Citrus Sinensis ID: 010308

---

Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510---
Protein Sequence
MGVVTISSSPARSPIGLSTISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETPKRHQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYADGVVKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKNEDEKVVTKTRKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV
Secondary Structure (PSIPRED)
ccEEEEcccccccccccccccccccccccHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHcHHHHHHHHHHccHHHHHHHHccccHHHHHHHHHHHHHHcccccHHHHHHHHcccccccccHHHHHHHHHHcccHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHccccccccccHHHHHHcccccHHHHHHHHHHHHHHcccccHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccEEEEEccccccccccccccccccccccEEEEEEccccccEEEEccccccccccccccccccEccccccccccccEEEEEEcccccccccHHHHHHHHHHHHHcccccccccHHHHcccEEcccccEEEEcccccccccccccEEEEccccccccccHHHHHHHccccHHHccccccccccccHHHHHHHHHHHccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHccccHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHcccccEccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccHHHccEEEEEEcccccccccHHHHHHHHcccHHHHHHHHHHHHHHcccccHHHHHHHHcc
Coil and Loop (DISEMBL)
mgvvtisssparspiglstishrstskrpLIVAFKadksnnqalfspqeqiplpietpkrhQKRRENSRKRLERVkgvfsdeaspctldvDYNEAAAKLENIyklspavttsevkyadgvvkRGRQRRKRIgevekksddvsgkpvvrnqvkrpkrlsldkRIELRKNEDEKVVtktrktdskdeHEKIEKLVREYSYstdlvsldwkkmkippvlssteHTWLFKLMQPMKVFVQVKEQLQKdlgreptdvELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFqdfangprfqdLCQAGVKGLITAIDrfepkrrfrlstyGLFWIRHAIIRSMtvssftrvpfglesVRGEIQRAKLELLFElkrvptdeeiiqgvnispeRYREVMKASKpilslhsrhgvtqeefingitdvdgvenenqrQPALLRLALDDVldslkpkesLVIRQRfgldgkgdrtlgeiagnlniSREMVRKHEVKGlmklkhptrvdyLRQHMV
Flexible Loop (DISEMBL)
mgvvtisssparspiglstishrstskRPLIVAFKADKSNNQalfspqeqiplpietpkrhqkrrensrkrlervkgvfsdeaspctlDVDYNEAAAKLENiyklspavttsevkyadgvvkrgrqrrkrigevekksddvsgkpvvrnqvkrpkrlsldkrielrknedekvvtktrktdskdehekieklvreysystdlvsldwkkmkippVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLItaidrfepkrrFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLfelkrvptdeeiiqgvnisperyREVMKASKPILslhsrhgvtqeEFINGITDVDGVENENQRQPALLRLALDDVLdslkpkeslvirqrfgldgkgdrtlgeiagnlnisreMVRKHEvkglmklkhptrvdylrqhmv
Low Complexity Region (SEG)
MGVVTISSSPARSPIGLSTISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETPKRHQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYADgvvkrgrqrrkrIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKNEDEKVVTKTRKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAllrlalddvldslKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV
Disordered region (IsUnstruct)
************************************************************************************PCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYADGV**********************************************************************KLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQL********************AAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV*******PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM****************
Disordered Region (DISOPRED)
*******************************************************************************************YNEAAAKLENIYKLSPAVTTSE**************************************************************************************TDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQV**************VELAEATNMSAAQ*************KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV
Disordered Region (DISEMBL)
************SPIGLSTISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIET*************RLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYADGVVKRGRQRRKRIGE***********PVVRNQVKRPKRLSLDKRIELRKNE*****************EKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV
Disordered Region (DISPRO)
***********RSP**LST*SHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIET***************ERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYADGVVKRGRQRRKRIGEV******VSGKPVVRNQVK********************************************SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR**MV
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MGVVTISSSPARSPIGLSTISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETPKRHQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYADGVVKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKNEDEKVVTKTRKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV
Positional Conservation
no confident homologs detected

---

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	513	2.2.26 [Sep-21-2011]
Q9ZNX9	517	RNA polymerase sigma fact	yes	no	0.986	0.978	0.662	0.0
P26683	390	RNA polymerase sigma fact	yes	no	0.662	0.871	0.331	8e-44
P38023	399	RNA polymerase sigma fact	yes	no	0.610	0.784	0.324	2e-38
P52322	416	RNA polymerase sigma fact	yes	no	0.481	0.593	0.362	1e-36
P74565	425	RNA polymerase sigma fact	N/A	no	0.458	0.552	0.364	3e-36
Q59753	684	RNA polymerase sigma fact	yes	no	0.528	0.396	0.335	6e-35
O22056	572	RNA polymerase sigma fact	no	no	0.530	0.475	0.330	7e-35
Q03065	332	RNA polymerase sigma-B fa	no	no	0.590	0.912	0.322	1e-34
P77951	514	RNA polymerase principal	yes	no	0.497	0.496	0.358	1e-34
P18183	511	RNA polymerase principal	yes	no	0.483	0.485	0.357	1e-34

>sp|Q9ZNX9|SIGE_ARATH RNA polymerase sigma factor sigE, chloroplastic/mitochondrial OS=Arabidopsis thaliana GN=SIGE PE=1 SV=1

 Score =  678 bits (1750), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 347/524 (66%), Positives = 416/524 (79%), Gaps = 18/524 (3%)

Query: 1   MGVVTISSSPARSPIGLST--ISHRSTSKRPLIVAFKADKSNNQALF-SPQEQIPLPIET 57
           MGVV+ISSS ARSP+GL    ++HRS+ K+P IVAFKAD S+N AL   P+EQ+ +P E 
Sbjct: 1   MGVVSISSSAARSPLGLGNDLLTHRSSLKKPSIVAFKADDSSNSALIIPPREQVLIPAE- 59

Query: 58  PKRHQKRRENSRKRLERVK----GVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTT-S 112
            K ++K+RE +R++  +       +  + A  C+L VDYNEAAA+LE+IYKLSPA TT  
Sbjct: 60  -KHNEKKREVTRRKPCKTPKKPLSLEHNSAPSCSLGVDYNEAAARLESIYKLSPATTTLV 118

Query: 113 EVKYADGVVKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKNEDEK 172
           E    DG  K    RR++     +K      K VVRN VK+ KR+SLDKRI L++N  EK
Sbjct: 119 EDDVEDGGSKAKVSRRRK-----RKESGEEKKVVVRNNVKKEKRMSLDKRIALKRNVQEK 173

Query: 173 VVTKT---RKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQ 229
            V  +   + T  + E EKIE+LVR+YS S D+VSLDWKKMKIPPVLSSTEH WLFKLMQ
Sbjct: 174 PVVASVDKKVTKRQQEEEKIERLVRDYSASNDIVSLDWKKMKIPPVLSSTEHAWLFKLMQ 233

Query: 230 PMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLF 289
           PMK  ++VK+ LQK LGREP + E+A   NM+A +VKK +E+GRAARNKLIKHNLRLVLF
Sbjct: 234 PMKALLEVKDVLQKSLGREPREAEIAGEINMTAGEVKKKIEIGRAARNKLIKHNLRLVLF 293

Query: 290 VIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349
           V+ KYF +F NGP+FQDLCQAG++GLITAIDRFEPKR+FRLSTYGLFWIRHAIIRSMT S
Sbjct: 294 VMNKYFHEFTNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRSMTTS 353

Query: 350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSL 409
           +FTRVPFGLESVR EI +AK EL FE+ R PT++E+++ + I+PERYREV++A+KP+LSL
Sbjct: 354 NFTRVPFGLESVRVEIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAKPVLSL 413

Query: 410 HSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGK 469
           +S+H VTQEEFINGITDVDGV   N RQPALLRLALDDVLDSLKPKESLVIRQR+GLDGK
Sbjct: 414 NSKHSVTQEEFINGITDVDGVGANNSRQPALLRLALDDVLDSLKPKESLVIRQRYGLDGK 473

Query: 470 GDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 513
           GDRTLGEIAGNLNISREMVRKHEVK LMKLKH  RVDYLRQ++V
Sbjct: 474 GDRTLGEIAGNLNISREMVRKHEVKALMKLKHQARVDYLRQYIV 517

Essential protein. Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites (e.g. psbA and psbD) and are then released. Essential for blue light-mediated transcription of psbD, which encodes the photosystem II reaction center protein D2. Plays a role in reproduction.
Arabidopsis thaliana (taxid: 3702)

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

 Score =  178 bits (452), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 119/359 (33%), Positives = 196/359 (54%), Gaps = 19/359 (5%)

Query: 159 LDKRIELRKNEDE----KVVTKTRKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPP 214
           +D+ +E + +ED+    K     R+T SK +H           Y+ D + L  +++    
Sbjct: 45  IDEFLEPQTDEDDAKSGKAAKSRRRTQSKKKH-----------YTEDSIRLYLQEIGRIR 93

Query: 215 VLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRA 274
           +L + E   L + +  +    +V+E+L + L R+P D E AEA  +     +  L +GR 
Sbjct: 94  LLRADEEIELARKIADLLELERVRERLSEKLERDPRDSEWAEAVQLPLPAFRYRLHIGRR 153

Query: 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYG 334
           A++K+++ NLRLV+ + KKY      G  FQDL Q G  GLI A ++F+ ++ ++ STY 
Sbjct: 154 AKDKMVQSNLRLVVSIAKKYMN---RGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYA 210

Query: 335 LFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISP 393
            +WIR AI R++   S T R+P  L      I++    L  E+ R PT+EEI   + ++ 
Sbjct: 211 TWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTI 270

Query: 394 ERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLK 453
           E+ R + K+++  +SL +  G  ++  +    + DG   E+Q    LLR  L+ VLDSL 
Sbjct: 271 EKLRFIAKSAQLPISLETPIGKEEDSRLGDFIESDGETPEDQVSKNLLREDLEKVLDSLS 330

Query: 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512
           P+E  V+R R+GLD    +TL EI    N++RE +R+ E K L KL+HP R   L++++
Sbjct: 331 PRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 389

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

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

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

 Score =  160 bits (406), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 103/317 (32%), Positives = 178/317 (56%), Gaps = 4/317 (1%)

Query: 197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAE 256
           +Y+ D + L  +++    +L + E   L + +  +    +++++L + L R P+D E A 
Sbjct: 85  TYTEDSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAA 144

Query: 257 ATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLI 316
           A +    + ++ L  GR A++K+++ NLRLV+ + KKY      G  FQDL Q G  GLI
Sbjct: 145 AVDSPLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMN---RGLSFQDLIQEGSLGLI 201

Query: 317 TAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFE 375
            A ++F+ ++ ++ STY  +WIR AI R++   S T R+P  L      I++    L  E
Sbjct: 202 RAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQE 261

Query: 376 LKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQ 435
           + R PT+EEI   + ++ E+ R + K+++  +SL +  G  ++  +    + DG   E++
Sbjct: 262 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPEDE 321

Query: 436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 495
               LLR  L+ VL +L P+E  V+R R+GLD    +TL EI    N++RE +R+ E K 
Sbjct: 322 VAKNLLREDLEGVLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKA 381

Query: 496 LMKLKHPTRVDYLRQHM 512
           L KL+HP R   L++++
Sbjct: 382 LRKLRHPNRNSILKEYI 398

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

 Score =  154 bits (389), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 91/251 (36%), Positives = 147/251 (58%), Gaps = 4/251 (1%)

Query: 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRF 322
           +  K+ L  GR A+ K+++ NLRLV+ + KKY      G  FQDL Q G  GLI A ++F
Sbjct: 168 SAFKRRLYHGRRAKEKMVQSNLRLVVSIAKKYMN---RGLSFQDLIQEGSLGLIRAAEKF 224

Query: 323 EPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPT 381
           + ++ ++ STY  +WIR AI R++   S T R+P  L      I++    L  E++R PT
Sbjct: 225 DHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKILSQEMRRKPT 284

Query: 382 DEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALL 441
           +EEI   + ++ E+ R + K+++  +SL +  G  ++  +    + DG   E++    LL
Sbjct: 285 EEEIATKMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPEDEVSKNLL 344

Query: 442 RLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501
           R  L++VLD+L P+E  V+R R+GLD    +TL EI    N++RE +R+ E K L KL+H
Sbjct: 345 REDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRH 404

Query: 502 PTRVDYLRQHM 512
           P R   L++++
Sbjct: 405 PNRNSILKEYI 415

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

Microcystis aeruginosa (taxid: 1126)

>sp|P74565|RPOD_SYNY3 RNA polymerase sigma factor RpoD OS=Synechocystis sp. (strain PCC 6803 / Kazusa) GN=rpoD PE=3 SV=1

 Score =  153 bits (387), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 87/239 (36%), Positives = 143/239 (59%), Gaps = 4/239 (1%)

Query: 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYG 334
           A++K+++ NLRLV+ + KKY      G  FQDL Q G  GLI A ++F+ ++ ++ STY 
Sbjct: 189 AKDKMVQSNLRLVVSIAKKYMN---RGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYA 245

Query: 335 LFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISP 393
            +WIR AI R++   S T R+P  L      I++    L  E++R PT+EEI + + ++ 
Sbjct: 246 TWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKLLSQEMRRKPTEEEIAEKMEMTI 305

Query: 394 ERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLK 453
           E+ R + K+++  +SL +  G  ++  +    + DG   E++    LLR  L++VLD+L 
Sbjct: 306 EKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPEDEVSKNLLREDLENVLDTLS 365

Query: 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512
           P+E  V+R R+GLD    +TL EI    N++RE +R+ E K L KL+HP R   L++++
Sbjct: 366 PRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSILKEYI 424

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.

Synechocystis sp. (strain PCC 6803 / Kazusa) (taxid: 1111708)

>sp|Q59753|RPOD_RHIME RNA polymerase sigma factor RpoD OS=Rhizobium meliloti (strain 1021) GN=rpoD PE=3 SV=1

 Score =  149 bits (375), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 99/295 (33%), Positives = 161/295 (54%), Gaps = 24/295 (8%)

Query: 232 KVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEV-------GRAARNKLIKHNL 284
           K F + + Q  +D+ +E  +  LA  T +S A+ ++ + +        R A+ ++++ NL
Sbjct: 398 KEFARAENQTIRDIRQEIQN--LATETGISIAEFRRIVSMVQKGEREARIAKKEMVEANL 455

Query: 285 RLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344
           RLV+ + KKY      G +F DL Q G  GL+ A+D+FE +R ++ STY  +WIR AI R
Sbjct: 456 RLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 512

Query: 345 SMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS 403
           S+   + T R+P  +     +I R   ++L E+ R PT EE+ + + +  E+ R+V+K +
Sbjct: 513 SIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIA 572

Query: 404 KPILSLHSRHGVTQEEFINGITDVDGVENENQRQP------ALLRLALDDVLDSLKPKES 457
           K  +SL +  G  ++  +      D +E++N   P      A LR     VL SL P+E 
Sbjct: 573 KEPISLETPVGDEEDSHLG-----DFIEDKNALLPIDAAIQANLRETTTRVLASLTPREE 627

Query: 458 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512
            V+R RFG+    D TL E+    +++RE +R+ E K L KLKHP+R   LR  +
Sbjct: 628 RVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFL 682

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.

Rhizobium meliloti (strain 1021) (taxid: 266834)

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

 Score =  149 bits (375), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 93/281 (33%), Positives = 154/281 (54%), Gaps = 9/281 (3%)

Query: 239 EQLQKDL----GREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKY 294
           E+LQ +L    GR+PT  + A A  +    +++ +  G   ++K+IK N+RLV+ + K Y
Sbjct: 292 ERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRLVISIAKNY 351

Query: 295 FQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS-FTR 353
                 G   QDL Q G +GL+   ++F+  + F+ STY  +WI+ A+ +S++  S   R
Sbjct: 352 ---QGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKSLSDQSRMIR 408

Query: 354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRH 413
           +PF +      ++ A+ +L  E  + P +EEI +   +S +R   V+ + KP  SL  + 
Sbjct: 409 LPFHMVEATYRVKEARKQLYSETGKHPKNEEIAEATGLSMKRLMAVLLSPKPPRSLDQKI 468

Query: 414 GVTQE-EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 472
           G+ Q  +    I D + V +E+      +R  LD VLDSL  +E  VIR RFG++    +
Sbjct: 469 GMNQNLKPSEVIADPEAVTSEDILIKEFMRQDLDKVLDSLGTREKQVIRWRFGMEDGRMK 528

Query: 473 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 513
           TL EI   + +SRE VR+ E     KLK+  R ++L+Q++V
Sbjct: 529 TLQEIGEMMGVSRERVRQIESSAFRKLKNKKRNNHLQQYLV 569

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  148 bits (373), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 99/307 (32%), Positives = 162/307 (52%), Gaps = 4/307 (1%)

Query: 195 EYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVEL 254
           E+SY+ D VS+   K+   P+LS  +  +  + +Q M V    KE+L + L REPT  E 
Sbjct: 17  EFSYTADAVSIYLHKIGRVPLLSHEQEIFFAQQVQQMMVMFTAKEELAEKLQREPTLQEW 76

Query: 255 AEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKG 314
           A+   +    + + L  G+ A+ K+I+ NLRLV+ + KKY +       F DL Q G  G
Sbjct: 77  ADKMQLKEDVLLQQLSQGQIAKQKMIQANLRLVVSIAKKYQK---RNLEFLDLIQEGALG 133

Query: 315 LITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELL 373
           L   +++F+P   ++ STY  +WIR  I R++   S T R+P  +     +I+  + EL 
Sbjct: 134 LERGVEKFDPTLGYKFSTYAYWWIRQGITRAIAQQSRTIRLPIHMADKLNKIKCVQRELS 193

Query: 374 FELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENE 433
            +L  +    EI Q +N+ P + RE ++  +  +SL  R G  Q+  +  +   DG+  E
Sbjct: 194 QKLGYIAGVTEIAQALNLEPSQIREYLQLVRQPVSLDMRIGFEQDTQLQDLLKDDGMSPE 253

Query: 434 NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV 493
              +  LL   + ++L  L P++  V+  RFGL G  + TL +I+  + ISRE VR+ E 
Sbjct: 254 RYAERELLYQDIHNLLAKLTPQQKEVLILRFGLAGGCELTLVQISQRMGISRERVRQVEK 313

Query: 494 KGLMKLK 500
           + L  L+
Sbjct: 314 QALTLLR 320

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

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

>sp|P77951|HRDB_STRGR RNA polymerase principal sigma factor HrdB OS=Streptomyces griseus GN=hrdB PE=1 SV=1

 Score =  148 bits (373), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 95/265 (35%), Positives = 153/265 (57%), Gaps = 10/265 (3%)

Query: 254 LAEATNMSAAQVKKCLEV----GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQ 309
           LA A  + A ++K+ LE+    GR A+N L++ NLRLV+ + K+Y      G  F DL Q
Sbjct: 253 LANADKL-APKLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYT---GRGMLFLDLIQ 308

Query: 310 AGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRA 368
            G  GLI A+++F+  + ++ STY  +WIR AI R+M   + T R+P  +  V  ++ R 
Sbjct: 309 EGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARV 368

Query: 369 KLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDV 427
           + ++L +L R PT EE+ + ++++PE+  EV K  +  +SLH+  G   + EF + I D 
Sbjct: 369 QRQMLQDLGREPTPEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDS 428

Query: 428 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREM 487
           + V   +     LL+  L  VLD+L  +E+ V+  RFGL     +TL EI     ++RE 
Sbjct: 429 EAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRER 488

Query: 488 VRKHEVKGLMKLKHPTRVDYLRQHM 512
           +R+ E K + KL+HP+R   LR ++
Sbjct: 489 IRQIESKTMSKLRHPSRSQVLRDYL 513

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

Streptomyces griseus (taxid: 1911)

>sp|P18183|HRDB_STRCO RNA polymerase principal sigma factor HrdB OS=Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) GN=hrdB PE=3 SV=2

 Score =  148 bits (373), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 92/257 (35%), Positives = 149/257 (57%), Gaps = 9/257 (3%)

Query: 262 AAQVKKCLEV----GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLIT 317
           A ++K+ LE+    GR A+N L++ NLRLV+ + K+Y      G  F DL Q G  GLI 
Sbjct: 257 APKLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYT---GRGMLFLDLIQEGNLGLIR 313

Query: 318 AIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFEL 376
           A+++F+  + ++ STY  +WIR AI R+M   + T R+P  +  V  ++ R + ++L +L
Sbjct: 314 AVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDL 373

Query: 377 KRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQ 435
            R PT EE+ + ++++PE+  EV K  +  +SLH+  G   + EF + I D + V   + 
Sbjct: 374 GREPTPEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAVVPADA 433

Query: 436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG 495
               LL+  L  VLD+L  +E+ V+  RFGL     +TL EI     ++RE +R+ E K 
Sbjct: 434 VSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKT 493

Query: 496 LMKLKHPTRVDYLRQHM 512
           + KL+HP+R   LR ++
Sbjct: 494 MSKLRHPSRSQVLRDYL 510

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

Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (taxid: 100226)

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	513
224110206	512	predicted protein [Populus trichocarpa]	0.992	0.994	0.730	0.0
255545052	501	RNA polymerase sigma factor rpoD, putati	0.970	0.994	0.707	0.0
224116898	512	predicted protein [Populus trichocarpa]	0.992	0.994	0.709	0.0
356546249	512	PREDICTED: RNA polymerase sigma factor r	0.992	0.994	0.687	0.0
388556562	512	RNA polymerase sigma factor rpoD-like [G	0.992	0.994	0.691	0.0
449518953	515	PREDICTED: RNA polymerase sigma factor s	0.986	0.982	0.681	0.0
449463472	514	PREDICTED: RNA polymerase sigma factor s	0.986	0.984	0.689	0.0
356516017	507	PREDICTED: RNA polymerase sigma factor r	0.982	0.994	0.684	0.0
382365034	507	sigma-like factor 5B [Glycine max]	0.982	0.994	0.682	0.0
356509297	509	PREDICTED: RNA polymerase sigma factor r	0.986	0.994	0.664	0.0

>gi|224110206|ref|XP_002333134.1| predicted protein [Populus trichocarpa] gi|222834948|gb|EEE73397.1| predicted protein [Populus trichocarpa]

 Score =  744 bits (1920), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/516 (73%), Positives = 441/516 (85%), Gaps = 7/516 (1%)

Query: 1   MGVVTISSSPARSPIGLST--ISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETP 58
           MGVV++SSS +R+P+GLST   ++ ST+KRPLIVAFKADKSNN +L +P EQIPLP+ET 
Sbjct: 1   MGVVSVSSSASRTPLGLSTKFSTYGSTAKRPLIVAFKADKSNNTSLVAPHEQIPLPVETT 60

Query: 59  KRHQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYAD 118
           K  +KR   S+K   R+K V + E SPCTL VDYNEAAAKLENIYKLSP   TS+V+ A 
Sbjct: 61  K-GKKRLGKSKKSSNRLKAVRT-EVSPCTLLVDYNEAAAKLENIYKLSPGTDTSDVEDAS 118

Query: 119 GVVKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELR-KNEDEKVVTKT 177
           GV++RGRQR+++I E  K+++D +GK +VRN+ K+ KRLSL+KRI LR KNE++ V +  
Sbjct: 119 GVIRRGRQRKRKISEGGKETEDRTGKIIVRNRAKKAKRLSLEKRISLRIKNEEKLVSSAG 178

Query: 178 RKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQV 237
           ++ D K+E+EKI+ LVREYS STDLVSLDWKKMKIPPVL+S+EH WLFKLMQPMK  +QV
Sbjct: 179 KRKDRKNENEKIDDLVREYSASTDLVSLDWKKMKIPPVLTSSEHVWLFKLMQPMKALLQV 238

Query: 238 KEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQD 297
           KE LQ++LG EPTDVELA+A NM   QV+K + VGRAARNKLIKHNLRLVLFVIKKYFQD
Sbjct: 239 KEHLQENLGGEPTDVELAKAINMDVLQVRKQIAVGRAARNKLIKHNLRLVLFVIKKYFQD 298

Query: 298 FANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFG 357
           FANG +FQD CQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT+SSFTRV FG
Sbjct: 299 FANGTKFQDFCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTLSSFTRVSFG 358

Query: 358 LESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 417
           LES+R EIQ+AKLEL F+LKR P ++EII+ V ISPERY EV +ASKP+LSLHSRH  TQ
Sbjct: 359 LESIRSEIQKAKLELWFQLKRQPMEDEIIEKVRISPERYHEVTRASKPVLSLHSRHKTTQ 418

Query: 418 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEI 477
           EEFI GI DVDG   +++RQ ALLRLALDDVLDSLKPKESLV+RQR+GLDGKGDRTLGEI
Sbjct: 419 EEFIGGIADVDG--GDDRRQSALLRLALDDVLDSLKPKESLVVRQRYGLDGKGDRTLGEI 476

Query: 478 AGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 513
           AGNLNISREMVRKHEVK LMKLKHPTRVDYLR+++V
Sbjct: 477 AGNLNISREMVRKHEVKALMKLKHPTRVDYLRRYVV 512

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255545052|ref|XP_002513587.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis] gi|223547495|gb|EEF48990.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]

 Score =  729 bits (1881), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 365/516 (70%), Positives = 434/516 (84%), Gaps = 18/516 (3%)

Query: 1   MGVVTISSSPARSPIGLST--ISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETP 58
           MGVVT SSS AR+P+GLS    ++RST KR L+VAFK DK+N+  L  P+E+ PLPIET 
Sbjct: 1   MGVVTASSSAARTPLGLSLKFSTYRSTVKRSLVVAFKEDKANDIILVPPRERTPLPIETS 60

Query: 59  KRHQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYAD 118
           K  ++R + +R            E S  TL+VDYNEAAAKLENIYKLSPA  TS+V   +
Sbjct: 61  KGKKRRGKTNR------------EVSSGTLEVDYNEAAAKLENIYKLSPATDTSDVDI-N 107

Query: 119 GVVKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKNEDEKVVTKTR 178
           G++++GRQR+++ GE ++K+++ + + +VRN+ K+ KRLSLDKRI L+KNE+E+VV   R
Sbjct: 108 GLIRKGRQRKRKTGEGDEKAENRTSRTIVRNRAKKTKRLSLDKRIALKKNEEEEVVGPIR 167

Query: 179 KT-DSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQV 237
           K  DSKD++EKIE+LVR YS ST+LVSLDW+KMKIPPVL STEH WLFKLMQPMK  + V
Sbjct: 168 KKKDSKDDNEKIEELVRTYSASTNLVSLDWRKMKIPPVLPSTEHAWLFKLMQPMKTLLPV 227

Query: 238 KEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQD 297
           K  LQK+LGR+PTD ELAEATNM+  +V+K LEVGRAARNKLIKHNLRLV+FV+ KYFQD
Sbjct: 228 KADLQKNLGRDPTDGELAEATNMNVEKVRKQLEVGRAARNKLIKHNLRLVMFVMNKYFQD 287

Query: 298 FANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFG 357
           FANGPRFQDLCQAGVKGLITAIDRFEP+RRF+LSTY LFWIRHAIIRSMT+SSFT+V FG
Sbjct: 288 FANGPRFQDLCQAGVKGLITAIDRFEPQRRFQLSTYSLFWIRHAIIRSMTLSSFTKVSFG 347

Query: 358 LESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 417
           LESVR EIQ+AKLELL EL+R PT+EEII+ V IS ERY EV++A+KP LSLH+RH VTQ
Sbjct: 348 LESVRTEIQKAKLELLIELQRRPTEEEIIERVGISAERYHEVIRAAKPALSLHARHAVTQ 407

Query: 418 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEI 477
           EEFINGITD+DG   +N+RQPALLRLALDDVLDSLKPKESLVIRQR+GLDGKGDRTLGEI
Sbjct: 408 EEFINGITDIDG--GDNRRQPALLRLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEI 465

Query: 478 AGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 513
           AGNLNISREMVRK+EVK LMKLKHP RVDYLR+++V
Sbjct: 466 AGNLNISREMVRKYEVKALMKLKHPARVDYLRRYVV 501

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224116898|ref|XP_002331841.1| predicted protein [Populus trichocarpa] gi|222875079|gb|EEF12210.1| predicted protein [Populus trichocarpa]

 Score =  727 bits (1877), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 366/516 (70%), Positives = 430/516 (83%), Gaps = 7/516 (1%)

Query: 1   MGVVTISSSPARSPIGLST--ISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETP 58
           MG+V++SSS + +P+G ST   + RST+KRPLIVAFKADKSN  AL +P EQIPLPIET 
Sbjct: 1   MGIVSVSSSASWTPLGFSTKFSTCRSTAKRPLIVAFKADKSNETALVAPHEQIPLPIETT 60

Query: 59  KRHQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYAD 118
           K  ++R ++ +   +R+K V + E SPCTL VDYNEAAAKLENIYKLSP   TS+V+  +
Sbjct: 61  KEKKRRGKSKKSS-DRLKAVRT-EVSPCTLGVDYNEAAAKLENIYKLSPGTDTSDVEDVN 118

Query: 119 GVVKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKNEDEKVVTKT- 177
           GV++R RQR+++  E EK+ D  + K +VRNQ K+ KRLSL KRI LR   DEK+VT   
Sbjct: 119 GVIRRCRQRKRKTSECEKEDDGRTSKIIVRNQAKKAKRLSLQKRIALRIKSDEKLVTSVG 178

Query: 178 RKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQV 237
           ++   K+E+EKI++LVREYS STDL SLDWKKMKIPPVL+S EH WLFKLMQPMK  +QV
Sbjct: 179 KRKGRKNENEKIDELVREYSSSTDLASLDWKKMKIPPVLTSAEHAWLFKLMQPMKASLQV 238

Query: 238 KEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQD 297
           KE LQ++ GREPT+ ELAEAT+M   QV+K +EVGRAARNKLIKHNLRLVLFVI KYFQD
Sbjct: 239 KEHLQENSGREPTEGELAEATDMDVLQVRKQIEVGRAARNKLIKHNLRLVLFVINKYFQD 298

Query: 298 FANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFG 357
           +ANGPR+QDLCQAGVKGL+TAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT+SSFTRV FG
Sbjct: 299 YANGPRYQDLCQAGVKGLMTAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTLSSFTRVSFG 358

Query: 358 LESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 417
           LES+R EIQ+AKLEL F+L R PT EEII+ V IS ERY EVM+ASKP+LSLHSRH  TQ
Sbjct: 359 LESIRSEIQKAKLELWFQLLRKPTGEEIIEKVGISIERYHEVMRASKPVLSLHSRHKTTQ 418

Query: 418 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEI 477
           EE I+G+ DV+G   +++RQ ALLRLALDDVLDSLKPKESLV+RQRFGLDGKGDRTLGEI
Sbjct: 419 EELISGVADVNG--GDDRRQSALLRLALDDVLDSLKPKESLVVRQRFGLDGKGDRTLGEI 476

Query: 478 AGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 513
           AGNLNISREMVRKHE K LMKLKHPTRVDYL +++V
Sbjct: 477 AGNLNISREMVRKHEAKALMKLKHPTRVDYLCRYVV 512

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356546249|ref|XP_003541542.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max]

 Score =  716 bits (1849), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 355/516 (68%), Positives = 426/516 (82%), Gaps = 7/516 (1%)

Query: 1   MGVVTISSSPARSPIGLST--ISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETP 58
           MGV+T+S+S AR+P+ L+T  ISH+   KRP+I+AFK +KSN   L SPQE+IPLP+ET 
Sbjct: 1   MGVITVSTSAARTPLRLNTRLISHQQVHKRPIILAFKGNKSNKTTLVSPQEKIPLPLETA 60

Query: 59  KRHQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYAD 118
           K+HQKR   + + L+RV+ V + E SPCTLDVDYNEAAAKLENIYKLSP   T  V+  D
Sbjct: 61  KKHQKRVGKTSESLKRVRAVSTVETSPCTLDVDYNEAAAKLENIYKLSPVSDTCNVEDID 120

Query: 119 GVVKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKNEDEKVVTKT- 177
             ++R  +RRK++ E   + DD +   VVRNQ K+ KRLSLDKRI L+ N  E+V+ +T 
Sbjct: 121 SKIERVLRRRKKVSE---ERDDGNCDNVVRNQNKKAKRLSLDKRIALKNNAKEEVIDQTQ 177

Query: 178 RKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQV 237
           +K + K+  + I+ L+R+YS STDLVS+DWKKMKIPPVL S+EH WLFKLMQPMK  +Q 
Sbjct: 178 KKRNVKNRVQNIDVLIRDYSASTDLVSMDWKKMKIPPVLPSSEHAWLFKLMQPMKALLQA 237

Query: 238 KEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQD 297
           KE L K++ +E T  ELA+ATNMS  QV+K +EVGRAARNKLIKHNLRLVLFVI KYFQD
Sbjct: 238 KEDL-KEVDKEITGGELADATNMSIIQVRKAIEVGRAARNKLIKHNLRLVLFVINKYFQD 296

Query: 298 FANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFG 357
           FA+GPRFQDLCQAGVKGLITAIDRFEPKRR +LSTY LFWIRH+I+RS+T+SSFTRVPFG
Sbjct: 297 FASGPRFQDLCQAGVKGLITAIDRFEPKRRLQLSTYSLFWIRHSIVRSITLSSFTRVPFG 356

Query: 358 LESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 417
           LE VR +IQR KL+L FEL+R PT+EE+++ + IS ERY EVMKASKPILSLHSRH  TQ
Sbjct: 357 LERVRVDIQRTKLKLTFELQRSPTEEELVERIGISLERYHEVMKASKPILSLHSRHITTQ 416

Query: 418 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEI 477
           EE+INGITDVDGV  +N+RQ A+LRLALDDVLDSLKPKESLVIRQR+GLDGKGDRTLGEI
Sbjct: 417 EEYINGITDVDGVNGDNRRQLAVLRLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEI 476

Query: 478 AGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 513
           AGNLNISRE+VRKHEVK LMKLKHP R+DYLR+++V
Sbjct: 477 AGNLNISREIVRKHEVKALMKLKHPARLDYLRRYVV 512

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388556562|ref|NP_001254001.1| RNA polymerase sigma factor rpoD-like [Glycine max] gi|382365028|dbj|BAM05477.1| sigma-like factor 5A [Glycine max]

 Score =  712 bits (1837), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 357/516 (69%), Positives = 421/516 (81%), Gaps = 7/516 (1%)

Query: 1   MGVVTISSSPARSPIGLST--ISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETP 58
           MGVVT+S+  AR+P+ L+T   SH+   KRPLIVAFK +K N  AL SPQEQIPLPIET 
Sbjct: 1   MGVVTVSTLAARTPLRLNTRLTSHQQVHKRPLIVAFKGNKLNKAALVSPQEQIPLPIETA 60

Query: 59  KRHQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYAD 118
           K+ QKR   + + L+RV+ V   E SPCTLD+DYNEAAAKLENIYKLSP   T  ++  D
Sbjct: 61  KKDQKRVGKTSESLKRVRAVSIVETSPCTLDMDYNEAAAKLENIYKLSPVSDTCNMEDID 120

Query: 119 GVVKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKNEDEKVVTKTR 178
             V+R   RR+++G    + DD +   VVRNQ K+ KRLSLDKRI L+ N  E+V+ +T+
Sbjct: 121 SKVERVLWRRRKVGN---EHDDENCDIVVRNQNKKAKRLSLDKRITLKNNAKEEVIDQTQ 177

Query: 179 KT-DSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQV 237
           K  + K+  + I+ L+R+YS STDLVS+DWKKMKIP VL S+EH WLFKLMQPMK  +Q 
Sbjct: 178 KIRNVKNRVQNIDVLIRDYSASTDLVSMDWKKMKIPAVLPSSEHAWLFKLMQPMKALLQA 237

Query: 238 KEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQD 297
           KE LQ  +G+E TD ELA+ATNMS  QV+K +EVGRAARNKLIKHNLRLVLFVI KYFQD
Sbjct: 238 KEDLQ-SVGKEITDGELADATNMSIIQVRKAIEVGRAARNKLIKHNLRLVLFVISKYFQD 296

Query: 298 FANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFG 357
           FA+G RFQDLCQAGVKGLITAIDRFEPKRR +LSTY LFWIRH+I+RS+T+SSFTRVPFG
Sbjct: 297 FASGRRFQDLCQAGVKGLITAIDRFEPKRRLQLSTYSLFWIRHSIVRSITLSSFTRVPFG 356

Query: 358 LESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 417
           LE VR +IQR KL+L FEL+R PT+EE+++ + ISPERY EVMKASKPILSLHSRH  TQ
Sbjct: 357 LERVRVDIQRTKLKLTFELQRSPTEEELVERIGISPERYYEVMKASKPILSLHSRHITTQ 416

Query: 418 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEI 477
           EE+INGITDVDGV  +N+RQ A+LRLALDDVLDSLKPKESLVIRQR+GLDGKGDRTLGEI
Sbjct: 417 EEYINGITDVDGVNGDNRRQLAVLRLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEI 476

Query: 478 AGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 513
           AGNLNISREMVRKHEVK LMKLKHP R+DYLR+++V
Sbjct: 477 AGNLNISREMVRKHEVKALMKLKHPARLDYLRRYVV 512

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449518953|ref|XP_004166500.1| PREDICTED: RNA polymerase sigma factor sigE, chloroplastic/mitochondrial-like [Cucumis sativus]

 Score =  707 bits (1825), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/522 (68%), Positives = 420/522 (80%), Gaps = 16/522 (3%)

Query: 1   MGVVTISSSPARSP--IGLSTISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETP 58
           MGVVT+SS+ AR+P  +G+   +H ST KRP IVAFKADK  N  L SP EQ+ LP+E+ 
Sbjct: 1   MGVVTVSSAAARTPFRLGVKFSNHSSTLKRPSIVAFKADKHTNTTLVSPHEQVTLPVESN 60

Query: 59  KRHQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYAD 118
            R +KR  N+ K L+RVK V  DEA+PC+LD+DYNEAAAKLENI+KLSP    S+ +  D
Sbjct: 61  NRRKKRSGNTSKPLKRVKAVLIDEATPCSLDLDYNEAAAKLENIFKLSPMTEDSDKECKD 120

Query: 119 GVVKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKN-------EDE 171
           G  KRG++R        KKS +  G  +VRNQ KR KRL LDKRI L+         E +
Sbjct: 121 GRSKRGQKR-------SKKSANRPGDGIVRNQTKRIKRLDLDKRIALKNKRKAKRNKEGK 173

Query: 172 KVVTKTRKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPM 231
            V +  ++ ++K+E ++I++LVR+YS STDLVSLDWKKMKIPPVL S+EHT LFKL+QPM
Sbjct: 174 AVPSLRKQKETKNEDDEIDRLVRDYSASTDLVSLDWKKMKIPPVLPSSEHTRLFKLVQPM 233

Query: 232 KVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVI 291
           K  V+V+E+LQK LGREPT+ ELA ATNM+  QV++ LEVGRAARNKLIKHNLRLVLFVI
Sbjct: 234 KALVEVQEELQKGLGREPTEGELANATNMNVIQVRRQLEVGRAARNKLIKHNLRLVLFVI 293

Query: 292 KKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSF 351
            KYF+DFA+GP+FQDLCQAGVKGLITAIDRFEPKR+FRLSTY LFWIRHAIIRSMT+SSF
Sbjct: 294 NKYFEDFASGPKFQDLCQAGVKGLITAIDRFEPKRKFRLSTYALFWIRHAIIRSMTLSSF 353

Query: 352 TRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHS 411
           TRV FGL+SVR EIQRAKLELL EL R+PT+ EI   V IS ERY EVM+A+KP+ SLHS
Sbjct: 354 TRVSFGLDSVRVEIQRAKLELLCELHRLPTEGEITAKVGISQERYLEVMRATKPVYSLHS 413

Query: 412 RHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGD 471
           RH  T EE INGITDV+G   +N+RQPALLRLALDDVLDSLKPKESLVIRQR+GLDGKG+
Sbjct: 414 RHSTTSEELINGITDVEGTGGDNRRQPALLRLALDDVLDSLKPKESLVIRQRYGLDGKGN 473

Query: 472 RTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 513
           RTLGEIAGNLNISREMVRKHEVK LMKLKHP RVDYLR++++
Sbjct: 474 RTLGEIAGNLNISREMVRKHEVKALMKLKHPARVDYLRRYLI 515

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449463472|ref|XP_004149458.1| PREDICTED: RNA polymerase sigma factor sigE, chloroplastic/mitochondrial-like [Cucumis sativus]

 Score =  706 bits (1822), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 359/521 (68%), Positives = 420/521 (80%), Gaps = 15/521 (2%)

Query: 1   MGVVTISSSPARSP--IGLSTISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETP 58
           MGVVT+SS+ AR+P  +G+   +H ST KRP IVAFKADK  N  L SP EQ+ LP+E+ 
Sbjct: 1   MGVVTVSSAAARTPFRLGVKFSNHSSTLKRPSIVAFKADKHTNTTLVSPHEQVTLPVESN 60

Query: 59  KRHQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYAD 118
            R +KR  N+ K L+RVK V  DEA+PC+LD+DYNEAAAKLENI+KLSP    S+ +  D
Sbjct: 61  NRRKKRSGNTSKPLKRVKAVLIDEATPCSLDLDYNEAAAKLENIFKLSPMTEDSDKECKD 120

Query: 119 GVVKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKNEDEKVVTKTR 178
           G  KRG++R        KKS +  G  +VRNQ KR KRL LDKRI L+  ++ K V   R
Sbjct: 121 GRSKRGQKR-------SKKSANRPGDGIVRNQTKRIKRLDLDKRIALKNKKEGKAVALLR 173

Query: 179 KT-DSKDE-----HEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMK 232
           K  D+K+E      ++I++LVR+YS STDLVSLDWKKMKIPPVL S+EHT LFKL+QPMK
Sbjct: 174 KQKDTKNEADEIDDDEIDRLVRDYSASTDLVSLDWKKMKIPPVLPSSEHTRLFKLVQPMK 233

Query: 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIK 292
             V+V+E+LQK LGREPT+ ELA ATNM+  QV++ LEVGRAARNKLIKHNLRLVLFVI 
Sbjct: 234 ALVEVQEELQKGLGREPTEGELANATNMNVIQVRRQLEVGRAARNKLIKHNLRLVLFVIN 293

Query: 293 KYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT 352
           KYF+DFA+GP+FQDLCQAGVKGLITAIDRFEPKR+FRLSTY LFWIRHAIIRSMT+SSFT
Sbjct: 294 KYFEDFASGPKFQDLCQAGVKGLITAIDRFEPKRKFRLSTYALFWIRHAIIRSMTLSSFT 353

Query: 353 RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSR 412
           RV FGL+SVR EIQRAKLELL EL R+PT+ EI   V IS ERY EVM+A+KP+ SLHSR
Sbjct: 354 RVSFGLDSVRVEIQRAKLELLCELHRLPTEGEITAKVGISQERYLEVMRATKPVYSLHSR 413

Query: 413 HGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 472
           H  T EE INGITDV+G   +N+RQPALLRLALDDVLDSLKPKESLVIRQR+GLDGKG+R
Sbjct: 414 HSTTSEELINGITDVEGTGGDNRRQPALLRLALDDVLDSLKPKESLVIRQRYGLDGKGNR 473

Query: 473 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 513
           TLGEIAGNLNISREMVRKHEVK LMKLKHP RVDYLR++++
Sbjct: 474 TLGEIAGNLNISREMVRKHEVKALMKLKHPARVDYLRRYLI 514

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356516017|ref|XP_003526693.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max]

 Score =  700 bits (1806), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 353/516 (68%), Positives = 420/516 (81%), Gaps = 12/516 (2%)

Query: 1   MGVVTISSSPARSPIGLSTISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETPKR 60
           MGVVT+SSS AR+P+GL+T    +  KRPLIVAFK DK N+ AL + QE+IP+P+ET K+
Sbjct: 1   MGVVTVSSSAARTPLGLNTKFCNNRLKRPLIVAFKGDKHNDSALVATQEKIPVPVETAKK 60

Query: 61  HQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYADGV 120
            QK+R     +L +       E+SP ++DVDYNEAAA LEN+YKLSPA   +E    DG 
Sbjct: 61  TQKKRIGKTNKLPK------RESSPSSMDVDYNEAAAMLENLYKLSPASDNAEC--IDGK 112

Query: 121 VKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVK--RPKRLSLDKRIELRKNEDEKVVTKTR 178
           +KR  +R K++ + E +  ++ G  VVRNQ K  +PKRL+LD+RI L+ N+    V  TR
Sbjct: 113 IKRVSRRGKKVVD-ESEEKELKGDWVVRNQNKNKKPKRLNLDQRISLKNNKSGDEVIPTR 171

Query: 179 KT-DSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQV 237
           K  +  ++ EKIE+L+REYS STD VS+DWK+M+IPPVLSS+EH WLFKLMQPMK  +QV
Sbjct: 172 KKRNVGNKIEKIEELIREYSVSTDFVSMDWKRMRIPPVLSSSEHAWLFKLMQPMKALLQV 231

Query: 238 KEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQD 297
           KE LQ++L REP D ELA+ATNMS  QV+K ++VG+AARNKLIKHNLRLVLFVI KYF D
Sbjct: 232 KEDLQQELTREPADGELADATNMSITQVRKAIDVGQAARNKLIKHNLRLVLFVINKYFTD 291

Query: 298 FANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFG 357
           FA+GPRFQDLCQAGVKGLITAIDRFEP RRFRLSTY LFWIRHAIIRSMT+S+FTRVPFG
Sbjct: 292 FASGPRFQDLCQAGVKGLITAIDRFEPNRRFRLSTYSLFWIRHAIIRSMTLSNFTRVPFG 351

Query: 358 LESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 417
           LESVR EIQ+AK EL FEL+R PT+EEII+ V+ISPERY +V+KASK ILSL+SRH  TQ
Sbjct: 352 LESVRAEIQKAKTELTFELQRSPTEEEIIERVHISPERYHDVIKASKSILSLNSRHTTTQ 411

Query: 418 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEI 477
           EEFINGI D DGV  +N++QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEI
Sbjct: 412 EEFINGIVDDDGVNGDNRKQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEI 471

Query: 478 AGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 513
           AGNLNISREMVRKHEVK LMKLKH  R+DYLR+++V
Sbjct: 472 AGNLNISREMVRKHEVKALMKLKHSARLDYLRRYVV 507

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|382365034|dbj|BAM05478.1| sigma-like factor 5B [Glycine max]

 Score =  697 bits (1799), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 352/516 (68%), Positives = 419/516 (81%), Gaps = 12/516 (2%)

Query: 1   MGVVTISSSPARSPIGLSTISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETPKR 60
           MGVVT+SSS AR+P+GL+T    +  KRPLIVAFK DK N+ AL + QE+IP+P+ET K+
Sbjct: 1   MGVVTVSSSAARTPLGLNTKFCNNRLKRPLIVAFKGDKHNDSALVATQEKIPVPVETAKK 60

Query: 61  HQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYADGV 120
            QK+R     +L +       E+SP ++DVDYNEAAA LEN+YKLSPA   +E    DG 
Sbjct: 61  TQKKRIGKTNKLPK------RESSPSSMDVDYNEAAAMLENLYKLSPASDNAEC--IDGK 112

Query: 121 VKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVK--RPKRLSLDKRIELRKNEDEKVVTKTR 178
           +KR  +R K++ + E +  ++ G  VVRNQ K  +PKRL+LD+RI L+ N+    V  TR
Sbjct: 113 IKRVSRRGKKVVD-ESEEKELKGDWVVRNQNKNKKPKRLNLDQRISLKNNKSGDEVIPTR 171

Query: 179 KT-DSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQV 237
           K  +  ++ EKIE+L+REYS STD VS+DWK+M+IPPVLSS+EH WLFKLMQPMK  +QV
Sbjct: 172 KKRNVGNKIEKIEELIREYSVSTDFVSMDWKRMRIPPVLSSSEHAWLFKLMQPMKALLQV 231

Query: 238 KEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQD 297
           KE LQ++L REP D ELA+ATNMS  QV+K ++VG+AARNKLIKHNLRLVLFVI KYF D
Sbjct: 232 KEDLQQELTREPADGELADATNMSITQVRKAIDVGQAARNKLIKHNLRLVLFVINKYFTD 291

Query: 298 FANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFG 357
           FA+GPRFQDLCQAGVKGLITAIDRFEP RRFRLSTY LFWIRHAIIRSMT+S+FTRVPFG
Sbjct: 292 FASGPRFQDLCQAGVKGLITAIDRFEPNRRFRLSTYSLFWIRHAIIRSMTLSNFTRVPFG 351

Query: 358 LESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 417
           LESVR EIQ+AK EL FEL+R PT+EEII+ V+ISPERY +V+KASK ILSL+SRH  TQ
Sbjct: 352 LESVRAEIQKAKTELTFELQRSPTEEEIIERVHISPERYHDVIKASKSILSLNSRHTTTQ 411

Query: 418 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEI 477
           EEFINGI D DGV  +N++QPALLRLALDDVLDSLKPKESLVIR RFGLDGKGDRTLGEI
Sbjct: 412 EEFINGIVDDDGVNGDNRKQPALLRLALDDVLDSLKPKESLVIRXRFGLDGKGDRTLGEI 471

Query: 478 AGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 513
           AGNLNISREMVRKHEVK LMKLKH  R+DYLR+++V
Sbjct: 472 AGNLNISREMVRKHEVKALMKLKHSARLDYLRRYVV 507

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356509297|ref|XP_003523387.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max]

 Score =  688 bits (1776), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 343/516 (66%), Positives = 414/516 (80%), Gaps = 10/516 (1%)

Query: 1   MGVVTISSSPARSPIGLSTISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETPKR 60
           MGVVT+S S +R+P+G +T       KRPLIVAFK DK N+ AL + QE+IP+P+ET K+
Sbjct: 1   MGVVTVSGSASRTPLGFNTKFSTHRLKRPLIVAFKGDKHNDSALVATQEKIPVPVETAKK 60

Query: 61  HQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYADGV 120
            QK+R     +L +       E+SP ++DVDYNEAAA LENIYKLSPA  T   +  D  
Sbjct: 61  TQKKRIGKSNKLPK------RESSPSSMDVDYNEAAAMLENIYKLSPASHTGNAECIDDK 114

Query: 121 VKRGRQRRKRIGEVEKKSDDVSGKPVVR--NQVKRPKRLSLDKRIELRKNE-DEKVVTKT 177
           +KR  +R K++ + E +  ++ G  VVR  N+ K+ KRL+LD+RI L+ N+  ++V+   
Sbjct: 115 IKRVSRRGKKVVD-ESEEKELKGDRVVRRQNKNKKAKRLTLDQRISLKNNKRGDEVIPTR 173

Query: 178 RKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQV 237
           +K + ++  EKIE+L+REYS S D +S+DWK+M+IPPVLSS+EH WLFKLMQPMK  +QV
Sbjct: 174 KKRNFRNRIEKIEELIREYSVSNDFISMDWKRMRIPPVLSSSEHAWLFKLMQPMKALLQV 233

Query: 238 KEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQD 297
           KE LQK+L REP D ELA+ATNMS  QVKK ++VG+AARNKLIKHNLRLVLFVI KYF D
Sbjct: 234 KEDLQKELAREPADGELADATNMSITQVKKAIDVGQAARNKLIKHNLRLVLFVINKYFTD 293

Query: 298 FANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFG 357
           FA+GPRFQDLCQAGVKGLITAIDRFEP RRFRLSTY LFWIRHAIIRSMT+SSF RVPFG
Sbjct: 294 FASGPRFQDLCQAGVKGLITAIDRFEPNRRFRLSTYSLFWIRHAIIRSMTLSSFIRVPFG 353

Query: 358 LESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ 417
           LESVR EIQ+AK EL F+L+R PT+EEII+ V+ISPERY +++KASK ILSL+SRH  TQ
Sbjct: 354 LESVRAEIQKAKTELTFKLQRSPTEEEIIERVHISPERYHDIIKASKSILSLNSRHTTTQ 413

Query: 418 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEI 477
           EEFINGI D DGV  +N++QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEI
Sbjct: 414 EEFINGIVDDDGVNGDNRKQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEI 473

Query: 478 AGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 513
           AGNLNISREMVRKHEVK LMKL H  R+DYLR+++V
Sbjct: 474 AGNLNISREMVRKHEVKALMKLNHSARLDYLRRYVV 509

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	513
TAIR|locus:2167413	517	SIGE "AT5G24120" [Arabidopsis	0.988	0.980	0.640	4.2e-166
UNIPROTKB|Q84JN3	500	SIG5 "Os05g0586600 protein" [O	0.812	0.834	0.542	4.5e-114
TIGR_CMR|SPO_1750	660	SPO_1750 "RNA polymerase sigma	0.514	0.4	0.320	5.6e-35
UNIPROTKB|Q9KUK1	625	VC_0517 "RNA polymerase sigma	0.569	0.467	0.293	2.2e-33
TIGR_CMR|VC_0517	625	VC_0517 "RNA polymerase sigma	0.569	0.467	0.293	2.2e-33
TIGR_CMR|APH_0576	627	APH_0576 "RNA polymerase sigma	0.475	0.389	0.364	3.7e-33
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.682	0.606	0.289	1.8e-32
TIGR_CMR|ECH_0760	622	ECH_0760 "RNA polymerase sigma	0.471	0.389	0.36	7e-32
TIGR_CMR|CBU_1596	698	CBU_1596 "RNA polymerase sigma	0.563	0.414	0.294	2.9e-30
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.764	0.716	0.264	9.7e-30

TAIR|locus:2167413 SIGE "AT5G24120" [Arabidopsis thaliana (taxid:3702)]

 Score = 1616 (573.9 bits), Expect = 4.2e-166, P = 4.2e-166
 Identities = 335/523 (64%), Positives = 399/523 (76%)

Query:     1 MGVVTISSSPARSPIGLST--ISHRSTSKRPLIVAFKADKSNNQALF-SPQEQIPLPIET 57
             MGVV+ISSS ARSP+GL    ++HRS+ K+P IVAFKAD S+N AL   P+EQ+ +P E 
Sbjct:     1 MGVVSISSSAARSPLGLGNDLLTHRSSLKKPSIVAFKADDSSNSALIIPPREQVLIPAE- 59

Query:    58 PKRHQKRRENSRKR-LERVKGVFSDE---ASPCTLDVDYNEAAAKLENIYKLSPAVTTSE 113
              K ++K+RE +R++  +  K   S E   A  C+L VDYNEAAA+LE+IYKLSPA TT  
Sbjct:    60 -KHNEKKREVTRRKPCKTPKKPLSLEHNSAPSCSLGVDYNEAAARLESIYKLSPATTTL- 117

Query:   114 VKYADXXXXXXXXXXXXIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKNEDEK- 172
                 D                 K+S +   K VVRN VK+ KR+SLDKRI L++N  EK 
Sbjct:   118 --VEDDVEDGGSKAKVSRRRKRKESGEEK-KVVVRNNVKKEKRMSLDKRIALKRNVQEKP 174

Query:   173 VVTKTRK--TDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQP 230
             VV    K  T  + E EKIE+LVR+YS S D+VSLDWKKMKIPPVLSSTEH WLFKLMQP
Sbjct:   175 VVASVDKKVTKRQQEEEKIERLVRDYSASNDIVSLDWKKMKIPPVLSSTEHAWLFKLMQP 234

Query:   231 MKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFV 290
             MK  ++VK+ LQK LGREP + E+A   NM+A +VKK +E+GRAARNKLIKHNLRLVLFV
Sbjct:   235 MKALLEVKDVLQKSLGREPREAEIAGEINMTAGEVKKKIEIGRAARNKLIKHNLRLVLFV 294

Query:   291 IKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS 350
             + KYF +F NGP+FQDLCQAG++GLITAIDRFEPKR+FRLSTYGLFWIRHAIIRSMT S+
Sbjct:   295 MNKYFHEFTNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRSMTTSN 354

Query:   351 FTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLH 410
             FTRVPFGLESVR EI +AK EL FE+ R PT++E+++ + I+PERYREV++A+KP+LSL+
Sbjct:   355 FTRVPFGLESVRVEIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAKPVLSLN 414

Query:   411 SRHGVTQEEFINGITDVDGVENENQRQPAXXXXXXXXXXXXXKPKESLVIRQRFGLDGKG 470
             S+H VTQEEFINGITDVDGV   N RQPA             KPKESLVIRQR+GLDGKG
Sbjct:   415 SKHSVTQEEFINGITDVDGVGANNSRQPALLRLALDDVLDSLKPKESLVIRQRYGLDGKG 474

Query:   471 DRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 513
             DRTLGEIAGNLNISREMVRKHEVK LMKLKH  RVDYLRQ++V
Sbjct:   475 DRTLGEIAGNLNISREMVRKHEVKALMKLKHQARVDYLRQYIV 517

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

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

GO:0016987 "sigma factor activity" evidence=ISS

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

GO:0005739 "mitochondrion" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

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

GO:0010207 "photosystem II assembly" evidence=IMP

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

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

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

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

GO:0009658 "chloroplast organization" evidence=IMP

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

GO:0010264 "myo-inositol hexakisphosphate biosynthetic process" evidence=RCA

UNIPROTKB|Q84JN3 SIG5 "Os05g0586600 protein" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 1125 (401.1 bits), Expect = 4.5e-114, P = 4.5e-114
 Identities = 230/424 (54%), Positives = 298/424 (70%)

Query:    91 DYNEAAAKLENIYKLSPAVTTSEVKYADXXXXXXXXXXXXI-GEVEKKSDDVSGKPVVRN 149
             DYNE AA LE+IYKLSPAV   E K AD              G V +  +        R 
Sbjct:    82 DYNEVAAALESIYKLSPAVV--EEKDADEEDEKSKQTKRKRKGRVGRSRNATVTVRSSRR 139

Query:   150 QVKRPKRLSLDKRIELRKNEDEKVVTKTRKTDSKDEHEKIEK-LVREYSYSTDLVSLDWK 208
             + +R +R+ L KR+E+R+ E+E+      K +  DE    E+ L+RE++ STD+ SLDWK
Sbjct:   140 R-RRGQRMDLGKRVEMRRREEEEGGGGAGKVE--DEERGFEEMLLREHAVSTDMGSLDWK 196

Query:   209 KMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268
             +MKIPPVL+S +   LF++MQPMK  +++KE L+ ++  EP D +LAEA NMS  Q+++ 
Sbjct:   197 RMKIPPVLTSAQSIRLFRIMQPMKAIMEMKENLENEVQSEPNDAQLAEAMNMSVLQMRRH 256

Query:   269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRF 328
             LEVGRAARNKLIKHNLRLVL+ I KY+ D +N  RF D+CQAG  GLITAIDRFEPKR F
Sbjct:   257 LEVGRAARNKLIKHNLRLVLYTINKYYPDMSNDERFDDICQAGANGLITAIDRFEPKRGF 316

Query:   329 RLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQG 388
             R+STY LFWIRH+I+R++T+S+FTR PF +ES R EI RA+ EL FEL R PT+EE+++ 
Sbjct:   317 RISTYALFWIRHSIVRAITLSNFTRFPFAMESERQEIHRAREELAFELGRAPTEEEVMKK 376

Query:   389 VNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXXXXXXXXX 448
             V +SP RYR+V++ ++P  SLH+R+ VTQEE IN +TD D +  +               
Sbjct:   377 VGLSPARYRDVVRMTRPTYSLHARNRVTQEELINEVTDDDAIGVDTSSHNTLLRLAIDDL 436

Query:   449 XXXXKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL 508
                 KPKES+VIRQRFGLDG+G RTL EIAGNLNISREMVRK+E+K LMKLKHPTRV+YL
Sbjct:   437 LDSLKPKESVVIRQRFGLDGRGKRTLSEIAGNLNISREMVRKYELKALMKLKHPTRVEYL 496

Query:   509 RQHM 512
             R++M
Sbjct:   497 RRYM 500

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

GO:0009536 "plastid" evidence=IDA

GO:0016987 "sigma factor activity" evidence=IDA

TIGR_CMR|SPO_1750 SPO_1750 "RNA polymerase sigma-70 factor RpoD" [Ruegeria pomeroyi DSS-3 (taxid:246200)]

 Score = 359 (131.4 bits), Expect = 5.6e-35, Sum P(2) = 5.6e-35
 Identities = 91/284 (32%), Positives = 154/284 (54%)

Query:   239 EQLQKDLGR--EPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQ 296
             E+L+ D+ +  +   ++++E   +   QV+K  +  R A+ ++++ NLRLV+ + KKY  
Sbjct:   385 EELRADMAQVGQYVGLDISEFRRI-VQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTN 443

Query:   297 DFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVP 355
                 G +F DL Q G  GL+ A+D+FE +R ++ STY  +WIR AI RS+   + T R+P
Sbjct:   444 ---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP 500

Query:   356 FGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV 415
               +     ++ R   ++L E+ R PT EE+ + + +  E+ R+VMK +K  +SL +  G 
Sbjct:   501 VHMIETINKLVRTGRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPIGD 560

Query:   416 TQE----EFI---NGITDVDGVENENQRQPAXXXXXXXXXXXXXKPKESLVIRQRFGLDG 468
              ++    +FI   N +  +D    EN ++                P+E  V+R RFG+  
Sbjct:   561 EEDSQLGDFIEDKNAVLPLDSAIQENLKETTTRVLASLT------PREERVLRMRFGIGM 614

Query:   469 KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512
               D TL E+    +++RE +R+ E K L KLKHP+R   LR  +
Sbjct:   615 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFL 658

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

GO:0016987 "sigma factor activity" evidence=ISS

UNIPROTKB|Q9KUK1 VC_0517 "RNA polymerase sigma factor" [Vibrio cholerae O1 biovar El Tor str. N16961 (taxid:243277)]

 Score = 369 (135.0 bits), Expect = 2.2e-33, P = 2.2e-33
 Identities = 90/307 (29%), Positives = 166/307 (54%)

Query:   217 SSTEHTWLFKLMQPMKVFV-QVKEQLQKDLGREPTDVELAEA-TNMSAAQVK---KCLEV 271
             + +   WL K++   K +V +V+EQ ++++ R    +++ E  T++S  ++K   + + +
Sbjct:   321 NESNEEWLDKVLASDKPYVAKVREQ-EEEIRRSIQKLQMIEQETSLSVERIKDISRRMSI 379

Query:   272 GRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRR 327
             G A    A+ ++++ NLRLV+ + KKY      G +F DL Q G  GL+ A+D+FE +R 
Sbjct:   380 GEAKARRAKKEMVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRG 436

Query:   328 FRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEII 386
             ++ STY  +WIR AI RS+   + T R+P  +     ++ R   ++L E+ R P  EE+ 
Sbjct:   437 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELA 496

Query:   387 QGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXXXXXXX 446
             + + +  ++ R+V+K +K  +S+ +  G  ++  +    +   +E       A       
Sbjct:   497 ERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAAT 556

Query:   447 XXXXXX-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 505
                     P+E+ V+R RFG+D   D TL E+    +++RE +R+ E K L KL+HP+R 
Sbjct:   557 RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 616

Query:   506 DYLRQHM 512
             + LR  +
Sbjct:   617 EVLRSFL 623

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|VC_0517 VC_0517 "RNA polymerase sigma factor RpoD" [Vibrio cholerae O1 biovar El Tor (taxid:686)]

 Score = 369 (135.0 bits), Expect = 2.2e-33, P = 2.2e-33
 Identities = 90/307 (29%), Positives = 166/307 (54%)

Query:   217 SSTEHTWLFKLMQPMKVFV-QVKEQLQKDLGREPTDVELAEA-TNMSAAQVK---KCLEV 271
             + +   WL K++   K +V +V+EQ ++++ R    +++ E  T++S  ++K   + + +
Sbjct:   321 NESNEEWLDKVLASDKPYVAKVREQ-EEEIRRSIQKLQMIEQETSLSVERIKDISRRMSI 379

Query:   272 GRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRR 327
             G A    A+ ++++ NLRLV+ + KKY      G +F DL Q G  GL+ A+D+FE +R 
Sbjct:   380 GEAKARRAKKEMVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRG 436

Query:   328 FRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEII 386
             ++ STY  +WIR AI RS+   + T R+P  +     ++ R   ++L E+ R P  EE+ 
Sbjct:   437 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELA 496

Query:   387 QGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXXXXXXX 446
             + + +  ++ R+V+K +K  +S+ +  G  ++  +    +   +E       A       
Sbjct:   497 ERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATSLKAAT 556

Query:   447 XXXXXX-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 505
                     P+E+ V+R RFG+D   D TL E+    +++RE +R+ E K L KL+HP+R 
Sbjct:   557 RDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 616

Query:   506 DYLRQHM 512
             + LR  +
Sbjct:   617 EVLRSFL 623

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 367 (134.2 bits), Expect = 3.7e-33, P = 3.7e-33
 Identities = 91/250 (36%), Positives = 135/250 (54%)

Query:   263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRF 322
             A+++K       A+ ++IK NLRLV+ + KKY      G +F DL Q G  GL+ A+D+F
Sbjct:   378 AKIQKHERTANRAKQEMIKANLRLVVSIAKKYSN---RGLQFLDLVQEGNIGLMKAVDKF 434

Query:   323 EPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPT 381
             + KR ++ STY  +W+R AI R++   + T R+P  +     +I R   ++L E+ R PT
Sbjct:   435 DYKRGYKFSTYATWWVRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEIGREPT 494

Query:   382 DEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE-FINGITDVDGVENENQRQPAX 440
              EE+   +NI+ E+ R+VMK  K  +SL S  G      F + I D   V+ EN    A 
Sbjct:   495 LEELSARLNINVEKIRKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPENAAVLAD 554

Query:   441 XXXXXXXXXXXXKPKESLVIRQRFGLDGKG-DRTLGEIAGNLNISREMVRKHEVKGLMKL 499
                          PKE  ++R RFG+   G D TL E+    N++RE +R+ E K L KL
Sbjct:   555 LREITTKVLSTLTPKEERILRMRFGIGKSGKDHTLEEVGRLFNVTRERIRQIEAKALRKL 614

Query:   500 KHPTRVDYLR 509
             +HP+R   LR
Sbjct:   615 RHPSRARKLR 624

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 359 (131.4 bits), Expect = 1.8e-32, P = 1.8e-32
 Identities = 107/370 (28%), Positives = 185/370 (50%)

Query:   157 LSLDKRIEL---RKNEDEKVVTKTRKTDSKDEH-EKIEKLVREYSYSTDLVSLDWKKM-K 211
             LS  +R EL   R+   EK+         KD H  KI + ++E S   D +  +   + K
Sbjct:   207 LSASRRQELLAERQELKEKLAEMVTSLRLKDRHIAKIAQRLKELSAKVDTIMAEIAAIEK 266

Query:   212 IPPVLSST--EHTWLFKLMQPMKVFVQVKEQLQKDL-GREPTDVELAEATNMSAAQVKKC 268
                V + T  E      + + +K+ ++  ++ +K +   E    ++ E +   A ++   
Sbjct:   267 EAGVSADTLKEIAASEAVGKGIKLSLEDAQKHEKKVRSAEKKLKKVEEESGFKARELSDA 326

Query:   269 LEV---GRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDR 321
             L     G A    A+++L++ NLRLV+ + KKY      G +F DL Q G  GL+ A+D+
Sbjct:   327 LRAIDRGEAKSKLAKSELVEANLRLVVSIAKKYTN---RGLQFLDLIQEGNIGLMKAVDK 383

Query:   322 FEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVP 380
             FE +R ++ STY  +WIR AI R++   + T R+P  +     ++ R   +L+ E+ R P
Sbjct:   384 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETINKLIRTSRQLVQEIGREP 443

Query:   381 TDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQ-PA 439
             + EEI + +N+  ++ R+V+K +K  +SL +  G  ++  +    +  GV +  +    A
Sbjct:   444 SPEEIAERMNLPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLEAVIKA 503

Query:   440 XXXXXXXXXXXXXKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 499
                           P+E  V+R RFG+  K D TL E+  +  ++RE +R+ E K L KL
Sbjct:   504 NLSEQTARVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKL 563

Query:   500 KHPTRVDYLR 509
             +HP+R   LR
Sbjct:   564 RHPSRAKKLR 573

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|ECH_0760 ECH_0760 "RNA polymerase sigma factor RpoD" [Ehrlichia chaffeensis str. Arkansas (taxid:205920)]

 Score = 358 (131.1 bits), Expect = 7.0e-32, P = 7.0e-32
 Identities = 90/250 (36%), Positives = 136/250 (54%)

Query:   264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFE 323
             +++K       A+ ++IK NLRLV+ + KKY      G +F DL Q G  GL+ A+D+F+
Sbjct:   374 KIQKHERAANQAKQEMIKANLRLVVSIAKKYSN---RGLQFLDLVQEGNIGLMKAVDKFD 430

Query:   324 PKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTD 382
              KR ++ STY  +W+R AI R++   + T R+P  +     +I R   ++L E+ R PT 
Sbjct:   431 YKRGYKFSTYATWWVRQAITRAIADQARTIRIPVHMIETVNKINRTLRQMLHEMGREPTL 490

Query:   383 EEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE-FINGITDVDGVENENQRQPAXX 441
             EE+   +NI+ ++ R+VMK  K  +SL S  G      F + I D   V+ E+    A  
Sbjct:   491 EELSARLNINVDKIRKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPEDAAVLADL 550

Query:   442 XXXXXXXXXXXKPKESLVIRQRFGLDGKG--DRTLGEIAGNLNISREMVRKHEVKGLMKL 499
                         PKE  ++R RFG+ GKG  D TL E+    N++RE +R+ E K L KL
Sbjct:   551 REITTKVLSTLTPKEERILRMRFGI-GKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKL 609

Query:   500 KHPTRVDYLR 509
             +HP+R   LR
Sbjct:   610 RHPSRARKLR 619

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 346 (126.9 bits), Expect = 2.9e-30, Sum P(2) = 2.9e-30
 Identities = 89/302 (29%), Positives = 158/302 (52%)

Query:   217 SSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDV-ELAEATNMSAAQVKKC---LEVG 272
             + T   WL +     K   +  E+  K++ R   ++ +L E  N++  ++K+    + +G
Sbjct:   392 NETNMKWLEQYKNENKEQAKRLEKYSKEIYRAQRNLAQLEEQNNLNIQEIKEINRRVAIG 451

Query:   273 RA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRF 328
              A    A+ ++I+ NLRLV+ + KKY      G +F DL Q G  GL+ A+D+FE +R +
Sbjct:   452 EAKSRRAKKEMIEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGY 508

Query:   329 RLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQ 387
             + STY  +WIR AI RS+   + T R+P  +     ++ R   ++L E     T EE+ +
Sbjct:   509 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQILQETGIEATPEELGR 568

Query:   388 GVNISPERYREVMKASKPILSLHSRHGVTQEEFING-ITDVDGVENENQRQPAXXXXXXX 446
              +++  E+ R+V+K +K  +S+ +  G  ++  +   I D++     +    A       
Sbjct:   569 RMDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGLMEATR 628

Query:   447 XXXXXXKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506
                    P+E+ V+R RFG+D   D TL E+    +++RE +R+ E K L KL+HP+R +
Sbjct:   629 EILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAE 688

Query:   507 YL 508
              L
Sbjct:   689 KL 690

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 345 (126.5 bits), Expect = 9.7e-30, P = 9.7e-30
 Identities = 107/404 (26%), Positives = 190/404 (47%)

Query:   105 LSPAVTTSEVKYADXXXXXXXXXXXXIGEVEKK-SDDVSGKPVVRNQVKRPKRLSL--DK 161
             L+ A     V  A             + + E   SD++       + +  P++ ++   K
Sbjct:   132 LADAELCDVVALAQKALSASKQAALLVDDTEANPSDNIKDSLSTSSSMSLPEKGNIVRSK 191

Query:   162 RIELRKNEDEKVVTKTRKTDSKD---EHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSS 218
             R +L +    +   K+   D +    +    +K  ++ + + D + L     +   +L++
Sbjct:   192 R-QLERRAKNRRAPKSNDVDDEGYVPQKTSAKKKYKQGADNDDALQLFLWGPETKQLLTA 250

Query:   219 TEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNK 278
              E   L   +Q +    +VK +L+   G EPT  E AEA  +S+  +K  +  GR++R K
Sbjct:   251 KEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRSSREK 310

Query:   279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWI 338
             LI  NLRLV+ + K+Y Q+   G  FQDL Q G  GL+ ++++F+P+   R +TY  +WI
Sbjct:   311 LITANLRLVVHIAKQY-QN--RGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWI 367

Query:   339 RHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYR 397
             R +I +S+  +S T R+P  +  + G++  A+   + E    P+ EE+   V +S E+  
Sbjct:   368 RQSIRKSIFQNSRTIRLPENVYMLLGKVSEARKTCVQEGNYRPSKEELAGHVGVSTEKLD 427

Query:   398 EVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQ-PAXXXXXXXXXXXXXKPKE 456
             +++  ++  LS+       Q+     IT   G+E                       PKE
Sbjct:   428 KLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQLMRNHVRNLLNVLSPKE 487

Query:   457 SLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500
               +I+ RFG+DG   R+L EI     +S+E VR+ E + L +LK
Sbjct:   488 RRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLK 531

GO:0003677 "DNA binding" evidence=ISS

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009507 "chloroplast" evidence=IDA

GO:0009536 "plastid" evidence=IDA

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

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

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

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

GO:0090351 "seedling development" evidence=IMP

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

GO:0005515 "protein binding" evidence=IPI

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

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

GO:0030154 "cell differentiation" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9ZNX9	SIGE_ARATH	No assigned EC number	0.6622	0.9863	0.9787	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.03830006 hypothetical protein (512 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	513
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	3e-56
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	7e-46
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	9e-46
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	9e-45
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	2e-42
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	3e-41
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	1e-37
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	8e-36
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	2e-35
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	8e-35
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	4e-31
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	2e-29
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	8e-25
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	9e-23
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	9e-23
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	7e-22
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	1e-19
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	2e-17
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	3e-17
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	1e-15
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	2e-14
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	7e-14
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	1e-12
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	2e-12
PRK05911	257	PRK05911, PRK05911, RNA polymerase sigma factor si	6e-12
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	3e-11
TIGR02392	270	TIGR02392, rpoH_proteo, alternative sigma factor R	7e-11
pfam04542	71	pfam04542, Sigma70_r2, Sigma-70 region 2	8e-10
PRK06288	268	PRK06288, PRK06288, RNA polymerase sigma factor Wh	1e-09
pfam04545	50	pfam04545, Sigma70_r4, Sigma-70, region 4	2e-09
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	5e-09
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	2e-08
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	5e-08
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	1e-07
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	2e-07
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	8e-07
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	9e-07
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	7e-06
PRK07670	251	PRK07670, PRK07670, RNA polymerase sigma factor Si	1e-05
cd06171	55	cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers	8e-05

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

 Score =  189 bits (483), Expect = 3e-56
 Identities = 111/301 (36%), Positives = 176/301 (58%), Gaps = 4/301 (1%)

Query: 201 DLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNM 260
           DLV L  +++   P+L+  E   L + +Q M V  +++E+L++ LGREP+  E A A  +
Sbjct: 1   DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGL 60

Query: 261 SAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAID 320
           S A++++ L  G+ A+ K+IK NLRLV+ V KKY      G    DL Q G  GL  A++
Sbjct: 61  SEAELRQRLRQGQRAKEKMIKANLRLVVSVAKKYQN---RGLELLDLIQEGSLGLERAVE 117

Query: 321 RFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRV 379
           +F+P R ++ STY  +WIR  I R++   S T R+P  +     +I++ + EL  +L R 
Sbjct: 118 KFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRT 177

Query: 380 PTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA 439
           P++ EI + + + PE+ RE+++ ++  +SL +  G  ++  +  + + DG   E Q +  
Sbjct: 178 PSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGESPEEQVERE 237

Query: 440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 499
            LR  L+ +L  L P+E  V+R RFGLDG    TL EI   LN+SRE VR+ E K L KL
Sbjct: 238 SLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKL 297

Query: 500 K 500
           +
Sbjct: 298 R 298

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

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

 Score =  164 bits (416), Expect = 7e-46
 Identities = 101/278 (36%), Positives = 163/278 (58%), Gaps = 4/278 (1%)

Query: 236 QVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYF 295
           +++EQ + +LGREP+D E AE  +M   + ++ L +GR A+ K+++ NLRLV+ + KKY 
Sbjct: 98  ELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYM 157

Query: 296 QDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RV 354
                G  FQDL Q G  GLI A ++F+ ++ ++ STY  +WIR AI R++   S T R+
Sbjct: 158 N---RGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRL 214

Query: 355 PFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHG 414
           P  L      I++    L  E  R PT+EEI + + ++ E+ R + K+++  +SL +  G
Sbjct: 215 PVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIG 274

Query: 415 VTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTL 474
             ++  +    + DG   E+     LLR  L+ VL +L P+E  V+R R+GLD    +TL
Sbjct: 275 KEEDSRLGDFIEADGETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTL 334

Query: 475 GEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512
            EI    N++RE +R+ E K L KL+HP R   L++++
Sbjct: 335 EEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372

Length = 373

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

 Score =  159 bits (405), Expect = 9e-46
 Identities = 81/237 (34%), Positives = 136/237 (57%), Gaps = 5/237 (2%)

Query: 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYG 334
           A+ +L++ NLRLV+ + KKY      G  F DL Q G  GL+ A+++F+ ++ ++ STY 
Sbjct: 1   AKKQLVESNLRLVVSIAKKYTN---RGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYA 57

Query: 335 LFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISP 393
            +WIR AI R++   + T R+P  +     ++ +A+ +L  EL R PTDEE+ + + +  
Sbjct: 58  TWWIRQAITRAIADQARTIRIPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPA 117

Query: 394 ERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQRQPALLRLALDDVLDSL 452
           E+ RE+ K ++  +SL +  G  ++    + I D      ++     LLR  LD+VL++L
Sbjct: 118 EKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDYAAKELLREQLDEVLETL 177

Query: 453 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 509
             +E  V+R R+GL      TL E+    N++RE +R+ E K L KL+HP+R   L+
Sbjct: 178 TEREEKVLRMRYGLLDGQPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLK 234

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|180321 PRK05949, PRK05949, RNA polymerase sigma factor; Validated

 Score =  160 bits (405), Expect = 9e-45
 Identities = 99/314 (31%), Positives = 172/314 (54%), Gaps = 4/314 (1%)

Query: 188 KIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGR 247
                 ++ ++S D+V     ++   P+L+  +     K +Q M   ++ KE L K LGR
Sbjct: 5   NTNTKTKQPTFSADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGR 64

Query: 248 EPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDL 307
           EP+  E AEA N+S  ++K+ L+ G+ A+ K+I+ NLRLV+ + KKY +       F DL
Sbjct: 65  EPSLPEWAEAVNLSETELKQTLKQGKRAKQKMIEANLRLVVAIAKKYQK---RNMEFLDL 121

Query: 308 CQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQ 366
            Q G  GL   +++F+P R ++ STY  +WIR AI R++   + T R+P  +     +I+
Sbjct: 122 IQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIK 181

Query: 367 RAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD 426
           + + EL  +L R  T  EI + + + P + RE +  ++  +SL  R G  Q+  ++ + +
Sbjct: 182 KTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLE 241

Query: 427 VDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISRE 486
            +G   +      LLR  L+++L  L P++  V+  RFGL+   + +L ++   LN+SRE
Sbjct: 242 DEGPSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRE 301

Query: 487 MVRKHEVKGLMKLK 500
            VR+ E + L  L+
Sbjct: 302 RVRQLEHQALAHLR 315

Length = 327

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

 Score =  153 bits (388), Expect = 2e-42
 Identities = 101/303 (33%), Positives = 174/303 (57%), Gaps = 4/303 (1%)

Query: 199 STDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEAT 258
           STDLV    +++   P+L+  E     K +Q +    +++E+L ++LGREPTD E A+A 
Sbjct: 6   STDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAA 65

Query: 259 NMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITA 318
            +S  +++  +  G AA+ K+++ NLRLV+ V KKY +   +     DL Q G  G+   
Sbjct: 66  KLSEEELRSAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVD---LLDLIQEGTIGMQRG 122

Query: 319 IDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELK 377
           +++F+P + +R STY  +WIR AI R++   S T R+P  +     +I++A+ +L  +L 
Sbjct: 123 VEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLG 182

Query: 378 RVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQ 437
           R  T  E+ + + ++P++ RE ++ ++  LSL  R G  Q+  +  + +  G   E+   
Sbjct: 183 RAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASPEDFAT 242

Query: 438 PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 497
            + L+L L+ +++ L P++  VI  RFGL+     TL +I   LNISRE VR+ E + L 
Sbjct: 243 QSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALS 302

Query: 498 KLK 500
           KL+
Sbjct: 303 KLR 305

Length = 317

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

 Score =  150 bits (382), Expect = 3e-41
 Identities = 113/337 (33%), Positives = 172/337 (51%), Gaps = 27/337 (8%)

Query: 198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQL-QKDLGREPTDVELAE 256
            S D V     ++   P+L       L K ++  ++ V++ E L    LGREP++     
Sbjct: 6   LSADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRP 65

Query: 257 ATNMSA-------------------AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQD 297
           A  +S                    A+  K  E    A+ KL++ NLRLV+ + KKY   
Sbjct: 66  AGRLSFYIRAIEAAPLLTPEEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGR 125

Query: 298 FANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPF 356
              G  F DL Q G  GL+ A+++F+P++ F+ STY  +WIR AI R++   + T R+P 
Sbjct: 126 ---GLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPV 182

Query: 357 GLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVT 416
               +  +++R K ELL EL R PT EEI + + +SP++ RE++K +   +SL +  G  
Sbjct: 183 HQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGDD 242

Query: 417 QE-EFINGITDVDGVENENQRQPALLRLALDDVLDS-LKPKESLVIRQRFGLDGKGDRTL 474
           ++ E  + + D   V  E+  +   L+  L++VL   L  +E  VIR RFGLD    +TL
Sbjct: 243 EDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTL 302

Query: 475 GEIAGNLNISREMVRKHEVKGLMKLK-HPTRVDYLRQ 510
            E+     ISRE VR+ E K L KL+ HP R   LR 
Sbjct: 303 EELGEEFGISRERVRQIEAKALRKLRRHPERSALLRS 339

Length = 342

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

 Score =  143 bits (361), Expect = 1e-37
 Identities = 93/306 (30%), Positives = 154/306 (50%), Gaps = 26/306 (8%)

Query: 230 PMKVFVQVKEQLQKDLGREPTDVELA----------------------EATNMSAAQVKK 267
           P    ++V+E+L  +LG  P+    A                      E   ++  ++++
Sbjct: 109 PYLRLIEVRERLTSELGHRPSLERWAKTADISLADLKPTLAEGKRRWAEIAKLTVEELEQ 168

Query: 268 CLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRR 327
             + G  A+  +IK NLRLV+ V KKY Q+   G    DL Q G  GL  A+++F+P + 
Sbjct: 169 IQKQGLRAKEHMIKANLRLVVSVAKKY-QN--RGLELLDLVQEGTLGLERAVEKFDPTKG 225

Query: 328 FRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEII 386
           +R STY  +WIR  I R++   S T R+P  +     +I++A+ ++  E  R PT E+I 
Sbjct: 226 YRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIA 285

Query: 387 QGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALD 446
           Q + ++P + REV+      +SL ++ G  ++  +  + + D +  E       L+  L 
Sbjct: 286 QELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLETDDISPEEMLMRESLQRDLQ 345

Query: 447 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506
            +L  L  +E  VIR RFGL      +L EI   L++SRE VR+ E K L KL+ P R +
Sbjct: 346 HLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRN 405

Query: 507 YLRQHM 512
            +R ++
Sbjct: 406 RIRDYL 411

Length = 415

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

 Score =  136 bits (345), Expect = 8e-36
 Identities = 87/245 (35%), Positives = 142/245 (57%), Gaps = 15/245 (6%)

Query: 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYG 334
           A+ +L + NLRLV+ + K+Y      G  F DL Q G  GL+ A+++F+ ++ F+ STY 
Sbjct: 130 AKQRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYA 186

Query: 335 LFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISP 393
            +WIR AI R++   + T R+P  +     ++ R + +LL EL R PT EEI + +++ P
Sbjct: 187 TWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPP 246

Query: 394 ERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA------LLRLALDD 447
           E+ RE++K ++  +SL +  G   +  +      D +E+++   PA      LL+  L+D
Sbjct: 247 EKVREILKIAQEPVSLETPIGEEDDSHLG-----DFIEDQDATSPADHAAYELLKEQLED 301

Query: 448 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 507
           VLD+L  +E  V+R RFGLD    RTL E+     ++RE +R+ E K L KL+HP+R   
Sbjct: 302 VLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQ 361

Query: 508 LRQHM 512
           L+  +
Sbjct: 362 LKDFL 366

Length = 367

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

 Score =  134 bits (339), Expect = 2e-35
 Identities = 96/263 (36%), Positives = 136/263 (51%), Gaps = 12/263 (4%)

Query: 254 LAEATNMSAAQVKKCLEV----GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQ 309
           L     +S A+ K+ L      G AAR  L++ NLRLV+ + K+Y      G    DL Q
Sbjct: 63  LETRKRLSEAR-KRDLAAVVRDGEAARRHLLEANLRLVVSLAKRYT---GRGMPLLDLIQ 118

Query: 310 AGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRA 368
            G  GLI A+++F+  + F+ STY  +WIR AI R M   S T R+P  L     ++ R 
Sbjct: 119 EGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARI 178

