Citrus Sinensis ID: 010092

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------52
Protein Sequence
MGVVTISSSPARSPIGLSTISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETPKRHQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYADGVVKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKNEDEKVVTKTRKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccEEcccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccHHHHHcHHHHHHHHHHHcHHHHHHHHcccccHHHHHHHHHHHHHcccccHHHHHHHHcccccccccHHHHHHHHHHcccHHHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHccccccccccHHHHHHcccccHHHHHHHHHHHHHHcccccHHHHHHHccc
Secondary Structure Prediction (SSPRO)
ccEEEEEccccccccccccccccccccccEEEEEEccccccEEEEccccccccccccccccccEccccccccccccEEEEEEcccccccccHHHHHHHHHHHHHcccccccccHHHHcccEEcccccEEEEcccccccccccccEEEEccccccccccHHHHHHHccccHHHHcccccccccccHHHHHHHHHHHccccccHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHccccHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHcccEccccccccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHcccccEccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccHHHccEEEEEEcccccccccHHHHHHHHcccHHHHHHHHHHHHHHcccccHHHHHHHHcc
Coil and Loop (DISEMBL)
mgvvtisssparspiglstishrstskrpLIVAFKadksnnqalfspqeqiplpietpkrhQKRRENSRKRLERVkgvfsdeaspctldvDYNEAAAKLENIyklspavttsevkyadgvvkRGRQRRKRIgevekksddvsgkpvvrnqvkrpkrlsldkRIELRKNEDEKVVtktrktdskdeHEKIEKLVREYSYstdlvsldwkkmkippvlssteHTWLFKLMQPMKVFVQVKEQLQKdlgreptdvELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFqdfangprfqdLCQAGVKGLITAIDrfepkrrfrlstyGLFWIRHAIIRSMtvssftrvpfglestSIMQVRGEIQRAKLELLFElkrvptdeeiiqgvnispeRYREVMKASKpilslhsrhgvtqeefingitdvdgvenenqrQPALLRLALDDVldslkpkesLVIRQRfgldgkgdrtlgeiagnlniSREMVRKHEVKGlmklkhptrvdyLRQHMV
Flexible Loop (DISEMBL)
mgvvtisssparspiglstishrstskRPLIVAFKADKSNNQalfspqeqiplpietpkrhqkrrensrkrlervkgvfsdeaspctlDVDYNEAAAKLENiyklspavttsevkyadgvvkrgrqrrkrigevekksddvsgkpvvrnqvkrpkrlsldkrielrknedekvvtktrktdskdehekieklvreysystdlvsldwkkmkippVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLItaidrfepkrrFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFelkrvptdeeiiqgvnisperyREVMKASKPILslhsrhgvtqeEFINGITDVDGVENENQRQPALLRLALDDVLdslkpkeslvirqrfgldgkgdrtlgeiagnlnisreMVRKHEvkglmklkhptrvdylrqhmv
Low Complexity Region (SEG)
MGVVTISSSPARSPIGLSTISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETPKRHQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYADgvvkrgrqrrkrIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKNEDEKVVTKTRKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAllrlalddvldslKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV
Disordered region (IsUnstruct)
************************************************************************************PCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYADGV**********************************************************************KLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQL********************AAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV*******PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM****************
Disordered Region (DISOPRED)
*******************************************************************************************YNEAAAKLENIYKLSPAVTTSE**************************************************************************************TDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQV**************VELAEATNMSAAQV************KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV
Disordered Region (DISEMBL)
************SPIGLSTISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIET*************RLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYADGVVKRGRQRRKRIGE***********PVVRNQVKRPKRLSLDKRIELRKNE*****************EKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV
Disordered Region (DISPRO)
***********RSP**LST*SHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIET***************ERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYADGVVKRGRQRRKRIGEV******VSGKPVVRNQVK*****S**************************************SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRH*VTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR**MV
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGVVTISSSPARSPIGLSTISHRSTSKRPLIVAFKADKSNNQALFSPQEQIPLPIETPKRHQKRRENSRKRLERVKGVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTTSEVKYADGVVKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKNEDEKVVTKTRKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	518	2.2.26 [Sep-21-2011]
Q9ZNX9	517	RNA polymerase sigma fact	yes	no	0.976	0.978	0.655	0.0
P26683	390	RNA polymerase sigma fact	yes	no	0.656	0.871	0.329	1e-42
P38023	399	RNA polymerase sigma fact	yes	no	0.604	0.784	0.322	3e-37
P52322	416	RNA polymerase sigma fact	yes	no	0.476	0.593	0.359	2e-35
P74565	425	RNA polymerase sigma fact	N/A	no	0.453	0.552	0.360	4e-35
Q59753	684	RNA polymerase sigma fact	yes	no	0.523	0.396	0.33	7e-34
O22056	572	RNA polymerase sigma fact	no	no	0.525	0.475	0.325	9e-34
P18183	511	RNA polymerase principal	yes	no	0.478	0.485	0.351	2e-33
P77951	514	RNA polymerase principal	yes	no	0.492	0.496	0.351	2e-33
P26480	617	RNA polymerase sigma fact	yes	no	0.552	0.463	0.289	5e-33

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

 Score =  673 bits (1737), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 347/529 (65%), Positives = 416/529 (78%), Gaps = 23/529 (4%)

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 SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK 409
           +FTRVPFGLES     VR EI +AK EL FE+ R PT++E+++ + I+PERYREV++A+K
Sbjct: 354 NFTRVPFGLES-----VRVEIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAK 408

Query: 410 PILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRF 469
           P+LSL+S+H VTQEEFINGITDVDGV   N RQPALLRLALDDVLDSLKPKESLVIRQR+
Sbjct: 409 PVLSLNSKHSVTQEEFINGITDVDGVGANNSRQPALLRLALDDVLDSLKPKESLVIRQRY 468

Query: 470 GLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 518
           GLDGKGDRTLGEIAGNLNISREMVRKHEVK LMKLKH  RVDYLRQ++V
Sbjct: 469 GLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHQARVDYLRQYIV 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 =  174 bits (442), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 120/364 (32%), Positives = 197/364 (54%), Gaps = 24/364 (6%)

