMTLTPDEVKSLLLKY---LDCRPQDLP-REVLTTNPRRLSI--IAESIRDGLATWDNW 347

Query: 255 -------LQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIF 299
                  L +I +E SL    L  +  R      + +D +          +F
Sbjct: 348 KHVNCDKLTTI-IESSL--NVLEPAEYR------KMFDRL---------SVF 381

>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 = 48.7 bits (115), Expect = 2e-06
 Identities = 51/370 (13%), Positives = 115/370 (31%), Gaps = 118/370 (31%)

Query: 21  FYYSDISEKF--SYINDLGSANSQVGSTKNVVAAKKSSNYNPSFPSSNRQTQPI------ 72
           + Y DI   F  +++++    + Q    K+++        +    S +  +  +      
Sbjct: 16  YQYKDILSVFEDAFVDNFDCKDVQ-DMPKSIL---SKEEIDHIIMSKDAVSGTLRLFWTL 71

Query: 73  ---------KALKEHVDTNFASTAEPWAEPPN--SIEEE--SSELD-----------YSV 108
                    K ++E +  N+     P        S+       + D           Y+V
Sbjct: 72  LSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV 131

Query: 109 ---EALLLLQKSMLE----------------KQWNLSFERTVLTDSPSKKTHKKVPVTCS 149
              +  L L++++LE                K W ++ +  V       K   K+     
Sbjct: 132 SRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTW-VALD--VCLS---YKVQCKMD---F 182

Query: 150 GV---SARQRRLNSKKKILSQNKSILQQ---NGSKQLRSMISPELIQNRLKGYVKGVVSE 203
            +   + +    NS + +L   + +L Q   N + +     + +L  + ++  ++ ++  
Sbjct: 183 KIFWLNLKNC--NSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKS 240

Query: 204 E-----LLT-----HAEVVR--------------------LSKKIKTGLSLDDHKLRLKE 233
           +     LL      +A+                       LS    T +SLD H + L  
Sbjct: 241 KPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTP 300

Query: 234 RLGCEPSMEQLAASLRIS----RPELQSIL-MECSLAREKLVMSNVRLVMSIAQRYDNMG 288
               +     L   L         E+ +      S+  E +     R  ++    + ++ 
Sbjct: 301 ----DEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESI-----RDGLATWDNWKHVN 351

Query: 289 ADMADLVQVI 298
            D   L  +I
Sbjct: 352 CD--KLTTII 359

>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 = 50.6 bits (122), Expect = 1e-07
 Identities = 14/33 (42%), Positives = 23/33 (69%)

Query: 265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQV 297
           AR++++  N+RLV S+ QR+ N G +  DL Q+
Sbjct: 29  ARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQI 61

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

 Score = 45.6 bits (108), Expect = 1e-05
 Identities = 27/131 (20%), Positives = 48/131 (36%), Gaps = 30/131 (22%)

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 NMGADMADLVQ 296
             G    DL+Q
Sbjct: 204 GRGLSFLDLIQ 214

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

 Score = 44.9 bits (106), Expect = 1e-05
 Identities = 29/130 (22%), Positives = 59/130 (45%), Gaps = 5/130 (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 MGADMADLVQ 296
            G    DL+Q
Sbjct: 133 RGLSFLDLIQ 142

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

 Score = 43.4 bits (102), Expect = 5e-05
 Identities = 36/227 (15%), Positives = 64/227 (28%), Gaps = 17/227 (7%)

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

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

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

Query: 250 ISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
                   I  E   AR+ L+ +N+RLV+SIA++Y   G    DL+Q
Sbjct: 184 -ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQ 229

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

 Score = 40.3 bits (94), Expect = 4e-04
 Identities = 15/43 (34%), Positives = 27/43 (62%)

Query: 254 ELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQ 296
            +     +   A++++V +N+RLV+SIA++Y N G    DL+Q
Sbjct: 255 RMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 297

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	301
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	99.74
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	99.7
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	99.66
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	98.11
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	97.52
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	97.15
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	96.55
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	92.12
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	89.29

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

Probab=99.74  E-value=4.1e-18  Score=153.90  Aligned_cols=115  Identities=25%  Similarity=0.341  Sum_probs=93.1