Query: 369 KLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING--ITD 426
           K EL  +L R  TDEE+ +   I  E+  ++++ S+  +SL    G + EE   G  I D
Sbjct: 179 KRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVG-SDEEAPLGDFIED 237

Query: 427 VDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISRE 486
            +    EN     LL   +  VL +L  +E  VIR RFGLD    RTL +I     +SRE
Sbjct: 238 SEATSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRE 297

Query: 487 MVRKHEVKGLMKLKHPTRVDYLR 509
            VR+ E + + KL++  R D LR
Sbjct: 298 RVRQIEREVMSKLRNGERADRLR 320

Length = 324

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

 Score =  136 bits (345), Expect = 8e-35
 Identities = 100/278 (35%), Positives = 149/278 (53%), Gaps = 42/278 (15%)

Query: 254 LAEATNMSAAQVKKCLE----VGRAARNKLIKHNLRLVLFVIKKYFQDFAN-GPRFQDLC 308
           LAE   +     ++ L+     G+ A+N L++ NLRLV+ + K+Y     N G  F DL 
Sbjct: 248 LAEGEKLDPEL-RRDLQWIGRDGKRAKNHLLEANLRLVVSLAKRY----TNRGLSFLDLI 302

Query: 309 QAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM-----TVSSFTRVPFGLESVRG 363
           Q G  GLI A+++F+  + ++ STY  +WIR AI R+M     T+    R+P  +     
Sbjct: 303 QEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTI----RIPVHMVETIN 358

Query: 364 EIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMK-ASKPILSLHSRHGVTQEE--- 419
           ++ R + ELL EL R PT EE+ + +  +PE+ RE+ K   +PI SL    G  +E    
Sbjct: 359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPI-SLDKTIG--KEGDSQ 415

Query: 420 ---FI---NGITDVDGVE-NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGL-DGKGD 471
              FI     ++ VD V     Q Q       L +VL++L  +E+ VIR RFGL DG+  
Sbjct: 416 FGDFIEDSEAVSPVDAVSFTLLQDQ-------LQEVLETLSEREAGVIRMRFGLTDGQ-P 467

Query: 472 RTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 509
           +TL EI     ++RE +R+ E K L KL+HP+R   LR
Sbjct: 468 KTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLR 505

Length = 509

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

 Score =  126 bits (320), Expect = 4e-31
 Identities = 96/258 (37%), Positives = 144/258 (55%), Gaps = 43/258 (16%)

Query: 273 RAARNKLIKHNLRLVLFVIKKYFQDFAN-GPRFQDLCQAGVKGLITAIDRFEPKRRFRLS 331
           R A+ ++++ NLRLV+ + KKY     N G +F DL Q G  GL+ A+D+FE +R ++ S
Sbjct: 379 RRAKKEMVEANLRLVISIAKKY----TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 434

Query: 332 TYGLFWIRHAIIRSM-----TVSSFTRVPFGL-ES----VRGEIQRAKLELLFELKRVPT 381
           TY  +WIR AI RS+     T+    R+P  + E+     R  I R   ++L E+ R PT
Sbjct: 435 TYATWWIRQAITRSIADQARTI----RIPVHMIETINKLNR--ISR---QMLQEIGREPT 485

Query: 382 DEEIIQGVNISPERYREVMKASK-PILSLHSRHGVTQEE------FI---NGITDVDGVE 431
            EE+ + + +  ++ R+V+K +K PI SL +  G   +E      FI   N    +D   
Sbjct: 486 PEELAERLGMPEDKVRKVLKIAKEPI-SLETPIG--DDEDSHLGDFIEDKNAELPIDAAI 542

Query: 432 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH 491
            E+      LR A  DVL SL P+E+ V+R RFG+D   D TL E+    +++RE +R+ 
Sbjct: 543 QES------LREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 596

Query: 492 EVKGLMKLKHPTRVDYLR 509
           E K L KL+HP+R   LR
Sbjct: 597 EAKALRKLRHPSRSRKLR 614

Length = 619

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

 Score =  116 bits (293), Expect = 2e-29
 Identities = 72/230 (31%), Positives = 120/230 (52%), Gaps = 5/230 (2%)

Query: 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTY 333
            AR  +I+ NLRLV+ + K Y      G    DL + G  GL+ A+++F+P+R FR STY
Sbjct: 46  EARKVMIESNLRLVVSIAKHYVN---RGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTY 102

Query: 334 GLFWIRHAIIRS-MTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNIS 392
             +WIR  I R+ M  +   R+P  +        RA  +L  +L R P+ EEI + ++  
Sbjct: 103 ATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKP 162

Query: 393 PERYREVMKASKPILSLHSRHGV-TQEEFINGITDVDGVENENQRQPALLRLALDDVLDS 451
            E    V+  ++ I SL +     + +  ++ I D   ++ E+  Q   L+  ++  L  
Sbjct: 163 VEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAE 222

Query: 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501
           L  ++  V+ +RFGL G    TL E+A  + ++RE VR+ +V+ L KL+ 
Sbjct: 223 LNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRR 272

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

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

 Score =  102 bits (257), Expect = 8e-25
 Identities = 76/256 (29%), Positives = 117/256 (45%), Gaps = 23/256 (8%)

Query: 255 AEATNMSAAQVKKCLEV---GRAARNKLIKHNLRLVLFVIKKYFQDFANG--PRFQDLCQ 309
                +S  + +K LE    G     +LI+  L LV  + +K    F N     + DL Q
Sbjct: 1   NAPQPLSKEEEEKLLEYYAEGDEEARRLIERYLPLVKSIARK----FENRGPSEYDDLIQ 56

Query: 310 AGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAK 369
            G+ GLI AI+R++P +  + STY +  IR  I+  +  +   +VP  L  +   I+ A 
Sbjct: 57  IGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKNDSVKVPRSLRELGRRIEEAI 116

Query: 370 LELLFELKRVPTDEEIIQGVNISPERYREVMKA---SKPILSLHSRHGVTQEEFINGITD 426
            EL  EL R PTDEEI + + I  E Y E + A   S+ +           ++  + I +
Sbjct: 117 DELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDDVDDQIEN 176

Query: 427 V-DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISR 485
             DGVE E   +       L + ++ L  +E LV+  R+    K + T  EIA  L IS 
Sbjct: 177 PDDGVEKEELLE------ILKEAIEPLPEREKLVLVLRY----KEELTQKEIAEVLGISE 226

Query: 486 EMVRKHEVKGLMKLKH 501
             V +   K + KL+ 
Sbjct: 227 SRVSRLHKKAIKKLRK 242

Length = 247

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

 Score = 98.9 bits (247), Expect = 9e-23
 Identities = 70/229 (30%), Positives = 121/229 (52%), Gaps = 5/229 (2%)

Query: 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTY 333
           AAR ++I+ NLRLV+ + K+Y      G    DL + G  GLI A+++F+P+R FR STY
Sbjct: 86  AARQRMIESNLRLVVKIAKRYLN---RGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTY 142

Query: 334 GLFWIRHAIIRS-MTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNIS 392
             +WIR  I R+ M  +   R+P  +        RA  EL  +L   P+ EEI + ++  
Sbjct: 143 ATWWIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKP 202

Query: 393 PERYREVMKASKPILSLHSRHGV-TQEEFINGITDVDGVENENQRQPALLRLALDDVLDS 451
            +    ++  ++ I SL +  G   ++  ++ + D      E+  Q   ++ ++   L  
Sbjct: 203 VDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFE 262

Query: 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500
           L  K+  V+ +RFGL G    TL ++A  + ++RE VR+ +V+ L +L+
Sbjct: 263 LNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311

Length = 325

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

 Score = 96.5 bits (241), Expect = 9e-23
 Identities = 71/235 (30%), Positives = 113/235 (48%), Gaps = 20/235 (8%)

Query: 273 RAARNKLIKHNLRLVLFVIKKYFQDFAN-GPRFQDLCQAGVKGLITAIDRFEPKRRFRLS 331
           + AR KL++ NL LV  + ++    F N G   +DL Q G  GL+ AIDRF+P    + S
Sbjct: 2   KEAREKLVELNLPLVRSIARR----FRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFS 57

Query: 332 TYGLFWI-----RHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEII 386
           T+ +  I     R    R  T +   RVP  L+ +  +I +A  EL   L R PT  EI 
Sbjct: 58  TFAVPTIMGEIKRF--FRDDTWA--VRVPRRLKELGVKINKATEELTQRLGRSPTIAEIA 113

Query: 387 QGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV-ENENQRQPALLRLAL 445
           + + +S E   E ++A        S     +++  + I  +D + + ++  +    RLAL
Sbjct: 114 ERLGVSEEEVVEALEAGNA-YQALSLDASIEDDDGDPIALLDTLGDEDDALETVEDRLAL 172

Query: 446 DDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500
             +L +L  +E  ++  RF      D+T  EIA  L IS+  V +   + L KL+
Sbjct: 173 KPLLAALPERERRILLLRF----FEDKTQSEIAERLGISQMHVSRLLRRALKKLR 223

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|131931 TIGR02885, spore_sigF, RNA polymerase sigma-F factor

 Score = 94.0 bits (234), Expect = 7e-22
 Identities = 70/238 (29%), Positives = 118/238 (49%), Gaps = 13/238 (5%)

Query: 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFAN-GPRFQDLCQAGVKGLITAIDRFE 323
           +K      + AR+KLI+ NLRLV  ++K+    F N G   +DL Q G  GL+ AID+F+
Sbjct: 2   IKLAQNGDKEARDKLIECNLRLVWSIVKR----FLNRGYEPEDLFQIGCIGLVKAIDKFD 57

Query: 324 PKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDE 383
                + STY +  I   I R +      +V   L+ +  +I+  K EL  EL R PT  
Sbjct: 58  LSYDVKFSTYAVPMIMGEIKRFLRDDGIIKVSRSLKELARKIRYMKEELSKELGREPTIN 117

Query: 384 EIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALL-R 442
           E+ + + +SPE     +++++   SL+       ++  + I  +D + ++       L +
Sbjct: 118 ELAEALGVSPEEIVMALESARSPQSLYD---TVHQDDGDPIYLLDQIADKGSEDSDWLEK 174

Query: 443 LALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500
           +AL + +  L  +E  +I  R+      D+T  E+A  L IS+  V + E K L K+K
Sbjct: 175 IALKEAISKLDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKMK 228

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

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

 Score = 87.7 bits (218), Expect = 1e-19
 Identities = 65/254 (25%), Positives = 101/254 (39%), Gaps = 71/254 (27%)

Query: 260 MSAAQVKKCLEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGL 315
           +S  + +K LE+ +     ARN LI+ NLRLV  ++KK+  +   G    DL   G  GL
Sbjct: 31  LSEEEERKYLELMKEGDEEARNILIERNLRLVAHIVKKF--EN-TGEDVDDLISIGTIGL 87

Query: 316 ITAIDRFEPKRRFRLSTYGLFWIRHAI---IRSMTVSSFTRVPFGLESVRGEIQRAKLEL 372
           I AI+ F+  +  +L+TY    I + I   +R+            L+  + E+       
Sbjct: 88  IKAIESFDAGKGTKLATYAARCIENEILMHLRN------------LKKTKKEV------- 128

Query: 373 LFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN 432
                                              SL    GV +E   N I+ +D + +
Sbjct: 129 -----------------------------------SLQDPIGVDKEG--NEISLIDILGS 151

Query: 433 ENQRQPALLRLALD-----DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREM 487
           E       + L ++       +D L  +E  VI  R+GL    ++T  EIA  L ISR  
Sbjct: 152 EEDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSY 211

Query: 488 VRKHEVKGLMKLKH 501
           V + E + L KL  
Sbjct: 212 VSRIEKRALKKLFK 225

Length = 233

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

 Score = 81.3 bits (201), Expect = 2e-17
 Identities = 67/232 (28%), Positives = 95/232 (40%), Gaps = 61/232 (26%)

Query: 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYG 334
           ARN LI+ NLRLV  ++KK+      G    DL   G  GLI AID F+P +  RL+TY 
Sbjct: 49  ARNVLIERNLRLVAHIVKKF---SNTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYA 105

Query: 335 LFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPE 394
              I + I+  M + +       L+  +GE+                             
Sbjct: 106 ARCIENEIL--MHLRA-------LKKTKGEV----------------------------- 127

Query: 395 RYREVMKASKPILSLHSRHGVTQEEFINGIT--DVDGVENENQRQPALLRLALDDV---L 449
                        SL    GV +E   N I+  D+ G + ++  +   L L +  +   L
Sbjct: 128 -------------SLQDPIGVDKEG--NEISLIDILGSDGDSVIEQVELNLEIKKLYKKL 172

Query: 450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501
             L  +E  VI  R+GL     +T  EIA  L ISR  V + E + LMKL  
Sbjct: 173 SVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYK 224

The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K [Transcription, Transcription factors, Cellular processes, Sporulation and germination]. Length = 227

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

 Score = 81.2 bits (201), Expect = 3e-17
 Identities = 71/251 (28%), Positives = 122/251 (48%), Gaps = 17/251 (6%)

Query: 255 AEATNMSAAQVKKCLEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFAN-GPRFQDLCQ 309
            +   +   + K+ ++  +     AR+ L++ NLRLV  V+++    F N G    DL Q
Sbjct: 9   KKKPQLKDEENKELIKKSQDGDQEARDTLVEKNLRLVWSVVQR----FLNRGYEPDDLFQ 64

Query: 310 AGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAK 369
            G  GL+ A+D+F+     + STY +  I   I R +      +V   L+    +I++ K
Sbjct: 65  IGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDGTVKVSRSLKETANKIRKDK 124

Query: 370 LELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG 429
            EL  EL R PT EE+ + + ++PE   EV+ A +   S  S H    E   + IT +D 
Sbjct: 125 DELSKELGREPTIEELAEYLGVTPE---EVVLAQEASRSPQSIHETVHENDGDPITLLDQ 181

Query: 430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVR 489
           +  +   +    ++AL + +  L  +E L++  R+      D+T  E+A  L IS+  V 
Sbjct: 182 IA-DQSEEDWFDKIALKEAIRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVS 236

Query: 490 KHEVKGLMKLK 500
           + E K L ++K
Sbjct: 237 RLEKKILKQMK 247

Length = 252

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

 Score = 76.5 bits (189), Expect = 1e-15
 Identities = 70/234 (29%), Positives = 110/234 (47%), Gaps = 21/234 (8%)

Query: 273 RAARNKLIKHNLRLVLFVIKKYFQDFAN-GPRFQDLCQAGVKGLITAIDRFEPKRRFRLS 331
           + AR KLI  NLRLVL VI    Q F N G    DL Q G  GL+ AID F+  +  + S
Sbjct: 36  KEAREKLINGNLRLVLSVI----QRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFS 91

Query: 332 TYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNI 391
           TY +  I   I R +  ++  RV   L  +  +  + + +L+ E  + PT EEI + + +
Sbjct: 92  TYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEV 151

Query: 392 SPERYREVMKASKPILSLHSRHGVTQEEFINGITD----VDGVENE-NQRQPALLRLALD 446
             E     + A +  +SL        E   +   D    +D + +E N+ +  L  +AL 
Sbjct: 152 PREEVVFALDAIQDPVSL-------FEPIYHDGGDPIYVMDQISDEKNKDENWLEEIALK 204

Query: 447 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500
           + +  L  +E L++  RF   GK   T  E+A  + IS+  V + E   L  ++
Sbjct: 205 EAMKKLNDREKLILNLRF-FQGK---TQMEVAEEIGISQAQVSRLEKAALKHMR 254

Length = 258

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

 Score = 71.9 bits (177), Expect = 2e-14
 Identities = 57/221 (25%), Positives = 101/221 (45%), Gaps = 32/221 (14%)

Query: 279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWI 338
           LI+  L LV  +  +      +     DL QAG+ GL+ AI+R++P R  +  TY +  I
Sbjct: 1   LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRI 60

Query: 339 RHAII---RSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPER 395
           R A++   R +       VP  L     +++RA  EL   L R PT+EEI + + +  + 
Sbjct: 61  RGAMLDELRRLDW-----VPRSLRQKARKLERAIRELEARLGREPTEEEIAEELGMDLKE 115

Query: 396 YREVMKA--SKPILSLHSRHGVTQEEFINGITD-------VDGVENENQRQPAL---LRL 443
           YR+ +    +  ++SL        +E +    D       ++  ++E+  +      LR 
Sbjct: 116 YRQALNEINALSLVSL--------DELLESGDDGGSLIDRIEDDKSEDPEEELEREELRE 167

Query: 444 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNIS 484
           AL + ++SL  +E LV+   +      +  L EI   L ++
Sbjct: 168 ALAEAIESLSEREQLVLSLYY----YEELNLKEIGEVLGLT 204

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

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

 Score = 71.6 bits (176), Expect = 7e-14
 Identities = 74/249 (29%), Positives = 112/249 (44%), Gaps = 34/249 (13%)

Query: 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLST 332
             A +++I  ++RLV+ +  K F+ F  G    DL Q G  GL+ A  RFEP R  R ST
Sbjct: 39  EDALHRIISAHMRLVISMAGK-FRRF--GLPMNDLIQEGYVGLLEAAARFEPDREVRFST 95

Query: 333 YGLFWIRHAI----------IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTD 382
           Y  +WIR +I          +R  T S+   + F L  +R  + +A  EL        T 
Sbjct: 96  YATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLAQADEEL--------TK 147

Query: 383 EEIIQGVNIS---PERYREVMKA--SKPILSLHSRHGVTQE---EFINGITDVDGVENEN 434
           +EI + +  +        E+M A  S P  SL++      E   E ++ + D   + +E 
Sbjct: 148 QEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSPLPDEQ 207

Query: 435 QRQP---ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH 491
                     R  L   L +L  +E  +IR+R  L   G  TL  +   L IS+E VR+ 
Sbjct: 208 VESSIDGERRRRWLTQALQTLNERELRIIRER-RLREDG-ATLEALGEELGISKERVRQI 265

Query: 492 EVKGLMKLK 500
           E + L KL+
Sbjct: 266 EARALEKLR 274

Length = 289

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

 Score = 67.6 bits (166), Expect = 1e-12
 Identities = 75/238 (31%), Positives = 117/238 (49%), Gaps = 27/238 (11%)

Query: 276 RNKLIKHNLRLVLFVIKKYFQDFANGPR--FQDLCQAGVKGLITAIDRFEPKRRFRLSTY 333
           RN+L++ NL LV    +K    ++N     ++DL Q G  GLI AI+RF+P +    S++
Sbjct: 27  RNQLVELNLGLV----RKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSF 82

Query: 334 GLFWIRHAII-----RSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQG 388
            + +IR  I      +S TV    R+P   + ++ + ++ + EL  EL R PTD+EI Q 
Sbjct: 83  AIPYIRGEIQHYLRDKSPTV----RIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQA 138

Query: 389 VNISPERYREVMKAS--KPILSLHSRHGVTQEEFINGITDVDGVENENQR--QPALL-RL 443
           ++IS E ++E+  A   +  LSL +   V Q+E     +  D + +   R  Q A   R+
Sbjct: 139 LDISLEEWQEIKLALQNRTPLSLDAP--VNQDED-GSTSLGDLLPDPRYRSFQLAQEDRI 195

Query: 444 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501
            L   L  L+ +   V+   F      D T  E A  L IS   V +   KGL +LK 
Sbjct: 196 RLQQALAQLEERTREVLEFVF----LHDLTQKEAAERLGISPVTVSRRVKKGLDQLKK 249

Length = 256

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

 Score = 66.8 bits (163), Expect = 2e-12
 Identities = 67/229 (29%), Positives = 107/229 (46%), Gaps = 13/229 (5%)

Query: 274 AARNKLIKHNLRLVLFVIKKYFQDFAN-GPRFQDLCQAGVKGLITAIDRFEPKRRFRLST 332
            AR KLI  NLRLVL VI    Q F N G    DL Q G  GL+ +ID F+  +  + ST
Sbjct: 34  TAREKLINGNLRLVLSVI----QRFNNRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFST 89

Query: 333 YGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNIS 392
           Y +  I   I R +  ++  RV   L  +  +  + + +L+ E  + PT  EI + + + 
Sbjct: 90  YAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVRDKLISENSKEPTVSEIAKELKVP 149

Query: 393 PERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALL-RLALDDVLDS 451
            E   EV+ A   I    S       +  + I  +D + +E  +    L  +AL + +  
Sbjct: 150 QE---EVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKNKDSQWLEGIALKEAMKR 206

Query: 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500
           L  +E +++  RF  +GK   T  E+A  + IS+  V + E   L  ++
Sbjct: 207 LNEREKMILNMRF-FEGK---TQMEVAEEIGISQAQVSRLEKAALKHMR 251

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

>gnl|CDD|235644 PRK05911, PRK05911, RNA polymerase sigma factor sigma-28; Reviewed

 Score = 65.4 bits (159), Expect = 6e-12
 Identities = 63/235 (26%), Positives = 110/235 (46%), Gaps = 19/235 (8%)

Query: 276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGL 335
           R+ LI+  L LV  V  +      +  + +DL  +GV+GL+ A++RF+P++  R   Y L
Sbjct: 25  RDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYAL 84

Query: 336 FWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPER 395
           F I+ AII  +    +  VP  +     ++  A   L   L + PTD E+ + +NIS + 
Sbjct: 85  FLIKAAIIDDLRKQDW--VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQE 142

Query: 396 YREVMKASKP--ILSLHSR--------HGVTQEEFINGITDVDGVENENQRQPALLRLAL 445
                 +++P  ILSL+           G+  EE I       G +  ++++ + +   L
Sbjct: 143 LSGWFSSARPALILSLNEEFPCQSDDEAGLALEERIADERAETGYDVVDKKEFSSI---L 199

Query: 446 DDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500
            + + +L+ KE    R+   L    +  L EI   L +S   V +   K L+KL+
Sbjct: 200 AEAILALEEKE----RKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLR 250

Length = 257

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

 Score = 59.2 bits (144), Expect = 3e-11
 Identities = 27/75 (36%), Positives = 43/75 (57%), Gaps = 1/75 (1%)

Query: 362 RGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EF 420
             +I+RA+ EL  EL R PT EEI + + IS E+ REV++A++  +SL    G  ++ E 
Sbjct: 3   LNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDGEL 62

Query: 421 INGITDVDGVENENQ 435
            + + D D    E+ 
Sbjct: 63  GDLLEDDDAESPEDA 77

Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme. Length = 78

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

 Score = 62.7 bits (153), Expect = 7e-11
 Identities = 64/249 (25%), Positives = 111/249 (44%), Gaps = 41/249 (16%)

Query: 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTY 333
           AA+ KL+  +LR V+ + + Y      G    DL Q G  GL+ A+ RF+P+R  RL ++
Sbjct: 36  AAK-KLVLSHLRFVVKIARGYR---GYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSF 91

Query: 334 GLFWIRHAI----IRS------MTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDE 383
            + WI+  I    +R+       T  +  ++ F L  ++  +Q               + 
Sbjct: 92  AVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLQGW------------LNP 139

Query: 384 EIIQGV----NISPERYREVMKA--SKPILSLHSRHGVTQEEFINGITD-VDGVEN---- 432
           E ++ +     +S    RE M++  S   +SL++     +++    I   VD   +    
Sbjct: 140 EEVEAIAEELGVSEREVRE-MESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKRSDPEDT 198

Query: 433 -ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH 491
            E ++   L R AL + L SL  +   +I  R+  D K   TL E+A    +S E +R+ 
Sbjct: 199 LEEEQWEELQRQALANALGSLDARSRRIIEARWLDDDK--LTLQELAAEYGVSAERIRQI 256

Query: 492 EVKGLMKLK 500
           E   + KLK
Sbjct: 257 EKNAMKKLK 265

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|218138 pfam04542, Sigma70_r2, Sigma-70 region 2

 Score = 54.5 bits (132), Expect = 8e-10
 Identities = 25/68 (36%), Positives = 41/68 (60%), Gaps = 3/68 (4%)

Query: 279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWI 338
           L++  L LV  + ++Y  D A+    +DL Q G  GL+ A++RF+P+R    ST+    I
Sbjct: 1   LVERYLPLVYSLARRYLGDGAD---AEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTII 57

Query: 339 RHAIIRSM 346
           R+AII ++
Sbjct: 58  RNAIIDAL 65

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|235770 PRK06288, PRK06288, RNA polymerase sigma factor WhiG; Reviewed

 Score = 58.5 bits (142), Expect = 1e-09
 Identities = 45/129 (34%), Positives = 61/129 (47%), Gaps = 8/129 (6%)

Query: 276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGL 335
           R  LI     LV +V  +          F DL   GV GLI AI++F+P+R  +  TY +
Sbjct: 33  REYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAV 92

Query: 336 FWIRHAIIRSMTVSSFTRVPFGLESVRG---EIQRAKLELLFELKRVPTDEEIIQGVNIS 392
             IR AI   +   S   +P    SVR    +I+RA   L   L R P+DEEI   + IS
Sbjct: 93  TRIRGAIFDEL--RSIDWIP---RSVRQKARQIERAIAMLEARLGRTPSDEEIADELGIS 147

Query: 393 PERYREVMK 401
            E Y  ++ 
Sbjct: 148 LEEYNSLLS 156

Length = 268

>gnl|CDD|218139 pfam04545, Sigma70_r4, Sigma-70, region 4

 Score = 52.8 bits (128), Expect = 2e-09
 Identities = 24/54 (44%), Positives = 29/54 (53%), Gaps = 4/54 (7%)

Query: 448 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501
            L SL P+E  V+  RFG       TL EI   L ISRE VR+ E + L KL+ 
Sbjct: 1   ALASLPPREREVLVLRFG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50

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

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

 Score = 56.8 bits (137), Expect = 5e-09
 Identities = 61/253 (24%), Positives = 113/253 (44%), Gaps = 14/253 (5%)

Query: 255 AEATNMSAAQVKKCLE-----VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQ 309
           ++ TN++   V + +          A+ KL+ H   LV  +  KY +    GP  +DL Q
Sbjct: 5   SQPTNLTKEDVIQWIAEFQQNQNGEAQEKLVDHYQNLVYSIAYKYSK---GGPMHEDLVQ 61

Query: 310 AGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRA 368
            G+ GL+ AI R++         + +  I   I R +   +++  VP  ++ +  +I++A
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKA 121

Query: 369 KLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD 428
             EL   L+R P   EI   + +S E   E+M+  +   +L     +  +   + +  +D
Sbjct: 122 IDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARLD 181

Query: 429 GV-ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREM 487
            V E E+       R+ L+ +L  L  +E  +I   F  +    +  GE  G   IS+  
Sbjct: 182 SVGEVEDGYDQTERRMVLEKILPILSEREKSIIHCTF-EENLSQKETGERLG---ISQMH 237

Query: 488 VRKHEVKGLMKLK 500
           V + + + + KLK
Sbjct: 238 VSRLQRQAISKLK 250

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

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

 Score = 55.2 bits (134), Expect = 2e-08
 Identities = 61/249 (24%), Positives = 104/249 (41%), Gaps = 42/249 (16%)

Query: 274 AARNKLIKHNLRLVLFVIKKYFQDFANG---PRFQDLCQAGVKGLITAIDRFEPKRRFRL 330
           AA+ +L+  +LR V+ + + Y      G   P+  DL Q G  GL+ A+ RF+P+   RL
Sbjct: 49  AAK-QLVLSHLRFVVHIARGY-----RGYGLPQ-ADLIQEGNIGLMKAVKRFDPEVGVRL 101

Query: 331 STYGLFWIRHAI----IRSM------TVSSFTRVPFGLESVRGEIQRAKLELLFELKRVP 380
            ++ + WI+  I    +R+       T  +  ++ F L   +  +     E   E++ V 
Sbjct: 102 VSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLNPE---EVEMVA 158

Query: 381 TDEEIIQGVNISPERYREV---MKASKPILSLHSRHGVTQE-EFINGITD-----VDGVE 431
            +      + +S E  RE+   +      L         +     + + D      D +E
Sbjct: 159 EE------LGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDKSSDPADVLE 212

Query: 432 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH 491
            +N        LA  D L+ L  +   +I  R+  D K   TL E+A    +S E VR+ 
Sbjct: 213 EDNWEDQRRALLA--DALEGLDERSRDIIEARWLDDDK--STLQELAAEYGVSAERVRQI 268

Query: 492 EVKGLMKLK 500
           E   + KLK
Sbjct: 269 EKNAMKKLK 277

Length = 284

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

 Score = 53.9 bits (130), Expect = 5e-08
 Identities = 66/247 (26%), Positives = 109/247 (44%), Gaps = 35/247 (14%)

Query: 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPK--RRFRLST 332
           A+ KL+KH   LV  +  KY +        +DL Q G+ GL+ AI R++P   R F    
Sbjct: 30  AQEKLVKHYKNLVESLAYKYSK---GQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEA-- 84

Query: 333 YGLFWIRHAI------IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEII 386
              F +   I      +R  T S    VP  ++ +  +I++A  EL  EL+R P   EI 
Sbjct: 85  ---FAVPTIIGEIKRYLRDKTWS--VHVPRRIKELGPKIKKAVDELTTELQRSPKISEIA 139

Query: 387 QGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD-------GVENENQRQPA 439
             + +S E   E M+  K   +L   H +  +   + +T +D       G E   Q    
Sbjct: 140 DRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLLDIVGQQEDGYELTEQ---- 195

Query: 440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 499
             R+ L+ +L  L  +E  +I+  F ++    +  GE  G   IS+  V + + + + KL
Sbjct: 196 --RMILEKILPVLSDREKSIIQCTF-IENLSQKETGERLG---ISQMHVSRLQRQAIKKL 249

Query: 500 KHPTRVD 506
           +    +D
Sbjct: 250 REAAFLD 256

Length = 257

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

 Score = 50.8 bits (122), Expect = 1e-07
 Identities = 45/227 (19%), Positives = 75/227 (33%), Gaps = 72/227 (31%)

Query: 274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTY 333
            A  +L +  L LV    ++Y  D A+    +DL Q     L+ A+DRF+P+  F+   +
Sbjct: 1   EAFEELYERYLPLVYRYARRYLGDDAD---AEDLVQEAFLKLLEALDRFDPEGSFK--AW 55

Query: 334 GLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISP 393
                R+ I+  +                    R K  L  EL  +    +         
Sbjct: 56  LFRIARNLILDYL--------------------RRKRRLRRELDLLEELLDSDPSP---- 91

Query: 394 ERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLK 453
                                             + +E E +R+   LR AL    + L 
Sbjct: 92  ---------------------------------EEELEQEEERE--ALREAL----EKLP 112

Query: 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500
            +E  V+  R+        +  EIA  L IS   V++   +   KL+
Sbjct: 113 EREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKLR 155

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

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

 Score = 51.8 bits (125), Expect = 2e-07
 Identities = 49/168 (29%), Positives = 78/168 (46%), Gaps = 27/168 (16%)

Query: 306 DLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI---IRSMTVSSFTRVPFGLESVR 362
           DL QAG+ GL+ A  R++ ++     TY    IR A+   +RS+       VP    SVR
Sbjct: 40  DLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLDW-----VP---RSVR 91

Query: 363 GEIQR---AKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK--PILSLHSRHGVTQ 417
              +    A  +L  EL R PTD E+ + + +S E YRE++  +    + S+    G   
Sbjct: 92  RNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHG 151

Query: 418 EEFINGITDVD-----GVENENQRQPALLRLALDDVLDSLKPKESLVI 460
           +  +      D      +E+E       LR AL + ++SL  +E LV+
Sbjct: 152 DSILVTEDHQDEDPLQQLEDEE------LREALVEAIESLPEREQLVL 193

Length = 236

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

 Score = 49.9 bits (120), Expect = 8e-07
 Identities = 25/61 (40%), Positives = 39/61 (63%), Gaps = 5/61 (8%)

Query: 274 AARNKLIKHNLRLVLFVIKKYFQDFAN-GPRFQDLCQAGVKGLITAIDRFEPKRRFRLST 332
           A R+ LI+ NLRLV+++ +K    F N G   +DL   G  GLI A++ F P+++ +L+T
Sbjct: 52  AVRSLLIERNLRLVVYIARK----FENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLAT 107

Query: 333 Y 333
           Y
Sbjct: 108 Y 108

Length = 234

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

 Score = 49.8 bits (119), Expect = 9e-07
 Identities = 28/81 (34%), Positives = 48/81 (59%), Gaps = 5/81 (6%)

Query: 274 AARNKLIKHNLRLVLFVIKKYFQDFAN-GPRFQDLCQAGVKGLITAIDRFEPKRRFRLST 332
           +A++ LI+ NLRLV+++ +K    F N G   +DL   G  GLI A++ F P ++ +L+T
Sbjct: 52  SAKSTLIERNLRLVVYIARK----FENTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLAT 107

Query: 333 YGLFWIRHAIIRSMTVSSFTR 353
           Y    I + I+  +  ++ TR
Sbjct: 108 YASRCIENEILMYLRRNNKTR 128

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

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

 Score = 43.7 bits (104), Expect = 7e-06
 Identities = 15/41 (36%), Positives = 26/41 (63%)

Query: 236 QVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAAR 276
           + + +L+++LGREPT  E+AE   +S  +V++ LE  R   
Sbjct: 8   RAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPV 48

Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme. Length = 78

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

 Score = 46.6 bits (111), Expect = 1e-05
 Identities = 61/236 (25%), Positives = 99/236 (41%), Gaps = 16/236 (6%)

Query: 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLST 332
             A ++LI+  + LV + +++            DL   G+ GL  A+++F+P R  +  T
Sbjct: 21  PDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDT 80

Query: 333 YGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQR---AKLELLFELKRVPTDEEIIQGV 389
           Y  F IR AII  +       +P    S+R + ++   A  +L     R  T +E+   +
Sbjct: 81  YASFRIRGAIIDGLRKED--WLP---RSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAEL 135

Query: 390 NISPERYREVMKAS--KPILSLHSR-HGVTQEEFIN-GITDVDGVENENQRQPALLRLAL 445
            ++ E     M       +LS+  + H     E ++  I D      E +     L   L
Sbjct: 136 GMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEEL 195

Query: 446 DDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 501
            + +  L  KE LVI     L  K + TL EI   LN+S   + +   K L KLK 
Sbjct: 196 AEKIKQLSEKEQLVI----SLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247

Length = 251

>gnl|CDD|100119 cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

 Score = 40.2 bits (95), Expect = 8e-05
 Identities = 23/59 (38%), Positives = 30/59 (50%), Gaps = 4/59 (6%)

Query: 442 RLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500
           R  L++ LD L  +E  VI  RFG       +  EIA  L ISR  VR+   + L KL+
Sbjct: 1   RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	513
PRK07598	415	RNA polymerase sigma factor SigC; Validated	100.0
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05949	327	RNA polymerase sigma factor; Validated	100.0
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	100.0
PRK07405	317	RNA polymerase sigma factor SigD; Validated	100.0
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	100.0
PRK05901	509	RNA polymerase sigma factor; Provisional	100.0
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	100.0
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	100.0
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	100.0
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	100.0
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	100.0
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	100.0
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	100.0
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	100.0
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	100.0
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	100.0
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	100.0
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	100.0
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	100.0
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	100.0
PRK08215	258	sporulation sigma factor SigG; Reviewed	100.0
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	100.0
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	100.0
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	100.0
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	100.0
PRK07670	251	RNA polymerase sigma factor SigD; Validated	100.0
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	100.0
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	100.0
PRK05572	252	sporulation sigma factor SigF; Validated	100.0
PRK08583	257	RNA polymerase sigma factor SigB; Validated	100.0
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	100.0
PRK05803	233	sporulation sigma factor SigK; Reviewed	99.95
PRK08301	234	sporulation sigma factor SigE; Reviewed	99.92
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.92
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.9
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.87
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.86
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.86
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.86
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.86
PRK12513	194	RNA polymerase sigma factor; Provisional	99.86
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.85
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.85
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.85
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.85
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.84
PRK11922	231	RNA polymerase sigma factor; Provisional	99.84
PRK12519	194	RNA polymerase sigma factor; Provisional	99.84
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.84
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.83
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.83
PRK11924	179	RNA polymerase sigma factor; Provisional	99.83
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.82
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.82
PRK12514	179	RNA polymerase sigma factor; Provisional	99.82
PRK12524	196	RNA polymerase sigma factor; Provisional	99.82
PRK12538	233	RNA polymerase sigma factor; Provisional	99.82
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.82
PRK12531	194	RNA polymerase sigma factor; Provisional	99.82
PRK12542	185	RNA polymerase sigma factor; Provisional	99.81
PRK12534	187	RNA polymerase sigma factor; Provisional	99.81
PRK12526	206	RNA polymerase sigma factor; Provisional	99.81
PRK12537	182	RNA polymerase sigma factor; Provisional	99.81
PRK12515	189	RNA polymerase sigma factor; Provisional	99.81
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	99.8
PRK12536	181	RNA polymerase sigma factor; Provisional	99.8
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.8
PRK12543	179	RNA polymerase sigma factor; Provisional	99.8
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.79
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.79
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.79
PRK12512	184	RNA polymerase sigma factor; Provisional	99.79
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.79
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.79
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.78
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.78
PRK12522	173	RNA polymerase sigma factor; Provisional	99.78
PRK12539	184	RNA polymerase sigma factor; Provisional	99.78
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.78
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.78
PRK12518	175	RNA polymerase sigma factor; Provisional	99.77
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.77
PRK12520	191	RNA polymerase sigma factor; Provisional	99.76
PRK12529	178	RNA polymerase sigma factor; Provisional	99.76
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.76
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.76
PRK12533	216	RNA polymerase sigma factor; Provisional	99.75
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.75
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.75
PRK12516	187	RNA polymerase sigma factor; Provisional	99.74
PRK12541	161	RNA polymerase sigma factor; Provisional	99.74
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.74
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.74
PRK12528	161	RNA polymerase sigma factor; Provisional	99.73
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.73
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.73
PRK12535	196	RNA polymerase sigma factor; Provisional	99.73
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.73
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.72
PRK12547	164	RNA polymerase sigma factor; Provisional	99.72
PRK12532	195	RNA polymerase sigma factor; Provisional	99.72
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.72
PRK12545	201	RNA polymerase sigma factor; Provisional	99.71
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.71
PRK12530	189	RNA polymerase sigma factor; Provisional	99.71
PRK12544	206	RNA polymerase sigma factor; Provisional	99.69
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.69
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.69
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.69
PRK12540	182	RNA polymerase sigma factor; Provisional	99.68
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.68
PRK12517	188	RNA polymerase sigma factor; Provisional	99.68
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.67
PRK12546	188	RNA polymerase sigma factor; Provisional	99.67
PRK12511	182	RNA polymerase sigma factor; Provisional	99.66
PRK12525	168	RNA polymerase sigma factor; Provisional	99.65
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.64
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.61
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.59
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.58
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.57
PRK09191	261	two-component response regulator; Provisional	99.46
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.42
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.4
PF07638	185	Sigma70_ECF: ECF sigma factor	99.36
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	99.19
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.13
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	98.97
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	98.93
PRK06930	170	positive control sigma-like factor; Validated	98.47
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	98.3
PRK00118	104	putative DNA-binding protein; Validated	98.22
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	98.13
PRK03975	141	tfx putative transcriptional regulator; Provisiona	98.05
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	97.96
PRK04217	110	hypothetical protein; Provisional	97.93
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	97.86
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	97.84
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	97.75
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	97.74
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	97.7
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	97.66
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	97.52
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	97.52
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	97.51
PRK15201	198	fimbriae regulatory protein FimW; Provisional	97.28
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	97.26
PRK10840	216	transcriptional regulator RcsB; Provisional	97.22
TIGR03020	247	EpsA transcriptional regulator EpsA. Proteins in t	97.22
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	97.21
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	97.21
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	97.16
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	97.16
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	97.12
PRK13870	234	transcriptional regulator TraR; Provisional	97.07
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	97.06
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	96.99
COG4566	202	TtrR Response regulator [Signal transduction mecha	96.98
COG2197	211	CitB Response regulator containing a CheY-like rec	96.9
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	96.82
PRK09483	217	response regulator; Provisional	96.82
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	96.81
COG3413	215	Predicted DNA binding protein [General function pr	96.79
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	96.69
PRK01381	99	Trp operon repressor; Provisional	96.65
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	96.59
PRK09390	202	fixJ response regulator FixJ; Provisional	96.56
PRK15369	211	two component system sensor kinase SsrB; Provision	96.49
COG1356	143	tfx Transcriptional regulator [DNA replication, re	96.44
TIGR01637	132	phage_arpU phage transcriptional regulator, ArpU f	96.43
PRK10651	216	transcriptional regulator NarL; Provisional	96.38
PRK10403	215	transcriptional regulator NarP; Provisional	95.95
PRK15320	251	transcriptional activator SprB; Provisional	95.93
COG1342	99	Predicted DNA-binding proteins [General function p	95.84
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	95.79
PRK13558	665	bacterio-opsin activator; Provisional	95.44
PRK09935	210	transcriptional regulator FimZ; Provisional	95.34
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	95.24
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	95.18
COG4941	415	Predicted RNA polymerase sigma factor containing a	95.16
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	95.13
PRK04841	903	transcriptional regulator MalT; Provisional	94.97
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	94.86
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	94.7
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	94.69
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	94.55
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	94.14
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	94.09
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	93.99
PRK15418	318	transcriptional regulator LsrR; Provisional	93.96
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	93.73
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	93.64
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	93.38
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	93.37
PRK05901	509	RNA polymerase sigma factor; Provisional	93.24
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	93.08
PF06530	125	Phage_antitermQ: Phage antitermination protein Q;	92.69
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	92.33
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	92.21
PF10668	60	Phage_terminase: Phage terminase small subunit; In	92.07
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	91.83
PF13730	55	HTH_36: Helix-turn-helix domain	91.74
PF13518	52	HTH_28: Helix-turn-helix domain	91.73
PRK07598	415	RNA polymerase sigma factor SigC; Validated	91.57
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	91.52
smart00351	125	PAX Paired Box domain.	91.17
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	90.72
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	90.45
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	90.34
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	90.19
PHA00675	78	hypothetical protein	90.09
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	90.02
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	89.85
PF02650	85	HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IP	89.73
PRK05949	327	RNA polymerase sigma factor; Validated	89.47
PHA02591	83	hypothetical protein; Provisional	89.2
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	89.12
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	89.09
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	88.75
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	88.71
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	88.62
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	88.21
cd00131	128	PAX Paired Box domain	87.9
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	87.4
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	86.75
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	86.57
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	86.53
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	86.14
COG3355	126	Predicted transcriptional regulator [Transcription	85.96
PRK10046	225	dpiA two-component response regulator DpiA; Provis	85.96
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	85.88
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	85.84
PHA02547	179	55 RNA polymerase sigma factor; Provisional	85.79
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	85.69
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	85.59
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	85.28
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	85.16
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	84.88
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	84.83
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	84.37
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	84.2
PF12728	51	HTH_17: Helix-turn-helix domain	84.12
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	84.03
PRK07405	317	RNA polymerase sigma factor SigD; Validated	84.0
PRK07670	251	RNA polymerase sigma factor SigD; Validated	83.94
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	83.85
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	83.74
PRK12423	202	LexA repressor; Provisional	83.58
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	83.44
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	83.41
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	83.1
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	82.55
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	82.45
PRK11083	228	DNA-binding response regulator CreB; Provisional	82.35
PRK13413	200	mpi multiple promoter invertase; Provisional	82.33
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	82.18
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	82.13
TIGR01764	49	excise DNA binding domain, excisionase family. An	81.94
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	81.93
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	81.83
COG3415	138	Transposase and inactivated derivatives [DNA repli	81.7
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	81.42
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	81.3
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	81.1
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	80.94
PRK15479	221	transcriptional regulatory protein TctD; Provision	80.64
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	80.16

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=4e-64  Score=528.64  Aligned_cols=314  Identities=31%  Similarity=0.489  Sum_probs=290.6

Q ss_pred             hhcCCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHH--------------------HHHHHHHHHHHhCCCCCHHHH
Q 010308          195 EYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKV--------------------FVQVKEQLQKDLGREPTDVEL  254 (513)
Q Consensus       195 ~~~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~--------------------l~~~~~~l~~~l~r~p~~~e~  254 (513)
                      ..+.++|+|+.||++|+++|+||++||+.|+++||.++.                    |+++++.|+..+|++|+..||
T Consensus        54 ~~~~~~d~v~~yl~~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ew  133 (415)
T PRK07598         54 RNRRSTDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERW  133 (415)
T ss_pred             cCCCCCChHHHHHHhcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHH
Confidence            445678999999999999999999999999999999998                    889999999999999999999


Q ss_pred             HHHcc----------------------CCHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHH
Q 010308          255 AEATN----------------------MSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV  312 (513)
Q Consensus       255 A~~~~----------------------~s~e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~  312 (513)
                      |.++|                      ++.++|.+.+..|..|+++||.+|++||+++|++|.   ++|++++||||||+
T Consensus       134 a~~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~---~~g~~~eDLiQEG~  210 (415)
T PRK07598        134 AKTADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQ---NRGLELLDLVQEGT  210 (415)
T ss_pred             HHHhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHc---cCCCCHHHHHHHHH
Confidence            95554                      556666666677899999999999999999999998   78999999999999


Q ss_pred             HHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCC
Q 010308          313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNI  391 (513)
Q Consensus       313 iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgi  391 (513)
                      +|||+|+++|||++|++|||||+||||++|.++++ ++++||+|.|+.+.+++++++...|.+++||.||.+|||+.+||
T Consensus       211 iGL~ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~i  290 (415)
T PRK07598        211 LGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEM  290 (415)
T ss_pred             HHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCC
Confidence            99999999999999999999999999999999999 99999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHhccCcccccCCCCCchhh-hhccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCC
Q 010308          392 SPERYREVMKASKPILSLHSRHGVTQEE-FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKG  470 (513)
Q Consensus       392 s~e~v~~~l~~~~~~~SLd~~~~~~~~e-~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~  470 (513)
                      ++++|+.++.....++|||.+++++++. +.+.+. ++..+|++.....++...|..+|+.|||+|+.||.|||||+|++
T Consensus       291 s~~~vr~~l~~~~~~~SLd~~vg~~~d~~l~d~l~-~~~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~  369 (415)
T PRK07598        291 TPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLE-TDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGH  369 (415)
T ss_pred             CHHHHHHHHHHccCCcccccccCCCccccHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCC
Confidence            9999999999999999999998766554 444443 44456787788888999999999999999999999999999999


Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010308          471 DRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  512 (513)
Q Consensus       471 ~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl  512 (513)
                      ++|++|||+.||||+++||+++++|++|||++.+...|++|+
T Consensus       370 ~~Tl~EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~  411 (415)
T PRK07598        370 TYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYL  411 (415)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHH
Confidence            999999999999999999999999999999999999999996

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=3.3e-60  Score=495.49  Aligned_cols=310  Identities=34%  Similarity=0.539  Sum_probs=291.7

Q ss_pred             CChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHH
Q 010308          200 TDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKL  279 (513)
Q Consensus       200 ~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~L  279 (513)
                      .|.+..||++|+++|+||++||..|++.++.+..++..+.+|+...|++|+..+||.+.|++...|.+.+..|..|++.|
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            58899999999999999999999999999999999999999999999999999999999999999999999889999999


Q ss_pred             HHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccch
Q 010308          280 IKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGL  358 (513)
Q Consensus       280 I~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~  358 (513)
                      |.+|+++|+++|++|.   +++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+ ++++||+|.|+
T Consensus       142 i~~~l~lV~~iA~ry~---~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~~  218 (373)
T PRK07406        142 VQSNLRLVVSIAKKYM---NRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHL  218 (373)
T ss_pred             HHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHHH
Confidence            9999999999999998   7899999999999999999999999999999999999999999999999 89999999999


Q ss_pred             hHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchhhhH
Q 010308          359 ESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQRQ  437 (513)
Q Consensus       359 ~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~~~  437 (513)
                      ...+++++++...|.+++||.||.+|||+.+|+++++|..++.....++|||.+.+.+++ .+.+.+.++ ..+|++...
T Consensus       219 ~~~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~-~~~pee~~~  297 (373)
T PRK07406        219 YETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEAD-GETPEDDVA  297 (373)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCC-CCCHHHHHH
Confidence            999999999999999999999999999999999999999999988999999999765444 344555443 355777778


Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhccC
Q 010308          438 PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV  513 (513)
Q Consensus       438 ~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl~  513 (513)
                      ...+...|..+|+.||++|+.||.+||||+|++++|++|||+.||||+++|||++.+|++|||++.....|..|+.
T Consensus       298 ~~~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~~~  373 (373)
T PRK07406        298 KNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYIR  373 (373)
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHhC
Confidence            8888999999999999999999999999998889999999999999999999999999999999999999999874

>PRK05949 RNA polymerase sigma factor; Validated

Probab=100.00  E-value=7.8e-60  Score=486.51  Aligned_cols=309  Identities=33%  Similarity=0.541  Sum_probs=287.7

Q ss_pred             CCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHH
Q 010308          198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN  277 (513)
Q Consensus       198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~  277 (513)
                      .+.|.+..||++|+++|+||++||..|++.++.+..+++.++.|+..+|++|+..+||.+++++...|...+.+|..|++
T Consensus        15 ~~~d~~~~yl~~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A~~   94 (327)
T PRK05949         15 FSADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQ   94 (327)
T ss_pred             CCCCHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHHHH
Confidence            34699999999999999999999999999999999999999999999999999999999999999888888888889999


Q ss_pred             HHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccccc
Q 010308          278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF  356 (513)
Q Consensus       278 ~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~  356 (513)
                      .||.+|+++|+++|++|.   +++.+++|||||||+|||+|+++|||++|++|+|||+||||++|.+++. ++++||+|.
T Consensus        95 ~Li~~~~~~V~~iA~~y~---~~~~~~eDLvQEg~igL~~a~~kfd~~~G~rFsTYa~wwIrq~I~r~i~~~~r~iRlP~  171 (327)
T PRK05949         95 KMIEANLRLVVAIAKKYQ---KRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPI  171 (327)
T ss_pred             HHHHHHHHHHHHHHHHHc---cCCCCHHHHHHHHHHHHHHHHHhcCCcCCCChhhhhHHHHHHHHHHHHHHcCCceeCCH
Confidence            999999999999999998   7899999999999999999999999999999999999999999999999 999999999


Q ss_pred             chhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchhh
Q 010308          357 GLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQ  435 (513)
Q Consensus       357 ~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~  435 (513)
                      |+...+++++++...+..++||.||.+|||+.+|+++++|..++.....++|||.+.+++++ .+.+.+.+. ..+|++.
T Consensus       172 ~~~~~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~-~~~pe~~  250 (327)
T PRK05949        172 HITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDE-GPSPDQY  250 (327)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCC-CCCHHHH
Confidence            99999999999999999999999999999999999999999999999999999999865544 344444443 3567877


Q ss_pred             hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010308          436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  512 (513)
Q Consensus       436 ~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl  512 (513)
                      .....+...|..+|+.|||+|+.||.+||||+|++++|++|||+.||||+++|||++.+|++|||+  ....|..|+
T Consensus       251 ~~~~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~--~~~~l~~~~  325 (327)
T PRK05949        251 ITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR--RRANVKEYL  325 (327)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH--HHHHHHHHH
Confidence            888888999999999999999999999999999999999999999999999999999999999998  346677775

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

Probab=100.00  E-value=1.8e-58  Score=471.10  Aligned_cols=296  Identities=38%  Similarity=0.613  Sum_probs=277.0

Q ss_pred             ChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHH
Q 010308          201 DLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLI  280 (513)
Q Consensus       201 d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI  280 (513)
                      |.+..|+++|+.+|+||++||..|++.++.+..+++.++.|+.++|++|+..+||+++|++...+...+..|..|++.||
T Consensus         1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv   80 (298)
T TIGR02997         1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI   80 (298)
T ss_pred             CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence            46789999999999999999999999999999999999999999999999999999999999888888888899999999


Q ss_pred             HHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchh
Q 010308          281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLE  359 (513)
Q Consensus       281 ~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~  359 (513)
                      .+|+++|+++|++|.   ++|.+++|||||||+|||+|+++|||++|++|+|||+||||++|.+++. +.+++|+|.++.
T Consensus        81 ~~~lrlV~~iA~~y~---~~~~~~eDLiQEg~igL~~a~~kfd~~~g~rFsTya~~wIr~~I~r~i~~~~r~vr~p~~~~  157 (298)
T TIGR02997        81 KANLRLVVSVAKKYQ---NRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHIT  157 (298)
T ss_pred             HHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCccCCCChHHHHHHHHHHHHHHHHHhcCCCeeCcHHHH
Confidence            999999999999999   7899999999999999999999999999999999999999999999999 899999999999


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchhhhHH
Q 010308          360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQRQP  438 (513)
Q Consensus       360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~~~~  438 (513)
                      ..+++++++...+.+.+|+.||.+|||+.+|+++++|..++.....++|||.+.+++++ .+.+.+.+ ...+|++....
T Consensus       158 ~~~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~-~~~~pe~~~~~  236 (298)
T TIGR02997       158 EKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLED-DGESPEEQVER  236 (298)
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccC-CCCCHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999998755433 33343444 34567777788


Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010308          439 ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       439 ~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR  500 (513)
                      .++...|..+|+.|||+|+.||.+||||+|++++|++|||+.||||+++|||++.+|++|||
T Consensus       237 ~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr  298 (298)
T TIGR02997       237 ESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR  298 (298)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            88888999999999999999999999999999999999999999999999999999999997

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

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=4.5e-58  Score=471.88  Aligned_cols=309  Identities=33%  Similarity=0.543  Sum_probs=286.5

Q ss_pred             CCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHH
Q 010308          198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN  277 (513)
Q Consensus       198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~  277 (513)
                      .++|.+..||++|+.+|+||++||..|++.++.+..+++.+..|++++|++|+..+||.+++++...|...+.+|..|++
T Consensus         5 ~~~~~~~~yl~~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~~   84 (317)
T PRK07405          5 TSTDLVRTYLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKR   84 (317)
T ss_pred             CCCcHHHHHHHHccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHHH
Confidence            34688999999999999999999999999999999999999999999999999999999999999888888887889999


Q ss_pred             HHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccccc
Q 010308          278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF  356 (513)
Q Consensus       278 ~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~  356 (513)
                      .||.+|+++|+++|++|.   +++.+++||+||||+|||+|+++|||++|++|+|||+||||++|.++|. ++++||+|.
T Consensus        85 ~L~~~~~~~V~~~a~~~~---~~~~~~eDLvQEg~i~L~~a~~~fd~~~g~rf~tYa~~wIR~~I~~~i~~~~~~ir~p~  161 (317)
T PRK07405         85 KMVEANLRLVVSVAKKYL---KRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPI  161 (317)
T ss_pred             HHHHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHHhCcCCCCChHHHHHHHHHHHHHHHHHhcCCCccCCh
Confidence            999999999999999999   7899999999999999999999999999999999999999999999999 999999999


Q ss_pred             chhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchhh
Q 010308          357 GLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQ  435 (513)
Q Consensus       357 ~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~  435 (513)
                      |+...+++++++...+...+|+.||.+|||+.+|++++++..+++....++|||.+.+++++ .+.+.+.+. ..+|++.
T Consensus       162 ~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~-~~~pe~~  240 (317)
T PRK07405        162 HITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDT-GASPEDF  240 (317)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCC-CCCHHHH
Confidence            99999999999999999999999999999999999999999999888889999998765544 344444443 3567887


Q ss_pred             hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010308          436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  512 (513)
Q Consensus       436 ~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl  512 (513)
                      ....++...|..+|+.|||+|+.||.+||||+|++++|++|||+.||||+++|||++.+|++|||+.  ...|..|+
T Consensus       241 ~~~~~~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~~~  315 (317)
T PRK07405        241 ATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQEYL  315 (317)
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHHHH
Confidence            8888889999999999999999999999999999999999999999999999999999999999984  45666664

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

Probab=100.00  E-value=3e-58  Score=470.59  Aligned_cols=313  Identities=35%  Similarity=0.537  Sum_probs=282.6

Q ss_pred             cCCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHH-HhCCCCCHH---------------HHHHHccC
Q 010308          197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQK-DLGREPTDV---------------ELAEATNM  260 (513)
Q Consensus       197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~-~l~r~p~~~---------------e~A~~~~~  260 (513)
                      ..++|.+..|+.+++..++++.+++..+.+.++....+......+.. .+++.|+..               +|+.....
T Consensus         5 ~~~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~   84 (342)
T COG0568           5 RLSADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTP   84 (342)
T ss_pred             ccchhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccCh
Confidence            45789999999999999999999999999999888877666667655 677777765               44443333


Q ss_pred             CH-HHHH-HHHHH--hHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHH
Q 010308          261 SA-AQVK-KCLEV--GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLF  336 (513)
Q Consensus       261 s~-e~L~-~~~~g--d~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~  336 (513)
                      +. ..|. .+..|  +..|+.+||.+|++||++||++|.   ++|++|.||||||+||||+|+++|||++||+|||||+|
T Consensus        85 ~Ee~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~---~rGL~~~DLIQEGniGLmkAVekFdp~rG~kFsTYA~w  161 (342)
T COG0568          85 EEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYT---GRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATW  161 (342)
T ss_pred             HHHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhh---cCCCcHHHHHhcccHHHHHHHHhcCcccCCcchhHHHH
Confidence            32 2333 34455  677999999999999999999999   89999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCC
Q 010308          337 WIRHAIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV  415 (513)
Q Consensus       337 wIR~aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~  415 (513)
                      |||++|.++|. +.++||+|.|+.+.++++.++.++|.+++|++|+.+|||+.+|+++++|+.++.....++|||.++++
T Consensus       162 WIrqaI~raI~~q~rtIRipvh~~e~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd~~ig~  241 (342)
T COG0568         162 WIRQAITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDTPIGD  241 (342)
T ss_pred             HHHHHHHHHHHHhcchhhHhHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccCCcCCC
Confidence            99999999999 99999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             chh-hhhccccCCCCCCchhhhHHHHHHHHHHHHHhc-CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          416 TQE-EFINGITDVDGVENENQRQPALLRLALDDVLDS-LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       416 ~~~-e~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~-L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      +++ .+.+.+.|+...+|++.+....+.+.+...|.. |+|+|+.||++||||+|+.+.|++|||+.+|||+++||||+.
T Consensus       242 ded~~l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERvRQIE~  321 (342)
T COG0568         242 DEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEA  321 (342)
T ss_pred             CcccHHHHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHHHHHHH
Confidence            655 466888888777899999999999999999999 999999999999999999999999999999999999999999


Q ss_pred             HHHHHHh-Ccchhhhhhhcc
Q 010308          494 KGLMKLK-HPTRVDYLRQHM  512 (513)
Q Consensus       494 rALkKLR-~~~~~~~L~~yl  512 (513)
                      +|++||| ++.+...+++|+
T Consensus       322 kAl~KLr~~~~~~~~~~~~l  341 (342)
T COG0568         322 KALRKLRRHPERSALLRSYL  341 (342)
T ss_pred             HHHHHHHHhhhhhhHHHHhh
Confidence            9999999 888888788886

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=7.4e-58  Score=491.79  Aligned_cols=304  Identities=32%  Similarity=0.474  Sum_probs=271.4

Q ss_pred             HHhhcCCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHh
Q 010308          193 VREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVG  272 (513)
Q Consensus       193 ~~~~~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd  272 (513)
                      ....+...|.+..||++|+.+|+||++||..|++.++.+..+++.   +.       ...+|+..   ....+++.+..+
T Consensus       203 ~~~~~~~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~~~---~~~~l~~~~~~g  269 (509)
T PRK05901        203 DAKLTATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLDPE---LRRDLQWIGRDG  269 (509)
T ss_pred             hhhccccccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccchhh---hhhhhhhhccch
Confidence            445667789999999999999999999999999999876433321   11       11223322   345577788889


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccc
Q 010308          273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSF  351 (513)
Q Consensus       273 ~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~  351 (513)
                      ..|+++||.+|+|||+++|++|.   ++|++++||||||+||||+|+++|||++|++|||||+||||++|.++|. +.++
T Consensus       270 ~~Ar~~LI~sNLrLVvsIAkrY~---~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~  346 (509)
T PRK05901        270 KRAKNHLLEANLRLVVSLAKRYT---NRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQART  346 (509)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCc
Confidence            99999999999999999999998   7899999999999999999999999999999999999999999999999 8999


Q ss_pred             cccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCC
Q 010308          352 TRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGV  430 (513)
Q Consensus       352 iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~  430 (513)
                      ||+|.|+.+.++++.++..+|.+.+||.||.+|||+.||+++++|..++.....++|||.+.+.+++ .+.+.+.+....
T Consensus       347 IRvP~~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~~~~  426 (509)
T PRK05901        347 IRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAV  426 (509)
T ss_pred             eecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCCCCC
Confidence            9999999999999999999999999999999999999999999999999999999999999765444 355666666666


Q ss_pred             CchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhh
Q 010308          431 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQ  510 (513)
Q Consensus       431 ~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~  510 (513)
                      .|++.+....++..|..+|..|+++|+.||.+||||++++++|++|||+.||||+++||||+.+||.|||++.+...|+.
T Consensus       427 ~p~~~~~~~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~l~~  506 (509)
T PRK05901        427 SPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRD  506 (509)
T ss_pred             CHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            77887888889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cc
Q 010308          511 HM  512 (513)
Q Consensus       511 yl  512 (513)
                      |+
T Consensus       507 ~l  508 (509)
T PRK05901        507 FL  508 (509)
T ss_pred             hh
Confidence            86

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=4.1e-56  Score=458.03  Aligned_cols=298  Identities=32%  Similarity=0.443  Sum_probs=264.2

Q ss_pred             CCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHH
Q 010308          199 STDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNK  278 (513)
Q Consensus       199 ~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~  278 (513)
                      ..|.+..||++|+.+|+||++||..|++.++.+..++..           |...+|....  ....+...+..|..|++.
T Consensus        24 ~~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~~   90 (324)
T PRK07921         24 AADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARRH   90 (324)
T ss_pred             CCChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHHH
Confidence            358899999999999999999999999999866544332           1122221110  234577778888999999


Q ss_pred             HHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccc
Q 010308          279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFG  357 (513)
Q Consensus       279 LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~  357 (513)
                      ||.+|+++|+++|++|.   +++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+ +.+.||+|.|
T Consensus        91 Lv~~~~~lV~~iA~r~~---~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~~  167 (324)
T PRK07921         91 LLEANLRLVVSLAKRYT---GRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVH  167 (324)
T ss_pred             HHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCHH
Confidence            99999999999999999   7899999999999999999999999999999999999999999999999 8999999999


Q ss_pred             hhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchhhh
Q 010308          358 LESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQR  436 (513)
Q Consensus       358 ~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~~  436 (513)
                      +.+.+++++++...|.+++||.||.+|||+.+|+++++|..++.....++|||.+.+++++ .+.+.+.+....+|++..
T Consensus       168 ~~~~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~pe~~~  247 (324)
T PRK07921        168 LVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAV  247 (324)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCCCHHHHH
Confidence            9999999999999999999999999999999999999999999988899999999765444 355566665555677777


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010308          437 QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  512 (513)
Q Consensus       437 ~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl  512 (513)
                      ...++...|..+|..|+++|+.||.+||||+|++++|++|||+.||||+++||||+.+||+|||.......|..|+
T Consensus       248 ~~~~~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~~~  323 (324)
T PRK07921        248 IAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSYA  323 (324)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHHhh
Confidence            8888899999999999999999999999999889999999999999999999999999999999998888898886

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=6.1e-54  Score=449.33  Aligned_cols=273  Identities=34%  Similarity=0.557  Sum_probs=254.8

Q ss_pred             cCCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHH
Q 010308          197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAAR  276 (513)
Q Consensus       197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar  276 (513)
                      ....|++.+||++|+..|+||++||..|++.+                                        ..|+..|+
T Consensus        92 ~~~~d~~~~yl~~i~~~~~l~~~ee~~L~~~~----------------------------------------~~Gd~~A~  131 (367)
T PRK09210         92 VKINDPVRMYLKEIGRVPLLTAEEEIELAKRI----------------------------------------EEGDEEAK  131 (367)
T ss_pred             cccCcHHHHHHHHhhccCCCCHHHHHHHHHHH----------------------------------------HhhHHHHH
Confidence            34579999999999999999999999997665                                        35788999


Q ss_pred             HHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccc
Q 010308          277 NKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVP  355 (513)
Q Consensus       277 ~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP  355 (513)
                      +.||.+|+++|+++|++|.   +++.+++||+||||+|||+|+++|||.+|++|+|||+||||++|.++|. +.+++|+|
T Consensus       132 ~~Li~~~~~lV~~iA~~~~---~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip  208 (367)
T PRK09210        132 QRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIP  208 (367)
T ss_pred             HHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceecc
Confidence            9999999999999999998   7899999999999999999999999999999999999999999999999 99999999


Q ss_pred             cchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchh
Q 010308          356 FGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENEN  434 (513)
Q Consensus       356 ~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee  434 (513)
                      .|+++.++++.++.+.|..++||.||.+|||+.||+++++|+.++.....++|||.+.+.+++ .+.+.+.+....+|++
T Consensus       209 ~~~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~~~p~~  288 (367)
T PRK09210        209 VHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPAD  288 (367)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCCCCHHH
Confidence            999999999999999999999999999999999999999999999999899999999765533 4556666666667888


Q ss_pred             hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010308          435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  512 (513)
Q Consensus       435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl  512 (513)
                      ......++..|..+|..||++|+.||.+||||+|++++|++|||+.||||+++|||++.+||+|||++.+...|+.|+
T Consensus       289 ~~~~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~~~~  366 (367)
T PRK09210        289 HAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDFL  366 (367)
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHHHhh
Confidence            888889999999999999999999999999999999999999999999999999999999999999999999999986

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=1.5e-50  Score=449.24  Aligned_cols=237  Identities=36%  Similarity=0.593  Sum_probs=223.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccc
Q 010308          273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSF  351 (513)
Q Consensus       273 ~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~  351 (513)
                      ..|+++||.+|++||++||++|.   ++|++++||||||+||||+|+++|||++|++|||||+||||++|.++|+ +.++
T Consensus       379 ~~a~~~Li~~nlrlV~~iA~ky~---~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~~i~~~~r~  455 (619)
T PRK05658        379 RRAKKEMVEANLRLVISIAKKYT---NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART  455 (619)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHh---hCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHHHHHHcCCc
Confidence            47899999999999999999998   7899999999999999999999999999999999999999999999999 8999


Q ss_pred             cccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCC
Q 010308          352 TRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGV  430 (513)
Q Consensus       352 iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~  430 (513)
                      ||+|.|+.+.++++.++...|.+++||.||.+|||+.||+++++|+.++.....++|||.+++++++ .+.+.+.+....
T Consensus       456 irip~~~~~~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~~~l~d~i~d~~~~  535 (619)
T PRK05658        456 IRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAE  535 (619)
T ss_pred             eecCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCCCchhhhcCCCCCC
Confidence            9999999999999999999999999999999999999999999999999999999999999765544 355666666666


Q ss_pred             CchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhh
Q 010308          431 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQ  510 (513)
Q Consensus       431 ~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~  510 (513)
                      +|++......++..|..+|..||++|+.||++||||++..++|++|||+.||||+++|||++.+||+|||++.+...|+.
T Consensus       536 ~p~~~~~~~~~~~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~~~~~~l~~  615 (619)
T PRK05658        536 LPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRS  615 (619)
T ss_pred             ChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhchHHHHHHHH
Confidence            77887888889999999999999999999999999998899999999999999999999999999999999999999999


Q ss_pred             cc
Q 010308          511 HM  512 (513)
Q Consensus       511 yl  512 (513)
                      |+
T Consensus       616 ~~  617 (619)
T PRK05658        616 FL  617 (619)
T ss_pred             Hh
Confidence            86

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

Probab=100.00  E-value=7.5e-47  Score=373.48  Aligned_cols=235  Identities=34%  Similarity=0.570  Sum_probs=218.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccc
Q 010308          275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR  353 (513)
Q Consensus       275 Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iR  353 (513)
                      |+++||.+|+++|+++|++|.   +++.+++||+|||++||++|+++|||++|++|+|||+||||++|.+++. +.+.++
T Consensus         1 a~~~Li~~~~~lv~~ia~~~~---~~~~~~eDLiQeG~igL~~A~~~fd~~~g~~FstYA~~~Ir~~I~~~l~~~~~~vr   77 (238)
T TIGR02393         1 AKKQLVESNLRLVVSIAKKYT---NRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIR   77 (238)
T ss_pred             CHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCCCCCCChHHHhHHHHHHHHHHHHHHcCCcEE
Confidence            578999999999999999998   7899999999999999999999999999999999999999999999999 889999


Q ss_pred             cccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCc
Q 010308          354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVEN  432 (513)
Q Consensus       354 lP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~  432 (513)
                      +|.++.+.++++.++...|.+++|+.||.+|||+.||++++++..++......+|||.+.+.+++ .+.+.+.++...+|
T Consensus        78 ip~~~~~~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~~p  157 (238)
T TIGR02393        78 IPVHMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESP  157 (238)
T ss_pred             eCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCCCCCCh
Confidence            99999999999999999999999999999999999999999999999888889999998765444 34455666555667


Q ss_pred             hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010308          433 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  512 (513)
Q Consensus       433 ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl  512 (513)
                      ++.....++...|..+|+.||++|+.||.++|||++++++|++|||+.||||.++|+|++.+|++|||+....+.|+.|+
T Consensus       158 ~~~~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~~~~~~  237 (238)
T TIGR02393       158 DDYAAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKSFL  237 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhHHHHhh
Confidence            77777888889999999999999999999999999999999999999999999999999999999999999889898885

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.

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=100.00  E-value=2.5e-44  Score=371.16  Aligned_cols=269  Identities=29%  Similarity=0.445  Sum_probs=243.9

Q ss_pred             CCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHH
Q 010308          198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN  277 (513)
Q Consensus       198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~  277 (513)
                      ...|.+++|+++|+..|+||+++|..|...+                                        ..|+..|++
T Consensus        50 ~~~~~~~~y~~~~~~~~~l~~~ee~~li~~~----------------------------------------~~Gd~~A~~   89 (325)
T PRK05657         50 RVLDATQLYLNEIGYSPLLTAEEEVYFARRA----------------------------------------LRGDFAARQ   89 (325)
T ss_pred             ccccHHHHHHHHHhcCCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHH
Confidence            4679999999999999999999999886554                                        468899999


Q ss_pred             HHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccccc
Q 010308          278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF  356 (513)
Q Consensus       278 ~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~  356 (513)
                      .||..|.++|+++|++|.   +++.+++||+||||+|||+++++||+.+|++|+|||+||||++|.+++. +.+.+++|.
T Consensus        90 ~Li~~y~~~V~~~a~~~~---~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p~  166 (325)
T PRK05657         90 RMIESNLRLVVKIAKRYL---NRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPV  166 (325)
T ss_pred             HHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccCH
Confidence            999999999999999998   7889999999999999999999999999999999999999999999998 889999999


Q ss_pred             chhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchhh
Q 010308          357 GLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQ  435 (513)
Q Consensus       357 ~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~  435 (513)
                      ++...++.+.++...|...+|+.||.+|||+.+|+++++|..++.......|||.+...+.. .+.+.+.+....+|++.
T Consensus       167 ~~~~~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~~~pe~~  246 (325)
T PRK05657        167 HVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDT  246 (325)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCCCCHHHH
Confidence            99999999999999999999999999999999999999999999988888999988654433 34455555544567777


Q ss_pred             hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhh
Q 010308          436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR  509 (513)
Q Consensus       436 ~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~  509 (513)
                      ....+....|..+|..||+++|.||.++|||.+++++|++|||+.||||.++|++++++|+++||+......+.
T Consensus       247 ~~~~e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~  320 (325)
T PRK05657        247 TQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS  320 (325)
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccc
Confidence            78888888999999999999999999999999999999999999999999999999999999999876655543

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=1.9e-43  Score=358.45  Aligned_cols=258  Identities=24%  Similarity=0.285  Sum_probs=213.9

Q ss_pred             CChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHH
Q 010308          200 TDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKL  279 (513)
Q Consensus       200 ~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~L  279 (513)
                      .+.+..|+++++..|+||.++|..|+...                                       ...||..|++.|
T Consensus        13 ~~~~~~y~~~~~~~~~l~~~~e~~l~~~~---------------------------------------~~~Gd~~a~~~L   53 (284)
T PRK06596         13 EGNLDAYIQAVNKIPMLTAEEEYMLAKRL---------------------------------------REHGDLEAAKQL   53 (284)
T ss_pred             ccHHHHHHHHHhccCCCCHHHHHHHHHHH---------------------------------------HHcCCHHHHHHH
Confidence            47899999999999999999998886653                                       135889999999


Q ss_pred             HHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccch
Q 010308          280 IKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGL  358 (513)
Q Consensus       280 I~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~  358 (513)
                      |.+|+++|+++|++|.   +.+.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++++ +.+.+++|.+.
T Consensus        54 v~~~~~lV~~ia~~~~---~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~~  130 (284)
T PRK06596         54 VLSHLRFVVHIARGYR---GYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTK  130 (284)
T ss_pred             HHHhHHHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccchH
Confidence            9999999999999998   7899999999999999999999999999999999999999999999999 66778999875


Q ss_pred             hH--HHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh-ccCcccccCCCCCchh---hhhccccCCCCCCc
Q 010308          359 ES--VRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA-SKPILSLHSRHGVTQE---EFINGITDVDGVEN  432 (513)
Q Consensus       359 ~~--~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~-~~~~~SLd~~~~~~~~---e~~d~l~d~~~~~~  432 (513)
                      ..  ....+.+...++.  .+++||.+|||+.||+++++|..++.. ...++|||.+.+++++   .+.+.+.+. ..+|
T Consensus       131 ~~~~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~-~~~p  207 (284)
T PRK06596        131 AQRKLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDK-SSDP  207 (284)
T ss_pred             HHHHHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCC-CCCc
Confidence            42  2333444444443  349999999999999999999998753 3478999998654322   244455544 3445


Q ss_pred             hhhhHHH----HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          433 ENQRQPA----LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       433 ee~~~~~----~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ++..+..    ++...|..+|+.||++|+.||.+|||.+  +++|++|||+.||||+++|+|++.+|++|||+...
T Consensus       208 ~~~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~~--~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~  281 (284)
T PRK06596        208 ADVLEEDNWEDQRRALLADALEGLDERSRDIIEARWLDD--DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIE  281 (284)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCC--CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            5544433    4678899999999999999999999642  68999999999999999999999999999997543

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=2.9e-43  Score=357.87  Aligned_cols=262  Identities=26%  Similarity=0.293  Sum_probs=220.7

Q ss_pred             CCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHH
Q 010308          198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN  277 (513)
Q Consensus       198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~  277 (513)
                      ...++++.|++++..+|+||+++|..|++.++                                       ..||..|++
T Consensus         3 ~~~~~~~~y~~~~~~~~~l~~~~e~~L~~~~~---------------------------------------~~gd~~A~~   43 (289)
T PRK07500          3 ADASADRSMIRSAMKAPYLEREEEHALAYRWK---------------------------------------DHRDEDALH   43 (289)
T ss_pred             cchhHHHHHHHHHhcCCCCCHHHHHHHHHHHH---------------------------------------HCCCHHHHH
Confidence            35688999999999999999999999977651                                       247899999


Q ss_pred             HHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccccc
Q 010308          278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF  356 (513)
Q Consensus       278 ~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~  356 (513)
                      .||..|+++|+++|++|.   +++.+++||+||||+|||+|+++|||.+|++|+|||+|||+++|.++++ +.+.+|+|.
T Consensus        44 ~Lv~~~~~lV~~~a~~~~---~~~~~~eDLvQeg~i~L~~a~~~fd~~~~~~f~tya~~~Ir~~I~~~lr~~~~~iR~p~  120 (289)
T PRK07500         44 RIISAHMRLVISMAGKFR---RFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGT  120 (289)
T ss_pred             HHHHHhHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHCCCceecCc
Confidence            999999999999999998   7789999999999999999999999999999999999999999999999 788999999


Q ss_pred             chhH--HHHHHHHHHHHHHH---HhCCCCCHHHHHHhcCCCHHHHHHHHH-hccCcccccCCCCCchh---hhhccccCC
Q 010308          357 GLES--VRGEIQRAKLELLF---ELKRVPTDEEIIQGVNISPERYREVMK-ASKPILSLHSRHGVTQE---EFINGITDV  427 (513)
Q Consensus       357 ~~~~--~~~ki~ka~~~L~~---elgR~PT~eELA~~lgis~e~v~~~l~-~~~~~~SLd~~~~~~~~---e~~d~l~d~  427 (513)
                      +...  ...++.+....+..   .+|+.||.+|||+.||+++++|..++. ....++|||.+.+++++   .+.+.+.++
T Consensus       121 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d~i~d~  200 (289)
T PRK07500        121 SSAQKALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDD  200 (289)
T ss_pred             cHHHHHHHHHHHHHHHHHHhhhcccCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcccHHHhccCC
Confidence            8655  33455555555554   689999999999999999999988753 45579999998765433   245555554


Q ss_pred             CCCCchhhhH----HHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          428 DGVENENQRQ----PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       428 ~~~~~ee~~~----~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      . .+|++...    ..++...|..+|+.||++|+.||.++|+.  .+++|++|||+.||||+++|+|++.+|+++||...
T Consensus       201 ~-~~pe~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~~--~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l  277 (289)
T PRK07500        201 S-PLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLR--EDGATLEALGEELGISKERVRQIEARALEKLRRAL  277 (289)
T ss_pred             C-CCchHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            3 34554433    23456789999999999999999999952  47999999999999999999999999999999765


Q ss_pred             h
Q 010308          504 R  504 (513)
Q Consensus       504 ~  504 (513)
                      .
T Consensus       278 ~  278 (289)
T PRK07500        278 L  278 (289)
T ss_pred             H
Confidence            4

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=7.3e-43  Score=350.69  Aligned_cols=221  Identities=24%  Similarity=0.306  Sum_probs=195.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccc
Q 010308          273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSF  351 (513)
Q Consensus       273 ~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~  351 (513)
                      ..++++||.+|++||+++|++|.   ++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++++ +..+
T Consensus        39 ~~~r~~Lv~~~l~LV~~iA~~y~---~~g~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~~~Irg~I~~~lr~~~~~  115 (264)
T PRK07122         39 QRQRDRIVTRCLPLADHIARRFD---GRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWS  115 (264)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHH---hCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHcCCc
Confidence            45899999999999999999998   6799999999999999999999999999999999999999999999999 7889


Q ss_pred             cccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh--ccCcccccCCCCCchhhhhccccCCCC
Q 010308          352 TRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEEFINGITDVDG  429 (513)
Q Consensus       352 iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLd~~~~~~~~e~~d~l~d~~~  429 (513)
                      ||+|.++.+..++++++..+|.+++|+.||.+|||+.||+++++|.+++..  ...++|||.+.+++++.. ..+.+. .
T Consensus       116 ir~Pr~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~-~~~~d~-~  193 (264)
T PRK07122        116 VKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDA-RAIADT-L  193 (264)
T ss_pred             cccCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCc-ccchhc-c
Confidence            999999999999999999999999999999999999999999999998865  456899999865432210 111111 1


Q ss_pred             CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      .+++...+..+....|..+|+.||++|+.||.++|    ++++|++|||+.||||.++|++++.+|+++||..
T Consensus       194 ~~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y----~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~  262 (264)
T PRK07122        194 GDVDAGLDQIENREALRPLLAALPERERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTLARLRDQ  262 (264)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHh----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            22344456667788899999999999999999999    6899999999999999999999999999999964

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=100.00  E-value=2.2e-42  Score=348.03  Aligned_cols=255  Identities=25%  Similarity=0.314  Sum_probs=208.7

Q ss_pred             hHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHHH
Q 010308          202 LVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIK  281 (513)
Q Consensus       202 ~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI~  281 (513)
                      .+..|+++|+.+|+|++++|..|+..+                                       ...||..|++.||.
T Consensus         2 ~~~~yl~~~~~~~~l~~~~e~~l~~~~---------------------------------------~~~gd~~a~~~Lv~   42 (270)
T TIGR02392         2 SLDAYIRAVNRIPMLTPEEEYQLAKRL---------------------------------------REHGDLDAAKKLVL   42 (270)
T ss_pred             hHHHHHHHHhcCCCCCHHHHHHHHHHH---------------------------------------HHCCCHHHHHHHHH
Confidence            467899999999999999998886653                                       13588999999999


Q ss_pred             HHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchh-
Q 010308          282 HNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLE-  359 (513)
Q Consensus       282 ~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~-  359 (513)
                      +|+++|+++|++|.   +++.+++||+|||++|||+|+++|||++|++|+|||+|||+++|.++++ +...+|+|.+.. 
T Consensus        43 ~~~~lV~~~a~~~~---~~~~~~eDLvQeg~igl~~a~~~fd~~~~~~FsTYA~~~Ir~~i~~~l~~~~~~ir~p~~~~~  119 (270)
T TIGR02392        43 SHLRFVVKIARGYR---GYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQ  119 (270)
T ss_pred             HhHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHHhCcccCCChHHhhHHHHHHHHHHHHHHcCCceecCchHHH
Confidence            99999999999998   7899999999999999999999999999999999999999999999999 666789997643 


Q ss_pred             -HHHHHHHHHHHHHHHHhCCCC-CHHHHHHhcCCCHHHHHHHHHh-ccCcccccCCCCCchh---hhhccccCCCCCCch
Q 010308          360 -SVRGEIQRAKLELLFELKRVP-TDEEIIQGVNISPERYREVMKA-SKPILSLHSRHGVTQE---EFINGITDVDGVENE  433 (513)
Q Consensus       360 -~~~~ki~ka~~~L~~elgR~P-T~eELA~~lgis~e~v~~~l~~-~~~~~SLd~~~~~~~~---e~~d~l~d~~~~~~e  433 (513)
                       ....++.+....+.  .++.| +.+|||+.||+++++|..++.. ...++|||.+.+++++   .+.+.+.++. .+|+
T Consensus       120 ~~~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~-~~pe  196 (270)
T TIGR02392       120 RKLFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT-SDPE  196 (270)
T ss_pred             HHHHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCC-CChH
Confidence             33444454444432  22566 6999999999999999998653 3357999998755332   2344454443 3455


Q ss_pred             hhhHH----HHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          434 NQRQP----ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       434 e~~~~----~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      +....    ..+...|..+|..||++|+.||.++||.  .+++|++|||+.||||.++|+|++.+||+|||...
T Consensus       197 ~~~~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~--~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l  268 (270)
T TIGR02392       197 DTLEEEQWEELQRQALANALGSLDARSRRIIEARWLD--DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAAL  268 (270)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcC--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            54433    3466789999999999999999999953  35899999999999999999999999999999753

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

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=100.00  E-value=2.1e-40  Score=335.98  Aligned_cols=265  Identities=29%  Similarity=0.443  Sum_probs=238.1

Q ss_pred             CCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHH
Q 010308          199 STDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNK  278 (513)
Q Consensus       199 ~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~  278 (513)
                      -+|++++||++|..+|.||.+++..|...+                                        .+|+..|++.
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~~li~~~----------------------------------------~~gd~~a~~~   50 (285)
T TIGR02394        11 VADVTQLYLREIGFKPLLTAEEEIAYARRA----------------------------------------LAGDFEARKV   50 (285)
T ss_pred             cchHHHHHHHHHhccCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHHH
Confidence            379999999999999999999998885554                                        4688999999


Q ss_pred             HHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccc
Q 010308          279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFG  357 (513)
Q Consensus       279 LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~  357 (513)
                      |+..|.++|+++|++|.   +++.+++||+||||+|||+|+++||+..|++|+||++|||+.++++++. +.+.+++|.+
T Consensus        51 L~~~y~~~v~~~a~~~~---~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~~  127 (285)
T TIGR02394        51 MIESNLRLVVSIAKHYV---NRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVH  127 (285)
T ss_pred             HHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcHH
Confidence            99999999999999998   7899999999999999999999999999999999999999999999999 8889999999


Q ss_pred             hhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchhhh
Q 010308          358 LESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQR  436 (513)
Q Consensus       358 ~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~~  436 (513)
                      +...++.+.+..+.+...+|+.|+.+++|+.+|++++++..++.......|+|.+...+.. .+.+.+.+....+|++..
T Consensus       128 ~~~~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~pe~~~  207 (285)
T TIGR02394       128 VIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLV  207 (285)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCCCHHHHH
Confidence            9999999999888888999999999999999999999999999988888999986544332 233344444445577777


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          437 QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       437 ~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ...+....|..+|..||+++|.||.++|||.+++++|++|||+.||||.++|++++++|+++||+.....
T Consensus       208 ~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~  277 (285)
T TIGR02394       208 QNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERD  277 (285)
T ss_pred             HHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            8888889999999999999999999999999999999999999999999999999999999999866543

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).