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-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQG 393
            +WIR AI R++   S T R+P  L  T        I++    L  E+ R PT+EEI   
Sbjct: 211 TWWIRQAITRAIADQSRTIRLPVHLYETI-----SRIKKTTKLLSQEMGRKPTEEEIATR 265

Query: 394 VNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDV 453
           + ++ E+ R + K+++  +SL +  G  ++  +    + DG   E+Q    LLR  L+ V
Sbjct: 266 MEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIESDGETPEDQVSKNLLREDLEKV 325

Query: 454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL 513
           LDSL P+E  V+R R+GLD    +TL EI    N++RE +R+ E K L KL+HP R   L
Sbjct: 326 LDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVL 385

Query: 514 RQHM 517
           ++++
Sbjct: 386 KEYI 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 =  156 bits (395), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 104/322 (32%), Positives = 179/322 (55%), Gaps = 9/322 (2%)

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-RVPFGLESTSIMQVRGEIQRAKL 375
            A ++F+ ++ ++ STY  +WIR AI R++   S T R+P  L  T        I++   
Sbjct: 202 RAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI-----SRIKKTTK 256

Query: 376 ELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV 435
            L  E+ R PT+EEI   + ++ E+ R + K+++  +SL +  G  ++  +    + DG 
Sbjct: 257 LLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGE 316

Query: 436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRK 495
             E++    LLR  L+ VL +L P+E  V+R R+GLD    +TL EI    N++RE +R+
Sbjct: 317 TPEDEVAKNLLREDLEGVLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQ 376

Query: 496 HEVKGLMKLKHPTRVDYLRQHM 517
            E K L KL+HP R   L++++
Sbjct: 377 IEAKALRKLRHPNRNSILKEYI 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 =  150 bits (379), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 92/256 (35%), Positives = 148/256 (57%), Gaps = 9/256 (3%)

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-RVPFGLESTSIMQVRGEIQRAKLELLFEL 381
           + ++ ++ STY  +WIR AI R++   S T R+P  L  T        I++    L  E+
Sbjct: 225 DHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI-----SRIKKTTKILSQEM 279

Query: 382 KRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQR 441
           +R PT+EEI   + ++ E+ R + K+++  +SL +  G  ++  +    + DG   E++ 
Sbjct: 280 RRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPEDEV 339

Query: 442 QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 501
              LLR  L++VLD+L P+E  V+R R+GLD    +TL EI    N++RE +R+ E K L
Sbjct: 340 SKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKAL 399

Query: 502 MKLKHPTRVDYLRQHM 517
            KL+HP R   L++++
Sbjct: 400 RKLRHPNRNSILKEYI 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 =  149 bits (377), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 88/244 (36%), Positives = 144/244 (59%), Gaps = 9/244 (3%)

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

Query: 335 LFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQG 393
            +WIR AI R++   S T R+P  L  T        I++    L  E++R PT+EEI + 
Sbjct: 246 TWWIRQAITRAIADQSRTIRLPVHLYETI-----SRIKKTTKLLSQEMRRKPTEEEIAEK 300

Query: 394 VNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDV 453
           + ++ E+ R + K+++  +SL +  G  ++  +    + DG   E++    LLR  L++V
Sbjct: 301 MEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPEDEVSKNLLREDLENV 360

Query: 454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL 513
           LD+L P+E  V+R R+GLD    +TL EI    N++RE +R+ E K L KL+HP R   L
Sbjct: 361 LDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSIL 420

Query: 514 RQHM 517
           ++++
Sbjct: 421 KEYI 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 =  145 bits (366), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 99/300 (33%), Positives = 163/300 (54%), Gaps = 29/300 (9%)

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-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYRE 403
           S+   + T R+P       +++   +I R   ++L E+ R PT EE+ + + +  E+ R+
Sbjct: 513 SIADQARTIRIPV-----HMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRK 567

Query: 404 VMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQP------ALLRLALDDVLDSL 457
           V+K +K  +SL +  G  ++  +      D +E++N   P      A LR     VL SL
Sbjct: 568 VLKIAKEPISLETPVGDEEDSHLG-----DFIEDKNALLPIDAAIQANLRETTTRVLASL 622

Query: 458 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
            P+E  V+R RFG+    D TL E+    +++RE +R+ E K L KLKHP+R   LR  +
Sbjct: 623 TPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFL 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 =  145 bits (365), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 93/286 (32%), Positives = 156/286 (54%), Gaps = 14/286 (4%)

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 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILS 413
           +PF +     ++    ++ A+ +L  E  + P +EEI +   +S +R   V+ + KP  S
Sbjct: 409 LPFHM-----VEATYRVKEARKQLYSETGKHPKNEEIAEATGLSMKRLMAVLLSPKPPRS 463

Query: 414 LHSRHGVTQE-EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLD 472
           L  + G+ Q  +    I D + V +E+      +R  LD VLDSL  +E  VIR RFG++
Sbjct: 464 LDQKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDLDKVLDSLGTREKQVIRWRFGME 523

Query: 473 GKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 518
               +TL EI   + +SRE VR+ E     KLK+  R ++L+Q++V
Sbjct: 524 DGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRNNHLQQYLV 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|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 =  144 bits (363), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 92/262 (35%), Positives = 151/262 (57%), Gaps = 14/262 (5%)

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-RVPFGLESTSIMQVRGEIQRAKLE 376
           A+++F+  + ++ STY  +WIR AI R+M   + T R+P       +++V  ++ R + +
Sbjct: 314 AVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPV-----HMVEVINKLARVQRQ 368

Query: 377 LLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGV 435
           +L +L R PT EE+ + ++++PE+  EV K  +  +SLH+  G   + EF + I D + V
Sbjct: 369 MLQDLGREPTPEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAV 428

Query: 436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRK 495
              +     LL+  L  VLD+L  +E+ V+  RFGL     +TL EI     ++RE +R+
Sbjct: 429 VPADAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQ 488

Query: 496 HEVKGLMKLKHPTRVDYLRQHM 517
            E K + KL+HP+R   LR ++
Sbjct: 489 IESKTMSKLRHPSRSQVLRDYL 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)

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

 Score =  144 bits (363), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 95/270 (35%), Positives = 155/270 (57%), Gaps = 15/270 (5%)

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-RVPFGLESTSIMQVRG 368
            G  GLI A+++F+  + ++ STY  +WIR AI R+M   + T R+P       +++V  
Sbjct: 309 EGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPV-----HMVEVIN 363