Q ss_pred             chhhcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHH-HHHHH--HHH-----------------------hCCCC
Q 022167          186 PELIQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDD-HKLRL--KER-----------------------LGCEP  239 (301)
Q Consensus       186 pel~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~-~r~eL--ee~-----------------------LGreP  239 (301)
                      |...+|+++.||++|+++||||++||++|+++|+.|..... +....  +..                       .+.+|
T Consensus         2 ~~~~~d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~   81 (245)
T 3ugo_A            2 PHMTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDP   81 (245)
T ss_dssp             ---CCHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCH
T ss_pred             CCCCCCcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccc
Confidence            44567999999999999999999999999999998876332 21100  000                       14688


Q ss_pred             CHHHHHHHhccChH----HHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          240 SMEQLAASLRISRP----ELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       240 t~eEwA~a~g~S~~----eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      +..+||++.+++..    +|.+....+..|+++|+..|+++|.++|++|.+++.+.+||+|||+|
T Consensus        82 ~~~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi  146 (245)
T 3ugo_A           82 KTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQ  146 (245)
T ss_dssp             HHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHH
T ss_pred             hhHHHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHH
Confidence            89999999999764    44556677899999999999999999999999999999999999986

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

Probab=99.70  E-value=1.2e-17  Score=163.18  Aligned_cols=110  Identities=25%  Similarity=0.351  Sum_probs=92.3

Q ss_pred             chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHH------------------HHHHHHhCCCCCHHHHHHH-----
Q 022167          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHK------------------LRLKERLGCEPSMEQLAAS-----  247 (301)
Q Consensus       191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r------------------~eLee~LGrePt~eEwA~a-----  247 (301)
                      |.++.||++|+++|+||++||++|+++|+.|..++...                  .+....+++.|+.++|+..     
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            78999999999999999999999999999986544322                  1222346788888887542     


Q ss_pred             -------hccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          248 -------LRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       248 -------~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                             ++++..+|...+..+..|+++||.+|+|||++||++|.|+|++++||||||+|
T Consensus       174 ~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~I  233 (438)
T 1l9z_H          174 VDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQ  233 (438)
T ss_pred             hhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence                   34566778888888899999999999999999999999999999999999986

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

Probab=99.66  E-value=1.1e-17  Score=161.59  Aligned_cols=111  Identities=27%  Similarity=0.351  Sum_probs=88.4

Q ss_pred             cchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHH------------------HHHHHhCCCCCHHHHH------
Q 022167          190 QNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKL------------------RLKERLGCEPSMEQLA------  245 (301)
Q Consensus       190 ~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~------------------eLee~LGrePt~eEwA------  245 (301)
                      .|+++.||++|++.|+||++||++|+++|+.|..+.....                  +....+++.|+.++|+      
T Consensus        78 ~d~~~~Yl~ei~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  157 (423)
T 2a6h_F           78 SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVE  157 (423)
T ss_dssp             HHHHHHHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTHHHH
T ss_pred             CcHHHHHHHHhcccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhhhhh
Confidence            4889999999999999999999999999998754332111                  0112334566644432      


Q ss_pred             ---H---HhccChHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          246 ---A---SLRISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       246 ---~---a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                         .   +++++..+|...+..+..|+++||.+|+|||++||++|.|+|++++||||||||
T Consensus       158 ~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~i  218 (423)
T 2a6h_F          158 EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQ  218 (423)
T ss_dssp             HHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHH
T ss_pred             hhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence               2   235667778888888999999999999999999999999999999999999986

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

Probab=98.11  E-value=1.1e-06  Score=81.30  Aligned_cols=56  Identities=27%  Similarity=0.381  Sum_probs=43.9

Q ss_pred             HHHhccChHHHHH---HhhhHH----HHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          245 AASLRISRPELQS---ILMECS----LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       245 A~a~g~S~~eLrr---~L~eG~----~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      ...+|++..+...   .+..|.    .|.+.|+..|+++|+++|++|.++|.+++||+|||+|
T Consensus       239 e~~~~l~~~~~~~l~~~~~~gd~~~~~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i  301 (339)
T 1sig_A          239 EEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI  301 (339)
T ss_dssp             HHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHH
T ss_pred             HHHcCCChHHHHHHHHHHHhccccchhhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHH
Confidence            3444555544433   333343    6999999999999999999999999999999999986

>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=97.52  E-value=3.3e-06  Score=84.79  Aligned_cols=36  Identities=42%  Similarity=0.618  Sum_probs=34.6

Q ss_pred             HHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          265 AREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       265 ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      |.+.|+..|+++|+++|++|.++|..++||||||+|
T Consensus       375 A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi  410 (613)
T 3iyd_F          375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI  410 (613)
T ss_dssp             HHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence            499999999999999999999999999999999986