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=2e-40  Score=331.51  Aligned_cols=227  Identities=29%  Similarity=0.382  Sum_probs=196.0

Q ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-
Q 010308          269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-  347 (513)
Q Consensus       269 ~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-  347 (513)
                      ..|+..|++.||.+|+++|+++|++|..  ..+.+++||+|||+||||+|+++|||++|++|+|||+|||+++|.++++ 
T Consensus        20 ~~gd~~a~~~Lv~~~~~lV~~ia~~~~~--~~~~~~eDL~Qeg~igL~~a~~~fd~~~g~~F~tya~~~Ir~~i~~~lr~   97 (256)
T PRK07408         20 QNPSIALRNQLVELNLGLVRKEAHRWSN--QCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRD   97 (256)
T ss_pred             HCCCHHHHHHHHHHhHHHHHHHHHHHhc--cCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHH
Confidence            3678899999999999999999999973  2366799999999999999999999999999999999999999999999 


Q ss_pred             hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh--ccCcccccCCCCCchhh---hhc
Q 010308          348 VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEE---FIN  422 (513)
Q Consensus       348 ~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLd~~~~~~~~e---~~d  422 (513)
                      +..+||+|.++.+.++++.++..+|.+++|+.||.+|||+.||+++++|..++..  ....+|||.+...+++.   +.+
T Consensus        98 ~~~~vr~pr~~~~~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~~~l~d  177 (256)
T PRK07408         98 KSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGSTSLGD  177 (256)
T ss_pred             cCCeeeeCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCcccccc
Confidence            8899999999999999999999999999999999999999999999999998753  45688999986543332   223


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      .+.+... .+  .....+....|..+|..||++++.||.++|    ++++|++|||+.||||.++|++++.+|+++||+.
T Consensus       178 ~~~d~~~-~~--~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y----~~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~  250 (256)
T PRK07408        178 LLPDPRY-RS--FQLAQEDRIRLQQALAQLEERTREVLEFVF----LHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKL  250 (256)
T ss_pred             ccCCccc-ch--hhhhHHHHHHHHHHHHcCCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            3333221 11  112345567799999999999999999999    6899999999999999999999999999999976


Q ss_pred             ch
Q 010308          503 TR  504 (513)
Q Consensus       503 ~~  504 (513)
                      ..
T Consensus       251 l~  252 (256)
T PRK07408        251 LQ  252 (256)
T ss_pred             hh
Confidence            54

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=100.00  E-value=1e-39  Score=326.56  Aligned_cols=228  Identities=26%  Similarity=0.354  Sum_probs=199.7

Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhc
Q 010308          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS  349 (513)
Q Consensus       270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~  349 (513)
                      .|+..|++.||.+|+++|+++|++|...+..+++++||+|||++|||+|+++|||++|++|+|||+||||++|.++++..
T Consensus        19 ~~~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~ai~~fd~~~g~~F~tya~~~Ir~~i~~~lr~~   98 (257)
T PRK05911         19 TQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQ   98 (257)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhc
Confidence            57889999999999999999999986444456789999999999999999999999999999999999999999999932


Q ss_pred             cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhcc--CcccccCCCCC--chh---hhhc
Q 010308          350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK--PILSLHSRHGV--TQE---EFIN  422 (513)
Q Consensus       350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~--~~~SLd~~~~~--~~~---e~~d  422 (513)
                        .++|.++.+..+++..+...|.+.+||.||.+|||+.+|+++++|..++....  .++|||.+...  +++   .+.+
T Consensus        99 --~~~pr~~~~~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~~~l~~  176 (257)
T PRK05911         99 --DWVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEE  176 (257)
T ss_pred             --CCCCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccccchhh
Confidence              24899999999999999999999999999999999999999999999987654  46899986532  111   2344


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      .+.+.....|++.....++...|..+|+.|||+|+.||.++|    ++++|++|||+.||||.++|++++.+|+++||+.
T Consensus       177 ~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y----~e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~  252 (257)
T PRK05911        177 RIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKALLKLRAT  252 (257)
T ss_pred             hccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            555554445666777778888999999999999999999999    6899999999999999999999999999999975


Q ss_pred             c
Q 010308          503 T  503 (513)
Q Consensus       503 ~  503 (513)
                      .
T Consensus       253 l  253 (257)
T PRK05911        253 L  253 (257)
T ss_pred             H
Confidence            4

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=100.00  E-value=3.8e-39  Score=321.64  Aligned_cols=241  Identities=27%  Similarity=0.353  Sum_probs=210.6

Q ss_pred             cCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Q 010308          210 MKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLF  289 (513)
Q Consensus       210 i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI~~nlrLV~s  289 (513)
                      ...+|+||++|+..|+..+                                        ..||..|++.|+..|+++|++
T Consensus        10 ~~~~~~l~~~~~~~li~~~----------------------------------------~~gd~~a~~~L~~~~~~~v~~   49 (254)
T TIGR02850        10 TSKLPVLKNQEMRELFIRM----------------------------------------QSGDTTAREKLINGNLRLVLS   49 (254)
T ss_pred             ccCCCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHHHHHHHhHHHHHH
Confidence            4578999999998775544                                        357889999999999999999


Q ss_pred             HHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccchhHHHHHHHHHH
Q 010308          290 VIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAK  369 (513)
Q Consensus       290 IAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~~~~~~~ki~ka~  369 (513)
                      +|++|.   +++.+++||+||||+|||+|+++|||.+|.+|+||++|||+++|.++++....+|+|.++.+..+++.++.
T Consensus        50 ~a~~~~---~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~~ir~p~~~~~~~~~~~~~~  126 (254)
T TIGR02850        50 VIQRFN---NRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR  126 (254)
T ss_pred             HHHHHh---CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCCCccCchHHHHHHHHHHHHH
Confidence            999998   77899999999999999999999999999999999999999999999996568999999999999999999


Q ss_pred             HHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh---hhhccccCCCCCCchhhhHHHHHHHHHH
Q 010308          370 LELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE---EFINGITDVDGVENENQRQPALLRLALD  446 (513)
Q Consensus       370 ~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~---e~~d~l~d~~~~~~ee~~~~~~l~~~L~  446 (513)
                      .++..++|+.||.+|||+.||++++++..++.....+.|||.+...+++   .+.+.+.++..  +.   ........|.
T Consensus       127 ~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~--~~---~~~~~~~~l~  201 (254)
T TIGR02850       127 DKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN--KD---SQWLEGIALK  201 (254)
T ss_pred             HHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc--cH---HHHHhHHHHH
Confidence            9999999999999999999999999999999988888999987643322   13334433321  11   2234556789


Q ss_pred             HHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          447 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       447 ~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      .+|+.|+++++.||.++|    ++++|++|||+.||+|.++|++++.+|+++||+.
T Consensus       202 ~~l~~L~~rer~vi~~~~----~~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~  253 (254)
T TIGR02850       202 EAMKRLNEREKMILNMRF----FEGKTQMEVAEEIGISQAQVSRLEKAALKHMRKY  253 (254)
T ss_pred             HHHHcCCHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence            999999999999999999    5799999999999999999999999999999963

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.

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

Probab=100.00  E-value=1.3e-38  Score=315.11  Aligned_cols=225  Identities=32%  Similarity=0.429  Sum_probs=198.0

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCC-cHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHH
Q 010308          267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGP-RFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS  345 (513)
Q Consensus       267 ~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~-~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~ra  345 (513)
                      ...+|+..++ .||++|+|||.++|++|.   +++. .++||+|-|+|||++|+++|||++|.+|+|||...|+++|.++
T Consensus        17 ~~~~g~~~~~-~Li~~ylpLV~~ia~k~~---~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~   92 (247)
T COG1191          17 YYAEGDEEAR-RLIERYLPLVKSIARKFE---NRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDY   92 (247)
T ss_pred             HHHhcCHHHH-HHHHHHHHHHHHHHHHHH---hcCCCchhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHH
Confidence            3456889999 999999999999999999   4444 9999999999999999999999999999999999999999999


Q ss_pred             HHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhcc--CcccccCCCCCchhhhhcc
Q 010308          346 MTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK--PILSLHSRHGVTQEEFING  423 (513)
Q Consensus       346 I~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~--~~~SLd~~~~~~~~e~~d~  423 (513)
                      ++....+++|+.+++..+++..+..+|..++||+||++|||+.||++.++|..++...+  ..+|+|.....+++..   
T Consensus        93 LR~~~~v~vpR~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d~~---  169 (247)
T COG1191          93 LRKNDSVKVPRSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDD---  169 (247)
T ss_pred             HHhCCCccCcHHHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccccc---
Confidence            99433999999999999999999999999999999999999999999999999998765  6677777554332221   


Q ss_pred             ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                       .++...++++..+..++...|..++..|+++|+.||.+||    ++++|++|||+.||||.++|+|++.+|+++||...
T Consensus       170 -~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y----~eelt~kEI~~~LgISes~VSql~kkai~kLr~~l  244 (247)
T COG1191         170 -VDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRY----KEELTQKEIAEVLGISESRVSRLHKKAIKKLRKEL  244 (247)
T ss_pred             -hhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHH----HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHh
Confidence             1222334556677778888888888899999999999999    89999999999999999999999999999999654

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=100.00  E-value=1.1e-37  Score=311.69  Aligned_cols=240  Identities=29%  Similarity=0.382  Sum_probs=209.1

Q ss_pred             CCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 010308          211 KIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFV  290 (513)
Q Consensus       211 ~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI~~nlrLV~sI  290 (513)
                      ..+|+|+++|+..|+..+                                        ..||..|++.||..|+++|+++
T Consensus        14 ~~~~~l~~~~~~~l~~~~----------------------------------------~~gd~~a~~~l~~~~~~~v~~~   53 (258)
T PRK08215         14 SKLPVLKNEEMRELFERM----------------------------------------QNGDKEAREKLINGNLRLVLSV   53 (258)
T ss_pred             CCCCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHHHHHHHHHHHHHHH
Confidence            467899999888775544                                        3578899999999999999999


Q ss_pred             HHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccchhHHHHHHHHHHH
Q 010308          291 IKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKL  370 (513)
Q Consensus       291 Akky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~~~~~~~ki~ka~~  370 (513)
                      |++|.   +++.+++||+|||++|||+|+++||+.+|.+|+||++|||+++|.++++....+|+|.++.....++.++..
T Consensus        54 a~~~~---~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~~~~vrip~~~~~~~~~~~~~~~  130 (258)
T PRK08215         54 IQRFN---NRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVRE  130 (258)
T ss_pred             HHHHh---CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHhCCceEecHHHHHHHHHHHHHHH
Confidence            99998   778999999999999999999999999999999999999999999999955688999999999999999999


Q ss_pred             HHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhh---hhccccCCCCCCchhhhHHHHHHHHHHH
Q 010308          371 ELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE---FINGITDVDGVENENQRQPALLRLALDD  447 (513)
Q Consensus       371 ~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e---~~d~l~d~~~~~~ee~~~~~~l~~~L~~  447 (513)
                      ++..++|+.||.+|||+.||++++++..++.....+.|||.+...+++.   +.+.+.+...     ..+.......|..
T Consensus       131 ~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~l~~  205 (258)
T PRK08215        131 KLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQISDEKN-----KDENWLEEIALKE  205 (258)
T ss_pred             HHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhhhhhccCccc-----cHHHHHhHHHHHH
Confidence            9999999999999999999999999999998888888999886443321   2233333211     1223345567889


Q ss_pred             HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          448 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       448 aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      +|+.||++++.||.++|    ++++|++|||+.||+|.++|++++.+|+++||+.
T Consensus       206 ~l~~L~~~er~vi~~~~----~~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~  256 (258)
T PRK08215        206 AMKKLNDREKLILNLRF----FQGKTQMEVAEEIGISQAQVSRLEKAALKHMRKY  256 (258)
T ss_pred             HHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999    6899999999999999999999999999999964

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=100.00  E-value=1.9e-36  Score=304.35  Aligned_cols=249  Identities=23%  Similarity=0.349  Sum_probs=214.9

Q ss_pred             CCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q 010308          211 KIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFV  290 (513)
Q Consensus       211 ~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI~~nlrLV~sI  290 (513)
                      |.+|+||+++|..|+..++                                       ..||..|++.|+..|.++|+.+
T Consensus         7 ~~~~~~~~~~e~~l~~~~~---------------------------------------~~~d~~a~~~l~~~y~~lv~~~   47 (268)
T PRK06288          7 GKIPKYAQQDETELWREYK---------------------------------------KTGDPKIREYLILKYSPLVKYV   47 (268)
T ss_pred             CCCccccchHHHHHHHHHH---------------------------------------HcCCHHHHHHHHHHHHHHHHHH
Confidence            6789999999999877652                                       2468899999999999999999


Q ss_pred             HHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccchhHHHHHHHHHHH
Q 010308          291 IKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKL  370 (513)
Q Consensus       291 Akky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~~~~~~~ki~ka~~  370 (513)
                      |++|......+.+++||+||||+|||+|+++||+.+|++|+||++|||++.|.++++.  .+++|.++....+++.++..
T Consensus        48 a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~--~~~~p~~~~~~~~~i~~~~~  125 (268)
T PRK06288         48 AGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRS--IDWIPRSVRQKARQIERAIA  125 (268)
T ss_pred             HHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHh--cCccCHHHHHHHHHHHHHHH
Confidence            9998632235778999999999999999999999999999999999999999999982  35689999999999999999


Q ss_pred             HHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhc--cCcccccCCCCC--chh--hhhccccCCCCCCchhhhHHHHHHHH
Q 010308          371 ELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGV--TQE--EFINGITDVDGVENENQRQPALLRLA  444 (513)
Q Consensus       371 ~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLd~~~~~--~~~--e~~d~l~d~~~~~~ee~~~~~~l~~~  444 (513)
                      .|.+++|+.||.+|||+.+|++.+++..++...  ...+|||.....  +.+  .+.+.+.+....+|++.....+....
T Consensus       126 ~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~e~~~~  205 (268)
T PRK06288        126 MLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAEREEIKRV  205 (268)
T ss_pred             HHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHHHHHHH
Confidence            999999999999999999999999999998654  456888876531  111  23444555555667777778888889


Q ss_pred             HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          445 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       445 L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      |..+|+.||++++.||.++|    ++++|++|||+.||+|.++|++++.+|+++||....
T Consensus       206 l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~  261 (268)
T PRK06288        206 IVEAIKTLPEREKKVLILYY----YEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLA  261 (268)
T ss_pred             HHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999    789999999999999999999999999999997643

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=100.00  E-value=3.2e-36  Score=295.77  Aligned_cols=224  Identities=30%  Similarity=0.401  Sum_probs=197.1

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHH
Q 010308          267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM  346 (513)
Q Consensus       267 ~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI  346 (513)
                      ++..|+..|++.|+..|.++|+++|++|.   +++.+++||+|||++|||+++++|||..|.+|+||++|||++.|.+++
T Consensus         4 ~~~~gd~~a~~~l~~~y~~~v~~~a~~~~---~~~~~aeDl~Qe~~i~l~~a~~~f~~~~~~~f~tyl~~~i~~~i~~~l   80 (231)
T TIGR02885         4 LAQNGDKEARDKLIECNLRLVWSIVKRFL---NRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFL   80 (231)
T ss_pred             HHHcCCHHHHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHH
Confidence            34578999999999999999999999998   778999999999999999999999999999999999999999999999


Q ss_pred             HhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh---hhhcc
Q 010308          347 TVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE---EFING  423 (513)
Q Consensus       347 ~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~---e~~d~  423 (513)
                      +....+++|.++....+++.++...|..++|+.||.+|||+.+|++++++..++.....+.|||....++++   .+++.
T Consensus        81 r~~~~i~~p~~~~~~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~  160 (231)
T TIGR02885        81 RDDGIIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQ  160 (231)
T ss_pred             HhCCCeECCHHHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcchhhhh
Confidence            955689999999999999999999999999999999999999999999999999888888999987654332   12333


Q ss_pred             ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      +.++..  +   .........|..+|+.||++|+.||.++|    ++++|++|||+.||+|+++|++++++|+++||..
T Consensus       161 ~~~~~~--~---~~~~~~~~~l~~~l~~L~~~e~~i~~~~~----~~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~  230 (231)
T TIGR02885       161 IADKGS--E---DSDWLEKIALKEAISKLDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKMKEK  230 (231)
T ss_pred             cCCCCc--c---HHhHHHHHHHHHHHHcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence            333211  1   12334566788999999999999999999    5799999999999999999999999999999963

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.

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=100.00  E-value=2.4e-35  Score=294.04  Aligned_cols=225  Identities=25%  Similarity=0.301  Sum_probs=197.5

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hc
Q 010308          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VS  349 (513)
Q Consensus       271 gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~  349 (513)
                      ||..|++.|+..|.++|+.+|++|.   +++.+.+||+||||+|||+|+++||++.|..|+||+++||++.|.++++ +.
T Consensus        26 gd~~a~~~l~~~y~~~v~~~a~~~~---~~~~~aeDlvQe~~i~l~~a~~~~~~~~~~~f~tyl~~~i~n~~~~~lr~~~  102 (255)
T TIGR02941        26 QNGEAQEKLVDHYQNLVYSIAYKYS---KGGPMHEDLVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKT  102 (255)
T ss_pred             CCHHHHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHcCCcCCCCcHhHHHHHHHHHHHHHHHHcC
Confidence            6789999999999999999999998   7889999999999999999999999999999999999999999999999 67


Q ss_pred             cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhc--cCcccccCCCCCchhhhhccccCC
Q 010308          350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQEEFINGITDV  427 (513)
Q Consensus       350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLd~~~~~~~~e~~d~l~d~  427 (513)
                      ..+++|.++.+..++++++...+...+|+.||.+|+|+.+|++.+++..++...  ....|||.++..+++.......+.
T Consensus       103 ~~iri~~~~~~~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~  182 (255)
T TIGR02941       103 WSVHVPRRIKELGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTVARLDS  182 (255)
T ss_pred             CCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCcccccccc
Confidence            789999999999999999999999999999999999999999999999887754  467888887654333211111111


Q ss_pred             CCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          428 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       428 ~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                       ..++++.....+....|..+|+.||++++.||.++|    ++++|++|||+.||||.++|++++.+|+++||...
T Consensus       183 -~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~ii~l~~----~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~  253 (255)
T TIGR02941       183 -VGEVEDGYDQTERRMVLEKILPILSEREKSIIHCTF----EENLSQKETGERLGISQMHVSRLQRQAISKLKEAA  253 (255)
T ss_pred             -cCCcchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence             122455566677778899999999999999999999    68999999999999999999999999999999753

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

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

Probab=100.00  E-value=4.2e-35  Score=286.94  Aligned_cols=222  Identities=31%  Similarity=0.396  Sum_probs=194.2

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcc
Q 010308          272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSS  350 (513)
Q Consensus       272 d~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r  350 (513)
                      |..|++.||..|.++|+++|++|.   +++.+.+||+|||++|||+|+++||+++|.+|+||++|||++.|.++++ +..
T Consensus         1 ~~~a~~~lv~~y~~~v~~~a~~~~---~~~~~~eDl~Qe~~i~l~~a~~~f~~~~~~~F~ty~~~~i~~~~~~~~r~~~~   77 (227)
T TIGR02980         1 DKEAREKLVELNLPLVRSIARRFR---NRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRFFRDDTW   77 (227)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHhcCcccCCCcHHHHHHHHHHHHHHHHHHcCC
Confidence            457999999999999999999998   6788999999999999999999999999999999999999999999999 667


Q ss_pred             ccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccC--cccccCCCCCchhhhhccccCCC
Q 010308          351 FTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKP--ILSLHSRHGVTQEEFINGITDVD  428 (513)
Q Consensus       351 ~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~--~~SLd~~~~~~~~e~~d~l~d~~  428 (513)
                      .+++|.++.+..++++++...+.+.+|+.||.+|||+.+|++++++..++.....  ..|||.+..++++. ...+.+ .
T Consensus        78 ~~ri~~~~~~~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~-~~~~~d-~  155 (227)
T TIGR02980        78 AVRVPRRLKELGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGD-PIALLD-T  155 (227)
T ss_pred             ceecCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCC-Cccccc-c
Confidence            9999999999999999999999999999999999999999999999998887654  88999876522211 111111 1


Q ss_pred             CCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          429 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       429 ~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ..++++..+..+....|..+|..||++|+.||.++|    ++++|++|||+.||+|.++|++++.+|+++||+.
T Consensus       156 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y----~~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~  225 (227)
T TIGR02980       156 LGDEDDALETVEDRLALKPLLAALPERERRILLLRF----FEDKTQSEIAERLGISQMHVSRLLRRALKKLREQ  225 (227)
T ss_pred             cCCcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            122344455667778899999999999999999999    6899999999999999999999999999999964

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

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=100.00  E-value=2.6e-34  Score=286.20  Aligned_cols=229  Identities=25%  Similarity=0.329  Sum_probs=198.8

Q ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh
Q 010308          269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV  348 (513)
Q Consensus       269 ~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~  348 (513)
                      ..||..|++.||..|.++|+++|.+|..++.++.+.+||+||||+|||+++++||+.+|.+|+||++|||++.|.++++.
T Consensus        17 ~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~d~lR~   96 (251)
T PRK07670         17 EERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRK   96 (251)
T ss_pred             HcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHh
Confidence            35689999999999999999999999743346889999999999999999999999999999999999999999999993


Q ss_pred             ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh--ccCcccccCCCCCchhh--hhccc
Q 010308          349 SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEE--FINGI  424 (513)
Q Consensus       349 ~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLd~~~~~~~~e--~~d~l  424 (513)
                      .  .++|.++.+.+++++++...+.+.+|+.|+.+|||+.+|+++++|..++..  .....|||.+..++++.  +...+
T Consensus        97 ~--~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~  174 (251)
T PRK07670         97 E--DWLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTI  174 (251)
T ss_pred             c--CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhh
Confidence            2  269999999999999999999999999999999999999999999999764  45778999886433322  22233


Q ss_pred             cCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          425 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       425 ~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      .+....++++.....+....|..+|+.||+++|.||.++|    ++++|++|||+.||+|.++|++++.+|+++||...
T Consensus       175 ~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l  249 (251)
T PRK07670        175 RDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLKKLL  249 (251)
T ss_pred             cCcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            3444445666667777788899999999999999999999    79999999999999999999999999999999643

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=100.00  E-value=3.9e-34  Score=282.18  Aligned_cols=212  Identities=21%  Similarity=0.281  Sum_probs=180.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcccccc
Q 010308          275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRV  354 (513)
Q Consensus       275 Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRl  354 (513)
                      ....|+..|++||.++|++|......+.+.+||+|||++|||+|+++||+..| +|+|||+|||+++|.++++..  .++
T Consensus        16 ~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~--~~~   92 (231)
T PRK12427         16 EEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELREL--DWR   92 (231)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhc--CCC
Confidence            45688999999999999999865556789999999999999999999998666 899999999999999999932  247


Q ss_pred             ccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh--ccCcccccCCCCCchhhhhccccCCCCCCc
Q 010308          355 PFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEEFINGITDVDGVEN  432 (513)
Q Consensus       355 P~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~  432 (513)
                      |.++....++++++...|.+++|+.||.+|||+.||+++++|.+++..  .....|||.+.+.++..  +.+ +  ..++
T Consensus        93 ~r~vr~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~--~~~-~--~~~~  167 (231)
T PRK12427         93 PRRLRQKTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHN--DIL-Q--SRDL  167 (231)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCcc--ccc-C--CCCH
Confidence            888999999999999999999999999999999999999999998764  45789999986543321  111 1  1112


Q ss_pred             hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          433 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       433 ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                      +   +.......|..+|..||++++.||.++|    ++++|++|||+.||||.++|+|++.+|+++||.
T Consensus       168 ~---~~~~~~~~l~~~l~~L~~~er~vi~l~~----~~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~  229 (231)
T PRK12427        168 E---ENIIIEDNLKQALSQLDEREQLILHLYY----QHEMSLKEIALVLDLTEARICQLNKKIAQKIKS  229 (231)
T ss_pred             H---HHHHHHHHHHHHHHcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence            2   2334566789999999999999999999    689999999999999999999999999999985

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

Probab=100.00  E-value=3.5e-34  Score=280.27  Aligned_cols=218  Identities=28%  Similarity=0.411  Sum_probs=190.3

Q ss_pred             HHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccch
Q 010308          279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGL  358 (513)
Q Consensus       279 LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~~  358 (513)
                      |+..|.++|+++|++|..+++++.+++||+|||++|||+|+++|||++|++|+||+++||++.+.++++..  .++|.++
T Consensus         1 L~~~~~~lv~~~a~~~~~~~~~~~~~eDl~Qe~~~~l~~a~~~fd~~~~~~f~t~~~~~i~~~~~~~lr~~--~~~p~~~   78 (224)
T TIGR02479         1 LIRRYLPLVKRIAGRLSVGLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRL--DWVPRSL   78 (224)
T ss_pred             CHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHHc--CccCHHH
Confidence            68899999999999998544478999999999999999999999999999999999999999999999832  3699999


Q ss_pred             hHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhc--cCcccccCCCCCc--hhhhhccccCCCCCCchh
Q 010308          359 ESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVT--QEEFINGITDVDGVENEN  434 (513)
Q Consensus       359 ~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLd~~~~~~--~~e~~d~l~d~~~~~~ee  434 (513)
                      ...++++.++..+|.+++|+.|+.+|||+.+|+++++|..++...  ...+|+|....+.  ...+.+.+.++...++++
T Consensus        79 ~~~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~  158 (224)
T TIGR02479        79 RQKARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPEE  158 (224)
T ss_pred             HHHHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhccccccCCHHH
Confidence            999999999999999999999999999999999999999998643  4567888754432  122333444444556777


Q ss_pred             hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      .....+....|..+|+.||++++.||.++|    .+++|++|||+.||+|.++|++++.+|+++||..
T Consensus       159 ~~~~~~~~~~l~~~l~~L~~~~r~il~l~y----~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~  222 (224)
T TIGR02479       159 ELEREELREALAEAIESLSEREQLVLSLYY----YEELNLKEIGEVLGLTESRVSQIHSQALKKLRAK  222 (224)
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            777888888999999999999999999999    7899999999999999999999999999999964

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

>PRK05572 sporulation sigma factor SigF; Validated

Probab=100.00  E-value=1e-33  Score=282.17  Aligned_cols=242  Identities=29%  Similarity=0.404  Sum_probs=208.5

Q ss_pred             HhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 010308          208 KKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLV  287 (513)
Q Consensus       208 ~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI~~nlrLV  287 (513)
                      +.-+..|.||.+++..|...+                                        ..|+..|++.|+..|.++|
T Consensus         6 ~~~~~~~~l~~~~~~~li~~~----------------------------------------~~gd~~a~~~L~~~y~~~v   45 (252)
T PRK05572          6 KNKKKKPQLKDEENKELIKKS----------------------------------------QDGDQEARDTLVEKNLRLV   45 (252)
T ss_pred             ccCcCCCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHHHHHHHhHHHH
Confidence            345678999998887774433                                        3578899999999999999


Q ss_pred             HHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccchhHHHHHHHH
Q 010308          288 LFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQR  367 (513)
Q Consensus       288 ~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~~~~~~~ki~k  367 (513)
                      +.+|++|.   +++.+++||+||||+++|+++++|++.+|.+|+||+++||++.|.++++..+.+++|.++....+++++
T Consensus        46 ~~~a~~~~---~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~~~~~r~~~~~~~~~~~~~~  122 (252)
T PRK05572         46 WSVVQRFL---NRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDGTVKVSRSLKETANKIRK  122 (252)
T ss_pred             HHHHHHHc---cCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH
Confidence            99999998   788999999999999999999999999888999999999999999999966789999999999999999


Q ss_pred             HHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhh---hhccccCCCCCCchhhhHHHHHHHH
Q 010308          368 AKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE---FINGITDVDGVENENQRQPALLRLA  444 (513)
Q Consensus       368 a~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e---~~d~l~d~~~~~~ee~~~~~~l~~~  444 (513)
                      +...+..++||.|+.+|+|+.+|++++++..++.....+.||+.+..+++..   ..+.+.++.       .........
T Consensus       123 ~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~~d~~~~~~-------~~~~~~~~~  195 (252)
T PRK05572        123 DKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITLLDQIADQS-------EEDWFDKIA  195 (252)
T ss_pred             HHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchhhhhcCCCc-------hhhHHHHHH
Confidence            9999999999999999999999999999999988888888998775433221   112222211       122345678


Q ss_pred             HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          445 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       445 L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      |..+|+.||++++.||.++|    ++++|++|||+.||+|.++|++++.+|+++||...
T Consensus       196 l~~~l~~L~~~~~~v~~l~~----~~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l  250 (252)
T PRK05572        196 LKEAIRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKL  250 (252)
T ss_pred             HHHHHHcCCHHHHHHHHHHH----hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            89999999999999999999    68999999999999999999999999999999643

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=100.00  E-value=2.9e-33  Score=279.29  Aligned_cols=227  Identities=25%  Similarity=0.299  Sum_probs=196.7

Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-h
Q 010308          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-V  348 (513)
Q Consensus       270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~  348 (513)
                      .||..|++.|+..|.++|+++|++|.   +++.+++||+||||++||+++++||+..|.+|+||+++||++.|.++++ +
T Consensus        25 ~gd~~a~~~l~~~~~~~v~~~a~~~~---~~~~~aeDlvQe~~l~l~~~~~~f~~~~~~~f~tyl~~~i~n~~~~~lr~~  101 (257)
T PRK08583         25 NQDEEAQEKLVKHYKNLVESLAYKYS---KGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDK  101 (257)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHcCccCCCChHHHHHHHHHHHHHHHHHhc
Confidence            37889999999999999999999998   7788999999999999999999999999989999999999999999999 6


Q ss_pred             ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhc--cCcccccCCCCCchhhhhccccC
Q 010308          349 SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQEEFINGITD  426 (513)
Q Consensus       349 ~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLd~~~~~~~~e~~d~l~d  426 (513)
                      ...+++|.++.+..+++..+...+...++|.|+.+|+|+.+|++.+++...+...  ....|+|.+.+.+++.....+.+
T Consensus       102 ~~~~~i~r~~~~~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~  181 (257)
T PRK08583        102 TWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLLD  181 (257)
T ss_pred             CCCcCCCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCccchHhh
Confidence            7789999999999999999999999999999999999999999999998887654  35678887764433221111111


Q ss_pred             CCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          427 VDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       427 ~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                       ...++++.....+....|..+|..||++++.||.++|    ++++|++|||+.||||.++|++++++|+++||....
T Consensus       182 -~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~  254 (257)
T PRK08583        182 -IVGQQEDGYELTEQRMILEKILPVLSDREKSIIQCTF----IENLSQKETGERLGISQMHVSRLQRQAIKKLREAAF  254 (257)
T ss_pred             -hcCCcchhHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence             1123455556667778899999999999999999999    689999999999999999999999999999997543

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=100.00  E-value=7.8e-33  Score=272.97  Aligned_cols=226  Identities=24%  Similarity=0.358  Sum_probs=193.6

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcc
Q 010308          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS  350 (513)
Q Consensus       271 gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r  350 (513)
                      .|.-+++.|+..|.++|+++|++|..+++++.+++||+||||+|||+++++|||+.|.+|+||+++||++.+.+++++..
T Consensus         5 ~~~~~~~~L~~~~~~~v~~~a~~~~~~~~~~~~aeDlvQe~~i~l~~~~~~f~~~~~~~f~tyl~~~irn~~~~~lR~~~   84 (236)
T PRK06986          5 EGKMDQDELVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLD   84 (236)
T ss_pred             cccccHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHcC
Confidence            45678999999999999999999974445788999999999999999999999999999999999999999999999322


Q ss_pred             ccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhc--cCcccccCCCCCchhhhhccccCCC
Q 010308          351 FTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQEEFINGITDVD  428 (513)
Q Consensus       351 ~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLd~~~~~~~~e~~d~l~d~~  428 (513)
                        ++|.++.....++.++...+.+.+|+.||.+|||+.+|++.++|..++...  ...+|++...+.+++.+. ...++.
T Consensus        85 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~-~~~~~~  161 (236)
T PRK06986         85 --WVPRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSIL-VTEDHQ  161 (236)
T ss_pred             --CCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcccc-cccCCC
Confidence              368888888888999999999999999999999999999999999998764  356678877554433322 122233


Q ss_pred             CCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          429 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       429 ~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      ..++++.....+....|..+|+.||++++.||.++|    .+++|++|||+.||||.++|++++.+|+++||+..
T Consensus       162 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l  232 (236)
T PRK06986        162 DEDPLQQLEDEELREALVEAIESLPEREQLVLSLYY----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARL  232 (236)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHh----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            345666677777888999999999999999999999    78999999999999999999999999999999753

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.95  E-value=5.1e-27  Score=231.30  Aligned_cols=207  Identities=30%  Similarity=0.382  Sum_probs=164.4

Q ss_pred             hHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHHH
Q 010308          202 LVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIK  281 (513)
Q Consensus       202 ~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI~  281 (513)
                      ++..|+.++++.|+||++++..|...+                                        ..|+..|++.|+.
T Consensus        17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~----------------------------------------~~gd~~a~~~l~~   56 (233)
T PRK05803         17 FLVSYVKNNSFPQPLSEEEERKYLELM----------------------------------------KEGDEEARNILIE   56 (233)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHHHHHH
Confidence            677899999999999999988775444                                        3578899999999


Q ss_pred             HHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchhH
Q 010308          282 HNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLES  360 (513)
Q Consensus       282 ~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~~  360 (513)
                      .|.++|+++|.+|.   +++.+.+||+|||+++||+++++||+++|.+|.||+++|+++.+.++++ ..+..        
T Consensus        57 ~y~~~l~~~a~~~~---~~~~daeDlvQE~fi~l~~~~~~f~~~~~~~f~~wl~~i~rn~~id~~Rk~~~~~--------  125 (233)
T PRK05803         57 RNLRLVAHIVKKFE---NTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNLKKTK--------  125 (233)
T ss_pred             HhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHhcCcccCCChHHHHHHHHHHHHHHHHHHHhccc--------
Confidence            99999999999998   7889999999999999999999999998889999999999999999988 32110        


Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCc--h--hhhhccccCCCCCCchhhh
Q 010308          361 VRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVT--Q--EEFINGITDVDGVENENQR  436 (513)
Q Consensus       361 ~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~--~--~e~~d~l~d~~~~~~ee~~  436 (513)
                                                                  ...+++.....+  +  ..+.+...+ ...++++..
T Consensus       126 --------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  160 (233)
T PRK05803        126 --------------------------------------------KEVSLQDPIGVDKEGNEISLIDILGS-EEDDVIEQV  160 (233)
T ss_pred             --------------------------------------------cCCCccccccCCCCcCcccHHHHccC-CCCCHHHHH
Confidence                                                        001111111000  0  011111111 122345555


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          437 QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       437 ~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ........|..+|+.||+++|+||.++|++.+++++|++|||+.||||.++|++++.+|+++||....
T Consensus       161 ~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~  228 (233)
T PRK05803        161 ELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELY  228 (233)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            66667778999999999999999999998877799999999999999999999999999999997654

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=99.92  E-value=1.8e-23  Score=205.82  Aligned_cols=180  Identities=26%  Similarity=0.409  Sum_probs=137.8

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH
Q 010308          268 CLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT  347 (513)
Q Consensus       268 ~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~  347 (513)
                      +..||..|++.|+..|.++|+.+|++|.   +++.+.+|++||+|+++|+++++|++..+++|.||+++++++.+.++++
T Consensus        46 ~~~gd~~af~~l~~~y~~~l~~~a~~~~---~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~lR  122 (234)
T PRK08301         46 LPKGDEAVRSLLIERNLRLVVYIARKFE---NTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLR  122 (234)
T ss_pred             HHccCHHHHHHHHHHhHHHHHHHHHHhh---cCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHHHH
Confidence            4568899999999999999999999998   7788999999999999999999999988889999999999999999998


Q ss_pred             -hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCC--chh-h-hhc
Q 010308          348 -VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV--TQE-E-FIN  422 (513)
Q Consensus       348 -~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~--~~~-e-~~d  422 (513)
                       +.+..                                                    ...+++.....  ++. . ..+
T Consensus       123 k~~~~~----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~  150 (234)
T PRK08301        123 RNNKVK----------------------------------------------------AEVSFDEPLNIDWDGNELLLSD  150 (234)
T ss_pred             HHhccc----------------------------------------------------cccccccccccccCCCcccHHH
Confidence             32110                                                    00111111000  000 0 001


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ...+ ....+............|..+|++||+++|.||.++|+|...+++|++|||+.||||.++|++++++|+++||+.
T Consensus       151 ~~~~-~~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~  229 (234)
T PRK08301        151 VLGT-DNDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE  229 (234)
T ss_pred             hccC-cccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            1111 111122233344556679999999999999999999987667899999999999999999999999999999975


Q ss_pred             c
Q 010308          503 T  503 (513)
Q Consensus       503 ~  503 (513)
                      .
T Consensus       230 l  230 (234)
T PRK08301        230 I  230 (234)
T ss_pred             H
Confidence            3

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.92  E-value=2.7e-23  Score=204.23  Aligned_cols=179  Identities=35%  Similarity=0.438  Sum_probs=137.5

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH
Q 010308          268 CLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT  347 (513)
Q Consensus       268 ~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~  347 (513)
                      +..|+..|++.|+..|.++|+++|.+|.   ++..+.+||+||+|+++|+++++|+++.+..|.||+++++++.+.++++
T Consensus        42 ~~~gd~~af~~l~~~y~~~v~~~~~~~~---~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~R  118 (227)
T TIGR02846        42 LKEGDEEARNVLIERNLRLVAHIVKKFS---NTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHLR  118 (227)
T ss_pred             HHcCCHHHHHHHHHHhHHHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHHH
Confidence            3568899999999999999999999998   6788999999999999999999999988888999999999999999998


Q ss_pred             -hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCC--ch--hhhhc
Q 010308          348 -VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV--TQ--EEFIN  422 (513)
Q Consensus       348 -~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~--~~--~e~~d  422 (513)
                       ..+..+                                                    ..+++.....  +.  ....+
T Consensus       119 k~~r~~~----------------------------------------------------~~~~~~~~~~~~~~~~~~~~~  146 (227)
T TIGR02846       119 ALKKTKG----------------------------------------------------EVSLQDPIGVDKEGNEISLID  146 (227)
T ss_pred             HHhcccc----------------------------------------------------ceeccccccCCcccCcccHHH
Confidence             321100                                                    0011110000  00  00111


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ... .....+++.....+....|..+|+.||+++|+||.++|.++.++++|++|||+.||+|.++|++++++|+++||+.
T Consensus       147 ~~~-~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~  225 (227)
T TIGR02846       147 ILG-SDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKE  225 (227)
T ss_pred             Hhc-CCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            111 1122244444555666779999999999999999999955444899999999999999999999999999999964

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.

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=99.90  E-value=3.4e-22  Score=197.20  Aligned_cols=184  Identities=26%  Similarity=0.402  Sum_probs=139.0

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010308          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (513)
Q Consensus       265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r  344 (513)
                      +..+..|+..|++.|+..|.+.|+++|.+|.   +++.+.+||+||+|+++|+++++|++..+++|+||++.++++.+.+
T Consensus        43 ~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~---~~~~~AEDlvQE~fl~l~~~~~~f~~~~~~~f~~wl~~iarN~~~d  119 (234)
T TIGR02835        43 LQKLTQGDESAKSTLIERNLRLVVYIARKFE---NTGIGIEDLVSIGTIGLIKAVNTFNPSKKIKLATYASRCIENEILM  119 (234)
T ss_pred             HHHHHcCCHHHHHHHHHHhHHHHHHHHHHhc---cCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHH
Confidence            3444678899999999999999999999998   7888999999999999999999999888888999999999999999


Q ss_pred             HHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCC---Cchhhh
Q 010308          345 SMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHG---VTQEEF  420 (513)
Q Consensus       345 aI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~---~~~~e~  420 (513)
                      +++ +.+...                                                    ..+++....   .++...
T Consensus       120 ~~Rk~~r~~~----------------------------------------------------~~~~~~~~~~~~~~~~~~  147 (234)
T TIGR02835       120 YLRRNNKTRS----------------------------------------------------EVSFDEPLNVDWDGNELL  147 (234)
T ss_pred             HHHHhccccC----------------------------------------------------cccccccccCCCCCCcch
Confidence            998 322100                                                    001111100   000000


Q ss_pred             hccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010308          421 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       421 ~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR  500 (513)
                      .....+.+...+++..........|..+|+.||++++.||.++|.|.+++++|++|||+.||||..+|++++.+|+++||
T Consensus       148 ~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR  227 (234)
T TIGR02835       148 LSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLK  227 (234)
T ss_pred             HHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            00111111111223334445566799999999999999999999665558999999999999999999999999999999


Q ss_pred             Ccc
Q 010308          501 HPT  503 (513)
Q Consensus       501 ~~~  503 (513)
                      +..
T Consensus       228 ~~l  230 (234)
T TIGR02835       228 KEI  230 (234)
T ss_pred             HHh
Confidence            754

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

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=99.87  E-value=3.7e-21  Score=184.93  Aligned_cols=186  Identities=18%  Similarity=0.228  Sum_probs=138.2

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010308          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (513)
Q Consensus       264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~  343 (513)
                      .+..+..|+..|++.|+..|.++|+.+|.+|.   ++..+.+||+||+|++||+++++|++.++.+|.||++.++++.+.
T Consensus        14 l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~---~~~~~aeDlvQe~~l~l~~~~~~~~~~~~~~f~twl~~i~~n~~~   90 (208)
T PRK08295         14 LVELARSGDKEALEYLIEKYKNFVRAKARSYF---LIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCITRQII   90 (208)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHH
Confidence            34556789999999999999999999999998   788999999999999999999999998877999999999999999


Q ss_pred             HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCch--hhh
Q 010308          344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ--EEF  420 (513)
Q Consensus       344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~--~e~  420 (513)
                      ++++ ..+..+.+.                                               ....|++.....+.  ..+
T Consensus        91 d~~r~~~r~~~~~~-----------------------------------------------~~~~s~~~~~~~~~~~~~~  123 (208)
T PRK08295         91 TAIKTANRQKHIPL-----------------------------------------------NSYVSLDKPIYDEESDRTL  123 (208)
T ss_pred             HHHHHhhhhccccc-----------------------------------------------cceeecCCcccCCccchhH
Confidence            8887 222111110                                               00112222111101  111


Q ss_pred             hccccCCCCCCchhhhHHHHHHHHH-HHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010308          421 INGITDVDGVENENQRQPALLRLAL-DDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL  499 (513)
Q Consensus       421 ~d~l~d~~~~~~ee~~~~~~l~~~L-~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKL  499 (513)
                      .+.+.++...+|++.....+....+ ..+++.||+.++.||.+ |    .+++|++|||+.||+|.++|+..+.+|+++|
T Consensus       124 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~----~e~~s~~EIA~~lgis~~tV~~~l~rar~~L  198 (208)
T PRK08295        124 LDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-Y----LDGKSYQEIAEELNRHVKSIDNALQRVKRKL  198 (208)
T ss_pred             HHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-H----HccCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            1212222223455444444444445 56779999999999999 7    5899999999999999999999999999999


Q ss_pred             hCcch
Q 010308          500 KHPTR  504 (513)
Q Consensus       500 R~~~~  504 (513)
                      |....
T Consensus       199 r~~l~  203 (208)
T PRK08295        199 EKYLE  203 (208)
T ss_pred             HHHHH
Confidence            97654

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.86  E-value=1.6e-20  Score=178.48  Aligned_cols=171  Identities=17%  Similarity=0.168  Sum_probs=134.5

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhcc-CCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010308          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDF-ANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (513)
Q Consensus       265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~-~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~  343 (513)
                      +.....|+..|++.|+..|.+.|+.+|.++..+. +...+.+|++||+|++||+++.+|++. +..|.+|++..+++.+.
T Consensus        15 ~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~~~~wl~~i~~n~~~   93 (189)
T PRK09648         15 VAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITALPRYRDQ-GRPFLAFVYGIAAHKVA   93 (189)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHHHHHHhcc-CCcHHHHHHHHHHHHHH
Confidence            5566789999999999999999999999987321 124689999999999999999999864 45799999999999999


Q ss_pred             HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      ++++ +.+....+                                                     .+        ...+
T Consensus        94 d~~r~~~r~~~~~-----------------------------------------------------~~--------~~~~  112 (189)
T PRK09648         94 DAHRAAGRDKAVP-----------------------------------------------------TE--------EVPE  112 (189)
T ss_pred             HHHHHhCCCcccc-----------------------------------------------------cc--------cccc
Confidence            9888 32210000                                                     00        0000


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      .. + ...++++.....+....|..+|..||+++|.||.++|    ++++|++|||+.||||..+|++.+.||+++||+.
T Consensus       113 ~~-~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~  186 (189)
T PRK09648        113 RP-S-DDAGPEERALRSESSNRMRELLDTLPEKQREILILRV----VVGLSAEETAEAVGSTPGAVRVAQHRALARLRAE  186 (189)
T ss_pred             cc-c-cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            00 1 1123455555666777899999999999999999999    7899999999999999999999999999999965


Q ss_pred             c
Q 010308          503 T  503 (513)
Q Consensus       503 ~  503 (513)
                      .
T Consensus       187 l  187 (189)
T PRK09648        187 I  187 (189)
T ss_pred             h
Confidence            3

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.86  E-value=1.4e-20  Score=178.48  Aligned_cols=170  Identities=12%  Similarity=0.130  Sum_probs=136.6

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010308          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (513)
Q Consensus       263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI  342 (513)
                      ..+..+..|+..|++.|+..|.++|+.+|.+|.   +++.+.+|++||+|++||+++.+|++. +..|.+|++..+++.+
T Consensus         9 ~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~~   84 (186)
T PRK05602          9 ELLARVAAGDPAAFRVLVARKLPRLLALATRML---GDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNLC   84 (186)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHHH
Confidence            345667889999999999999999999999998   778899999999999999999999986 4579999999999999


Q ss_pred             HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      .++++..+..  +                                                     .+.     ..+   
T Consensus        85 ~d~~R~~~~~--~-----------------------------------------------------~~~-----~~~---  101 (186)
T PRK05602         85 YDRLRRRREV--P-----------------------------------------------------VED-----APD---  101 (186)
T ss_pred             HHHHHhcCCC--C-----------------------------------------------------ccc-----ccc---
Confidence            8888721100  0                                                     000     000   


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                       ..+ ....++......+....+..+|+.||++++.||.++|    ++++|++|||+.||+|..+|++.+++|+++||+.
T Consensus       102 -~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~  175 (186)
T PRK05602        102 -VPD-PAPGPDAGLEARQRARRVEQALAALPERQREAIVLQY----YQGLSNIEAAAVMDISVDALESLLARGRRALRAQ  175 (186)
T ss_pred             -cCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHH----hcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence             001 1112344444556667799999999999999999999    7999999999999999999999999999999976


Q ss_pred             chh
Q 010308          503 TRV  505 (513)
Q Consensus       503 ~~~  505 (513)
                      ...
T Consensus       176 l~~  178 (186)
T PRK05602        176 LAD  178 (186)
T ss_pred             HHh
Confidence            543

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

Probab=99.86  E-value=2.6e-20  Score=172.95  Aligned_cols=167  Identities=17%  Similarity=0.179  Sum_probs=134.4

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010308          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (513)
Q Consensus       265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r  344 (513)
                      +.+..+||..|++.|+..|.+.+++++.++.   ++..+++|++||+|+.+|++.++|+...+ .|.+|++..+++.+.+
T Consensus         2 i~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d   77 (170)
T TIGR02952         2 LERAQDREEDAFARIYETYSDRVYRYIYYRV---GCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVND   77 (170)
T ss_pred             hHHHHccCHHHHHHHHHHHHHHHHHHHHHHH---CChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHH
Confidence            3456779999999999999999999999887   67789999999999999999999997555 7999999999999999


Q ss_pred             HHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010308          345 SMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING  423 (513)
Q Consensus       345 aI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~  423 (513)
                      +++ +.+....                                                     +++        .....
T Consensus        78 ~~R~~~~~~~~-----------------------------------------------------~~~--------~~~~~   96 (170)
T TIGR02952        78 YFRGSKRHPLF-----------------------------------------------------SLD--------VFKEL   96 (170)
T ss_pred             HHHhcCCCCCC-----------------------------------------------------cHH--------HHhhc
Confidence            998 3221000                                                     000        00000


Q ss_pred             ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ..  ...++++.....+....+..+|..|||+++.||.++|    .+++|++|||+.||||.++|++.+.||+++||+.
T Consensus        97 ~~--~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~  169 (170)
T TIGR02952        97 LS--NEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRF----GQNLPIAEVARILGKTEGAVKILQFRAIKKLARQ  169 (170)
T ss_pred             CC--CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence            00  1123455555566677899999999999999999999    7899999999999999999999999999999964

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

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.86  E-value=2.1e-20  Score=178.13  Aligned_cols=185  Identities=18%  Similarity=0.229  Sum_probs=136.8

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010308          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (513)
Q Consensus       263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI  342 (513)
                      +.+..+..|+..|++.|+..|.+.|+.+|.++.   ++..+++||+||+|+.+|+++.+|++..+..|+||++.+|++.+
T Consensus         8 ~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~---~~~~~aeDlvQe~fl~~~~~~~~~~~~~~~~f~~wl~~~~~~~~   84 (198)
T TIGR02859         8 EIVELARQGNTHALEYLINKYKNFVRAKARSYF---LIGADKEDIIQEGMIGLYKAIRDFRPDKLSSFKAFAELCVTRQI   84 (198)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHc---cccCcHHHHHHHHHHHHHHHHHHhCcccCCChHHHHHHHHHHHH
Confidence            345566788999999999999999999999998   67889999999999999999999999887799999999999998


Q ss_pred             HHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCC--chhh
Q 010308          343 IRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV--TQEE  419 (513)
Q Consensus       343 ~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~--~~~e  419 (513)
                      .++++ ..+..+.+                                               .....|++.+...  .+++
T Consensus        85 ~~~~r~~~~~~~~~-----------------------------------------------~~~~~~~~~~~~~~~~~~~  117 (198)
T TIGR02859        85 ITAIKTATRQKHIP-----------------------------------------------LNSYVSLNKPIYDEESDRT  117 (198)
T ss_pred             HHHHHHHHHhcccc-----------------------------------------------hhhhcCcccccccccccch
Confidence            88877 21111100                                               0011222222111  1111


Q ss_pred             hhccccCCCCCCchhhhHHHHHHHHHHHHHhcC-CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010308          420 FINGITDVDGVENENQRQPALLRLALDDVLDSL-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  498 (513)
Q Consensus       420 ~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L-~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkK  498 (513)
                      +.+.+.+....++++.....+....|..+|+.| ++.++.|+. +|    .+++|++|||+.||+|.++|+..+++|+++
T Consensus       118 ~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~-~~----~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~  192 (198)
T TIGR02859       118 LLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQ-SY----LDGKSYQEIACDLNRHVKSIDNALQRVKRK  192 (198)
T ss_pred             HHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHH-HH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            222222122234566666667777889999995 666666665 46    589999999999999999999999999999


Q ss_pred             HhCc
Q 010308          499 LKHP  502 (513)
Q Consensus       499 LR~~  502 (513)
                      ||+.
T Consensus       193 L~~~  196 (198)
T TIGR02859       193 LEKY  196 (198)
T ss_pred             HHHh
Confidence            9964

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

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=99.86  E-value=1.2e-20  Score=180.11  Aligned_cols=176  Identities=20%  Similarity=0.196  Sum_probs=140.4

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHH
Q 010308          262 AAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHA  341 (513)
Q Consensus       262 ~e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~a  341 (513)
                      .+.+..+..||..|++.|+..|.+.|+++|.++.   ++..+.+|++||+|+++|++.++|++..  .|.+|++..+++.
T Consensus        14 ~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~---~~~~daeDlvQe~fi~l~~~~~~~~~~~--~f~~wl~~i~~n~   88 (194)
T PRK12513         14 EALMLRYRAGDAAAFEALYARHRTGLYRFLLRLA---RDRALAEDIFQETWLRVIRARAQYQPRA--RFRTWLYQIARNL   88 (194)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHHH
Confidence            3457777889999999999999999999999998   7788999999999999999999999743  6999999999999


Q ss_pred             HHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhh
Q 010308          342 IIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEF  420 (513)
Q Consensus       342 I~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~  420 (513)
                      +.++++ ..+..+.+                                                     .+.     +...
T Consensus        89 ~~~~~R~~~~~~~~~-----------------------------------------------------~~~-----~~~~  110 (194)
T PRK12513         89 LIDHWRRHGARQAPS-----------------------------------------------------LDA-----DEQL  110 (194)
T ss_pred             HHHHHHHhccccccc-----------------------------------------------------ccc-----chhh
Confidence            999988 32211110                                                     000     0000


Q ss_pred             hccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010308          421 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       421 ~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR  500 (513)
                       .... ....+++...+..+....|..+|+.||++++.||.++|    .+++|++|||+.||+|.++|++++.+|+++||
T Consensus       111 -~~~~-~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr  184 (194)
T PRK12513        111 -HALA-DDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLRE----HGDLELEEIAELTGVPEETVKSRLRYALQKLR  184 (194)
T ss_pred             -hhcC-CCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeeh----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence             0001 11223455556667778899999999999999999999    78999999999999999999999999999999


Q ss_pred             Ccchhh
Q 010308          501 HPTRVD  506 (513)
Q Consensus       501 ~~~~~~  506 (513)
                      ......
T Consensus       185 ~~l~~~  190 (194)
T PRK12513        185 ELLAEE  190 (194)
T ss_pred             HHHHHh
Confidence            765543

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.85  E-value=1.7e-20  Score=175.09  Aligned_cols=173  Identities=16%  Similarity=0.108  Sum_probs=134.9

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHH
Q 010308          267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM  346 (513)
Q Consensus       267 ~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI  346 (513)
                      ++.+||..|++.|+..|.++|+.++++|.   +++.+.+|++||++++||++++.|+  .+.+|.+|++..+++.+.+.+
T Consensus         3 ~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDl~Qe~~l~l~~~~~~~~--~~~~~~~~l~~~~~~~~~~~~   77 (182)
T PRK09652          3 RVQRGDRAAFALLVRRYQPRVKRLLSRLT---RDPADAEDLVQETFIKAYRALHSFR--GGAAFYTWLYRIARNTAINYL   77 (182)
T ss_pred             hhhcCCHHHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHHHHhcC--CCcchHHHHHHHHHHHHHHHH
Confidence            45679999999999999999999999998   6788999999999999999999999  455899999999999999988


Q ss_pred             Hh-ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcccc
Q 010308          347 TV-SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT  425 (513)
Q Consensus       347 ~~-~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~  425 (513)
                      ++ .+....+                                                  ..+.+..   ++....+.. 
T Consensus        78 r~~~~~~~~~--------------------------------------------------~~~~~~~---~~~~~~~~~-  103 (182)
T PRK09652         78 RKQGRRPPAS--------------------------------------------------DVDAEEA---EDFDLADAL-  103 (182)
T ss_pred             HcccCCCCcc--------------------------------------------------ccccccc---ccccccccc-
Confidence            83 2211000                                                  0000000   000001111 


Q ss_pred             CCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          426 DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       426 d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      + ...++++.....+....+..+|..|||+++.||.++|    ..++|++|||+.||+|..+|++.+.+|+++||+..
T Consensus       104 ~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l  176 (182)
T PRK09652        104 R-DISTPENELLSAELEQRVRAAIESLPEELRTAITLRE----IEGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL  176 (182)
T ss_pred             c-cccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            1 1123555556666778899999999999999999998    68999999999999999999999999999999754

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.85  E-value=2.4e-20  Score=175.96  Aligned_cols=177  Identities=19%  Similarity=0.209  Sum_probs=136.9

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010308          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (513)
Q Consensus       263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI  342 (513)
                      ..+..+.+|+..|+..|+..|.++|+.+|.+|.   +++.+++|++||+|+++|+++..|++..  .|.+|++..+++.+
T Consensus         7 ~li~~~~~gd~~a~~~l~~~y~~~v~~~~~~~~---~~~~~aeDlvQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~   81 (187)
T TIGR02948         7 KRIKEVRKGDENAFADLVDLYKDKIYQLCYRML---GNVHEAEDVAQEAFIRAYTNIDTYDIQR--KFSTWLYRIATNLT   81 (187)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhHHhcCCCC--chHHHHHHHHHHHH
Confidence            346677889999999999999999999999998   7788999999999999999999999865  69999999999999


Q ss_pred             HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCC-CCchhhhh
Q 010308          343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRH-GVTQEEFI  421 (513)
Q Consensus       343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~-~~~~~e~~  421 (513)
                      .++++..+. . .                                                    .++... ..+.....
T Consensus        82 ~~~~rk~~~-~-~----------------------------------------------------~~~~~~~~~~~~~~~  107 (187)
T TIGR02948        82 IDRLRKRKP-D-F----------------------------------------------------YLDDEVQGTDGLTME  107 (187)
T ss_pred             HHHHHhhcc-c-c----------------------------------------------------cccccccCccccccc
Confidence            988872110 0 0                                                    000000 00000001


Q ss_pred             ccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          422 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       422 d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                      +...+ ...++++.....+....+..+|+.|||+++.||.++|    .+++|++|||+.||+|.++|++.+.||+++||.
T Consensus       108 ~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~  182 (187)
T TIGR02948       108 SQLAA-DEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKY----MEDLSLKEISEILDLPVGTVKTRIHRGREALRK  182 (187)
T ss_pred             ccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            11111 1223445555556667799999999999999999998    689999999999999999999999999999996


Q ss_pred             cc
Q 010308          502 PT  503 (513)
Q Consensus       502 ~~  503 (513)
                      ..
T Consensus       183 ~l  184 (187)
T TIGR02948       183 QL  184 (187)
T ss_pred             Hh
Confidence            54

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

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.85  E-value=3.3e-20  Score=177.50  Aligned_cols=170  Identities=15%  Similarity=0.190  Sum_probs=134.1

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010308          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (513)
Q Consensus       265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r  344 (513)
                      +.....|+..|++.|+..|.++|+.+|.+|.   ++..+.+|++||+|+++|+++++||+.+| .|.+|++..+++.+.+
T Consensus        21 i~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~---~~~~dAeDivQe~fi~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~d   96 (194)
T PRK09646         21 LRRVARGDQDAFAELYDRTSSRVYGLVRRVL---RDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLLTLAHRRAVD   96 (194)
T ss_pred             HHHHHccCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhhhhcCcccc-cHHHHHHHHHHHHHHH
Confidence            4556778999999999999999999999999   78899999999999999999999998765 6999999999999999


Q ss_pred             HHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010308          345 SMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING  423 (513)
Q Consensus       345 aI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~  423 (513)
                      .++ +.+..+.-                                                   .+..       ..  + 
T Consensus        97 ~~r~~~~~~~~~---------------------------------------------------~~~~-------~~--~-  115 (194)
T PRK09646         97 RVRSEQAASQRE---------------------------------------------------VRYG-------AR--N-  115 (194)
T ss_pred             HHHhhccccccc---------------------------------------------------cccc-------cc--c-
Confidence            888 32110000                                                   0000       00  0 


Q ss_pred             ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      . +.....+++.....+....|..+|..||++++.||.++|    .+++|++|||+.||+|..+|++++++|+++||...
T Consensus       116 ~-~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l  190 (194)
T PRK09646        116 V-DPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAY----YGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCL  190 (194)
T ss_pred             c-cccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence            0 000111233333445567899999999999999999999    78999999999999999999999999999999765


Q ss_pred             h
Q 010308          504 R  504 (513)
Q Consensus       504 ~  504 (513)
                      .
T Consensus       191 ~  191 (194)
T PRK09646        191 G  191 (194)
T ss_pred             c
Confidence            3

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.85  E-value=3.3e-20  Score=169.95  Aligned_cols=152  Identities=22%  Similarity=0.246  Sum_probs=122.0

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccc
Q 010308          272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSF  351 (513)
Q Consensus       272 d~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~  351 (513)
                      +..|++.|+..|.++|+++++++.    ...+++|++||+++++|++++.|++..| .|.+|++..+++.+.+++++...
T Consensus         2 ~~~af~~l~~~y~~~l~~~~~~~~----~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~~   76 (154)
T PRK06759          2 KPATFTEAVVLYEGLIVNQIKKLG----IYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFA   76 (154)
T ss_pred             CcccHHHHHHHHHHHHHHHHHHhC----CcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHHh
Confidence            457899999999999999998864    4568999999999999999999998766 69999999999999998882100


Q ss_pred             cccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCC
Q 010308          352 TRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVE  431 (513)
Q Consensus       352 iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~  431 (513)
                                         .  .                                   +...  .         +   ..
T Consensus        77 -------------------~--~-----------------------------------~~~~--~---------~---~~   86 (154)
T PRK06759         77 -------------------V--Q-----------------------------------EKCV--C---------V---GE   86 (154)
T ss_pred             -------------------h--c-----------------------------------cccc--c---------c---CC
Confidence                               0  0                                   0000  0         0   00


Q ss_pred             chhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          432 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       432 ~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      +++.....+....|..+|.+||++++.||.++|    .+++|.+|||+.||+|..+|++++.+|+++||+.
T Consensus        87 ~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~----~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~  153 (154)
T PRK06759         87 YEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERF----FVGKTMGEIALETEMTYYQVRWIYRQALEKMRNS  153 (154)
T ss_pred             CcccccHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence            111222334456789999999999999999999    7899999999999999999999999999999963

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.84  E-value=7.2e-20  Score=172.76  Aligned_cols=176  Identities=16%  Similarity=0.160  Sum_probs=136.8

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010308          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (513)
Q Consensus       264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~  343 (513)
                      .+.....|+..|+..|+..|.++|+.+|.+|.   ++..+++|++||++++||+++++|++..  .|.+|++..+++.+.
T Consensus         8 li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDivQe~~l~l~~~~~~~~~~~--~~~~wl~~iarn~~~   82 (187)
T PRK09641          8 LIKQVKKGDQNAFAELVDLYKDKIYQLCYRML---GNRHEAEDAAQEAFIRAYVNIDSYDINR--KFSTWLYRIATNLTI   82 (187)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHHhhCCCc--chhHHHHHHHHHHHH
Confidence            45566789999999999999999999999998   7888999999999999999999999853  699999999999999


Q ss_pred             HHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCC-chhhhhc
Q 010308          344 RSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV-TQEEFIN  422 (513)
Q Consensus       344 raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~-~~~e~~d  422 (513)
                      +++++.+..                                                      .+++..... +.....+
T Consensus        83 d~~R~~~~~------------------------------------------------------~~~~~~~~~~~~~~~~~  108 (187)
T PRK09641         83 DRLRKRKPD------------------------------------------------------YYLDAEVAGTEGLTMYS  108 (187)
T ss_pred             HHHHhcCcc------------------------------------------------------ccccccccCCcchhhhc
Confidence            988832100                                                      000000000 0000111


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ...+ ...++++.....+....|..+|+.||++++.||.++|    ..++|++|||+.||||.++|++.++||+++||..
T Consensus       109 ~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~----~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~  183 (187)
T PRK09641        109 QLAA-DDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKY----IEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ  183 (187)
T ss_pred             cccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----hhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            1111 1223455555666677899999999999999999999    6899999999999999999999999999999965


Q ss_pred             c
Q 010308          503 T  503 (513)
Q Consensus       503 ~  503 (513)
                      .
T Consensus       184 l  184 (187)
T PRK09641        184 L  184 (187)
T ss_pred             H
Confidence            4

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=6.8e-20  Score=180.44  Aligned_cols=174  Identities=16%  Similarity=0.135  Sum_probs=134.8

Q ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-
Q 010308          269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-  347 (513)
Q Consensus       269 ~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-  347 (513)
                      ..|+..|++.|+..|.++|+++|.++.   ++..+.+||+||+|++||++++.|++.  ..|.+|++..+++.+.++++ 
T Consensus        25 ~~gd~~a~~~l~~~y~~~l~~~a~~~~---~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~Rk   99 (231)
T PRK11922         25 LAGDEAAFEALMRRHNRRLYRTARAIL---RNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLRR   99 (231)
T ss_pred             HcCCHHHHHHHHHHHHHHHHHHHHHHh---CChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHHh
Confidence            568899999999999999999999998   678899999999999999999999975  36999999999999998887 


Q ss_pred             hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCC
Q 010308          348 VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV  427 (513)
Q Consensus       348 ~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~  427 (513)
                      ..+...++                            +                        ... .....++.... ...
T Consensus       100 ~~r~~~~~----------------------------~------------------------~~~-~~~~~~~~~~~-~~~  125 (231)
T PRK11922        100 RRRLVNLA----------------------------E------------------------MVM-ASTIAGGERTP-LAD  125 (231)
T ss_pred             hcccccch----------------------------h------------------------ccc-ccccccccccc-cCc
Confidence            32211100                            0                        000 00000000000 111


Q ss_pred             CCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010308          428 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  505 (513)
Q Consensus       428 ~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~  505 (513)
                      ...++++.....+..+.|..+|+.||+++++||.++|    .+++|++|||+.||+|.++|++.+.+|+++||+....
T Consensus       126 ~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~  199 (231)
T PRK11922        126 PAEDPERAAARREIRALLERAIDALPDAFRAVFVLRV----VEELSVEETAQALGLPEETVKTRLHRARRLLRESLAR  199 (231)
T ss_pred             ccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeeh----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            1233555566677778899999999999999999998    7899999999999999999999999999999986543

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=9.9e-20  Score=173.57  Aligned_cols=170  Identities=23%  Similarity=0.218  Sum_probs=132.6

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010308          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (513)
Q Consensus       264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~  343 (513)
                      .+.....||..|++.|+..|.+.|+.+++++.   ++..+.+|++||+|+++|+. ..|++..+ .|.||++.++++.+.
T Consensus        19 l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~---~~~~~aeDlvQe~fl~l~~~-~~~~~~~~-~f~~wl~~iarn~~~   93 (194)
T PRK12519         19 LFSALKAGQSAALGVLYDRHAGLVYGLALKIL---GNSQEAEDLTQEIFLSLWRK-SSYDPKRG-SLSSYLLTLTRSRAI   93 (194)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHh-cCCCcccc-cHHHHHHHHHHHHHH
Confidence            45566789999999999999999999999998   67788999999999999976 67887655 799999999999999


Q ss_pred             HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      ++++ +.+.....                                                      +.    ...... 
T Consensus        94 d~~Rk~~~~~~~~------------------------------------------------------~~----~~~~~~-  114 (194)
T PRK12519         94 DRLRSRRSRQRLL------------------------------------------------------ER----WQQELL-  114 (194)
T ss_pred             HHHHhcccccchh------------------------------------------------------hh----hhhhhc-
Confidence            9988 32100000                                                      00    000000 


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                        .+....++++.....+....|..+|..||++++.||.++|    .+++|++|||+.||+|.++|++++.||+++||+.
T Consensus       115 --~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~  188 (194)
T PRK12519        115 --GEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAY----YEGLSQSEIAKRLGIPLGTVKARARQGLLKLREL  188 (194)
T ss_pred             --ccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhh----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence              0001122344444555566789999999999999999999    7899999999999999999999999999999965


Q ss_pred             c
Q 010308          503 T  503 (513)
Q Consensus       503 ~  503 (513)
                      .
T Consensus       189 l  189 (194)
T PRK12519        189 L  189 (194)
T ss_pred             H
Confidence            3

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.84  E-value=1.1e-19  Score=173.10  Aligned_cols=174  Identities=13%  Similarity=0.138  Sum_probs=136.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010308          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (513)
Q Consensus       263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI  342 (513)
                      ..+.....|+..|++.|+..|.++|+.++.++..+.....+.+|++||++++||+++++|+++.+ .|.||++..+++.+
T Consensus         7 ~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~~~~~~~~~~-~~~~wl~~iarn~~   85 (189)
T PRK06811          7 NFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKG-SFKKWIAAISKYKA   85 (189)
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHhHHHhccccc-cHHHHHHHHHHHHH
Confidence            34666778999999999999999999999999832112357999999999999999999997655 79999999999999


Q ss_pred             HHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhh
Q 010308          343 IRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFI  421 (513)
Q Consensus       343 ~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~  421 (513)
                      .++++ +.+.....                                                    +.+       +.. 
T Consensus        86 ~d~~rk~~~~~~~~----------------------------------------------------~~~-------~~~-  105 (189)
T PRK06811         86 IDYKRKLTKNNEID----------------------------------------------------SID-------EFI-  105 (189)
T ss_pred             HHHHHHhccccccc----------------------------------------------------cch-------hhh-
Confidence            99988 32210000                                                    000       000 


Q ss_pred             ccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          422 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       422 d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                         .+ ...++++.....+....|..+|..|||+++.||.++|    .+++|++|||+.||+|..+|++.+.||+++||.
T Consensus       106 ---~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~  177 (189)
T PRK06811        106 ---LI-SEESIENEIILKENKEEILKLINDLEKLDREIFIRRY----LLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK  177 (189)
T ss_pred             ---hc-ccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence               00 1122444455566667799999999999999999998    689999999999999999999999999999998


Q ss_pred             cchh
Q 010308          502 PTRV  505 (513)
Q Consensus       502 ~~~~  505 (513)
                      ...+
T Consensus       178 ~~~~  181 (189)
T PRK06811        178 NKLN  181 (189)
T ss_pred             cccC
Confidence            6544

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.83  E-value=1.6e-19  Score=170.88  Aligned_cols=171  Identities=19%  Similarity=0.202  Sum_probs=130.6

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010308          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (513)
Q Consensus       264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~  343 (513)
                      .+.....|+..|++.|+..|.+.|+.++++|.   +++.+.+|++||+|+.+|+++++|++..+ .|.+|++..+++.+.
T Consensus        13 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~---~~~~~aeDlvQe~~i~l~~~~~~~~~~~~-~~~~wl~~ia~n~~~   88 (186)
T PRK13919         13 LLALVARGEEEALRALFRRYAGAFLALARRMG---LDGAAAEDVVQEVFIRVWKKAKEFDPRRG-SARAWLLALAHHAAV   88 (186)
T ss_pred             HHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHh---cCHHHHHHHHHHHHHHHHHhhhccCcccc-chHHHHHHHHHHHHH
Confidence            35556789999999999999999999999998   67889999999999999999999987543 599999999999999


Q ss_pred             HHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010308          344 RSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING  423 (513)
Q Consensus       344 raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~  423 (513)
                      +++++.......                                                     ++.    ...+. ..
T Consensus        89 d~~rk~~~~~~~-----------------------------------------------------~~~----~~~~~-~~  110 (186)
T PRK13919         89 DHVRRRAARPQP-----------------------------------------------------LEP----DEREP-EA  110 (186)
T ss_pred             HHHHhhhccccc-----------------------------------------------------ccc----ccccc-cc
Confidence            988831100000                                                     000    00000 00


Q ss_pred             ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                       .+.  .+++......+....|..+|+.||++++.||.++|    .+++|++|||+.||+|..+|+..++||+++||...
T Consensus       111 -~~~--~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l  183 (186)
T PRK13919        111 -FDL--PGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLY----YQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVL  183 (186)
T ss_pred             -ccC--CCccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence             000  01111112233456789999999999999999999    79999999999999999999999999999999643

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.83  E-value=4.1e-19  Score=168.04  Aligned_cols=177  Identities=12%  Similarity=0.087  Sum_probs=135.5

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010308          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (513)
Q Consensus       264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~  343 (513)
                      .+.....|+..|+..|+..|.+.|+.+|.++.   ++..+.+||+||+|++||+++++|++.  ..|.+|++...++.+.
T Consensus        10 l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDlvQe~fi~l~~~~~~~~~~--~~~~~wl~~iarn~~~   84 (190)
T TIGR02939        10 LVERVQRGEKQAFDLLVRKYQHKVVALVGRYV---RDSSEVEDVAQEAFVKAYRALSSFRGD--SAFYTWLYRIAVNTAK   84 (190)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHhHHhcCCC--CccHhHHHHHHHHHHH
Confidence            45566789999999999999999999999998   778899999999999999999999975  3699999999999988


Q ss_pred             HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      +.++ +.+.....                                                  ..+.+.     .+....
T Consensus        85 ~~~r~~~r~~~~~--------------------------------------------------~~~~~~-----~~~~~~  109 (190)
T TIGR02939        85 NHLVAQGRRPPTS--------------------------------------------------DVEIED-----AEHFEG  109 (190)
T ss_pred             HHHHHhccCCCcc--------------------------------------------------cccccc-----hhhhcc
Confidence            8776 32211000                                                  000000     000000


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ........++++.....+....|..+|+.||++++.||.++|    .+++|++|||+.||+|..+|++.+++|+++||+.
T Consensus       110 ~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~  185 (190)
T TIGR02939       110 ADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRE----LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR  185 (190)
T ss_pred             cccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhh----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            000001123455555666777899999999999999999999    7899999999999999999999999999999976


Q ss_pred             ch
Q 010308          503 TR  504 (513)
Q Consensus       503 ~~  504 (513)
                      .+
T Consensus       186 l~  187 (190)
T TIGR02939       186 LR  187 (190)
T ss_pred             hh
Confidence            53

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

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=3.5e-19  Score=165.84  Aligned_cols=170  Identities=15%  Similarity=0.044  Sum_probs=137.1

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010308          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (513)
Q Consensus       265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r  344 (513)
                      +..+..|+..|++.|+..|.+.|+.+|+++.   ++..+.+|++||+++.||.+.+.|+  .+..|.+|++..+++.+.+
T Consensus         4 ~~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~---~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d   78 (179)
T PRK11924          4 MPVDATGDKEAFSELFRPHAPDLLRYARRQL---GDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYD   78 (179)
T ss_pred             HHHHHccCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHH
Confidence            3445789999999999999999999999998   7888999999999999999999998  3457999999999999998


Q ss_pred             HHHh-ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010308          345 SMTV-SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING  423 (513)
Q Consensus       345 aI~~-~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~  423 (513)
                      ++++ .+.....                                                     .+.     ..   ..
T Consensus        79 ~~r~~~~~~~~~-----------------------------------------------------~~~-----~~---~~   97 (179)
T PRK11924         79 LLRRRRREKAVL-----------------------------------------------------SDD-----AL---EP   97 (179)
T ss_pred             HHHhcccccccC-----------------------------------------------------ccc-----cc---cc
Confidence            8873 2110000                                                     000     00   00


Q ss_pred             ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      ..+....++++.....+....|..+|..||++++.||.++|    ..++|+.|||+.||+|+.+|++.+.+|+++||+..
T Consensus        98 ~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l  173 (179)
T PRK11924         98 EFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRY----VEGLSYREIAEILGVPVGTVKSRLRRARQLLRECL  173 (179)
T ss_pred             ccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            00002334666677778888999999999999999999999    68999999999999999999999999999999754


Q ss_pred             h
Q 010308          504 R  504 (513)
Q Consensus       504 ~  504 (513)
                      .
T Consensus       174 ~  174 (179)
T PRK11924        174 E  174 (179)
T ss_pred             H
Confidence            4

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.82  E-value=2.2e-19  Score=170.79  Aligned_cols=159  Identities=18%  Similarity=0.226  Sum_probs=125.7

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh-c
Q 010308          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-S  349 (513)
Q Consensus       271 gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~-~  349 (513)
                      ||..|++.|+..|.+.|+++|.+|.   ++..+.+|++||+|+.||+++++|++.  ..|.+|++.++++.+.+.++. .
T Consensus        23 gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDlvQe~f~~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~~R~~~   97 (188)
T PRK09640         23 HVTRAYEELMRRYQRTLFNVCARYL---GNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLYSITYNECITQYRKER   97 (188)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHHHHHhcCC--CcchHHHHHHHHHHHHHHHHHhc
Confidence            6999999999999999999999998   778899999999999999999999863  479999999999999998882 1


Q ss_pred             cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCC
Q 010308          350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG  429 (513)
Q Consensus       350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~  429 (513)
                      +.....                                                     .+        ...+...+.  
T Consensus        98 ~~~~~~-----------------------------------------------------~~--------~~~~~~~~~--  114 (188)
T PRK09640         98 RKRRLM-----------------------------------------------------DA--------LSLDPLEEA--  114 (188)
T ss_pred             ccccCc-----------------------------------------------------ch--------hhhcccccc--
Confidence            100000                                                     00        000000000  


Q ss_pred             CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                        .++.....+....|..+|+.||++++.||.++|    .+++|++|||+.||||..+|+..+.||+++||...
T Consensus       115 --~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l  182 (188)
T PRK09640        115 --SEEKAPKPEERGGLDRWLVHVNPIDREILVLRF----VAELEFQEIADIMHMGLSATKMRYKRALDKLREKF  182 (188)
T ss_pred             --cccccccHHHHHHHHHHHHhcChhheeeeeeHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence              001111224456789999999999999999999    78999999999999999999999999999999753

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.82  E-value=8.4e-19  Score=167.03  Aligned_cols=176  Identities=12%  Similarity=0.050  Sum_probs=135.0

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010308          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (513)
Q Consensus       264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~  343 (513)
                      .+..+..|+..|++.|+..|.+.|+.++.+|.   ++..+.+|++||+|+++|+++..|++..  .|.+|++...++.+.
T Consensus        10 ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~---~~~~daeDlvQe~~i~l~~~~~~~~~~~--~~~~wl~~ia~n~~~   84 (193)
T PRK11923         10 LVERVQRGDKRAFDLLVLKYQHKILGLIVRFV---HDTAEAQDVAQEAFIKAYRALGNFRGDS--AFYTWLYRIAINTAK   84 (193)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHhHhCcCCCC--ccHhHHHHHHHHHHH
Confidence            35556778999999999999999999999998   6778999999999999999999999864  489999999999888


Q ss_pred             HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      ++++ +.+.....                                                  ..+++..     +.+..
T Consensus        85 d~~rk~~~~~~~~--------------------------------------------------~~~~~~~-----~~~~~  109 (193)
T PRK11923         85 NHLVSRGRRPPDS--------------------------------------------------DVSSEDA-----EFYDG  109 (193)
T ss_pred             HHHHHhcCCCccc--------------------------------------------------cccccch-----hhhcc
Confidence            8887 32210000                                                  0000000     00000


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      .....+..+|++.....+....+..+|..||++++.||.++|    .+++|++|||+.||+|..+|++...||+++||..
T Consensus       110 ~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~  185 (193)
T PRK11923        110 DHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLRE----FDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKA  185 (193)
T ss_pred             cccccCcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            000001123455555667778899999999999999999998    7999999999999999999999999999999965


Q ss_pred             c
Q 010308          503 T  503 (513)
Q Consensus       503 ~  503 (513)
                      .
T Consensus       186 l  186 (193)
T PRK11923        186 L  186 (193)
T ss_pred             H
Confidence            4

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=4.5e-19  Score=166.98  Aligned_cols=169  Identities=14%  Similarity=0.149  Sum_probs=132.6

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010308          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (513)
Q Consensus       264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~  343 (513)
                      .+..+..|+..|+..|+..|.+.|+.+|.+|.   ++..+.+|++||+|+++|+++++|++..+ .|.||++..+++.+.
T Consensus         9 li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~~   84 (179)
T PRK12514          9 LIVRVSLGDRDAFSSLYDATSAKLFGICLRVL---KDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHAI   84 (179)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH---cCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHH
Confidence            35556789999999999999999999999998   77889999999999999999999997543 599999999999999


Q ss_pred             HHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010308          344 RSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING  423 (513)
Q Consensus       344 raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~  423 (513)
                      +++++.+....+                                                     ++.     ...    
T Consensus        85 d~~R~~~~~~~~-----------------------------------------------------~~~-----~~~----  102 (179)
T PRK12514         85 DRLRARKAVAVD-----------------------------------------------------IDE-----AHD----  102 (179)
T ss_pred             HHHHhcCCcccc-----------------------------------------------------ccc-----chh----
Confidence            988731100000                                                     000     000    


Q ss_pred             ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      ..+ ...++++.....+....|..+|..||++++.||.++|    .+++|++|||+.||+|..+|++.+.||+++||+..
T Consensus       103 ~~~-~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l  177 (179)
T PRK12514        103 LAD-PSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAY----LEGLSYKELAERHDVPLNTMRTWLRRSLLKLRECL  177 (179)
T ss_pred             ccc-cCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHHh
Confidence            000 1112344343344445788999999999999999999    78999999999999999999999999999999753

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=5.2e-19  Score=169.48  Aligned_cols=171  Identities=18%  Similarity=0.102  Sum_probs=136.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010308          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (513)
Q Consensus       263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI  342 (513)
                      ..+.++..|+..|++.|+..|.+.|+.+|.++.   ++..+.+|++||+++.+|+..+.|++.. ..|.+|++..+++.+
T Consensus        15 ~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQe~~l~l~~~~~~~~~~~-~~~~~wl~~ia~n~~   90 (196)
T PRK12524         15 ALLVLYANGDPAAARALTLRLAPRALAVATRVL---GDRAEAEDVTQEAMLRLWRIAPDWRQGE-ARVSTWLYRVVCNLC   90 (196)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhhhcccccc-chHHHHHHHHHHHHH
Confidence            456667889999999999999999999999998   7888999999999999999999998533 469999999999999


Q ss_pred             HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      .+.+++.+...                                                     ..++..     .+   
T Consensus        91 ~d~~Rk~~~~~-----------------------------------------------------~~~~~~-----~~---  109 (196)
T PRK12524         91 TDRLRRRRRAS-----------------------------------------------------VDLDDA-----PE---  109 (196)
T ss_pred             HHHHHhhcCCC-----------------------------------------------------CCcccc-----cc---
Confidence            98887211000                                                     000000     00   


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      . .+ ...++++.....+....|..+|+.||++++.||.|+|    .+++|++|||+.||||..+|+++++||+++||..
T Consensus       110 ~-~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~----~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~  183 (196)
T PRK12524        110 P-AD-AAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRH----IEGLSNPEIAEVMEIGVEAVESLTARGKRALAAL  183 (196)
T ss_pred             c-cc-cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            0 01 1122344455556677899999999999999999999    7899999999999999999999999999999975


Q ss_pred             ch
Q 010308          503 TR  504 (513)
Q Consensus       503 ~~  504 (513)
                      ..
T Consensus       184 l~  185 (196)
T PRK12524        184 LA  185 (196)
T ss_pred             HH
Confidence            54

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=4.2e-19  Score=175.59  Aligned_cols=169  Identities=15%  Similarity=0.160  Sum_probs=134.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010308          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (513)
Q Consensus       263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI  342 (513)
                      +.+..+..||..|++.|+..|.+.|+.++.++.   ++..+.+|++||+|+.+|+..++|++..+ .|.+|++..+++.+
T Consensus        52 ~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~---~d~~dAEDivQEvfl~l~~~~~~~~~~~~-~f~~WL~~IarN~~  127 (233)
T PRK12538         52 ELLDRLATDDEAAFRLLVERHIDRAYAIALRIV---GNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSNRC  127 (233)
T ss_pred             HHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHHcccccc-cHHHHHHHHHHHHH
Confidence            345667789999999999999999999999998   67789999999999999999999986544 69999999999999


Q ss_pred             HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      .+++++.+...                                                       ++.     ..+   
T Consensus       128 id~~Rk~~~~~-------------------------------------------------------~~~-----~~~---  144 (233)
T PRK12538        128 IDLRRKPRTEN-------------------------------------------------------VDA-----VPE---  144 (233)
T ss_pred             HHHHHhhcccc-------------------------------------------------------ccc-----ccc---
Confidence            88776211000                                                       000     000   


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      . .+ ....+++.....+....|..+|..||+++|+||.|+|    .+++|++|||+.||+|.++|+++++||+++||+.
T Consensus       145 ~-~~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~----~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~  218 (233)
T PRK12538        145 V-AD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSY----HENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDL  218 (233)
T ss_pred             c-cc-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            0 00 0112333344556667899999999999999999999    7999999999999999999999999999999976


Q ss_pred             ch
Q 010308          503 TR  504 (513)
Q Consensus       503 ~~  504 (513)
                      ..
T Consensus       219 l~  220 (233)
T PRK12538        219 LR  220 (233)
T ss_pred             HH
Confidence            54

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

Probab=99.82  E-value=6.4e-19  Score=166.36  Aligned_cols=180  Identities=15%  Similarity=0.123  Sum_probs=135.0

Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHchhc-cCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh
Q 010308          270 EVGRAARNKLIKHNLRLVLFVIKKYFQD-FANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV  348 (513)
Q Consensus       270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~-~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~  348 (513)
                      .|+..|++.|+..|.+.|+.+|++|... +++..+.+|++||+++.+|+++..|++..+..|.+|++..+++.+.+++++
T Consensus         3 ~~~~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeD~vQe~~l~l~~~~~~~~~~~~~~~~~wl~~i~~n~~~d~~r~   82 (189)
T TIGR02984         3 GGDQEALGELLDRYRNYLRLLARVQLDPRLRRRVDPSDLVQETLLEAHRRFDQFRGKTEGEFAGWLRGILSNVLADALRR   82 (189)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHhhhhcCCccCHHHHHHHHHHHHHHHHHhccCcccchHHHHHHHHHHHHHHHHHHH
Confidence            5789999999999999999999987521 235678999999999999999999997666689999999999999988872


Q ss_pred             c--cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCC-Cc-hhhhhccc
Q 010308          349 S--SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHG-VT-QEEFINGI  424 (513)
Q Consensus       349 ~--r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~-~~-~~e~~d~l  424 (513)
                      .  +..+.+                                                ....+++.... .+ ...+.+.+
T Consensus        83 ~~~~~~r~~------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~  114 (189)
T TIGR02984        83 HLGAQKRDI------------------------------------------------RREQSLDAGGRLDESSVRLAAQL  114 (189)
T ss_pred             HHHHHhhhc------------------------------------------------ccccCCCcccccCCcchhHHHHc
Confidence            1  000000                                                00112221110 00 11112222


Q ss_pred             cCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          425 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       425 ~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      .+ ...++++.....+....|..+|..|||+++.||.++|    ..++|++|||..||||.++|++.+++|+++||+.
T Consensus       115 ~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~  187 (189)
T TIGR02984       115 AA-DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRH----LEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQI  187 (189)
T ss_pred             cC-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            22 2234555556666677899999999999999999999    6899999999999999999999999999999964