Query: 369 EIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFIN 427
           ++ R + ++L +L R PT EE+ + ++++PE+  EV K  +  +SLH+  G   + EF +
Sbjct: 364 KLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGD 423

Query: 428 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN 487
            I D + V   +     LL+  L  VLD+L  +E+ V+  RFGL     +TL EI     
Sbjct: 424 LIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYG 483

Query: 488 ISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
           ++RE +R+ E K + KL+HP+R   LR ++
Sbjct: 484 VTRERIRQIESKTMSKLRHPSRSQVLRDYL 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|P26480|RPOD_PSEAE RNA polymerase sigma factor RpoD OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) GN=rpoD PE=3 SV=1

 Score =  142 bits (359), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 91/314 (28%), Positives = 173/314 (55%), Gaps = 28/314 (8%)

Query: 219 TEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEA-TNMSAAQVK---KCLEVGRA 274
           T+  W+  +++    + +  E+L+ D+ R    +   E+   ++ A++K   + + +G A
Sbjct: 315 TDEKWVDSVLKSKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAMSIGEA 374

Query: 275 ----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRL 330
               A+ ++++ NLRLV+ + KKY      G +F DL Q G  GL+ A+D+FE +R ++ 
Sbjct: 375 KARRAKKEMVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 431

Query: 331 STYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEE 389
           STY  +WIR AI RS+   + T R+P       +++   ++ R   ++L E+ R PT EE
Sbjct: 432 STYATWWIRQAITRSIADQARTIRIP-----VHMIETINKLNRISRQMLQEMGREPTPEE 486

Query: 390 IIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQP------ 443
           + + +++  ++ R+V+K +K  +S+ +  G  ++  +      D +E+   + P      
Sbjct: 487 LGERMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLG-----DFIEDSTMQSPIEMATS 541

Query: 444 ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503
             L+ +  +VL  L  +E+ V+R RFG+D   D TL E+    +++RE +R+ E K L K
Sbjct: 542 ESLKESTREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 601

Query: 504 LKHPTRVDYLRQHM 517
           L+HP+R ++LR  +
Sbjct: 602 LRHPSRSEHLRSFL 615

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.

Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (taxid: 208964)

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	518
224110206	512	predicted protein [Populus trichocarpa]	0.982	0.994	0.723	0.0
255545052	501	RNA polymerase sigma factor rpoD, putati	0.961	0.994	0.700	0.0
224116898	512	predicted protein [Populus trichocarpa]	0.982	0.994	0.702	0.0
356546249	512	PREDICTED: RNA polymerase sigma factor r	0.982	0.994	0.681	0.0
388556562	512	RNA polymerase sigma factor rpoD-like [G	0.982	0.994	0.685	0.0
449518953	515	PREDICTED: RNA polymerase sigma factor s	0.976	0.982	0.675	0.0
449463472	514	PREDICTED: RNA polymerase sigma factor s	0.976	0.984	0.682	0.0
356516017	507	PREDICTED: RNA polymerase sigma factor r	0.972	0.994	0.677	0.0
382365034	507	sigma-like factor 5B [Glycine max]	0.972	0.994	0.675	0.0
356509297	509	PREDICTED: RNA polymerase sigma factor r	0.976	0.994	0.658	0.0

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

 Score =  738 bits (1904), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 377/521 (72%), Positives = 441/521 (84%), Gaps = 12/521 (2%)

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 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSR 417
           LES     +R EIQ+AKLEL F+LKR P ++EII+ V ISPERY EV +ASKP+LSLHSR
Sbjct: 359 LES-----IRSEIQKAKLELWFQLKRQPMEDEIIEKVRISPERYHEVTRASKPVLSLHSR 413

Query: 418 HGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 477
           H  TQEEFI GI DVDG   +++RQ ALLRLALDDVLDSLKPKESLV+RQR+GLDGKGDR
Sbjct: 414 HKTTQEEFIGGIADVDG--GDDRRQSALLRLALDDVLDSLKPKESLVVRQRYGLDGKGDR 471

Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 518
           TLGEIAGNLNISREMVRKHEVK LMKLKHPTRVDYLR+++V
Sbjct: 472 TLGEIAGNLNISREMVRKHEVKALMKLKHPTRVDYLRRYVV 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 =  723 bits (1865), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 365/521 (70%), Positives = 434/521 (83%), Gaps = 23/521 (4%)

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 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSR 417
           LES     VR EIQ+AKLELL EL+R PT+EEII+ V IS ERY EV++A+KP LSLH+R
Sbjct: 348 LES-----VRTEIQKAKLELLIELQRRPTEEEIIERVGISAERYHEVIRAAKPALSLHAR 402

Query: 418 HGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 477
           H VTQEEFINGITD+DG   +N+RQPALLRLALDDVLDSLKPKESLVIRQR+GLDGKGDR
Sbjct: 403 HAVTQEEFINGITDIDG--GDNRRQPALLRLALDDVLDSLKPKESLVIRQRYGLDGKGDR 460

Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 518
           TLGEIAGNLNISREMVRK+EVK LMKLKHP RVDYLR+++V
Sbjct: 461 TLGEIAGNLNISREMVRKYEVKALMKLKHPARVDYLRRYVV 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 =  721 bits (1860), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 366/521 (70%), Positives = 430/521 (82%), Gaps = 12/521 (2%)

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 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSR 417
           LES     +R EIQ+AKLEL F+L R PT EEII+ V IS ERY EVM+ASKP+LSLHSR
Sbjct: 359 LES-----IRSEIQKAKLELWFQLLRKPTGEEIIEKVGISIERYHEVMRASKPVLSLHSR 413

Query: 418 HGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 477
           H  TQEE I+G+ DV+G   +++RQ ALLRLALDDVLDSLKPKESLV+RQRFGLDGKGDR
Sbjct: 414 HKTTQEELISGVADVNG--GDDRRQSALLRLALDDVLDSLKPKESLVVRQRFGLDGKGDR 471

Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 518
           TLGEIAGNLNISREMVRKHE K LMKLKHPTRVDYL +++V
Sbjct: 472 TLGEIAGNLNISREMVRKHEAKALMKLKHPTRVDYLCRYVV 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 =  711 bits (1835), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 355/521 (68%), Positives = 427/521 (81%), Gaps = 12/521 (2%)