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

Probab=97.15  E-value=6.3e-05  Score=63.06  Aligned_cols=61  Identities=28%  Similarity=0.419  Sum_probs=0.0

Q ss_pred             cCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHHHHHHHHHHHhHHHHHH
Q 022167          200 VVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECSLAREKLVMSNVRLVMS  279 (301)
Q Consensus       200 i~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~~ARekLV~aNLRLVVS  279 (301)
                      |...+.++.+++.+|...++.|..                                        .|.+.|+..|.++|..
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            345566788888888888877665                                        7888999999999999


Q ss_pred             HHhhccCCCCChhhHhhhccC
Q 022167          280 IAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       280 IAKRY~grGLsfeDLIQEGnI  300 (301)
                      +|.+|.+...+.+||+|||.+
T Consensus        44 ~~~~~~~~~~~aeDl~Qe~~l   64 (243)
T 1l0o_C           44 VVQRFLNRGYEADDLFQIGCI   64 (243)
T ss_dssp             ---------------------
T ss_pred             HHHHHhccCCCHHHHHHHHHH
Confidence            999999999999999999976

>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=96.55  E-value=0.00025  Score=71.20  Aligned_cols=35  Identities=23%  Similarity=0.487  Sum_probs=14.6

Q ss_pred             hcchHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCc
Q 022167          189 IQNRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLS  223 (301)
Q Consensus       189 ~~D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~  223 (301)
                      ++||+++||++||.+||||+++|++|+++|..|..
T Consensus        94 ~~dpvrmyl~emg~~~ll~~~~e~~~ak~ie~g~~  128 (613)
T 3iyd_F           94 TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGIN  128 (613)
T ss_dssp             -----------C--------CSSSTTTHHHHHHHH
T ss_pred             CCCcHHHHHHHhcccccCCchhHHHHHHHHHHhHH
Confidence            56999999999999999999999999999998764

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

Probab=89.29  E-value=0.21  Score=37.91  Aligned_cols=36  Identities=19%  Similarity=0.134  Sum_probs=31.9

Q ss_pred             HHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          264 LAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       264 ~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      .|-+.|+..+.+.|..+|.+| +....-+|++||..+
T Consensus        24 ~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl   59 (112)
T 2o7g_A           24 RALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFL   59 (112)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHH
Confidence            677889999999999999999 877889999999753

---

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	301
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	3e-06
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	3e-05
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	0.002

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

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

 Score = 44.4 bits (104), Expect = 3e-06
 Identities = 32/135 (23%), Positives = 57/135 (42%), Gaps = 30/135 (22%)

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 RYDNMGADMADLVQV 297
           +Y   G    DL+Q 
Sbjct: 124 KYTGRGLSFLDLIQE 138

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

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

 Score = 42.6 bits (99), Expect = 3e-05
 Identities = 30/229 (13%), Positives = 77/229 (33%)

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 RISRPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQV 297
           +     +     +   A++++V +N+RLV+SIA++Y N G    DL+Q 
Sbjct: 247 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 295

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

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

 Score = 34.5 bits (79), Expect = 0.002
 Identities = 10/38 (26%), Positives = 18/38 (47%), Gaps = 3/38 (7%)

Query: 264 LAREKLVMSNVRLVMSIAQRYDNM---GADMADLVQVI 298
           + RE+L++  + LV +IA           D+ DL+   
Sbjct: 10  IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYG 47

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	301
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.87
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.26
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.28
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	97.42
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	97.35
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	96.2
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	91.62

>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=99.87  E-value=2.5e-23  Score=175.74  Aligned_cols=110  Identities=25%  Similarity=0.370  Sum_probs=85.0

Q ss_pred             chHHHHHhhcCCCCCCCHHHHHHHHHHHHcCCcHHHHHHHHH------------------HHhCCCCCHHH---------
Q 022167          191 NRLKGYVKGVVSEELLTHAEVVRLSKKIKTGLSLDDHKLRLK------------------ERLGCEPSMEQ---------  243 (301)
Q Consensus       191 D~l~~YLkei~~~~LLT~EEEveLs~kIq~g~~Le~~r~eLe------------------e~LGrePt~eE---------  243 (301)
                      |+++.||++|+++||||+|||++|+++|+.|..+.....+..                  ...++.|...+         
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            899999999999999999999999999998776544332221                  01223333332         