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

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=5.4e-19  Score=169.10  Aligned_cols=174  Identities=14%  Similarity=0.120  Sum_probs=132.2

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010308          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (513)
Q Consensus       265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r  344 (513)
                      +.+...|+..|++.|+..|.+.|+.+|.++.   ++..+.+|++||+|+.+|+..++|++..+ .|.+|++..+++.+.+
T Consensus        18 i~~~~~~d~~af~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQev~l~l~~~~~~~~~~~~-~~~~wL~~iarn~~ld   93 (194)
T PRK12531         18 MEKVKSRDKQAFALVFSYYAPKLKQFAMKHV---GNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTIIRNLCFD   93 (194)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhcCcccc-hHHHHHHHHHHHHHHH
Confidence            5667789999999999999999999999998   67788999999999999999999997544 6999999999999999


Q ss_pred             HHHh-ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010308          345 SMTV-SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING  423 (513)
Q Consensus       345 aI~~-~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~  423 (513)
                      ++++ .+.....                                                    +.+...  ........
T Consensus        94 ~~Rk~~~~~~~~----------------------------------------------------~~~~~~--~~~~~~~~  119 (194)
T PRK12531         94 LLRKQKGKDLHI----------------------------------------------------HADDIW--PSDYYPPD  119 (194)
T ss_pred             HHHHhccccccc----------------------------------------------------chhhcc--cccccccc
Confidence            8883 2100000                                                    000000  00000000


Q ss_pred             ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      ..  ....++    .......+..+|.+||++++.||.++|    .+++|++|||+.||||.++|+..+++|+++||...
T Consensus       120 ~~--~~~~~e----~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l  189 (194)
T PRK12531        120 LV--DHYSPE----QDMLKEQVMKFLDRLPKAQRDVLQAVY----LEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM  189 (194)
T ss_pred             cc--cccCHH----HHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence            00  001111    223345688999999999999999999    79999999999999999999999999999999765


Q ss_pred             hhh
Q 010308          504 RVD  506 (513)
Q Consensus       504 ~~~  506 (513)
                      ..+
T Consensus       190 ~~~  192 (194)
T PRK12531        190 DAE  192 (194)
T ss_pred             hhc
Confidence            543

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=1.7e-19  Score=171.01  Aligned_cols=169  Identities=15%  Similarity=0.144  Sum_probs=130.5

Q ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh
Q 010308          269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV  348 (513)
Q Consensus       269 ~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~  348 (513)
                      ..||..|+..|+..|.+.++.+|.++.   ++..+.+|++||.|+.+|++.++|++..+..|.||++..+++.+.+++++
T Consensus         4 ~~gd~~a~~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQe~fl~~~~~~~~~~~~~~~~~~~wL~~Iarn~~~d~~Rk   80 (185)
T PRK12542          4 TNNDYEKMEELYELYEQKVYYVAYSIL---NNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRK   80 (185)
T ss_pred             cccCHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHHHH
Confidence            468899999999999999999999998   67788999999999999999999986544579999999999999998882


Q ss_pred             -ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCC
Q 010308          349 -SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV  427 (513)
Q Consensus       349 -~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~  427 (513)
                       .+...                  +.                                    +. .   ..   ..... 
T Consensus        81 ~~~~~~------------------~~------------------------------------~~-~---~~---~~~~~-   98 (185)
T PRK12542         81 NKRHET------------------FL------------------------------------EE-Y---ER---ESIEA-   98 (185)
T ss_pred             hhhhhh------------------hh------------------------------------hh-c---cc---cchhh-
Confidence             11000                  00                                    00 0   00   00000 


Q ss_pred             CCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          428 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       428 ~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ....+++.....+....|..+|..|||++++||.|+|    .+++|++|||+.||+|.++|+..+.||+++||+.....
T Consensus        99 ~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~  173 (185)
T PRK12542         99 VDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKV----FYNLTYQEISSVMGITEANVRKQFERARKRVQNMIGGI  173 (185)
T ss_pred             hhccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence            0011222223334456789999999999999999998    78999999999999999999999999999999865443

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=4.2e-19  Score=168.31  Aligned_cols=170  Identities=20%  Similarity=0.210  Sum_probs=133.3

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010308          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (513)
Q Consensus       265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r  344 (513)
                      +.....|+..+++.|+..|.++|+++|.+|.   ++..+.+|++||+|+.+|++.++|++..+ .|.+|++..+++.+.+
T Consensus        16 ~~~~~~~~~~~~~~l~~~y~~~l~~~~~~~~---~~~~~aeDlvQe~fl~~~~~~~~~~~~~~-~~~~wl~~I~~n~~~d   91 (187)
T PRK12534         16 LTATAGGDRHAFEALYRQTSPKLFGVCLRMI---PQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLTWLAMIARNKAID   91 (187)
T ss_pred             HHHHHcCCHHHHHHHHHHhhHHHHHHHHHHh---cCHHHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHHH
Confidence            5556678999999999999999999999998   77889999999999999999999998654 5889999999999998


Q ss_pred             HHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccc
Q 010308          345 SMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGI  424 (513)
Q Consensus       345 aI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l  424 (513)
                      ++++....+ .                                                  ..+++.     ....    
T Consensus        92 ~~R~~~~~~-~--------------------------------------------------~~~~~~-----~~~~----  111 (187)
T PRK12534         92 HLRANAPQR-R--------------------------------------------------NVALDD-----AGEL----  111 (187)
T ss_pred             HHHhccccc-c--------------------------------------------------cccccc-----hhhh----
Confidence            887311000 0                                                  000000     0000    


Q ss_pred             cCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          425 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       425 ~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      .+ ...++++.....+....|..+|+.||++++.|+.++|    .+++|++|||+.||+|.++|++++++|+++||...
T Consensus       112 ~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l  185 (187)
T PRK12534        112 RA-ADASPLERTERASTRRRIDHCLAELEPPRSELIRTAF----FEGITYEELAARTDTPIGTVKSWIRRGLAKLKACL  185 (187)
T ss_pred             cc-ccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Confidence            00 0112333334456677899999999999999999999    79999999999999999999999999999999643

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=7.1e-19  Score=170.20  Aligned_cols=173  Identities=12%  Similarity=0.120  Sum_probs=131.9

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010308          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (513)
Q Consensus       265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r  344 (513)
                      +.....|+..|++.|+..|.++|+.++.++.   ++..+.+|++||+|+.+|++++.|++.++ .|.||++.++++.+.+
T Consensus        29 ~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~---~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wl~~I~rn~~~d  104 (206)
T PRK12526         29 ILVAISRDKQAFTHLFQFFAPKIKRFGIKQL---GNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYTVMRNAAFD  104 (206)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHhHHhcCCccc-chhHHHHHHHHHHHHH
Confidence            3445679999999999999999999999998   67788999999999999999999997665 5999999999999999


Q ss_pred             HHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010308          345 SMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING  423 (513)
Q Consensus       345 aI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~  423 (513)
                      +++ +.+.....                                                     ++    .+.....+.
T Consensus       105 ~~Rk~~~~~~~~-----------------------------------------------------~~----~~~~~~~~~  127 (206)
T PRK12526        105 MLRKIKAKKEQN-----------------------------------------------------LG----DDIWPIEQA  127 (206)
T ss_pred             HHHHhccccccc-----------------------------------------------------cc----cccchhhhh
Confidence            988 32210000                                                     00    000000000


Q ss_pred             ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      +.+. .. .............|..+|..||++++.||.++|    ++++|++|||+.||+|..+|+..+++|+++||...
T Consensus       128 ~~~~-~~-~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l  201 (206)
T PRK12526        128 LAES-QS-ESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVY----FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM  201 (206)
T ss_pred             cccc-cC-chHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            0111 11 111222333446789999999999999999999    79999999999999999999999999999999765


Q ss_pred             h
Q 010308          504 R  504 (513)
Q Consensus       504 ~  504 (513)
                      .
T Consensus       202 ~  202 (206)
T PRK12526        202 G  202 (206)
T ss_pred             h
Confidence            4

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=6.9e-19  Score=166.58  Aligned_cols=168  Identities=16%  Similarity=0.131  Sum_probs=133.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010308          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (513)
Q Consensus       263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI  342 (513)
                      +.+..+..|+..|++.|+..|.+.|+.++.++.   ++..+.+|++||+|+.+|+..++|++..+ .|.+|++..+++.+
T Consensus        12 ~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~~   87 (182)
T PRK12537         12 ACLLACARGDRRALQALYQQESARLLGVARRIV---RDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHLA   87 (182)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHH
Confidence            346667789999999999999999999999998   78889999999999999999999986443 69999999999999


Q ss_pred             HHHHHh-ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhh
Q 010308          343 IRSMTV-SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFI  421 (513)
Q Consensus       343 ~raI~~-~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~  421 (513)
                      .++++. .+...                                                       .+.    ..   .
T Consensus        88 ~d~~r~~~~~~~-------------------------------------------------------~~~----~~---~  105 (182)
T PRK12537         88 LNVLRDTRREVV-------------------------------------------------------LDD----DA---E  105 (182)
T ss_pred             HHHHHhccccCc-------------------------------------------------------ccc----ch---h
Confidence            998883 11000                                                       000    00   0


Q ss_pred             ccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          422 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       422 d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                      +...+  ..++++..........|..+|+.||+++++||.++|    .+++|++|||+.||||.++|+..+.+|+++||.
T Consensus       106 ~~~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~  179 (182)
T PRK12537        106 ETAQT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAY----VDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRE  179 (182)
T ss_pred             hhccc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence            00000  111222333444556789999999999999999999    799999999999999999999999999999996


Q ss_pred             c
Q 010308          502 P  502 (513)
Q Consensus       502 ~  502 (513)
                      .
T Consensus       180 ~  180 (182)
T PRK12537        180 C  180 (182)
T ss_pred             H
Confidence            5

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=9.6e-19  Score=166.42  Aligned_cols=172  Identities=16%  Similarity=0.154  Sum_probs=137.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010308          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (513)
Q Consensus       263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI  342 (513)
                      +.+.....||..|++.|+..|.+.++.++.++.   ++..+.+|++||+|+.+|++.+.|++.  ..|.+|++..+++.+
T Consensus        11 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDivQe~f~~l~~~~~~~~~~--~~~~~wl~~i~~n~~   85 (189)
T PRK12515         11 MLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLV---RDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFKA   85 (189)
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHHhcCCC--CChHHHHHHHHHHHH
Confidence            456677889999999999999999999999998   678899999999999999999999964  379999999999999


Q ss_pred             HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      .+++++.+...+                                                       ..       +...
T Consensus        86 ~d~~r~~~~~~~-------------------------------------------------------~~-------~~~~  103 (189)
T PRK12515         86 LSALRRRKHEEI-------------------------------------------------------DD-------EAAA  103 (189)
T ss_pred             HHHHHccCCCCC-------------------------------------------------------cc-------cccc
Confidence            988873110000                                                       00       0000


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ...+ ...++++.....+....+..+|+.||+++++||.++|    .+++|++|||+.||+|..+|++.+.||+++||+.
T Consensus       104 ~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~  178 (189)
T PRK12515        104 AIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVY----YHEKSVEEVGEIVGIPESTVKTRMFYARKKLAEL  178 (189)
T ss_pred             ccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            0111 1123444445556667899999999999999999999    7999999999999999999999999999999986


Q ss_pred             chhh
Q 010308          503 TRVD  506 (513)
Q Consensus       503 ~~~~  506 (513)
                      ....
T Consensus       179 l~~~  182 (189)
T PRK12515        179 LKAA  182 (189)
T ss_pred             HHHh
Confidence            5543

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

Probab=99.80  E-value=1.4e-18  Score=155.59  Aligned_cols=155  Identities=23%  Similarity=0.279  Sum_probs=126.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccc
Q 010308          275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR  353 (513)
Q Consensus       275 Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iR  353 (513)
                      |++.|+..|.++|.++++++.   .++.+.+|++|||+++||++++.|++.  ..|.+|+.+++++.+.++++ +.+   
T Consensus         2 a~~~l~~~~~~~v~~~~~~~~---~~~~~~~D~~qe~~~~l~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~rk~~~---   73 (158)
T TIGR02937         2 AFEELYERYLPLLYRYARRYL---GDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR---   73 (158)
T ss_pred             HHHHHHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHHhHHhcCCc--chHHHHHHHHHHHHHHHHHHHhcc---
Confidence            789999999999999999998   677889999999999999999999998  68999999999999999998 322   


Q ss_pred             cccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCch
Q 010308          354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENE  433 (513)
Q Consensus       354 lP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~e  433 (513)
                      .+...                                                   .      ...   .. ......++
T Consensus        74 ~~~~~---------------------------------------------------~------~~~---~~-~~~~~~~~   92 (158)
T TIGR02937        74 LRREL---------------------------------------------------D------LLE---EL-LDSDPSPE   92 (158)
T ss_pred             CCcch---------------------------------------------------h------hhh---hc-ccccCCHH
Confidence            11000                                                   0      000   00 01112344


Q ss_pred             hhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          434 NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       434 e~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      +..........|..+|+.||+.++.||.++|    ..++|..|||+.||+|+++|+++..+++++||+.
T Consensus        93 ~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~----~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~  157 (158)
T TIGR02937        93 EELEQEEEREALREALEKLPEREREVLVLRY----LEGLSYKEIAEILGISVGTVKRRLKRARKKLREL  157 (158)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            4555666777899999999999999999998    5799999999999999999999999999999963

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

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=2e-18  Score=163.30  Aligned_cols=167  Identities=16%  Similarity=0.136  Sum_probs=129.5

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010308          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (513)
Q Consensus       264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~  343 (513)
                      .+..+..||..|++.|+..|.+.|+.++.++..  .+..+.+||+||+|+.||+.++.|++.  ..|.+|++..+++.+.
T Consensus        11 ~~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~--~~~~~aeDlvQevfl~l~~~~~~~~~~--~~~~~wl~~iarN~~~   86 (181)
T PRK12536         11 LLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLP--QLPDEVEDLVQEILLAVHNARHTYRAD--QPLTAWVHAIARYKLM   86 (181)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcC--CChhhHHHHHHHHHHHHHHhHHhcCCC--CchHHHHHHHHHHHHH
Confidence            467778899999999999999999999987651  346799999999999999999999974  3699999999999999


Q ss_pred             HHHHh-ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          344 RSMTV-SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       344 raI~~-~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      +++++ .+...                                                       .+....    +..+
T Consensus        87 d~~Rk~~~~~~-------------------------------------------------------~~~~~~----~~~~  107 (181)
T PRK12536         87 DFLRSRARREA-------------------------------------------------------LHDPLD----DESE  107 (181)
T ss_pred             HHHHHHhcccc-------------------------------------------------------ccCCcc----chhh
Confidence            99883 21100                                                       000000    0000


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ...+.   .++    ..+....+..+|..||++++.||.++|    .+++|++|||+.||+|.++|+..+++|+++||+.
T Consensus       108 ~~~~~---~~~----~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~  176 (181)
T PRK12536        108 LFATS---DDE----AAEARRDLGKLLEQLPDRQRLPIVHVK----LEGLSVAETAQLTGLSESAVKVGIHRGLKALAAK  176 (181)
T ss_pred             hcCCC---Ccc----hHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            00000   011    123445689999999999999999998    7999999999999999999999999999999976


Q ss_pred             ch
Q 010308          503 TR  504 (513)
Q Consensus       503 ~~  504 (513)
                      ..
T Consensus       177 l~  178 (181)
T PRK12536        177 IR  178 (181)
T ss_pred             hc
Confidence            54

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.80  E-value=2.9e-18  Score=164.10  Aligned_cols=167  Identities=13%  Similarity=0.096  Sum_probs=134.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010308          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (513)
Q Consensus       263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI  342 (513)
                      +.+.....|+..+++.|+..|.+.|++++.++.   ++..+.+|++||+|+.+|+++++|++..  .|.+|++..+++.+
T Consensus        16 ~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQEvfl~l~~~~~~~~~~~--~f~~wL~~i~rn~~   90 (192)
T PRK09643         16 ELLAAHVAGDRYAFGELFRRHHRRLWAVARRTS---GTREDAADALQDAMLSAHRAAGSFRGDA--AVSSWLHRIVVNAC   90 (192)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHHHHHhcCCCC--ccHHHHHHHHHHHH
Confidence            456667789999999999999999999999998   7788999999999999999999999653  69999999999999


Q ss_pred             HHHHHh-ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhh
Q 010308          343 IRSMTV-SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFI  421 (513)
Q Consensus       343 ~raI~~-~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~  421 (513)
                      .+++++ .+....                                                     +++.     ..   
T Consensus        91 ~d~~Rk~~~~~~~-----------------------------------------------------~~~~-----~~---  109 (192)
T PRK09643         91 LDRLRRAKARPTV-----------------------------------------------------PLDD-----VY---  109 (192)
T ss_pred             HHHHHccccCCCC-----------------------------------------------------Cccc-----cc---
Confidence            999883 211000                                                     0000     00   


Q ss_pred             ccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          422 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       422 d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                       ...    ..+++.....+....|..+|+.||+++++||.|+|    .+++|++|||+.||+|..+|+..+.+|+++||.
T Consensus       110 -~~~----~~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~----~~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~  180 (192)
T PRK09643        110 -PVA----QLERDPTARVETALAVQRALMRLPVEQRAALVAVD----MQGYSVADAARMLGVAEGTVKSRCARGRARLAE  180 (192)
T ss_pred             -ccc----CCcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence             000    01122234445567799999999999999999999    799999999999999999999999999999997


Q ss_pred             cch
Q 010308          502 PTR  504 (513)
Q Consensus       502 ~~~  504 (513)
                      ...
T Consensus       181 ~l~  183 (192)
T PRK09643        181 LLG  183 (192)
T ss_pred             HHH
Confidence            543

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=2e-18  Score=162.99  Aligned_cols=164  Identities=16%  Similarity=0.087  Sum_probs=129.0

Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhc
Q 010308          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS  349 (513)
Q Consensus       270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~  349 (513)
                      .|+..|++.|+..|.+.|+.++..|.   ++..+.+|++||+|+.+|+++..|++..  .|.+|++..+++.+.++++..
T Consensus         3 ~~d~~af~~l~~~~~~~l~~~~~~~~---~~~~daeDl~Qevfl~l~~~~~~~~~~~--~f~~wl~~iarn~~~~~~r~~   77 (179)
T PRK12543          3 SGDQEAFSEIYDVTIQEVYKTVHFLV---EDKQDVDDVVNEIYIQLWESLRKYDSNR--PFRFWLIGLVIKQIHSWRRKR   77 (179)
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHHcCCCC--ChHHHHHHHHHHHHHHHHHhh
Confidence            57889999999999999999999998   7888999999999999999999999864  699999999998888776621


Q ss_pred             cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCC
Q 010308          350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG  429 (513)
Q Consensus       350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~  429 (513)
                      .....                                                     .++..     .+..+.   ...
T Consensus        78 ~~~~~-----------------------------------------------------~~~~~-----~~~~~~---~~~   96 (179)
T PRK12543         78 WRRFR-----------------------------------------------------IFEKA-----EEQRKP---VSI   96 (179)
T ss_pred             ccccc-----------------------------------------------------ccccc-----cccccc---ccc
Confidence            10000                                                     00000     000000   001


Q ss_pred             CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ..++. ....+....|..+|..|||++|.||.++|    .+++|++|||+.||||..+|+..+.+|+++||+...
T Consensus        97 ~~~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~----~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~  166 (179)
T PRK12543         97 DFSED-VLSKESNQELIELIHKLPYKLRQVIILRY----LHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ  166 (179)
T ss_pred             cChHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            12333 45556677899999999999999999998    799999999999999999999999999999998654

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

Probab=99.79  E-value=2.3e-18  Score=157.42  Aligned_cols=158  Identities=15%  Similarity=0.161  Sum_probs=124.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccc
Q 010308          275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR  353 (513)
Q Consensus       275 Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iR  353 (513)
                      |++.|+..|.+.|+.+++++.   ++..+.+|++||+++++|+++.+|++..  +|.+|++.++++.+.++++ ..+.. 
T Consensus         2 a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~~~d~~r~~~~~~-   75 (161)
T TIGR02985         2 AFEQLYRRYYPKLCAFAYRYV---KDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNRSLNYLRHKQVEE-   75 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHHHHHHHHHHHhHh-
Confidence            789999999999999999998   6788899999999999999999998643  7999999999999999887 21100 


Q ss_pred             cccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCch
Q 010308          354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENE  433 (513)
Q Consensus       354 lP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~e  433 (513)
                                   .....+                                     ..       . ..  ......+++
T Consensus        76 -------------~~~~~~-------------------------------------~~-------~-~~--~~~~~~~~~   95 (161)
T TIGR02985        76 -------------KYQEEI-------------------------------------LE-------I-EV--DELSENDPE   95 (161)
T ss_pred             -------------HHHHHH-------------------------------------Hh-------h-cc--cccCCCCcH
Confidence                         000000                                     00       0 00  000111244


Q ss_pred             hhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          434 NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       434 e~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      +.....+....|..+|..||++++.||.++|    .+++|..|||+.||+|+++|++++.+|+++||+.
T Consensus        96 ~~~~~~e~~~~l~~~l~~L~~~~r~il~l~~----~~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~  160 (161)
T TIGR02985        96 EELEAKELQLIIYKAIEKLPEQCRKIFILSR----FEGKSYKEIAEELGISVKTVEYHISKALKELRKE  160 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            4455566777899999999999999999988    6899999999999999999999999999999963

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

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.79  E-value=1.9e-18  Score=161.94  Aligned_cols=166  Identities=16%  Similarity=0.117  Sum_probs=129.8

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010308          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (513)
Q Consensus       264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~  343 (513)
                      .+....+||..|++.|+..|.+.|+.+|.+|.   ++..+.+|++||+|+++|++++.|++.  .+|.+|++..+++.+.
T Consensus         8 l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~vQe~~l~l~~~~~~~~~~--~~~~~wl~~i~~n~~~   82 (176)
T PRK09638          8 LIQKAKKGDDAALTTLFQQHYSFLYKYLLKLT---LDPDLAEDLVQETMLKAIENLSSFQGR--SKFSTWLISIASRLYK   82 (176)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHc---CCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHH
Confidence            35566789999999999999999999999998   778889999999999999999999874  4799999999999999


Q ss_pred             HHHHh-ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          344 RSMTV-SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       344 raI~~-~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      ++++. .+.....                           +.                       ..+            
T Consensus        83 d~~r~~~~~~~~~---------------------------~~-----------------------~~~------------  100 (176)
T PRK09638         83 DHLRKQKREKLRL---------------------------QR-----------------------AKE------------  100 (176)
T ss_pred             HHHHHhccccchh---------------------------hh-----------------------ccc------------
Confidence            99883 2110000                           00                       000            


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ...+..  .. +..........|..+|..||++++.||.++|    ..++|++|||+.||+|..+|++.+.+|+++||+.
T Consensus       101 ~~~~~~--~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~  173 (176)
T PRK09638        101 ETLRKE--KW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKH----YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE  173 (176)
T ss_pred             ccCCcc--ch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehh----hcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence            000000  00 1112233445688999999999999999998    7899999999999999999999999999999974


Q ss_pred             c
Q 010308          503 T  503 (513)
Q Consensus       503 ~  503 (513)
                      .
T Consensus       174 l  174 (176)
T PRK09638        174 W  174 (176)
T ss_pred             h
Confidence            3

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.79  E-value=4.7e-18  Score=166.51  Aligned_cols=120  Identities=12%  Similarity=0.166  Sum_probs=104.5

Q ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHH
Q 010308          267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM  346 (513)
Q Consensus       267 ~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI  346 (513)
                      .+..||.. ++.||..|.|+|.++|.+|..+. .+.+.+||+|+|++|||+|+++|||++|.+|.|||.+||++.|.+++
T Consensus         3 ~~~~gd~~-~e~LI~~Y~plI~~~a~~~~~~~-~~~e~dDlvQ~glial~eAi~~yd~~kg~~F~sya~~~Ir~~i~dyl   80 (218)
T TIGR02895         3 PIQPGNEE-REELIRQYKPFIAKIVSSVCGRY-IDTKSDDELSIGLIAFNEAIESYDSNKGKSFLSFAKLIIKRRLIDYI   80 (218)
T ss_pred             hhhcCChH-HHHHHHHhHHHHHHHHHHHHccC-CCCChhHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence            34567777 99999999999999999997321 13589999999999999999999999999999999999999999999


Q ss_pred             H-hc---cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHh
Q 010308          347 T-VS---SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQG  388 (513)
Q Consensus       347 ~-~~---r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~  388 (513)
                      + ..   ..+++|....+....+..+..++..++++.|+.+||+..
T Consensus        81 Rk~~k~~~~v~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~eEI~~~  126 (218)
T TIGR02895        81 RKNQKYQNLLYLDEDYDENPLEFNKSMEEYRNEIENENRRLEILEY  126 (218)
T ss_pred             HhcccccCeeeCCchHHHHHHHHHHHHHHHHHHHccccHHHHHHHH
Confidence            9 44   466888777776778888888999999999999999764

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

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.79  E-value=6e-18  Score=159.98  Aligned_cols=167  Identities=16%  Similarity=0.185  Sum_probs=128.2

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccC-CCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010308          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFA-NGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (513)
Q Consensus       265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~-~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~  343 (513)
                      +..+..|+..|++.|+..|.+.|+.+|.++..+.+ +..+.+|++||+|+.+|...+.|+..  ..|.+|++..+++.+.
T Consensus        13 ~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~~~~~~~~~--~~~~~wl~~i~rn~~~   90 (184)
T PRK12512         13 MRSANAGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWLFAIARNKLI   90 (184)
T ss_pred             HHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHHhHHhcCcc--ccHHHHHHHHHHHHHH
Confidence            55567799999999999999999999999874211 34689999999999999999999863  3699999999999999


Q ss_pred             HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      ++++ +.+....+                                                     ++        ++.+
T Consensus        91 d~~Rr~~~~~~~~-----------------------------------------------------~~--------~~~~  109 (184)
T PRK12512         91 DALRRRGRRVFVD-----------------------------------------------------ID--------DFAE  109 (184)
T ss_pred             HHHHhhcccccCC-----------------------------------------------------ch--------hccc
Confidence            9887 22110000                                                     00        0000


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ...+..   ..    .......+..+|+.||+++++||.++|    .+++|++|||+.||+|..+|+...++|+++||..
T Consensus       110 ~~~~~~---~~----~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~  178 (184)
T PRK12512        110 TLPAEP---AT----ETLPAGDVGRHLETLPPRQRDVVQSIS----VEGASIKETAAKLSMSEGAVRVALHRGLAALAAK  178 (184)
T ss_pred             cccccc---hh----hHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            001100   00    112345688899999999999999998    7899999999999999999999999999999976


Q ss_pred             chh
Q 010308          503 TRV  505 (513)
Q Consensus       503 ~~~  505 (513)
                      .++
T Consensus       179 l~~  181 (184)
T PRK12512        179 FRS  181 (184)
T ss_pred             hhc
Confidence            543

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.79  E-value=4.1e-18  Score=161.03  Aligned_cols=163  Identities=15%  Similarity=0.060  Sum_probs=130.1

Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhc
Q 010308          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS  349 (513)
Q Consensus       270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~  349 (513)
                      ..+..|++.|+..|.+.|+.+|.++.   ++..+.+|++||+|+.||+++++|++.  ..|.+|++..+++.+.+++++.
T Consensus        12 ~~~~~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDlvQd~fl~l~~~~~~~~~~--~~~~awl~~ia~n~~~d~~Rk~   86 (179)
T PRK09415         12 EDKEDLIDEIMNEYGQEVLQLVYSYV---KNKEVAEDLTQEIFVKCYKSLHTYKGK--SSLKTWLYRIAINHCKDYLKSW   86 (179)
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHhcCCC--cccHHHHHHHHHHHHHHHHHhh
Confidence            45688999999999999999999998   778899999999999999999999864  3699999999999999988731


Q ss_pred             -cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCC
Q 010308          350 -SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD  428 (513)
Q Consensus       350 -r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~  428 (513)
                       +....+                                                     .+.        ..+... ..
T Consensus        87 ~~~~~~~-----------------------------------------------------~~~--------~~~~~~-~~  104 (179)
T PRK09415         87 HNKKVIV-----------------------------------------------------TED--------IFTYME-SQ  104 (179)
T ss_pred             ccccccc-----------------------------------------------------ccc--------cccccc-cc
Confidence             100000                                                     000        000000 11


Q ss_pred             CCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          429 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       429 ~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      ..++++.....+....|..+|+.||+++++||.++|    ++++|++|||+.||||..+|++.+.||+++||...
T Consensus       105 ~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l  175 (179)
T PRK09415        105 KESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFY----YEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL  175 (179)
T ss_pred             ccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            123455555566777899999999999999999999    78999999999999999999999999999999644

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

Probab=99.79  E-value=4.7e-18  Score=158.58  Aligned_cols=163  Identities=24%  Similarity=0.204  Sum_probs=128.6

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010308          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (513)
Q Consensus       263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI  342 (513)
                      +.+..+..||..|++.|+..|.+.|++++.++.   ++..+.+|++||+|+.+|+..+.|++..  .|.||++..+++.+
T Consensus         5 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~~   79 (169)
T TIGR02954         5 ELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYV---KNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINEC   79 (169)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHHH
Confidence            345667789999999999999999999999998   7888999999999999999999999753  69999999999999


Q ss_pred             HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      .+++++... ..|                                                     ++...         
T Consensus        80 ~d~~R~~~~-~~~-----------------------------------------------------~~~~~---------   96 (169)
T TIGR02954        80 IDLLKKKKK-VIP-----------------------------------------------------FDPNT---------   96 (169)
T ss_pred             HHHHHhcCC-cCc-----------------------------------------------------ccccc---------
Confidence            998873110 000                                                     00000         


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                        ... ...++.  + ......|..+|+.||+++++||.++|    .+++|.+|||+.||+|..+|+....+|+++||..
T Consensus        97 --~~~-~~~~~~--~-~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~  166 (169)
T TIGR02954        97 --SIE-KGECET--H-ADSRLDLYKAIDTLNDKYQTAIILRY----YHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR  166 (169)
T ss_pred             --ccc-cchhhh--c-hHHHHHHHHHHHhCCHHHhHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence              000 000010  0 11123688999999999999999999    7899999999999999999999999999999974


Q ss_pred             c
Q 010308          503 T  503 (513)
Q Consensus       503 ~  503 (513)
                      .
T Consensus       167 l  167 (169)
T TIGR02954       167 L  167 (169)
T ss_pred             h
Confidence            3

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

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.78  E-value=4.8e-18  Score=161.66  Aligned_cols=169  Identities=17%  Similarity=0.128  Sum_probs=129.2

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010308          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (513)
Q Consensus       264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~  343 (513)
                      .+.++..|+..|++.|+..|.+.++.++. +.   ++..+.+|++||.|+.+|+..++|++.  ..|.+|++..+++.+.
T Consensus        14 l~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~---~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~   87 (185)
T PRK09649         14 LALSAAKGNGRALEAFIKATQQDVWRFVA-YL---SDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVA   87 (185)
T ss_pred             HHHHHHccCHHHHHHHHHHHHHHHHHHHH-Hh---CCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHH
Confidence            35667789999999999999999999995 55   677899999999999999999999964  3699999999999999


Q ss_pred             HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      ++++ +.+..+..                                                     .+.    ..+.   
T Consensus        88 d~~Rk~~~~~~~~-----------------------------------------------------~~~----~~~~---  107 (185)
T PRK09649         88 DHIRHVRSRPRTT-----------------------------------------------------RGA----RPEH---  107 (185)
T ss_pred             HHHHHhccccccc-----------------------------------------------------ccc----chhh---
Confidence            9888 22110000                                                     000    0000   


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                       ..+     ++......+....|..+|++||+++|.||.|+|    ++++|++|||+.||+|.++|+..+.+|+++||+.
T Consensus       108 -~~~-----~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~  177 (185)
T PRK09649        108 -LID-----GDRHARGFEDLVEVTTMIADLTTDQREALLLTQ----LLGLSYADAAAVCGCPVGTIRSRVARARDALLAD  177 (185)
T ss_pred             -ccC-----hhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence             000     000011112234588899999999999999999    7999999999999999999999999999999986


Q ss_pred             chhhhh
Q 010308          503 TRVDYL  508 (513)
Q Consensus       503 ~~~~~L  508 (513)
                      ...+.|
T Consensus       178 ~~~~~~  183 (185)
T PRK09649        178 AEPDDL  183 (185)
T ss_pred             CCcccc
Confidence            655443

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.78  E-value=6.3e-18  Score=158.14  Aligned_cols=163  Identities=14%  Similarity=0.141  Sum_probs=126.8

Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhc
Q 010308          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS  349 (513)
Q Consensus       270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~  349 (513)
                      .++..|++.|+..|.+.|+.+|.++.   ++..+.+|++||.|+.+|+..++|++.. ..|.+|++..+++.+.+++++.
T Consensus         5 ~~~~~~~~~l~~~~~~~l~~~~~~~~---~~~~~AeD~vQevfl~~~~~~~~~~~~~-~~~~~wL~~iarn~~~d~~Rk~   80 (173)
T PRK09645          5 TAEAALMRALYDEHAAPLWRYALRLT---GDRARAEDVVQETLLRAWQHPEVLADTG-RSARAWLFTVARNLVIDERRSA   80 (173)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhcCccc-ccHHHHHHHHHHHHHHHHHHhh
Confidence            36789999999999999999999998   6778899999999999999999997532 3699999999999999988831


Q ss_pred             cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCC
Q 010308          350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG  429 (513)
Q Consensus       350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~  429 (513)
                      +... +                                                   ...+        +... ..+   
T Consensus        81 ~~~~-~---------------------------------------------------~~~~--------~~~~-~~~---   96 (173)
T PRK09645         81 RARP-V---------------------------------------------------EGGD--------DVLG-VPE---   96 (173)
T ss_pred             cccc-c---------------------------------------------------cccc--------cccc-CCC---
Confidence            1000 0                                                   0000        0000 000   


Q ss_pred             CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      .++++..........|..+|+.||+++++||.|+|    ++++|++|||+.||+|..+|+..+++|+++||+...
T Consensus        97 ~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~  167 (173)
T PRK09645         97 QSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSY----YRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQ  167 (173)
T ss_pred             CCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence            11122233334455789999999999999999999    799999999999999999999999999999997654

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=6.3e-18  Score=158.47  Aligned_cols=164  Identities=11%  Similarity=0.009  Sum_probs=126.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccc
Q 010308          274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFT  352 (513)
Q Consensus       274 ~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~i  352 (513)
                      ..++.|+..|.++|+.+|.+|.   ++..+++|++||+++.||++.+.|++..  +|.+|++..+++.+.++++ +.+..
T Consensus         3 ~~~~~l~~~y~~~i~~~~~~~~---~~~~daeDvvQe~~i~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~Rk~~~~~   77 (173)
T PRK12522          3 EKVEELIDIYKQQIYSLCYKLA---KTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKRWK   77 (173)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHHcCCcc--chHHHHHHHHHHHHHHHHHHhcccc
Confidence            4589999999999999999998   7889999999999999999999999754  7999999999999999988 32210


Q ss_pred             ccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCc
Q 010308          353 RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN  432 (513)
Q Consensus       353 RlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~  432 (513)
                      ..+.                                                   +..     +.+...+.........+
T Consensus        78 ~~~~---------------------------------------------------~~~-----~~~~~~~~~~~~~~~~~  101 (173)
T PRK12522         78 DRIL---------------------------------------------------DLF-----HKEDGGEIEFADDVNIS  101 (173)
T ss_pred             cccc---------------------------------------------------ccc-----chhhhhhhccccCCCCh
Confidence            0000                                                   000     00000000000111112


Q ss_pred             hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          433 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       433 ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      +. ....+..+.|..+|..||++++.||.|+|    .+++|++|||+.||+|..+|+..+.||+++||+..
T Consensus       102 ~~-~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l  167 (173)
T PRK12522        102 EE-FIQKVEAEMIREVIQLLNEKYKTVLVLYY----YEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHL  167 (173)
T ss_pred             HH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence            22 44455677899999999999999999999    79999999999999999999999999999999654

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=8.7e-18  Score=159.33  Aligned_cols=169  Identities=16%  Similarity=0.178  Sum_probs=128.6

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhcc-CCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010308          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDF-ANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (513)
Q Consensus       264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~-~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI  342 (513)
                      .+.+...||..|++.|+..|.+.|+.+|++...++ ++..+.+|++||+++.+|++.+.|++..  .|.+|++..+++.+
T Consensus        11 l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n~~   88 (184)
T PRK12539         11 LMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIARYKL   88 (184)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHHHH
Confidence            35566789999999999999999999987433211 5678999999999999999999999753  69999999999999


Q ss_pred             HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      .++++.......+                                                   .+++.      .   +
T Consensus        89 ~d~~R~~~~~~~~---------------------------------------------------~~~~~------~---~  108 (184)
T PRK12539         89 IDHLRRTRASLAD---------------------------------------------------VPIDD------A---D  108 (184)
T ss_pred             HHHHHHHhccccc---------------------------------------------------cChhh------h---c
Confidence            9988821100000                                                   00000      0   0


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ...      +.+.....+....|..+|..||+++++||.++|    .+++|++|||+.||+|..+|+..+++|+++||+.
T Consensus       109 ~~~------~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~  178 (184)
T PRK12539        109 ELV------AHDDHAAVESTLDLGRLLARLPEKMRLAIQAVK----LEGLSVAEAATRSGMSESAVKVSVHRGLKALAAL  178 (184)
T ss_pred             ccc------CCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            000      001112223456789999999999999999999    7899999999999999999999999999999975


Q ss_pred             ch
Q 010308          503 TR  504 (513)
Q Consensus       503 ~~  504 (513)
                      ..
T Consensus       179 l~  180 (184)
T PRK12539        179 IG  180 (184)
T ss_pred             Hh
Confidence            43

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

Probab=99.78  E-value=5.8e-18  Score=168.67  Aligned_cols=179  Identities=16%  Similarity=0.151  Sum_probs=138.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHH-------HHhhcCCcCCCccchHH
Q 010308          262 AAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLIT-------AIDRFEPKRRFRLSTYG  334 (513)
Q Consensus       262 ~e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLir-------AvekFDp~kG~rFSTYA  334 (513)
                      ...+..+..|+..|+..|+..|.+.|+.++.++.   ++..+.+|++||.|+.+|.       .+++|++.  ..|.||+
T Consensus        27 ~~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~---~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tWL  101 (244)
T TIGR03001        27 LYLACACAQGEPAALAALERHVLSKVPARLAGLR---PPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSWV  101 (244)
T ss_pred             HHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhHH
Confidence            3456667889999999999999999999999997   6788999999999999994       78889864  3699999


Q ss_pred             HHHHHHHHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCC
Q 010308          335 LFWIRHAIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRH  413 (513)
Q Consensus       335 ~~wIR~aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~  413 (513)
                      +..++|.+.++++ +.+...                                                       ++.  
T Consensus       102 ~~Ia~N~~id~lRk~~r~~~-------------------------------------------------------~~~--  124 (244)
T TIGR03001       102 RIVATRIALELQAQERRHSP-------------------------------------------------------VEE--  124 (244)
T ss_pred             HHHHHHHHHHHHHHhcccCc-------------------------------------------------------ccc--
Confidence            9999999999887 221100                                                       000  


Q ss_pred             CCchhhhhccccCCCCCCchhhhHH----HHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHH
Q 010308          414 GVTQEEFINGITDVDGVENENQRQP----ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVR  489 (513)
Q Consensus       414 ~~~~~e~~d~l~d~~~~~~ee~~~~----~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVR  489 (513)
                         .+...+ ..+ ...++++....    .+....|..+|++||+++|+||.|+|    .+++|++|||+.||||.++|+
T Consensus       125 ---~~~~~~-~~~-~~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~----~eg~S~~EIA~~Lgis~~TVk  195 (244)
T TIGR03001       125 ---PTELAA-LPA-PGSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHF----VDGLSMDRIGAMYQVHRSTVS  195 (244)
T ss_pred             ---cccccc-ccC-CCCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHH
Confidence               000000 001 11123332222    34567799999999999999999999    899999999999999999999


Q ss_pred             HHHHHHHHHHhCcchhhhhhhc
Q 010308          490 KHEVKGLMKLKHPTRVDYLRQH  511 (513)
Q Consensus       490 qi~~rALkKLR~~~~~~~L~~y  511 (513)
                      ..+.+|+++||+....+....|
T Consensus       196 ~rl~RAr~~Lr~~l~~~~~~~~  217 (244)
T TIGR03001       196 RWVAQARERLLERTRRRLAERL  217 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999998877665554

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

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

Probab=99.78  E-value=6e-18  Score=155.60  Aligned_cols=157  Identities=16%  Similarity=0.212  Sum_probs=122.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccc
Q 010308          274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFT  352 (513)
Q Consensus       274 ~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~i  352 (513)
                      +|++.++..|.++|+.+|+++.   ++..+.+|++||+++.+|+++++|++..  .|.+|++..+++.+.++++ +.+..
T Consensus         1 ~~~~~~~~~~~~~l~~~~~~~~---~~~~~aEDivQe~~l~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~r~~~~~~   75 (159)
T TIGR02989         1 EAFAALLQRHQRSLRAFVRSLV---PDRDDADDVLQETFVTAWRKFDEFDPGT--DFGAWARGIARNKVLNHRRKLGRDR   75 (159)
T ss_pred             CHHHHHHHHhHHHHHHHHHHHc---CChhhHHHHHHHHHHHHHHHHHhCCCCC--chHHHHHHHHHHHHHHHHHHhcccc
Confidence            3789999999999999999998   7888999999999999999999999764  6999999999999999988 32210


Q ss_pred             ccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCc
Q 010308          353 RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN  432 (513)
Q Consensus       353 RlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~  432 (513)
                      . +.                         .+++                                .+..   .+.  .++
T Consensus        76 ~-~~-------------------------~~~~--------------------------------~~~~---~~~--~~~   92 (159)
T TIGR02989        76 L-VF-------------------------DDEL--------------------------------LEAL---AAE--AEA   92 (159)
T ss_pred             c-cc-------------------------CHHH--------------------------------HHHH---Hhh--ccc
Confidence            0 00                         0000                                0000   000  011


Q ss_pred             hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          433 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       433 ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      .+..........|..+++.||++++.||.++|    .+++|.+|||+.||||..+|+...+||+++||+.
T Consensus        93 ~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~----~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~  158 (159)
T TIGR02989        93 TEADRSEDELQALEGCLEKLPERQRELLQLRY----QRGVSLTALAEQLGRTVNAVYKALSRLRVRLRDC  158 (159)
T ss_pred             chHhhHHHHHHHHHHHHHHCCHHHHHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence            11122233456788999999999999999998    7899999999999999999999999999999974

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

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.77  E-value=6.9e-18  Score=157.97  Aligned_cols=168  Identities=13%  Similarity=0.061  Sum_probs=127.2

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010308          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (513)
Q Consensus       265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r  344 (513)
                      +..+..||..|++.|+..|.+.|+.++.++.   + ..+.+|++||+|+.+|+.++.|++.  ..|.+|++..+++.+.+
T Consensus         2 ~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d   75 (175)
T PRK12518          2 ILRCQRGDRQSFRQLYRRYQQKVRSTLYQLC---G-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATD   75 (175)
T ss_pred             hhHHHcCCHHHHHHHHHHHHHHHHHHHHHHc---C-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHH
Confidence            3456789999999999999999999999976   3 4689999999999999999999974  46999999999999998


Q ss_pred             HHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccc
Q 010308          345 SMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGI  424 (513)
Q Consensus       345 aI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l  424 (513)
                      ++++....+ .                                                    ..+.     ... .+..
T Consensus        76 ~~R~~~~~~-~----------------------------------------------------~~~~-----~~~-~~~~   96 (175)
T PRK12518         76 ARRQFAQRP-S----------------------------------------------------RIQD-----DSL-NDQP   96 (175)
T ss_pred             HHHHhhccc-c----------------------------------------------------chhc-----ccc-cccc
Confidence            877211000 0                                                    0000     000 0000


Q ss_pred             cCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          425 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       425 ~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ..   ..+++.....+....+..+|+.||++++.||.|+|    .+++|++|||+.||+|..+|++.+.||+++||+...
T Consensus        97 ~~---~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~  169 (175)
T PRK12518         97 SR---PSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHD----LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ  169 (175)
T ss_pred             cC---CCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            00   01111122233445688999999999999999999    789999999999999999999999999999997654

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

Probab=99.77  E-value=1.2e-17  Score=157.43  Aligned_cols=168  Identities=14%  Similarity=0.122  Sum_probs=122.1

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCC-----cHHHHHHHHHHHHHH-HHhhcCCcCCCccchHHHHH
Q 010308          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGP-----RFQDLCQAGVKGLIT-AIDRFEPKRRFRLSTYGLFW  337 (513)
Q Consensus       264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~-----~~eDLIQEG~iGLir-AvekFDp~kG~rFSTYA~~w  337 (513)
                      .+..+..|+..|+..|+..|.+.|+.+|.+|.   ++..     +.+|++||+|+.+|+ ..++|++.  ..|.+|++.+
T Consensus         7 li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i   81 (183)
T TIGR02999         7 LLQQWQNGDAAARDQLFPQLYQELRRIARRQL---RRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKA   81 (183)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---hcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHH
Confidence            35556789999999999999999999999998   5555     899999999999998 78889754  3699999999


Q ss_pred             HHHHHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCc
Q 010308          338 IRHAIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVT  416 (513)
Q Consensus       338 IR~aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~  416 (513)
                      +++.+.+.++ +.+..+..                                                 .  ..+..    
T Consensus        82 ~~n~~~d~~R~~~~~~~~~-------------------------------------------------~--~~~~~----  106 (183)
T TIGR02999        82 MRRILVDHARRRRAQKRGG-------------------------------------------------G--AVRVP----  106 (183)
T ss_pred             HHHHHHHHHHHHHHHhccC-------------------------------------------------C--ccccc----
Confidence            9999998887 21100000                                                 0  00000    


Q ss_pred             hhhhhccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010308          417 QEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  496 (513)
Q Consensus       417 ~~e~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rAL  496 (513)
                          .+......  .++.. +.......+...|++|||+++.||.|+|    .+++|++|||+.||+|.++|+..+.||+
T Consensus       107 ----~~~~~~~~--~~~~~-~~~~~l~~~~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar  175 (183)
T TIGR02999       107 ----LDEVLPDA--EADLD-EELLDLDDALDKLAQVDPRQAEVVELRF----FAGLTVEEIAELLGVSVRTVERDWRFAR  175 (183)
T ss_pred             ----cccccCCC--CccHH-HHHHHHHHHHHHhhcCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence                00000000  11111 1111122334456779999999999999    7999999999999999999999999999


Q ss_pred             HHHhCc
Q 010308          497 MKLKHP  502 (513)
Q Consensus       497 kKLR~~  502 (513)
                      ++||+.
T Consensus       176 ~~Lr~~  181 (183)
T TIGR02999       176 AWLADE  181 (183)
T ss_pred             HHHHHH
Confidence            999964

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

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=99.76  E-value=1.3e-17  Score=158.88  Aligned_cols=180  Identities=14%  Similarity=0.142  Sum_probs=130.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccc
Q 010308          275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR  353 (513)
Q Consensus       275 Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iR  353 (513)
                      +++.|+..|.+.|+.+|.++.   ++..+.+|++||.|+.+|+.+++|++..  .|.+|++..+++.+.++++ +.+...
T Consensus         3 ~~~~l~~~~~~~l~~~a~~~~---~~~~~AeDivQevfl~~~~~~~~~~~~~--~~~~WL~~ia~n~~~d~~Rk~~r~~~   77 (191)
T PRK12520          3 IAPAQLEALRPHLLRFARLQL---RDPALAEDAVSETLLAVLEHPERFAGQS--SLKTYLVGILKHKIIDAIRSGRREVR   77 (191)
T ss_pred             chHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhhhhhcccc--cHHHHHHHHHHHHHHHHHHhhcCcCc
Confidence            688999999999999999998   7788999999999999999999998543  6999999999999999988 332111


Q ss_pred             cccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCch
Q 010308          354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENE  433 (513)
Q Consensus       354 lP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~e  433 (513)
                      .+....                  ......++                       ++...  ..+.......+ ...+++
T Consensus        78 ~~~~~~------------------~~~~~~~~-----------------------~~~~~--~~~~~~~~~~~-~~~~~~  113 (191)
T PRK12520         78 LSLDDA------------------DEQSDDDL-----------------------FDALF--AADGHYREPPS-DWGDPD  113 (191)
T ss_pred             cccccc------------------ccchhhhh-----------------------hhhhc--ccccccccCcc-ccCCHH
Confidence            110000                  00000000                       00000  00000000111 112355


Q ss_pred             hhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          434 NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       434 e~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      +.....+....|..+|..||+++|.||.|+|    .+++|++|||+.||+|.++|++.+.||+++||+......
T Consensus       114 ~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~  183 (191)
T PRK12520        114 AALSRREFFEVLQACVDRLPPRTGRVFMMRE----WLELETEEICQELQITATNAWVLLYRARMRLRECLDLHW  183 (191)
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            5555666677899999999999999999999    789999999999999999999999999999998765443

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.76  E-value=1.3e-17  Score=157.62  Aligned_cols=168  Identities=14%  Similarity=0.087  Sum_probs=127.8

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHchhccC-CCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHH
Q 010308          268 CLEVGRAARNKLIKHNLRLVLFVIKKYFQDFA-NGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM  346 (513)
Q Consensus       268 ~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~-~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI  346 (513)
                      ...|+..|++.|+..|.+.|+.++..+..  . +..+.+|++||.|+.+|+..+.|++.....|.||++...++.+.+++
T Consensus         7 ~~~~d~~af~~ly~~~~~~l~~~~~~~~~--~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~~   84 (178)
T PRK12529          7 CLSADRDKVATLYRENHAWLRNWLAYRLR--SWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSWR   84 (178)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHhC--CCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHHH
Confidence            45789999999999999999998766551  1 35689999999999999999999854445799999999999998877


Q ss_pred             HhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccC
Q 010308          347 TVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD  426 (513)
Q Consensus       347 ~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d  426 (513)
                      ++.+. + .               .                                    ..+        .... ...
T Consensus        85 Rk~~~-~-~---------------~------------------------------------~~~--------~~~~-~~~  102 (178)
T PRK12529         85 RRQSL-E-L---------------A------------------------------------WLE--------ALAT-LPE  102 (178)
T ss_pred             HHHHH-H-h---------------h------------------------------------hhh--------Hhhh-ccC
Confidence            62110 0 0               0                                    000        0000 000


Q ss_pred             CCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          427 VDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       427 ~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      ....++++.....+....|..+|.+|||++|.||.|+|    .+++|++|||+.||||.++|+..+.+|+.+|+..+
T Consensus       103 ~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~~  175 (178)
T PRK12529        103 PLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMAT----LDGMKQKDIAQALDIALPTVKKYIHQAYVTCLSLM  175 (178)
T ss_pred             cCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence            11123444445555567799999999999999999999    79999999999999999999999999999998653

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

Probab=99.76  E-value=3e-17  Score=155.57  Aligned_cols=170  Identities=18%  Similarity=0.135  Sum_probs=133.0

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010308          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (513)
Q Consensus       265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r  344 (513)
                      +.....++..++..++..+.+.++.++.++.   ++..+.+||+||+|+.+|+++..| .. +..|.||++..++|.+.+
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~---~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD   80 (182)
T COG1595           6 LAEALRGDRAAFEELLERLRPRLRRLARRLL---GDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAID   80 (182)
T ss_pred             HHHHHhcchHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHhhc-CC-CCchHHHHHHHHHHHHHH
Confidence            4455688899999999999999999999999   666699999999999999999999 33 447999999999999999


Q ss_pred             HHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcc
Q 010308          345 SMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING  423 (513)
Q Consensus       345 aI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~  423 (513)
                      .++ +.+.....                                                      +.      .+....
T Consensus        81 ~~R~~~r~~~~~------------------------------------------------------~~------~~~~~~  100 (182)
T COG1595          81 RLRKRKRRRARV------------------------------------------------------EE------ADLLPE  100 (182)
T ss_pred             HHHHhccccccc------------------------------------------------------cc------cccccc
Confidence            998 33211100                                                      00      000000


Q ss_pred             ccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          424 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       424 l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      ..+...... +.....+....|..+|..||+++|.+|.++|    .+++|++|||+.||||.++|+..+++|+.+|+...
T Consensus       101 ~~~~~~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~----~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l  175 (182)
T COG1595         101 EADPAPDLA-ELLLAEEELERLRRALARLPPRQREAFLLRY----LEGLSYEEIAEILGISVGTVKSRLHRARKKLREQL  175 (182)
T ss_pred             ccCcccccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHh----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            000000000 2345567778899999999999999999999    79999999999999999999999999999999765


Q ss_pred             h
Q 010308          504 R  504 (513)
Q Consensus       504 ~  504 (513)
                      .
T Consensus       176 ~  176 (182)
T COG1595         176 E  176 (182)
T ss_pred             h
Confidence            4

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.76  E-value=2.9e-17  Score=159.12  Aligned_cols=165  Identities=17%  Similarity=0.199  Sum_probs=131.6

Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhc
Q 010308          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS  349 (513)
Q Consensus       270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~  349 (513)
                      .|+..+++.|+..|.+.++.++.++.   ++..+.+|++||+|+.+|+...+|++  + .|.+|++..+++.+.+++++.
T Consensus        24 ~~d~~a~~~l~~~~~~~L~~~~~~~~---~~~~~AEDivQEvflkl~~~~~~~~~--~-~~~~wL~~iarn~~~d~~Rk~   97 (203)
T PRK09647         24 KATMPSWEELVRQHADRVYRLAYRLS---GNQHDAEDLTQETFIRVFRSLQNYQP--G-TFEGWLHRITTNLFLDMVRRR   97 (203)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHHhHHhcCC--c-ccHHHHHHHHHHHHHHHHHhc
Confidence            46889999999999999999999998   67789999999999999999999985  3 599999999999999998832


Q ss_pred             cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCC
Q 010308          350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG  429 (513)
Q Consensus       350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~  429 (513)
                      ...+..                                                    .++       +++ +... ...
T Consensus        98 ~~~~~~----------------------------------------------------~~~-------~~~-~~~~-~~~  116 (203)
T PRK09647         98 ARIRME----------------------------------------------------ALP-------EDY-DRVP-GDE  116 (203)
T ss_pred             ccCccc----------------------------------------------------ccc-------ccc-cccC-CCC
Confidence            111000                                                    000       000 0001 112


Q ss_pred             CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010308          430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  505 (513)
Q Consensus       430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~  505 (513)
                      .+++......++...|..+|+.||++++.||.|+|    .+++|++|||+.||||..+|++.+.||+++||+....
T Consensus       117 ~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~----~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~  188 (203)
T PRK09647        117 PNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCD----IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAA  188 (203)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            23444455666777899999999999999999999    7899999999999999999999999999999975543

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=4.2e-17  Score=159.65  Aligned_cols=169  Identities=14%  Similarity=0.079  Sum_probs=130.4

Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-h
Q 010308          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-V  348 (513)
Q Consensus       270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~  348 (513)
                      .....++..|+..|.+.++.++.++.   ++..+.+|++||.|+.+|+.+++|++.   .|.+|++..++|.+.+.++ +
T Consensus        14 ~~~~~~f~~l~~~~~~~l~~~~~~~~---~d~~dAEDlvQEvflkl~~~~~~~~~~---~~~aWL~~IarN~~~d~~Rk~   87 (216)
T PRK12533         14 AARGERFRQLVLPHLDAAYNLARWLC---GNASDADDVVQEACMRALRFFDSFRGD---NARPWLLAIVRHTWYSEWRRR   87 (216)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHhHHhcCcc---chHhHHHHHHHHHHHHHHHhh
Confidence            34567999999999999999999998   778899999999999999999999853   4999999999999998887 3


Q ss_pred             ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCC
Q 010308          349 SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD  428 (513)
Q Consensus       349 ~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~  428 (513)
                      .+.....                                                    ..+. .  ......+.. ++.
T Consensus        88 ~~~~~~~----------------------------------------------------~~~~-~--~~~~~~~~~-~~~  111 (216)
T PRK12533         88 ANAHEVA----------------------------------------------------APDT-L--DDADSLDDW-QPA  111 (216)
T ss_pred             ccccccc----------------------------------------------------cccc-c--ccccccccc-ccC
Confidence            2110000                                                    0000 0  000000000 111


Q ss_pred             CCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          429 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       429 ~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ..++++.....+....|..+|+.||+++++||.|+|    .+++|++|||+.||||.++|++++++|+++||+...
T Consensus       112 ~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y----~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~  183 (216)
T PRK12533        112 GEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRE----LEDMSYREIAAIADVPVGTVMSRLARARRRLAALLG  183 (216)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence            223555556667778899999999999999999999    799999999999999999999999999999997553

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

Probab=99.75  E-value=1.6e-17  Score=158.51  Aligned_cols=173  Identities=14%  Similarity=0.082  Sum_probs=127.5

Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-h
Q 010308          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-V  348 (513)
Q Consensus       270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~  348 (513)
                      .++..+++.|+..|.+.|+.+|.++.   ++..+.+|++||.|+.+|+..+.|++.  ..|.+|++..+++.+.++++ +
T Consensus         7 ~~~~~~f~~l~~~~~~~l~~~~~~~~---~~~~~AEDlvQevfl~~~~~~~~~~~~--~~~~~wL~~iarN~~~d~~Rk~   81 (193)
T TIGR02947         7 TQRAQRFERDALEYLDQLYGAALRMT---RNPADAEDLVQEAYAKAFSSFHQFKPG--TNLKAWLYRILTNTYINSYRKA   81 (193)
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhhcccCCC--CcchHHHHHHHHHHHHHHHHHh
Confidence            45678999999999999999999998   677889999999999999999999864  36999999999999999888 3


Q ss_pred             ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCC
Q 010308          349 SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD  428 (513)
Q Consensus       349 ~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~  428 (513)
                      .+.....                         ..+++.           ..        .+.        . ........
T Consensus        82 ~~~~~~~-------------------------~~~~~~-----------~~--------~~~--------~-~~~~~~~~  108 (193)
T TIGR02947        82 QRRPQQS-------------------------DDDDIE-----------DW--------QLA--------K-AASHTSNG  108 (193)
T ss_pred             cCCcccc-------------------------cchhhh-----------hh--------hhc--------c-cccccccc
Confidence            2210000                         000000           00        000        0 00000000


Q ss_pred             CCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          429 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       429 ~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ...++......+....|..+|++||++++.||.|+|    .+++|++|||+.||||..+|+.++.||+++||+...
T Consensus       109 ~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~  180 (193)
T TIGR02947       109 LRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLAD----VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV  180 (193)
T ss_pred             ccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehh----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            011222223334456788999999999999999999    799999999999999999999999999999997654

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

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

Probab=99.75  E-value=3.1e-17  Score=151.70  Aligned_cols=157  Identities=17%  Similarity=0.163  Sum_probs=125.1

Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhc
Q 010308          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS  349 (513)
Q Consensus       270 ~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~  349 (513)
                      .|+..+++.|+..|.+.|+.+|..+.   ++..+.+|++||+|+.+|++.++|+.  ...|.+|++..+++.+.+++++.
T Consensus         2 ~~~~~~~~~l~~~~~~~l~~~~~~~~---~~~~~aeDivQe~f~~~~~~~~~~~~--~~~~~~wl~~i~~n~~~d~~rk~   76 (162)
T TIGR02983         2 SATEEEFTAFVAARYPRLLRTAYLLT---GDPHEAEDLVQEALVRTYVRWDRIRD--PDAPDAYVRRVLVNLARSRWRRR   76 (162)
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHhhcCC--cccHHHHHHHHHHHHHHHHHHhh
Confidence            47899999999999999999999998   77889999999999999999999964  34799999999999998888721


Q ss_pred             cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCC
Q 010308          350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG  429 (513)
Q Consensus       350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~  429 (513)
                      ....++                                                      +       +..    .... 
T Consensus        77 ~~~~~~------------------------------------------------------~-------~~~----~~~~-   90 (162)
T TIGR02983        77 RLLELP------------------------------------------------------T-------REL----PDAA-   90 (162)
T ss_pred             cccccc------------------------------------------------------c-------ccc----Cccc-
Confidence            100000                                                      0       000    0000 


Q ss_pred             CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                        +++.....+....|..+|..||++++.||.|+|    .+++|.+|||+.||+|.++|++.+.+|+++||+..
T Consensus        91 --~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l  158 (162)
T TIGR02983        91 --APDPAPDVALRAALARALRRLPARQRAVVVLRY----YEDLSEAQVAEALGISVGTVKSRLSRALARLRELL  158 (162)
T ss_pred             --CCccchhHHHHHHHHHHHHhCCHHHHHHhhhHH----HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence              011112334556788999999999999999999    78999999999999999999999999999999754

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

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=99.74  E-value=4.3e-17  Score=155.71  Aligned_cols=159  Identities=13%  Similarity=0.094  Sum_probs=124.4

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh-c
Q 010308          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-S  349 (513)
Q Consensus       271 gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~-~  349 (513)
                      +|..++..|+..|.+.++.+|.++.   ++..+.+|++||.|+.+|+..++|+...  .|.+|++..+++.+.+++++ .
T Consensus         7 ~~~~~f~~l~~~~~~~L~~~a~~~~---~~~~~AEDivQevfl~~~~~~~~~~~~~--~~~awL~~Ia~n~~~d~~R~~~   81 (187)
T PRK12516          7 EGTPPFKRELLAALPSLRAFAVSLI---GRHDRADDLVQDTIMKAWAKQDHFEVGT--NMKAWLFTILRNEFYSQMRKRG   81 (187)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHc---CCHhHHHHHHHHHHHHHHHhhhccCCcc--cHHHHHHHHHHHHHHHHHHhhc
Confidence            5688999999999999999999998   7788999999999999999999998643  59999999999999998883 2


Q ss_pred             cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCC
Q 010308          350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG  429 (513)
Q Consensus       350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~  429 (513)
                      +...                                                      ..+       +...+.. +.  
T Consensus        82 ~~~~------------------------------------------------------~~~-------~~~~~~~-~~--   97 (187)
T PRK12516         82 REVQ------------------------------------------------------DTD-------GMFTEQL-AV--   97 (187)
T ss_pred             CCcc------------------------------------------------------ccc-------ccccccc-CC--
Confidence            1000                                                      000       0000000 00  


Q ss_pred             CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010308          430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  505 (513)
Q Consensus       430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~  505 (513)
                       .++.  ........|..+|+.||+++++||.|+|    .+++|++|||+.||||.++|+.++.+|+++||+....
T Consensus        98 -~~~~--~~~~~~~~l~~~L~~Lp~~~r~i~~L~~----~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~  166 (187)
T PRK12516         98 -HPSQ--YGTLDLQDFRAALDQLPDDQREAIILVG----ASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQI  166 (187)
T ss_pred             -Ccch--hhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence             0111  1112235688999999999999999999    7999999999999999999999999999999976553

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.74  E-value=6.1e-17  Score=149.89  Aligned_cols=158  Identities=15%  Similarity=0.070  Sum_probs=121.5

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcc
Q 010308          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS  350 (513)
Q Consensus       271 gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r  350 (513)
                      ++..|++.++..|.+.|+.++.++.   ++..+.+|++||+++.+|+..++|++.   .|.||++..+++.+.+++++.+
T Consensus         2 ~~~~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDv~Qe~f~~~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~   75 (161)
T PRK12541          2 KRKQSLEEIYSEHMQDLFRYLLSLT---GDSHFAEDLMQETFYRMLVHIDYYKGE---EIRPWLFTIAYNAFIDWYRKEK   75 (161)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHh---cCHHHHHHHHHHHHHHHHHhHHHccCC---ChHHHHHHHHHHHHHHHHHhcc
Confidence            4568999999999999999999998   778899999999999999999999863   5999999999999999888321


Q ss_pred             ccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCC
Q 010308          351 FTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV  430 (513)
Q Consensus       351 ~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~  430 (513)
                      ... .                                                   ...        ++.. .  .....
T Consensus        76 ~~~-~---------------------------------------------------~~~--------~~~~-~--~~~~~   92 (161)
T PRK12541         76 KYK-T---------------------------------------------------TTI--------EEFH-L--PNVPS   92 (161)
T ss_pred             ccc-c---------------------------------------------------cch--------hhhh-c--cCCCC
Confidence            000 0                                                   000        0000 0  00000


Q ss_pred             CchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          431 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       431 ~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ++++.....+. ..+..+|..||++++.||.|+|    .+++|++|||+.||+|..+|++.++||+++||..
T Consensus        93 ~~~~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~  159 (161)
T PRK12541         93 TEHEYFIKHEI-ASWLDSLSSLPLERRNVLLLRD----YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI  159 (161)
T ss_pred             cHHHHHHHhHH-HHHHHHHHHCCHHHHHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            11222222233 3455789999999999999999    7899999999999999999999999999999964

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.74  E-value=2.8e-17  Score=151.88  Aligned_cols=153  Identities=15%  Similarity=0.105  Sum_probs=119.6

Q ss_pred             HHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchh
Q 010308          281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLE  359 (513)
Q Consensus       281 ~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~  359 (513)
                      +.|.+.|+.+|.++.   ++..+.+|++||.|+.+|++.++|++.   .|.+|++..+++.+.++++ +.+..+.     
T Consensus         2 ~~y~~~l~~~~~~~~---~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wl~~ia~n~~~d~~Rk~~~~~~~-----   70 (160)
T PRK09642          2 QTYRHYIFQVIFSIL---RHEEDAKDVTQEVFVKIHASLPNYQFR---GLKTWMARIATNHAIDYKRKKARENEE-----   70 (160)
T ss_pred             chHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHhcccccccc---hhHHHHHHHHHHHHHHHHHHhcccccc-----
Confidence            578999999999998   778899999999999999999999863   4999999999999999888 3211000     


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhHHH
Q 010308          360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA  439 (513)
Q Consensus       360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~~~  439 (513)
                                                                     .++.    ....   +...  ...++++.....
T Consensus        71 -----------------------------------------------~~~~----~~~~---~~~~--~~~~~~~~~~~~   94 (160)
T PRK09642         71 -----------------------------------------------LSLC----KETE---ENIK--SSHNIEDLLLTK   94 (160)
T ss_pred             -----------------------------------------------cccc----hhhh---hhcc--CCCChHHHHHHH
Confidence                                                           0000    0000   0000  112244445555


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      +....|..+|+.||+.++.||.|+|    .+++|++|||+.||+|.++|++.+.+|+++||+...
T Consensus        95 e~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~  155 (160)
T PRK09642         95 EQKLLIAQKLRELPENYRDVVLAHY----LEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWK  155 (160)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence            6677899999999999999999999    799999999999999999999999999999997654

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.74  E-value=5.2e-17  Score=152.30  Aligned_cols=163  Identities=16%  Similarity=0.118  Sum_probs=124.6

Q ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh
Q 010308          269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV  348 (513)
Q Consensus       269 ~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~  348 (513)
                      ..|+..|+..|+..|.+.|+.++.++.   ++..+.+|++||.|+.+|+. ..|...  ..|.+|++..+++.+.++++.
T Consensus         5 ~~~~~~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDlvQevflk~~~~-~~~~~~--~~~~~wL~~Iarn~~~d~~Rk   78 (172)
T PRK12523          5 QSPHSELVGALYRDHRGWLLAWLRRNV---ACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRR   78 (172)
T ss_pred             CCCCcHHHHHHHHHHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHcc-cccCcc--hhHHHHHHHHHHHHHHHHHHH
Confidence            468899999999999999999999998   77889999999999999987 446543  369999999999999998882


Q ss_pred             ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCC
Q 010308          349 SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD  428 (513)
Q Consensus       349 ~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~  428 (513)
                      ...               . . ...         .++                        .           . .....
T Consensus        79 ~~~---------------~-~-~~~---------~~~------------------------~-----------~-~~~~~   96 (172)
T PRK12523         79 AAL---------------E-Q-AYL---------AEL------------------------A-----------L-VPEAE   96 (172)
T ss_pred             HHH---------------H-H-HHH---------HHH------------------------h-----------h-ccccc
Confidence            110               0 0 000         000                        0           0 00001


Q ss_pred             CCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          429 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       429 ~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      ...++......+....|..+|+.||++++.||.|+|    .+++|++|||+.||+|.++|++.+.+|+++||...
T Consensus        97 ~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l  167 (172)
T PRK12523         97 QPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNR----LDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIAL  167 (172)
T ss_pred             CCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            112333333334445799999999999999999999    79999999999999999999999999999998644

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.73  E-value=1e-16  Score=148.39  Aligned_cols=157  Identities=17%  Similarity=0.147  Sum_probs=121.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccc
Q 010308          274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTR  353 (513)
Q Consensus       274 ~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iR  353 (513)
                      .|++.|+..|.+.|+.++.++.   ++..+.+|++||.|+.+|+..+.|++   ..|.+|.+.++++.+.+.++....  
T Consensus         4 ~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDivQe~flk~~~~~~~~~~---~~~~~wl~~i~~n~~~d~~R~~~~--   75 (161)
T PRK12528          4 ATVEGLYSAHHHWLTGWLRRRL---GCPQSAADLAQDTFVKVLVARETAQI---IEPRAFLTTIAKRVLCNHYRRQDL--   75 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHc---CCcccHHHHHHHHHHHHHhccccccc---cCHHHHHHHHHHHHHHHHHHHHHH--
Confidence            6899999999999999999998   67789999999999999999888864   259999999999999988872110  


Q ss_pred             cccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCch
Q 010308          354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENE  433 (513)
Q Consensus       354 lP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~e  433 (513)
                                  ..   ...         ..                        +            ....+.....++
T Consensus        76 ------------~~---~~~---------~~------------------------~------------~~~~~~~~~~~~   95 (161)
T PRK12528         76 ------------ER---AYL---------EA------------------------L------------AQLPERVAPSEE   95 (161)
T ss_pred             ------------HH---hhH---------HH------------------------h------------hccccccCCCHH
Confidence                        00   000         00                        0            000000111122


Q ss_pred             hhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          434 NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       434 e~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ......+....|..+|..||++++.||.|+|    .+++|++|||+.||+|.++|+..+.+|+++||..
T Consensus        96 ~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~----~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~  160 (161)
T PRK12528         96 ERAIILETLVELDQLLDGLPPLVKRAFLLAQ----VDGLGYGEIATELGISLATVKRYLNKAAMRCYFA  160 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence            2233334456789999999999999999999    7999999999999999999999999999999853

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.73  E-value=6.3e-17  Score=150.57  Aligned_cols=154  Identities=16%  Similarity=0.117  Sum_probs=123.9

Q ss_pred             HHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh-cccccc
Q 010308          276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRV  354 (513)
Q Consensus       276 r~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~-~r~iRl  354 (513)
                      ++.|+..|.+.|+.+|.++.   ++..+.+|++||.|+.+|++++.|++.   .|.+|++..+++.+.+++++ .+...+
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQe~fl~~~~~~~~~~~~---~~~~wL~~i~~n~~~d~~R~~~~~~~~   76 (165)
T PRK09644          3 IEEIYKMYINDVYRYLFSLT---KSHHAAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVSFV   76 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhcccc---chHHHHHHHHHHHHHHHHHhhhhcccc
Confidence            57899999999999999998   778899999999999999999999863   59999999999999999883 110000


Q ss_pred             ccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchh
Q 010308          355 PFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN  434 (513)
Q Consensus       355 P~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee  434 (513)
                      .                          .+                                   . .+.+..   .++++
T Consensus        77 ~--------------------------~~-----------------------------------~-~~~~~~---~~~~~   91 (165)
T PRK09644         77 G--------------------------TD-----------------------------------E-IEAIQA---ESTEE   91 (165)
T ss_pred             c--------------------------hh-----------------------------------H-Hhhhcc---cChHH
Confidence            0                          00                                   0 000000   12444


Q ss_pred             hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      .....+....|..+|..||+++++||.++|    .+++|++|||+.||+|..+|+..+.||+++||+...
T Consensus        92 ~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~  157 (165)
T PRK09644         92 YVVAKNSYEKLIQIIHTLPVIEAQAILLCD----VHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK  157 (165)
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHhHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            444556667899999999999999999998    789999999999999999999999999999997654

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.73  E-value=1.4e-16  Score=164.96  Aligned_cols=187  Identities=17%  Similarity=0.163  Sum_probs=134.4

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010308          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (513)
Q Consensus       263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI  342 (513)
                      +.+.++..|+..|++.|+..|.+.|+.+|.++.   ++..+.+|++||.|+.+|+.+++|++.  ..|.+|++...+|.+
T Consensus         8 ~l~~~~~~gd~~af~~l~~~y~~~l~~~~~~~~---~~~~dAEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~   82 (339)
T PRK08241          8 ALLARAAAGDRDAFAALVEPHRRELLAHCYRML---GSVHDAEDAVQETLLRAWRGYDRFEGR--SSLRTWLYRIATNVC   82 (339)
T ss_pred             HHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHh---CChhhHHHHHHHHHHHHHhhhhccccc--cchHHHHHHHHHHHH
Confidence            457778899999999999999999999999998   677899999999999999999999853  369999999999999


Q ss_pred             HHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhh
Q 010308          343 IRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFI  421 (513)
Q Consensus       343 ~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~  421 (513)
                      .++++ +.+. ..+..                  .+. +..++                        .+.........+.
T Consensus        83 ~d~~Rk~~~~-~~~~~------------------~~~-~~~~~------------------------~~~~~~~~~~~~~  118 (339)
T PRK08241         83 LDALEGRARR-PLPTD------------------LGA-PAADP------------------------VDELVERPEVPWL  118 (339)
T ss_pred             HHHHHhhccc-cCccc------------------cCC-CcCcc------------------------ccccccccccccc
Confidence            99888 3211 00000                  000 00000                        0000000000011


Q ss_pred             ccccCC----CCCCchhhhHHHH-HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010308          422 NGITDV----DGVENENQRQPAL-LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  496 (513)
Q Consensus       422 d~l~d~----~~~~~ee~~~~~~-l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rAL  496 (513)
                      +.+.+.    ...++++.....+ ....|..+|++||+++|.||.|+|    .+++|++|||+.||+|..+|+++++||+
T Consensus       119 ~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~RAr  194 (339)
T PRK08241        119 EPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRD----VLGWSAAEVAELLDTSVAAVNSALQRAR  194 (339)
T ss_pred             CCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHH----hhCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            111110    0223444333333 455688999999999999999999    7999999999999999999999999999


Q ss_pred             HHHhCc
Q 010308          497 MKLKHP  502 (513)
Q Consensus       497 kKLR~~  502 (513)
                      ++||+.
T Consensus       195 ~~Lr~~  200 (339)
T PRK08241        195 ATLAER  200 (339)
T ss_pred             HHHhhc
Confidence            999983

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.73  E-value=1.4e-16  Score=153.28  Aligned_cols=167  Identities=16%  Similarity=0.118  Sum_probs=127.1

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHH
Q 010308          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (513)
Q Consensus       264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~  343 (513)
                      .+..+..|+..|++.|+..|.+.++.+++ +.   ++..+.+|++||.|+.||+..++|++.  ..|.+|++..+++.+.
T Consensus        15 l~~~~~~~d~~a~~~l~~~y~~~l~~~~~-~~---~~~~~AEDivQevflkl~~~~~~~~~~--~~~~~WL~~Iarn~~i   88 (196)
T PRK12535         15 LALAAGRGDRAALTEFIRETQDDVWRLLA-HL---GGHDIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARRVWV   88 (196)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHH-Hh---CCHHHHHHHHHHHHHHHHHHhhhcCCc--ccHHHHHHHHHHHHHH
Confidence            35667789999999999999999999975 45   577899999999999999999999863  3699999999999999


Q ss_pred             HHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          344 RSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       344 raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      ++++ ..+..+..                                                     .+.     ..... 
T Consensus        89 d~~Rk~~~~~~~~-----------------------------------------------------~~~-----~~~~~-  109 (196)
T PRK12535         89 DNIRHDMARPRKS-----------------------------------------------------ATE-----YEDAA-  109 (196)
T ss_pred             HHHHhhccCCCcc-----------------------------------------------------ccc-----ccccc-
Confidence            9988 32110000                                                     000     00000 


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                         +. ...++... .......|..+|+.||+++++||.|+|    ++++|++|||+.||+|..+|+..++||+++||+.
T Consensus       110 ---~~-~~~~~~~~-~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~  180 (196)
T PRK12535        110 ---AT-TASNETTG-SWSEWIDVRTLIDALPPERREALILTQ----VLGYTYEEAAKIADVRVGTIRSRVARARADLIAA  180 (196)
T ss_pred             ---cc-cCCcchhH-HHHHHHHHHHHHHcCCHHHHHHhhhHH----HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence               00 01111111 112234688999999999999999999    8999999999999999999999999999999965


Q ss_pred             ch
Q 010308          503 TR  504 (513)
Q Consensus       503 ~~  504 (513)
                      ..
T Consensus       181 l~  182 (196)
T PRK12535        181 TA  182 (196)
T ss_pred             hc
Confidence            43

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.73  E-value=1.3e-16  Score=147.87  Aligned_cols=158  Identities=14%  Similarity=0.077  Sum_probs=123.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccc
Q 010308          273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSF  351 (513)
Q Consensus       273 ~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~  351 (513)
                      ..+++.|+..|.+.|+.+|.++.   ++..+.+|++||+|+.+|++  .|+.  +..|.+|++..+++.+.++++ ..+.
T Consensus         2 ~~~f~~l~~~y~~~l~~~~~~~~---~~~~~aeDlvQe~fi~~~~~--~~~~--~~~~~~wl~~i~rn~~~d~~rk~~~~   74 (166)
T PRK09639          2 DETFEDLFEQYYPDVVQQIFYIV---KDRTQAEDLAQEVFLRLYRS--DFKG--IENEKGWLIKSARNVAYNYLRSEKRR   74 (166)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHH--hccc--ccchHHHHHHHHHHHHHHHHHHhccc
Confidence            36899999999999999999998   67889999999999999999  6764  347999999999999999888 3211


Q ss_pred             cccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCC
Q 010308          352 TRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVE  431 (513)
Q Consensus       352 iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~  431 (513)
                      .+..                                                      +.     ..+.. .+  +....
T Consensus        75 ~~~~------------------------------------------------------~~-----~~~~~-~~--~~~~~   92 (166)
T PRK09639         75 RARI------------------------------------------------------LG-----EFQWQ-EV--DNEPS   92 (166)
T ss_pred             cccc------------------------------------------------------cc-----hhhhh-hc--cCCCC
Confidence            1000                                                      00     00000 00  11223


Q ss_pred             chhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          432 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       432 ~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      +++.....+....|..+|..||++++.||.++|     +++|++|||+.||+|..+|+..+.+|+++||....
T Consensus        93 ~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~  160 (166)
T PRK09639         93 PEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYE  160 (166)
T ss_pred             hHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            455555556666789999999999999999999     58999999999999999999999999999997654

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

Probab=99.72  E-value=1.1e-16  Score=152.77  Aligned_cols=177  Identities=15%  Similarity=0.128  Sum_probs=127.2

Q ss_pred             HHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccc
Q 010308          277 NKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVP  355 (513)
Q Consensus       277 ~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP  355 (513)
                      .+++..|.+.|+.+|.++.   ++..+.+|++||+|+.+|+..++|++.  ..|.+|++..+++.+.++++ +.+....+
T Consensus         5 ~~~~~~~~~~l~~~~~~~~---~~~~dAeDivQevfl~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R~~~r~~~~~   79 (188)
T TIGR02943         5 PQELEQLRRDLLRFARLQL---RDRDLAEDAVQETLLAALSHRDSFAGR--SALKTWLFAILKNKIIDALRAKGREVKVS   79 (188)
T ss_pred             HHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhhhhhccc--cHHHHHHHHHHHHHHHHHHHhhcccCCcc
Confidence            4578889999999999998   778899999999999999999999965  37999999999999999988 32211110


Q ss_pred             cchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhh
Q 010308          356 FGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQ  435 (513)
Q Consensus       356 ~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~  435 (513)
                      . +                       .++.    .  ..             .++... .+.+.............++..
T Consensus        80 ~-~-----------------------~~~~----~--~~-------------~~~~~~-~~~~~~~~~~~~~~~~~~e~~  115 (188)
T TIGR02943        80 D-L-----------------------DDEL----D--DE-------------AFNALF-TQNGHWAQHGQPQHWNTPEKQ  115 (188)
T ss_pred             c-c-----------------------cccc----c--cc-------------hhhhhh-ccccchhccccccccCCHHHH
Confidence            0 0                       0000    0  00             000000 000000001111112234555


Q ss_pred             hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       436 ~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ....+....|..+|..||+++++||.++|    .+++|++|||+.||+|.++|++++.||+++||+.....
T Consensus       116 ~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~  182 (188)
T TIGR02943       116 LENKEFWEVFEACLYHLPEQTARVFMMRE----VLGFESDEICQELEISTSNCHVLLYRARLSLRACLSIN  182 (188)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            56666677899999999999999999999    79999999999999999999999999999999866543

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

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.72  E-value=1.8e-16  Score=147.69  Aligned_cols=156  Identities=12%  Similarity=0.058  Sum_probs=121.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh-ccc
Q 010308          273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSF  351 (513)
Q Consensus       273 ~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~-~r~  351 (513)
                      ...+..|+..|.+.|+.+|.++.   ++..+.+|++||+|+.+|+..+.|++..  .|.+|++..+++.+.+.++. .+.
T Consensus         5 ~~~f~~~~~~~~~~l~~~a~~~~---~~~~~AeDivQe~fl~l~~~~~~~~~~~--~~~~wl~~i~~n~~~d~~R~~~~~   79 (164)
T PRK12547          5 SKNFKQELLLALPALRAFAVSLS---SKHDKAEDLVQDTLMKAWAKQDSFEMGT--NLKAWLFTILRNEFYSQMRKRGRE   79 (164)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHHhhhhcCCcc--cHHHHHHHHHHHHHHHHHHhhccc
Confidence            46789999999999999999998   7888999999999999999999998543  59999999999999998882 210


Q ss_pred             cccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCC
Q 010308          352 TRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVE  431 (513)
Q Consensus       352 iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~  431 (513)
                         +                         .                            +.     ....... .+   ..
T Consensus        80 ---~-------------------------~----------------------------~~-----~~~~~~~-~~---~~   94 (164)
T PRK12547         80 ---V-------------------------Q----------------------------DS-----DGVFTAR-VA---VH   94 (164)
T ss_pred             ---c-------------------------c----------------------------cc-----ccccccc-CC---CC
Confidence               0                         0                            00     0000000 00   00


Q ss_pred             chhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          432 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       432 ~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ++.  ........|..+|..||+.+++||.|+|    .+++|++|||+.||||.++|++.+.||+++||....
T Consensus        95 ~~~--~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~  161 (164)
T PRK12547         95 PAQ--YGSLDLQDFKKALNLLSADQREAIILIG----ASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLK  161 (164)
T ss_pred             chh--hhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence            111  1122345688999999999999999999    799999999999999999999999999999997554

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.72  E-value=1.8e-16  Score=151.49  Aligned_cols=180  Identities=16%  Similarity=0.137  Sum_probs=126.6

Q ss_pred             HHHHHHHHHHHHHHHHHchhccCCCCc-HHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccc
Q 010308          277 NKLIKHNLRLVLFVIKKYFQDFANGPR-FQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRV  354 (513)
Q Consensus       277 ~~LI~~nlrLV~sIAkky~~~~~~g~~-~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRl  354 (513)
                      +..+..|.+.|+.+|.++.   ++..+ .+|++||+|+.+|++.++|++.  ..|.+|++..+++.+.++++ +.+....
T Consensus         8 ~~~~~~~~~~l~~~a~~~~---~~~~~~AEDivQevfl~~~~~~~~~~~~--~~~~~wL~~Ia~n~~~d~~Rk~~~~~~~   82 (195)
T PRK12532          8 DAELIESRKLLLHFARLQL---PDHPDLAEDLVQETLLSAYSAGDSFQGR--ALVNSWLFAILKNKIIDALRQIGRQRKV   82 (195)
T ss_pred             hhhHHHHHHHHHHHHHHHc---CChhhhHHHHHHHHHHHHHHhccccccc--chHHHHHHHHHHHHHHHHHHHhcccccc
Confidence            3567788999999999998   66777 9999999999999999999864  37999999999999999988 3221110


Q ss_pred             ccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchh
Q 010308          355 PFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN  434 (513)
Q Consensus       355 P~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee  434 (513)
                      ....                      ..+.+           ....      .+...   .+.....+. ......+++.
T Consensus        83 ~~~~----------------------~~~~~-----------~~~~------~~~~~---~~~~~~~~~-~~~~~~~~e~  119 (195)
T PRK12532         83 FTLL----------------------DDELL-----------DEAF------ESHFS---QNGHWTPEG-QPQHWNTPEK  119 (195)
T ss_pred             cccc----------------------ccccc-----------chhh------hhhhc---ccccccccc-CccccCCHHH
Confidence            0000                      00000           0000      00000   000000000 0111223555