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 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSR 417
           LE     +VR +IQR KL+L FEL+R PT+EE+++ + IS ERY EVMKASKPILSLHSR
Sbjct: 357 LE-----RVRVDIQRTKLKLTFELQRSPTEEELVERIGISLERYHEVMKASKPILSLHSR 411

Query: 418 HGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 477
           H  TQEE+INGITDVDGV  +N+RQ A+LRLALDDVLDSLKPKESLVIRQR+GLDGKGDR
Sbjct: 412 HITTQEEYINGITDVDGVNGDNRRQLAVLRLALDDVLDSLKPKESLVIRQRYGLDGKGDR 471

Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 518
           TLGEIAGNLNISRE+VRKHEVK LMKLKHP R+DYLR+++V
Sbjct: 472 TLGEIAGNLNISREIVRKHEVKALMKLKHPARLDYLRRYVV 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 =  707 bits (1824), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 357/521 (68%), Positives = 422/521 (80%), Gaps = 12/521 (2%)

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 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSR 417
           LE     +VR +IQR KL+L FEL+R PT+EE+++ + ISPERY EVMKASKPILSLHSR
Sbjct: 357 LE-----RVRVDIQRTKLKLTFELQRSPTEEELVERIGISPERYYEVMKASKPILSLHSR 411

Query: 418 HGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 477
           H  TQEE+INGITDVDGV  +N+RQ A+LRLALDDVLDSLKPKESLVIRQR+GLDGKGDR
Sbjct: 412 HITTQEEYINGITDVDGVNGDNRRQLAVLRLALDDVLDSLKPKESLVIRQRYGLDGKGDR 471

Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 518
           TLGEIAGNLNISREMVRKHEVK LMKLKHP R+DYLR+++V
Sbjct: 472 TLGEIAGNLNISREMVRKHEVKALMKLKHPARLDYLRRYVV 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 =  701 bits (1809), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 356/527 (67%), Positives = 420/527 (79%), Gaps = 21/527 (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 TRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPI 411
           TRV FGL+S     VR EIQRAKLELL EL R+PT+ EI   V IS ERY EVM+A+KP+
Sbjct: 354 TRVSFGLDS-----VRVEIQRAKLELLCELHRLPTEGEITAKVGISQERYLEVMRATKPV 408

Query: 412 LSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGL 471
            SLHSRH  T EE INGITDV+G   +N+RQPALLRLALDDVLDSLKPKESLVIRQR+GL
Sbjct: 409 YSLHSRHSTTSEELINGITDVEGTGGDNRRQPALLRLALDDVLDSLKPKESLVIRQRYGL 468

Query: 472 DGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 518
           DGKG+RTLGEIAGNLNISREMVRKHEVK LMKLKHP RVDYLR++++
Sbjct: 469 DGKGNRTLGEIAGNLNISREMVRKHEVKALMKLKHPARVDYLRRYLI 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 =  701 bits (1808), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 359/526 (68%), Positives = 420/526 (79%), Gaps = 20/526 (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 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 RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPIL 412
           RV FGL+S     VR EIQRAKLELL EL R+PT+ EI   V IS ERY EVM+A+KP+ 
Sbjct: 354 RVSFGLDS-----VRVEIQRAKLELLCELHRLPTEGEITAKVGISQERYLEVMRATKPVY 408

Query: 413 SLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLD 472
           SLHSRH  T EE INGITDV+G   +N+RQPALLRLALDDVLDSLKPKESLVIRQR+GLD
Sbjct: 409 SLHSRHSTTSEELINGITDVEGTGGDNRRQPALLRLALDDVLDSLKPKESLVIRQRYGLD 468

Query: 473 GKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 518
           GKG+RTLGEIAGNLNISREMVRKHEVK LMKLKHP RVDYLR++++
Sbjct: 469 GKGNRTLGEIAGNLNISREMVRKHEVKALMKLKHPARVDYLRRYLI 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 =  694 bits (1790), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 353/521 (67%), Positives = 420/521 (80%), Gaps = 17/521 (3%)

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 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSR 417
           LES     VR EIQ+AK EL FEL+R PT+EEII+ V+ISPERY +V+KASK ILSL+SR
Sbjct: 352 LES-----VRAEIQKAKTELTFELQRSPTEEEIIERVHISPERYHDVIKASKSILSLNSR 406

Query: 418 HGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 477
           H  TQEEFINGI D DGV  +N++QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR
Sbjct: 407 HTTTQEEFINGIVDDDGVNGDNRKQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 466

Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 518
           TLGEIAGNLNISREMVRKHEVK LMKLKH  R+DYLR+++V
Sbjct: 467 TLGEIAGNLNISREMVRKHEVKALMKLKHSARLDYLRRYVV 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 =  691 bits (1784), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 352/521 (67%), Positives = 419/521 (80%), Gaps = 17/521 (3%)

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 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSR 417
           LES     VR EIQ+AK EL FEL+R PT+EEII+ V+ISPERY +V+KASK ILSL+SR
Sbjct: 352 LES-----VRAEIQKAKTELTFELQRSPTEEEIIERVHISPERYHDVIKASKSILSLNSR 406

Query: 418 HGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 477
           H  TQEEFINGI D DGV  +N++QPALLRLALDDVLDSLKPKESLVIR RFGLDGKGDR
Sbjct: 407 HTTTQEEFINGIVDDDGVNGDNRKQPALLRLALDDVLDSLKPKESLVIRXRFGLDGKGDR 466

Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 518
           TLGEIAGNLNISREMVRKHEVK LMKLKH  R+DYLR+++V
Sbjct: 467 TLGEIAGNLNISREMVRKHEVKALMKLKHSARLDYLRRYVV 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 =  682 bits (1761), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 343/521 (65%), Positives = 414/521 (79%), Gaps = 15/521 (2%)

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 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSR 417
           LES     VR EIQ+AK EL F+L+R PT+EEII+ V+ISPERY +++KASK ILSL+SR
Sbjct: 354 LES-----VRAEIQKAKTELTFKLQRSPTEEEIIERVHISPERYHDIIKASKSILSLNSR 408

Query: 418 HGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 477
           H  TQEEFINGI D DGV  +N++QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR
Sbjct: 409 HTTTQEEFINGIVDDDGVNGDNRKQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 468

Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 518
           TLGEIAGNLNISREMVRKHEVK LMKL H  R+DYLR+++V
Sbjct: 469 TLGEIAGNLNISREMVRKHEVKALMKLNHSARLDYLRRYVV 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	518
TAIR|locus:2167413	517	SIGE "AT5G24120" [Arabidopsis	0.978	0.980	0.634	2.7e-164
UNIPROTKB|Q84JN3	500	SIG5 "Os05g0586600 protein" [O	0.805	0.834	0.536	2.2e-112
UNIPROTKB|Q9KUK1	625	VC_0517 "RNA polymerase sigma	0.563	0.467	0.288	1.7e-31
TIGR_CMR|VC_0517	625	VC_0517 "RNA polymerase sigma	0.563	0.467	0.288	1.7e-31
TIGR_CMR|SPO_1750	660	SPO_1750 "RNA polymerase sigma	0.509	0.4	0.314	2.4e-31
TIGR_CMR|APH_0576	627	APH_0576 "RNA polymerase sigma	0.471	0.389	0.356	4.2e-31
TIGR_CMR|GSU_3089	577	GSU_3089 "RNA polymerase sigma	0.675	0.606	0.285	4.5e-30
TIGR_CMR|ECH_0760	622	ECH_0760 "RNA polymerase sigma	0.467	0.389	0.352	9.3e-30
TIGR_CMR|CBU_1596	698	CBU_1596 "RNA polymerase sigma	0.557	0.414	0.289	1.5e-28
TIGR_CMR|BA_4515	373	BA_4515 "RNA polymerase sigma-	0.555	0.772	0.309	2.1e-28

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

 Score = 1599 (567.9 bits), Expect = 2.7e-164, P = 2.7e-164
 Identities = 335/528 (63%), Positives = 399/528 (75%)

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 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKP 410
             FTRVPFGLES     VR EI +AK EL FE+ R PT++E+++ + I+PERYREV++A+KP
Sbjct:   355 FTRVPFGLES-----VRVEIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAKP 409

Query:   411 ILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXXXXXXXXXXXXXKPKESLVIRQRFG 470
             +LSL+S+H VTQEEFINGITDVDGV   N RQPA             KPKESLVIRQR+G
Sbjct:   410 VLSLNSKHSVTQEEFINGITDVDGVGANNSRQPALLRLALDDVLDSLKPKESLVIRQRYG 469

Query:   471 LDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 518
             LDGKGDRTLGEIAGNLNISREMVRKHEVK LMKLKH  RVDYLRQ++V
Sbjct:   470 LDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHQARVDYLRQYIV 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 = 1109 (395.4 bits), Expect = 2.2e-112, P = 2.2e-112
 Identities = 230/429 (53%), Positives = 298/429 (69%)

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 RLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDE 388
             R+STY LFWIRH+I+R++T+S+FTR PF +ES      R EI RA+ EL FEL R PT+E
Sbjct:   317 RISTYALFWIRHSIVRAITLSNFTRFPFAMESE-----RQEIHRAREELAFELGRAPTEE 371

Query:   389 EIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXXXX 448
             E+++ V +SP RYR+V++ ++P  SLH+R+ VTQEE IN +TD D +  +          
Sbjct:   372 EVMKKVGLSPARYRDVVRMTRPTYSLHARNRVTQEELINEVTDDDAIGVDTSSHNTLLRL 431

Query:   449 XXXXXXXXXKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508
                      KPKES+VIRQRFGLDG+G RTL EIAGNLNISREMVRK+E+K LMKLKHPT
Sbjct:   432 AIDDLLDSLKPKESVVIRQRFGLDGRGKRTLSEIAGNLNISREMVRKYELKALMKLKHPT 491

Query:   509 RVDYLRQHM 517
             RV+YLR++M
Sbjct:   492 RVEYLRRYM 500

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

GO:0009536 "plastid" evidence=IDA

GO:0016987 "sigma factor activity" evidence=IDA

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

 Score = 359 (131.4 bits), Expect = 1.7e-31, P = 1.7e-31
 Identities = 90/312 (28%), Positives = 168/312 (53%)

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-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPT 386
             ++ STY  +WIR AI RS+   + T R+P       +++   ++ R   ++L E+ R P 
Sbjct:   437 YKFSTYATWWIRQAITRSIADQARTIRIP-----VHMIETINKLNRISRQMLQEMGREPL 491

Query:   387 DEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXX 446
              EE+ + + +  ++ R+V+K +K  +S+ +  G  ++  +    +   +E       A  
Sbjct:   492 PEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATS 551

Query:   447 XXXXXXXXXXX-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505
                          P+E+ V+R RFG+D   D TL E+    +++RE +R+ E K L KL+
Sbjct:   552 LKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 611

Query:   506 HPTRVDYLRQHM 517
             HP+R + LR  +
Sbjct:   612 HPSRSEVLRSFL 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 = 359 (131.4 bits), Expect = 1.7e-31, P = 1.7e-31
 Identities = 90/312 (28%), Positives = 168/312 (53%)

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-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPT 386
             ++ STY  +WIR AI RS+   + T R+P       +++   ++ R   ++L E+ R P 
Sbjct:   437 YKFSTYATWWIRQAITRSIADQARTIRIP-----VHMIETINKLNRISRQMLQEMGREPL 491

Query:   387 DEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXX 446
              EE+ + + +  ++ R+V+K +K  +S+ +  G  ++  +    +   +E       A  
Sbjct:   492 PEELAERMQMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATATS 551

Query:   447 XXXXXXXXXXX-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505
                          P+E+ V+R RFG+D   D TL E+    +++RE +R+ E K L KL+
Sbjct:   552 LKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 611

Query:   506 HPTRVDYLRQHM 517
             HP+R + LR  +
Sbjct:   612 HPSRSEVLRSFL 623

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 349 (127.9 bits), Expect = 2.4e-31, Sum P(2) = 2.4e-31
 Identities = 91/289 (31%), Positives = 156/289 (53%)

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 FGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLH 415
                    +++   ++ R   ++L E+ R PT EE+ + + +  E+ R+VMK +K  +SL 
Sbjct:   501 -----VHMIETINKLVRTGRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLE 555