Q ss_pred             HHHHhccC---hHHHHHHhhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          244 LAASLRIS---RPELQSILMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       244 wA~a~g~S---~~eLrr~L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      +.......   ..++.+.+..|..||++||++|+|||++||++|.++|++|+||||||+|
T Consensus        82 ~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl~q~g~~  141 (180)
T d1ku2a2          82 VDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQ  141 (180)
T ss_dssp             HHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHHHHHHHH
T ss_pred             HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHHHHHHHH
Confidence            22222322   3456677888999999999999999999999999999999999999986

>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=99.26  E-value=1.9e-12  Score=115.78  Aligned_cols=57  Identities=28%  Similarity=0.434  Sum_probs=47.6

Q ss_pred             HHHHhccChHHHHHH-------hhhHHHHHHHHHHHhHHHHHHHHhhccCCCCChhhHhhhccC
Q 022167          244 LAASLRISRPELQSI-------LMECSLAREKLVMSNVRLVMSIAQRYDNMGADMADLVQVIFY  300 (301)
Q Consensus       244 wA~a~g~S~~eLrr~-------L~eG~~ARekLV~aNLRLVVSIAKRY~grGLsfeDLIQEGnI  300 (301)
                      +...+|++..+++.+       ..++..||++||++|||||++||+||.++|++|+||||+|||
T Consensus       235 ie~~~gl~~~elk~i~~~i~~ge~~~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~  298 (334)
T d1siga_         235 IEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI  298 (334)
T ss_dssp             HHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHH
T ss_pred             HHHHhhhhHHHHHHHHHHHHHHHhhccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHH
Confidence            344466766655544       445788999999999999999999999999999999999986

>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=98.28  E-value=1.7e-07  Score=71.32  Aligned_cols=37  Identities=27%  Similarity=0.429  Sum_probs=33.8

Q ss_pred             HHHHHHHHHhHHHHHHHHhhccCC---CCChhhHhhhccC
Q 022167          264 LAREKLVMSNVRLVMSIAQRYDNM---GADMADLVQVIFY  300 (301)
Q Consensus       264 ~ARekLV~aNLRLVVSIAKRY~gr---GLsfeDLIQEGnI  300 (301)
                      ..|++||+.|++||.+||++|.++   |++++||+|+|++
T Consensus        10 ~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~i   49 (87)
T d1rp3a3          10 IEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVI   49 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHH
Confidence            468999999999999999999765   8999999999975

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

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

Probab=97.42  E-value=0.00011  Score=51.54  Aligned_cols=41  Identities=20%  Similarity=0.248  Sum_probs=36.1

Q ss_pred             cHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhhHH
Q 022167          223 SLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILMECS  263 (301)
Q Consensus       223 ~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~eG~  263 (301)
                      ++.+...+|.+.+||+||.+|+|+.+|++.+++..+|..++
T Consensus        16 ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~r   56 (57)
T d1l0oc_          16 KIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVR   56 (57)
T ss_dssp             HHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHhc
Confidence            34567889999999999999999999999999998887654

>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=97.35  E-value=0.00017  Score=52.38  Aligned_cols=40  Identities=38%  Similarity=0.467  Sum_probs=35.3

Q ss_pred             CcHHHHHHHHHHHhCCCCCHHHHHHHhccChHHHHHHhhh
Q 022167          222 LSLDDHKLRLKERLGCEPSMEQLAASLRISRPELQSILME  261 (301)
Q Consensus       222 ~~Le~~r~eLee~LGrePt~eEwA~a~g~S~~eLrr~L~e  261 (301)
                      .++++...+|++.+||+||.+|+|..+||+.+++++++..
T Consensus        10 ~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~   49 (77)
T d1rp3a1          10 RRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDK   49 (77)
T ss_dssp             HHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3467788999999999999999999999999999877654

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

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

Probab=96.20  E-value=0.0033  Score=44.38  Aligned_cols=39  Identities=26%  Similarity=0.390  Sum_probs=31.7

Q ss_pred             cHHHHHHHHHHHhCCCCCHHHHHHHhccC--hHHHHHHhhh
Q 022167          223 SLDDHKLRLKERLGCEPSMEQLAASLRIS--RPELQSILME  261 (301)
Q Consensus       223 ~Le~~r~eLee~LGrePt~eEwA~a~g~S--~~eLrr~L~e  261 (301)
                      ++.+...+|.+.+||+||.+|+|+++|++  ++.++.++.-
T Consensus        13 rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~~   53 (60)
T d1ku2a1          13 KLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKI   53 (60)
T ss_dssp             HHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGGG
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHH
Confidence            35568889999999999999999999855  5667776654