Q ss_pred             hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010308          435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  508 (513)
Q Consensus       435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L  508 (513)
                      .....+....+..+|..||+++++||.|+|    .+++|++|||+.||+|..+|++.++||+++||+......+
T Consensus       120 ~~~~~e~~~~l~~~l~~L~~~~r~i~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~  189 (195)
T PRK12532        120 SLNNNEFQKILQSCLYNLPENTARVFTLKE----ILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF  189 (195)
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            556667777899999999999999999999    7999999999999999999999999999999987665543

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

Probab=99.72  E-value=2.3e-16  Score=162.09  Aligned_cols=182  Identities=17%  Similarity=0.112  Sum_probs=129.5

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcc
Q 010308          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS  350 (513)
Q Consensus       271 gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r  350 (513)
                      |+..|++.|+..|.+.|+.+|.++.   ++..+.+|++||.|+.+|+..++|++.  ..|.+|++..++|.+.+++++.+
T Consensus         2 gd~~af~~l~~~~~~~l~~~a~~~~---~~~~~AEDivQe~fl~~~~~~~~~~~~--~~~~~WL~~Ia~n~~~d~~Rk~~   76 (324)
T TIGR02960         2 VDGAAFTALAEPHRRELLAHCYRML---GSLHEAEDLVQETLLRAWRARDRFEGR--SSVRTWLYRIATNACLDALEARQ   76 (324)
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHhc---CChhhHHHHHHHHHHHHHhhhhccCcc--cchHHHHHHHHHHHHHHHHHhcc
Confidence            6789999999999999999999998   778899999999999999999999864  36999999999999999988321


Q ss_pred             ccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhcccc-----
Q 010308          351 FTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT-----  425 (513)
Q Consensus       351 ~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~-----  425 (513)
                      ....+.                          .+.                 ...................+.+.     
T Consensus        77 ~~~~~~--------------------------~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~  113 (324)
T TIGR02960        77 RRPRPV--------------------------GLG-----------------APSADGTAAASEAAEVTWLEPLPDLTLD  113 (324)
T ss_pred             CCcCcc--------------------------ccC-----------------CCCCcccccccccccccccCCCCccccc
Confidence            100000                          000                 00000000000000000000000     


Q ss_pred             --CCCCCCchhhhHHHH-HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          426 --DVDGVENENQRQPAL-LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       426 --d~~~~~~ee~~~~~~-l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                        .....++++.....+ +...|..+|++||+++|.||.|+|    .+++|++|||+.||+|.++|+++++||+++||+.
T Consensus       114 ~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~  189 (324)
T TIGR02960       114 LDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRD----VLGWRAAETAELLGTSTASVNSALQRARATLDEV  189 (324)
T ss_pred             cccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence              011123444333333 456688999999999999999999    7899999999999999999999999999999986


Q ss_pred             ch
Q 010308          503 TR  504 (513)
Q Consensus       503 ~~  504 (513)
                      ..
T Consensus       190 l~  191 (324)
T TIGR02960       190 GP  191 (324)
T ss_pred             cc
Confidence            54

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

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.71  E-value=1.7e-16  Score=152.96  Aligned_cols=178  Identities=13%  Similarity=0.075  Sum_probs=123.9

Q ss_pred             HHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccccc
Q 010308          278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF  356 (513)
Q Consensus       278 ~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~  356 (513)
                      .++..|.+.++.+|.++.   ++..+.+|++||.|+.+|+..++|++..  .|.+|++..+++.+.++++ +.+...++.
T Consensus        12 ~~~~~~~~~l~~~~~~~~---~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~   86 (201)
T PRK12545         12 AYLAQLRHDLLRFARLQL---RDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSA   86 (201)
T ss_pred             HHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhcccccccc
Confidence            448889999999999998   7778999999999999999999999753  6999999999999999988 322111100


Q ss_pred             chhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhh
Q 010308          357 GLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQR  436 (513)
Q Consensus       357 ~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~  436 (513)
                                     +         ..++.                  ....++.........+......+...++++..
T Consensus        87 ---------------~---------~~~~~------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (201)
T PRK12545         87 ---------------L---------DAELD------------------GEALLDRELFKDNGHWAAHAKPRPWPKPETIL  124 (201)
T ss_pred             ---------------c---------ccccc------------------hhhhhhhhhhcccccccccccCcCCCCHHHHH
Confidence                           0         00000                  00000000000000000000011112234444


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          437 QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       437 ~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ...+....|..+|..||+++|.||.|+|    ++++|++|||+.||+|.++|+..+.||+++||+.....
T Consensus       125 ~~~~~~~~l~~~L~~Lp~~~r~v~~L~~----~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~  190 (201)
T PRK12545        125 QQQQFWTLFETCLDHLPEQIGRVFMMRE----FLDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEK  190 (201)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            4455556788999999999999999999    79999999999999999999999999999999866543

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.71  E-value=9e-17  Score=147.02  Aligned_cols=150  Identities=15%  Similarity=0.117  Sum_probs=117.0

Q ss_pred             HHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchh
Q 010308          281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLE  359 (513)
Q Consensus       281 ~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~  359 (513)
                      ..|.+.|+.++.++.   ++..+.+|++||+++.+|+++++|++   .+|.||++..+++.+.++++ +.+....+    
T Consensus         2 ~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~~----   71 (154)
T TIGR02950         2 REYMHDVFRYLYRLT---KDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTID----   71 (154)
T ss_pred             chHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhcccc----
Confidence            578899999999998   67789999999999999999999997   37999999999999998887 32100000    


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhHHH
Q 010308          360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA  439 (513)
Q Consensus       360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~~~  439 (513)
                                             .                                  +. ......+...++++.....
T Consensus        72 -----------------------~----------------------------------~~-~~~~~~~~~~~~~~~~~~~   93 (154)
T TIGR02950        72 -----------------------D----------------------------------DA-IGDLEQHPVESPEHHLLIK   93 (154)
T ss_pred             -----------------------H----------------------------------hh-hhhccccccCChhHHHHHH
Confidence                                   0                                  00 0000000111244444455


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      +....|..+|..||+.++.||.++|    .+++|++|||+.||+|..+|++..++|+++||+.
T Consensus        94 ~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~  152 (154)
T TIGR02950        94 IEQEEITHHLSRLPENYRTVLILRE----FKEFSYKEIAELLNLSLAKVKSNLFRARKELKKL  152 (154)
T ss_pred             HHHHHHHHHHHhCCHhheeeeeehh----hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            5667799999999999999999998    6899999999999999999999999999999963

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

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.71  E-value=2.6e-16  Score=150.22  Aligned_cols=173  Identities=16%  Similarity=0.103  Sum_probs=123.8

Q ss_pred             HHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccc
Q 010308          277 NKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVP  355 (513)
Q Consensus       277 ~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP  355 (513)
                      ...|..|.+.++.+|.+|.   ++..+.+|++||.|+.+|+..+.|++..  .|.+|++..+++.+.++++ +.+.....
T Consensus        10 ~~~~~~~~~~l~~~~~~~~---~d~~~AeDivQe~flk~~~~~~~~~~~~--~~~~wL~~Ia~n~~~d~~Rk~~~~~~~~   84 (189)
T PRK12530         10 SLEIEEIRLQMLKFATLQL---KDADLAEDVVQEALVSAYKNADSFKGQS--ALKTWIFAILKNKIIDLIRYRKRFVNES   84 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHhchhccCCc--cHHHHHHHHHHHHHHHHHHhhccCCCcc
Confidence            3457778899999999998   6778999999999999999999998653  6999999999999999888 32211000


Q ss_pred             cchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhh
Q 010308          356 FGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQ  435 (513)
Q Consensus       356 ~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~  435 (513)
                       ..              .         ++                   ........   .......+........+++..
T Consensus        85 -~~--------------~---------~~-------------------~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~  118 (189)
T PRK12530         85 -EL--------------I---------EE-------------------DSPNSFFD---EKGHWKPEYYEPSEWQEVENT  118 (189)
T ss_pred             -cc--------------c---------cc-------------------ccchhhhc---ccccccccccCCccccCHHHH
Confidence             00              0         00                   00000000   000000000001111234445


Q ss_pred             hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       436 ~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ....+....|..+|++||+++|+||.|+|    .+++|++|||+.||+|.++|+.+++||+++||+...
T Consensus       119 ~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~  183 (189)
T PRK12530        119 VYKEEFWLIFEACLNHLPAQQARVFMMRE----YLELSSEQICQECDISTSNLHVLLYRARLQLQACLS  183 (189)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            55667777899999999999999999999    789999999999999999999999999999997654

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.69  E-value=5.3e-16  Score=150.62  Aligned_cols=180  Identities=13%  Similarity=0.134  Sum_probs=128.3

Q ss_pred             HHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccc
Q 010308          276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRV  354 (513)
Q Consensus       276 r~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRl  354 (513)
                      -..|+..|.+.|+.+|.++.   ++..+.+|++||.|+.+|+.++.|++.  .+|.+|++..+++.+.++++ ..+....
T Consensus        20 ~~~~~~~~~~~l~~~~~~~~---~d~~~AEDivQEvfikl~~~~~~~~~~--~~~~~WL~~IarN~~~d~~Rk~~~~~~~   94 (206)
T PRK12544         20 DPVFLEDLRKQMIKFATLQL---SDLHLAEDAVQEALIGALKNADSFAGR--AAFKTWVFAILKNKIIDLLRQKKRHVSA   94 (206)
T ss_pred             hHHHHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhhcccccc
Confidence            36788999999999999999   778899999999999999999999864  36999999999999999998 3321111


Q ss_pred             ccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchh
Q 010308          355 PFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN  434 (513)
Q Consensus       355 P~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee  434 (513)
                      +...                  .  +...         ...+..+.         +     ...............+|+.
T Consensus        95 ~~~~------------------~--~~~~---------~~~~~~~~---------~-----~~~~~~~~~~~~~~~~~e~  131 (206)
T PRK12544         95 SSLL------------------R--DEEE---------EEDFEELF---------D-----ESGHWQKDERPQAWGNPEE  131 (206)
T ss_pred             cccc------------------c--ccch---------hhHHHHhh---------c-----ccccccccccccccCCHHH
Confidence            1000                  0  0000         00000000         0     0000000000111123455


Q ss_pred             hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      .....+....+..+|..||++++.||.++|    ++++|++|||+.||+|..+|++.++||+++||+......
T Consensus       132 ~~~~~e~~~~l~~~L~~L~~~~r~v~~L~~----~~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~  200 (206)
T PRK12544        132 SLEQEQFWRIFEACLDGLPAKYARVFMMRE----FIELETNEICHAVDLSVSNLNVLLYRARLRLRECLENKW  200 (206)
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            555566667789999999999999999999    799999999999999999999999999999998765433

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.69  E-value=5e-16  Score=143.73  Aligned_cols=155  Identities=14%  Similarity=0.114  Sum_probs=118.0

Q ss_pred             HHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccccc
Q 010308          278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF  356 (513)
Q Consensus       278 ~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~  356 (513)
                      .++..|.+.++.+|.++.   ++..+.+|++||+++.+|+....|++.   .|.+|++..+++.+.++++ +......  
T Consensus         2 ~~~~~~~~~l~~~~~~~~---~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~~--   73 (163)
T PRK07037          2 DVFVDNRSMLVKIAARIV---GCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENKY--   73 (163)
T ss_pred             hHHHHHHHHHHHHHHHHc---CCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhcccccc--
Confidence            357788899999999998   678899999999999999998877753   4789999999999998887 3210000  


Q ss_pred             chhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhh
Q 010308          357 GLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQR  436 (513)
Q Consensus       357 ~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~  436 (513)
                                                                         + +    .+.+. .. .... ..+++...
T Consensus        74 ---------------------------------------------------~-~----~~~~~-~~-~~~~-~~~~~~~~   94 (163)
T PRK07037         74 ---------------------------------------------------H-G----DEEDG-LD-VPSP-EASPEAAL   94 (163)
T ss_pred             ---------------------------------------------------c-c----ccccc-cc-cCCC-CCCHHHHH
Confidence                                                               0 0    00000 00 0111 12244444


Q ss_pred             HHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          437 QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       437 ~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      ...+..+.|..+|+.|||+++.||.++|    .+++|.+|||+.||+|.++|+..+.+|+++||+..
T Consensus        95 ~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l  157 (163)
T PRK07037         95 INRDTLRHVADALSELPARTRYAFEMYR----LHGETQKDIARELGVSPTLVNFMIRDALVHCRKCL  157 (163)
T ss_pred             HHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            4555667789999999999999999999    78999999999999999999999999999999754

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.69  E-value=7.5e-16  Score=146.30  Aligned_cols=152  Identities=16%  Similarity=0.151  Sum_probs=122.1

Q ss_pred             HHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccc
Q 010308          276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRV  354 (513)
Q Consensus       276 r~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRl  354 (513)
                      ++.|+..|.+.|+.+|.++.   ++..+.+|++||.++.+|+.+..|++.  ..|.+|++..+++.+.++++ +.+...+
T Consensus         3 ~~~l~~~y~~~l~~~~~~~~---~~~~~aeDi~QEvflkl~~~~~~~~~~--~~~~~wL~~i~~n~~~d~~Rk~~~~~~~   77 (181)
T PRK09637          3 LESIWSEYKAQLKAFLHSRV---SNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRSEEL   77 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHh---CChhhHHHHHHHHHHHHHHhHHHhccc--cchHHHHHHHHHHHHHHHHHhccccCCc
Confidence            57899999999999999998   788999999999999999999999853  47999999999999999988 3211000


Q ss_pred             ccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchh
Q 010308          355 PFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN  434 (513)
Q Consensus       355 P~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee  434 (513)
                      +                                                             .+...   .+    ++++
T Consensus        78 ~-------------------------------------------------------------~~~~~---~~----~~~~   89 (181)
T PRK09637         78 P-------------------------------------------------------------DDLLF---ED----EERE   89 (181)
T ss_pred             c-------------------------------------------------------------hhhhc---cC----CChh
Confidence            0                                                             00000   00    0112


Q ss_pred             hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      .....+....+..+|+.||++++.||.++|    .+++++.|||+.||+|..+|+..+.+|+++||+...
T Consensus        90 ~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~  155 (181)
T PRK09637         90 ENAKKELAPCLRPFIDALPEKYAEALRLTE----LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE  155 (181)
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence            223345567799999999999999999999    799999999999999999999999999999997543

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.69  E-value=9.9e-16  Score=143.89  Aligned_cols=159  Identities=13%  Similarity=0.096  Sum_probs=120.8

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcc
Q 010308          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS  350 (513)
Q Consensus       271 gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r  350 (513)
                      .+..|++.++..|.+.++.++.++.   ++..+.+||+||.|+.+|+. ..|++-.  .|.+|++..+++.+.+++++.+
T Consensus         7 ~~~~af~~l~~~~~~~l~~~~~~~~---~~~~~AEDlvQe~flkl~~~-~~~~~~~--~~~~wL~~iarn~~~d~~R~~~   80 (172)
T PRK09651          7 TASLTFESLYGTHHGWLKSWLTRKL---QSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNA   80 (172)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHc---CCHhHHHHHHHHHHHHHHhh-ccccccc--CHHHHHHHHHHHHHHHHHHHHH
Confidence            4578999999999999999999998   77889999999999999998 4565432  5889999999999988887211


Q ss_pred             ccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCC
Q 010308          351 FTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV  430 (513)
Q Consensus       351 ~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~  430 (513)
                      ...                 ..                                    .+     ...    .+.+....
T Consensus        81 ~~~-----------------~~------------------------------------~~-----~~~----~~~~~~~~   98 (172)
T PRK09651         81 LEK-----------------AY------------------------------------LE-----MLA----LMPEGGAP   98 (172)
T ss_pred             HHh-----------------hh------------------------------------hh-----HHh----hccccCCC
Confidence            000                 00                                    00     000    00000111


Q ss_pred             CchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          431 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       431 ~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                      +++......+....|..+|+.|||++++||.++|    ++++|++|||+.||+|..+|+..+.+|+++|+.
T Consensus        99 ~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~  165 (172)
T PRK09651         99 SPEERESQLETLQLLDSMLDGLNGKTREAFLLSQ----LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLL  165 (172)
T ss_pred             ChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhh----ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            2333333444556789999999999999999999    799999999999999999999999999999985

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.68  E-value=8.6e-16  Score=146.13  Aligned_cols=158  Identities=14%  Similarity=0.095  Sum_probs=121.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccc
Q 010308          274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFT  352 (513)
Q Consensus       274 ~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~i  352 (513)
                      .+...++..|.+.|+.+|.++.   ++..+.+|++||.|+.+|+..+.|++..  .|.+|++..+++.+.+.++ +.+..
T Consensus         5 ~~~~~~~~~~~~~l~~~~~~~~---~~~~~AEDivQevflkl~~~~~~~~~~~--~~~~WL~~Ia~n~~~d~~Rk~~~~~   79 (182)
T PRK12540          5 DSLRDDILAAVPSLRAFAISLS---GNGDRADDLVQETLLRALANIDSFQPGS--NLPAWLFTILRNLFRSDYRKRRREV   79 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhHHhcCCCc--hHHHHHHHHHHHHHHHHHHhccccc
Confidence            5678899999999999999998   7788999999999999999999998653  6999999999999988877 22100


Q ss_pred             ccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCc
Q 010308          353 RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN  432 (513)
Q Consensus       353 RlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~  432 (513)
                      ..                                                      .+       +...... + .  .+
T Consensus        80 ~~------------------------------------------------------~~-------~~~~~~~-~-~--~~   94 (182)
T PRK12540         80 ED------------------------------------------------------AD-------GSYAKTL-K-S--QP   94 (182)
T ss_pred             cc------------------------------------------------------cc-------ccccccc-c-C--CC
Confidence            00                                                      00       0000000 0 0  01


Q ss_pred             hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          433 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       433 ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      +..  .......|..+|+.||+++++||.|+|    .+++|++|||+.||+|..+|++.++||+++||+......
T Consensus        95 ~~~--~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~  163 (182)
T PRK12540         95 GQN--AHLEFEEFRAALDKLPQDQREALILVG----ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDG  163 (182)
T ss_pred             chH--HHHHHHHHHHHHHhCCHHHHHHhhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence            111  112234688999999999999999999    799999999999999999999999999999998766443

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.68  E-value=6.9e-16  Score=142.59  Aligned_cols=152  Identities=13%  Similarity=0.090  Sum_probs=116.9

Q ss_pred             HHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchh
Q 010308          281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLE  359 (513)
Q Consensus       281 ~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~  359 (513)
                      ..|.+.++.++.++.   ++..+.+|++||.|+.||+..+.|++.   +|.||++..+++.+.++++ +.....      
T Consensus         2 ~~~~~~l~~~~~~~~---~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n~~~d~~R~~~~~~~------   69 (159)
T PRK12527          2 ENYYRELVRFLSARL---GNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALNLVVDRHRRHRVRQA------   69 (159)
T ss_pred             hhHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHHHHHHHHHHHhcccc------
Confidence            467788888888888   677889999999999999999998752   6899999999999999887 211000      


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhHHH
Q 010308          360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA  439 (513)
Q Consensus       360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~~~  439 (513)
                                                                     .+++.        ..+. ......++++.....
T Consensus        70 -----------------------------------------------~~~~~--------~~~~-~~~~~~~~~~~~~~~   93 (159)
T PRK12527         70 -----------------------------------------------EPLEV--------LDEE-ERLHSPSPQTRLDLG   93 (159)
T ss_pred             -----------------------------------------------cchhh--------hhcc-ccccCCCHHHHHHHH
Confidence                                                           00000        0000 000112345555555


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      +....|..+|.+||++++.||.|+|    ++++|++|||+.||+|.++|+..+.+|+++||+...
T Consensus        94 ~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~  154 (159)
T PRK12527         94 QRLALLQRALAELPPACRDSFLLRK----LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR  154 (159)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence            6667899999999999999999999    799999999999999999999999999999997644

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.68  E-value=1.1e-15  Score=146.03  Aligned_cols=160  Identities=14%  Similarity=0.135  Sum_probs=122.7

Q ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh
Q 010308          269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV  348 (513)
Q Consensus       269 ~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~  348 (513)
                      +.++..+++.++..|.+.|+.+|.++.   ++..+.+|++||.|+.+|+.++.|++.  ..|.+|++..+++.+.+..++
T Consensus        18 ~~~~~~~f~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQdvflkl~~~~~~~~~~--~~~~~wL~~Iarn~~~~~~r~   92 (188)
T PRK12517         18 MLSKQRRYEALVKALHADIYRYAYWLC---KDKHIAEDLVQETFLRAWRSLDSLKDE--KAAKAWLITILRRENARRFER   92 (188)
T ss_pred             hhccHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhhcCc--cchHHHHHHHHHHHHHHHHHH
Confidence            466899999999999999999999998   778899999999999999999999864  368999998888866544331


Q ss_pred             ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCC
Q 010308          349 SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD  428 (513)
Q Consensus       349 ~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~  428 (513)
                      ...                                                     ...+.+       +.   ...+..
T Consensus        93 ~~~-----------------------------------------------------~~~~~~-------~~---~~~~~~  109 (188)
T PRK12517         93 KQF-----------------------------------------------------DLVDIE-------DD---SIEDDA  109 (188)
T ss_pred             hcc-----------------------------------------------------CccCcc-------cc---cccCcc
Confidence            000                                                     000000       00   000111


Q ss_pred             CCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          429 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       429 ~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ..+++.    ......|..+|..||++++.||.++|    .+++|++|||+.||||..+|+.++.||+++||....
T Consensus       110 ~~~~e~----~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~  177 (188)
T PRK12517        110 SHSSEE----EMEQEWLRRQIAKLDPEYREPLLLQV----IGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALE  177 (188)
T ss_pred             ccChhH----HHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            111221    22335688999999999999999999    789999999999999999999999999999997654

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.67  E-value=1.4e-15  Score=142.74  Aligned_cols=146  Identities=16%  Similarity=0.135  Sum_probs=115.8

Q ss_pred             HHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh-ccccccccchh
Q 010308          281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRVPFGLE  359 (513)
Q Consensus       281 ~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~-~r~iRlP~~~~  359 (513)
                      ..|.+.++.++.++.   ++..+.+|++||+|+.+|++++.|++.  ..|.+|++..+++.+.++++. .+...++    
T Consensus         2 ~~~~~~l~~~~~~~~---~~~~~AeDlvQe~fl~l~~~~~~~~~~--~~f~~wl~~iarn~~~d~~Rk~~~~~~~~----   72 (170)
T TIGR02959         2 DEFRSELKAFIKSRV---SDASDVEDLLQEVFIKIHRNLPSLKDG--QKIQSWLYQIARNTIIDFYRSKSRSVELP----   72 (170)
T ss_pred             chHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHHHHHhcCCc--ccHHHHHHHHHHHHHHHHHHhccCccccc----
Confidence            467888999999998   778899999999999999999999963  479999999999999999883 2110000    


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhHHH
Q 010308          360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA  439 (513)
Q Consensus       360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~~~  439 (513)
                                                                                +...    ..  .++++.....
T Consensus        73 ----------------------------------------------------------~~~~----~~--~~~~~~~~~~   88 (170)
T TIGR02959        73 ----------------------------------------------------------ESLL----AA--DSAREETFVK   88 (170)
T ss_pred             ----------------------------------------------------------hhhc----cc--CCccHHHHHH
Confidence                                                                      0000    00  0112222334


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      +....|..+|+.||++++.||.++|    .+++|++|||+.||+|..+|++.+.+|+++||...
T Consensus        89 e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l  148 (170)
T TIGR02959        89 ELSQCIPPMIKELPDEYREAIRLTE----LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL  148 (170)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            4556789999999999999999999    78999999999999999999999999999999754

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

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.67  E-value=1.7e-15  Score=144.93  Aligned_cols=156  Identities=13%  Similarity=0.095  Sum_probs=118.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcccc
Q 010308          273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT  352 (513)
Q Consensus       273 ~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~i  352 (513)
                      ..+++.|.. |.+.|+++|..+.   ++..+.+|++||.|+.+|+.+..|+..  ..|.+|++..+++.+.+.+++..  
T Consensus         7 ~~~~~~l~~-~~~~l~~~a~~~l---~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~--   78 (188)
T PRK12546          7 RDPRDELVE-HLPALRAFAISLT---RNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHK--   78 (188)
T ss_pred             hhHHHHHHH-HHHHHHHHHHHHc---CChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhc--
Confidence            456667766 6799999999998   788999999999999999999999864  36999999999999998877311  


Q ss_pred             ccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCc
Q 010308          353 RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN  432 (513)
Q Consensus       353 RlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~  432 (513)
                      +.+                         .                          ..+       ....+...+.    +
T Consensus        79 r~~-------------------------~--------------------------~~~-------~~~~~~~~~~----~   96 (188)
T PRK12546         79 REV-------------------------P--------------------------DPE-------GVHAASLAVK----P   96 (188)
T ss_pred             ccc-------------------------c--------------------------Ccc-------cccccccccC----C
Confidence            000                         0                          000       0000000000    0


Q ss_pred             hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          433 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       433 ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      .  .........+..+|+.|||+++.||.|+|    .+++|.+|||+.||||..+|+..+.+|+++||+...
T Consensus        97 ~--~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~----~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~  162 (188)
T PRK12546         97 A--HDGRLAMSDFRAAFAQLPDEQREALILVG----ASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQ  162 (188)
T ss_pred             c--chhHHHHHHHHHHHHhCCHHHhHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence            0  01122234688999999999999999999    799999999999999999999999999999997554

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=99.66  E-value=2.8e-15  Score=142.74  Aligned_cols=153  Identities=12%  Similarity=0.073  Sum_probs=116.9

Q ss_pred             HHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hcccccc
Q 010308          276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRV  354 (513)
Q Consensus       276 r~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRl  354 (513)
                      +...+..+++.|+.+|.++.   ++..+.+|++||.|+.+|+....|++.  ..|.+|++..+++.+.++++ +.+....
T Consensus         6 ~~~~~~~~~~~l~~~~~~~~---~~~~dAEDivQe~flkl~~~~~~~~~~--~~~~~WL~~Iarn~~id~~Rk~~~~~~~   80 (182)
T PRK12511          6 KRFDVLDQLVPLRRYARSLT---RDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRRVEARR   80 (182)
T ss_pred             hhhhHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhHHhcCCc--cchHHHHHHHHHHHHHHHHHhhcccccc
Confidence            44557788999999999998   778899999999999999999999864  36999999999999999888 3211000


Q ss_pred             ccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchh
Q 010308          355 PFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN  434 (513)
Q Consensus       355 P~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee  434 (513)
                      .                           ++                                ...    ..+.....+. 
T Consensus        81 ~---------------------------~~--------------------------------~~~----~~~~~~~~~~-   96 (182)
T PRK12511         81 A---------------------------DE--------------------------------LAV----LADASLPAAQ-   96 (182)
T ss_pred             c---------------------------cc--------------------------------hhh----ccccCCCcch-
Confidence            0                           00                                000    0000000011 


Q ss_pred             hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                        ........|..+|.+||+++++||.|+|    .+++|++|||+.||||.++|+..+.+|+++||...
T Consensus        97 --~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~  159 (182)
T PRK12511         97 --EHAVRLAQIRDAFFDLPEEQRAALHLVA----IEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFE  159 (182)
T ss_pred             --HHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence              1122345688999999999999999999    79999999999999999999999999999999644

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.65  E-value=3.7e-15  Score=139.38  Aligned_cols=159  Identities=14%  Similarity=0.078  Sum_probs=121.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcccc
Q 010308          273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT  352 (513)
Q Consensus       273 ~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~i  352 (513)
                      ..++..++..|.+.++++|.+|.   ++..+.+|++||.|+.+|+..+.++.   ..|.+|++..+++.+.++++..+. 
T Consensus         8 ~~~~~~~~~~~~~~l~~~~~~~~---~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~~-   80 (168)
T PRK12525          8 NTLIGQMFQQDYDWLCKKLSRQL---GCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQDL-   80 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHc---CCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHHH-
Confidence            46789999999999999999998   67789999999999999986555542   269999999999999887772110 


Q ss_pred             ccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCc
Q 010308          353 RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN  432 (513)
Q Consensus       353 RlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~  432 (513)
                                   .+.   ...                                 +.+           + .......++
T Consensus        81 -------------~~~---~~~---------------------------------~~~-----------~-~~~~~~~~~   99 (168)
T PRK12525         81 -------------ERA---YLQ---------------------------------SLA-----------E-APEAVQPSP   99 (168)
T ss_pred             -------------HHH---HHH---------------------------------HHh-----------c-ccccccCCh
Confidence                         000   000                                 000           0 000011234


Q ss_pred             hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          433 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       433 ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      ++.....+....|..+|+.||++++.||.|+|    .+++|++|||+.||+|..+|+..+.+|+++||...
T Consensus       100 ~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~----~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~  166 (168)
T PRK12525        100 EEQWMVIETLLAIDRLLDGLSGKARAAFLMSQ----LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGF  166 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhh
Confidence            44444555567899999999999999999998    79999999999999999999999999999999653

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.64  E-value=4.3e-15  Score=151.32  Aligned_cols=159  Identities=14%  Similarity=0.037  Sum_probs=119.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccc
Q 010308          274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTR  353 (513)
Q Consensus       274 ~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iR  353 (513)
                      .....|+..|.+.++.+|+++.   ++..+.+|++||.|+. |.....|+   ...|.+|++..+++.+.+++++.+..+
T Consensus         4 ~~~~~l~~~~~~~l~~~a~~~~---~~~~dAEDlvQe~fl~-~~~~~~~~---~~~~~~WL~~Ia~n~~~d~lR~~~~~~   76 (293)
T PRK09636          4 ADAAAEFEPLRPHLLSVAYRML---GSVADAEDIVQEAWLR-WNNADRAQ---IRDPRAWLTRVVTRLCLDRLRSARHRR   76 (293)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHH-HHhccccc---ccCHHHHHHHHHHHHHHHHHHhhhccc
Confidence            3467899999999999999998   7788999999999999 66667776   246999999999999999888211000


Q ss_pred             cccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCch
Q 010308          354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENE  433 (513)
Q Consensus       354 lP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~e  433 (513)
                       .                                                   ....       ..+.+...+.. .+++
T Consensus        77 -~---------------------------------------------------~~~~-------~~~~e~~~~~~-~~~~   96 (293)
T PRK09636         77 -E---------------------------------------------------TYVG-------PWLPEPVVEEL-DDPL   96 (293)
T ss_pred             -c---------------------------------------------------cccC-------CcCCcCCCCCC-CChH
Confidence             0                                                   0000       00000011111 1233


Q ss_pred             h-hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          434 N-QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       434 e-~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      + ......+...+..+|++|||++|.||.|+|    ..++|++|||+.||+|..+|+++++||+++||+..
T Consensus        97 ~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~----~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~  163 (293)
T PRK09636         97 EAVVAAEDLSLALMLALERLSPLERAAFLLHD----VFGVPFDEIASTLGRSPAACRQLASRARKHVRAAR  163 (293)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence            2 233445566789999999999999999999    78999999999999999999999999999999854

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=99.61  E-value=7.3e-15  Score=135.35  Aligned_cols=152  Identities=11%  Similarity=0.084  Sum_probs=106.0

Q ss_pred             CCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhC
Q 010308          299 ANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELK  377 (513)
Q Consensus       299 ~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elg  377 (513)
                      ++..+.+|++||.|+.+|+..+.+ +  +..|.+|++..+++.+.++++ +.+......                     
T Consensus         2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~---------------------   57 (161)
T PRK09047          2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVS---------------------   57 (161)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhcccccccc---------------------
Confidence            345679999999999999998863 3  446999999999999999988 321100000                     


Q ss_pred             CCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCC--CCCchhhhHHHHHHHHHHHHHhcCCHH
Q 010308          378 RVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD--GVENENQRQPALLRLALDDVLDSLKPK  455 (513)
Q Consensus       378 R~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~--~~~~ee~~~~~~l~~~L~~aL~~L~~r  455 (513)
                                                 ...++......+..+..+.+.+..  ..++++.....+....|..+|+.||++
T Consensus        58 ---------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~  110 (161)
T PRK09047         58 ---------------------------LFSSFSDDDDDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQKLPAR  110 (161)
T ss_pred             ---------------------------cccccccccccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHHhCCHH
Confidence                                       000000000000011111111111  133555566667778899999999999


Q ss_pred             HHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010308          456 ESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  505 (513)
Q Consensus       456 Er~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~  505 (513)
                      ++.||.|+|    ++++|++|||+.||||..+|+.++.+|+++||+....
T Consensus       111 ~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~  156 (161)
T PRK09047        111 QREAFLLRY----WEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEA  156 (161)
T ss_pred             HHHHHHHHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            999999999    7999999999999999999999999999999976543

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.59  E-value=2.1e-14  Score=141.81  Aligned_cols=158  Identities=18%  Similarity=0.127  Sum_probs=121.1

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010308          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (513)
Q Consensus       263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI  342 (513)
                      ..|.+...++..+++.+++.| +.++.++.++.   ++..+.+||+||.|+.+|+.   |+..  ..|.+|++...++.+
T Consensus         7 ~~~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~---~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~   77 (228)
T PRK06704          7 HILKNHIDMNHSNINFLIEQY-GELKRYCTFLT---KNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRW   77 (228)
T ss_pred             HHHhcccCCCHHHHHHHHHHH-HHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHH
Confidence            356777888999999998888 68999999988   77889999999999999986   5543  248999999999999


Q ss_pred             HHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhc
Q 010308          343 IRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  422 (513)
Q Consensus       343 ~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d  422 (513)
                      .+.+++....  +                                                    .+.       +.   
T Consensus        78 id~~Rk~k~~--~----------------------------------------------------~~~-------~~---   93 (228)
T PRK06704         78 LDQIKSKSVH--E----------------------------------------------------KIR-------DQ---   93 (228)
T ss_pred             HHHHhccccc--c----------------------------------------------------ccc-------cc---
Confidence            9888721100  0                                                    000       00   


Q ss_pred             cccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          423 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       423 ~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                       ....   .++..  ..+....+..+|+.||+++|.||.|+|    .+++|++|||+.||+|.++|++.+.||+++||+.
T Consensus        94 -~~~~---~~~~~--~~~~~~~l~~~L~~Lp~~~R~v~lL~~----~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~  163 (228)
T PRK06704         94 -ITFE---EPHEK--IADLHEMVGKVLSSLNVQQSAILLLKD----VFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTV  163 (228)
T ss_pred             -cccC---ChHHH--HHHHHHHHHHHHHhCCHHHhhHhhhHH----hhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence             0000   01111  122345688999999999999999999    7899999999999999999999999999999975


Q ss_pred             c
Q 010308          503 T  503 (513)
Q Consensus       503 ~  503 (513)
                      .
T Consensus       164 l  164 (228)
T PRK06704        164 S  164 (228)
T ss_pred             H
Confidence            4

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

Probab=99.58  E-value=3.1e-14  Score=144.46  Aligned_cols=155  Identities=14%  Similarity=0.047  Sum_probs=114.7

Q ss_pred             HHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccc
Q 010308          278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFG  357 (513)
Q Consensus       278 ~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~  357 (513)
                      +++..|.+.++.+|+++.   ++..+.+|++||.|+.+++.  .|+.  ...|.+|++..+++.+.++++..+..+..  
T Consensus         1 ~l~~~~~~~l~~~a~r~l---g~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~~~--   71 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRML---GSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARREV--   71 (281)
T ss_pred             ChHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcccc--
Confidence            368899999999999998   77889999999999997775  4543  23699999999999999988821100000  


Q ss_pred             hhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhH
Q 010308          358 LESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQ  437 (513)
Q Consensus       358 ~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~  437 (513)
                                                                        ..+ +      .+.+...+ ...++++...
T Consensus        72 --------------------------------------------------~~~-~------~~~e~~~~-~~~~~~~~~~   93 (281)
T TIGR02957        72 --------------------------------------------------YVG-P------WLPEPLLT-TSADPAESVE   93 (281)
T ss_pred             --------------------------------------------------cCC-C------CCCcccCC-CCCChHHHHH
Confidence                                                              000 0      00000001 1122333332


Q ss_pred             -HHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          438 -PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       438 -~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                       ...+...+..+|++|||+||.||.|+|    ..++|++|||+.||+|..+|+++++||+++||+..
T Consensus        94 ~~e~~~~~l~~~l~~L~~~~R~v~~L~~----~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~  156 (281)
T TIGR02957        94 LAESLSMAYLLLLERLSPLERAVFVLRE----VFDYPYEEIASIVGKSEANCRQLVSRARRHLDARR  156 (281)
T ss_pred             HHHHHHHHHHHHHhhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence             334556788899999999999999999    78999999999999999999999999999999743

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

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=99.57  E-value=4.9e-14  Score=143.87  Aligned_cols=160  Identities=13%  Similarity=0.070  Sum_probs=119.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccc
Q 010308          274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTR  353 (513)
Q Consensus       274 ~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iR  353 (513)
                      ..+..++..|.+.++++|.++.   ++..+.||++||.|+.+|++...+.    ..|.+|++...++.+.++++..+..+
T Consensus         5 ~~~~~l~~~~~~~L~~~a~r~l---gs~~dAEDvvQE~flr~~~~~~~~~----~~~~aWL~~Ia~n~~id~lRk~~~rr   77 (290)
T PRK09635          5 DPVSAAWRAHRAYLVDLAFRMV---GDIGVAEDMVQEAFSRLLRAPVGDI----DDERGWLIVVTSRLCLDHIKSASTRR   77 (290)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHhcCcccc----ccHHHHHHHHHHHHHHHHHhhhhccC
Confidence            4678899999999999999999   7888999999999999999865431    25899999999999999887311100


Q ss_pred             cccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCch
Q 010308          354 VPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENE  433 (513)
Q Consensus       354 lP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~e  433 (513)
                      ..                                                  ....+...   .+   +...  ...+++
T Consensus        78 ~~--------------------------------------------------~~~~~~~~---~~---~~~~--~~~~~~   99 (290)
T PRK09635         78 ER--------------------------------------------------PQDIAAWH---DG---DASV--SSVDPA   99 (290)
T ss_pred             cC--------------------------------------------------cccccccC---cc---ccCC--CCCCcH
Confidence            00                                                  00000000   00   0000  111232


Q ss_pred             h-hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          434 N-QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       434 e-~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      + .....+....+..+|+.|||+++.||.|+|    ..++|++|||+.||+|..+|+++++||+++||..
T Consensus       100 ~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~----~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~  165 (290)
T PRK09635        100 DRVTLDDEVRLALLIMLERLGPAERVVFVLHE----IFGLPYQQIATTIGSQASTCRQLAHRARRKINES  165 (290)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHH----HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence            2 234455667889999999999999999999    7899999999999999999999999999999974

>PRK09191 two-component response regulator; Provisional

Probab=99.46  E-value=7.8e-13  Score=130.37  Aligned_cols=136  Identities=8%  Similarity=-0.041  Sum_probs=108.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhcccccc
Q 010308          275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRV  354 (513)
Q Consensus       275 Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRl  354 (513)
                      ++..|+..|.+.|+.+|.++.   ++..+.+|++||+|+.+|+....|++.  ..|.+|++.++++.....         
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~---~~~~~aeDi~qd~~~~~~~~~~~~~~~--~~~~~wl~~~~~~~~~~~---------   67 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALT---GSQSSGDAYVAATLEALLADPSIFPEA--SSPRVGLYRLFHRLWSSA---------   67 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhc---CChhhHHHHHHHHHHHHHHhHHhcCCC--cchhhHHHHHHHHHhccc---------
Confidence            478899999999999999998   678899999999999999999999864  358888887654421000         


Q ss_pred             ccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchh
Q 010308          355 PFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN  434 (513)
Q Consensus       355 P~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee  434 (513)
                                                                               ...        .... .  .+..
T Consensus        68 ---------------------------------------------------------~~~--------~~~~-~--~~~~   79 (261)
T PRK09191         68 ---------------------------------------------------------GAN--------DPEP-G--SPFE   79 (261)
T ss_pred             ---------------------------------------------------------ccc--------CCCC-C--CCch
Confidence                                                                     000        0000 0  0110


Q ss_pred             hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          435 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       435 ~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                              ..+..+|+.||+++|.||.|+|    .+++|++|||+.||+|.++|+....+|+++|+....
T Consensus        80 --------~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~  137 (261)
T PRK09191         80 --------ARAERRLAGLTPLPRQAFLLTA----LEGFSVEEAAEILGVDPAEAEALLDDARAEIARQVA  137 (261)
T ss_pred             --------HHHHHHHHhCCHHHhHHHHHHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence                    1688999999999999999999    799999999999999999999999999999997554

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.42  E-value=1.4e-12  Score=118.39  Aligned_cols=136  Identities=18%  Similarity=0.230  Sum_probs=97.6

Q ss_pred             HHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhh-----cCCcCCCccchHHHHHHHHHHHHHHH-hc
Q 010308          276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDR-----FEPKRRFRLSTYGLFWIRHAIIRSMT-VS  349 (513)
Q Consensus       276 r~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvek-----FDp~kG~rFSTYA~~wIR~aI~raI~-~~  349 (513)
                      ++.|+..|.++++.+|++|.   .    .+| +||.++.+|....+     |++.  ..|.||++..+++.+.+.++ +.
T Consensus         1 f~~~~~~y~~~l~~~~~~~~---~----~~~-~qdvf~~~w~~~~~~~~~~~~~~--~~~~~wL~~iarN~~id~~Rk~~   70 (142)
T TIGR03209         1 FEEIYMNFKNTIDIFTRKYN---L----YYD-YNDILYHLWIILKKIDLNKFNTE--NDLEKYISTSLKRYCLDICNKKN   70 (142)
T ss_pred             ChHHHHHHHHHHHHHHHHhc---c----hhh-HHHHHHHHHHHHHHhhhhhcCch--hHHHHHHHHHHHHHHHHHHHHHh
Confidence            36799999999999999997   2    224 49999999999875     5532  46999999999999999888 21


Q ss_pred             cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCC
Q 010308          350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG  429 (513)
Q Consensus       350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~  429 (513)
                      +...                  ...                                   +       .+..+    .. 
T Consensus        71 ~~~~------------------~~~-----------------------------------~-------~~~~~----~~-   85 (142)
T TIGR03209        71 RDKK------------------IIY-----------------------------------N-------SEITD----IK-   85 (142)
T ss_pred             hhhh------------------hhh-----------------------------------h-------hhhhc----cc-
Confidence            1000                  000                                   0       00000    00 


Q ss_pred             CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHH
Q 010308          430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRK  490 (513)
Q Consensus       430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRq  490 (513)
                      ..+++.....+....|..+|+.||+.+|+||.|+|    .+++|++|||+.||+|.++|+.
T Consensus        86 ~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~~~s~~EIA~~l~is~~tV~~  142 (142)
T TIGR03209        86 LSLINVYSSNDLEFEFNDLISILPNKQKKIIYMKF----FEDMKEIDIAKKLHISRQSVYK  142 (142)
T ss_pred             cchhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHhhcC
Confidence            00112223334455688999999999999999999    7999999999999999999973

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

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.40  E-value=1.1e-11  Score=123.32  Aligned_cols=80  Identities=15%  Similarity=0.207  Sum_probs=73.4

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCC--cHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010308          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGP--RFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (513)
Q Consensus       265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~--~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI  342 (513)
                      +..+..||..|++.|+..|.++|+++|.+|.   ++..  +.+|++|||++++|+|+++|++++|..|.+|+..+|++.+
T Consensus         9 i~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~---~~~~~~eaeDlvQe~fi~l~eai~~y~~~kg~sF~awl~~Iirn~~   85 (237)
T PRK08311          9 LEKIKNGDEELREELIEEYKPFIAKVVSSVC---GRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRL   85 (237)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHh---cccCCCCchHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            4556789999999999999999999999998   4443  5899999999999999999999988889999999999999


Q ss_pred             HHHHH
Q 010308          343 IRSMT  347 (513)
Q Consensus       343 ~raI~  347 (513)
                      .++++
T Consensus        86 iDylR   90 (237)
T PRK08311         86 IDYFR   90 (237)
T ss_pred             HHHHH
Confidence            99999

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=99.36  E-value=1.9e-11  Score=116.79  Aligned_cols=175  Identities=19%  Similarity=0.184  Sum_probs=118.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHH--HHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHH
Q 010308          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQD--LCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRH  340 (513)
Q Consensus       263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eD--LIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~  340 (513)
                      +.|.++.+||..|.+.|+..|++-++.+|+++......+.+.+|  |++|.|+.++..-...+.+.-..|..|+...+++
T Consensus         6 ~ll~~~~~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~lv~ea~lrl~~~~~~~~~~~~~~f~~~~~~~~rr   85 (185)
T PF07638_consen    6 ELLDRWRQGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTALVHEAFLRLARRGRFVQFSDRRHFWALLARIMRR   85 (185)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHHHHHHHHHHhccccccCCCCHHHHHHHHHHHHHH
Confidence            45777889999999999999999999999987654344555555  4677777776633322333333588888888888


Q ss_pred             HHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhh
Q 010308          341 AIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE  419 (513)
Q Consensus       341 aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e  419 (513)
                      .+.+.++ +....|-.                      .                         ....+|+...      
T Consensus        86 ~lid~~R~~~a~KRg~----------------------~-------------------------~~~~~l~~~~------  112 (185)
T PF07638_consen   86 KLIDHARRRQAQKRGG----------------------D-------------------------QVRVELDERA------  112 (185)
T ss_pred             HHHHHHHHHHHHhcCC----------------------C-------------------------Ccccchhhhh------
Confidence            8888777 32211110                      0                         0001111100      


Q ss_pred             hhccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010308          420 FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL  499 (513)
Q Consensus       420 ~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKL  499 (513)
                        +   +.+...++.   ..++.+.+..+.. |+|++..+|.++|    +.|+|.+|||+.||||..+|++....|..+|
T Consensus       113 --~---~~~~~~~~~---~~~l~e~l~~L~~-l~~~~~~~v~l~~----~~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l  179 (185)
T PF07638_consen  113 --D---SGDEPSPEE---LLELEEALERLLA-LDPRQRRVVELRF----FEGLSVEEIAERLGISERTVRRRLRRARAWL  179 (185)
T ss_pred             --c---cccCCCHHH---HHHHHHHHHHHHc-cCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence              0   001122222   2345555655555 9999999999998    7899999999999999999999999999999


Q ss_pred             hCcc
Q 010308          500 KHPT  503 (513)
Q Consensus       500 R~~~  503 (513)
                      +...
T Consensus       180 ~~~l  183 (185)
T PF07638_consen  180 RREL  183 (185)
T ss_pred             HHHh
Confidence            8643

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=99.19  E-value=4.3e-11  Score=90.40  Aligned_cols=50  Identities=46%  Similarity=0.587  Sum_probs=46.1

Q ss_pred             HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          448 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       448 aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                      +|+.|||+|+.||.++|    ++++|+.|||+.||+|.++|++++.+|+++||+
T Consensus         1 Al~~L~~~er~vi~~~y----~~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~   50 (50)
T PF04545_consen    1 ALDQLPPREREVIRLRY----FEGLTLEEIAERLGISRSTVRRILKRALKKLRK   50 (50)
T ss_dssp             HHCTS-HHHHHHHHHHH----TST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             ChhhCCHHHHHHHHHHh----cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence            68899999999999999    799999999999999999999999999999984

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

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

Probab=99.13  E-value=1.8e-10  Score=91.53  Aligned_cols=66  Identities=21%  Similarity=0.312  Sum_probs=63.4

Q ss_pred             HHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH
Q 010308          279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT  347 (513)
Q Consensus       279 LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~  347 (513)
                      |++.|.++|+.++.+|.   +++.+.+|++||++++||+++++||++.|..|.+|++..+++.+.+.++
T Consensus         1 L~~~~~~~l~~~~~~~~---~~~~~~eD~~qe~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~r   66 (71)
T PF04542_consen    1 LYERYYPLLYRYARRYT---GDPEDAEDLVQEAFIKLWRAIDSYDPDRGDSFRAWLFRIARNRILDYLR   66 (71)
T ss_dssp             HHHHTHHHHHHHHHTCT---TCSSHHHHHHHHHHHHHHHHHHHTSTTSSSHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHh---CCHhhHHHHhhHHHHHHHhhhhcccccccCCHHHHHHHHHHHHHHHHHH
Confidence            78999999999999998   7788999999999999999999999999988999999999999999998

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 ....

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=98.97  E-value=1.5e-09  Score=89.21  Aligned_cols=75  Identities=37%  Similarity=0.415  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhccccCCCCCCchh
Q 010308          360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENEN  434 (513)
Q Consensus       360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee  434 (513)
                      +++++|.++..+|.+++||.||.+|||+.|||++++|+.++...+.++||+.+...+++ .+.+.+.|....+|++
T Consensus         1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e   76 (78)
T PF04539_consen    1 EKLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEE   76 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHH
T ss_pred             ChHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhh
Confidence            46789999999999999999999999999999999999999999999999998876644 4666677776766665

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 ....

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=98.93  E-value=3.3e-09  Score=81.11  Aligned_cols=54  Identities=28%  Similarity=0.329  Sum_probs=46.3

Q ss_pred             HHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010308          442 RLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL  499 (513)
Q Consensus       442 ~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKL  499 (513)
                      ++.|..+|..|||+++.||.++|    .+++|+.|||+.+|+|.++|++.+.+|+++|
T Consensus         1 r~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L   54 (54)
T PF08281_consen    1 REALQQALAQLPERQREIFLLRY----FQGMSYAEIAEILGISESTVKRRLRRARKKL   54 (54)
T ss_dssp             HHHHHHHHHCS-HHHHHHHHHHH----TS---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHH----HHCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence            35788999999999999999999    7999999999999999999999999999987

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>PRK06930 positive control sigma-like factor; Validated

Probab=98.47  E-value=5.6e-07  Score=85.34  Aligned_cols=65  Identities=20%  Similarity=0.187  Sum_probs=58.5

Q ss_pred             hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       436 ~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ....+....|..+|+.|||+++.||.++|    .+++|++|||+.||+|.++|++++.+|+++|+....
T Consensus        99 ~~~~e~~~~l~~al~~L~~rer~V~~L~~----~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~  163 (170)
T PRK06930         99 VISEWDKIRIEDALSVLTEREKEVYLMHR----GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQIN  163 (170)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            34455667899999999999999999998    689999999999999999999999999999997554

>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

Probab=98.30  E-value=2.5e-06  Score=63.16  Aligned_cols=54  Identities=39%  Similarity=0.467  Sum_probs=49.9

Q ss_pred             HHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010308          443 LALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       443 ~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR  500 (513)
                      ..+..++..||+.++.++.++|    .+++|..+||+.||+|..+|+++..++..+|+
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~----~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~   55 (55)
T cd06171           2 ERLEEALDKLPEREREVILLRF----GEGLSYEEIAEILGISRSTVRQRLHRALKKLR   55 (55)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            3577889999999999999999    68999999999999999999999999998875

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

>PRK00118 putative DNA-binding protein; Validated

Probab=98.22  E-value=3.2e-06  Score=73.92  Aligned_cols=57  Identities=25%  Similarity=0.233  Sum_probs=51.3

Q ss_pred             HHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          444 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       444 ~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      .++-....||++++.|+.++|    .+++|..|||+.||+|+.+|++++.+|+++||+...
T Consensus        10 l~d~~~~~L~ekqRevl~L~y----~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~   66 (104)
T PRK00118         10 LFDFYGSLLTEKQRNYMELYY----LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEE   66 (104)
T ss_pred             HHHHHhccCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            444566789999999999999    789999999999999999999999999999997554

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=98.13  E-value=4.3e-06  Score=76.57  Aligned_cols=54  Identities=19%  Similarity=0.164  Sum_probs=47.5

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhh
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR  509 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~  509 (513)
                      -||++|++||.+++     +++|++|||+.||+|+++|++++++|+++|+.....-.+-
T Consensus         6 ~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~   59 (137)
T TIGR00721         6 FLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFV   59 (137)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHH
Confidence            49999999999976     7999999999999999999999999999999755444443

Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=98.05  E-value=7e-06  Score=75.50  Aligned_cols=50  Identities=26%  Similarity=0.213  Sum_probs=45.9

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ..|||+|++||.+++     +++|++|||+.||+|+.+|++++++|+++||+...
T Consensus         5 ~~Lt~rqreVL~lr~-----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~   54 (141)
T PRK03975          5 SFLTERQIEVLRLRE-----RGLTQQEIADILGTSRANVSSIEKRARENIEKARE   54 (141)
T ss_pred             cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            469999999999965     79999999999999999999999999999997543

>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT)

Probab=97.96  E-value=3.4e-05  Score=67.04  Aligned_cols=55  Identities=29%  Similarity=0.330  Sum_probs=43.6

Q ss_pred             HHHHHHhc-CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          444 ALDDVLDS-LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       444 ~L~~aL~~-L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      .|.+.... ||++|+.++.++|    .+++|+.|||+.+|||+.+|.....||.++|...
T Consensus         9 ~L~d~Yg~LLT~kQ~~~l~lyy----~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~y   64 (101)
T PF04297_consen    9 LLFDFYGELLTEKQREILELYY----EEDLSLSEIAEELGISRQAVYDSIKRAEKKLEEY   64 (101)
T ss_dssp             HHHHHHGGGS-HHHHHHHHHHC----TS---HHHHHHHCTS-HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCHHHHHHHHHHH----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            34445544 9999999999999    7999999999999999999999999999999753

Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.

>PRK04217 hypothetical protein; Provisional

Probab=97.93  E-value=1.4e-05  Score=70.60  Aligned_cols=55  Identities=15%  Similarity=-0.040  Sum_probs=49.5

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  508 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L  508 (513)
                      ..|++.|++||.++|    .+++|++|||+.||||..+|++++.+|.++|+.......+
T Consensus        41 ~~Lt~eereai~l~~----~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~   95 (110)
T PRK04217         41 IFMTYEEFEALRLVD----YEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRE   95 (110)
T ss_pred             ccCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccc
Confidence            479999999999999    7899999999999999999999999999999986654443

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=97.86  E-value=4.4e-05  Score=57.45  Aligned_cols=50  Identities=36%  Similarity=0.358  Sum_probs=44.5

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ..|++.|+.|+.+.+     .++|..|||+.||+|+.+|+++..+++++|.-...
T Consensus         2 ~~l~~~e~~i~~~~~-----~g~s~~eia~~l~is~~tv~~~~~~~~~kl~~~~~   51 (58)
T smart00421        2 ASLTPREREVLRLLA-----EGLTNKEIAERLGISEKTVKTHLSNIMRKLGVRSR   51 (58)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCH
Confidence            468999999997754     68999999999999999999999999999986554

lux regulon (activates the bioluminescence operon

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=97.84  E-value=0.00011  Score=66.92  Aligned_cols=61  Identities=18%  Similarity=0.194  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      .....|..+|+.|++.++.||.++|. . ...+|+.+||..||+|..+|+++..+|+.+|+..
T Consensus        71 ~~~~~I~~~l~~Ld~~er~II~~rY~-~-~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~  131 (134)
T TIGR01636        71 RNRDAIENCLNEADEQTRVIIQELYM-K-KRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEE  131 (134)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHc-c-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            45667999999999999999999993 1 1235999999999999999999999999999854

This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.

>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19

Probab=97.75  E-value=0.00011  Score=63.62  Aligned_cols=56  Identities=32%  Similarity=0.485  Sum_probs=50.5

Q ss_pred             HHHHHHHHHHhcCC-HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010308          440 LLRLALDDVLDSLK-PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL  499 (513)
Q Consensus       440 ~l~~~L~~aL~~L~-~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKL  499 (513)
                      ..+..+..++++|. +.++.||.++|    ...+++.+||..||+|+.++..++.+|++.|
T Consensus        43 ~~k~ei~~~I~~l~d~~~r~iL~~~Y----i~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L   99 (100)
T PF07374_consen   43 KEKLEIRRAINKLEDPDERLILRMRY----INKLTWEQIAEELNISRRTYYRIHKKALKEL   99 (100)
T ss_pred             HHHHHHHHHHHHccChhHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence            44566888999985 89999999999    7899999999999999999999999999876

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=97.74  E-value=1.1e-05  Score=57.58  Aligned_cols=33  Identities=21%  Similarity=0.245  Sum_probs=29.2

Q ss_pred             CChHHHHHHhcCCCCCCChHHHHHHHHHHhHhH
Q 010308          200 TDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMK  232 (513)
Q Consensus       200 ~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~  232 (513)
                      +|.+..||++|+.+|+||++||..|++.|+.+.
T Consensus         1 ~D~l~~Yl~ei~~~~LLt~eeE~~LA~~i~~g~   33 (37)
T PF00140_consen    1 SDSLRLYLKEIGRYPLLTAEEEIELARRIRKGD   33 (37)
T ss_dssp             HHHHHHHHHHHHHS-EETTHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhH
Confidence            378999999999999999999999999997654

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 ....

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=97.70  E-value=0.0001  Score=57.17  Aligned_cols=52  Identities=31%  Similarity=0.319  Sum_probs=44.8

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      +.|+++|.+||.+..     .++|.+|||..||||..+|+.+..++++||.-..+.+
T Consensus         2 ~~LT~~E~~vl~~l~-----~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~~~   53 (58)
T PF00196_consen    2 PSLTERELEVLRLLA-----QGMSNKEIAEELGISEKTVKSHRRRIMKKLGVKNRAE   53 (58)
T ss_dssp             GSS-HHHHHHHHHHH-----TTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSHHH
T ss_pred             CccCHHHHHHHHHHH-----hcCCcchhHHhcCcchhhHHHHHHHHHHHhCCCCHHH
Confidence            579999999999987     7999999999999999999999999999998766544

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=97.66  E-value=0.00017  Score=54.37  Aligned_cols=49  Identities=35%  Similarity=0.366  Sum_probs=43.9

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  505 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~  505 (513)
                      |+++|+.|+.+.+     .++|.+|||+.||+|+.+|+.+..+++++|.-....
T Consensus         1 l~~~e~~i~~~~~-----~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~~~~   49 (57)
T cd06170           1 LTPREREVLRLLA-----EGKTNKEIADILGISEKTVKTHLRNIMRKLGVKSRT   49 (57)
T ss_pred             CCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCCHH
Confidence            6899999998855     689999999999999999999999999999976543

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=97.52  E-value=0.00018  Score=58.89  Aligned_cols=46  Identities=22%  Similarity=0.204  Sum_probs=41.0

Q ss_pred             HHHHHhcCCHHHHHHHhHH-hcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          445 LDDVLDSLKPKESLVIRQR-FGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       445 L~~aL~~L~~rEr~VL~lR-yGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      +..-|+.||++.+.++.|. |    .+++|++|||+.||+|..+|+.++.+
T Consensus         9 ~~~~l~~l~~~~r~af~L~R~----~eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879         9 LAERLTWVDSLAEAAAALARE----EAGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             HHHHHhcCCHHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            5567889999999999994 4    58999999999999999999999874

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=97.52  E-value=0.00012  Score=62.67  Aligned_cols=50  Identities=20%  Similarity=0.268  Sum_probs=43.1

Q ss_pred             HHHHHHHh-cCCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHH
Q 010308          443 LALDDVLD-SLKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRKHE  492 (513)
Q Consensus       443 ~~L~~aL~-~L~~rEr~VL~lRyGL~~---~~~~Tl~EIA~~LgISrerVRqi~  492 (513)
                      +.+..+|. -|+|+|+.+|.+||||.+   ..++|+.|||+.+|||+.+|.+..
T Consensus        23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~s   76 (94)
T TIGR01321        23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGS   76 (94)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHH
Confidence            34666774 499999999999999987   678999999999999999998654

This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=97.51  E-value=0.00034  Score=53.91  Aligned_cols=48  Identities=27%  Similarity=0.373  Sum_probs=41.4

Q ss_pred             CCHHHHHHHhHHh--cCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRF--GLDGK-GDRTLGEIAGNLNISREMVRKHEVKGLMKL  499 (513)
Q Consensus       452 L~~rEr~VL~lRy--GL~~~-~~~Tl~EIA~~LgISrerVRqi~~rALkKL  499 (513)
                      |+++|++||..-|  |..+. .+-|+.|||+.||||.+++..++.+|.+||
T Consensus         1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~kl   51 (53)
T PF04967_consen    1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERKL   51 (53)
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            7899999998855  43332 468999999999999999999999999987

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=97.28  E-value=0.00066  Score=64.51  Aligned_cols=52  Identities=19%  Similarity=0.194  Sum_probs=47.5

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      .||++|++||.+.-     +|+|.+|||+.|++|..||+....++++||.-..+.+.
T Consensus       133 ~LSpRErEVLrLLA-----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV~SRaEL  184 (198)
T PRK15201        133 HFSVTERHLLKLIA-----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHVKTEQQF  184 (198)
T ss_pred             CCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHH
Confidence            59999999999987     89999999999999999999999999999987666543

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=97.26  E-value=0.00048  Score=67.04  Aligned_cols=50  Identities=24%  Similarity=0.268  Sum_probs=46.2

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  505 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~  505 (513)
                      .|+|+|++||.+.-     +|+|.+|||+.||+|..||+.+..+.++||.-..+.
T Consensus       137 ~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v~nr~  186 (207)
T PRK15411        137 SLSRTESSMLRMWM-----AGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTHNKQ  186 (207)
T ss_pred             cCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCCCcHH
Confidence            59999999999987     899999999999999999999999999999865553

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=97.22  E-value=0.00056  Score=65.87  Aligned_cols=52  Identities=31%  Similarity=0.328  Sum_probs=46.7

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ..|+++|++||.+.-     +|+|.+|||+.||+|..||+.+..+.++||--..+.+
T Consensus       149 ~~Lt~rE~evl~~~~-----~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v~~~~~  200 (216)
T PRK10840        149 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIA  200 (216)
T ss_pred             ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence            359999999999987     7999999999999999999999999999997654443

>TIGR03020 EpsA transcriptional regulator EpsA

Probab=97.22  E-value=0.00065  Score=68.27  Aligned_cols=54  Identities=24%  Similarity=0.202  Sum_probs=48.8

Q ss_pred             HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      +..||++|++||.+..     +++|.+|||+.||||..||+....++++||.-..+.+.
T Consensus       188 ~~~LT~RE~evl~l~a-----~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~nr~qA  241 (247)
T TIGR03020       188 AGLITAREAEILAWVR-----DGKTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQA  241 (247)
T ss_pred             ccCCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCHHHH
Confidence            4579999999999976     79999999999999999999999999999997766554

Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=97.21  E-value=0.00055  Score=66.87  Aligned_cols=52  Identities=21%  Similarity=0.279  Sum_probs=47.0

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ..||++|++||.+.-     +|+|.+|||+.|+||..||+.+..+.++||--..+.+
T Consensus       133 ~~LT~RE~eVL~ll~-----~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv~n~~e  184 (207)
T PRK11475        133 RMLSPTEREILRFMS-----RGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVSSDAG  184 (207)
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence            469999999999987     7999999999999999999999999999997655443

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=97.21  E-value=0.00072  Score=67.02  Aligned_cols=53  Identities=26%  Similarity=0.204  Sum_probs=47.7

Q ss_pred             HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ...||++|++||.+..     +++|..|||++||||..+|+.++.++++||.-..+.+
T Consensus       169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~~~  221 (232)
T TIGR03541       169 AGVLSEREREVLAWTA-----LGRRQADIAAILGISERTVENHLRSARRKLGVATTAQ  221 (232)
T ss_pred             hccCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHH
Confidence            3469999999999965     7999999999999999999999999999999766544

Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=97.16  E-value=0.00088  Score=65.78  Aligned_cols=56  Identities=14%  Similarity=-0.043  Sum_probs=50.6

Q ss_pred             HHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          446 DDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       446 ~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ..+...|+|+|++||.+.-     +|+|.+|||+.|++|..||+.+..+.++||--..+.+
T Consensus       138 ~~~~~~LS~RE~eVL~Lia-----~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~sR~e  193 (217)
T PRK13719        138 LEAKNKVTKYQNDVFILYS-----FGFSHEYIAQLLNITVGSSKNKISEILKFFGISSRDE  193 (217)
T ss_pred             hhccCCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence            4566789999999999987     7999999999999999999999999999998766654

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=97.16  E-value=0.0008  Score=66.13  Aligned_cols=52  Identities=23%  Similarity=0.210  Sum_probs=47.7

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ..||++|++||.+..     +++|.+|||+.|++|..||+.+..++++||.-..+.+
T Consensus       154 ~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~nr~e  205 (216)
T PRK10100        154 ALLTHREKEILNKLR-----IGASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQ  205 (216)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence            469999999999998     6999999999999999999999999999998766654

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=97.12  E-value=0.00064  Score=50.20  Aligned_cols=41  Identities=27%  Similarity=0.328  Sum_probs=24.8

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .+|++.|+..|...+    ..++|..+||+.||+|++||...+.|
T Consensus         3 ~~Lt~~eR~~I~~l~----~~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen    3 KHLTPEERNQIEALL----EQGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             ---------HHHHHH----CS---HHHHHHHTT--HHHHHHHHHH
T ss_pred             cchhhhHHHHHHHHH----HcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            469999999999888    78999999999999999999988776

>PRK13870 transcriptional regulator TraR; Provisional

Probab=97.07  E-value=0.00095  Score=66.42  Aligned_cols=51  Identities=22%  Similarity=0.244  Sum_probs=46.5

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      .||+||++||.+-=     +|+|..|||.+||||..||..++..|.+||--..+.+
T Consensus       173 ~LT~RE~E~L~W~A-----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga~nr~q  223 (234)
T PRK13870        173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAH  223 (234)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence            49999999999986     8999999999999999999999999999997665544

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=97.06  E-value=0.001  Score=66.34  Aligned_cols=52  Identities=23%  Similarity=0.288  Sum_probs=47.1

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      .|+++|++||.+..     .|+|..|||.+||||..||+.++.++++||--..+.+.
T Consensus       179 ~LT~rE~evl~~~a-----~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~nr~q~  230 (240)
T PRK10188        179 NFSKREKEILKWTA-----EGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQI  230 (240)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHH
Confidence            59999999999997     79999999999999999999999999999986655443

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=96.99  E-value=0.0027  Score=49.32  Aligned_cols=54  Identities=31%  Similarity=0.359  Sum_probs=47.3

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  508 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L  508 (513)
                      ..|+++|.+|+.+.-     .++|..|||..+|+|..+|+....++..||.-..+...+
T Consensus         3 ~~Lt~rE~~v~~l~~-----~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~~r~~~~   56 (65)
T COG2771           3 ADLTPREREILRLVA-----QGKSNKEIARILGISEETVKTHLRNIYRKLGVKNRVELV   56 (65)
T ss_pred             ccCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHH
Confidence            359999999998876     579999999999999999999999999999876665443

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=96.98  E-value=0.0027  Score=61.11  Aligned_cols=65  Identities=23%  Similarity=0.256  Sum_probs=56.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhh
Q 010308          440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR  509 (513)
Q Consensus       440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~  509 (513)
                      .....+...|.+|+|+||+|+...-     .++..++||..||||..||..+..+.+.||+.....+-++
T Consensus       131 ~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr  195 (202)
T COG4566         131 DRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVR  195 (202)
T ss_pred             HHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHH
Confidence            4456788899999999999999886     7899999999999999999999999999999766655444

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=96.90  E-value=0.0019  Score=63.27  Aligned_cols=52  Identities=33%  Similarity=0.360  Sum_probs=47.2

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ..||+||++||++.-     +|+|.+|||+.|++|..||+.+.++.++||.-..+.+
T Consensus       147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~~Rte  198 (211)
T COG2197         147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRNRTE  198 (211)
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCCCCHHH
Confidence            469999999999986     7999999999999999999999999999998766544

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=96.82  E-value=0.0023  Score=56.24  Aligned_cols=48  Identities=19%  Similarity=0.091  Sum_probs=44.6

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      .|+..|-+.|+|.+    ++++|++|.|+.||||+.|+..++..|.+|+-..
T Consensus        41 ~L~~dElEAiRL~D----~egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~A   88 (106)
T PF02001_consen   41 VLTVDELEAIRLVD----YEGLSQEEAAERMGVSRPTFQRILESARKKIADA   88 (106)
T ss_pred             EeeHHHHHHHHHHH----HcCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHH
Confidence            58889999999998    7899999999999999999999999999999754

>PRK09483 response regulator; Provisional

Probab=96.82  E-value=0.0021  Score=60.74  Aligned_cols=50  Identities=22%  Similarity=0.237  Sum_probs=44.8

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ..|+++|++||.+..     .++|.+|||+.|++|..||+.+..+.++||--..+
T Consensus       147 ~~Lt~rE~~vl~~~~-----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v~~~  196 (217)
T PRK09483        147 ASLSERELQIMLMIT-----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGD  196 (217)
T ss_pred             cccCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCH
Confidence            469999999998865     78999999999999999999999999999965444

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=96.81  E-value=0.0028  Score=71.62  Aligned_cols=38  Identities=16%  Similarity=0.156  Sum_probs=34.5

Q ss_pred             hhcCCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhH
Q 010308          195 EYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMK  232 (513)
Q Consensus       195 ~~~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~  232 (513)
                      +++.++|+|+|||++||.+||||.|+|+.+|++|+.+.
T Consensus        98 ~~~rt~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~  135 (619)
T PRK05658         98 EIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGE  135 (619)
T ss_pred             ccCCCCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHH
Confidence            45668999999999999999999999999999998664

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=96.79  E-value=0.0028  Score=62.08  Aligned_cols=51  Identities=24%  Similarity=0.310  Sum_probs=43.9

Q ss_pred             cCCHHHHHHHhHHh--cCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          451 SLKPKESLVIRQRF--GLDGK-GDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       451 ~L~~rEr~VL~lRy--GL~~~-~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                      .|+++|++||+.-|  |..+. ...|++|||+.||||.+++.+++.+|.+||=.
T Consensus       155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~  208 (215)
T COG3413         155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIE  208 (215)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            59999999999865  44333 45899999999999999999999999999854

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

Probab=96.69  E-value=0.0067  Score=48.69  Aligned_cols=60  Identities=25%  Similarity=0.230  Sum_probs=48.6

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhc-c--CCCCcHHHHHHHHHHHHHHHHhhcC
Q 010308          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQD-F--ANGPRFQDLCQAGVKGLITAIDRFE  323 (513)
Q Consensus       264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~-~--~~g~~~eDLIQEG~iGLirAvekFD  323 (513)
                      .|.++.+||..|.++++.+|.+++.+++.+-..+ .  ..+.--+||-|+-...|+.++-+|+
T Consensus         3 vI~~A~~GD~~A~~~IL~~y~~yI~kls~r~~~d~~g~~~~~vDedl~q~l~~kLi~~I~~F~   65 (65)
T PF12645_consen    3 VIKAAKQGDPEAMEEILKHYEPYISKLSTRTLYDEYGNVYGYVDEDLKQRLEIKLIEAILKFE   65 (65)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHhhcccccCCcCceeCHHHHHHHHHHHHHHHHccC
Confidence            4677899999999999999999999988762211 0  1234449999999999999999996

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

>PRK01381 Trp operon repressor; Provisional

Probab=96.65  E-value=0.0016  Score=56.35  Aligned_cols=50  Identities=18%  Similarity=0.224  Sum_probs=41.6

Q ss_pred             HHHHHHHHHhc-CCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHH
Q 010308          441 LRLALDDVLDS-LKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRK  490 (513)
Q Consensus       441 l~~~L~~aL~~-L~~rEr~VL~lRyGL~~---~~~~Tl~EIA~~LgISrerVRq  490 (513)
                      ..+.+..+|.. |+|.|+.+|..||++..   ..++|+.|||+.+|||..+|.+
T Consensus        21 ~~~~~~~~l~~llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITR   74 (99)
T PRK01381         21 EEDLHLPLLTLLLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITR   74 (99)
T ss_pred             cHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehh
Confidence            34456666766 89999999999999965   4579999999999999998873

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.59  E-value=0.0036  Score=54.11  Aligned_cols=46  Identities=24%  Similarity=0.307  Sum_probs=42.4

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                      |+.+|+..+.++|    ..++|+.|||+.++||+++|...+.|.-+.|-.
T Consensus        18 LT~KQ~~Y~~lyy----~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~   63 (105)
T COG2739          18 LTKKQKNYLELYY----LDDLSLSEIAEEFNVSRQAIYDNIKRTEKILED   63 (105)
T ss_pred             HhHHHHHHHHHHH----HhhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence            8999999999999    789999999999999999999999998776643

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=96.56  E-value=0.0082  Score=55.08  Aligned_cols=59  Identities=19%  Similarity=0.195  Sum_probs=51.0

Q ss_pred             HHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          444 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       444 ~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      .+...+..|+++|++||.+.+     .+++.++||+.+|+|..+|+.+..++++||+...+.+-
T Consensus       134 ~~~~~~~~l~~~e~~vl~~~~-----~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~~  192 (202)
T PRK09390        134 DIRARIASLSERERQVMDGLV-----AGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSEL  192 (202)
T ss_pred             HHHHHHHhhhhhHHHHHHHHH-----ccCchHHHHHHcCCCHHHHHHHHHHHHHHHccccHHHH
Confidence            455667889999999999755     67899999999999999999999999999987766543

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=96.49  E-value=0.0073  Score=55.67  Aligned_cols=50  Identities=26%  Similarity=0.290  Sum_probs=45.0

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ..|+++|++||.+.-     +++|.++||+.|++|..||+.+..++++||.-..+
T Consensus       148 ~~lt~~e~~vl~l~~-----~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~  197 (211)
T PRK15369        148 PLLTPRERQILKLIT-----EGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKV  197 (211)
T ss_pred             cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCH
Confidence            459999999999843     78999999999999999999999999999986554

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=96.44  E-value=0.0019  Score=57.92  Aligned_cols=49  Identities=24%  Similarity=0.222  Sum_probs=45.4

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  505 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~  505 (513)
                      |+++|-.||.||-     +|+|.+|||++||-|+..|+-++.+|+.++.+..+.
T Consensus         9 lte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekarnT   57 (143)
T COG1356           9 LTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKARNT   57 (143)
T ss_pred             eehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHHHH
Confidence            8999999999997     899999999999999999999999999999876543

>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family

Probab=96.43  E-value=0.016  Score=52.40  Aligned_cols=57  Identities=11%  Similarity=0.166  Sum_probs=50.1

Q ss_pred             HHHHHHHH-hcCCHHHHHHHhHHhcCCCCC--CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          442 RLALDDVL-DSLKPKESLVIRQRFGLDGKG--DRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       442 ~~~L~~aL-~~L~~rEr~VL~lRyGL~~~~--~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ...+..++ +.|++.+|.||.++|    ..  .++..+|+..||+|+.+...+..+|+.+|-..
T Consensus        69 ~~~i~~ai~~~l~~~~r~Il~~~Y----l~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~  128 (132)
T TIGR01637        69 ARAIVNAIVNQLDEISRQILYDKY----LEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFATL  128 (132)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHH----cCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHH
Confidence            34566777 999999999999999    44  78999999999999999999999999988643

This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.

>PRK10651 transcriptional regulator NarL; Provisional

Probab=96.38  E-value=0.0072  Score=56.46  Aligned_cols=52  Identities=27%  Similarity=0.337  Sum_probs=46.3

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ..|+++|++|+.+..     ++++.++||..|++|..||+.+..+.++||.-..+.+
T Consensus       154 ~~Lt~rE~~vl~~l~-----~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~~~~~  205 (216)
T PRK10651        154 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVE  205 (216)
T ss_pred             ccCCHHHHHHHHHHH-----cCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence            459999999999876     7899999999999999999999999999997655543

>PRK10403 transcriptional regulator NarP; Provisional

Probab=95.95  E-value=0.016  Score=53.91  Aligned_cols=55  Identities=29%  Similarity=0.222  Sum_probs=47.8

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhh
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR  509 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~  509 (513)
                      ..|+++|.+|+.+..     .++|.++||+.+|+|..||+.+..+.++||.-..+.+...
T Consensus       152 ~~Lt~~e~~vl~~~~-----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~~~~~~~  206 (215)
T PRK10403        152 SVLTERELDVLHELA-----QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAATI  206 (215)
T ss_pred             ccCCHHHHHHHHHHH-----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHHHHH
Confidence            359999999998876     6799999999999999999999999999997766655433

>PRK15320 transcriptional activator SprB; Provisional

Probab=95.93  E-value=0.014  Score=56.60  Aligned_cols=51  Identities=10%  Similarity=0.068  Sum_probs=45.6

Q ss_pred             HHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          447 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       447 ~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      .+--.|+++|.+||.+--     +|+|.+|||+.|++|..+|+....+.+.||.-.
T Consensus       160 ~~~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgAk  210 (251)
T PRK15320        160 NLPPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGMD  210 (251)
T ss_pred             cCCCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcCCC
Confidence            334579999999999886     799999999999999999999999999999753

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=95.84  E-value=0.016  Score=49.64  Aligned_cols=48  Identities=21%  Similarity=0.067  Sum_probs=43.7

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      .|+..|-+.|+|..    +.++|++|-|..||||+.|+-+.+..|++|.-..
T Consensus        33 ~lt~eElEAlRLvD----~~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~a   80 (99)
T COG1342          33 ILTIEELEALRLVD----YEGLTQEEAALRMGISRQTFWRLLTSARKKVADA   80 (99)
T ss_pred             eecHHHHHHHHHHh----HhhccHHHHHHHhcccHHHHHHHHHHHHHHHHHH
Confidence            47888999999988    7899999999999999999999999999998643

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=95.79  E-value=0.025  Score=52.50  Aligned_cols=55  Identities=27%  Similarity=0.320  Sum_probs=48.1

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhh
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR  509 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~  509 (513)
                      ..|+++|.+|+.+..     +++|.++||+.|++|..+|+.+..+.++||.-..+.+-..
T Consensus       136 ~~Lt~~E~~il~~l~-----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~~~~~l~~  190 (196)
T PRK10360        136 DPLTKRERQVAEKLA-----QGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELAR  190 (196)
T ss_pred             cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHH
Confidence            369999999999976     5799999999999999999999999999998766655443

>PRK13558 bacterio-opsin activator; Provisional

Probab=95.44  E-value=0.026  Score=63.80  Aligned_cols=52  Identities=17%  Similarity=0.172  Sum_probs=43.3

Q ss_pred             HhcCCHHHHHHHhHHhcCC--C-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010308          449 LDSLKPKESLVIRQRFGLD--G-KGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       449 L~~L~~rEr~VL~lRyGL~--~-~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR  500 (513)
                      ...|+++|+++|..-|-.+  + -.+-|++|||+.||||++++.+++++|.+||=
T Consensus       605 ~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~  659 (665)
T PRK13558        605 ENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLV  659 (665)
T ss_pred             hhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence            3579999999999977221  1 12349999999999999999999999999984

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=95.34  E-value=0.034  Score=51.89  Aligned_cols=49  Identities=24%  Similarity=0.209  Sum_probs=43.2

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      .|+++|..|+.+..     +++|.+|||+.|++|..+|+.+..++++||.-..+
T Consensus       149 ~lt~re~~vl~~l~-----~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~~~~  197 (210)
T PRK09935        149 VLSNREVTILRYLV-----SGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSI  197 (210)
T ss_pred             cCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCH
Confidence            48999999998754     67999999999999999999999999999975443

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=95.24  E-value=0.037  Score=51.64  Aligned_cols=51  Identities=27%  Similarity=0.305  Sum_probs=45.1

Q ss_pred             HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      +..|+++|.+|+.+..     .+.|.++||+.+++|..+|+.+..+.++||--..+
T Consensus       141 ~~~lt~~E~~vl~~l~-----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~~~~  191 (204)
T PRK09958        141 LDSLSKQEISVMRYIL-----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSL  191 (204)
T ss_pred             cccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCH
Confidence            3569999999999887     67899999999999999999999999999964443

>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=95.18  E-value=0.043  Score=44.68  Aligned_cols=40  Identities=35%  Similarity=0.671  Sum_probs=31.3

Q ss_pred             hHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHH
Q 010308          231 MKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLE  270 (513)
Q Consensus       231 ~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~  270 (513)
                      +..+.++..+|+..+||+|+.+|+|..+|++.+.+..++.
T Consensus         3 l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~   42 (78)
T PF04539_consen    3 LRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQ   42 (78)
T ss_dssp             HHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHH
Confidence            3456778889999999999999999999999988877653

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 ....

>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]

Probab=95.16  E-value=0.49  Score=49.54  Aligned_cols=58  Identities=19%  Similarity=0.321  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                      .++...--+---|++.+|-.|.+|.    ..++|..|||..|=|+..++-|.+.||..+++.
T Consensus       109 ~LRLiFvccHPal~~~~riALtLR~----v~GLs~~eIArAFLv~e~am~QRivRAK~ri~~  166 (415)
T COG4941         109 RLRLIFVCCHPALPPEQRIALTLRL----VGGLSTAEIARAFLVPEAAMAQRIVRAKARIRE  166 (415)
T ss_pred             hHHhhhhhcCCCCChhhHHHHHHHH----HcCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHh
Confidence            3444344444559999999999999    789999999999999999999999999999996

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=95.13  E-value=0.044  Score=46.63  Aligned_cols=37  Identities=16%  Similarity=0.196  Sum_probs=31.4

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHE  492 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~  492 (513)
                      +.|++| ..|+.+.-     .++|..+||+.+|||+.||.++.
T Consensus        35 ~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyRi~   71 (88)
T TIGR02531        35 QSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISRVK   71 (88)
T ss_pred             HhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHH
Confidence            358899 78877765     57899999999999999999844

This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=94.97  E-value=0.046  Score=63.70  Aligned_cols=53  Identities=21%  Similarity=0.277  Sum_probs=47.7

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      ..||++|.+|+.+..     +++|.+|||..|+||..||+.++.+...||.-..+.+.
T Consensus       837 ~~lt~~e~~v~~~~~-----~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~v~~r~~~  889 (903)
T PRK04841        837 SPLTQREWQVLGLIY-----SGYSNEQIAGELDVAATTIKTHIRNLYQKLGIAHRQEA  889 (903)
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHH
Confidence            349999999999977     89999999999999999999999999999987666543

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=94.86  E-value=0.1  Score=47.65  Aligned_cols=57  Identities=26%  Similarity=0.345  Sum_probs=47.1

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010308          441 LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL  499 (513)
Q Consensus       441 l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKL  499 (513)
                      ....|..+++.|.+.++.||.+||+-  ..++|+.+||..|++|..+++.....-...+
T Consensus        71 ~k~~id~~~~~l~de~k~Ii~lry~~--r~~~TW~~IA~~l~i~erta~r~~~~fK~~i  127 (130)
T PF05263_consen   71 QKEAIDRWLETLIDEEKRIIKLRYDR--RSRRTWYQIAQKLHISERTARRWRDRFKNDI  127 (130)
T ss_pred             HHHHHHHHHHhhCHHHHHHHHHHHcc--cccchHHHHHHHhCccHHHHHHHHHHHHHHh
Confidence            45567888999999999999999952  3469999999999999999998876654433

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=94.70  E-value=0.069  Score=40.80  Aligned_cols=48  Identities=17%  Similarity=0.168  Sum_probs=41.7

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                      +|+..++.++.+.|-   ..+.|++++|..+|||+++|+++.+..+.-|-.
T Consensus         2 kLs~~d~lll~L~~L---R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~   49 (53)
T PF13613_consen    2 KLSLEDQLLLTLMYL---RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQ   49 (53)
T ss_pred             CCCHHHHHHHHHHHH---HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHH
Confidence            688899999888763   678999999999999999999999998877654

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=94.69  E-value=0.028  Score=41.84  Aligned_cols=33  Identities=27%  Similarity=0.256  Sum_probs=23.0

Q ss_pred             HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          458 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       458 ~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      .||.+..     +++|..+||+.||||+.+|+++..+-
T Consensus         9 ~ii~l~~-----~G~s~~~ia~~lgvs~~Tv~~w~kr~   41 (50)
T PF13384_consen    9 QIIRLLR-----EGWSIREIAKRLGVSRSTVYRWIKRY   41 (50)
T ss_dssp             -HHHHHH-----HT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred             HHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence            3555555     58999999999999999999987663

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=94.55  E-value=0.038  Score=40.82  Aligned_cols=33  Identities=18%  Similarity=0.118  Sum_probs=24.0

Q ss_pred             HHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          456 ESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       456 Er~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      ..+|+.|+-     .++|..+||+.||||+.+|.+++.
T Consensus        11 ~~~i~~l~~-----~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen   11 IEEIKELYA-----EGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             HHHHHHHHH-----TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             HHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHh
Confidence            455666665     679999999999999999998763

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=94.14  E-value=0.48  Score=50.35  Aligned_cols=130  Identities=22%  Similarity=0.297  Sum_probs=72.1

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHH
Q 010308          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV  312 (513)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~  312 (513)
                      .+......|...+|++|+.+|+|..+|++.+.+..++....    .        .+++-...    +.+   +|      
T Consensus       217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~----~--------~~SLd~~~----~~~---~~------  271 (367)
T PRK09210        217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQ----E--------PVSLETPI----GEE---DD------  271 (367)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhc----C--------CCCcCCCC----CCC---Cc------
Confidence            34556677888999999999999999999988876543211    0        01110000    000   01      


Q ss_pred             HHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccchhHHHHHHHHHHHHHHHH--hCCCCCHHHHHHhcC
Q 010308          313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFE--LKRVPTDEEIIQGVN  390 (513)
Q Consensus       313 iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~e--lgR~PT~eELA~~lg  390 (513)
                      ..|...+.  |+.............++..+..++..     +|..        .+..-.+..-  -|..-|.+|||+.+|
T Consensus       272 ~~l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~~-----L~~r--------Er~Vl~lrygl~~~~~~tl~EIa~~lg  336 (367)
T PRK09210        272 SHLGDFIE--DQDATSPADHAAYELLKEQLEDVLDT-----LTDR--------EENVLRLRFGLDDGRTRTLEEVGKVFG  336 (367)
T ss_pred             chhhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHHh-----CCHH--------HHHHHHHHhccCCCCCccHHHHHHHHC
Confidence            01111111  11112223344455666667666651     3311        1111122211  237789999999999


Q ss_pred             CCHHHHHHHHHh
Q 010308          391 ISPERYREVMKA  402 (513)
Q Consensus       391 is~e~v~~~l~~  402 (513)
                      +|.++|+++...
T Consensus       337 vs~erVrQi~~~  348 (367)
T PRK09210        337 VTRERIRQIEAK  348 (367)
T ss_pred             CCHHHHHHHHHH
Confidence            999999988543

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=94.09  E-value=0.13  Score=38.01  Aligned_cols=41  Identities=24%  Similarity=0.167  Sum_probs=30.2

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      |++.++.||..-+-   ..+.|..|||+.+|+|..+|+++..+-
T Consensus         1 l~~~~~~Il~~l~~---~~~~t~~ela~~~~is~~tv~~~l~~L   41 (48)
T PF13412_consen    1 LDETQRKILNYLRE---NPRITQKELAEKLGISRSTVNRYLKKL   41 (48)
T ss_dssp             --HHHHHHHHHHHH---CTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            56788888877662   456999999999999999999876653

...