Query:   416 SRHGVTQE----EFI---NGITDVDGVENENQRQPAXXXXXXXXXXXXXKPKESLVIRQR 468
             +  G  ++    +FI   N +  +D    EN ++                P+E  V+R R
Sbjct:   556 TPIGDEEDSQLGDFIEDKNAVLPLDSAIQENLKETTTRVLASLT------PREERVLRMR 609

Query:   469 FGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
             FG+    D TL E+    +++RE +R+ E K L KLKHP+R   LR  +
Sbjct:   610 FGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFL 658

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 = 357 (130.7 bits), Expect = 4.2e-31, P = 4.2e-31
 Identities = 91/255 (35%), Positives = 137/255 (53%)

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-RVPFGLESTSIMQVRGEIQRAKLELLFEL 381
             + KR ++ STY  +W+R AI R++   + T R+P       +++   +I R   ++L E+
Sbjct:   435 DYKRGYKFSTYATWWVRQAITRAIADQARTIRIP-----VHMIETVNKINRTLRQMLHEI 489

Query:   382 KRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE-FINGITDVDGVENENQ 440
              R PT EE+   +NI+ E+ R+VMK  K  +SL S  G      F + I D   V+ EN 
Sbjct:   490 GREPTLEELSARLNINVEKIRKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPENA 549

Query:   441 RQPAXXXXXXXXXXXXXKPKESLVIRQRFGLDGKG-DRTLGEIAGNLNISREMVRKHEVK 499
                A              PKE  ++R RFG+   G D TL E+    N++RE +R+ E K
Sbjct:   550 AVLADLREITTKVLSTLTPKEERILRMRFGIGKSGKDHTLEEVGRLFNVTRERIRQIEAK 609

Query:   500 GLMKLKHPTRVDYLR 514
              L KL+HP+R   LR
Sbjct:   610 ALRKLRHPSRARKLR 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 = 349 (127.9 bits), Expect = 4.5e-30, P = 4.5e-30
 Identities = 107/375 (28%), Positives = 187/375 (49%)

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-RVPFGLESTSIMQVRGEIQRAKLELLFE 380
             FE +R ++ STY  +WIR AI R++   + T R+P       +++   ++ R   +L+ E
Sbjct:   384 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIP-----VHMIETINKLIRTSRQLVQE 438

Query:   381 LKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQ 440
             + R P+ EEI + +N+  ++ R+V+K +K  +SL +  G  ++  +    +  GV +  +
Sbjct:   439 IGREPSPEEIAERMNLPLDKVRKVLKIAKEPISLETPIGEEEDSHLGDFIEDKGVVSPLE 498

Query:   441 RQ-PAXXXXXXXXXXXXXKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499
                 A              P+E  V+R RFG+  K D TL E+  +  ++RE +R+ E K
Sbjct:   499 AVIKANLSEQTARVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAK 558

Query:   500 GLMKLKHPTRVDYLR 514
              L KL+HP+R   LR
Sbjct:   559 ALRKLRHPSRAKKLR 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 = 348 (127.6 bits), Expect = 9.3e-30, P = 9.3e-30
 Identities = 90/255 (35%), Positives = 138/255 (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-RVPFGLESTSIMQVRGEIQRAKLELLFELK 382
              KR ++ STY  +W+R AI R++   + T R+P       +++   +I R   ++L E+ 
Sbjct:   431 YKRGYKFSTYATWWVRQAITRAIADQARTIRIP-----VHMIETVNKINRTLRQMLHEMG 485

Query:   383 RVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE-FINGITDVDGVENENQR 441
             R PT EE+   +NI+ ++ R+VMK  K  +SL S  G      F + I D   V+ E+  
Sbjct:   486 REPTLEELSARLNINVDKIRKVMKIVKDPVSLESPIGDDDSSTFGDCIEDKRAVKPEDAA 545

Query:   442 QPAXXXXXXXXXXXXXKPKESLVIRQRFGLDGKG--DRTLGEIAGNLNISREMVRKHEVK 499
               A              PKE  ++R RFG+ GKG  D TL E+    N++RE +R+ E K
Sbjct:   546 VLADLREITTKVLSTLTPKEERILRMRFGI-GKGGKDHTLEEVGKLFNVTRERIRQIEAK 604

Query:   500 GLMKLKHPTRVDYLR 514
              L KL+HP+R   LR
Sbjct:   605 ALRKLRHPSRARKLR 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 = 336 (123.3 bits), Expect = 1.5e-28, Sum P(2) = 1.5e-28
 Identities = 89/307 (28%), Positives = 160/307 (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-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTD 387
             + STY  +WIR AI RS+   + T R+P       +++   ++ R   ++L E     T 
Sbjct:   509 KFSTYATWWIRQAITRSIADQARTIRIP-----VHMIETINKLNRISRQILQETGIEATP 563

Query:   388 EEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING-ITDVDGVENENQRQPAXX 446
             EE+ + +++  E+ R+V+K +K  +S+ +  G  ++  +   I D++     +    A  
Sbjct:   564 EELGRRMDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGL 623

Query:   447 XXXXXXXXXXXKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506
                         P+E+ V+R RFG+D   D TL E+    +++RE +R+ E K L KL+H
Sbjct:   624 MEATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 683

Query:   507 PTRVDYL 513
             P+R + L
Sbjct:   684 PSRAEKL 690

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

GO:0016987 "sigma factor activity" evidence=ISS

TIGR_CMR|BA_4515 BA_4515 "RNA polymerase sigma-43 factor" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 319 (117.4 bits), Expect = 2.1e-28, P = 2.1e-28
 Identities = 95/307 (30%), Positives = 158/307 (51%)

Query:   216 LSSTEHTW-LFKLMQP--MKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVG 272
             ++ TE  + L  L  P  +K+   V+  L K++GR   D+  AE     A +++   E  
Sbjct:    80 ITKTEEEFDLNDLSVPPGVKINDPVRMYL-KEIGR--VDLLSAEEEIRLATRIE---EGD 133

Query:   273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLST 332
               A+ +L + NLRLV+ + K+Y      G  F DL Q G  GLI A+++F+ ++ F+ ST
Sbjct:   134 EEAKRRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFST 190

Query:   333 YGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEII 391
             Y  +WIR AI R++   + T R+P  +  T    +R  +QR   +LL +L R P+ EEI 
Sbjct:   191 YATWWIRQAITRAIADQARTIRIPVHMVETINKLIR--VQR---QLLQDLGREPSPEEIG 245

Query:   392 QGVNISPERYREVMKASKPILSLHSRHGVTQEEFING-ITDVDGVENENQRQPAXXXXXX 450
             + ++++PE+ RE++K ++  +SL +  G   +  +   I D +     +           
Sbjct:   246 EEMDLAPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPADHAAYELLKEQL 305

Query:   451 XXXXXXXKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV 510
                      +E  V+R RFGLD    RTL E+     ++RE +R+ E K L KL+HP+R 
Sbjct:   306 EDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 365

Query:   511 DYLRQHM 517
               L+  +
Sbjct:   366 KRLKDFL 372

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

GO:0016987 "sigma factor activity" evidence=ISS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9ZNX9	SIGE_ARATH	No assigned EC number	0.6559	0.9768	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	518
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	7e-55
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	1e-44
TIGR02393	238	TIGR02393, RpoD_Cterm, RNA polymerase sigma factor	1e-44
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	2e-43
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	2e-41
COG0568	342	COG0568, RpoD, DNA-directed RNA polymerase, sigma	5e-40
PRK07598	415	PRK07598, PRK07598, RNA polymerase sigma factor Si	1e-36
PRK09210	367	PRK09210, PRK09210, RNA polymerase sigma factor Rp	4e-36
PRK07921	324	PRK07921, PRK07921, RNA polymerase sigma factor Si	9e-35
PRK05901	509	PRK05901, PRK05901, RNA polymerase sigma factor; P	3e-34
PRK05658	619	PRK05658, PRK05658, RNA polymerase sigma factor Rp	8e-31
TIGR02394	285	TIGR02394, rpoS_proteo, RNA polymerase sigma facto	2e-28
COG1191	247	COG1191, FliA, DNA-directed RNA polymerase special	2e-24
PRK05657	325	PRK05657, PRK05657, RNA polymerase sigma factor Rp	1e-22
TIGR02980	227	TIGR02980, SigBFG, RNA polymerase sigma-70 factor,	1e-21
TIGR02885	231	TIGR02885, spore_sigF, RNA polymerase sigma-F fact	3e-21
PRK05572	252	PRK05572, PRK05572, sporulation sigma factor SigF;	4e-17
TIGR02846	227	TIGR02846, spore_sigmaK, RNA polymerase sigma-K fa	1e-16
PRK08215	258	PRK08215, PRK08215, sporulation sigma factor SigG;	9e-15
TIGR02479	224	TIGR02479, FliA_WhiG, RNA polymerase sigma factor,	5e-14
PRK07500	289	PRK07500, rpoH2, RNA polymerase factor sigma-32; R	5e-12
PRK05911	257	PRK05911, PRK05911, RNA polymerase sigma factor si	1e-11
TIGR02850	254	TIGR02850, spore_sigG, RNA polymerase sigma-G fact	2e-11
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	3e-11
PRK07408	256	PRK07408, PRK07408, RNA polymerase sigma factor Si	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
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	1e-09
PRK05803	233	PRK05803, PRK05803, sporulation sigma factor SigK;	2e-09
pfam04545	50	pfam04545, Sigma70_r4, Sigma-70, region 4	2e-09
TIGR02941	255	TIGR02941, Sigma_B, RNA polymerase sigma-B factor	9e-08
PRK08583	257	PRK08583, PRK08583, RNA polymerase sigma factor Si	4e-07
TIGR02835	234	TIGR02835, spore_sigmaE, RNA polymerase sigma-E fa	5e-07
PRK08301	234	PRK08301, PRK08301, sporulation sigma factor SigE;	8e-07
PRK06986	236	PRK06986, fliA, flagellar biosynthesis sigma facto	2e-06
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	5e-06
pfam04539	78	pfam04539, Sigma70_r3, Sigma-70 region 3	7e-06
TIGR02937	158	TIGR02937, sigma70-ECF, RNA polymerase sigma facto	6e-05
PRK07670	251	PRK07670, PRK07670, RNA polymerase sigma factor Si	7e-05
cd06171	55	cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers	8e-05
PRK06596	284	PRK06596, PRK06596, RNA polymerase factor sigma-32	1e-04

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

 Score =  185 bits (473), Expect = 7e-55
 Identities = 112/306 (36%), Positives = 177/306 (57%), Gaps = 9/306 (2%)

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-RVPFGLESTSIMQVRGEIQRAKLELLF 379
           +F+P R ++ STY  +WIR  I R++   S T R+P       I +   +I++ + EL  
Sbjct: 118 KFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLP-----IHITEKLNKIKKVQRELSQ 172

Query: 380 ELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN 439
           +L R P++ EI + + + PE+ RE+++ ++  +SL +  G  ++  +  + + DG   E 
Sbjct: 173 KLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGESPEE 232

Query: 440 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499
           Q +   LR  L+ +L  L P+E  V+R RFGLDG    TL EI   LN+SRE VR+ E K
Sbjct: 233 QVERESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAK 292

Query: 500 GLMKLK 505
            L KL+
Sbjct: 293 ALRKLR 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 =  161 bits (408), Expect = 1e-44
 Identities = 102/283 (36%), Positives = 164/283 (57%), Gaps = 9/283 (3%)

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 PFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSL 414
           P  L  T        I++    L  E  R PT+EEI + + ++ E+ R + K+++  +SL
Sbjct: 215 PVHLYETI-----SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISL 269

Query: 415 HSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGK 474
            +  G  ++  +    + DG   E+     LLR  L+ VL +L P+E  V+R R+GLD  
Sbjct: 270 ETPIGKEEDSRLGDFIEADGETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDG 329

Query: 475 GDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
             +TL EI    N++RE +R+ E K L KL+HP R   L++++
Sbjct: 330 RMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372

Length = 373

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

 Score =  157 bits (398), Expect = 1e-44
 Identities = 82/242 (33%), Positives = 137/242 (56%), Gaps = 10/242 (4%)

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-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQG 393
            +WIR AI R++   + T R+P  +  T       ++ +A+ +L  EL R PTDEE+ + 
Sbjct: 58  TWWIRQAITRAIADQARTIRIPVHMVETI-----NKLIKAERQLTQELGREPTDEELAER 112