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=93.99  E-value=0.1  Score=34.39  Aligned_cols=36  Identities=25%  Similarity=0.385  Sum_probs=28.2

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH  491 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi  491 (513)
                      +++.++..+...|    ..+.|..+||+.+|+|+.+|..+
T Consensus         6 ~~~~~~~~i~~~~----~~~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569           6 LTPEQIEEARRLL----AAGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             CCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHh
Confidence            5556666665556    45779999999999999999875

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=93.96  E-value=0.072  Score=55.53  Aligned_cols=36  Identities=22%  Similarity=0.204  Sum_probs=32.7

Q ss_pred             HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010308          458 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  497 (513)
Q Consensus       458 ~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALk  497 (513)
                      .|-.|||    .+++|.+|||++||+||.+|.+++.+|.+
T Consensus        20 ~vA~lYY----~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~   55 (318)
T PRK15418         20 RIAWFYY----HDGLTQSEIGERLGLTRLKVSRLLEKGRQ   55 (318)
T ss_pred             HHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            4567888    79999999999999999999999999976

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=93.73  E-value=0.079  Score=42.47  Aligned_cols=45  Identities=20%  Similarity=0.243  Sum_probs=28.2

Q ss_pred             HhcCCHHHHHHHhHH--hcCCCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 010308          449 LDSLKPKESLVIRQR--FGLDGKGDRTLGEIAGNLNIS-REMVRKHEV  493 (513)
Q Consensus       449 L~~L~~rEr~VL~lR--yGL~~~~~~Tl~EIA~~LgIS-rerVRqi~~  493 (513)
                      |..|+++|++||...  |-...+.+-|+.|||+.||++ .++|.+.+.
T Consensus         1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~   48 (65)
T PF01726_consen    1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK   48 (65)
T ss_dssp             -----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence            457999999998763  212223467999999999997 999987664

The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=93.64  E-value=0.073  Score=36.85  Aligned_cols=26  Identities=38%  Similarity=0.431  Sum_probs=18.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010308          471 DRTLGEIAGNLNISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       471 ~~Tl~EIA~~LgISrerVRqi~~rALkKLR  500 (513)
                      ++|.+|||..+|+|+++|++    ++++|+
T Consensus         2 ~mtr~diA~~lG~t~ETVSR----~l~~l~   27 (32)
T PF00325_consen    2 PMTRQDIADYLGLTRETVSR----ILKKLE   27 (32)
T ss_dssp             E--HHHHHHHHTS-HHHHHH----HHHHHH
T ss_pred             CcCHHHHHHHhCCcHHHHHH----HHHHHH
Confidence            47899999999999999985    555555

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

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

Probab=93.38  E-value=1.1  Score=44.51  Aligned_cols=36  Identities=44%  Similarity=0.712  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010308          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC  268 (513)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~  268 (513)
                      .+......+...+|++|+.+|+|..+|++.+.+..+
T Consensus        88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~  123 (238)
T TIGR02393        88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVREI  123 (238)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            344556778889999999999999999998887654

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.

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=93.37  E-value=0.18  Score=44.83  Aligned_cols=50  Identities=28%  Similarity=0.256  Sum_probs=44.2

Q ss_pred             HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          448 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       448 aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                      .+..|++.+..-|....    ...=+++|+++.||||..|||..+.+.+.+|-.
T Consensus        30 ~~~~L~~E~~~Fi~~Fi----~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~   79 (113)
T PF09862_consen   30 WFARLSPEQLEFIKLFI----KNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY   79 (113)
T ss_pred             hhhcCCHHHHHHHHHHH----HhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence            46789999998887776    445599999999999999999999999999987

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=93.24  E-value=1  Score=50.08  Aligned_cols=37  Identities=30%  Similarity=0.527  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010308          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (513)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~  269 (513)
                      .+...+.+|...+|++|+.+|+|..+|++.+.+..++
T Consensus       359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~  395 (509)
T PRK05901        359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQ  395 (509)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence            4455677788899999999999999999988776653

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=93.08  E-value=1.1  Score=46.91  Aligned_cols=36  Identities=33%  Similarity=0.593  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010308          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC  268 (513)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~  268 (513)
                      .+......|...+|++|+..|+|..+|++.+.+..+
T Consensus       174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~  209 (324)
T PRK07921        174 KLARIKRELHQQLGREATDEELAEESGIPEEKIADL  209 (324)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence            445566778889999999999999999998777654

>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ

Probab=92.69  E-value=0.53  Score=42.50  Aligned_cols=52  Identities=17%  Similarity=0.091  Sum_probs=46.1

Q ss_pred             HHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          447 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       447 ~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ..|.+-.|.+-.+|.++|    ..++|...||..+++|...||+.+.+|-.-+...
T Consensus        58 ~~L~~~~~~~~~ll~~~Y----v~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~  109 (125)
T PF06530_consen   58 ARLKKRDPEEYDLLILYY----VYGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGC  109 (125)
T ss_pred             HHHHccCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhh
Confidence            334557999999999999    6899999999999999999999999998888765

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=92.33  E-value=0.13  Score=39.43  Aligned_cols=40  Identities=28%  Similarity=0.322  Sum_probs=28.9

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .|+..|+.=|..+|    ..+.+..+||..|||+.++|+.|...
T Consensus         6 ~LTl~eK~~iI~~~----e~g~s~~~ia~~fgv~~sTv~~I~K~   45 (53)
T PF04218_consen    6 SLTLEEKLEIIKRL----EEGESKRDIAREFGVSRSTVSTILKN   45 (53)
T ss_dssp             S--HHHHHHHHHHH----HCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred             cCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence            47777777666667    56779999999999999999999865

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=92.21  E-value=0.36  Score=35.32  Aligned_cols=39  Identities=23%  Similarity=0.368  Sum_probs=26.9

Q ss_pred             CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          453 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       453 ~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ++-.+.||..--.   ....|+.+||+.+|+|..+|.+...+
T Consensus         2 D~~D~~Il~~Lq~---d~r~s~~~la~~lglS~~~v~~Ri~r   40 (42)
T PF13404_consen    2 DELDRKILRLLQE---DGRRSYAELAEELGLSESTVRRRIRR   40 (42)
T ss_dssp             -HHHHHHHHHHHH----TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH---cCCccHHHHHHHHCcCHHHHHHHHHH
Confidence            4455666665442   35799999999999999999987654

...

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=92.07  E-value=0.25  Score=39.12  Aligned_cols=39  Identities=23%  Similarity=0.336  Sum_probs=28.5

Q ss_pred             HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      |.--..+.++...  ...+++.+||+.||||..+||....+
T Consensus         7 p~rdkA~e~y~~~--~g~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen    7 PNRDKAFEIYKES--NGKIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             cCHHHHHHHHHHh--CCCccHHHHHHHHCCCHHHHHHHhhh
Confidence            3333445555422  45899999999999999999988654

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []

Probab=91.83  E-value=0.32  Score=38.15  Aligned_cols=26  Identities=23%  Similarity=0.270  Sum_probs=24.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          470 GDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       470 ~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      ++++..|||+.||+++.+|.....+-
T Consensus        12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~   37 (58)
T PF06056_consen   12 QGWSIKEIAEELGVPRSTVYSWKDRY   37 (58)
T ss_pred             cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence            79999999999999999999988764

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>PF13730 HTH_36: Helix-turn-helix domain

Probab=91.74  E-value=0.51  Score=35.73  Aligned_cols=46  Identities=24%  Similarity=0.362  Sum_probs=33.6

Q ss_pred             cCCHHHHHHHhHHhcCCCCCC---CCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010308          451 SLKPKESLVIRQRFGLDGKGD---RTLGEIAGNLNISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~---~Tl~EIA~~LgISrerVRqi~~rALkKLR  500 (513)
                      .|++.++.|+..-.-+.+..+   .|.+.||+.+|+|+.+|+    ++++.|.
T Consensus         2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~----~~i~~L~   50 (55)
T PF13730_consen    2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQ----RAIKELE   50 (55)
T ss_pred             CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHH----HHHHHHH
Confidence            588999988776544432222   399999999999999998    4555554

>PF13518 HTH_28: Helix-turn-helix domain

Probab=91.73  E-value=0.26  Score=36.62  Aligned_cols=27  Identities=26%  Similarity=0.254  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010308          470 GDRTLGEIAGNLNISREMVRKHEVKGL  496 (513)
Q Consensus       470 ~~~Tl~EIA~~LgISrerVRqi~~rAL  496 (513)
                      ++.|+.+||..+|||+.+|+++..+-.
T Consensus        11 ~g~s~~~~a~~~gis~~tv~~w~~~y~   37 (52)
T PF13518_consen   11 EGESVREIAREFGISRSTVYRWIKRYR   37 (52)
T ss_pred             cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence            456999999999999999998887653

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=91.57  E-value=1.4  Score=47.80  Aligned_cols=37  Identities=19%  Similarity=0.226  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHH
Q 010308          364 EIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVM  400 (513)
Q Consensus       364 ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l  400 (513)
                      .+.+....|..++|+.||.+|.|..+|+++.+++..+
T Consensus       112 ~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~l  148 (415)
T PRK07598        112 RLIEVRERLTSELGHRPSLERWAKTADISLADLKPTL  148 (415)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHhh
Confidence            4566677899999999999999988877766655443

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=91.52  E-value=0.35  Score=47.35  Aligned_cols=48  Identities=23%  Similarity=0.165  Sum_probs=37.0

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  498 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkK  498 (513)
                      .|+++|.+++.....-....++|.+|||+.||+|..||+.+..++...
T Consensus       158 ~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~  205 (239)
T PRK10430        158 GLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNC  205 (239)
T ss_pred             CCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhC
Confidence            488999777654331011478999999999999999999999988554

>smart00351 PAX Paired Box domain

Probab=91.17  E-value=0.49  Score=42.63  Aligned_cols=42  Identities=19%  Similarity=0.059  Sum_probs=34.0

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  497 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALk  497 (513)
                      |+..+|.-|...|    .++.|..+||+.||||+.+|.++..+...
T Consensus        18 ~s~~~R~riv~~~----~~G~s~~~iA~~~gvs~~tV~kwi~r~~~   59 (125)
T smart00351       18 LPDEERQRIVELA----QNGVRPCDISRQLCVSHGCVSKILGRYYE   59 (125)
T ss_pred             CCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            5555666666666    46889999999999999999999998754

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=90.72  E-value=0.97  Score=45.44  Aligned_cols=37  Identities=32%  Similarity=0.554  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010308          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (513)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~  269 (513)
                      .+.....+|...+|++|+..|+|..+|++.+.+..+.
T Consensus       114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~  150 (256)
T PRK07408        114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIK  150 (256)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHH
Confidence            4455677888899999999999999999988776543

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=90.45  E-value=0.34  Score=50.67  Aligned_cols=35  Identities=29%  Similarity=0.203  Sum_probs=31.1

Q ss_pred             HHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010308          459 VIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  497 (513)
Q Consensus       459 VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALk  497 (513)
                      +-.+||    .+++|..|||+.||||+.+|++++.+|.+
T Consensus        18 ~A~lYY----~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~   52 (321)
T COG2390          18 AAWLYY----VEGLTQSEIAERLGISRATVSRLLAKARE   52 (321)
T ss_pred             HHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            445788    79999999999999999999999999865

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=90.34  E-value=2.7  Score=44.90  Aligned_cols=36  Identities=25%  Similarity=0.490  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010308          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC  268 (513)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~  268 (513)
                      .+......|...+|++|+.+|+|..+|++.+.+..+
T Consensus       224 ~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~  259 (373)
T PRK07406        224 RIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFI  259 (373)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            445566778889999999999999999998777543

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=90.19  E-value=0.86  Score=36.53  Aligned_cols=43  Identities=21%  Similarity=0.195  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCC-HHHHHHHHHh
Q 010308          360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNIS-PERYREVMKA  402 (513)
Q Consensus       360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis-~e~v~~~l~~  402 (513)
                      +.-.++-.+..++..+.|..||..|||+.+|++ ...+...+..
T Consensus         6 ~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~   49 (65)
T PF01726_consen    6 ERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA   49 (65)
T ss_dssp             HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence            344556666777888899999999999999997 8888887765

The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.

>PHA00675 hypothetical protein

Probab=90.09  E-value=0.56  Score=38.82  Aligned_cols=41  Identities=17%  Similarity=0.100  Sum_probs=31.4

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      ..|++-+-+.|+..+-   ..+.|+.+||..||||+++|.+|.+
T Consensus        21 AKLt~~qV~~IR~l~~---r~G~s~~~IA~~fGVsrstV~~I~~   61 (78)
T PHA00675         21 AKLTDAEVERIRELHE---VEGMSYAVLAEKFEQSKGAIAKICR   61 (78)
T ss_pred             cccCHHHHHHHHHHHH---hcCccHHHHHHHhCCCHHHHHHHHc
Confidence            3566666666655541   2577999999999999999999875

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=90.02  E-value=0.47  Score=35.92  Aligned_cols=39  Identities=21%  Similarity=0.332  Sum_probs=27.5

Q ss_pred             HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          455 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       455 rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      |+..||.+-+  ....+.|.+|||+.||||+.+|++.+..-
T Consensus         1 R~~~il~~L~--~~~~~it~~eLa~~l~vS~rTi~~~i~~L   39 (55)
T PF08279_consen    1 RQKQILKLLL--ESKEPITAKELAEELGVSRRTIRRDIKEL   39 (55)
T ss_dssp             HHHHHHHHHH--HTTTSBEHHHHHHHCTS-HHHHHHHHHHH
T ss_pred             CHHHHHHHHH--HcCCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence            4556666643  11345999999999999999999776543

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=89.85  E-value=3.9  Score=41.13  Aligned_cols=36  Identities=33%  Similarity=0.559  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010308          234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (513)
Q Consensus       234 l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~  269 (513)
                      +......+...+|++|+.+|+|..+|++.+.+...+
T Consensus       112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~  147 (257)
T PRK05911        112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWF  147 (257)
T ss_pred             HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHH
Confidence            344555677889999999999999999988775543

>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA

Probab=89.73  E-value=0.65  Score=39.31  Aligned_cols=44  Identities=30%  Similarity=0.240  Sum_probs=34.1

Q ss_pred             HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh--CCCHHHHHHHHHHH
Q 010308          449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNL--NISREMVRKHEVKG  495 (513)
Q Consensus       449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~L--gISrerVRqi~~rA  495 (513)
                      ++.||+..+++..+|.-   ..+.|+.|+|+.|  .||.+.|.-+..+-
T Consensus        35 ~~~l~~~l~~~a~lRl~---~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl   80 (85)
T PF02650_consen   35 LDKLPEKLREFAELRLE---NPDASLKELGELLEPPISKSGVNHRLRKL   80 (85)
T ss_dssp             GGGS-HHHHHHHHHHHH----TTS-HHHHHHTT--T--HHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHH---CccccHHHHHHHHcCcCcHHHHHHHHHHH
Confidence            57899999999999884   5789999999999  99999998877654

It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.

>PRK05949 RNA polymerase sigma factor; Validated

Probab=89.47  E-value=8.6  Score=40.31  Aligned_cols=37  Identities=24%  Similarity=0.486  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010308          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (513)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~  269 (513)
                      .+......+...+|++|+..|+|..+|++.+.+..++
T Consensus       179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~  215 (327)
T PRK05949        179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYL  215 (327)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence            3445556677889999999999999999987776543

>PHA02591 hypothetical protein; Provisional

Probab=89.20  E-value=0.62  Score=38.65  Aligned_cols=24  Identities=29%  Similarity=0.209  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          470 GDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       470 ~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      .|+|.++||..||+|.++|+++..
T Consensus        58 qGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         58 KGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHh
Confidence            589999999999999999999875

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B

Probab=89.12  E-value=0.78  Score=35.25  Aligned_cols=43  Identities=26%  Similarity=0.286  Sum_probs=32.3

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .|++.|..||..-+.-++ .+.|..|||+.+++++.+|.++..+
T Consensus         2 glt~~q~~vL~~l~~~~~-~~~t~~~la~~l~~~~~~vs~~v~~   44 (62)
T PF12802_consen    2 GLTPSQFRVLMALARHPG-EELTQSELAERLGISKSTVSRIVKR   44 (62)
T ss_dssp             TSTHHHHHHHHHHHHSTT-SGEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHCCC-CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            378888888887664221 2389999999999999999876654

...

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=89.09  E-value=0.79  Score=33.92  Aligned_cols=37  Identities=27%  Similarity=0.391  Sum_probs=28.1

Q ss_pred             HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      |.-..||.+-.    .++++..||++.+|+|+++|++.+..
T Consensus         2 ~~R~~Il~~L~----~~~~~~~el~~~l~~s~~~vs~hL~~   38 (47)
T PF01022_consen    2 PTRLRILKLLS----EGPLTVSELAEELGLSQSTVSHHLKK   38 (47)
T ss_dssp             HHHHHHHHHHT----TSSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHH----hCCCchhhHHHhccccchHHHHHHHH
Confidence            34455666655    47899999999999999999987654

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

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

Probab=88.75  E-value=7.8  Score=39.18  Aligned_cols=38  Identities=32%  Similarity=0.561  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010308          232 KVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (513)
Q Consensus       232 ~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~  269 (513)
                      ..+..+...|+.++||+|++.|+|...|++.+++..++
T Consensus       110 ~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~  147 (247)
T COG1191         110 RRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEAL  147 (247)
T ss_pred             HHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHH
Confidence            34567778899999999999999999999987776544

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=88.71  E-value=0.55  Score=54.41  Aligned_cols=50  Identities=28%  Similarity=0.177  Sum_probs=46.1

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ||.||.+|+.+.|     .|+|.+|||++|.||-.||+.+.+.--.||.-..+.+
T Consensus       832 Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV~~Rtq  881 (894)
T COG2909         832 LSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLGVANRTQ  881 (894)
T ss_pred             ccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhCcchHHH
Confidence            8999999999999     7999999999999999999999999999997655544

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=88.62  E-value=10  Score=38.15  Aligned_cols=37  Identities=27%  Similarity=0.418  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010308          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (513)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~  269 (513)
                      .+......|+..+|++|+..|+|...|++.+.+..+.
T Consensus       119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~  155 (268)
T PRK06288        119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLL  155 (268)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHH
Confidence            4455666788899999999999999999987765543

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=88.21  E-value=6.4  Score=39.82  Aligned_cols=36  Identities=33%  Similarity=0.478  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010308          234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (513)
Q Consensus       234 l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~  269 (513)
                      +......+...+|++|+..|+|..+|++.+.+..++
T Consensus       129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~  164 (264)
T PRK07122        129 LGRATAELSQRLGRAPTASELAAELGMDREEVVEGL  164 (264)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence            344566777889999999999999999988776544

>cd00131 PAX Paired Box domain

Probab=87.90  E-value=1.2  Score=40.34  Aligned_cols=42  Identities=17%  Similarity=0.022  Sum_probs=32.9

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  497 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALk  497 (513)
                      ||...|.-|...|    .+++|..+||+.||||+.+|..+..+-..
T Consensus        18 lS~d~R~rIv~~~----~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e   59 (128)
T cd00131          18 LPDSIRQRIVELA----QSGIRPCDISRQLRVSHGCVSKILNRYYE   59 (128)
T ss_pred             CCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            5555555555556    47899999999999999999999888653

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=87.40  E-value=3.9  Score=40.11  Aligned_cols=34  Identities=50%  Similarity=0.656  Sum_probs=27.4

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010308          236 QVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (513)
Q Consensus       236 ~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~  269 (513)
                      ...+.+...+|+.|+..|+|...|++.+.+...+
T Consensus       101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~  134 (231)
T TIGR02885       101 YMKEELSKELGREPTINELAEALGVSPEEIVMAL  134 (231)
T ss_pred             HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHH
Confidence            4456677889999999999999999987775543

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.

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=86.75  E-value=8.4  Score=38.53  Aligned_cols=36  Identities=28%  Similarity=0.447  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHH
Q 010308          235 VQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLE  270 (513)
Q Consensus       235 ~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~  270 (513)
                      ......+..++|++|+.+|+|...|++.+.+..++.
T Consensus       123 ~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~  158 (254)
T TIGR02850       123 LQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALD  158 (254)
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344566778899999999999999999888766543

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.

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=86.57  E-value=1.5  Score=36.03  Aligned_cols=52  Identities=15%  Similarity=0.146  Sum_probs=36.3

Q ss_pred             HHHHHHHHhcCCHHHHHHHhHHhc-CCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          442 RLALDDVLDSLKPKESLVIRQRFG-LDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       442 ~~~L~~aL~~L~~rEr~VL~lRyG-L~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      ...|....+.|++.|+.|.....- .+....+|..|||+..|||..+|.+...
T Consensus         4 ~~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~k   56 (77)
T PF01418_consen    4 LEKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCK   56 (77)
T ss_dssp             HHHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHH
T ss_pred             HHHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHH
Confidence            456777788999999999766441 0123479999999999999999987654

Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=86.53  E-value=2.3  Score=33.04  Aligned_cols=37  Identities=30%  Similarity=0.376  Sum_probs=28.1

Q ss_pred             HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      |.-..||.+-.+   ..++|..|||+.+|++.++|+..+.
T Consensus        10 p~R~~Il~~L~~---~~~~t~~ela~~l~~~~~t~s~hL~   46 (61)
T PF12840_consen   10 PTRLRILRLLAS---NGPMTVSELAEELGISQSTVSYHLK   46 (61)
T ss_dssp             HHHHHHHHHHHH---CSTBEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            666666666522   5899999999999999999987654

...

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=86.14  E-value=1.7  Score=32.41  Aligned_cols=25  Identities=24%  Similarity=0.320  Sum_probs=22.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          471 DRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       471 ~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      ..|+++||+.+|||..+|+.+..+.
T Consensus        27 ~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   27 SRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            3699999999999999999998764

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=85.96  E-value=2.7  Score=38.24  Aligned_cols=51  Identities=25%  Similarity=0.247  Sum_probs=39.6

Q ss_pred             HHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010308          444 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       444 ~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR  500 (513)
                      .+-.+.-.|++.+-+|+..-.-  ...+.|..|||+.||.|+++|.    ||+++|=
T Consensus        17 dvl~c~~GLs~~Dv~v~~~LL~--~~~~~tvdelae~lnr~rStv~----rsl~~L~   67 (126)
T COG3355          17 DVLKCVYGLSELDVEVYKALLE--ENGPLTVDELAEILNRSRSTVY----RSLQNLL   67 (126)
T ss_pred             HHHHHHhCCcHHHHHHHHHHHh--hcCCcCHHHHHHHHCccHHHHH----HHHHHHH
Confidence            3556666799999998766541  2468999999999999999987    6666664

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=85.96  E-value=0.77  Score=44.59  Aligned_cols=39  Identities=23%  Similarity=0.135  Sum_probs=29.4

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      .|+++  +|+.+.-  .|..++|.+|||+.||||+.||+.+..
T Consensus       161 ~Lt~r--~Vl~~~~--~g~~g~s~~eIa~~l~iS~~Tv~~~~~  199 (225)
T PRK10046        161 PLTLN--AVRKLFK--EPGVQHTAETVAQALTISRTTARRYLE  199 (225)
T ss_pred             HHHHH--HHHHHHH--cCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence            45665  5665543  223479999999999999999999875

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=85.88  E-value=1.5  Score=34.30  Aligned_cols=42  Identities=26%  Similarity=0.246  Sum_probs=27.6

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      |++.|..||..-.  ....++|..+||+.++++..+|++.+.+-
T Consensus         1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~L   42 (68)
T PF13463_consen    1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKKL   42 (68)
T ss_dssp             --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            5677777776655  23578999999999999999998555443

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=85.84  E-value=0.78  Score=34.30  Aligned_cols=22  Identities=23%  Similarity=0.271  Sum_probs=19.7

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHH
Q 010308          473 TLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       473 Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      |++|||+..|||..+|+..++.
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~   22 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNG   22 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTT
T ss_pred             CHHHHHHHHCcCHHHHHHHHhC
Confidence            7899999999999999987754

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=85.79  E-value=2.6  Score=40.06  Aligned_cols=62  Identities=11%  Similarity=0.160  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHchhccCCCCc---HHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH
Q 010308          283 NLRLVLFVIKKYFQDFANGPR---FQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT  347 (513)
Q Consensus       283 nlrLV~sIAkky~~~~~~g~~---~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~  347 (513)
                      .+..+..++++|.   -.+..   -+|+|.+|.-..++.++.|||++...+-.|.+..+-++..+-|.
T Consensus        46 imkIa~glS~r~n---F~~Yt~~wKedMI~DgIe~~i~ylhNFD~~k~~Np~aYiT~~~~~AF~~RI~  110 (179)
T PHA02547         46 IMKIAEGLSRRPN---FSGYTQTWKEDMIADGIEACIKGLHNFDETKYKNPHAYITQACFNAFVQRIK  110 (179)
T ss_pred             HHHHHhccccCCc---cccchHHHHHHHHHHHHHHHHHHhhcCCcccccChHHHHHHHHHHHHHHHHH
Confidence            3444444555543   23433   68999999999999999999999877877777777777666555

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=85.69  E-value=1.7  Score=37.38  Aligned_cols=41  Identities=15%  Similarity=0.191  Sum_probs=31.7

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      |++.++.||....-   ....|+.+||+.+|+|+.+|++...+-
T Consensus         1 ld~~D~~il~~L~~---~~~~~~~~la~~l~~s~~tv~~~l~~L   41 (108)
T smart00344        1 LDEIDRKILEELQK---DARISLAELAKKVGLSPSTVHNRVKRL   41 (108)
T ss_pred             CCHHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            46677888866542   246899999999999999999766543

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=85.59  E-value=1.3  Score=33.82  Aligned_cols=41  Identities=29%  Similarity=0.383  Sum_probs=31.3

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      |++.|-.||..-+-   ..+.|..+||+.+++++.+|.++..+-
T Consensus         1 lt~~q~~iL~~l~~---~~~~~~~~la~~~~~~~~~~t~~i~~L   41 (59)
T PF01047_consen    1 LTPSQFRILRILYE---NGGITQSELAEKLGISRSTVTRIIKRL   41 (59)
T ss_dssp             STHHHHHHHHHHHH---HSSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCCChhHHHHHHHHH
Confidence            56677777777653   457999999999999999998776554

This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=85.28  E-value=9.2  Score=33.98  Aligned_cols=28  Identities=32%  Similarity=0.458  Sum_probs=22.8

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010308          469 KGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       469 ~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR  500 (513)
                      ..+.|+.|||+.||||.++|.    ++|++|.
T Consensus        69 ~pd~tl~Ela~~l~Vs~~ti~----~~Lkrlg   96 (119)
T PF01710_consen   69 NPDATLRELAERLGVSPSTIW----RALKRLG   96 (119)
T ss_pred             CCCcCHHHHHHHcCCCHHHHH----HHHHHcC
Confidence            368999999999999988887    5555554

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=85.16  E-value=2  Score=34.49  Aligned_cols=23  Identities=22%  Similarity=0.238  Sum_probs=20.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Q 010308          471 DRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       471 ~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      +.|..|||+.+||+..+|++++.
T Consensus        22 ~~ta~eLa~~lgl~~~~v~r~L~   44 (68)
T smart00550       22 TSTALQLAKNLGLPKKEVNRVLY   44 (68)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHH
Confidence            59999999999999999886554

Helix-turn-helix-containing domain. Also known as Zab.

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=84.88  E-value=1.2  Score=35.11  Aligned_cols=45  Identities=24%  Similarity=0.295  Sum_probs=31.0

Q ss_pred             CCHHHHHHHhHHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010308          452 LKPKESLVIRQRFGLD-GKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~-~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR  500 (513)
                      |++....-|...|-|. +....+..+||+.||+|+.+|..    ++++|.
T Consensus         2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~----ml~~L~   47 (60)
T PF01325_consen    2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTE----MLKRLA   47 (60)
T ss_dssp             CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHH----HHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHH----HHHHHH
Confidence            4555555555555553 45678999999999999999985    455554

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=84.83  E-value=0.61  Score=37.01  Aligned_cols=40  Identities=33%  Similarity=0.310  Sum_probs=30.7

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      .|++.|..|+..-.-   ..+.|..|||+.+|+|+.+|+..+.
T Consensus         5 gLs~~E~~vy~~Ll~---~~~~t~~eIa~~l~i~~~~v~~~L~   44 (68)
T PF01978_consen    5 GLSENEAKVYLALLK---NGPATAEEIAEELGISRSTVYRALK   44 (68)
T ss_dssp             CHHHHHHHHHHHHHH---HCHEEHHHHHHHHTSSHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            367788888755431   3689999999999999999985543

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression

Probab=84.37  E-value=1.2  Score=37.99  Aligned_cols=46  Identities=20%  Similarity=0.265  Sum_probs=32.4

Q ss_pred             CCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRKHEVKGLMK  498 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~---~~~~Tl~EIA~~LgISrerVRqi~~rALkK  498 (513)
                      |+|.|..-|..|+-+-.   .+++|+.||++.+|+|..+|.+. +++|+.
T Consensus        27 ~T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRv-sr~Lk~   75 (87)
T PF01371_consen   27 CTPDELEALAQRWQVAKELLDEGKSYREIAEETGVSIATITRV-SRCLKY   75 (87)
T ss_dssp             SSHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHH-HHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHH-HHHHHc
Confidence            67777766665553321   26899999999999999999753 445443

The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=84.20  E-value=2  Score=32.86  Aligned_cols=39  Identities=23%  Similarity=0.211  Sum_probs=26.3

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      .|++-|+.-|-...    ..++|+.|||..+|-|+..|+..+.
T Consensus         4 ~Lt~~Eqaqid~m~----qlG~s~~~isr~i~RSr~~Ir~yl~   42 (50)
T PF11427_consen    4 TLTDAEQAQIDVMH----QLGMSLREISRRIGRSRTCIRRYLK   42 (50)
T ss_dssp             ---HHHHHHHHHHH----HTT--HHHHHHHHT--HHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH----HhchhHHHHHHHhCccHHHHHHHhc
Confidence            47777777777766    4689999999999999999998743

>PF12728 HTH_17: Helix-turn-helix domain

Probab=84.12  E-value=1.1  Score=33.36  Aligned_cols=24  Identities=38%  Similarity=0.338  Sum_probs=21.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          472 RTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       472 ~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      +|.+|+|+.||||+.+|+++..+.
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g   25 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQG   25 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcC
Confidence            589999999999999999998654

>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress

Probab=84.03  E-value=1.9  Score=36.00  Aligned_cols=43  Identities=16%  Similarity=0.173  Sum_probs=34.4

Q ss_pred             cCCHHHHHHHhHHhcC--CCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGL--DGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL--~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      .|+++|+.||...--+  ..+++-.-++||+.+++|..+||+...
T Consensus         1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~   45 (78)
T PF03444_consen    1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMA   45 (78)
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHH
Confidence            3899999998764322  345788999999999999999998764

Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=84.00  E-value=10  Score=39.55  Aligned_cols=36  Identities=33%  Similarity=0.448  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010308          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC  268 (513)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~  268 (513)
                      .+......+...+|+.|+..|+|..+|++.+.+...
T Consensus       169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~  204 (317)
T PRK07405        169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVREY  204 (317)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence            445566677788999999999999999987766544

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=83.94  E-value=14  Score=36.73  Aligned_cols=37  Identities=22%  Similarity=0.274  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHH
Q 010308          234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLE  270 (513)
Q Consensus       234 l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~  270 (513)
                      +.+....+...+|++|+..++|...|++.+.+..++.
T Consensus       111 ~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~  147 (251)
T PRK07670        111 VEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMN  147 (251)
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence            3445566777899999999999999999888776543

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

Probab=83.85  E-value=15  Score=37.64  Aligned_cols=35  Identities=34%  Similarity=0.641  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010308          234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC  268 (513)
Q Consensus       234 l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~  268 (513)
                      +......+...+|+.|+..|+|..+|++.+.+..+
T Consensus       163 ~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~  197 (298)
T TIGR02997       163 IKKVQRELSQKLGRTPSEAEIAEALELEPEQVREL  197 (298)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            34445667778999999999999999998887654

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).

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=83.74  E-value=12  Score=29.45  Aligned_cols=73  Identities=18%  Similarity=0.179  Sum_probs=45.3

Q ss_pred             CCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHH
Q 010308          379 VPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESL  458 (513)
Q Consensus       379 ~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~  458 (513)
                      ++|.++||+.+|++...+..++.....                        .++.+...    ...+.           .
T Consensus         1 ~~~~~~la~~~~~s~~~l~~~f~~~~~------------------------~s~~~~~~----~~r~~-----------~   41 (84)
T smart00342        1 PLTLEDLAEALGMSPRHLQRLFKKETG------------------------TTPKQYLR----DRRLE-----------R   41 (84)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHhC------------------------cCHHHHHH----HHHHH-----------H
Confidence            378899999999999988887654210                        11111110    11121           1


Q ss_pred             HHhHHhcCCCCCCCCHHHHHHHhCC-CHHHHHHHHHH
Q 010308          459 VIRQRFGLDGKGDRTLGEIAGNLNI-SREMVRKHEVK  494 (513)
Q Consensus       459 VL~lRyGL~~~~~~Tl~EIA~~LgI-SrerVRqi~~r  494 (513)
                      ++.+..    ..+.|+.+||..+|+ |.....+...+
T Consensus        42 a~~~l~----~~~~~~~~ia~~~g~~s~~~f~r~Fk~   74 (84)
T smart00342       42 ARRLLR----DTDLSVTEIALRVGFSSQSYFSRAFKK   74 (84)
T ss_pred             HHHHHH----cCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence            222222    237899999999999 98877766544

>PRK12423 LexA repressor; Provisional

Probab=83.58  E-value=1.6  Score=42.44  Aligned_cols=48  Identities=27%  Similarity=0.343  Sum_probs=33.8

Q ss_pred             hcCCHHHHHHHhHHhcC--CCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHhC
Q 010308          450 DSLKPKESLVIRQRFGL--DGKGDRTLGEIAGNLN-ISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL--~~~~~~Tl~EIA~~Lg-ISrerVRqi~~rALkKLR~  501 (513)
                      ..|++++++|+..---.  .++-.-|..|||+.|| +|+.+|+.    +|+.|.+
T Consensus         2 ~~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~----~l~~L~~   52 (202)
T PRK12423          2 DTLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK----HVQALAE   52 (202)
T ss_pred             CcCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH----HHHHHHH
Confidence            35899999998763311  1223469999999999 59999995    4555544

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=83.44  E-value=9.7  Score=39.10  Aligned_cols=26  Identities=27%  Similarity=0.266  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHhcCCCHHHHHHHHHhc
Q 010308          378 RVPTDEEIIQGVNISPERYREVMKAS  403 (513)
Q Consensus       378 R~PT~eELA~~lgis~e~v~~~l~~~  403 (513)
                      ..-|..|||+.||+|.++|+.++..+
T Consensus       244 ~~~t~~EIa~~lgvs~~~V~q~~~~A  269 (289)
T PRK07500        244 DGATLEALGEELGISKERVRQIEARA  269 (289)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            56799999999999999999887543

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=83.41  E-value=2.5  Score=35.83  Aligned_cols=43  Identities=19%  Similarity=0.236  Sum_probs=37.0

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  496 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rAL  496 (513)
                      .|+|.-+..|..+.-   .++++..++|+.||||+.+++++..|=.
T Consensus         8 ~Lt~~gR~~lv~~vv---~~g~~~a~aA~~~gVS~~Ta~kW~~Ryr   50 (85)
T PF13011_consen    8 RLTPRGRLRLVRRVV---EQGWPVAHAAAEFGVSRRTAYKWLARYR   50 (85)
T ss_pred             CCCHHHHHHHHHHHH---HcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence            589999999888762   3589999999999999999999988754

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=83.10  E-value=42  Score=34.87  Aligned_cols=177  Identities=14%  Similarity=0.013  Sum_probs=88.9

Q ss_pred             HHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccccchh
Q 010308          280 IKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLE  359 (513)
Q Consensus       280 I~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP~~~~  359 (513)
                      +...+..+..++....        +.+-+.|...-+++-+.....-+|.....++.-.|.-+    .+            
T Consensus       122 l~~a~~~I~~~~~~L~--------Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiA----CR------------  177 (310)
T PRK00423        122 LAFALSELDRIASQLG--------LPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAA----CR------------  177 (310)
T ss_pred             HHHHHHHHHHHHHHcC--------CCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHH----HH------------
Confidence            3444455556655553        33667777777877776666667766544443333222    22            


Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhhhHHH
Q 010308          360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA  439 (513)
Q Consensus       360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~~~~~  439 (513)
                                     ..|-+-|..||+..++++..++....+.....+.++.+.. +..+++..+.+.-..+ .+..  .
T Consensus       178 ---------------~~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~-~p~~~i~r~~~~L~L~-~~v~--~  238 (310)
T PRK00423        178 ---------------RCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPT-DPIDYVPRFASELGLS-GEVQ--K  238 (310)
T ss_pred             ---------------HcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCC-CHHHHHHHHHHHcCCC-HHHH--H
Confidence                           1233456778888888888777655443322222222221 1122222221111111 1111  1


Q ss_pred             HHHHHHHHHHhc-C----CHHH--HHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010308          440 LLRLALDDVLDS-L----KPKE--SLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       440 ~l~~~L~~aL~~-L----~~rE--r~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR  500 (513)
                      .....+..+.+. |    +|.-  ..+|.+-.-+. +.+.|++|||...|||..+|++....-.+.|-
T Consensus       239 ~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~-g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~  305 (310)
T PRK00423        239 KAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLL-GERRTQREVAEVAGVTEVTVRNRYKELAEKLD  305 (310)
T ss_pred             HHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHh-CCCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence            111222222211 1    2221  11222211112 35799999999999999999988777666554

>TIGR00498 lexA SOS regulatory protein LexA

Probab=82.55  E-value=1.8  Score=41.52  Aligned_cols=44  Identities=14%  Similarity=0.114  Sum_probs=33.6

Q ss_pred             hcCCHHHHHHHhHHhc--CCCCCCCCHHHHHHHhCCC-HHHHHHHHH
Q 010308          450 DSLKPKESLVIRQRFG--LDGKGDRTLGEIAGNLNIS-REMVRKHEV  493 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyG--L~~~~~~Tl~EIA~~LgIS-rerVRqi~~  493 (513)
                      ..|+++|+.||..-.-  ..++.+.|..|||+.||++ +.+|+.++.
T Consensus         2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~   48 (199)
T TIGR00498         2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLK   48 (199)
T ss_pred             CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHH
Confidence            3589999999887541  2234568999999999998 999985543

LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=82.45  E-value=1.3  Score=31.70  Aligned_cols=25  Identities=28%  Similarity=0.244  Sum_probs=22.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010308          472 RTLGEIAGNLNISREMVRKHEVKGL  496 (513)
Q Consensus       472 ~Tl~EIA~~LgISrerVRqi~~rAL  496 (513)
                      +|..|+|+.||||+.+|+++...+.
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g~   25 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGK   25 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence            5889999999999999999988764

Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=82.35  E-value=1.9  Score=40.47  Aligned_cols=50  Identities=14%  Similarity=0.018  Sum_probs=42.7

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHHhC
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNIS-----REMVRKHEVKGLMKLKH  501 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgIS-----rerVRqi~~rALkKLR~  501 (513)
                      .|+++|.+||.+..- +.+..+|.++|++.++.+     ..+|+.+..+.++||..
T Consensus       154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~l~~Kl~~  208 (228)
T PRK11083        154 TLTRYEFLLLKTLLL-SPGRVFSRQQLMDIVWEDAQDSYDRTVDTHIKTLRAKLRA  208 (228)
T ss_pred             ecCHHHHHHHHHHHh-CCCceECHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhcc
Confidence            599999999988762 223469999999999986     78999999999999974

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=82.33  E-value=2.2  Score=41.15  Aligned_cols=35  Identities=23%  Similarity=0.209  Sum_probs=28.0

Q ss_pred             HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          455 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       455 rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .++.|..++.     .++|+.+||+.||||+++|.++...
T Consensus       161 ~~~~i~~~~~-----~g~s~~~iak~lgis~~Tv~r~~k~  195 (200)
T PRK13413        161 KEEKIKKLLD-----KGTSKSEIARKLGVSRTTLARFLKT  195 (200)
T ss_pred             hHHHHHHHHH-----CCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            3455666644     5799999999999999999998863

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=82.18  E-value=4.8  Score=34.37  Aligned_cols=49  Identities=22%  Similarity=0.210  Sum_probs=36.0

Q ss_pred             HhcCCHHHHHHHhHH----hcCC-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          449 LDSLKPKESLVIRQR----FGLD-GKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       449 L~~L~~rEr~VL~lR----yGL~-~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                      ...|++++..+|...    ||.. .....|..|||+.+|+|+++|+    ++|++|.+
T Consensus        20 ~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVs----r~L~~Le~   73 (95)
T TIGR01610        20 GADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVS----DAIKSLAR   73 (95)
T ss_pred             hCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            356899999987642    4422 2457999999999999999988    55555543

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

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

Probab=82.13  E-value=21  Score=34.84  Aligned_cols=37  Identities=32%  Similarity=0.530  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010308          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (513)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~  269 (513)
                      .+......+...+|++|+.+|+|..+|++.+.+..+.
T Consensus        84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~  120 (224)
T TIGR02479        84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQAL  120 (224)
T ss_pred             HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHH
Confidence            4455667788889999999999999999987776644

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

>TIGR01764 excise DNA binding domain, excisionase family

Probab=81.94  E-value=1.6  Score=31.39  Aligned_cols=24  Identities=29%  Similarity=0.339  Sum_probs=21.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          472 RTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       472 ~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      +|.+|+|+.||||+.+|+++....
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g   25 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEG   25 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcC
Confidence            589999999999999999998665

An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=81.93  E-value=2.8  Score=38.77  Aligned_cols=41  Identities=10%  Similarity=0.169  Sum_probs=32.5

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .|++.++.||..---   ....|+.+||+.+|+|+.+|+....+
T Consensus         6 ~lD~~D~~Il~~Lq~---d~R~s~~eiA~~lglS~~tV~~Ri~r   46 (153)
T PRK11179          6 QIDNLDRGILEALME---NARTPYAELAKQFGVSPGTIHVRVEK   46 (153)
T ss_pred             ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            377788888776541   35789999999999999999977654

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=81.83  E-value=2  Score=40.86  Aligned_cols=50  Identities=14%  Similarity=0.131  Sum_probs=43.8

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhC
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg-----ISrerVRqi~~rALkKLR~  501 (513)
                      .|+++|.+|+.+... +.+...|.++|++.+.     +|..+|+.+..+.++||..
T Consensus       160 ~Lt~~e~~il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~  214 (240)
T PRK10710        160 DLTPAEFRLLKTLSH-EPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLES  214 (240)
T ss_pred             ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhc
Confidence            599999999998773 3345799999999998     9999999999999999974

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=81.70  E-value=2.5  Score=39.04  Aligned_cols=28  Identities=14%  Similarity=0.007  Sum_probs=25.1

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010308          469 KGDRTLGEIAGNLNISREMVRKHEVKGL  496 (513)
Q Consensus       469 ~~~~Tl~EIA~~LgISrerVRqi~~rAL  496 (513)
                      .+++|..|||++||||.++|.....+--
T Consensus        19 ~~G~S~re~Ak~~gvs~sTvy~wv~r~~   46 (138)
T COG3415          19 GEGLSCREAAKRFGVSISTVYRWVRRYR   46 (138)
T ss_pred             HcCccHHHHHHHhCccHHHHHHHHHHhc
Confidence            3799999999999999999999888754

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=81.42  E-value=1.9  Score=40.27  Aligned_cols=50  Identities=22%  Similarity=0.154  Sum_probs=41.9

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhC
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg-----ISrerVRqi~~rALkKLR~  501 (513)
                      .|+++|.+||.+.. -+.+..+|.++|+..+.     ++..+|+.+..+..+||..
T Consensus       149 ~Lt~~E~~il~~l~-~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl~~  203 (219)
T PRK10336        149 TLKPKEFALLELLM-RNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKLGS  203 (219)
T ss_pred             ecCHHHHHHHHHHH-hCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhcCC
Confidence            49999999998765 12234589999999996     9999999999999999963

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=81.30  E-value=2.7  Score=31.51  Aligned_cols=28  Identities=32%  Similarity=0.469  Sum_probs=22.4

Q ss_pred             CCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          470 GDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       470 ~~~-Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                      ... |..|||+.||+|+.+|+    +++++|.+
T Consensus        18 ~~l~s~~~la~~~~vs~~tv~----~~l~~L~~   46 (60)
T smart00345       18 DKLPSERELAAQLGVSRTTVR----EALSRLEA   46 (60)
T ss_pred             CcCcCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            445 99999999999999998    55555654

>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]

Probab=81.10  E-value=2.1  Score=31.00  Aligned_cols=38  Identities=26%  Similarity=0.269  Sum_probs=25.9

Q ss_pred             HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      +-|+.+|...+-   ..+.+..+.|+.||||+.+++..+.+
T Consensus         4 ~~E~~~i~~aL~---~~~gn~~~aA~~Lgisr~tL~~klkk   41 (42)
T PF02954_consen    4 EFEKQLIRQALE---RCGGNVSKAARLLGISRRTLYRKLKK   41 (42)
T ss_dssp             HHHHHHHHHHHH---HTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            446666665442   24568999999999999999876643

It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism

Probab=80.94  E-value=2.4  Score=32.76  Aligned_cols=35  Identities=17%  Similarity=0.283  Sum_probs=25.7

Q ss_pred             HHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          456 ESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       456 Er~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      +..|+.+-.   .....|.+|+|+.||||..|||+-+.
T Consensus         2 ~~~Il~~l~---~~~~~s~~ela~~~~VS~~TiRRDl~   36 (57)
T PF08220_consen    2 QQQILELLK---EKGKVSVKELAEEFGVSEMTIRRDLN   36 (57)
T ss_pred             HHHHHHHHH---HcCCEEHHHHHHHHCcCHHHHHHHHH
Confidence            344554432   24578999999999999999996554

This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=80.64  E-value=2.7  Score=39.30  Aligned_cols=50  Identities=14%  Similarity=0.094  Sum_probs=41.8

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhC
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg-----ISrerVRqi~~rALkKLR~  501 (513)
                      .|+++|.+|+.+..- +-+...|.++|++.+.     +|..+|..+..+.++||..
T Consensus       148 ~Lt~~E~~il~~l~~-~~~~~~~~~~i~~~l~~~~~~~~~~tv~~~i~~ir~kl~~  202 (221)
T PRK15479        148 ALTPREQALLTVLMY-RRTRPVSRQQLFEQVFSLNDEVSPESIELYIHRLRKKLQG  202 (221)
T ss_pred             ecCHHHHHHHHHHHh-CCCCcCcHHHHHHHhcCCCCCCCcccHHHHHHHHHHhcCC
Confidence            599999999987651 1124579999999986     9999999999999999964

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=80.16  E-value=6.9  Score=34.24  Aligned_cols=48  Identities=15%  Similarity=0.151  Sum_probs=35.9

Q ss_pred             HHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          443 LALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       443 ~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      ..+...+.  .|++.|..||...+.   ..+.|..|||+.+|+++.+|.++..
T Consensus        15 ~~~~~~l~~~~lt~~q~~iL~~l~~---~~~~t~~ela~~~~~~~~tvs~~l~   64 (118)
T TIGR02337        15 SFFRPILAQHGLTEQQWRILRILAE---QGSMEFTQLANQACILRPSLTGILA   64 (118)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHH---cCCcCHHHHHHHhCCCchhHHHHHH
Confidence            34444443  589999988876652   4679999999999999999875443

This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	513
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		1e-30
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		1e-30
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		2e-26
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		5e-26
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		5e-26
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		5e-26
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		9e-26
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		7e-19
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		8e-19
3les_A	179	2f5 Epitope Scaffold Es2 Length = 179		2e-13
1sig_A	339	Crystal Structure Of A Sigma70 Subunit Fragment Fro		6e-13
1l0o_C	243	Crystal Structure Of The Bacillus Stearothermophilu		5e-11
1tty_A	87	Solution Structure Of Sigma A Region 4 From Thermot		4e-08
1tlh_B	81	T4 Asia Bound To Sigma70 Region 4 Length = 81		2e-07
2p7v_B	68	Crystal Structure Of The Escherichia Coli Regulator		2e-07
3t72_q	99	Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna		4e-07
4g6d_A	73	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		9e-06
4g94_A	62	G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Comp		2e-04
3n97_A	72	Rna Polymerase Alpha C-Terminal Domain (E. Coli) An		4e-04

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

Iteration: 1
 Score =  131 bits (329), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 147/275 (53%), Gaps = 24/275 (8%)
Query: 253 ELAEATNMSAAQVKKC---LEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQ 305
           ++ E T ++  QVK     + +G A    A+ ++++ NLRLV+ + KKY      G +F 
Sbjct: 346 QIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN---RGLQFL 402
Query: 306 DLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGE 364
           DL Q G  GL+ A+D+FE +R ++ STY  +WIR AI RS+   + T R+P  +     +
Sbjct: 403 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 462
Query: 365 IQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE----EF 420
           + R   ++L E+ R PT EE+ + + +  ++ R+V+K +K  +S+ +  G  ++    +F
Sbjct: 463 LNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDF 522
Query: 421 INGIT---DVDGVENENQRQPAXXXXXXXXXXXXXKPKESLVIRQRFGLDGKGDRTLGEI 477
           I   T    +D    E+ R                  +E+ V+R RFG+D   D TL E+
Sbjct: 523 IEDTTLELPLDSATTESLRAATHDVLAGLT------AREAKVLRMRFGIDMNTDHTLEEV 576
Query: 478 AGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512
               +++RE +R+ E K L KL+HP+R + LR  +
Sbjct: 577 GKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 611

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

Iteration: 1
 Score =  130 bits (328), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 147/275 (53%), Gaps = 24/275 (8%)
Query: 253 ELAEATNMSAAQVKKC---LEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQ 305
           ++ E T ++  QVK     + +G A    A+ ++++ NLRLV+ + KKY      G +F 
Sbjct: 346 QIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN---RGLQFL 402
Query: 306 DLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGE 364
           DL Q G  GL+ A+D+FE +R ++ STY  +WIR AI RS+   + T R+P  +     +
Sbjct: 403 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 462
Query: 365 IQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE----EF 420
           + R   ++L E+ R PT EE+ + + +  ++ R+V+K +K  +S+ +  G  ++    +F
Sbjct: 463 LNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDF 522
Query: 421 INGIT---DVDGVENENQRQPAXXXXXXXXXXXXXKPKESLVIRQRFGLDGKGDRTLGEI 477
           I   T    +D    E+ R                  +E+ V+R RFG+D   D TL E+
Sbjct: 523 IEDTTLELPLDSATTESLRAATHDVLAGLT------AREAKVLRMRFGIDMNTDYTLEEV 576
Query: 478 AGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512
               +++RE +R+ E K L KL+HP+R + LR  +
Sbjct: 577 GKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 611

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

Iteration: 1
 Score =  117 bits (292), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 87/262 (33%), Positives = 133/262 (50%), Gaps = 21/262 (8%)
Query: 264 QVKKCLEV---GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAID 320
           ++K+ L +   G AAR  LI+ NLRLV+ + KKY      G  F DL Q G +GLI A++
Sbjct: 184 ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVE 240
Query: 321 RFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRV 379
           +FE KRRF+ STY  +WIR AI R++   + T R+P  +     ++ R   +L  EL R 
Sbjct: 241 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGRE 300
Query: 380 PTDEEIIQ--GVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQ 437
           P+ EEI +  G     +R  E +K ++  +SL +  G  ++ F       D + +EN   
Sbjct: 301 PSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYG-----DFIPDENLPS 355
Query: 438 PAXXXXXXXXXXXXXKP------KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH 491
           P              K       +E++V++ R GL    + TL E+     ++RE +R+ 
Sbjct: 356 PVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQI 415
Query: 492 EVKGLMKLK-HPTRVDYLRQHM 512
           E K L KLK H +R   LR  +
Sbjct: 416 ENKALRKLKYHESRTRKLRDFL 437

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

Iteration: 1
 Score =  115 bits (289), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 127/251 (50%), Gaps = 18/251 (7%)
Query: 272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLS 331
           G AAR  LI+ NLRLV+ + KKY      G  F DL Q G +GLI A+++FE KRRF+ S
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS 236
Query: 332 TYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQ--G 388
           TY  +WIR AI R++   + T R+P  +     ++ R   +L  EL R PT EEI +  G
Sbjct: 237 TYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMG 296
Query: 389 VNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXXXXXXXXX 448
                +R  E +K ++  +SL +  G  ++ F       D + +E+   P          
Sbjct: 297 PGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYG-----DFIPDEHLPSPVDAATQSLLS 351
Query: 449 XXXXKP------KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK-H 501
               K       +E++V++ R GL    + TL E+     ++RE +R+ E K L KLK H
Sbjct: 352 EELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYH 411
Query: 502 PTRVDYLRQHM 512
            +R   LR  +
Sbjct: 412 ESRTRKLRDFL 422

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

Iteration: 1
 Score =  115 bits (289), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 127/251 (50%), Gaps = 18/251 (7%)
Query: 272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLS 331
           G AAR  LI+ NLRLV+ + KKY      G  F DL Q G +GLI A+++FE KRRF+ S
Sbjct: 180 GEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS 236
Query: 332 TYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQ--G 388
           TY  +WIR AI R++   + T R+P  +     ++ R   +L  EL R PT EEI +  G
Sbjct: 237 TYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMG 296
Query: 389 VNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXXXXXXXXX 448
                +R  E +K ++  +SL +  G  ++ F       D + +E+   P          
Sbjct: 297 PGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYG-----DFIPDEHLPSPVDAATQSLLS 351
Query: 449 XXXXKP------KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK-H 501
               K       +E++V++ R GL    + TL E+     ++RE +R+ E K L KLK H
Sbjct: 352 EELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYH 411
Query: 502 PTRVDYLRQHM 512
            +R   LR  +
Sbjct: 412 ESRTRKLRDFL 422

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

Iteration: 1
 Score =  115 bits (289), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 87/262 (33%), Positives = 133/262 (50%), Gaps = 21/262 (8%)
Query: 264 QVKKCLEV---GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAID 320
           ++K+ L +   G AAR  LI+ NLRLV+ + KKY      G  F DL Q G +GLI A++
Sbjct: 78  ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVE 134
Query: 321 RFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRV 379
           +FE KRRF+ STY  +WIR AI R++   + T R+P  +     ++ R   +L  EL R 
Sbjct: 135 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGRE 194
Query: 380 PTDEEIIQ--GVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQ 437
           P+ EEI +  G     +R  E +K ++  +SL +  G  ++ F       D + +EN   
Sbjct: 195 PSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYG-----DFIPDENLPS 249
Query: 438 PAXXXXXXXXXXXXXKP------KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH 491
           P              K       +E++V++ R GL    + TL E+     ++RE +R+ 
Sbjct: 250 PVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQI 309
Query: 492 EVKGLMKLK-HPTRVDYLRQHM 512
           E K L KLK H +R   LR  +
Sbjct: 310 ENKALRKLKYHESRTRKLRDFL 331

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

Iteration: 1
 Score =  114 bits (286), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 127/251 (50%), Gaps = 18/251 (7%)
Query: 272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLS 331
           G AAR  LI+ NLRLV+ + KKY      G  F DL Q G +GLI A+++FE KRRF+ S
Sbjct: 200 GEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS 256
Query: 332 TYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQ--G 388
           TY  +WIR AI R++   + T R+P  +     ++ R   +L  EL R PT EEI +  G
Sbjct: 257 TYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMG 316
Query: 389 VNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXXXXXXXXX 448
                +R  E +K ++  +SL +  G  ++ F       D + +E+   P          
Sbjct: 317 PGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYG-----DFIPDEHLPSPVDAATQSLLS 371
Query: 449 XXXXKP------KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK-H 501
               K       +E++V++ R GL    + TL E+     ++RE +R+ E K L KLK H
Sbjct: 372 EELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYH 431
Query: 502 PTRVDYLRQHM 512
            +R   LR  +
Sbjct: 432 ESRTRKLRDFL 442

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

Iteration: 1
 Score = 92.0 bits (227), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 59/152 (38%), Positives = 87/152 (57%), Gaps = 9/152 (5%)
Query: 264 QVKKCLEV---GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAID 320
           ++K+ L +   G AAR  LI+ NLRLV+ + KKY      G  F DL Q G +GLI A++
Sbjct: 97  ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVE 153
Query: 321 RFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRV 379
           +FE KRRF+ STY  +WIR AI R++   + T R+P  +     ++ R   +L  EL R 
Sbjct: 154 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGRE 213
Query: 380 PTDEEIIQ--GVNISPERYREVMKASKPILSL 409
           P+ EEI +  G     +R  E +K ++  +SL
Sbjct: 214 PSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 245

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

Iteration: 1
 Score = 92.0 bits (227), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 57/141 (40%), Positives = 81/141 (57%), Gaps = 6/141 (4%)
Query: 272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLS 331
           G AAR  LI+ NLRLV+ + KKY      G  F DL Q G +GLI A+++FE KRRF+ S
Sbjct: 104 GEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFS 160
Query: 332 TYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQ--G 388
           TY  +WIR AI R++   + T R+P  +     ++ R   +L  EL R P+ EEI +  G
Sbjct: 161 TYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMG 220
Query: 389 VNISPERYREVMKASKPILSL 409
                +R  E +K ++  +SL
Sbjct: 221 PGWDAKRVEETLKIAQEPVSL 241

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

Iteration: 1
 Score = 74.3 bits (181), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/87 (45%), Positives = 54/87 (62%), Gaps = 6/87 (6%)
Query: 264 QVKKCLEV---GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAID 320
           ++K+ L +   G AAR  LI+ NLRLV+ + KKY      G  F DL Q G +GLI A++
Sbjct: 92  ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVE 148
Query: 321 RFEPKRRFRLSTYGLFWIRHAIIRSMT 347
           +FE KR F  STY  +WIR AI R++ 
Sbjct: 149 KFEYKRGFAFSTYATWWIRQAINRAIA 175

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

Iteration: 1
 Score = 72.4 bits (176), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 39/102 (38%), Positives = 61/102 (59%), Gaps = 10/102 (9%)
Query: 253 ELAEATNMSAAQVKKC---LEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQ 305
           ++ E T ++  QVK     + +G A    A+ ++++ NLRLV+ + KKY      G +F 
Sbjct: 237 QIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN---RGLQFL 293
Query: 306 DLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT 347
           DL Q G  GL+ A+D+FE +R ++ STY  +WIR AI RS+ 
Sbjct: 294 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 335

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

Iteration: 1
 Score = 65.9 bits (159), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 110/236 (46%), Gaps = 11/236 (4%)
Query: 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEP 324
           +++  E  + AR+++I+ N+RLV  V++++      G    DL Q G  GL+ ++D+F+ 
Sbjct: 19  IRRSQEGDQEARDEIIEKNMRLVWSVVQRFLN---RGYEADDLFQIGCIGLLKSVDKFDL 75
Query: 325 KRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEE 384
               + STY +  I   I R +      +V   L+ +  +I++AK EL     R PT  E
Sbjct: 76  SYDVKFSTYAVPMIIGEIQRFLRDDGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTE 135
Query: 385 IIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXXXXX 444
           I   + ISPE   +V+ A + +    S H    E   + IT +D + + ++         
Sbjct: 136 IADHLGISPE---DVVLAQEAVRLPTSIHETVYENDGDPITLLDQIADADE-ASWFDKIA 191
Query: 445 XXXXXXXXKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500
                     +E L++  R+      D+T  E+A  L IS+  + + E K L  +K
Sbjct: 192 LKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLEKKILQHIK 243

>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga Maritima Length = 87

Iteration: 1
 Score = 56.6 bits (135), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 42/57 (73%), Gaps = 2/57 (3%)
Query: 454 PKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 509
           P+E++V+R R+GL DGK  +TL E+    N++RE +R+ EVK L KL+HP+R  YL+
Sbjct: 21  PREAMVLRMRYGLLDGK-PKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLK 76

>pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4 Length = 81

Iteration: 1
 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 38/59 (64%)
Query: 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512
            +E+ V+R RFG+D   D TL E+    +++RE +R+ E K L KL+HP+R + LR  +
Sbjct: 21  AREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 79

>pdb|2P7V|B Chain B, Crystal Structure Of The Escherichia Coli Regulator Of Sigma 70, Rsd, In Complex With Sigma 70 Domain 4 Length = 68

Iteration: 1
 Score = 53.9 bits (128), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 38/59 (64%)
Query: 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512
            +E+ V+R RFG+D   D TL E+    +++RE +R+ E K L KL+HP+R + LR  +
Sbjct: 8   AREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 66

>pdb|3T72|QQ Chain q, Phob(E)-Sigma70(4)-(Rnap-Betha-Flap-Tip-Helix)-Dna Transcription Activation Sub-Complex Length = 99

Iteration: 1
 Score = 53.1 bits (126), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 37/56 (66%)
Query: 454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 509
            +E+ V+R RFG+D   D TL E+    +++RE +R+ E K L KL+HP+R + LR
Sbjct: 22  AREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLR 77

>pdb|4G6D|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 73

Iteration: 1
 Score = 48.5 bits (114), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 35/58 (60%)
Query: 455 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512
           +E  V+R RFGLD    RTL E+     ++RE +R+ E K L KL+HP+R   L+  M
Sbjct: 15  REENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFM 72

>pdb|4G94|A Chain A, G1 Orf67 / Staphyloccus Aureus Sigmaa Domain 4 Complex Length = 62

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/48 (45%), Positives = 30/48 (62%)
Query: 455 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502
           +E  V+R RFGLD    RTL E+     ++RE +R+ E K L KL+HP
Sbjct: 15  REENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 62

>pdb|3N97|A Chain A, Rna Polymerase Alpha C-Terminal Domain (E. Coli) And Sigma Region 4 (T. Aq. Mutant) Bound To (Up,-35 Element) Dna Length = 72

Iteration: 1
 Score = 42.7 bits (99), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 455 KESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 512
           +E++V++ R GL DG+ + TL E+     ++RE +R+ E K L KL+HP+R + LR  +
Sbjct: 14  REAMVLKMRKGLIDGR-EHTLEEVGAYFGVTRERIRQIENKALRKLRHPSRSEKLRDFL 71

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	513
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	2e-44
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	3e-05
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	1e-42
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	1e-41
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	7e-41
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	2e-37
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	8e-05
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	4e-23
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	8e-17
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	2e-16
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	5e-15
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	6e-15
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	5e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	6e-05

>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 =  155 bits (395), Expect = 2e-44
 Identities = 64/229 (27%), Positives = 111/229 (48%), Gaps = 13/229 (5%)

Query: 273 RAARNKLIKHNLRLVLFVIKKYFQDFAN-GPRFQDLCQAGVKGLITAIDRFEPKRRFRLS 331
           + AR+++I+ N+RLV  V+++    F N G    DL Q G  GL+ ++D+F+     + S
Sbjct: 27  QEARDEIIEKNMRLVWSVVQR----FLNRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFS 82

Query: 332 TYGLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNI 391
           TY +  I   I R +      +V   L+ +  +I++AK EL     R PT  EI   + I
Sbjct: 83  TYAVPMIIGEIQRFLRDDGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGI 142

Query: 392 SPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDS 451
           SPE      +A +   S+H        +    IT +D + + ++      ++AL   ++ 
Sbjct: 143 SPEDVVLAQEAVRLPTSIHETVYENDGDP---ITLLDQIADADEASW-FDKIALKKAIEE 198

Query: 452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500
           L  +E L++  R+      D+T  E+A  L IS+  + + E K L  +K
Sbjct: 199 LDERERLIVYLRYYK----DQTQSEVASRLGISQVQMSRLEKKILQHIK 243

>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 = 44.5 bits (106), Expect = 3e-05
 Identities = 13/40 (32%), Positives = 19/40 (47%)

Query: 235 VQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRA 274
            + K++L K  GR PT  E+A+   +S   V    E  R 
Sbjct: 117 RKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRL 156

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

 Score =  159 bits (403), Expect = 1e-42
 Identities = 93/301 (30%), Positives = 158/301 (52%), Gaps = 13/301 (4%)

Query: 219 TEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDV-ELAEATNMSAAQVKKCLE------- 270
           T  TW    +   K + +    + +++ R    + ++ E T ++  QVK           
Sbjct: 311 TSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEA 370

Query: 271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRL 330
             R A+ ++++ NLRLV+ + KKY      G +F DL Q G  GL+ A+D+FE +R ++ 
Sbjct: 371 KARRAKKEMVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 427

Query: 331 STYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGV 389
           STY  +WIR AI RS+   + T R+P  +     ++ R   ++L E+ R PT EE+ + +
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERM 487

Query: 390 NISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQRQPALLRLALDDV 448
            +  ++ R+V+K +K  +S+ +  G  ++    + I D       +      LR A  DV
Sbjct: 488 LMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDV 547

Query: 449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL 508
           L  L  +E+ V+R RFG+D   D TL E+    +++RE +R+ E K L KL+HP+R + L
Sbjct: 548 LAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVL 607

Query: 509 R 509
           R
Sbjct: 608 R 608

>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 =  153 bits (389), Expect = 1e-41
 Identities = 103/386 (26%), Positives = 170/386 (44%), Gaps = 24/386 (6%)

Query: 132 GEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKNEDEKVVTKTRKTDSKDEHEKIEK 191
           G +E       G      +     ++S    +    +E  +V   T + +  D   K+E+
Sbjct: 65  GPLEADLLPEEGLLEEEEEELSLPKVSTSDPVRQYLHEIGQVPLLTLE-EEIDLARKVEE 123

Query: 192 LVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWL-FKLMQPMKVFVQVKEQLQKDLGREPT 250
            +      ++   LD + ++            +        K   +  E++   L   P 
Sbjct: 124 GMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPK 183

Query: 251 DVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQA 310
           +++                  G AAR  LI+ NLRLV+ + KKY      G  F DL Q 
Sbjct: 184 ELKRY----------LHIAREGEAARQHLIEANLRLVVSIAKKYTG---RGLSFLDLIQE 230

Query: 311 GVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAK 369
           G +GLI A+++FE KRRF+ STY  +WIR AI R++   + T R+P  +     ++ R  
Sbjct: 231 GNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTA 290

Query: 370 LELLFELKRVPTDEEIIQ--GVNISPERYREVMKASKPILSLHSRHGVTQEE---FINGI 424
            +L  EL R P+ EEI +  G     +R  E +K ++  +SL +  G   E+   + + I
Sbjct: 291 RQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIG--DEKDSFYGDFI 348

Query: 425 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNIS 484
            D +          +LL   L+  L  L  +E++V++ R GL    + TL E+     ++
Sbjct: 349 PDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVT 408

Query: 485 REMVRKHEVKGLMKLK-HPTRVDYLR 509
           RE +R+ E K L KLK H +R   LR
Sbjct: 409 RERIRQIENKALRKLKYHESRTRKLR 434

>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 =  151 bits (382), Expect = 7e-41
 Identities = 103/379 (27%), Positives = 164/379 (43%), Gaps = 32/379 (8%)

Query: 158 SLDKRIELRKNEDEKVVTKTRKTDSKDEHEKIEKLVREYSYSTDLVSL--------DWKK 209
           +L+  +     E E +  +  + D           VR+Y +    V L          +K
Sbjct: 46  ALEDDLLDLPEEGEGLDLEEEEEDLPIPKISTSDPVRQYLHEIGQVPLLTLEEEVELARK 105

Query: 210 MKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDV-----ELAEATNMSAAQ 264
           ++                   ++  V+ K      +   P        +  E  +     
Sbjct: 106 VEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVEEIDQKLKS 165

Query: 265 VKKCLEV-------GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLIT 317
           + K  +        G AAR  LI+ NLRLV+ + KKY      G  F DL Q G +GLI 
Sbjct: 166 LPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTG---RGLSFLDLIQEGNQGLIR 222

Query: 318 AIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESVRGEIQRAKLELLFEL 376
           A+++FE KRRF+ STY  +WIR AI R++   + T R+P  +     ++ R   +L  EL
Sbjct: 223 AVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQEL 282

Query: 377 KRVPTDEEIIQ--GVNISPERYREVMKASKPILSLHSRHGVTQEE---FINGITDVDGVE 431
            R PT EEI +  G     +R  E +K ++  +SL +  G   E+   + + I D     
Sbjct: 283 GREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIG--DEKDSFYGDFIPDEHLPS 340

Query: 432 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH 491
             +    +LL   L+  L  L  +E++V++ R GL    + TL E+     ++RE +R+ 
Sbjct: 341 PVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQI 400

Query: 492 EVKGLMKLK-HPTRVDYLR 509
           E K L KLK H +R   LR
Sbjct: 401 ENKALRKLKYHESRTRKLR 419

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

 Score =  136 bits (346), Expect = 2e-37
 Identities = 57/234 (24%), Positives = 90/234 (38%), Gaps = 16/234 (6%)

Query: 272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLS 331
            +  R +LI   L LV  +     +        +DL   GV GLI A+D    +   R  
Sbjct: 10  NQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAE 69

Query: 332 TYGLFWIRHAII---RSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQG 388
            Y    I+ AI    RS+           +      I+    +L  +L R PTDEE+ + 
Sbjct: 70  AYIKLRIKGAIYDYLRSL-----DFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKE 124

Query: 389 VNISPERYREVMKASKP--ILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALD 446
           + IS E   + +       ILSL         ++   I     VE E  ++   L   + 
Sbjct: 125 LGISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIPSSTNVEEEVIKR--ELTEKVK 182

Query: 447 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500
           + +  L  +E LVI+  F      +    E+A  L  S   V + + K L +L+
Sbjct: 183 EAVSKLPEREKLVIQLIFYE----ELPAKEVAKILETSVSRVSQLKAKALERLR 232

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

 Score = 42.9 bits (102), Expect = 8e-05
 Identities = 15/41 (36%), Positives = 26/41 (63%)

Query: 236 QVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAAR 276
           +V E+L++ LGREPTD E+A+   +S  ++ K L+    + 
Sbjct: 103 EVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSY 143

>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 = 97.3 bits (242), Expect = 4e-23
 Identities = 59/187 (31%), Positives = 92/187 (49%), Gaps = 6/187 (3%)

Query: 226 KLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLR 285
           K++   ++      + + D           ++      +       G AAR  LI+ NLR
Sbjct: 62  KILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLR 121

Query: 286 LVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS 345
           LV+ + KKY      G  F DL Q G +GLI A+++FE KRRF+ STY  +WIR AI R+
Sbjct: 122 LVVSIAKKYTG---RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRA 178

Query: 346 MTVSSFT-RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQ--GVNISPERYREVMKA 402
           +   + T R+P  +     ++ R   +L  EL R P+ EEI +  G     +R  E +K 
Sbjct: 179 IADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKI 238

Query: 403 SKPILSL 409
           ++  +SL
Sbjct: 239 AQEPVSL 245

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B Length = 99

 Score = 74.8 bits (184), Expect = 8e-17
 Identities = 31/71 (43%), Positives = 44/71 (61%)

Query: 439 ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 498
             LR A  DVL  L  +E+ V+R RFG+D   D TL E+    +++RE +R+ E K L K
Sbjct: 7   ESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRK 66

Query: 499 LKHPTRVDYLR 509
           L+HP+R + LR
Sbjct: 67  LRHPSRSEVLR 77

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2 Length = 87

 Score = 73.2 bits (180), Expect = 2e-16
 Identities = 31/71 (43%), Positives = 48/71 (67%)

Query: 439 ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 498
            L+R  L+ VL +L P+E++V+R R+GL     +TL E+    N++RE +R+ EVK L K
Sbjct: 6   MLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRK 65

Query: 499 LKHPTRVDYLR 509
           L+HP+R  YL+
Sbjct: 66  LRHPSRSKYLK 76

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2 Length = 68

 Score = 68.8 bits (169), Expect = 5e-15
 Identities = 28/63 (44%), Positives = 41/63 (65%)

Query: 447 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506
           DVL  L  +E+ V+R RFG+D   D TL E+    +++RE +R+ E K L KL+HP+R +
Sbjct: 1   DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 60

Query: 507 YLR 509
            LR
Sbjct: 61  VLR 63

>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 = 74.9 bits (184), Expect = 6e-15
 Identities = 52/194 (26%), Positives = 89/194 (45%), Gaps = 17/194 (8%)

Query: 161 KRIELRKNEDEKVVTKTRKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTE 220
           K+  L   + + +V   R     D     E+L+ +       +               T 
Sbjct: 148 KQFRLVPKQFDYLVNSMR--VMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE--TS 203

Query: 221 HTWLFKLMQPMKVFVQVKEQLQKDLGREPTDV-ELAEATNMSAAQVKKC---LEVG---- 272
            TW    +   K + +    + +++ R    + ++ E T ++  QVK     + +G    
Sbjct: 204 DTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKA 263

Query: 273 RAARNKLIKHNLRLVLFVIKKYFQDFAN-GPRFQDLCQAGVKGLITAIDRFEPKRRFRLS 331
           R A+ ++++ NLRLV+ + KKY     N G +F DL Q G  GL+ A+D+FE +R ++ S
Sbjct: 264 RRAKKEMVEANLRLVISIAKKY----TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 319

Query: 332 TYGLFWIRHAIIRS 345
           TY  +WIR AI RS
Sbjct: 320 TYATWWIRQAITRS 333

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A* Length = 73

 Score = 63.2 bits (154), Expect = 5e-13
 Identities = 24/67 (35%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 444 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK-HP 502
            L+  L  L  +E++V++ R GL    + TL E+     ++RE +R+ E K L KLK H 
Sbjct: 3   ELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHE 62

Query: 503 TRVDYLR 509
           +R   LR
Sbjct: 63  SRTRKLR 69

>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 = 55.6 bits (133), Expect = 3e-08
 Identities = 72/550 (13%), Positives = 141/550 (25%), Gaps = 189/550 (34%)

Query: 62  QKRRENSRKRL--------ERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTS- 112
            K   +   RL        E +   F +E     L ++Y    + ++   +  P++ T  
Sbjct: 57  SKDAVSGTLRLFWTLLSKQEEMVQKFVEEV----LRINYKFLMSPIKTEQR-QPSMMTRM 111

Query: 113 -----EVKYADGVV--KRGRQRRKRIGEVEKK------SDDV-------SGKPVVRNQVK 152
                +  Y D  V  K    R +   ++ +       + +V       SGK  V   V 
Sbjct: 112 YIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVC 171

Query: 153 RPKRLSLDKRIEL------------RKNEDEKVV--------------------TKTRKT 180
                    +++               N  E V+                    +   K 
Sbjct: 172 L------SYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL 225

Query: 181 DSKDEHEKIEKLVREYSYSTDLVSLD-------WKKMKIP-PVLSSTEHTWLFKLMQPMK 232
                  ++ +L++   Y   L+ L        W    +   +L +T    +   +    
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAAT 285

Query: 233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIK 292
                 +     L  +     L +  +     + +  EV        +  N    L +I 
Sbjct: 286 TTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPR--EV--------LTTNP-RRLSIIA 334

Query: 293 KYFQDFANGPRFQDLCQAGVKGLITAIDRF-------EPKRRFR------------LSTY 333
           +  +D      + +        L T I+         E ++ F                 
Sbjct: 335 ESIRDGLA--TWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILL 392

Query: 334 GLFWIRHAIIRSMTVSSFTRVPFGLESVRGEIQRAKL-------------ELLFELKRVP 380
            L W             F  +   +  V  ++ +  L              +  ELK   
Sbjct: 393 SLIW-------------FDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKL 439

Query: 381 TDE-----EIIQGVNI---------SP------------------ERYREVMKASKPILS 408
            +E      I+   NI          P                  E    +       L 
Sbjct: 440 ENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLD 499

Query: 409 LH-----SRHGVTQEEFINGITDVDG---------VENENQRQPALLRLALDDVLDSLKP 454
                   RH  T       I +             +N+ + +    RL ++ +LD L  
Sbjct: 500 FRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYE----RL-VNAILDFLPK 554

Query: 455 KESLVIRQRF 464
            E  +I  ++
Sbjct: 555 IEENLICSKY 564

>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 = 52.9 bits (126), Expect = 2e-07
 Identities = 60/393 (15%), Positives = 114/393 (29%), Gaps = 137/393 (34%)

Query: 186 HEKIEKLVREYSYSTDLVS---------LDWKKMK--IPPVLSSTE--HT---------- 222
           H   E    +Y Y  D++S          D K ++     +LS  E  H           
Sbjct: 6   HMDFETGEHQYQYK-DILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGT 64

Query: 223 ----WLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNK 278
               W     Q   V   V+E L+ +         L         Q      +    R++
Sbjct: 65  LRLFWTLLSKQEEMVQKFVEEVLRINYKF------LMSPIKTEQRQPSMMTRMYIEQRDR 118

Query: 279 LIKHNLRLVLFVIKKYFQDFANGPRFQD-------LCQA---------GVKG-----L-I 316
           L   N      V  KY     N  R Q        L +          GV G     + +
Sbjct: 119 LYNDNQ-----VFAKY-----NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVAL 168

Query: 317 TAIDRFEPKRRFRLSTYGLFWIR-------HAIIRSMT------VSSFTRVPFGLESVRG 363
                ++ + +     + +FW+          ++  +         ++T       +++ 
Sbjct: 169 DVCLSYKVQCKM---DFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL 225

Query: 364 EIQRAKLEL--LFELKRVPT---------DEEIIQGVNIS-----PERYREVM-----KA 402
            I   + EL  L + K             + +     N+S       R+++V        
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAAT 285

Query: 403 SKPILSLHSRHGVTQEE-------FIN-GITDV--------------------DGVE-NE 433
           +  I   H    +T +E       +++    D+                    DG+   +
Sbjct: 286 TTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD 345

Query: 434 NQRQPALLRL--ALDDVLDSLKPKESLVIRQRF 464
           N +     +L   ++  L+ L+P E    R+ F
Sbjct: 346 NWKHVNCDKLTTIIESSLNVLEPAE---YRKMF 375

>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 = 44.8 bits (105), Expect = 6e-05
 Identities = 65/458 (14%), Positives = 125/458 (27%), Gaps = 145/458 (31%)

Query: 38  KSNNQALFSPQEQIPLPIETPKRHQKRRENSRKRLERVKGVFSDEASPCTLDVD--YNEA 95
             N  +       I L I + +  + RR    K  E            C L +    N  
Sbjct: 210 DPNWTSRSDHSSNIKLRIHSIQ-AELRRLLKSKPYEN-----------CLLVLLNVQNAK 257

Query: 96  AAKLENIY-KLSPAVTTSEVKYADGVVKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVKRP 154
           A    N+  K+   +TT               R K++      +D +S            
Sbjct: 258 AWNAFNLSCKI--LLTT---------------RFKQV------TDFLSA--------ATT 286

Query: 155 KRLSLDKRIE-LRKNEDEKVVTK---TRKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKM 210
             +SLD     L  +E + ++ K    R  D   E                 +S+  + +
Sbjct: 287 THISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRR---------LSIIAESI 337

Query: 211 KIPPVLSSTEHTWLF-------KLMQPMKVFVQVKEQLQKDLGRE--------PTDVELA 255
           +          TW         KL   ++  +     L+    R+        P    + 
Sbjct: 338 RDGL------ATWDNWKHVNCDKLTTIIESSL---NVLEPAEYRKMFDRLSVFPPSAHIP 388

Query: 256 EAT------NMSAAQV--------KKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANG 301
                    ++  + V        K  L   +   + +   ++ L L             
Sbjct: 389 TILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLEL------------- 435

Query: 302 PRFQDLCQAGVKGLITAIDRFEPKRRF--------RLSTYGLFWI-RHAIIRSMT--VSS 350
            + +   +  +   I  +D +   + F         L  Y    I  H         ++ 
Sbjct: 436 -KVKLENEYALHRSI--VDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTL 492

Query: 351 FTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLH 410
           F  V      +  +I+            + T +++        + Y+  +  + P     
Sbjct: 493 FRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQL--------KFYKPYICDNDPKY--- 541

Query: 411 SRHGVTQEEFINGITD-VDGVENENQRQPA--LLRLAL 445
                  E  +N I D +  +E          LLR+AL
Sbjct: 542 -------ERLVNAILDFLPKIEENLICSKYTDLLRIAL 572

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	513
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	100.0
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	100.0
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	100.0
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	100.0
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	99.97
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	99.96
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	99.86
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	99.86
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	99.82
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.63
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.62
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	99.51
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.49
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	99.32
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	99.29
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	99.29
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	99.19
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	98.92
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	98.73
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	98.7
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	98.67
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	98.59
3c57_A	95	Two component transcriptional regulatory protein;	98.58
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	98.57
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	98.57
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	98.5
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	98.47
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	98.44
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	98.29
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	97.97
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	97.92
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	97.87
2q0o_A	236	Probable transcriptional activator protein TRAR; h	97.38
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	97.34
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	97.19
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	97.11
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.93
1yio_A	208	Response regulatory protein; transcription regulat	96.66
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	96.55
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	96.25
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	96.1
3c3w_A	225	Two component transcriptional regulatory protein;	95.69
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	95.11
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	95.06
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	94.99
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	93.44
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	92.39
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	92.05
2gwr_A	238	DNA-binding response regulator MTRA; two-component	91.87
2oqr_A	230	Sensory transduction protein REGX3; response regul	91.54
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	91.28
1u78_A	141	TC3 transposase, transposable element TC3 transpos	91.26
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	91.22
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	90.94
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	90.8
1ys7_A	233	Transcriptional regulatory protein PRRA; response	90.52
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	90.13
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	89.41
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	89.14
3q9s_A	249	DNA-binding response regulator; DNA binding protei	88.98
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	88.43
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	88.34
2hqr_A	223	Putative transcriptional regulator; phosporylation	88.27
3r0a_A	123	Putative transcriptional regulator; structural gen	88.23
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	87.83
1sfx_A	109	Conserved hypothetical protein AF2008; structural	87.8
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	87.58
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	87.58
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	87.0
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	86.95
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	86.89
3r0j_A	250	Possible two component system response transcript	86.32
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	86.07
2w25_A	150	Probable transcriptional regulatory protein; trans	86.05
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	85.92
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	85.84
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	85.69
2gxg_A	146	146AA long hypothetical transcriptional regulator;	85.53
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	85.52
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	85.44
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	85.37
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	85.31
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	85.26
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	85.04
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	84.97
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	84.8
1ku9_A	152	Hypothetical protein MJ223; putative transcription	84.57
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	84.42
3frw_A	107	Putative Trp repressor protein; structural genomic	84.29
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	84.16
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	84.15
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	84.13
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	83.83
2nnn_A	140	Probable transcriptional regulator; structural gen	83.44
3jth_A	98	Transcription activator HLYU; transcription factor	83.31
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	83.19
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	83.11
2k27_A	159	Paired box protein PAX-8; paired domain, solution	83.09
3iwf_A	107	Transcription regulator RPIR family; transcription	82.97
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	82.76
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	82.73
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	82.65
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	82.59
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	82.52
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	82.45
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	82.44
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	82.4
2pex_A	153	Transcriptional regulator OHRR; transcription regu	82.27
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	82.19
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	82.15
3mn2_A	108	Probable ARAC family transcriptional regulator; st	82.04
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	81.96
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	81.92
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	81.81
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	81.58
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	81.47
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	81.4
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	81.38
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	81.36
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	81.35
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	81.34
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	81.2
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	81.1
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	80.97
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	80.73
3nqo_A	189	MARR-family transcriptional regulator; structural	80.7
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	80.58
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	80.57
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	80.42
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	80.4
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	80.35
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	80.32
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	80.15
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	80.05

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

Probab=100.00  E-value=2.6e-53  Score=450.83  Aligned_cols=313  Identities=29%  Similarity=0.411  Sum_probs=274.4

Q ss_pred             cCCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHH------------------HHHHHhCCCCCHHHHHH--
Q 010308          197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKE------------------QLQKDLGREPTDVELAE--  256 (513)
Q Consensus       197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~------------------~l~~~l~r~p~~~e~A~--  256 (513)
                      ..+.|.+++||++|+++|+||++||+.|++.|+.+..+.....                  .....+++.|+..+|+.  
T Consensus        90 ~~~~d~~~~Yl~ei~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (438)
T 1l9z_H           90 VSTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPK  169 (438)
T ss_pred             CCCCChHHHHHHHhccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccch
Confidence            4677999999999999999999999999999998754432211                  11223566787777642  


Q ss_pred             ----------HccCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcC
Q 010308          257 ----------ATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKR  326 (513)
Q Consensus       257 ----------~~~~s~e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~k  326 (513)
                                ..+++...|.....+|..|+++||.+|+++|+++|++|.   +++.+++|||||||||||+|+++|||++
T Consensus       170 ~~~~~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~---~~g~~aeDLIQEg~IgL~kAvekFDp~k  246 (438)
T 1l9z_H          170 TVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVEKFEYKR  246 (438)
T ss_pred             hhhhhhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHhcCccc
Confidence                      124555677777888999999999999999999999999   7899999999999999999999999999


Q ss_pred             CCccchHHHHHHHHHHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcC--CCHHHHHHHHHhc
Q 010308          327 RFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVN--ISPERYREVMKAS  403 (513)
Q Consensus       327 G~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lg--is~e~v~~~l~~~  403 (513)
                      |++|+|||+||||++|.++|+ +.+.+++|.|+...+++++++.+.+.+.+||.|+.+|||+.+|  +++++|..+++..
T Consensus       247 G~rFsTYA~~wIR~~I~~~i~~~~R~irlp~~~~~~l~~lrr~~r~l~~~lgr~pt~eeiA~~l~~~v~~e~V~~~~~~~  326 (438)
T 1l9z_H          247 RFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIA  326 (438)
T ss_pred             CCChHHHHHHHHHHHHHHHHHHhcchhccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhc
Confidence            999999999999999999999 8899999999999999999999999999999999999999999  9999999999999


Q ss_pred             cCcccccCCCCCchh-hhhccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC
Q 010308          404 KPILSLHSRHGVTQE-EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN  482 (513)
Q Consensus       404 ~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg  482 (513)
                      ...+|||.+.+++++ .+.+.+.+....+|++.....++...|..+|+.||++|+.||.+||||+|++++|++|||+.||
T Consensus       327 ~~~~SLd~~~~~d~d~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~ereR~VI~LRygL~~~e~~TleEIAe~Lg  406 (438)
T 1l9z_H          327 QEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFG  406 (438)
T ss_pred             ccccccccccccccchhhhhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCCCCHHHHHHHHC
Confidence            999999988755433 3444455544455777777778889999999999999999999999999989999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHh-Ccchhhhhhhcc
Q 010308          483 ISREMVRKHEVKGLMKLK-HPTRVDYLRQHM  512 (513)
Q Consensus       483 ISrerVRqi~~rALkKLR-~~~~~~~L~~yl  512 (513)
                      ||+++|||++.+|++||| ++.+...|+.|+
T Consensus       407 IS~erVRqi~~RAlkKLR~~~~~~~~l~~yl  437 (438)
T 1l9z_H          407 VTRERIRQIENKALRKLKYHESRTRKLRDFL  437 (438)
T ss_pred             cCHHHHHHHHHHHHHHHHHhHhhHHHHHHhh
Confidence            999999999999999999 888889999986

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

Probab=100.00  E-value=3.4e-53  Score=449.82  Aligned_cols=313  Identities=30%  Similarity=0.415  Sum_probs=265.5

Q ss_pred             cCCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHH------------------HHHHhCCCCCHHH-----
Q 010308          197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQ------------------LQKDLGREPTDVE-----  253 (513)
Q Consensus       197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~------------------l~~~l~r~p~~~e-----  253 (513)
                      ...+|.+++||++|+.+|+||++||.+|++.++.+..+......                  ....+++.|+..+     
T Consensus        75 ~~~~d~~~~Yl~ei~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (423)
T 2a6h_F           75 ISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPK  154 (423)
T ss_dssp             CTTHHHHHHHHHHHHHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTTH
T ss_pred             cCCCcHHHHHHHHhcccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhhh
Confidence            45679999999999999999999999999999986433322111                  0112334555333     


Q ss_pred             ----HHH---HccCCHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcC
Q 010308          254 ----LAE---ATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKR  326 (513)
Q Consensus       254 ----~A~---~~~~s~e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~k  326 (513)
                          |+.   +++++...|.....+|..|+++||.+|+++|+++|++|.   ++|.+++|||||||+|||+|+++|||++
T Consensus       155 ~~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~---~~~~~~eDLiQEg~igL~kav~kFd~~~  231 (423)
T 2a6h_F          155 TVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVEKFEYKR  231 (423)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTC---TTTSCHHHHHHHHHHHHHHHHHHCCTTS
T ss_pred             hhhhhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHhcCccc
Confidence                222   234555666667778899999999999999999999998   7899999999999999999999999999


Q ss_pred             CCccchHHHHHHHHHHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcC--CCHHHHHHHHHhc
Q 010308          327 RFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVN--ISPERYREVMKAS  403 (513)
Q Consensus       327 G~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lg--is~e~v~~~l~~~  403 (513)
                      |++|+|||+||||++|.++|. +.+.+++|.|+.+.+++++++.+.+.+.+||.|+.+|||+.+|  +++++|..+++..
T Consensus       232 g~~FstYa~~wIr~~i~~~i~~~~r~ir~p~~~~~~~~~lrr~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~~~~~~~  311 (423)
T 2a6h_F          232 RFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIA  311 (423)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHccceeeccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHHHHHhc
Confidence            999999999999999999999 8999999999999999999999999999999999999999999  9999999999999


Q ss_pred             cCcccccCCCCCchh-hhhccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC
Q 010308          404 KPILSLHSRHGVTQE-EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN  482 (513)
Q Consensus       404 ~~~~SLd~~~~~~~~-e~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg  482 (513)
                      ...+|||.+.+++++ .+.+.+.+....+|++.....++...|..+|+.||++|+.||.+||||+|++++|++|||+.||
T Consensus       312 ~~~~Sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~~~~~L~~aL~~L~~rer~Vl~lr~~L~~~e~~Tl~EIA~~lg  391 (423)
T 2a6h_F          312 QEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFG  391 (423)
T ss_dssp             SCCEESSCBCSSSSSCBGGGSSCCSSSCCHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTCC-----CHHHHSSS
T ss_pred             cCCcccccccCCCCccchhhhhccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHC
Confidence            999999988755433 3455555544456777777788889999999999999999999999999989999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHh-Ccchhhhhhhcc
Q 010308          483 ISREMVRKHEVKGLMKLK-HPTRVDYLRQHM  512 (513)
Q Consensus       483 ISrerVRqi~~rALkKLR-~~~~~~~L~~yl  512 (513)
                      ||+++|||++.+|++||| ++.+...|+.|+
T Consensus       392 iS~erVrqi~~rAl~kLR~~~~~~~~l~~~l  422 (423)
T 2a6h_F          392 VTRERIRQIENKALRKLKYHESRTRKLRDFL  422 (423)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHHTTSSSSCC
T ss_pred             cCHHHHHHHHHHHHHHHHhhhhhhHHHHHhh
Confidence            999999999999999999 888888899886

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

Probab=100.00  E-value=2.6e-41  Score=373.80  Aligned_cols=246  Identities=33%  Similarity=0.539  Sum_probs=226.7

Q ss_pred             HHHHHHHHhHHH---HHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHH
Q 010308          264 QVKKCLEVGRAA---RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRH  340 (513)
Q Consensus       264 ~L~~~~~gd~~A---r~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~  340 (513)
                      .+.++..|+..|   ++.||.+|+++|+++|++|.   +++.+++||+||||+|||+++++||+.+|++|+||++||||+
T Consensus       361 Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~---~~~~~aeDlvQE~fi~l~~a~~~fd~~~g~~Fstyl~~~irn  437 (613)
T 3iyd_F          361 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYT---NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ  437 (613)
T ss_dssp             HHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSS---TTSSCSTTTTHHHHHHHHHHTTSCCTTSSSCSTTTHHHHHHH
T ss_pred             HHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHcCccccCcHHHHHHHHHHH
Confidence            466678899887   99999999999999999998   789999999999999999999999999999999999999999


Q ss_pred             HHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-
Q 010308          341 AIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-  418 (513)
Q Consensus       341 aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-  418 (513)
                      +|.++++ +.+++|+|.|+.+.+++++++...+.+++||.||++|||+.+|+++++++.++.....++||+.+.+.+.+ 
T Consensus       438 ~i~~~lr~~~r~~rip~~~~~~~~k~~r~~~~l~~~~gr~pt~eela~~l~~~~~~v~~~~~~~~~~~sld~~~~~~~~~  517 (613)
T 3iyd_F          438 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS  517 (613)
T ss_dssp             HHHHHTTTSCSSSCCCSHHHHTTTTTTTTTTTTTTTTCSCCCTTTTTTTSSCCSSHHHHHHHHSCCCCCSSCCCSSSSSC
T ss_pred             HHHHHHHhcCcceeCcHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhccCCcccCCCCCCCCCc
Confidence            9999999 88999999999999999999999999999999999999999999999999999999999999998765444 


Q ss_pred             hhhccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010308          419 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  498 (513)
Q Consensus       419 e~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkK  498 (513)
                      .+.+.+.+....+|++.....++...|..+|+.||++++.||.|+||+++.+++|++|||+.||||+++|++++++|+++
T Consensus       518 ~l~d~i~d~~~~~p~~~~~~~e~~~~l~~aL~~Lp~~er~Vl~Lr~~~~~~e~~s~~EIA~~lgis~~tVk~~~~rAl~k  597 (613)
T 3iyd_F          518 HLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK  597 (613)
T ss_dssp             CGGGSCCCSSSCCHHHHHHHHTTSSSHHHHTTSSCHHHHHHHHHHHTSSSCCCCSTTGGGTTTSSCSSHHHHHHHHHHTT
T ss_pred             cHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            34455555555567777777777888999999999999999999999988799999999999999999999999999999


Q ss_pred             HhCcchhhhhhhcc
Q 010308          499 LKHPTRVDYLRQHM  512 (513)
Q Consensus       499 LR~~~~~~~L~~yl  512 (513)
                      ||++.+...|+.|+
T Consensus       598 LR~~~~~~~l~~~l  611 (613)
T 3iyd_F          598 LRHPSRSEVLRSFL  611 (613)
T ss_dssp             TTSCSSSCSSTTCC
T ss_pred             hhCcchhhHHHHHh
Confidence            99999999999886

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

Probab=100.00  E-value=2e-36  Score=299.58  Aligned_cols=210  Identities=31%  Similarity=0.464  Sum_probs=129.6

Q ss_pred             cCCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHH-HHHHHH--HHH-----------------------hCCCCC
Q 010308          197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFV-QVKEQL--QKD-----------------------LGREPT  250 (513)
Q Consensus       197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~-~~~~~l--~~~-----------------------l~r~p~  250 (513)
                      ..++|++++||++|+++|+||++||++|++.|+.+.... .+....  +..                       ...+|+
T Consensus         3 ~~~~d~~~~yl~~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~   82 (245)
T 3ugo_A            3 HMTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPK   82 (245)
T ss_dssp             --CCHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHH
T ss_pred             CCCCCcHHHHHHHcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccch
Confidence            357899999999999999999999999999999876533 222110  000                       136788


Q ss_pred             HHHHHHHccCCH----HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcC
Q 010308          251 DVELAEATNMSA----AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKR  326 (513)
Q Consensus       251 ~~e~A~~~~~s~----e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~k  326 (513)
                      ..+||.+.+++.    ..|.+...||..|++.||..|+++|+++|++|.   +++.+++||+||||+|||+|+++|||++
T Consensus        83 ~~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~---~~~~~aeDLvQegfi~L~~a~~~fd~~~  159 (245)
T 3ugo_A           83 TVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVEKFEYKR  159 (245)
T ss_dssp             HHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGT---TSSSCHHHHHHHHHHHHHHHHHHCCGGG
T ss_pred             hHHHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHc---CCCCcHHHHHHHHHHHHHHHHHHcCccc
Confidence            899999988753    456677889999999999999999999999998   7889999999999999999999999999


Q ss_pred             CCccchHHHHHHHHHHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcC--CCHHHHHHHHHhc
Q 010308          327 RFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVN--ISPERYREVMKAS  403 (513)
Q Consensus       327 G~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lg--is~e~v~~~l~~~  403 (513)
                      |++|+||++||||++|+++++ +.+.+++|.++.+.++++..+.+.|...+|+.||.+|||+.||  ||+++|...+..+
T Consensus       160 g~~F~tya~~~ir~~i~~~ir~~~r~~r~p~~l~e~i~~l~~~~~~L~~~~~~~ps~~EIAe~Lg~~is~~tVk~~l~~a  239 (245)
T 3ugo_A          160 RFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIA  239 (245)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHTC-------------------------------------------------------
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHH
Confidence            999999999999999999999 8889999999999999999999999999999999999999999  9999999999988


Q ss_pred             cCcccc
Q 010308          404 KPILSL  409 (513)
Q Consensus       404 ~~~~SL  409 (513)
                      +..+||
T Consensus       240 r~~lsl  245 (245)
T 3ugo_A          240 QEPVSL  245 (245)
T ss_dssp             ------
T ss_pred             hhccCC
Confidence            877775

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

Probab=99.97  E-value=6.1e-31  Score=253.06  Aligned_cols=224  Identities=23%  Similarity=0.249  Sum_probs=188.6

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccc
Q 010308          272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSF  351 (513)
Q Consensus       272 d~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~  351 (513)
                      +..|++.|+..|.++|+.+|++|..+++++.+++||+|||+++||+++++||+.+|.+|+||+++||++.+.++++... 
T Consensus        10 ~~~a~~~l~~~~~~~v~~~a~~~~~~~~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~~~~~~~~d~~r~~~-   88 (239)
T 1rp3_A           10 NQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLRSLD-   88 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHHTSS-
T ss_pred             cchHHHHHHHHhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHhcC-
Confidence            3458999999999999999999974334678999999999999999999999999999999999999999999999332 


Q ss_pred             cccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhcc--CcccccCCCCCchhhhhccccCCCC
Q 010308          352 TRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK--PILSLHSRHGVTQEEFINGITDVDG  429 (513)
Q Consensus       352 iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~--~~~SLd~~~~~~~~e~~d~l~d~~~  429 (513)
                       +.|.+.....+++.++...+...+|+.|+.+++|+.+|++++++..++....  ...|++.+...+++...+. .+. .
T Consensus        89 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~-~~~-~  165 (239)
T 1rp3_A           89 -FGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDFARDYSEL-IPS-S  165 (239)
T ss_dssp             -TTCHHHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-GGG-S
T ss_pred             -ccchHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccCCCccccccccCCCcccccc-cCC-C
Confidence             5788888899999999999999999999999999999999999998876543  3456665432222211222 222 3


Q ss_pred             CCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          430 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       430 ~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      .+|++.....+....|..+|+.||++++.||.++|    .+++|++|||+.||||.++|++++.+|+++||+..
T Consensus       166 ~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~~V~~~~~ra~~~Lr~~l  235 (239)
T 1rp3_A          166 TNVEEEVIKRELTEKVKEAVSKLPEREKLVIQLIF----YEELPAKEVAKILETSVSRVSQLKAKALERLREML  235 (239)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHH----TSCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence            34566667777888999999999999999999999    68999999999999999999999999999999654

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

Probab=99.96  E-value=3.5e-31  Score=254.58  Aligned_cols=222  Identities=27%  Similarity=0.398  Sum_probs=53.1

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010308          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (513)
Q Consensus       265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r  344 (513)
                      +..+..||..|++.|+..|.++|+++|++|.   ++..+++||+||||++||+++++||+.+|..|+||+++|+++.+.+
T Consensus        19 ~~~~~~gd~~a~~~l~~~~~~~v~~~~~~~~---~~~~~aeDl~Qe~~l~l~~~~~~~~~~~~~~f~~~l~~i~~~~~~d   95 (243)
T 1l0o_C           19 IRRSQEGDQEARDEIIEKNMRLVWSVVQRFL---NRGYEADDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQR   95 (243)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHcCCHHHHHHHHHHhHHHHHHHHHHHh---ccCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHH
Confidence            3445678999999999999999999999998   6778999999999999999999999999889999999999999999


Q ss_pred             HHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhh---hh
Q 010308          345 SMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE---FI  421 (513)
Q Consensus       345 aI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e---~~  421 (513)
                      ++++...+++|.++.....+++++...+....|+.|+.++++..+|++.+.+...+.......|++.+..+++++   +.
T Consensus        96 ~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~  175 (243)
T 1l0o_C           96 FLRDDGTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLL  175 (243)
T ss_dssp             ----CCCCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHHC-------------------
T ss_pred             HHHhcCCccCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHhccccCccccccccCCcccchh
Confidence            999555889999999999999999999999999999999999999999999998888777777887764322211   11


Q ss_pred             ccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010308          422 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       422 d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR  500 (513)
                      +.       .+++.....+....|..+|+.||++++.||.++|    ++++|++|||+.||||.++|++++.+|+++||
T Consensus       176 ~~-------~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr  243 (243)
T 1l0o_C          176 DQ-------IADADEASWFDKIALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLEKKILQHIK  243 (243)
T ss_dssp             -------------------------------------------------------------------------------
T ss_pred             hc-------cCcchhHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            11       1222333445667889999999999999999999    68999999999999999999999999999997

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

Probab=99.86  E-value=3.6e-21  Score=179.83  Aligned_cols=176  Identities=15%  Similarity=0.129  Sum_probs=134.0

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHH
Q 010308          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (513)
Q Consensus       263 e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI  342 (513)
                      +.+..+..||..|++.|+..|.+.|+.+|.+|.   + ..+.+|++||+|+++|+++++|++..  .|.+|++.++++.+
T Consensus        12 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~-~~~aeDl~Qe~~l~~~~~~~~~~~~~--~~~~~l~~i~~n~~   85 (194)
T 1or7_A           12 VLVERVQKGDQKAFNLLVVRYQHKVASLVSRYV---P-SGDVPDVVQEAFIKAYRALDSFRGDS--AFYTWLYRIAVNTA   85 (194)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTS---C-GGGHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHH
T ss_pred             HHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHc---C-HHhHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHH
Confidence            345667789999999999999999999999998   7 88999999999999999999999865  59999999999999


Q ss_pred             HHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhh
Q 010308          343 IRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFI  421 (513)
Q Consensus       343 ~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~  421 (513)
                      .++++ +.+....                            ..+.           .. .    ...++..         
T Consensus        86 ~d~~R~~~~~~~~----------------------------~~~~-----------~~-~----~~~~~~~---------  112 (194)
T 1or7_A           86 KNYLVAQGRRPPS----------------------------SDVD-----------AI-E----AENFESG---------  112 (194)
T ss_dssp             HHHHHHHTTCCTH----------------------------HHHH-----------HH-H----HHSCCSS---------
T ss_pred             HHHHHHHhccCcc----------------------------cccc-----------cc-c----ccccccc---------
Confidence            99998 3221110                            0000           00 0    0000000         


Q ss_pred             ccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          422 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       422 d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                      ..+.+  ..+|++.....+....|..+|+.||++++.||.++|    .+++|++|||+.||||..+|++++.+|+++||+
T Consensus       113 ~~~~~--~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~  186 (194)
T 1or7_A          113 GALKE--ISNPENLMLSEELRQIVFRTIESLPEDLRMAITLRE----LDGLSYEEIAAIMDCPVGTVRSRIFRAREAIDN  186 (194)
T ss_dssp             CC----------CEEEHHHHHHHHHHHHHHSCHHHHHHHHHHH----TTCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             ccccC--CCChHHHHHHHHHHHHHHHHHHhCCHHHHHHhHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            00111  122344444556677889999999999999999999    789999999999999999999999999999996


Q ss_pred             cc
Q 010308          502 PT  503 (513)
Q Consensus       502 ~~  503 (513)
                      ..
T Consensus       187 ~l  188 (194)
T 1or7_A          187 KV  188 (194)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}

Probab=99.82  E-value=4.4e-20  Score=166.84  Aligned_cols=151  Identities=15%  Similarity=0.142  Sum_probs=102.7

Q ss_pred             CCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH-hccccccccchhHHHHHHHHHHHHHHHHhCCC
Q 010308          301 GPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLESVRGEIQRAKLELLFELKRV  379 (513)
Q Consensus       301 g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~-~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~  379 (513)
                      |.+++|++||||++||+++++||+.+ .+|.||+++++++.+.++++ +.+..+.+..                      
T Consensus         1 g~daeDl~Qe~~~~l~~~~~~~~~~~-~~f~~~l~~i~~n~~~d~~r~~~~~~~~~~~----------------------   57 (164)
T 3mzy_A            1 GAEKEDLVQEGILGLLKAIKFYDETK-SSFSSFAFLCIRREMISAIRKANTQKHMVLN----------------------   57 (164)
T ss_dssp             ----CTTHHHHHHHHHHHHHHCCTTT-SCHHHHHHHHHHHHHHHHHHHHHHCC---------------------------
T ss_pred             CCcHHHHHHHHHHHHHHHHHHhCccC-CChHHHhHHHHHHHHHHHHHHhhcccchhhH----------------------
Confidence            56899999999999999999999987 78999999999999999998 4322222100                      


Q ss_pred             CCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchh-hhhc---cccCCCCCCchhhhHHHHHHHHHHHHHh-cCCH
Q 010308          380 PTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFIN---GITDVDGVENENQRQPALLRLALDDVLD-SLKP  454 (513)
Q Consensus       380 PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~-e~~d---~l~d~~~~~~ee~~~~~~l~~~L~~aL~-~L~~  454 (513)
                                               ..++++....++.. .+.+   ........+|++.....+....|..+|. .||+
T Consensus        58 -------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~~~L~~  112 (164)
T 3mzy_A           58 -------------------------EALKTNAILEDSAYFDDEGHNINNYKSSESNPEEAYLLKEEIEEFKKFSENNFSK  112 (164)
T ss_dssp             ---------------------------------------------------------CHHHHHHHHHHHHHHHHHHHSCH
T ss_pred             -------------------------HHhhhhhhhccCCCCCcccchhhhhcccCCCHHHHHHHHHHHHHHHHHHHhhCCH
Confidence                                     00111111000000 0000   0011222345666677778888999999 9999


Q ss_pred             HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          455 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       455 rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      +++.||. +|    .+++|++|||+.||||.++|++++.+|+++||+...
T Consensus       113 ~~r~v~~-~~----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~  157 (164)
T 3mzy_A          113 FEKEVLT-YL----IRGYSYREIATILSKNLKSIDNTIQRIRKKSEEWIK  157 (164)
T ss_dssp             HHHHHHH-HH----TTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHH-HH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            9999999 67    689999999999999999999999999999997654

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=99.63  E-value=9.4e-18  Score=153.72  Aligned_cols=140  Identities=10%  Similarity=0.040  Sum_probs=114.7

Q ss_pred             HHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHhccccccc
Q 010308          276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVP  355 (513)
Q Consensus       276 r~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~~r~iRlP  355 (513)
                      ++.|+..|.+.|+.+|.++.   ++..+.+|++||+|+.+|++.++|++..  .|.+|++..+++.+.++++...     
T Consensus         3 f~~l~~~~~~~l~~~~~~~~---~~~~~AeDlvQe~fl~~~~~~~~~~~~~--~~~~wl~~ia~n~~~d~~R~~~-----   72 (157)
T 2lfw_A            3 LGQQLAPHLPFLRRYGRALT---GSQNQGDKYVRATLEAIVAAPDQFPRDV--DPRLGLYRMFQGIWASANADGE-----   72 (157)
T ss_dssp             GGGGTGGGGGGGTTTGGGTT---SCHHHHHHHHHHHHHTTTTCGGGCCCSS--CTTHHHHHHHHHHHHHHTTTTS-----
T ss_pred             HHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHHcCCCC--cHHHHHHHHHHHHHHHHhhccC-----
Confidence            56788999999999999998   6788999999999999999999999753  6999999999999888776200     


Q ss_pred             cchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCCCCCchhh
Q 010308          356 FGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQ  435 (513)
Q Consensus       356 ~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~~~~~ee~  435 (513)
                                               .                       .    +.       .     .+ .   .   
T Consensus        73 -------------------------~-----------------------~----~~-------~-----~e-~---~---   81 (157)
T 2lfw_A           73 -------------------------A-----------------------Q----TS-------Q-----SD-A---E---   81 (157)
T ss_dssp             -------------------------C-----------------------C----CC-------C-----CS-C---S---
T ss_pred             -------------------------c-----------------------c----cC-------C-----cc-h---H---
Confidence                                     0                       0    00       0     00 0   0   


Q ss_pred             hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       436 ~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                          +....|..+|+.||+++++||.|+|    .+++|++|||+.||||..+|++.+.+|+++||+...
T Consensus        82 ----~~~~~l~~~l~~Lp~~~r~vl~L~~----~~g~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~  142 (157)
T 2lfw_A           82 ----GTEAVARARLARMTPLSRQALLLTA----MEGFSPEDAAYLIEVDTSEVETLVTEALAEIEKQTR  142 (157)
T ss_dssp             ----SSSSTTTTTTTTSCTTHHHHHTTTS----SSCCCHHHHHHTTTSCHHHHHHHHHHHHHHHHTTSS
T ss_pred             ----HHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence                0112466788999999999999999    789999999999999999999999999999998654

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

Probab=99.62  E-value=1.4e-15  Score=156.49  Aligned_cols=81  Identities=40%  Similarity=0.686  Sum_probs=76.8

Q ss_pred             HHHHHHHHhH---HHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHH
Q 010308          264 QVKKCLEVGR---AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRH  340 (513)
Q Consensus       264 ~L~~~~~gd~---~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~  340 (513)
                      .+.++..|+.   .|++.||..|+++|+++|++|.   +++.+++||+||||+|||+++++|++.+|++|+||++|||+|
T Consensus       252 l~~~~~~gd~~~~~A~~~L~~~~~~~v~~~a~~~~---~~~~~aeDlvQe~~i~l~~a~~~f~~~~g~~f~twl~~iirn  328 (339)
T 1sig_A          252 INRRMSIGEAKARRAKKEMVEANLRLVISIAKKYT---NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ  328 (339)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTST---TSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHH
T ss_pred             HHHHHHhccccchhhhHHHHHHHHHHHHHHHHHHh---cCCCCHhHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHH
Confidence            4566778998   9999999999999999999999   789999999999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q 010308          341 AIIRSMT  347 (513)
Q Consensus       341 aI~raI~  347 (513)
                      +|.++++
T Consensus       329 ~~~~~lr  335 (339)
T 1sig_A          329 AITRSIA  335 (339)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999998

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B

Probab=99.51  E-value=3.3e-14  Score=121.80  Aligned_cols=77  Identities=40%  Similarity=0.625  Sum_probs=72.6

Q ss_pred             hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010308          436 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  512 (513)
Q Consensus       436 ~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl  512 (513)
                      +...++...|..+|+.|||+|+.||.+|||++|.+++|++|||+.||||.++|++++.+|+++||+......|+.|+
T Consensus         4 ~~~~el~~~l~~aL~~Lp~reR~Vi~Lry~l~~~e~~s~~EIA~~lgiS~~tVr~~~~rAlkkLR~~~~~~~l~~~~   80 (99)
T 3t72_q            4 ATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSGS   80 (99)
T ss_pred             HHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            45667888999999999999999999999998889999999999999999999999999999999999999999886

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.49  E-value=1.2e-14  Score=146.09  Aligned_cols=145  Identities=8%  Similarity=-0.079  Sum_probs=116.6

Q ss_pred             HHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHHh
Q 010308          269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV  348 (513)
Q Consensus       269 ~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~~  348 (513)
                      .+|+..+++.|+..|.+.++.+|.+|.   ++..+.+|++||.|+.+|+..++|++.  ..|.+|++..++|.+.+.++.
T Consensus        16 ~~g~~~~f~~l~~~~~~~l~~~a~~~~---~~~~~AeD~vQe~fl~~~~~~~~~~~~--~~~~~wL~~ia~n~~~d~~r~   90 (286)
T 3n0r_A           16 PRGSEMHLLARLAPHLPYIRRYARALT---GDQATGDHYVRVALEALAAGELVLDAN--LSPRVALYRVFHAIWLSSGAQ   90 (286)
T ss_dssp             ----CCCHHHHHGGGHHHHHHHHHHHH---SCHHHHHHHHHHHHHHHHTTSSCCCSS--SCHHHHHHHHHHHHHSCTTC-
T ss_pred             CCCCcCCHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHhCchhcCCC--cChHHHHHHHHHHHHHhhccc
Confidence            467788999999999999999999999   778899999999999999999999974  369999999888877654431


Q ss_pred             ccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhhhhccccCCC
Q 010308          349 SSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD  428 (513)
Q Consensus       349 ~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e~~d~l~d~~  428 (513)
                      ..                                                            ...           ....
T Consensus        91 ~~------------------------------------------------------------~~~-----------~~~~   99 (286)
T 3n0r_A           91 LE------------------------------------------------------------VGH-----------DQGL   99 (286)
T ss_dssp             ---------------------------------------------------------------CC-----------CCCC
T ss_pred             cc------------------------------------------------------------cCC-----------Cccc
Confidence            00                                                            000           0000


Q ss_pred             CCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          429 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       429 ~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                          +       ....|..+|++||+++|.||.|+|    .+++|++|||..||+|..+|+....+|+++|+....
T Consensus       100 ----~-------~~~~l~~al~~Lp~~~R~v~~L~~----~eg~s~~EIA~~lgis~~tVks~l~rA~~~Lr~~l~  160 (286)
T 3n0r_A          100 ----H-------AGDDAAQRLMRIAPRSRQAFLLTA----LEGFTPTEAAQILDCDFGEVERLIGDAQAEIDAELA  160 (286)
T ss_dssp             ----C-------TTSHHHHHHHHHSCHHHHHHHHHH----TTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCC
T ss_pred             ----c-------hHHHHHHHHHhCCHHHeeEEEEEe----eCCCCHHHHHHHhCcCHHHHHHHHHHHHhhhhccCC
Confidence                0       012478899999999999999999    899999999999999999999999999999997654

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=99.32  E-value=1.9e-12  Score=102.31  Aligned_cols=65  Identities=42%  Similarity=0.711  Sum_probs=61.3

Q ss_pred             HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010308          448 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  512 (513)
Q Consensus       448 aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl  512 (513)
                      +|+.|||+|++||.++|||+|++++|++|||+.||+|.++|++++.+|+++||.......+..|+
T Consensus         2 ~l~~L~~~er~il~l~~~l~~~~g~s~~eIA~~lgis~~tV~~~~~ra~~kLr~~~~~~~~~~~~   66 (68)
T 2p7v_B            2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL   66 (68)
T ss_dssp             CSCCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCCGGGGGSCTT
T ss_pred             HHHcCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            46789999999999999999889999999999999999999999999999999999988888875

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=99.29  E-value=6.4e-12  Score=104.37  Aligned_cols=70  Identities=41%  Similarity=0.735  Sum_probs=64.3

Q ss_pred             HHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010308          443 LALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  512 (513)
Q Consensus       443 ~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl  512 (513)
                      ..|..+|+.||++|+.||.++|+|+|.+++|++|||+.||||.++|++++.+|+++||.......+..|+
T Consensus        10 ~~l~~~l~~L~~~er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~kLr~~l~~~~~~~~~   79 (87)
T 1tty_A           10 EELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLKSLL   79 (87)
T ss_dssp             SHHHHHHTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTBSSHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence            3578899999999999999999888779999999999999999999999999999999988887777663

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=99.29  E-value=1.5e-12  Score=104.44  Aligned_cols=68  Identities=35%  Similarity=0.565  Sum_probs=55.6

Q ss_pred             HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh-Ccchhhhhhhcc
Q 010308          445 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK-HPTRVDYLRQHM  512 (513)
Q Consensus       445 L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR-~~~~~~~L~~yl  512 (513)
                      |..+|+.||++|+.||.++|+|+|.+++|++|||+.||+|.++|++++.+|+++|| .....+.|+.|+
T Consensus         4 l~~~l~~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~~~~~~~~~~~~   72 (73)
T 1ku3_A            4 LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFL   72 (73)
T ss_dssp             CSSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTC---------
T ss_pred             HHHHHHhCCHHHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHhhHHHHHHhh
Confidence            45678899999999999999888779999999999999999999999999999999 998888888875

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=99.19  E-value=5.6e-11  Score=99.39  Aligned_cols=73  Identities=21%  Similarity=0.276  Sum_probs=66.4

Q ss_pred             CCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          428 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       428 ~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ...++++.+...+....|..+|..||++++.||.++|    .+++|++|||+.||||..+|++++.+|+++||....
T Consensus        14 ~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~   86 (92)
T 3hug_A           14 PEQSTPDEVNAALDRLLIADALAQLSAEHRAVIQRSY----YRGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQ   86 (92)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHH----TSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCchHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            3445777788888999999999999999999999999    789999999999999999999999999999997654

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=98.92  E-value=2.1e-09  Score=84.31  Aligned_cols=64  Identities=8%  Similarity=-0.021  Sum_probs=54.2

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      +....|..+|+.|||+++.||.++|    ..++|++|||+.||+|..+|+++..+|+++||.......
T Consensus         4 e~~~~l~~~l~~L~~~~r~il~l~~----~~g~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~l~~~~   67 (70)
T 2o8x_A            4 EDLVEVTTMIADLTTDQREALLLTQ----LLGLSYADAAAVCGCPVGTIRSRVARARDALLADAEPDD   67 (70)
T ss_dssp             HHHHHHHTTTTSSCHHHHHHHHHHH----TSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHC------
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhhccc
Confidence            3456788899999999999999999    689999999999999999999999999999998765443

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

Probab=98.73  E-value=1.2e-08  Score=83.40  Aligned_cols=75  Identities=13%  Similarity=0.060  Sum_probs=68.6

Q ss_pred             HHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH
Q 010308          268 CLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT  347 (513)
Q Consensus       268 ~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~  347 (513)
                      +..|+..|++.|+..|.+.++.+|.++.   ++..+.+|++||+|+.+|+..+.|++.  ..|.+|++..+++.+.+.++
T Consensus         6 ~~~g~~~af~~l~~~~~~~l~~~~~~~~---~~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~R   80 (87)
T 1h3l_A            6 STAERSARFERDALEFLDQMYSAALRMT---RNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSYR   80 (87)
T ss_dssp             CHHHHHHHHHHHHHHTHHHHHHHHHHHH---SCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTCC
T ss_pred             cCcccHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHHHhcCCC--ccHHHHHHHHHHHHHHHHHH
Confidence            3578999999999999999999999998   678899999999999999999999975  37999999999999988776

>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3

Probab=98.70  E-value=3.5e-08  Score=86.01  Aligned_cols=65  Identities=22%  Similarity=0.146  Sum_probs=58.2

Q ss_pred             hHHHHHHHHHHHHH-hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          436 RQPALLRLALDDVL-DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       436 ~~~~~l~~~L~~aL-~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      .+..+....+..+| ..||++++.||.++|    .+++|++|||+.||+|..+|+.+..+|+++||....
T Consensus         9 ~e~~~~~~~l~~~l~~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~   74 (113)
T 1xsv_A            9 LVKTLRMNYLFDFYQSLLTNKQRNYLELFY----LEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEK   74 (113)
T ss_dssp             HHHHHHHHHHHHHHGGGSCHHHHHHHHHHH----TSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            44556667788899 999999999999998    789999999999999999999999999999997544

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

Probab=98.67  E-value=4.5e-08  Score=83.77  Aligned_cols=77  Identities=21%  Similarity=0.160  Sum_probs=68.9

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010308          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (513)
Q Consensus       265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r  344 (513)
                      +..+..|+..|++.|+..|.+.|+.+|.++ .   +..+.+|++||+|+.+|+.+.+|++.  ..|.+|++..+++.+.+
T Consensus        15 ~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~-~---~~~~aeD~vQe~fl~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d   88 (112)
T 2o7g_A           15 ALSAAKGNGRALEAFIKATQQDVWRFVAYL-S---DVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVAD   88 (112)
T ss_dssp             HHHHHTTCHHHHHHHHHHHHHHHHHHHHHH-S---CHHHHHHHHHHHHHHHHHHGGGCCCS--SCHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHh-C---CHHHHHHHHHHHHHHHHHHHHhcCCC--CCHHHHHHHHHHHHHHH
Confidence            555678999999999999999999999987 3   56789999999999999999999964  36999999999999999


Q ss_pred             HHH
Q 010308          345 SMT  347 (513)
Q Consensus       345 aI~  347 (513)
                      +++
T Consensus        89 ~~R   91 (112)
T 2o7g_A           89 HIR   91 (112)
T ss_dssp             HTC
T ss_pred             HHH
Confidence            887

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=98.59  E-value=2.8e-08  Score=82.70  Aligned_cols=64  Identities=19%  Similarity=0.128  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          439 ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       439 ~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      ......+..++..||++|++||.+++     +++|.+|||+.||||..+|+.+..++++||+...+.+.
T Consensus        17 ~~~~~~l~~~l~~Lt~~e~~vl~l~~-----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~~~l   80 (91)
T 2rnj_A           17 GSHMKKRAELYEMLTEREMEILLLIA-----KGYSNQEIASASHITIKTVKTHVSNILSKLEVQDRTQA   80 (91)
T ss_dssp             --------CTGGGCCSHHHHHHHHHH-----TTCCTTHHHHHHTCCHHHHHHHHHHHHHHTTCCSSHHH
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHHH
Confidence            34455688899999999999999954     79999999999999999999999999999998766553

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=98.58  E-value=7.8e-08  Score=80.94  Aligned_cols=63  Identities=19%  Similarity=0.143  Sum_probs=47.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      +....|..+|..||++|++||.+++     +++|.+|||+.||||..+|+.+..++++||+...+.+.
T Consensus        16 ~~~~~l~~~l~~Lt~~e~~vl~l~~-----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~~~l   78 (95)
T 3c57_A           16 PRGSHMQDPLSGLTDQERTLLGLLS-----EGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQA   78 (95)
T ss_dssp             -----------CCCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCCC-
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            3455678899999999999999975     78999999999999999999999999999998766543

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=98.57  E-value=1.1e-07  Score=76.28  Aligned_cols=61  Identities=21%  Similarity=0.229  Sum_probs=54.2

Q ss_pred             HHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010308          443 LALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  508 (513)
Q Consensus       443 ~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L  508 (513)
                      ..|..++..||++|++||.+++     .++|.+|||+.||+|..+|+++..++++||+.....+.+
T Consensus         8 ~~l~~~l~~L~~~e~~vl~l~~-----~g~s~~eIA~~l~is~~tV~~~~~r~~~kl~~~~~~~l~   68 (79)
T 1x3u_A            8 NDIRARLQTLSERERQVLSAVV-----AGLPNKSIAYDLDISPRTVEVHRANVMAKMKAKSLPHLV   68 (79)
T ss_dssp             HHHHHHHHHHCHHHHHHHHHHT-----TTCCHHHHHHHTTSCHHHHHHHHHHHHHHTTCCSHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHHHHH
Confidence            3577888999999999999943     799999999999999999999999999999987765543

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=98.57  E-value=3.5e-10  Score=111.55  Aligned_cols=159  Identities=10%  Similarity=-0.003  Sum_probs=111.0

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHH----HHHHHHHHHHHhhcCCcCCCccchHHHHHHH
Q 010308          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLC----QAGVKGLITAIDRFEPKRRFRLSTYGLFWIR  339 (513)
Q Consensus       264 ~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLI----QEG~iGLirAvekFDp~kG~rFSTYA~~wIR  339 (513)
                      .+.++-.+|..+.+.+...|.+++..+.....   .......|+.    ||.++.+|+....|++..  .|.+|++..++
T Consensus        87 ll~~i~p~D~~~~~~~~~~~~~fi~~l~~~~~---~~~~~~~dl~~~~~qe~fl~~~~~~~~~~~~~--~~~~WL~~ia~  161 (258)
T 3clo_A           87 IYRRIHPEDLVEKRLMEYKFFQKTFSMSPGER---LKYRGRCRLRMMNEKGVYQYIDNLVQIMQNTP--AGNVWLIFCLY  161 (258)
T ss_dssp             HHTTBCHHHHHHHHHHHHHHHHHHTTSCHHHH---TTEEEEEEEEEECTTSCEEEEEEEEEEEEECT--TSCEEEEEEEE
T ss_pred             HHHhCChHHHHHHHHHHHHHHHHHHhcCHHhc---cCCeeeEEeecCCcCHHHHHHHHhHHhcCCCC--chHHHHHHHHH
Confidence            44455567788899999999999999988765   4566677886    999999999999998654  68887765444


Q ss_pred             HHHHHHHHhccccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhccCcccccCCCCCchhh
Q 010308          340 HAIIRSMTVSSFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE  419 (513)
Q Consensus       340 ~aI~raI~~~r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLd~~~~~~~~e  419 (513)
                      +.+.+..+.      .                                                    .+.       +.
T Consensus       162 n~~~d~~r~------~----------------------------------------------------~~~-------~~  176 (258)
T 3clo_A          162 SLSADQRPE------Q----------------------------------------------------GIY-------AT  176 (258)
T ss_dssp             EECSCCCCC------S----------------------------------------------------SCC-------CE
T ss_pred             HHHcchhhh------h----------------------------------------------------HHH-------HH
Confidence            322211000      0                                                    000       00


Q ss_pred             hhccccCCCCCCchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010308          420 FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL  499 (513)
Q Consensus       420 ~~d~l~d~~~~~~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKL  499 (513)
                      .... .....  ....        .+..++..||++|++||.+++     +++|.+|||+.||+|..+|+.+..+|++||
T Consensus       177 ~~~~-~~~~~--~~~~--------~~~~~~~~L~~~erevl~L~~-----~G~s~~EIA~~L~iS~~TVk~~l~ra~~kL  240 (258)
T 3clo_A          177 ITQM-ERGEV--ETLS--------LSEEHRNILSEREKEILRCIR-----KGLSSKEIAATLYISVNTVNRHRQNILEKL  240 (258)
T ss_dssp             EEET-TTTEE--EECC--------CHHHHTTSSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHT
T ss_pred             HHhh-ccccc--ccch--------hhHHHHccCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            0000 00000  0000        145667899999999999986     799999999999999999999999999999


Q ss_pred             hCcchhhhh
Q 010308          500 KHPTRVDYL  508 (513)
Q Consensus       500 R~~~~~~~L  508 (513)
                      |...+.+..
T Consensus       241 ~~~~~~~~~  249 (258)
T 3clo_A          241 SVGNSIEAC  249 (258)
T ss_dssp             TCSSHHHHH
T ss_pred             cCCCHHHHH
Confidence            987665443

>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3

Probab=98.50  E-value=1.8e-07  Score=81.53  Aligned_cols=61  Identities=23%  Similarity=0.165  Sum_probs=54.2

Q ss_pred             HHHHHHHHH-hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010308          441 LRLALDDVL-DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  505 (513)
Q Consensus       441 l~~~L~~aL-~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~  505 (513)
                      ....+..++ ..|||+++.||.++|    .+++|++|||+.||+|..+|+.+..+|+++||.....
T Consensus        11 ~~~~l~~~l~~~L~~~~r~vl~l~y----~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~   72 (113)
T 1s7o_A           11 RMNALFEFYAALLTDKQMNYIELYY----ADDYSLAEIADEFGVSRQAVYDNIKRTEKILETYEMK   72 (113)
T ss_dssp             HHHHHHHHHGGGSCHHHHHHHHHHH----HTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            344577788 899999999999998    6899999999999999999999999999999975543

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=98.47  E-value=7.3e-08  Score=82.46  Aligned_cols=63  Identities=16%  Similarity=0.146  Sum_probs=53.4

Q ss_pred             HHHHHHHHH-hcCCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          441 LRLALDDVL-DSLKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       441 l~~~L~~aL-~~L~~rEr~VL~lRyGL~~---~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      ..+.+..+| +-|+++|+.+|.+||||.+   ..++|+.|||+.+|+|+++|+++ .++|++|....+
T Consensus        24 ~~~~l~~~l~~lLT~~Er~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L~~l~~~~k   90 (101)
T 1jhg_A           24 QNDLHLPLLNLMLTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSLKAAPVELR   90 (101)
T ss_dssp             HTTCHHHHHHHHSCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHHHHSCHHHH
T ss_pred             CHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHHHHccHHHH
Confidence            344566777 5699999999999999964   45699999999999999999999 899999986443

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=98.44  E-value=2e-07  Score=76.29  Aligned_cols=60  Identities=23%  Similarity=0.277  Sum_probs=51.5

Q ss_pred             HHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010308          444 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  508 (513)
Q Consensus       444 ~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L  508 (513)
                      .+..++..|+++|++||.+++     +++|.+|||+.||||..+|+.+..++++||+...+.+..
T Consensus        14 ~~~~~~~~Lt~~e~~vl~l~~-----~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~~~l~   73 (82)
T 1je8_A           14 TTERDVNQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAA   73 (82)
T ss_dssp             ---CCGGGSCHHHHHHHHHHT-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSSHHHHH
T ss_pred             HHHHHHccCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHHHHH
Confidence            356778899999999999954     789999999999999999999999999999987765543

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=98.29  E-value=8.9e-07  Score=69.78  Aligned_cols=59  Identities=29%  Similarity=0.241  Sum_probs=50.0

Q ss_pred             HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010308          445 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  508 (513)
Q Consensus       445 L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L  508 (513)
                      +...+..||++|+.||.+.+     +++|.+|||+.||+|..+|+++..+++++|+...+.+.+
T Consensus         5 ~~~~~~~L~~~e~~il~~~~-----~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~~~~~~~   63 (74)
T 1fse_A            5 EFQSKPLLTKREREVFELLV-----QDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAV   63 (74)
T ss_dssp             ---CCCCCCHHHHHHHHHHT-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHHHHH
T ss_pred             cCCCCCCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHH
Confidence            44567789999999999943     789999999999999999999999999999987765543

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=97.97  E-value=1.4e-05  Score=66.58  Aligned_cols=56  Identities=25%  Similarity=0.281  Sum_probs=47.6

Q ss_pred             HHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          447 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       447 ~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      .....||++|++||.+.+     +++|.+|||+.||||..+|+.+..++++||.-..+.+.
T Consensus        25 ~~~~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TV~~~~~~i~~Klgv~~r~~l   80 (90)
T 3ulq_B           25 KEQDVLTPRECLILQEVE-----KGFTNQEIADALHLSKRSIEYSLTSIFNKLNVGSRTEA   80 (90)
T ss_dssp             ----CCCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCSSHHHH
T ss_pred             ccccCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHHH
Confidence            446789999999999987     79999999999999999999999999999987665443

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=97.92  E-value=1e-05  Score=61.47  Aligned_cols=49  Identities=22%  Similarity=0.255  Sum_probs=43.7

Q ss_pred             HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      |+|++||.+ |    .+++|.+|||+.||+|..+|+.+..++++||+...+.+.
T Consensus         1 ~re~~vl~l-~----~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~~~~~l   49 (61)
T 2jpc_A            1 LRERQVLKL-I----DEGYTNHGISEKLHISIKTVETHRMNMMRKLQVHKVTEL   49 (61)
T ss_dssp             CHHHHHHHH-H----HTSCCSHHHHHHTCSCHHHHHHHHHHHHHHHTCSSHHHH
T ss_pred             CHHHHHHHH-H----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHCCCCHHHH
Confidence            479999999 5    479999999999999999999999999999998766544

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=97.87  E-value=2.1e-05  Score=66.88  Aligned_cols=53  Identities=30%  Similarity=0.321  Sum_probs=47.7

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      ..||++|++||.+.+     +++|.+|||+.||||..+|+....++++||.-..+.+.
T Consensus        33 ~~Lt~re~~Vl~l~~-----~G~s~~EIA~~L~iS~~TV~~~l~ri~~KLgv~~r~el   85 (99)
T 1p4w_A           33 KRLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIAL   85 (99)
T ss_dssp             SSCCHHHHHHHHHHH-----HTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHHHH
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHHH
Confidence            569999999999966     69999999999999999999999999999987666543

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=97.38  E-value=0.00028  Score=68.05  Aligned_cols=52  Identities=21%  Similarity=0.138  Sum_probs=47.1

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      .||++|++||.+.+     +++|.+|||++||||..||+.+..++++||.-..+.+.
T Consensus       175 ~Lt~~e~~vl~~~~-----~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~~~~~~  226 (236)
T 2q0o_A          175 MLSPREMLCLVWAS-----KGKTASVTANLTGINARTVQHYLDKARAKLDAESVPQL  226 (236)
T ss_dssp             SCCHHHHHHHHHHH-----TTCCHHHHHHHHCCCHHHHHHHHHHHHHHHTCSSHHHH
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCHHHH
Confidence            59999999999965     79999999999999999999999999999987666543

>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A*

Probab=97.34  E-value=0.00032  Score=67.58  Aligned_cols=52  Identities=21%  Similarity=0.240  Sum_probs=46.7

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      .||++|++||.+.+     +++|.+|||+.||||..+|+.+..++++||.-..+.+.
T Consensus       173 ~Lt~~e~~vl~~~~-----~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~~~~~~  224 (234)
T 1l3l_A          173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHL  224 (234)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCSSHHHH
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCHHHH
Confidence            49999999999965     79999999999999999999999999999987665443

>3szt_A QCSR, quorum-sensing control repressor; quorum sensing acyl-homoserine lactone, helix-turn-helix, transcription factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas aeruginosa}

Probab=97.19  E-value=0.00051  Score=66.54  Aligned_cols=53  Identities=25%  Similarity=0.330  Sum_probs=47.4

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      ..||++|++||.+..     +++|.+|||+.||||..||+.+..++++||.-..+.+.
T Consensus       174 ~~Lt~re~~vl~~~~-----~G~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~~~~~~  226 (237)
T 3szt_A          174 VRLTARETEMLKWTA-----VGKTYGEIGLILSIDQRTVKFHIVNAMRKLNSSNKAEA  226 (237)
T ss_dssp             CCCCHHHHHHHHHHH-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSSHHHH
T ss_pred             CCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCCHHHH
Confidence            359999999999976     79999999999999999999999999999987665443

>3qp6_A CVIR transcriptional regulator; quorum sensing, agonist, antagonist, LUXR, acylated homoseri lactone, transcription factor; HET: HL6; 2.00A {Chromobacterium violaceum} PDB: 3qp5_A*

Probab=97.11  E-value=0.00063  Score=67.19  Aligned_cols=51  Identities=29%  Similarity=0.245  Sum_probs=46.9

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      .||++|++||.+..     +++|.+|||++||||..||+.+..++++||.-..+.+
T Consensus       197 ~Lt~re~~vl~~~~-----~G~s~~eIA~~l~is~~TV~~~~~~~~~kl~~~~~~~  247 (265)
T 3qp6_A          197 PLSQREYDIFHWMS-----RGKTNWEIATILNISERTVKFHVANVIRKLNANNRTH  247 (265)
T ss_dssp             CCCHHHHHHHHHHH-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSSHHH
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCHHH
Confidence            59999999999987     7999999999999999999999999999998766544

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=96.93  E-value=0.00097  Score=47.25  Aligned_cols=40  Identities=18%  Similarity=0.116  Sum_probs=33.0

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .|++.++..+...|    ..++|..+||+.||||+.+|+.++.+
T Consensus         5 ~l~~~~~~~i~~~~----~~g~s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            5 ALSDTERAQLDVMK----LLNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             CCCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            47888886666666    46899999999999999999988754

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A

Probab=96.66  E-value=0.0062  Score=56.03  Aligned_cols=59  Identities=24%  Similarity=0.335  Sum_probs=50.0

Q ss_pred             HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010308          445 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  508 (513)
Q Consensus       445 L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L  508 (513)
                      +...+..|+++|++|+.+..     .++|.++||+.||+|..+|+.+..+.++||....+.+..
T Consensus       136 ~~~~~~~Lt~rE~~vl~~l~-----~g~s~~~Ia~~l~is~~TV~~~~~~i~~Kl~~~~~~~~i  194 (208)
T 1yio_A          136 LEQLFSSLTGREQQVLQLTI-----RGLMNKQIAGELGIAEVTVKVHRHNIMQKLNVRSLANLV  194 (208)
T ss_dssp             HHHHHHTSCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCSSHHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHH-----cCCcHHHHHHHcCCCHHHHHHHHHHHHHHhCCCCHHHHH
Confidence            34456679999999998865     678999999999999999999999999999876655443

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=96.55  E-value=0.0049  Score=52.51  Aligned_cols=46  Identities=11%  Similarity=0.143  Sum_probs=42.6

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR  500 (513)
                      .+++.-..|-.++|    .+++|..|||+.||||+.+|.+++.+|...+-
T Consensus        18 ~~~~~~~~~A~lyY----v~g~tQ~eIA~~lGiSR~~VsrlL~~Ar~~~~   63 (101)
T 2w7n_A           18 EVGQQTIEIARGVL----VDGKPQATFATSLGLTRGAVSQAVHRVWAAFE   63 (101)
T ss_dssp             CCCHHHHHHHHHHH----TTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            58888899999999    89999999999999999999999999998863

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=96.25  E-value=0.0025  Score=47.14  Aligned_cols=39  Identities=23%  Similarity=0.105  Sum_probs=30.0

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      +++..+.|+.+ |    ..++|..|||+.||||+.+|+++..+|
T Consensus        17 ~~~~~~~i~~l-~----~~g~s~~eIA~~lgis~~TV~~~l~~a   55 (55)
T 2x48_A           17 EDDLVSVAHEL-A----KMGYTVQQIANALGVSERKVRRYLESC   55 (55)
T ss_dssp             HHHHHHHHHHH-H----HTTCCHHHHHHHHTSCHHHHHHHHTC-
T ss_pred             CHHHHHHHHHH-H----HcCCCHHHHHHHHCcCHHHHHHHHHhC
Confidence            34455666666 4    368899999999999999999987654

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A

Probab=96.10  E-value=0.011  Score=54.59  Aligned_cols=53  Identities=26%  Similarity=0.317  Sum_probs=47.0

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      ..|+++|.+|+.+..     +++|.+|||+.+++|..+|+.+..+.++||.-..+.+.
T Consensus       153 ~~Lt~rE~~vl~~l~-----~g~s~~~Ia~~l~is~~TV~~hi~~i~~Kl~~~~r~~l  205 (215)
T 1a04_A          153 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEA  205 (215)
T ss_dssp             GGSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCCSHHHH
T ss_pred             cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHHH
Confidence            359999999999876     67899999999999999999999999999987665543

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=95.69  E-value=0.018  Score=54.17  Aligned_cols=52  Identities=19%  Similarity=0.172  Sum_probs=46.1

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ..|+++|.+||.+..     +++|.+|||+.|++|..||+.+..+.++||.-..+.+
T Consensus       148 ~~LT~rE~~vL~~l~-----~g~s~~eIa~~l~is~~TV~~hi~~l~~KL~~~~r~~  199 (225)
T 3c3w_A          148 SGLTDQERTLLGLLS-----EGLTNKQIADRMFLAEKTVKNYVSRLLAKLGMERRTQ  199 (225)
T ss_dssp             TTSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCCSSCH
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence            469999999998876     6799999999999999999999999999997655543

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=95.11  E-value=0.025  Score=52.90  Aligned_cols=53  Identities=23%  Similarity=0.250  Sum_probs=46.5

Q ss_pred             HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ...|+++|.+||.+..     .++|.++||+.|++|..+|+.+..+.++||.-..+.+
T Consensus       157 ~~~Lt~rE~~vL~~l~-----~g~s~~~Ia~~l~~s~~Tv~~~i~~l~~KL~~~~~~~  209 (225)
T 3klo_A          157 YAKLTKREQQIIKLLG-----SGASNIEIADKLFVSENTVKTHLHNVFKKINAKNRLQ  209 (225)
T ss_dssp             HHTSCHHHHHHHHHHT-----TTCCHHHHHHHTTCCHHHHHHHHHHHTTTSCCSSHHH
T ss_pred             cccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence            3469999999999865     6899999999999999999999999999997665544

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

Probab=95.06  E-value=0.006  Score=67.30  Aligned_cols=38  Identities=18%  Similarity=0.129  Sum_probs=13.3

Q ss_pred             hhcCCCChHHHHHHhcCCCCCCChHHHHHHHHHHhHhH
Q 010308          195 EYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMK  232 (513)
Q Consensus       195 ~~~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~  232 (513)
                      +.+..+|+|+|||++||.+||||.++|+.|++.|+.+.
T Consensus        90 ~~~~~~dpvrmyl~emg~~~ll~~~~e~~~ak~ie~g~  127 (613)
T 3iyd_F           90 EIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGI  127 (613)
T ss_dssp             ---------------C--------CSSSTTTHHHHHHH
T ss_pred             cccCCCCcHHHHHHHhcccccCCchhHHHHHHHHHHhH
Confidence            34567999999999999999999999999999997654

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=94.99  E-value=0.079  Score=50.07  Aligned_cols=64  Identities=23%  Similarity=0.244  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010308          440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  508 (513)
Q Consensus       440 ~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L  508 (513)
                      .........+..|+.+++.|+.+..     .+++..+||..||+|..+|+....++++||.-..+.+.+
T Consensus       187 ~~~~~~~~~l~~L~~r~~~i~~~~~-----~g~~~~eia~~l~~s~~tv~~~l~~i~~kl~~~~~~elv  250 (258)
T 3p7n_A          187 ARRERAAEMLKTLSPRQLEVTTLVA-----SGLRNKEVAARLGLSEKTVKMHRGLVMEKLNLKTSADLV  250 (258)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCSCHHHHH
T ss_pred             HHHHHHHHHHhhcCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHHHH
Confidence            3345667888999999999999876     578999999999999999999999999999877665443

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=93.44  E-value=0.059  Score=38.23  Aligned_cols=25  Identities=8%  Similarity=-0.065  Sum_probs=21.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          470 GDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       470 ~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .+.|..+||+.||||+.+|..++.+
T Consensus        20 ~g~s~~~ia~~lgvs~~Tv~r~l~~   44 (52)
T 1jko_C           20 KGHPRQQLAIIFGIGVSTLYRYFPA   44 (52)
T ss_dssp             TTCCHHHHHHTTSCCHHHHHHHSCT
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4689999999999999999987643

>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nns_A*

Probab=92.39  E-value=0.11  Score=48.06  Aligned_cols=51  Identities=12%  Similarity=-0.019  Sum_probs=43.2

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC---CCHHHHHHHHHHHHHHHhCc
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN---ISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg---ISrerVRqi~~rALkKLR~~  502 (513)
                      .|+++|.+||.+..- +.++..|.++||+.++   +|..+|+.+..+.++||...
T Consensus       145 ~Lt~rE~~vl~~l~~-~~~~~~s~~~Ia~~l~~~~~s~~tv~~~i~~l~~Kl~~~  198 (220)
T 1p2f_A          145 HLPKKEFEILLFLAE-NAGKVVTREKLLETFWEDPVSPRVVDTVIKRIRKAIEDD  198 (220)
T ss_dssp             CCCHHHHHHHHHHHH-TTTSCEEHHHHHHHHCSSCCCTHHHHHHHHHHHHHHCSS
T ss_pred             ecCHHHHHHHHHHHH-CCCceEcHHHHHHHHhCCCCCcchHHHHHHHHHHHHhcc
Confidence            599999999987651 1123599999999999   99999999999999999753

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=92.05  E-value=0.12  Score=41.36  Aligned_cols=41  Identities=12%  Similarity=0.184  Sum_probs=29.6

Q ss_pred             HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      +.++.||.+-.-...++..|..|||+.||||+.+|++++.+
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~   54 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYS   54 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            34566765544333345789999999999999999876544

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=91.87  E-value=0.16  Score=47.78  Aligned_cols=51  Identities=16%  Similarity=0.066  Sum_probs=42.3

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHhCc
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNL-----NISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~L-----gISrerVRqi~~rALkKLR~~  502 (513)
                      .|+++|.+||.+..- +.+...|.+|||+.+     ++|..+|+....+.++||...
T Consensus       153 ~LT~rE~~vL~~l~~-~~~~~~s~~eIa~~lw~~~~~~s~~tV~~hi~~lr~KL~~~  208 (238)
T 2gwr_A          153 SLTPLEFDLLVALAR-KPRQVFTRDVLLEQVWGYRHPADTRLVNVHVQRLRAKVEKD  208 (238)
T ss_dssp             CCCHHHHHHHHHHHH-STTCCBCHHHHHHHHTCCC--CCTHHHHHHHHHHHHHHCSS
T ss_pred             ccCHHHHHHHHHHHH-CCCceecHHHHHHHHcCCCCCCCcccHHHHHHHHHHHhccC
Confidence            599999999987651 112359999999999     999999999999999999753

>2oqr_A Sensory transduction protein REGX3; response regulator, winged-helix-turn-helix, DNA-binding, 3D swapping, two component system; 2.03A {Mycobacterium tuberculosis H37RV}

Probab=91.54  E-value=0.14  Score=47.53  Aligned_cols=51  Identities=14%  Similarity=0.063  Sum_probs=43.4

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHhCc
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNL-----NISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~L-----gISrerVRqi~~rALkKLR~~  502 (513)
                      .|+++|.+||.+-.- +.++..|.+|||+.+     ++|..+|+.+..+.++||...
T Consensus       156 ~Lt~rE~~vL~~l~~-~~~~~~s~~~Ia~~lw~~~~~~s~~tv~~hi~~i~~Kl~~~  211 (230)
T 2oqr_A          156 TLPLKEFDLLEYLMR-NSGRVLTRGQLIDRVWGADYVGDTKTLDVHVKRLRSKIEAD  211 (230)
T ss_dssp             CCCHHHHHHHHHHHH-TTTSCEEHHHHHHHHTSSCCTTHHHHHHHHHHHHHHHHCSS
T ss_pred             ecCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCCCCCCcCHHHHHHHHHHHHhhC
Confidence            599999999987651 123459999999999     999999999999999999753

>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein, ALPH-beta sandwich, winged-helix, helix helix, DNA binding protein; HET: DNA MSE; 1.50A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nnn_A*

Probab=91.28  E-value=0.13  Score=47.38  Aligned_cols=52  Identities=17%  Similarity=0.109  Sum_probs=43.3

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhCcc
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg-----ISrerVRqi~~rALkKLR~~~  503 (513)
                      .|+++|.+||.+..- +.+...|.+|||+.++     +|..+|+.+..+.++||....
T Consensus       151 ~Lt~rE~~vL~~l~~-~~~~~~s~~eIa~~l~~~~~~~s~~tv~~hi~~l~~Kl~~~~  207 (225)
T 1kgs_A          151 DLTKKEYQILEYLVM-NKNRVVTKEELQEHLWSFDDEVFSDVLRSHIKNLRKKVDKGF  207 (225)
T ss_dssp             CCCHHHHHHHHHHHH-TTTSCEEHHHHHHHCC-----CHHHHHHHHHHHHHHHHHTTC
T ss_pred             ecCHHHHHHHHHHHh-CCCcccCHHHHHHHhcCCCCCCCcchHHHHHHHHHHHhhCCC
Confidence            599999999987651 1123499999999998     999999999999999997543

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=91.26  E-value=0.2  Score=43.15  Aligned_cols=40  Identities=18%  Similarity=0.116  Sum_probs=33.4

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .|++.++..|...+    ..++|..+||+.||||+.+|+.+..+
T Consensus         6 ~~s~~~r~~i~~~~----~~G~s~~~ia~~lgis~~Tv~r~~~~   45 (141)
T 1u78_A            6 ALSDTERAQLDVMK----LLNVSLHEMSRKISRSRHCIRVYLKD   45 (141)
T ss_dssp             CCCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             cCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHc
Confidence            47778877776666    46899999999999999999998765

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=91.22  E-value=0.28  Score=39.78  Aligned_cols=42  Identities=17%  Similarity=0.275  Sum_probs=29.4

Q ss_pred             HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010308          455 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       455 rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR  500 (513)
                      .++.||.+......+...|..|||+.||||+.+|++.    |.+|.
T Consensus        11 ~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~----L~~Le   52 (81)
T 1qbj_A           11 QEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRV----LYSLA   52 (81)
T ss_dssp             HHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHH----HHHHH
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHH----HHHHH
Confidence            3555665544333345799999999999999888855    55554

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=90.94  E-value=0.3  Score=40.93  Aligned_cols=42  Identities=19%  Similarity=0.029  Sum_probs=32.9

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  496 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rAL  496 (513)
                      .+++.++.-+...+    ..++|..+||+.||||+.+|+++..+..
T Consensus        17 ~~s~~~r~~i~~~~----~~g~s~~~ia~~lgis~~Tv~~w~~~~~   58 (128)
T 1pdn_C           17 PLPNNIRLKIVEMA----ADGIRPCVISRQLRVSHGCVSKILNRYQ   58 (128)
T ss_dssp             CCCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            46666665555555    3678999999999999999999988754

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=90.80  E-value=0.19  Score=43.84  Aligned_cols=35  Identities=17%  Similarity=0.100  Sum_probs=28.0

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH  491 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi  491 (513)
                      .|+.| .+|+.+-.     +++|+.|||+.+|+|..||.+.
T Consensus        61 aLs~R-~eV~klL~-----~G~syreIA~~~g~S~aTIsRv   95 (119)
T 3kor_A           61 SLSQR-LQVAKMIK-----QGYTYATIEQESGASTATISRV   95 (119)
T ss_dssp             HHHHH-HHHHHHHH-----HTCCHHHHHHHHCCCHHHHHHH
T ss_pred             HHHHH-HHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHH
Confidence            45556 66777754     5799999999999999999863

>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA binding domain, phosphorylation; 1.58A {Mycobacterium tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A

Probab=90.52  E-value=0.13  Score=47.69  Aligned_cols=52  Identities=10%  Similarity=-0.095  Sum_probs=42.2

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhCcc
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg-----ISrerVRqi~~rALkKLR~~~  503 (513)
                      .|+++|.+||.+..- +.+...|.++||+.++     +|..+|+.+..+.++||....
T Consensus       159 ~Lt~rE~~vL~~l~~-g~~~~~s~~~Ia~~l~~~~~~~s~~tv~~hi~~l~~Kl~~~~  215 (233)
T 1ys7_A          159 DLTKREFDLLAVLAE-HKTAVLSRAQLLELVWGYDFAADTNVVDVFIGYLRRKLEAGG  215 (233)
T ss_dssp             CCCHHHHHHHHHHHH-TTTCCBCHHHHHHHHHCCCCC-CCCHHHHHHHHHHHHHHCC-
T ss_pred             ccCHHHHHHHHHHHh-CCCCeEcHHHHHHHhcCcccCCCccCHHHHHHHHHHHhccCC
Confidence            599999999987651 1123499999999998     999999999999999998643

>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=90.13  E-value=0.056  Score=52.77  Aligned_cols=52  Identities=12%  Similarity=0.157  Sum_probs=0.0

Q ss_pred             HHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC--CCHHHHHHHHHHHHHHHh
Q 010308          444 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN--ISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       444 ~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg--ISrerVRqi~~rALkKLR  500 (513)
                      .+...+..|++.++. |...|    +.+.|.+|||+.||  ||.++|+.++.+|++.|.
T Consensus       191 ~l~e~i~~l~~~~~~-L~~~~----~~~ps~~EIAe~Lg~~is~~tVk~~l~~ar~~ls  244 (245)
T 3ugo_A          191 HMVETINKLSRTARQ-LQQEL----GREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVS  244 (245)
T ss_dssp             -----------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHHH-HHHHh----CCCCCHHHHHHHHCCCCCHHHHHHHHHHHhhccC
Confidence            345566778887777 44556    36789999999999  999999999999987763

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=89.41  E-value=0.26  Score=46.53  Aligned_cols=35  Identities=14%  Similarity=0.101  Sum_probs=29.0

Q ss_pred             HHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010308          457 SLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  496 (513)
Q Consensus       457 r~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rAL  496 (513)
                      ..+..+ |    ..++|..|||+.||||+.+|++++..|.
T Consensus        15 ~ria~~-y----~~g~tQ~eIA~~lGiSr~~VSR~L~~A~   49 (192)
T 1zx4_A           15 LRLMRM-K----NDGMSQKDIAAKEGLSQAKVTRALQAAS   49 (192)
T ss_dssp             HHHHHH-H----HTTCCHHHHHHHHTCCHHHHHHHHHHHT
T ss_pred             HHHHHH-H----HcCCCHHHHHHHhCcCHHHHHHHHHHhc
Confidence            344445 5    4689999999999999999999988874

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=89.14  E-value=0.48  Score=41.60  Aligned_cols=43  Identities=16%  Similarity=-0.006  Sum_probs=33.9

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  497 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALk  497 (513)
                      .+++.++.-+...+    ..++|..+||+.||||+.+|+++..+...
T Consensus        32 ~~s~e~r~~iv~~~----~~G~s~~~iA~~lgis~~TV~rw~~~~~~   74 (149)
T 1k78_A           32 PLPDVVRQRIVELA----HQGVRPCDISRQLRVSHGCVSKILGRYYE   74 (149)
T ss_dssp             CCCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            46666666665555    35789999999999999999999887543

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=88.98  E-value=0.23  Score=47.41  Aligned_cols=54  Identities=20%  Similarity=0.121  Sum_probs=44.8

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHhCcchh
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAG-----NLNISREMVRKHEVKGLMKLKHPTRV  505 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~-----~LgISrerVRqi~~rALkKLR~~~~~  505 (513)
                      .|+++|.+||.+..- +.+..+|.+|||+     .+++|..+|+.+..+.++||....+.
T Consensus       182 ~LT~rE~evL~ll~~-g~~~~~s~~eIa~~l~~~~l~~s~~TV~~hi~~lr~KL~~~~~~  240 (249)
T 3q9s_A          182 RLSPKEFDILALLIR-QPGRVYSRQEIGQEIWQGRLPEGSNVVDVHMANLRAKLRDLDGY  240 (249)
T ss_dssp             CCCHHHHHHHHHHHH-STTCCCCHHHHHHHHHTTCSCTTCSHHHHHHHHHHHHHCCCSCC
T ss_pred             ecCHHHHHHHHHHHH-CCCceEcHHHHHHHhcCCCCCCCccCHHHHHHHHHHHhhcCCCC
Confidence            599999999998762 1234599999999     58899999999999999999865443

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=88.43  E-value=0.38  Score=39.25  Aligned_cols=24  Identities=21%  Similarity=0.285  Sum_probs=21.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          471 DRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       471 ~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      +.|..|||+.||||+++|++++.+
T Consensus        30 g~sa~eLAk~LgiSk~aVr~~L~~   53 (82)
T 1oyi_A           30 GATAAQLTRQLNMEKREVNKALYD   53 (82)
T ss_dssp             TEEHHHHHHHSSSCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHH
Confidence            399999999999999999988765

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=88.34  E-value=0.65  Score=37.53  Aligned_cols=27  Identities=7%  Similarity=0.126  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010308          470 GDRTLGEIAGNLNISREMVRKHEVKGL  496 (513)
Q Consensus       470 ~~~Tl~EIA~~LgISrerVRqi~~rAL  496 (513)
                      .+.|..+||..||||+.+|+++..+..
T Consensus        37 ~g~s~~~iA~~~gIs~sTl~rW~k~~~   63 (87)
T 2elh_A           37 DGESKASVARDIGVPESTLRGWCKNED   63 (87)
T ss_dssp             HTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            358999999999999999999986543

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=88.27  E-value=0.14  Score=47.43  Aligned_cols=51  Identities=10%  Similarity=0.049  Sum_probs=42.7

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhCc
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~Lg-----ISrerVRqi~~rALkKLR~~  502 (513)
                      .|+++|.+||.+-.- +.+...|.+|||+.++     +|..+|+.+..+.++||...
T Consensus       143 ~Lt~rE~~vL~~l~~-~~~~~~s~~~Ia~~l~~~~~~~s~~tv~~~i~~lr~KL~~~  198 (223)
T 2hqr_A          143 EVKGKPFEVLTHLAR-HRDQIVSKEQLLDAIWEEPEMVTPNVIEVAINQIRQKMDKP  198 (223)
T ss_dssp             CCCSTTTHHHHHHHH-TCSEEEEHHHHHHHHCCSSCSCGGGTHHHHHHHHHHHHHTT
T ss_pred             ecCHHHHHHHHHHHh-CCCCcCCHHHHHHHhcCCccCCCCcCHHHHHHHHHHHHhcC
Confidence            599999999988651 0112399999999999     99999999999999999854

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=88.23  E-value=0.79  Score=39.45  Aligned_cols=45  Identities=11%  Similarity=0.103  Sum_probs=34.7

Q ss_pred             HHhcCCHHHHHHHhHHhcCCCCCC-CCHHHHHHHhCCCHHHHHHHHHH
Q 010308          448 VLDSLKPKESLVIRQRFGLDGKGD-RTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       448 aL~~L~~rEr~VL~lRyGL~~~~~-~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ..-.|++.+..||..-..-  ..+ .|..|||+.+|+|+++|.+.+.+
T Consensus        20 ~~~gLt~~e~~il~~L~~~--~~~~~t~~eLa~~l~~s~sTV~r~L~~   65 (123)
T 3r0a_A           20 CALNLTKADLNVMKSFLNE--PDRWIDTDALSKSLKLDVSTVQRSVKK   65 (123)
T ss_dssp             HHHTCCHHHHHHHHHHHHS--TTCCEEHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHHC--CCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            4457999999998876531  223 89999999999999999855443

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=87.83  E-value=0.74  Score=40.59  Aligned_cols=42  Identities=19%  Similarity=0.196  Sum_probs=33.2

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ..|++.++.||.+-..   ....|+.|||+.+|+|+.+|+++..+
T Consensus         5 ~~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~   46 (151)
T 2dbb_A            5 RKLDRVDMQLVKILSE---NSRLTYRELADILNTTRQRIARRIDK   46 (151)
T ss_dssp             -CCCHHHHHHHHHHHH---CTTCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred             hhCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4588999999876442   35799999999999999999876544

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=87.80  E-value=1.1  Score=36.15  Aligned_cols=41  Identities=27%  Similarity=0.403  Sum_probs=33.1

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .|++.+..||..-..   ..+.|..|||+.+|+|+.+|++++.+
T Consensus        17 ~l~~~~~~il~~l~~---~~~~s~~ela~~l~is~~tv~~~l~~   57 (109)
T 1sfx_A           17 SFKPSDVRIYSLLLE---RGGMRVSEIARELDLSARFVRDRLKV   57 (109)
T ss_dssp             CCCHHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            478999988876542   35799999999999999999866544

>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20

Probab=87.58  E-value=1.2  Score=37.90  Aligned_cols=52  Identities=17%  Similarity=0.136  Sum_probs=39.9

Q ss_pred             HHHHHHHHhcCCHHHHHHHhHHhcC-CCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          442 RLALDDVLDSLKPKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       442 ~~~L~~aL~~L~~rEr~VL~lRyGL-~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      ...|...+..|++.|+.|......= +....+|..|||+..|+|..+|.+..+
T Consensus         9 ~~~i~~~~~~ls~~e~~ia~yil~~~~~~~~~si~elA~~~~vS~aTv~Rf~k   61 (111)
T 2o3f_A            9 LAIIQSMXHXLPPSERKLADYILAHPHXAIESTVNEISALANSSDAAVIRLCX   61 (111)
T ss_dssp             HHHHHHHGGGSCHHHHHHHHHHHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHhccCCHHHHHHHHHHHHChHHHHhcCHHHHHHHHCCCHHHHHHHHH
Confidence            3457777889999999998776520 011369999999999999999987654

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=87.58  E-value=0.62  Score=46.59  Aligned_cols=36  Identities=22%  Similarity=0.287  Sum_probs=31.5

Q ss_pred             HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010308          458 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  497 (513)
Q Consensus       458 ~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALk  497 (513)
                      .|..++|    .+++|..|||+.||||+.+||+.+..+.+
T Consensus        12 ~ia~l~~----~~~~~~~ela~~l~vS~~tIrRdL~~l~~   47 (315)
T 2w48_A           12 KIAQLYY----EQDMTQAQIARELGIYRTTISRLLKRGRE   47 (315)
T ss_dssp             HHHHHHH----TSCCCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4667777    68899999999999999999999988765

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=87.00  E-value=0.63  Score=35.95  Aligned_cols=40  Identities=5%  Similarity=0.043  Sum_probs=26.9

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      +++....||.+---  +..+.|..|||+.||+|+++|.+++.
T Consensus         8 m~~~~~~IL~~L~~--~~~~~s~~eLA~~lglsr~tv~~~l~   47 (67)
T 2heo_A            8 GDNLEQKILQVLSD--DGGPVAIFQLVKKCQVPKKTLNQVLY   47 (67)
T ss_dssp             -CHHHHHHHHHHHH--HCSCEEHHHHHHHHCSCHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHH--cCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            34445556554321  13579999999999999888886543

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=86.95  E-value=0.55  Score=43.66  Aligned_cols=42  Identities=17%  Similarity=0.090  Sum_probs=32.9

Q ss_pred             cCCHHHHHHHhHHhcC--CCCCCCCHHHHHHHhCCCHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGL--DGKGDRTLGEIAGNLNISREMVRKHE  492 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL--~~~~~~Tl~EIA~~LgISrerVRqi~  492 (513)
                      .|+++|++||.....+  ..+.+.|..|||+.||+|..+|++++
T Consensus         2 ~lt~~q~~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~l   45 (196)
T 3k2z_A            2 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHL   45 (196)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHHH
Confidence            5899999999875422  12357899999999999999887665

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=86.89  E-value=0.93  Score=39.80  Aligned_cols=41  Identities=12%  Similarity=0.159  Sum_probs=32.7

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .|++.++.||.+-..   ....|+.|||+.+|+|+++|+.+..+
T Consensus         2 ~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~   42 (144)
T 2cfx_A            2 KLDQIDLNIIEELKK---DSRLSMRELGRKIKLSPPSVTERVRQ   42 (144)
T ss_dssp             CCCHHHHHHHHHHHH---CSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            378888888876542   35799999999999999999866544

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=86.32  E-value=0.96  Score=42.68  Aligned_cols=50  Identities=16%  Similarity=0.038  Sum_probs=43.6

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHhC
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNL-----NISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~L-----gISrerVRqi~~rALkKLR~  501 (513)
                      .|+++|.+||.+..- +.++..|.++|++.+     +++..+|+.+..+.++||..
T Consensus       176 ~LT~rE~~iL~~l~~-~~~~~~s~~~i~~~lw~~~~~~~~~tv~~~i~~lr~KL~~  230 (250)
T 3r0j_A          176 SLSPTEFTLLRYFVI-NAGTVLSKPKILDHVWRYDFGGDVNVVESYVSYLRRKIDT  230 (250)
T ss_dssp             CCCHHHHHHHHHHHH-TTTCCBCHHHHHHHHTTTSCCSCTHHHHHHHHHHHHHHCC
T ss_pred             ecCHHHHHHHHHHHH-CCCceEcHHHHHHHHcCCCCCCCccCHHHHHHHHHHhhcC
Confidence            599999999988762 224679999999999     88999999999999999975

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=86.07  E-value=1.2  Score=36.14  Aligned_cols=44  Identities=16%  Similarity=0.154  Sum_probs=33.8

Q ss_pred             HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ...|++.+..+|...+.-  ..+.|..|||+.+|+|+.+|++++..
T Consensus        16 ~~~l~~~~~~~l~~l~~~--~~~~t~~ela~~l~is~~tv~~~l~~   59 (109)
T 2d1h_A           16 CYKITDTDVAVLLKMVEI--EKPITSEELADIFKLSKTTVENSLKK   59 (109)
T ss_dssp             HHTCCHHHHHHHHHHHHH--CSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hhcCCHHHHHHHHHHHHc--CCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            357899998887655411  35799999999999999999865543

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=86.05  E-value=1.1  Score=39.53  Aligned_cols=41  Identities=22%  Similarity=0.348  Sum_probs=33.2

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .|++.++.||.+-..   ....|+.|||+.+|+|+++|+++..+
T Consensus         4 ~ld~~~~~iL~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~   44 (150)
T 2w25_A            4 ALDDIDRILVRELAA---DGRATLSELATRAGLSVSAVQSRVRR   44 (150)
T ss_dssp             CCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            488899988876431   35799999999999999999876554

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=85.92  E-value=1.9  Score=36.43  Aligned_cols=51  Identities=10%  Similarity=0.136  Sum_probs=39.0

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          441 LRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       441 l~~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      +...+...+.  .|++.+..||..-+.   ..+.|..|||+.+|+|+.+|.++..+
T Consensus        14 ~~~~~~~~~~~~~l~~~~~~iL~~l~~---~~~~~~~ela~~l~~s~~tvs~~l~~   66 (138)
T 3bpv_A           14 HRVFIGRELGHLNLTDAQVACLLRIHR---EPGIKQDELATFFHVDKGTIARTLRR   66 (138)
T ss_dssp             HHHHHHHHSGGGTCCHHHHHHHHHHHH---STTCBHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            3444555554  489999999887663   36799999999999999999876544

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=85.84  E-value=1.4  Score=37.71  Aligned_cols=52  Identities=13%  Similarity=0.237  Sum_probs=37.9

Q ss_pred             HHHHHHHHHhc----CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          441 LRLALDDVLDS----LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       441 l~~~L~~aL~~----L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      +...+...+..    |++.|-.||..-+.   ..+.|..|||+.+|+|+++|.++..+-
T Consensus        20 ~~~~~~~~l~~~~~~lt~~~~~vL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L   75 (142)
T 3ech_A           20 VRTRIQSELDCQRLDLTPPDVHVLKLIDE---QRGLNLQDLGRQMCRDKALITRKIREL   75 (142)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHHHHH---TTTCCHHHHHHHHC---CHHHHHHHHH
T ss_pred             HHHHHHHHHhhccCCCCHHHHHHHHHHHh---CCCcCHHHHHHHhCCCHHHHHHHHHHH
Confidence            44556666654    99999999988763   358999999999999999999766543

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=85.69  E-value=1.1  Score=39.48  Aligned_cols=42  Identities=17%  Similarity=0.192  Sum_probs=33.2

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      .|++.++.||.+-..   ....|+.|||+.+|+|+++|+++..+=
T Consensus         4 ~ld~~~~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~L   45 (151)
T 2cyy_A            4 PLDEIDKKIIKILQN---DGKAPLREISKITGLAESTIHERIRKL   45 (151)
T ss_dssp             CCCHHHHHHHHHHHH---CTTCCHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            478888888876431   347999999999999999998776543

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=85.53  E-value=2.4  Score=36.20  Aligned_cols=47  Identities=21%  Similarity=0.290  Sum_probs=37.0

Q ss_pred             HHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          444 ALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       444 ~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .+...+.  .|++.|..||..-+    .++.|..|||+.+|+|+++|+++..+
T Consensus        25 ~~~~~~~~~~l~~~~~~iL~~l~----~~~~~~~ela~~l~~s~~tvs~~l~~   73 (146)
T 2gxg_A           25 ELNRRLGELNLSYLDFLVLRATS----DGPKTMAYLANRYFVTQSAITASVDK   73 (146)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHT----TSCBCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHh----cCCcCHHHHHHHhCCCchhHHHHHHH
Confidence            3444453  48999999988766    45899999999999999999876544

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=85.52  E-value=1.4  Score=35.94  Aligned_cols=40  Identities=18%  Similarity=0.113  Sum_probs=29.7

Q ss_pred             CCHHHHHHHh-HHhcCCCCC-CCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          452 LKPKESLVIR-QRFGLDGKG-DRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       452 L~~rEr~VL~-lRyGL~~~~-~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      .|+.++.-+. +..    .. +.|+.+||..+|||+.+|+++..+.
T Consensus         6 ys~e~k~~~v~~~~----~~~g~s~~~ia~~~gIs~~tl~rW~~~~   47 (97)
T 2jn6_A            6 YSEEFKRDAVALYE----NSDGASLQQIANDLGINRVTLKNWIIKY   47 (97)
T ss_dssp             CCHHHHHHHHHHHT----TGGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH----HcCCChHHHHHHHHCcCHHHHHHHHHHH
Confidence            5566664443 443    23 7899999999999999999987654

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=85.44  E-value=1.2  Score=39.92  Aligned_cols=41  Identities=12%  Similarity=0.118  Sum_probs=33.1

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .|++.++.||.+-..   ....|+.|||+.+|+|+.+|++++.+
T Consensus         7 ~ld~~~~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~   47 (162)
T 2p5v_A            7 TLDKTDIKILQVLQE---NGRLTNVELSERVALSPSPCLRRLKQ   47 (162)
T ss_dssp             CCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            488888888876542   34689999999999999999977654

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=85.37  E-value=1.1  Score=38.52  Aligned_cols=47  Identities=17%  Similarity=0.153  Sum_probs=33.5

Q ss_pred             HHhcCCHHHHHHHhHHhcC-CCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          448 VLDSLKPKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       448 aL~~L~~rEr~VL~lRyGL-~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .+..|++.+..+|...+-+ ....+.|..+||+.+|+|+.+|++++.+
T Consensus         7 ~~~~lt~~~~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~~~l~~   54 (139)
T 2x4h_A            7 QMSNLSRREFSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVFEEVSH   54 (139)
T ss_dssp             ----CCHHHHHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHhhcCHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHHHHHHH
Confidence            3456888888887765533 2235789999999999999999966544

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=85.31  E-value=2.1  Score=35.41  Aligned_cols=47  Identities=15%  Similarity=0.237  Sum_probs=33.7

Q ss_pred             HHHHHHhcCC-HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          444 ALDDVLDSLK-PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       444 ~L~~aL~~L~-~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .+..++..|. +....||.+-.    ..++|..|||+.+|+|+++|++++..
T Consensus        15 ~~~~~~~~l~~~~r~~IL~~L~----~~~~~~~ela~~l~is~stvs~~L~~   62 (106)
T 1r1u_A           15 RVTEIFKALGDYNRIRIMELLS----VSEASVGHISHQLNLSQSNVSHQLKL   62 (106)
T ss_dssp             HHHHHHHHTCSHHHHHHHHHHH----HCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH----hCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3445555554 55566766544    35789999999999999999976543

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=85.26  E-value=1.4  Score=37.79  Aligned_cols=40  Identities=23%  Similarity=0.184  Sum_probs=32.2

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .|++.|..||..-+.    .+.|..|||+.+|+|+.+|+++..+
T Consensus        35 ~lt~~~~~iL~~l~~----~~~t~~eLa~~l~~s~~tvs~~l~~   74 (146)
T 3tgn_A           35 ALTNTQEHILMLLSE----ESLTNSELARRLNVSQAAVTKAIKS   74 (146)
T ss_dssp             CCCHHHHHHHHHHTT----CCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh----CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            478888888877662    3399999999999999999966544

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=85.04  E-value=1  Score=39.00  Aligned_cols=40  Identities=23%  Similarity=0.315  Sum_probs=31.0

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      |++.++.||..-..   ....|+.|||+.+|+|+.+|++...+
T Consensus         2 ld~~~~~il~~L~~---~~~~~~~ela~~lg~s~~tv~~~l~~   41 (141)
T 1i1g_A            2 IDERDKIILEILEK---DARTPFTEIAKKLGISETAVRKRVKA   41 (141)
T ss_dssp             CCSHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            66778888775431   34689999999999999999866554

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=84.97  E-value=1.3  Score=39.18  Aligned_cols=42  Identities=14%  Similarity=0.216  Sum_probs=33.3

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      .|++.++.||.+-..   ....|+.|||+.+|+|+++|+++..+=
T Consensus         5 ~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~L   46 (152)
T 2cg4_A            5 LIDNLDRGILEALMG---NARTAYAELAKQFGVSPETIHVRVEKM   46 (152)
T ss_dssp             CCCHHHHHHHHHHHH---CTTSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            478888888876431   357899999999999999999776543

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=84.80  E-value=1.4  Score=38.64  Aligned_cols=40  Identities=15%  Similarity=0.177  Sum_probs=30.8

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      |++.+..||.+-.   .....|+.|||+.+|+|+++|+++..+
T Consensus         1 ld~~~~~il~~L~---~~~~~~~~ela~~lg~s~~tv~~~l~~   40 (150)
T 2pn6_A            1 MDEIDLRILKILQ---YNAKYSLDEIAREIRIPKATLSYRIKK   40 (150)
T ss_dssp             CCHHHHHHHHHHT---TCTTSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CChHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            5677778876543   134799999999999999999866544

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36

Probab=84.57  E-value=2.2  Score=36.32  Aligned_cols=50  Identities=20%  Similarity=0.210  Sum_probs=37.0

Q ss_pred             HHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          443 LALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       443 ~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ..+...+.  .|++.+..|+.+.+ +. ..+.|..|||+.+|+|+++|.++..+
T Consensus        13 ~~~~~~~~~~gl~~~~~~il~~L~-~~-~~~~t~~ela~~l~~~~stvs~~l~~   64 (152)
T 1ku9_A           13 ELFSELAKIHGLNKSVGAVYAILY-LS-DKPLTISDIMEELKISKGNVSMSLKK   64 (152)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHH-HC-SSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCChhHHHHHHHHH-Hc-CCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            33444443  48999999987764 22 25799999999999999999866543

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28

Probab=84.42  E-value=3  Score=35.32  Aligned_cols=53  Identities=8%  Similarity=0.031  Sum_probs=39.0

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          441 LRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       441 l~~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      +...+...+.  .|++.|..||..-+.- +..+.|..+||+.+|+|+.+|.++..+
T Consensus        19 ~~~~~~~~~~~~~lt~~~~~iL~~l~~~-~~~~~~~~ela~~l~~~~~tvs~~l~~   73 (141)
T 3bro_A           19 MSTRFDIFAKKYDLTGTQMTIIDYLSRN-KNKEVLQRDLESEFSIKSSTATVLLQR   73 (141)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHT-TTSCCBHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHC-CCCCcCHHHHHHHHCCCcchHHHHHHH
Confidence            3444555554  4899999998876642 123799999999999999999866544

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=84.29  E-value=2.2  Score=36.48  Aligned_cols=40  Identities=23%  Similarity=0.272  Sum_probs=29.6

Q ss_pred             CCHHHHHHHhHHhcCCC--CCCCCHHHHHHHhCCCHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDG--KGDRTLGEIAGNLNISREMVRKH  491 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~--~~~~Tl~EIA~~LgISrerVRqi  491 (513)
                      |++.|+.-|..|+-+-.  ..++|+.+|++.+|+|..+|.+.
T Consensus        37 ~T~~E~~alaqR~~Ia~lL~~G~SyreIa~~tG~StaTIsRv   78 (107)
T 3frw_A           37 CTINELLSLSQRFEVAKMLTDKRTYLDISEKTGASTATISRV   78 (107)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCccHHHHHHH
Confidence            67777766665553310  25799999999999999999863

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=84.16  E-value=2.9  Score=36.27  Aligned_cols=51  Identities=10%  Similarity=0.045  Sum_probs=38.9

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          441 LRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       441 l~~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      +...+...+.  .|++.|..||..-+.   ..+.|..+||+.+|+++.+|.++..+
T Consensus        28 ~~~~~~~~l~~~~lt~~~~~iL~~l~~---~~~~t~~ela~~l~i~~~tvs~~l~~   80 (155)
T 3cdh_A           28 ASAQFHDHIRAQGLRVPEWRVLACLVD---NDAMMITRLAKLSLMEQSRMTRIVDQ   80 (155)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHSS---CSCBCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHH---CCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            3344555553  499999999887663   35799999999999999999876654

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=84.15  E-value=1.5  Score=35.18  Aligned_cols=45  Identities=20%  Similarity=0.347  Sum_probs=32.2

Q ss_pred             HHHhcC-CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          447 DVLDSL-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       447 ~aL~~L-~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .++..| ++.+..||..-.   ...+.|..|||+.+|+|+.+|++++.+
T Consensus        16 ~~~~~l~~~~~~~il~~l~---~~~~~s~~ela~~l~is~~tvs~~l~~   61 (99)
T 3cuo_A           16 ALLKAMSHPKRLLILCMLS---GSPGTSAGELTRITGLSASATSQHLAR   61 (99)
T ss_dssp             HHHHHHCSHHHHHHHHHHT---TCCSEEHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHhCChHHHHHHHHHH---hCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            334444 466777776544   245799999999999999999876543

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=84.13  E-value=1.5  Score=39.30  Aligned_cols=40  Identities=10%  Similarity=0.154  Sum_probs=31.3

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      |++.++.||.+--.   ....|+.|||+.+|+|+.+|+..+.+
T Consensus         1 lD~~d~~il~~L~~---~~~~s~~~la~~lg~s~~tv~~rl~~   40 (162)
T 3i4p_A            1 MDRLDRKILRILQE---DSTLAVADLAKKVGLSTTPCWRRIQK   40 (162)
T ss_dssp             CCHHHHHHHHHHTT---CSCSCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---CCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            56677888776541   34689999999999999999977654

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=83.83  E-value=2.5  Score=35.71  Aligned_cols=53  Identities=11%  Similarity=-0.025  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          440 LLRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       440 ~l~~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      .+...+...+.  .|++.|..||..-+.   ..+.|..+||+.+|+|+.+|.++..+-
T Consensus        18 ~~~~~~~~~~~~~~lt~~~~~iL~~l~~---~~~~~~~~la~~l~~~~~tvs~~l~~L   72 (138)
T 1jgs_A           18 KKDRLLNEYLSPLDITAAQFKVLCSIRC---AACITPVELKKVLSVDLGALTRMLDRL   72 (138)
T ss_dssp             HHHHHHHHHHTTTTSCHHHHHHHHHHHH---HSSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhcCCCHHHHHHHHHHHh---cCCCCHHHHHHHHCCChHHHHHHHHHH
Confidence            34455666664  389999999887663   357899999999999999999766553

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=83.44  E-value=2  Score=36.30  Aligned_cols=49  Identities=6%  Similarity=0.072  Sum_probs=37.5

Q ss_pred             HHHHHHHh-cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          443 LALDDVLD-SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       443 ~~L~~aL~-~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ..+...+. .|++.|..||..-+.   .++.|..|||+.+|+|+.+|.++..+
T Consensus        26 ~~~~~~~~~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~tvs~~l~~   75 (140)
T 2nnn_A           26 ALFANGIGNGLTPTQWAALVRLGE---TGPCPQNQLGRLTAMDAATIKGVVER   75 (140)
T ss_dssp             HHHHHHCSSCCCHHHHHHHHHHHH---HSSBCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            33444443 699999999887653   34899999999999999999876544

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=83.31  E-value=1.9  Score=34.98  Aligned_cols=45  Identities=13%  Similarity=0.289  Sum_probs=31.1

Q ss_pred             HHHHHhcC-CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          445 LDDVLDSL-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       445 L~~aL~~L-~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      +..++..| ++....||.+-.    ..+.|..|||+.+|+|+.+|++.+.
T Consensus        13 ~~~~~~~l~~~~r~~Il~~L~----~~~~~~~ela~~l~is~~tvs~~L~   58 (98)
T 3jth_A           13 AVVLLKAMANERRLQILCMLH----NQELSVGELCAKLQLSQSALSQHLA   58 (98)
T ss_dssp             HHHHHHHHCSHHHHHHHHHTT----TSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHcCCHHHHHHHHHHh----cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            44445555 455555554433    2589999999999999999986544

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=83.19  E-value=1.2  Score=33.09  Aligned_cols=26  Identities=23%  Similarity=0.197  Sum_probs=22.2

Q ss_pred             CCCC----HHHHHHHhCCCHHHHHHHHHHH
Q 010308          470 GDRT----LGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       470 ~~~T----l~EIA~~LgISrerVRqi~~rA  495 (513)
                      .+.|    ..+||..|||++++|+++....
T Consensus        20 ~g~s~~~~~~~vA~~~gIs~~tl~~W~~~~   49 (59)
T 2glo_A           20 NDNDCKGNQRATARKYNIHRRQIQKWLQCE   49 (59)
T ss_dssp             HCTTTTTCHHHHHHHTTSCHHHHHHHHTTH
T ss_pred             cCCCcchHHHHHHHHHCcCHHHHHHHHHHH
Confidence            3567    9999999999999999997643

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=83.11  E-value=2.8  Score=35.44  Aligned_cols=42  Identities=12%  Similarity=0.094  Sum_probs=34.7

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      .|++.+..||..-+.   ..+.|..+||+.+|+|+.+|+++..+-
T Consensus        28 ~l~~~~~~iL~~l~~---~~~~~~~ela~~l~is~~~vs~~l~~L   69 (142)
T 3bdd_A           28 GISLTRYSILQTLLK---DAPLHQLALQERLQIDRAAVTRHLKLL   69 (142)
T ss_dssp             SSCHHHHHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            699999999887652   357999999999999999998765543

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=83.09  E-value=0.54  Score=41.90  Aligned_cols=40  Identities=18%  Similarity=0.038  Sum_probs=30.8

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .++..++.-|...+    ..++|..+||+.||||+.+|+++..+
T Consensus        25 ~~s~e~r~~ii~l~----~~G~s~~~IA~~lgis~~TV~rwl~r   64 (159)
T 2k27_A           25 PLPEVVRQRIVDLA----HQGVRPCDISRQLRVSHGCVSKILGR   64 (159)
T ss_dssp             SSCHHHHHHHHHHH----HHTCCHHHHHHHHTCCSHHHHHHHCC
T ss_pred             CCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45666665555545    35789999999999999999998865

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=82.97  E-value=2.1  Score=36.25  Aligned_cols=53  Identities=17%  Similarity=0.137  Sum_probs=41.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHhHHhcC-CCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          442 RLALDDVLDSLKPKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       442 ~~~L~~aL~~L~~rEr~VL~lRyGL-~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ...|...+..|++.|+.|......- +....+|..|+|+..|+|..+|-+..++
T Consensus         5 ~~~I~~~~~~lt~~e~~ia~yil~~~~~~~~~si~elA~~~~vS~aTv~Rf~kk   58 (107)
T 3iwf_A            5 LYKIDNQYPYFTKNEKKIAQFILNYPHKVVNMTSQEIANQLETSSTSIIRLSKK   58 (107)
T ss_dssp             HHHHHHHGGGSCHHHHHHHHHHHHCHHHHTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCHHHHHHHHHHHhCHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
Confidence            3567788899999999998765421 1124699999999999999999876543

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=82.76  E-value=2.7  Score=35.80  Aligned_cols=52  Identities=19%  Similarity=0.172  Sum_probs=38.6

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          441 LRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       441 l~~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      +...+...+.  .|++.|..||..-+.  ...+.|..+||+.+|+|+.+|.++..+
T Consensus        22 ~~~~~~~~~~~~~l~~~~~~iL~~l~~--~~~~~t~~~la~~l~~s~~~vs~~l~~   75 (146)
T 2fbh_A           22 WRAELDRRLSHLGLSQARWLVLLHLAR--HRDSPTQRELAQSVGVEGPTLARLLDG   75 (146)
T ss_dssp             HHHHHHHHTGGGCCTTTHHHHHHHHHH--CSSCCBHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHH--cCCCCCHHHHHHHhCCChhhHHHHHHH
Confidence            3344555554  389999999877722  145799999999999999999876554

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=82.73  E-value=3.3  Score=35.81  Aligned_cols=50  Identities=16%  Similarity=0.198  Sum_probs=38.6

Q ss_pred             HHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          443 LALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       443 ~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      ..+...+.  .|++.|-.||..-+.   .++.|..|||+.+|+++.+|.++..+-
T Consensus        28 ~~~~~~~~~~~lt~~q~~iL~~l~~---~~~~~~~eLa~~l~~~~~~vs~~l~~L   79 (149)
T 4hbl_A           28 QFYEKKLKQFGITYSQYLVMLTLWE---ENPQTLNSIGRHLDLSSNTLTPMLKRL   79 (149)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHH---SSSEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            34444443  499999999888763   468899999999999999999766553

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=82.59  E-value=2.4  Score=36.27  Aligned_cols=53  Identities=8%  Similarity=-0.005  Sum_probs=40.1

Q ss_pred             HHHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          440 LLRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       440 ~l~~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      .+...+...+.  .|++.|-.||..-+.   .++.|..|||+.+|+++++|.++..+-
T Consensus        20 ~~~~~~~~~~~~~glt~~q~~vL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L   74 (140)
T 3hsr_A           20 EIIKKYTNYLKEYDLTYTGYIVLMAIEN---DEKLNIKKLGERVFLDSGTLTPLLKKL   74 (140)
T ss_dssp             HHHHHHHHHHGGGTCCHHHHHHHHHSCT---TCEEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCChhhHHHHHHHH
Confidence            34445555554  399999998877653   468999999999999999999766543

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=82.52  E-value=3.2  Score=35.17  Aligned_cols=54  Identities=13%  Similarity=0.142  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHhc--CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          440 LLRLALDDVLDS--LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       440 ~l~~~L~~aL~~--L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .+...+...+..  |++.|..||..-+.- +.++.|..|||+.+|+|+.+|.++..+
T Consensus        15 ~~~~~~~~~~~~~~lt~~~~~vL~~l~~~-~~~~~t~~ela~~l~~~~~tvs~~l~~   70 (139)
T 3eco_A           15 EMKQKADQKLEQFDITNEQGHTLGYLYAH-QQDGLTQNDIAKALQRTGPTVSNLLRN   70 (139)
T ss_dssp             HHHHHHHHHHGGGTCCHHHHHHHHHHHHS-TTTCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHhc-CCCCcCHHHHHHHhCCCcccHHHHHHH
Confidence            344455555644  899999999877632 124899999999999999999876554

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}

Probab=82.45  E-value=2.8  Score=36.08  Aligned_cols=49  Identities=8%  Similarity=0.064  Sum_probs=37.7

Q ss_pred             HHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          443 LALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       443 ~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ..+...+.  .|++.|..||..-+.   ..+.|..+||+.+|+|+.+|.++..+
T Consensus        27 ~~~~~~~~~~~lt~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~~vs~~l~~   77 (152)
T 3bj6_A           27 AAVERGTLREGVTVGQRAILEGLSL---TPGATAPQLGAALQMKRQYISRILQE   77 (152)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHH---STTEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            34444443  499999999887663   35799999999999999999876554

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=82.44  E-value=3  Score=35.75  Aligned_cols=50  Identities=16%  Similarity=0.121  Sum_probs=38.0

Q ss_pred             HHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          442 RLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       442 ~~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ...+...+.  .|++.|-.||..-+.   ..+.|..|||+.+|+++.+|.++..+
T Consensus        17 ~~~~~~~~~~~~lt~~q~~iL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~   68 (145)
T 3g3z_A           17 CNVFDKWIGQQDLNYNLFAVLYTLAT---EGSRTQKHIGEKWSLPKQTVSGVCKT   68 (145)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            334445553  489999999887653   34699999999999999999866554

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=82.40  E-value=1.9  Score=33.98  Aligned_cols=25  Identities=20%  Similarity=0.127  Sum_probs=21.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          470 GDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       470 ~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .+.|..|||+.+|+|+.+|++.+..
T Consensus        13 ~~~s~~eLa~~lgvs~~tv~r~L~~   37 (81)
T 2htj_A           13 NGGKTAEIAEALAVTDYQARYYLLL   37 (81)
T ss_dssp             CCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4699999999999999999866544

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=82.27  E-value=2.5  Score=36.60  Aligned_cols=52  Identities=15%  Similarity=0.198  Sum_probs=39.3

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          441 LRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       441 l~~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      +...+...+.  .|++.|..||...+.   ..+.|..|||+.+|+|+.+|.++..+-
T Consensus        32 ~~~~~~~~~~~~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~s~~tvs~~l~~L   85 (153)
T 2pex_A           32 MHKLYRGLLKALDLTYPQYLVMLVLWE---TDERSVSEIGERLYLDSATLTPLLKRL   85 (153)
T ss_dssp             HHHHHHHHTTTTTCCHHHHHHHHHHHH---SCSEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHh---CCCcCHHHHHHHhCCCcccHHHHHHHH
Confidence            3344455553  389999999887663   357999999999999999999766553

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=82.19  E-value=4.5  Score=33.83  Aligned_cols=47  Identities=13%  Similarity=0.257  Sum_probs=35.0

Q ss_pred             HHHHHHhc-CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          444 ALDDVLDS-LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       444 ~L~~aL~~-L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .+..++.. .++.+..||..-.    ..+.|+.|||+.+|+|+.+|++++.+
T Consensus        21 ~~~~~~~~l~~~~~~~il~~L~----~~~~s~~ela~~l~is~stvsr~l~~   68 (119)
T 2lkp_A           21 QVASTLQALATPSRLMILTQLR----NGPLPVTDLAEAIGMEQSAVSHQLRV   68 (119)
T ss_dssp             HHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHSSCHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            34444444 3577777877665    24799999999999999999977654

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=82.15  E-value=3.4  Score=35.44  Aligned_cols=51  Identities=14%  Similarity=0.281  Sum_probs=39.0

Q ss_pred             HHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          442 RLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       442 ~~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      ...+...+.  .|++.|..||..-+.   ..+.|..+||+.+|+|+.+|.++..+-
T Consensus        28 ~~~~~~~~~~~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~tvs~~l~~L   80 (150)
T 2rdp_A           28 KQRGREILTNYPITPPQFVALQWLLE---EGDLTVGELSNKMYLACSTTTDLVDRM   80 (150)
T ss_dssp             HHHHHHHHTTSSSCHHHHHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCchhHHHHHHHH
Confidence            334555554  489999999887663   357999999999999999999766543

>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=82.04  E-value=13  Score=30.29  Aligned_cols=38  Identities=13%  Similarity=0.056  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh
Q 010308          365 IQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA  402 (513)
Q Consensus       365 i~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~  402 (513)
                      +.++...+...+...++.++||+.+|+|+..+..+.+.
T Consensus         4 i~~~~~~i~~~~~~~~~~~~lA~~~~~s~~~l~r~fk~   41 (108)
T 3mn2_A            4 VRQVEEYIEANWMRPITIEKLTALTGISSRGIFKAFQR   41 (108)
T ss_dssp             HHHHHHHHHHHTTSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHcccCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            44555566677778899999999999999999888765

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=81.96  E-value=3.4  Score=33.72  Aligned_cols=46  Identities=15%  Similarity=0.387  Sum_probs=31.6

Q ss_pred             HHHHHHhcC-CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          444 ALDDVLDSL-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       444 ~L~~aL~~L-~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      .+..++..| .|.-..||.+-.    ..++|..|||+.+|+|+.+|++++.
T Consensus        12 ~~~~~~~~l~~~~r~~Il~~L~----~~~~~~~ela~~l~is~~tvs~~L~   58 (102)
T 3pqk_A           12 EVANLLKTLSHPVRLMLVCTLV----EGEFSVGELEQQIGIGQPTLSQQLG   58 (102)
T ss_dssp             HHHHHHHHHCSHHHHHHHHHHH----TCCBCHHHHHHHHTCCTTHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHH----hCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344555555 444555555543    3579999999999999999986543

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=81.92  E-value=2.6  Score=36.86  Aligned_cols=54  Identities=15%  Similarity=0.090  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHhc--CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          440 LLRLALDDVLDS--LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       440 ~l~~~L~~aL~~--L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .+...+...|..  |+..|-.||.+-+.- ...+.|..|||+.+|+++++|.++..+
T Consensus        19 ~l~~~~~~~l~~~gLt~~q~~vL~~L~~~-~~~~~t~~eLa~~l~~~~~tvs~~v~~   74 (147)
T 4b8x_A           19 ILLGEVDAVVKPYGLTFARYEALVLLTFS-KSGELPMSKIGERLMVHPTSVTNTVDR   74 (147)
T ss_dssp             HHHHHHHHHHGGGTCCHHHHHHHHHHHTS-GGGEEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHC-CCCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            344556666653  999999998876521 124689999999999999999876654

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=81.81  E-value=4.7  Score=35.05  Aligned_cols=51  Identities=12%  Similarity=0.009  Sum_probs=39.2

Q ss_pred             HHHHHHHH---hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          442 RLALDDVL---DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       442 ~~~L~~aL---~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      ...+...+   ..|++.|..||..-+.   ..+.|..|||+.+|+|+.+|.++..+-
T Consensus        34 ~~~~~~~l~~~~~lt~~~~~iL~~l~~---~~~~t~~ela~~l~is~~tvs~~l~~L   87 (162)
T 2fa5_A           34 SGNIAKVYGDRYGMAIPEWRVITILAL---YPGSSASEVSDRTAMDKVAVSRAVARL   87 (162)
T ss_dssp             HHHHHHHHHHHHCCCHHHHHHHHHHHH---STTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            33444555   2599999999887763   358999999999999999998766543

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=81.58  E-value=1.2  Score=34.45  Aligned_cols=23  Identities=26%  Similarity=0.101  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q 010308          472 RTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       472 ~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      +|+.|||+.+|||+.+|+++++.
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLng   23 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVING   23 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcC
Confidence            48899999999999999998874

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=81.47  E-value=2.6  Score=34.77  Aligned_cols=46  Identities=22%  Similarity=0.317  Sum_probs=32.8

Q ss_pred             HHHHHhcCC-HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          445 LDDVLDSLK-PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       445 L~~aL~~L~-~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      +..++..|. +....||..-.    ..+.|..|||+.+|+|+.+|++++.+
T Consensus        11 ~~~~~~~l~~~~r~~IL~~L~----~~~~~~~ela~~l~is~~tv~~~l~~   57 (114)
T 2oqg_A           11 LASVFAALSDETRWEILTELG----RADQSASSLATRLPVSRQAIAKHLNA   57 (114)
T ss_dssp             HHHHHHHTTCHHHHHHHHHHH----HSCBCHHHHHHHSSSCHHHHHHHHHH
T ss_pred             HHHHHHHhCChHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            444555553 55666666542    35799999999999999999976554

>3oou_A LIN2118 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; HET: BTB; 1.57A {Listeria innocua}

Probab=81.40  E-value=19  Score=29.43  Aligned_cols=38  Identities=8%  Similarity=0.009  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh
Q 010308          365 IQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA  402 (513)
Q Consensus       365 i~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~  402 (513)
                      +.++...+...+....+.++||+.+|+|+..+....+.
T Consensus         7 i~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~   44 (108)
T 3oou_A            7 IQNVLSYITEHFSEGMSLKTLGNDFHINAVYLGQLFQK   44 (108)
T ss_dssp             HHHHHHHHHHHTTSCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            44555556667778899999999999999999888765

>3k0l_A Repressor protein; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.35A {Acinetobacter SP}

Probab=81.38  E-value=2.9  Score=36.70  Aligned_cols=52  Identities=12%  Similarity=0.052  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          440 LLRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       440 ~l~~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .+...+...+.  .|++.|..||..-+.   ..+.|..|||+.+|+++.+|.++..+
T Consensus        30 ~~~~~~~~~l~~~glt~~q~~iL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~   83 (162)
T 3k0l_A           30 IISKYLTEHLSALEISLPQFTALSVLAA---KPNLSNAKLAERSFIKPQSANKILQD   83 (162)
T ss_dssp             HHHHHHHHHHHTTTCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCGGGHHHHHHH
T ss_pred             HHHHHHHHHhhhcCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            34445555554  499999999987663   35899999999999999999876554

>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28

Probab=81.36  E-value=2.3  Score=36.33  Aligned_cols=52  Identities=13%  Similarity=0.051  Sum_probs=38.9

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          441 LRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       441 l~~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      +...+...+.  .|++.+..||..-+.   ..+.|..+||+.+|+|+.+|.++..+-
T Consensus        14 ~~~~~~~~~~~~~lt~~~~~iL~~l~~---~~~~t~~~la~~l~~s~~~vs~~l~~L   67 (144)
T 1lj9_A           14 LDSISNIEFKELSLTRGQYLYLVRVCE---NPGIIQEKIAELIKVDRTTAARAIKRL   67 (144)
T ss_dssp             HHHHHHHHTGGGTCTTTHHHHHHHHHH---STTEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHH---CcCcCHHHHHHHHCCCHhHHHHHHHHH
Confidence            3444555554  489999999877653   357899999999999999998765543

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=81.35  E-value=1.2  Score=37.09  Aligned_cols=38  Identities=16%  Similarity=0.190  Sum_probs=28.7

Q ss_pred             HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      +|...|+.+..    ..+.|+.+||+.+|||..||+..+...
T Consensus         7 ~R~~~I~~~l~----~~~~ti~dlA~~~gVS~~TVsR~L~~~   44 (93)
T 2l0k_A            7 ERTIKIGKYIV----ETKKTVRVIAKEFGVSKSTVHKDLTER   44 (93)
T ss_dssp             HHHHHHHHHHH----HHCCCHHHHHHHHTSCHHHHHHHHTTH
T ss_pred             HHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHcCC
Confidence            35555655544    234899999999999999999987653

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=81.34  E-value=2.1  Score=38.92  Aligned_cols=42  Identities=14%  Similarity=0.114  Sum_probs=32.6

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ..|++.++.||.+-..   ....|+.|||+.+|+|+.+|++++.+
T Consensus        13 ~~ld~~d~~IL~~L~~---~~~~s~~eLA~~lglS~~tv~~~l~~   54 (171)
T 2ia0_A           13 IHLDDLDRNILRLLKK---DARLTISELSEQLKKPESTIHFRIKK   54 (171)
T ss_dssp             -CCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4578888888876431   34689999999999999999976544

>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 3jso_A* 3jsp_A* 3k3r_E* 1jhc_A 1jhe_A 1lea_A 1leb_A

Probab=81.20  E-value=0.83  Score=42.32  Aligned_cols=45  Identities=18%  Similarity=0.119  Sum_probs=32.4

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCC--CHHHHHHHhCCC-HHHHHHHHHH
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDR--TLGEIAGNLNIS-REMVRKHEVK  494 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~--Tl~EIA~~LgIS-rerVRqi~~r  494 (513)
                      ..|+++|+.++...--+-...++  |..|+|+.+|+| +++|++++.+
T Consensus         2 ~~lt~~q~~i~~~i~~~~~~~g~~ps~~elA~~lgiss~~tv~~~~~~   49 (202)
T 1jhf_A            2 KALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKA   49 (202)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHHHHHhCCCccHHHHHHHhCCCChHHHHHHHHH
Confidence            35888888876543211112355  999999999999 9999998763

>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28

Probab=81.10  E-value=2.5  Score=35.95  Aligned_cols=41  Identities=15%  Similarity=0.303  Sum_probs=34.2

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .|++.|..||..-+.   ..+.|..+||+.+|+|+.+|..+..+
T Consensus        30 ~l~~~~~~iL~~l~~---~~~~~~~~la~~l~~s~~tvs~~l~~   70 (145)
T 2a61_A           30 GITPAQFDILQKIYF---EGPKRPGELSVLLGVAKSTVTGLVKR   70 (145)
T ss_dssp             TCCHHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCchhHHHHHHH
Confidence            499999999887663   35799999999999999999876554

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=80.97  E-value=3.6  Score=35.23  Aligned_cols=45  Identities=13%  Similarity=0.278  Sum_probs=32.2

Q ss_pred             HHHHhcC-CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          446 DDVLDSL-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       446 ~~aL~~L-~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ..++..| ++....||.+-.    ..+.|..|||+.+|+|+++|++++..
T Consensus        37 ~~~~kaL~~~~rl~IL~~L~----~~~~s~~ela~~lgis~stvs~~L~~   82 (122)
T 1r1t_A           37 AEFFAVLADPNRLRLLSLLA----RSELCVGDLAQAIGVSESAVSHQLRS   82 (122)
T ss_dssp             HHHHHHHCCHHHHHHHHHHT----TCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHhCCHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3333333 555667776554    35799999999999999999976544

>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}

Probab=80.73  E-value=10  Score=31.31  Aligned_cols=39  Identities=13%  Similarity=0.180  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHh
Q 010308          364 EIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA  402 (513)
Q Consensus       364 ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~  402 (513)
                      .+.++...+...+...++.++||+.+|+|...+..+.+.
T Consensus         8 ~i~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~   46 (113)
T 3oio_A            8 KLTEAVSLMEANIEEPLSTDDIAYYVGVSRRQLERLFKQ   46 (113)
T ss_dssp             HHHHHHHHHHTCSSSCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            345555556666778899999999999999999888765

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=80.70  E-value=3.7  Score=37.44  Aligned_cols=53  Identities=17%  Similarity=0.300  Sum_probs=40.5

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          441 LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       441 l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      +...+...+..|++.|..||..-+-.. .++.|..+||+.+|+|+++|.++..+
T Consensus        28 ~~~~~~~~~~~lt~~q~~vL~~L~~~~-~~~~t~~eLa~~l~is~~tvs~~l~~   80 (189)
T 3nqo_A           28 IQIEGDKYFGILTSRQYMTILSILHLP-EEETTLNNIARKMGTSKQNINRLVAN   80 (189)
T ss_dssp             HHHHHHHHHCSSCHHHHHHHHHHHHSC-GGGCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHccCCHHHHHHHHHHHhcc-CCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            344555666679999999998766221 24799999999999999999866544

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=80.58  E-value=3.8  Score=35.39  Aligned_cols=49  Identities=10%  Similarity=0.054  Sum_probs=37.7

Q ss_pred             HHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          444 ALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       444 ~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      .+...+.  .|++.|..||..-+.   ..+.|..+||+.+|+|+++|.++..+-
T Consensus        29 ~~~~~~~~~~lt~~~~~iL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L   79 (154)
T 2qww_A           29 YADQNAASLGLTIQQLAMINVIYS---TPGISVADLTKRLIITGSSAAANVDGL   79 (154)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHH---STTEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3444443  499999999887663   357999999999999999998766543

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=80.57  E-value=2.4  Score=33.95  Aligned_cols=26  Identities=12%  Similarity=0.101  Sum_probs=23.7

Q ss_pred             CCCCCHHHHHHhcCCCHHHHHHHHHh
Q 010308          377 KRVPTDEEIIQGVNISPERYREVMKA  402 (513)
Q Consensus       377 gR~PT~eELA~~lgis~e~v~~~l~~  402 (513)
                      |..||..|||+.+|+|...++..|..
T Consensus        22 g~~psv~EIa~~lgvS~~TVrr~L~~   47 (77)
T 2jt1_A           22 GAPVKTRDIADAAGLSIYQVRLYLEQ   47 (77)
T ss_dssp             TSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            88999999999999999999887765

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=80.42  E-value=2.7  Score=33.68  Aligned_cols=26  Identities=15%  Similarity=0.221  Sum_probs=20.7

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          469 KGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       469 ~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ++..|..+||+.||+|+..|.+.+.+
T Consensus        27 ~~~~Ta~~IAkkLg~sK~~vNr~LY~   52 (75)
T 1sfu_A           27 NDYTTAISLSNRLKINKKKINQQLYK   52 (75)
T ss_dssp             TCEECHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHCCCHHHHHHHHHH
Confidence            34589999999999998777765554

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=80.40  E-value=1.3  Score=36.85  Aligned_cols=43  Identities=35%  Similarity=0.260  Sum_probs=31.1

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  500 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR  500 (513)
                      +.+....||...+-  .++..|..|||+.||+|+.+|++    ++++|.
T Consensus        16 ~~~~~l~Il~~l~~--~g~~~s~~eLa~~lgvs~~tV~~----~L~~L~   58 (110)
T 1q1h_A           16 LGDDVIDVLRILLD--KGTEMTDEEIANQLNIKVNDVRK----KLNLLE   58 (110)
T ss_dssp             SCSTTHHHHHHHHH--HCSCBCHHHHHHTTTSCHHHHHH----HHHHHH
T ss_pred             cChHHHHHHHHHHH--cCCCCCHHHHHHHHCcCHHHHHH----HHHHHH
Confidence            45666777765531  13468999999999999999995    555554

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28

Probab=80.35  E-value=2.5  Score=36.48  Aligned_cols=49  Identities=14%  Similarity=0.249  Sum_probs=37.7

Q ss_pred             HHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          443 LALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       443 ~~L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ..+...+.  .|++.|..||...+.   ..+.|..+||+.+|+|+.+|.++..+
T Consensus        24 ~~~~~~~~~~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~s~~tvs~~l~~   74 (155)
T 1s3j_A           24 PEMLESMEKQGVTPAQLFVLASLKK---HGSLKVSEIAERMEVKPSAVTLMADR   74 (155)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHH---HSEEEHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHhhcCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            34444443  699999999887652   35789999999999999999876544

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=80.32  E-value=2.5  Score=36.08  Aligned_cols=51  Identities=18%  Similarity=0.057  Sum_probs=38.8

Q ss_pred             HHHHHHHHHhc--CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          441 LRLALDDVLDS--LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       441 l~~~L~~aL~~--L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      +...+...+..  |++.|..||..-+.   .++.|..|||+.+|+++.+|.++..+
T Consensus        22 ~~~~~~~~~~~~~lt~~~~~iL~~l~~---~~~~t~~eLa~~l~~~~~~vs~~l~~   74 (143)
T 3oop_A           22 MHLFLMRSIASYDVTPEQWSVLEGIEA---NEPISQKEIALWTKKDTPTVNRIVDV   74 (143)
T ss_dssp             HHHHHHHHTTTSSSCHHHHHHHHHHHH---HSSEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHhhhCCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCHhhHHHHHHH
Confidence            34445555543  89999999887653   36899999999999999999866554

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=80.15  E-value=2  Score=35.25  Aligned_cols=38  Identities=13%  Similarity=0.259  Sum_probs=28.4

Q ss_pred             CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          453 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       453 ~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      +|....||.....   .+++|..|||+.+|+|+++|++++.
T Consensus        26 ~~~Rl~IL~~l~~---~~~~~~~ela~~l~is~stvs~hL~   63 (99)
T 2zkz_A           26 HPMRLKIVNELYK---HKALNVTQIIQILKLPQSTVSQHLC   63 (99)
T ss_dssp             SHHHHHHHHHHHH---HSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH---CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            5666677733221   2579999999999999999997654

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=80.05  E-value=2.6  Score=36.88  Aligned_cols=42  Identities=7%  Similarity=-0.019  Sum_probs=34.7

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      .|++.|..||...+.   ..+.|..+||+.+|+|+.+|.+++.+-
T Consensus        49 ~lt~~~~~iL~~l~~---~~~~t~~ela~~l~is~~tvs~~l~~L   90 (162)
T 3cjn_A           49 GLSTAKMRALAILSA---KDGLPIGTLGIFAVVEQSTLSRALDGL   90 (162)
T ss_dssp             TCCHHHHHHHHHHHH---SCSEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCChhHHHHHHHHH
Confidence            399999999887663   357899999999999999998766543

---

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	513
d1siga_	334	a.177.1.1 (A:) Sigma70 {Escherichia coli [TaxId: 5	9e-17
d1ttya_	87	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga mar	1e-16
d1rp3a3	87	a.177.1.1 (A:0-86) Sigma factor sigma-28 (FliA) {A	3e-15
d2p7vb1	68	a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escheri	5e-15
d1ku3a_	61	a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquati	2e-12
d1ku2a2	180	a.177.1.1 (A:93-272) Sigma factor SigA {Thermus aq	3e-12
d1rp3a1	77	a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {	7e-06
d1rp3a1	77	a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {	7e-05
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	2e-05
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	1e-04
d1rp3a2	71	a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA)	1e-04
d1ku2a1	60	a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aq	7e-04

>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 = 79.2 bits (194), Expect = 9e-17
 Identities = 47/188 (25%), Positives = 79/188 (42%), Gaps = 6/188 (3%)

Query: 159 LDKRIELRKNEDEKVVTKTRKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSS 218
           + K+ +   N    ++ + R  +       +E+          L + +           +
Sbjct: 150 VPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIA 209

Query: 219 TEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNK 278
               W  KL    +   +V   LQK    E       E       ++       R A+ +
Sbjct: 210 MNKPWSEKLHDVSE---EVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKE 266

Query: 279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWI 338
           +++ NLRLV+ + KKY      G +F DL Q G  GL+ A+D+FE +R ++ STY  +WI
Sbjct: 267 MVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 323

Query: 339 RHAIIRSM 346
           R AI RS+
Sbjct: 324 RQAITRSI 331

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]} Length = 87

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

 Score = 72.9 bits (179), Expect = 1e-16
 Identities = 31/73 (42%), Positives = 49/73 (67%)

Query: 440 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 499
           L+R  L+ VL +L P+E++V+R R+GL     +TL E+    N++RE +R+ EVK L KL
Sbjct: 7   LMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKL 66

Query: 500 KHPTRVDYLRQHM 512
           +HP+R  YL+  +
Sbjct: 67  RHPSRSKYLKSLL 79

>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 = 68.8 bits (168), Expect = 3e-15
 Identities = 20/70 (28%), Positives = 27/70 (38%)

Query: 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYG 334
            R +LI   L LV  +     +        +DL   GV GLI A+D    +   R   Y 
Sbjct: 11  EREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYI 70

Query: 335 LFWIRHAIIR 344
              I+ AI  
Sbjct: 71  KLRIKGAIYD 80

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

 Score = 67.4 bits (165), Expect = 5e-15
 Identities = 28/66 (42%), Positives = 42/66 (63%)

Query: 447 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 506
           DVL  L  +E+ V+R RFG+D   D TL E+    +++RE +R+ E K L KL+HP+R +
Sbjct: 1   DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 60

Query: 507 YLRQHM 512
            LR  +
Sbjct: 61  VLRSFL 66

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]} Length = 61

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

 Score = 60.1 bits (146), Expect = 2e-12
 Identities = 20/58 (34%), Positives = 33/58 (56%)

Query: 445 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 502
           L+  L  L  +E++V++ R GL    + TL E+     ++RE +R+ E K L KLK+ 
Sbjct: 2   LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYH 59

>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 = 62.9 bits (152), Expect = 3e-12
 Identities = 49/176 (27%), Positives = 74/176 (42%), Gaps = 33/176 (18%)

Query: 200 TDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKV---FVQVKEQLQKDLGREPTDVELAE 256
           +D V     ++   P+L+  E   L + ++        +     L ++L RE    ++  
Sbjct: 1   SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILG 60

Query: 257 ATNMSA---------------------------AQVKKCLEVGRAARNKLIKHNLRLVLF 289
              +                              +       G AAR  LI+ NLRLV+ 
Sbjct: 61  TARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVS 120

Query: 290 VIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS 345
           + KKY      G  F DL Q G +GLI A+++FE KRRF+ STY  +WIR AI R+
Sbjct: 121 IAKKYTG---RGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRA 173

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 41.7 bits (98), Expect = 7e-06
 Identities = 15/41 (36%), Positives = 26/41 (63%)

Query: 236 QVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAAR 276
           +V E+L++ LGREPTD E+A+   +S  ++ K L+    + 
Sbjct: 14  EVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSY 54

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 77

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 39.0 bits (91), Expect = 7e-05
 Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 2/48 (4%)

Query: 364 EIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKP--ILSL 409
            I+    +L  +L R PTDEE+ + + IS E   + +       ILSL
Sbjct: 11  RIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSL 58

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]} Length = 57

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

 Score = 39.7 bits (93), Expect = 2e-05
 Identities = 17/52 (32%), Positives = 26/52 (50%)

Query: 353 RVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK 404
           +V   L+ +  +I++AK EL     R PT  EI   + ISPE      +A +
Sbjct: 5   KVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVR 56

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]} Length = 57

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

 Score = 37.7 bits (88), Expect = 1e-04
 Identities = 13/38 (34%), Positives = 19/38 (50%)

Query: 236 QVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGR 273
           + K++L K  GR PT  E+A+   +S   V    E  R
Sbjct: 19  KAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVR 56

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]} Length = 71

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

 Score = 38.3 bits (89), Expect = 1e-04
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 4/61 (6%)

Query: 441 LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 500
           L   + + +  L  +E LVI+  F  +        E+A  L  S   V + + K L +L+
Sbjct: 11  LTEKVKEAVSKLPEREKLVIQLIFYEE----LPAKEVAKILETSVSRVSQLKAKALERLR 66

Query: 501 H 501
            
Sbjct: 67  E 67

>d1ku2a1 a.4.13.1 (A:273-332) Sigma factor SigA {Thermus aquaticus [TaxId: 271]} Length = 60

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]

 Score = 35.8 bits (83), Expect = 7e-04
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 365 IQRAKLELLFELKRVPTDEEIIQ--GVNISPERYREVMKASKPILSL 409
           + R   +L  EL R P+ EEI +  G     +R  E +K ++  +SL
Sbjct: 14  LSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 60

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	513
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.98
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.84
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.79
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	99.65
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	99.64
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	99.55
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.27
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.14
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.06
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.03
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.99
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	98.67
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	98.67
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.65
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	98.4
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	98.32
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	98.04
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	97.85
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	97.84
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	97.49
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	95.94
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	95.78
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	95.13
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	94.57
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	94.0
d1hlva1	66	DNA-binding domain of centromere binding protein B	92.08
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	92.08
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	91.36
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	90.98
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	90.93
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.5
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	88.77
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	88.33
d1nr3a_	122	DNA-binding protein Tfx {Archaeon Methanobacterium	87.8
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	87.75
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	87.41
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	86.45
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	86.07
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	85.61
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	84.99
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	84.88
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	84.28
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	84.13
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	83.97
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	83.58
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	83.1
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	82.58
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	82.39
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	82.39
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	82.32
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	82.28
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	82.15
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	82.1
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	81.57
d1y7ya1	69	Restriction-modification controller protein C.AhdI	80.9
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	80.77
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	80.16

>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=99.98  E-value=3.4e-33  Score=261.29  Aligned_cols=148  Identities=32%  Similarity=0.447  Sum_probs=119.4

Q ss_pred             CChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHH------------------HHhCCCCCHHHH-------
Q 010308          200 TDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQ------------------KDLGREPTDVEL-------  254 (513)
Q Consensus       200 ~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~------------------~~l~r~p~~~e~-------  254 (513)
                      ||+|++||++|+.+|+||++||+.|++.|+.+..+.....+..                  ......|...+|       
T Consensus         1 tDpVr~YLreig~v~LLT~EEEieLAr~Ie~g~~~~~~~~e~~~~~~~l~~e~~~~~~~~~~~~~~~~~~~e~~~~~~~~   80 (180)
T d1ku2a2           1 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVE   80 (180)
T ss_dssp             CHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCSSCCCTTSCCSSCTTTHH
T ss_pred             CCcHHHHHHHhcCcCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHhhhHHHHhcchhhHHHhhHHHHH
Confidence            6899999999999999999999999999998765544322221                  012222332222       


Q ss_pred             --HHHccC---CHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCc
Q 010308          255 --AEATNM---SAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFR  329 (513)
Q Consensus       255 --A~~~~~---s~e~L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~r  329 (513)
                        ......   ....+.+....+..|+++||.+|++||+++|++|.   +.|.+++||||||+||||+|+++|||++|++
T Consensus        81 ~~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~---~~~~~~~dl~q~g~~gl~~a~~~fd~~~g~~  157 (180)
T d1ku2a2          81 EVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVEKFEYKRRFK  157 (180)
T ss_dssp             HHHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTC---SSSSCHHHHHHHHHHHHHHHHHHCCGGGCSC
T ss_pred             HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc---CCCcCHHHHHHHHHHHHHHHHHHcCCCCCCC
Confidence              222211   13455667778899999999999999999999998   7899999999999999999999999999999


Q ss_pred             cchHHHHHHHHHHHHHHH-hcc
Q 010308          330 LSTYGLFWIRHAIIRSMT-VSS  350 (513)
Q Consensus       330 FSTYA~~wIR~aI~raI~-~~r  350 (513)
                      |||||+|||+++|.++++ +++
T Consensus       158 f~tya~~~i~~~i~~~~~~~~r  179 (180)
T d1ku2a2         158 FSTYATWWIRQAINRAIADQAR  179 (180)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSCC
T ss_pred             HHHHHHHHHHHHHHHHHHHhCC
Confidence            999999999999999998 655

>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=99.84  E-value=1.7e-21  Score=196.63  Aligned_cols=80  Identities=41%  Similarity=0.725  Sum_probs=74.4

Q ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHH
Q 010308          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (513)
Q Consensus       265 L~~~~~gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~r  344 (513)
                      +.+.......|++.||.+|++||++||++|.   ++|++++||||+|++||++|+++|||.+|++|||||+||||++|.|
T Consensus       253 i~~ge~~~~~ak~~~~~~~~~lv~~~~~~~~---~~~~~~~dl~~~~~~~l~~~~~~~~~~~~~~f~~~~~~~~~~~~~~  329 (334)
T d1siga_         253 MSIGEAKARRAKKEMVEANLRLVISIAKKYT---NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR  329 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHHTHHHHHHHHTTST---TSSSCHHHHHHHHHHHHHHHHHHCCGGGCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHhhccchHHHHHHhHHHHHHHHHHhcc---CCCCCHHHHHHhhHHHHHHHHHhcCCCCCCchHhhhHHHHHHHHHH
Confidence            4444555678999999999999999999998   7899999999999999999999999999999999999999999999


Q ss_pred             HHH
Q 010308          345 SMT  347 (513)
Q Consensus       345 aI~  347 (513)
                      +|+
T Consensus       330 ~~~  332 (334)
T d1siga_         330 SIA  332 (334)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            997

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

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

Probab=99.79  E-value=1.2e-19  Score=150.09  Aligned_cols=75  Identities=27%  Similarity=0.353  Sum_probs=70.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHHH
Q 010308          273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT  347 (513)
Q Consensus       273 ~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI~  347 (513)
                      +..+++||..|++||.++|++|..+++.+++++||+|+|++||++|+++|||++|.+|+|||.+|||++|.++++
T Consensus         9 ~~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A~~~yd~~~g~~F~tYA~~~Irgai~d~lR   83 (87)
T d1rp3a3           9 QIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLRIKGAIYDYLR   83 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHHHHTCCCCCTHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence            345799999999999999999986666789999999999999999999999999999999999999999999998

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

Probab=99.65  E-value=5.2e-17  Score=127.85  Aligned_cols=65  Identities=42%  Similarity=0.711  Sum_probs=62.8

Q ss_pred             HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010308          448 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  512 (513)
Q Consensus       448 aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl  512 (513)
                      +|+.|+|+|+.||.+||||+++.++|++|||+.||||+++|||++.+|++|||++...+.|+.|+
T Consensus         2 ~L~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrerVrqie~~al~kLr~~~~~~~L~~yl   66 (68)
T d2p7vb1           2 VLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL   66 (68)
T ss_dssp             CSCCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCCGGGGGSCTT
T ss_pred             hhhcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhHHHHHHHHHh
Confidence            47889999999999999999999999999999999999999999999999999999999999997

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

Probab=99.64  E-value=9.5e-17  Score=132.22  Aligned_cols=72  Identities=42%  Similarity=0.749  Sum_probs=68.6

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhcc
Q 010308          441 LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  512 (513)
Q Consensus       441 l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~L~~yl  512 (513)
                      +++.|..+|+.|+|+|+.||.+||||+|++++|+.|||+.||||+++|||++.+|++|||++.....|+.|+
T Consensus         8 l~~~l~~~l~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrERVRQie~~al~kLr~~~~~~~L~~~l   79 (87)
T d1ttya_           8 MREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSKYLKSLL   79 (87)
T ss_dssp             CCSHHHHHHTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTBSSHHHHHHH
T ss_pred             HHHHHHHHHhcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcHHHHHHHHHH
Confidence            456789999999999999999999999999999999999999999999999999999999999999999885

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

Probab=99.55  E-value=8e-16  Score=118.52  Aligned_cols=59  Identities=34%  Similarity=0.510  Sum_probs=55.2

Q ss_pred             HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          445 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       445 L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      |..+|+.|+++|+.||.+||||++++++|+.|||+.||||+++|||++.+|++|||++.
T Consensus         2 l~~~L~~L~~rer~Ii~~ryGl~~~~~~tl~eIa~~lgiS~erVrqi~~~al~kLR~~~   60 (61)
T d1ku3a_           2 LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHE   60 (61)
T ss_dssp             CSSSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHhcCCHHHHHHHHHHhCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhcCC
Confidence            34678899999999999999999999999999999999999999999999999999753

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.27  E-value=4.1e-12  Score=99.43  Aligned_cols=68  Identities=24%  Similarity=0.241  Sum_probs=62.9

Q ss_pred             chhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010308          432 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  503 (513)
Q Consensus       432 ~ee~~~~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~  503 (513)
                      +++.+...++...|..+|+.|||+++.||.++|    ++++|++|||+.||+|.++|+++..+|+++||+..
T Consensus         2 ~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~~L   69 (71)
T d1rp3a2           2 VEEEVIKRELTEKVKEAVSKLPEREKLVIQLIF----YEELPAKEVAKILETSVSRVSQLKAKALERLREML   69 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHH----TSCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHH----hHhCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHc
Confidence            466677888899999999999999999999999    79999999999999999999999999999999643

>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=99.14  E-value=2.8e-11  Score=92.43  Aligned_cols=58  Identities=28%  Similarity=0.413  Sum_probs=54.9

Q ss_pred             cccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcC--CCHHHHHHHHHhccCcccc
Q 010308          352 TRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVN--ISPERYREVMKASKPILSL  409 (513)
Q Consensus       352 iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lg--is~e~v~~~l~~~~~~~SL  409 (513)
                      ||+|.|+.+.+++++++.++|.+++||+||.+|||+.+|  +++++|+.++..++.++||
T Consensus         1 IRlPvH~~e~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~~~~~p~SL   60 (60)
T d1ku2a1           1 IRIPVHMVETINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL   60 (60)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGGGSSSCCCC
T ss_pred             CccchhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHccCCCCC
Confidence            699999999999999999999999999999999999997  5588999999999998886

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=99.06  E-value=2.3e-10  Score=88.96  Aligned_cols=61  Identities=18%  Similarity=0.159  Sum_probs=57.3

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          438 PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       438 ~~~l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      ..++...|..+|+.||++++.||.++|    ++++|++|||+.||+|.++|++...+|+++||..
T Consensus         5 ~~e~~~~l~~~l~~Lp~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~   65 (68)
T d1or7a1           5 SEELRQIVFRTIESLPEDLRMAITLRE----LDGLSYEEIAAIMDCPVGTVRSRIFRAREAIDNK   65 (68)
T ss_dssp             HHHHHHHHHHHHHHSCHHHHHHHHHHH----TTCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHH----HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            456778899999999999999999999    8999999999999999999999999999999964

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

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

Probab=98.99  E-value=2.1e-10  Score=86.52  Aligned_cols=55  Identities=31%  Similarity=0.329  Sum_probs=52.2

Q ss_pred             cccccccchhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhcc
Q 010308          350 SFTRVPFGLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK  404 (513)
Q Consensus       350 r~iRlP~~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~~  404 (513)
                      ++||+|.|+.+.++++.++..+|.+++||+||.+|||+.||+|+++|..+|.+++
T Consensus         2 g~IrvPr~~~e~~~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~r   56 (57)
T d1l0oc_           2 GTVKVSRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVR   56 (57)
T ss_dssp             CCCTTHHHHHHHHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCEeCcHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHhc
Confidence            5799999999999999999999999999999999999999999999999987653

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=98.67  E-value=3.2e-08  Score=83.47  Aligned_cols=48  Identities=23%  Similarity=0.207  Sum_probs=46.1

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      -|||+||.||.++|    ++++|+.|||+.||||+++|+++++||+++||+.
T Consensus        18 LLpe~QR~vl~L~~----~e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~L~~y   65 (106)
T d1xsva_          18 LLTNKQRNYLELFY----LEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDY   65 (106)
T ss_dssp             GSCHHHHHHHHHHH----TSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHH----HhCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            39999999999999    8999999999999999999999999999999974

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=98.67  E-value=1.7e-08  Score=85.23  Aligned_cols=48  Identities=25%  Similarity=0.250  Sum_probs=45.9

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  502 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~  502 (513)
                      -|||+||.||.++|    ++++|++|||+.||||+++|+++++||+++|+..
T Consensus        16 lLp~~qR~v~~L~y----~~~ls~~EIA~~lgiS~~aV~~~l~RA~~~L~~~   63 (106)
T d1s7oa_          16 LLTDKQMNYIELYY----ADDYSLAEIADEFGVSRQAVYDNIKRTEKILETY   63 (106)
T ss_dssp             GSCHHHHHHHHHHH----HTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            39999999999999    8999999999999999999999999999999963

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=98.65  E-value=4.6e-09  Score=83.45  Aligned_cols=69  Identities=25%  Similarity=0.263  Sum_probs=56.5

Q ss_pred             chhHHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCCCHHHHHHHHHhc--cCcccccCCCCCchhhhhcccc
Q 010308          357 GLESVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQEEFINGIT  425 (513)
Q Consensus       357 ~~~~~~~ki~ka~~~L~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLd~~~~~~~~e~~d~l~  425 (513)
                      .+..+.+++.++...|.+++||.||.+|||+.|||++++|+.++...  ..++|||.+..+++.++.+.++
T Consensus         4 s~r~~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~~~~~~~~~SLD~~~~d~~~~~~e~lp   74 (77)
T d1rp3a1           4 QVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIP   74 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHHhcCCceecccCccCCCCchhccCC
Confidence            34578899999999999999999999999999999999999998754  3678999876554444444443

>d1h3la_ a.177.1.1 (A:) Sigma factor SigR {Streptomyces coelicolor a3(2) [TaxId: 100226]}

class: All alpha proteins
fold: Sigma2 domain of RNA polymerase sigma factors
superfamily: Sigma2 domain of RNA polymerase sigma factors
family: Sigma2 domain of RNA polymerase sigma factors
domain: Sigma factor SigR
species: Streptomyces coelicolor a3(2) [TaxId: 100226]

Probab=98.40  E-value=1.9e-07  Score=72.99  Aligned_cols=71  Identities=14%  Similarity=0.069  Sum_probs=63.4

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHchhccCCCCcHHHHHHHHHHHHHHHHhhcCCcCCCccchHHHHHHHHHHHHHH
Q 010308          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM  346 (513)
Q Consensus       271 gd~~Ar~~LI~~nlrLV~sIAkky~~~~~~g~~~eDLIQEG~iGLirAvekFDp~kG~rFSTYA~~wIR~aI~raI  346 (513)
                      +..+++++++..|.+.++.+|.++.   ++..+.+|++||.++.+|+..++|++.  ..|.+|++..+++.+.+.+
T Consensus         4 ~~~~~f~~~~~~y~~~l~~~~~~~~---~d~~~aeDivQd~f~~~~~~~~~~~~~--~~~~~wl~~i~~n~~~d~~   74 (75)
T d1h3la_           4 ERSARFERDALEFLDQMYSAALRMT---RNPADAEDLVQETYAKAYASFHQFREG--TNLKAWLYRILTNTFINSY   74 (75)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHHHHHH---SCHHHHHHHHHHHHHHHHHHGGGCCSS--SCHHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhhhhcCCC--CCHHHHHHHHHHHHHHHHh
Confidence            3456799999999999999999999   788999999999999999999999864  4699999999999887654

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=98.32  E-value=7.9e-07  Score=69.07  Aligned_cols=61  Identities=23%  Similarity=0.292  Sum_probs=54.2

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          441 LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       441 l~~~L~~aL~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ..+.+...++.|+|+|.+|+.+..     .|+|..|||..||||..||+.+..++++||--..+.+
T Consensus         2 ~~~~~~~~~~~LT~rE~~vl~~l~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv~~r~e   62 (70)
T d1yioa1           2 TQDQLEQLFSSLTGREQQVLQLTI-----RGLMNKQIAGELGIAEVTVKVHRHNIMQKLNVRSLAN   62 (70)
T ss_dssp             HHHHHHHHHHTSCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCSSHHH
T ss_pred             cHHHHHHHHccCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence            356778888999999999999976     7999999999999999999999999999998665544

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=98.04  E-value=4.8e-06  Score=63.84  Aligned_cols=53  Identities=26%  Similarity=0.342  Sum_probs=48.2

Q ss_pred             HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          449 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       449 L~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      ++.|+|+|.+|+.+.-     +|+|..|||+.||||..+|+++..+++.||.-..+.+
T Consensus         4 l~~LT~rE~~vl~ll~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv~~r~e   56 (67)
T d1a04a1           4 VNQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVE   56 (67)
T ss_dssp             GGGSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCCSHHH
T ss_pred             cccCCHHHHHHHHHHH-----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence            5689999999999987     7999999999999999999999999999998766544

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.85  E-value=1.7e-05  Score=60.26  Aligned_cols=51  Identities=22%  Similarity=0.244  Sum_probs=46.4

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      .|+|+|++||.+.-     +++|.+|||+.||+|..+|+.+..++++||.-..+.+
T Consensus         4 ~Lt~rE~~vl~l~~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv~~r~~   54 (65)
T d1l3la1           4 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAH   54 (65)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCSSHHH
T ss_pred             ccCHHHHHHHHHHH-----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence            69999999998886     7999999999999999999999999999998665544

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=97.84  E-value=1.5e-05  Score=60.97  Aligned_cols=52  Identities=33%  Similarity=0.327  Sum_probs=46.6

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  507 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~~  507 (513)
                      .|+|+|++|+.+.-     +|+|.+|||..||+|..+|+.+..+.++||--..+.+.
T Consensus         4 ~LT~rE~~vl~l~~-----~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v~~r~~l   55 (67)
T d1fsea_           4 LLTKREREVFELLV-----QDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQA   55 (67)
T ss_dssp             CCCHHHHHHHHHHT-----TTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHHHH
T ss_pred             CCCHHHHHHHHHHH-----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHHH
Confidence            49999999998875     89999999999999999999999999999987665443

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=97.49  E-value=8.9e-05  Score=59.49  Aligned_cols=51  Identities=31%  Similarity=0.330  Sum_probs=46.3

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  506 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~~~  506 (513)
                      .|+++|.+|+.+..     .|+|.+|||+.||+|..+|+....++++||.-..+.+
T Consensus        22 ~LT~rE~~vl~ll~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~~~~~~~   72 (87)
T d1p4wa_          22 RLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIA   72 (87)
T ss_dssp             SCCHHHHHHHHHHH-----HTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHHH
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence            59999999999987     7999999999999999999999999999997655433

>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=95.94  E-value=0.009  Score=43.64  Aligned_cols=40  Identities=30%  Similarity=0.409  Sum_probs=34.7

Q ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHH
Q 010308          232 KVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEV  271 (513)
Q Consensus       232 ~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~g  271 (513)
                      ..+.+...+|..++||+||.+|+|..+|++.+.+..++..
T Consensus        15 ~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a   54 (57)
T d1l0oc_          15 NKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEA   54 (57)
T ss_dssp             HHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3456778889999999999999999999999999887754

>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=95.78  E-value=0.0079  Score=46.31  Aligned_cols=41  Identities=37%  Similarity=0.553  Sum_probs=35.0

Q ss_pred             HhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHH
Q 010308          230 PMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLE  270 (513)
Q Consensus       230 ~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~~s~e~L~~~~~  270 (513)
                      ....+.+....|+.++||+|+.+|+|..+||+.+.+.+++.
T Consensus         8 ~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~   48 (77)
T d1rp3a1           8 KERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLD   48 (77)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34567788889999999999999999999999988877653

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=95.13  E-value=0.013  Score=41.17  Aligned_cols=38  Identities=11%  Similarity=0.069  Sum_probs=32.5

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHE  492 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~  492 (513)
                      .|++.+.+-++..+    ..+.|..+||..||||+.||.+++
T Consensus         5 ~lt~~q~~~a~~l~----~~G~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           5 AINKHEQEQISRLL----EKGHPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             SSCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             cCCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHhhC
Confidence            47888888887777    578999999999999999998763

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=94.57  E-value=0.017  Score=44.01  Aligned_cols=43  Identities=21%  Similarity=0.131  Sum_probs=34.2

Q ss_pred             cCCHHHHHHHhH--HhcCCCCCCCCHHHHHHHhCC-CHHHHHHHHH
Q 010308          451 SLKPKESLVIRQ--RFGLDGKGDRTLGEIAGNLNI-SREMVRKHEV  493 (513)
Q Consensus       451 ~L~~rEr~VL~l--RyGL~~~~~~Tl~EIA~~LgI-SrerVRqi~~  493 (513)
                      .|+++|+.||..  .|-...+.+-|+.|||+.||+ |.++|+.++.
T Consensus         2 ~LT~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~   47 (71)
T d1jhfa1           2 ALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLK   47 (71)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHH
Confidence            599999999876  332233467899999999999 8999998754

>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=94.00  E-value=0.051  Score=39.95  Aligned_cols=41  Identities=37%  Similarity=0.563  Sum_probs=32.2

Q ss_pred             HhHHHHHHHHHHHHHhCCCCCHHHHHHHcc--CCHHHHHHHHH
Q 010308          230 PMKVFVQVKEQLQKDLGREPTDVELAEATN--MSAAQVKKCLE  270 (513)
Q Consensus       230 ~~~~l~~~~~~l~~~l~r~p~~~e~A~~~~--~s~e~L~~~~~  270 (513)
                      .+..+.++..+|..++||+||.+|+|.++|  ++.+.+..++.
T Consensus        10 ~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~   52 (60)
T d1ku2a1          10 TINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLK   52 (60)
T ss_dssp             HHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGG
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHH
Confidence            344566778889999999999999999987  45677776553

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.08  E-value=0.079  Score=39.72  Aligned_cols=43  Identities=26%  Similarity=0.195  Sum_probs=33.3

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      .|+..|+.=|..+|-  .+..++..|||..|||++++|+.|+..-
T Consensus         7 ~LT~~eK~~ii~~~e--~g~k~sq~eIA~~fGv~~STvs~IlKnK   49 (66)
T d1hlva1           7 QLTFREKSRIIQEVE--ENPDLRKGEIARRFNIPPSTLSTILKNK   49 (66)
T ss_dssp             CCCHHHHHHHHHHHH--HCTTSCHHHHHHHHTCCHHHHHHHHHTH
T ss_pred             cCCHHHHHHHHHHHH--cCCcchHHHHHHHhCCChhHHHHHHHHH
Confidence            477777766666661  2344789999999999999999998764

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=92.08  E-value=0.068  Score=36.62  Aligned_cols=32  Identities=22%  Similarity=0.159  Sum_probs=27.0

Q ss_pred             HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          458 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       458 ~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .|..|+-     ++++-.+||+.|||++.+|.+++..
T Consensus        10 ~V~~L~~-----~G~gat~IAk~lgI~R~SVYR~L~~   41 (43)
T d1gdta1          10 AVLNMWQ-----QGLGASHISKTMNIARSTVYKVINE   41 (43)
T ss_dssp             HHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHhh
Confidence            4666665     7999999999999999999988764

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=91.36  E-value=0.17  Score=37.05  Aligned_cols=40  Identities=15%  Similarity=0.273  Sum_probs=33.0

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      |++.++.||..--.   ....|+.|||+.+|+|..+|+....+
T Consensus         3 lD~~D~~IL~~L~~---~~r~s~~eiA~~l~ls~~~v~~Ri~r   42 (63)
T d2cg4a1           3 IDNLDRGILEALMG---NARTAYAELAKQFGVSPETIHVRVEK   42 (63)
T ss_dssp             CCHHHHHHHHHHHH---CTTSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            67788888877652   45789999999999999999977655

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=90.98  E-value=0.21  Score=36.63  Aligned_cols=41  Identities=12%  Similarity=0.159  Sum_probs=32.8

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      +|++.++.||..--.   ....|+.|||+.+|+|+++|.+...+
T Consensus         2 klD~~D~~IL~~L~~---n~r~s~~~iA~~lgis~~tv~~Ri~~   42 (63)
T d2cfxa1           2 KLDQIDLNIIEELKK---DSRLSMRELGRKIKLSPPSVTERVRQ   42 (63)
T ss_dssp             CCCHHHHHHHHHHHH---CSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            477788888877542   35789999999999999999977654

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=90.93  E-value=0.22  Score=37.42  Aligned_cols=43  Identities=26%  Similarity=0.268  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHhcCC-CHHHHHHHHHh
Q 010308          360 SVRGEIQRAKLELLFELKRVPTDEEIIQGVNI-SPERYREVMKA  402 (513)
Q Consensus       360 ~~~~ki~ka~~~L~~elgR~PT~eELA~~lgi-s~e~v~~~l~~  402 (513)
                      ..-.++-.+...+..+.|..||..|||+.+|+ |...++..+..
T Consensus         5 ~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~   48 (71)
T d1jhfa1           5 ARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKA   48 (71)
T ss_dssp             HHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHH
Confidence            34456666777788889999999999999999 78888888765

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=90.50  E-value=0.18  Score=36.60  Aligned_cols=40  Identities=23%  Similarity=0.315  Sum_probs=31.2

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      |++.++.||.+--.   ....|+.|||+.+|+|.++|.+...+
T Consensus         1 lD~~D~kIl~~L~~---n~r~s~~~lA~~~gls~~~v~~Ri~~   40 (60)
T d1i1ga1           1 IDERDKIILEILEK---DARTPFTEIAKKLGISETAVRKRVKA   40 (60)
T ss_dssp             CCSHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45667778776542   35789999999999999999977654

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=88.77  E-value=0.39  Score=34.56  Aligned_cols=41  Identities=17%  Similarity=0.194  Sum_probs=30.7

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      |++-++.||..--.   ....|+.|||+.+|+|..+|.....+=
T Consensus         1 lD~~D~~Il~~L~~---n~r~s~~eiA~~l~ls~~~v~~Ri~~L   41 (60)
T d2cyya1           1 LDEIDKKIIKILQN---DGKAPLREISKITGLAESTIHERIRKL   41 (60)
T ss_dssp             CCHHHHHHHHHHHH---CTTCCHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            45566677766441   356899999999999999999776553

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=88.33  E-value=0.42  Score=36.95  Aligned_cols=52  Identities=17%  Similarity=0.123  Sum_probs=40.2

Q ss_pred             HHHHHHHhcCCHHHHHHHhHHhcC-CCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          443 LALDDVLDSLKPKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       443 ~~L~~aL~~L~~rEr~VL~lRyGL-~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ..|...+..||+.|+.|..+..-- +....+|..|||+..|||..+|-+..++
T Consensus         7 ~~i~~~~~~Ls~~e~~ia~yil~~~~~~~~~si~~lA~~~~vS~sTi~Rf~kk   59 (83)
T d2o3fa1           7 AIIQSMKHKLPPSERKLADYILAHPHKAIESTVNEISALANSSDAAVIRLCKS   59 (83)
T ss_dssp             HHHHHHGGGSCHHHHHHHHHHHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHhhCCHHHHHHHHHHHcCHHHHHHccHHHHHHHHCCCHHHHHHHHHH
Confidence            467788899999999997654410 1124699999999999999999876543

>d1nr3a_ d.236.1.1 (A:) DNA-binding protein Tfx {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a+b)
fold: DNA-binding protein Tfx
superfamily: DNA-binding protein Tfx
family: DNA-binding protein Tfx
domain: DNA-binding protein Tfx
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=87.80  E-value=0.008  Score=50.59  Aligned_cols=36  Identities=19%  Similarity=0.257  Sum_probs=32.8

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010308          469 KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  504 (513)
Q Consensus       469 ~~~~Tl~EIA~~LgISrerVRqi~~rALkKLR~~~~  504 (513)
                      .+|+|++|||+.||.|+.+|+.++.+|++++++...
T Consensus         3 ~kGltQ~eIA~~LgTSraNIs~IEk~A~eNIekAr~   38 (122)
T d1nr3a_           3 ERGWSQKKIARELKTTRQNVSAIERKAMENIEKSRN   38 (122)
T ss_dssp             CCSCSSCSTHHHHHHCCSSSCCHHHHHHTTCSSSSC
T ss_pred             cccCCHHHHHHHHCccHHHHHHHHHHHHHHHHHHHH
Confidence            368999999999999999999999999999987654

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=87.75  E-value=0.33  Score=40.28  Aligned_cols=41  Identities=20%  Similarity=0.027  Sum_probs=31.0

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010308          452 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  496 (513)
Q Consensus       452 L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rAL  496 (513)
                      ||...|.-|.-.|    ..+++..+||+.||||+.+|+++..+=.
T Consensus        17 Ls~dlR~rIv~~~----~~G~s~r~iA~~~~VS~~tV~k~l~r~~   57 (123)
T d1pdnc_          17 LPNNIRLKIVEMA----ADGIRPCVISRQLRVSHGCVSKILNRYQ   57 (123)
T ss_dssp             CCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH----HhcCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4444444444445    4789999999999999999999887643

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.41  E-value=0.52  Score=34.33  Aligned_cols=38  Identities=16%  Similarity=0.096  Sum_probs=28.2

Q ss_pred             CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          453 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       453 ~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      +.....||.+--   +....|.+|+|+.||||+.+|++.+.
T Consensus         4 ~~~~~~iL~~L~---~~~~~s~~eLa~~l~vS~~ti~r~i~   41 (63)
T d1biaa1           4 NTVPLKLIALLA---NGEFHSGEQLGETLGMSRAAINKHIQ   41 (63)
T ss_dssp             CHHHHHHHHHHT---TSSCBCHHHHHHHHTSCHHHHHHHHH
T ss_pred             cHHHHHHHHHHH---HCCcCCHHHHHHHHCcCHHHHHHHHH
Confidence            445555665443   34678999999999999999997654

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=86.45  E-value=0.36  Score=37.50  Aligned_cols=35  Identities=20%  Similarity=0.213  Sum_probs=27.9

Q ss_pred             HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          458 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       458 ~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      ++|.+..-   .+++|+.+||..||||.++|+++..+.
T Consensus        13 ~aV~l~~~---~~g~s~~~vA~~lGIs~~tl~~W~k~~   47 (89)
T d2jn6a1          13 DAVALYEN---SDGASLQQIANDLGINRVTLKNWIIKY   47 (89)
T ss_dssp             HHHHHHTT---GGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHH---cCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            45556540   137999999999999999999998765

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=86.07  E-value=0.3  Score=35.45  Aligned_cols=25  Identities=20%  Similarity=0.132  Sum_probs=22.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          470 GDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       470 ~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .++|.+|+|+.+|||+.+|+++++.
T Consensus        11 ~gltQ~elA~~lGvs~~tvs~~E~G   35 (62)
T d2ppxa1          11 LKLTQEEFSARYHIPLGTLRDWEQG   35 (62)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHTT
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence            4789999999999999999999973

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=85.61  E-value=0.65  Score=37.16  Aligned_cols=47  Identities=28%  Similarity=0.411  Sum_probs=36.0

Q ss_pred             HHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          445 LDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       445 L~~aL~--~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      |...|.  .|++.|-.|+..-+-   ..+.|..|||+.+|+++.+|...+.+
T Consensus         9 l~~~L~~lGlt~~e~~v~~~L~~---~g~~t~~eia~~~~i~~~~v~~~l~~   57 (109)
T d1sfxa_           9 LVKALEKLSFKPSDVRIYSLLLE---RGGMRVSEIARELDLSARFVRDRLKV   57 (109)
T ss_dssp             HHHHHHHTCCCHHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHh---cCCCCHHHHHHHhCCCcchHHHHHHH
Confidence            334444  489999999776552   36899999999999999999865543

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=84.99  E-value=0.97  Score=35.68  Aligned_cols=46  Identities=15%  Similarity=0.302  Sum_probs=32.6

Q ss_pred             HHHHHHhcCC-HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          444 ALDDVLDSLK-PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       444 ~L~~aL~~L~-~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      .+..++..|. |.-..||.+-.    ..++|..|||+.+|+|.++|++++.
T Consensus        12 ~la~~~kaL~~p~Rl~Il~~L~----~~~~~v~ela~~l~is~stvS~HL~   58 (98)
T d1r1ta_          12 SLAEFFAVLADPNRLRLLSLLA----RSELCVGDLAQAIGVSESAVSHQLR   58 (98)
T ss_dssp             HHHHHHHHHCCHHHHHHHHHHT----TCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH----cCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            4445555554 44445554443    4679999999999999999998764

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.88  E-value=0.54  Score=35.23  Aligned_cols=44  Identities=9%  Similarity=0.113  Sum_probs=38.0

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh-CCCHHHHHHHHH
Q 010308          450 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNL-NISREMVRKHEV  493 (513)
Q Consensus       450 ~~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~L-gISrerVRqi~~  493 (513)
                      +-|+|.++.|+.+.-.-.+.+|.+..||+..| |+|...|++...
T Consensus         2 nGLs~~q~~V~~~i~s~~~~eGi~~~el~~~l~~~~~~~i~~aid   46 (69)
T d1dpua_           2 NGLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVD   46 (69)
T ss_dssp             CCSCHHHHHHHHHHHHCCCTTTEEHHHHHHHSTTSCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHhCCCccCcCHHHHHHHccCCCHHHHHHHHH
Confidence            35899999999998877777899999999999 899999886543

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=84.28  E-value=0.92  Score=37.62  Aligned_cols=53  Identities=21%  Similarity=0.212  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHhc--CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          440 LLRLALDDVLDS--LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       440 ~l~~~L~~aL~~--L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .+.+.+..++..  |++-+-.|+.+-+ +. .+++|..|||+.+|+|+++|++...+
T Consensus        10 ~~~~~~~~~~~~~Gl~~~~~~i~~~L~-~~-~~plt~~ela~~l~vsk~~vs~~l~~   64 (151)
T d1ku9a_          10 LIIELFSELAKIHGLNKSVGAVYAILY-LS-DKPLTISDIMEELKISKGNVSMSLKK   64 (151)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHHHH-HC-SSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHH-hC-CCCcCHHHHHHHhCCCcchHHHHHHH
Confidence            344445555544  7999999998876 22 35799999999999999999865544

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=84.13  E-value=0.65  Score=33.86  Aligned_cols=39  Identities=15%  Similarity=0.183  Sum_probs=28.5

Q ss_pred             HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          454 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       454 ~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ++...||.+-.  ......|..|+|+.||||+.||++-+..
T Consensus         7 eR~~~Il~~L~--~~~~~vs~~~La~~l~VS~~TI~rdi~~   45 (65)
T d1j5ya1           7 ERLKSIVRILE--RSKEPVSGAQLAEELSVSRQVIVQDIAY   45 (65)
T ss_dssp             HHHHHHHHHHH--HCSSCBCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHH--HcCCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence            45556666543  1124579999999999999999987754

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=83.97  E-value=0.48  Score=37.76  Aligned_cols=42  Identities=17%  Similarity=0.196  Sum_probs=33.9

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      .|++.+..||..-+-.  .+++|..|||+.+|+++++|++++.+
T Consensus        18 gLs~~~~~iL~~L~~~--~~~~t~~eLa~~~~i~~~tvs~~l~~   59 (109)
T d2d1ha1          18 KITDTDVAVLLKMVEI--EKPITSEELADIFKLSKTTVENSLKK   59 (109)
T ss_dssp             TCCHHHHHHHHHHHHH--CSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHc--CCCCCHHHHHHHHCccHhHHHHHHHH
Confidence            5999999998655421  34699999999999999999976654

>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: HTH-motif protein NE1354
species: Nitrosomonas europaea [TaxId: 915]

Probab=83.58  E-value=0.59  Score=34.39  Aligned_cols=32  Identities=13%  Similarity=-0.020  Sum_probs=27.4

Q ss_pred             HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          458 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       458 ~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      .|-.+|.    ..++|.+|+|+.+|||+.+|..+++
T Consensus        10 ~i~~~r~----~~gltq~elA~~~gv~~~~is~ie~   41 (69)
T d2a6ca1          10 VLQEHLR----NSGLTQFKAAELLGVTQPRVSDLMR   41 (69)
T ss_dssp             HHHHHHH----TTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHH----HcCCCHHHHHHHHHcCHhHHHHHHc
Confidence            3445566    6899999999999999999999986

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=83.10  E-value=0.52  Score=36.83  Aligned_cols=43  Identities=14%  Similarity=0.114  Sum_probs=33.4

Q ss_pred             cCCHHHHHHHhHHh--cCCCCCCCCHHHHHHHhC--CCHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRF--GLDGKGDRTLGEIAGNLN--ISREMVRKHEV  493 (513)
Q Consensus       451 ~L~~rEr~VL~lRy--GL~~~~~~Tl~EIA~~Lg--ISrerVRqi~~  493 (513)
                      +|++|+++||....  -+..+.+-+.++|++.+|  +|..+||..+.
T Consensus         1 ~Lt~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~   47 (87)
T d1stza1           1 KLNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMK   47 (87)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHH
Confidence            48999999987532  134467999999999965  58999998764

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.58  E-value=0.69  Score=32.56  Aligned_cols=49  Identities=20%  Similarity=0.217  Sum_probs=39.0

Q ss_pred             cCCHHHHHHHhHHhcCCCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKG-DRTLGEIAGNLNISREMVRKHEVKGLMKL  499 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~-~~Tl~EIA~~LgISrerVRqi~~rALkKL  499 (513)
                      .|+|.+..||...|..+.+. .....+||..+|||...|+.+...-..+.
T Consensus         3 ~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~   52 (53)
T d1le8a_           3 SISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRS   52 (53)
T ss_dssp             CCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhcc
Confidence            58999999999999765432 24578999999999999999887665543

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=82.39  E-value=0.66  Score=34.23  Aligned_cols=36  Identities=11%  Similarity=0.012  Sum_probs=28.2

Q ss_pred             HHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          457 SLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       457 r~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      ..||.+-+-   ..+.|..|||+.+|+|+.+|+.+...=
T Consensus         9 ~~Il~~l~~---~g~~sr~eLa~~~glS~~Tv~~~l~~L   44 (71)
T d1z05a1           9 GRVYKLIDQ---KGPISRIDLSKESELAPASITKITREL   44 (71)
T ss_dssp             HHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHH---cCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            355555442   358999999999999999999887653

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=82.39  E-value=0.89  Score=33.74  Aligned_cols=24  Identities=33%  Similarity=0.342  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          470 GDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       470 ~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      .++|..|+|+.||||+.+|.+++.
T Consensus        13 ~gltQ~elA~~LGvs~~ti~~yE~   36 (67)
T d2auwa1          13 NNLSLTTAAEALGISRRMVSYYRT   36 (67)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Confidence            478999999999999999999876

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=82.32  E-value=0.49  Score=34.42  Aligned_cols=25  Identities=28%  Similarity=0.332  Sum_probs=23.1

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          469 KGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       469 ~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      ..++|..|+|+.+|||+++|.++++
T Consensus        12 ~~g~tq~elA~~~gis~~~is~~e~   36 (66)
T d1utxa_          12 KKKISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHhcccCHHHHHHHHc
Confidence            4689999999999999999999986

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=82.28  E-value=2  Score=34.81  Aligned_cols=51  Identities=8%  Similarity=0.021  Sum_probs=37.9

Q ss_pred             HHHHHHHHHhc--CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 010308          441 LRLALDDVLDS--LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHE  492 (513)
Q Consensus       441 l~~~L~~aL~~--L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~  492 (513)
                      +...+...+..  |++.|-.||..-+.. ++++.|..|||+.++++.++|..+.
T Consensus        14 ~~~~~~~~l~~~glt~~q~~vL~~l~~~-~~~~it~~ela~~~~~~~~~vs~~l   66 (135)
T d3broa1          14 MSTRFDIFAKKYDLTGTQMTIIDYLSRN-KNKEVLQRDLESEFSIKSSTATVLL   66 (135)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHT-TTSCCBHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHCcCHhHHHHHH
Confidence            34445555544  899999998776632 2356899999999999999998543

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.15  E-value=1.1  Score=32.83  Aligned_cols=26  Identities=19%  Similarity=0.072  Sum_probs=23.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010308          470 GDRTLGEIAGNLNISREMVRKHEVKG  495 (513)
Q Consensus       470 ~~~Tl~EIA~~LgISrerVRqi~~rA  495 (513)
                      +++|-.+||+.|+||.++|.++..+-
T Consensus        29 ~G~s~r~aA~rf~VS~s~v~k~l~r~   54 (63)
T d1k78a1          29 QGVRPCDISRQLRVSHGCVSKILGRY   54 (63)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            68999999999999999999998764

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Transcriptional repressor protein KorB DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=82.10  E-value=0.69  Score=37.35  Aligned_cols=40  Identities=25%  Similarity=0.351  Sum_probs=32.8

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          451 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       451 ~L~~rEr~VL~lRyGL~~~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      .|+|-|...-..++ +  ..++|.++||+.+|.|+.+|++++.
T Consensus        13 ~L~p~e~A~a~~~l-~--~~g~s~~eiA~~~G~s~~~V~~~l~   52 (114)
T d1r71a_          13 ELTPREIADFIGRE-L--AKGKKKGDIAKEIGKSPAFITQHVT   52 (114)
T ss_dssp             CCCHHHHHHHHHHH-H--HTTCCHHHHHHHHTCCHHHHHHHHG
T ss_pred             CCCHHHHHHHHHHH-H--HhCCCHHHHHHHHCCcHHHHHHHHH
Confidence            48888888766665 2  2478999999999999999998865

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=81.57  E-value=0.59  Score=36.25  Aligned_cols=25  Identities=16%  Similarity=0.155  Sum_probs=23.6

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          469 KGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       469 ~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      ..++|..++|+.+|+|+.+|.++++
T Consensus        22 ~~gltq~~lA~~~gis~~~is~ie~   46 (89)
T d2o38a1          22 RARLSQAAAAARLGINQPKVSALRN   46 (89)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHHhhHhHHHHHHc
Confidence            5789999999999999999999997

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

Probab=80.90  E-value=0.69  Score=33.85  Aligned_cols=25  Identities=16%  Similarity=-0.003  Sum_probs=23.2

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010308          469 KGDRTLGEIAGNLNISREMVRKHEV  493 (513)
Q Consensus       469 ~~~~Tl~EIA~~LgISrerVRqi~~  493 (513)
                      ..++|.+++|+.+|+|+++|+++++
T Consensus        20 ~~gltq~~lA~~~gis~~~i~~~E~   44 (69)
T d1y7ya1          20 AKGLSQETLAFLSGLDRSYVGGVER   44 (69)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHhHhCCCHHHHHHHHC
Confidence            4689999999999999999999986

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=80.77  E-value=0.56  Score=34.44  Aligned_cols=27  Identities=33%  Similarity=0.250  Sum_probs=22.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010308          471 DRTLGEIAGNLNISREMVRKHEVKGLMKLKH  501 (513)
Q Consensus       471 ~~Tl~EIA~~LgISrerVRqi~~rALkKLR~  501 (513)
                      +.|.+|||..+|+|+++|.    |.|++|++
T Consensus        29 ~lt~~~lA~~~G~sRetvs----r~L~~l~~   55 (69)
T d1i5za1          29 KITRQEIGQIVGCSRETVG----RILKMLED   55 (69)
T ss_dssp             ECCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            4899999999999999998    45555654

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

Probab=80.16  E-value=0.76  Score=32.87  Aligned_cols=26  Identities=12%  Similarity=0.147  Sum_probs=23.7

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010308          469 KGDRTLGEIAGNLNISREMVRKHEVK  494 (513)
Q Consensus       469 ~~~~Tl~EIA~~LgISrerVRqi~~r  494 (513)
                      ..++|.+|+|+.+|||+.+|+++++.
T Consensus        12 ~~g~sq~elA~~~gvs~~~is~~E~g   37 (63)
T d1r69a_          12 QLGLNQAELAQKVGTTQQSIEQLENG   37 (63)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             HcCCcHHHHHHHhCcCHHHHHHHHCC
Confidence            46899999999999999999999873