Query: 394 VNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQRQPALLRLALDD 452
           + +  E+ RE+ K ++  +SL +  G  ++    + I D      ++     LLR  LD+
Sbjct: 113 MGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDTSIESPDDYAAKELLREQLDE 172

Query: 453 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512
           VL++L  +E  V+R R+GL      TL E+    N++RE +R+ E K L KL+HP+R   
Sbjct: 173 VLETLTEREEKVLRMRYGLLDGQPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKK 232

Query: 513 LR 514
           L+
Sbjct: 233 LK 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 =  156 bits (397), Expect = 2e-43
 Identities = 100/319 (31%), Positives = 173/319 (54%), Gaps = 9/319 (2%)

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-RVPFGLESTSIMQV 366
            Q G  GL   +++F+P R ++ STY  +WIR AI R++   + T R+P       I + 
Sbjct: 122 IQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPI-----HITEK 176

Query: 367 RGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFI 426
             +I++ + EL  +L R  T  EI + + + P + RE +  ++  +SL  R G  Q+  +
Sbjct: 177 LNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTEL 236

Query: 427 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNL 486
           + + + +G   +      LLR  L+++L  L P++  V+  RFGL+   + +L ++   L
Sbjct: 237 SELLEDEGPSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERL 296

Query: 487 NISREMVRKHEVKGLMKLK 505
           N+SRE VR+ E + L  L+
Sbjct: 297 NLSRERVRQLEHQALAHLR 315

Length = 327

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

 Score =  150 bits (381), Expect = 2e-41
 Identities = 102/308 (33%), Positives = 175/308 (56%), Gaps = 9/308 (2%)

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-RVPFGLESTSIMQVRGEIQRAKLEL 377
           +++F+P + +R STY  +WIR AI R++   S T R+P       I +   +I++A+ +L
Sbjct: 123 VEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPI-----HITEKLNKIKKAQRQL 177

Query: 378 LFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN 437
             +L R  T  E+ + + ++P++ RE ++ ++  LSL  R G  Q+  +  + +  G   
Sbjct: 178 SQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASP 237

Query: 438 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHE 497
           E+    + L+L L+ +++ L P++  VI  RFGL+     TL +I   LNISRE VR+ E
Sbjct: 238 EDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIE 297

Query: 498 VKGLMKLK 505
            + L KL+
Sbjct: 298 REALSKLR 305

Length = 317

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

 Score =  147 bits (373), Expect = 5e-40
 Identities = 115/342 (33%), Positives = 172/342 (50%), Gaps = 32/342 (9%)

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 GLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHS 416
                 I ++R    R K ELL EL R PT EEI + + +SP++ RE++K +   +SL +
Sbjct: 183 HQVEL-INKLR----RVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLDT 237

Query: 417 RHGVTQE-EFINGITDVDGVENENQRQPALLRLALDDVLDS-LKPKESLVIRQRFGLDGK 474
             G  ++ E  + + D   V  E+  +   L+  L++VL   L  +E  VIR RFGLD  
Sbjct: 238 PIGDDEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDG 297

Query: 475 GDRTLGEIAGNLNISREMVRKHEVKGLMKLK-HPTRVDYLRQ 515
             +TL E+     ISRE VR+ E K L KL+ HP R   LR 
Sbjct: 298 EPKTLEELGEEFGISRERVRQIEAKALRKLRRHPERSALLRS 339

Length = 342

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

 Score =  140 bits (354), Expect = 1e-36
 Identities = 94/311 (30%), Positives = 155/311 (49%), Gaps = 31/311 (9%)

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-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPT 386
           +R STY  +WIR  I R++   S T R+P       I +   +I++A+ ++  E  R PT
Sbjct: 226 YRFSTYAYWWIRQGITRAIATQSRTIRLP-----VHITEKLNKIKKAQRKISQEKGRTPT 280

Query: 387 DEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALL 446
            E+I Q + ++P + REV+      +SL ++ G  ++  +  + + D +  E       L
Sbjct: 281 IEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLETDDISPEEMLMRESL 340

Query: 447 RLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506
           +  L  +L  L  +E  VIR RFGL      +L EI   L++SRE VR+ E K L KL+ 
Sbjct: 341 QRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQ 400

Query: 507 PTRVDYLRQHM 517
           P R + +R ++
Sbjct: 401 PKRRNRIRDYL 411

Length = 415

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

 Score =  137 bits (347), Expect = 4e-36
 Identities = 92/250 (36%), Positives = 146/250 (58%), Gaps = 20/250 (8%)

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-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQG 393
            +WIR AI R++   + T R+P  +  T    +R  +QR   +LL EL R PT EEI + 
Sbjct: 187 TWWIRQAITRAIADQARTIRIPVHMVETINKLIR--VQR---QLLQELGREPTPEEIAEE 241

Query: 394 VNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA------LLR 447
           +++ PE+ RE++K ++  +SL +  G   EE  + + D   +E+++   PA      LL+
Sbjct: 242 MDMPPEKVREILKIAQEPVSLETPIG---EEDDSHLGDF--IEDQDATSPADHAAYELLK 296

Query: 448 LALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507
             L+DVLD+L  +E  V+R RFGLD    RTL E+     ++RE +R+ E K L KL+HP
Sbjct: 297 EQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 356

Query: 508 TRVDYLRQHM 517
           +R   L+  +
Sbjct: 357 SRSKQLKDFL 366

Length = 367

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

 Score =  132 bits (335), Expect = 9e-35
 Identities = 98/268 (36%), Positives = 139/268 (51%), Gaps = 17/268 (6%)

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-RVPFGLESTSIMQVRG 368
            G  GLI A+++F+  + F+ STY  +WIR AI R M   S T R+P  L    + QV  
Sbjct: 119 EGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHL----VEQV-N 173

Query: 369 EIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING 428
           ++ R K EL  +L R  TDEE+ +   I  E+  ++++ S+  +SL    G + EE   G
Sbjct: 174 KLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVG-SDEEAPLG 232

Query: 429 --ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNL 486
             I D +    EN     LL   +  VL +L  +E  VIR RFGLD    RTL +I    
Sbjct: 233 DFIEDSEATSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLF 292

Query: 487 NISREMVRKHEVKGLMKLKHPTRVDYLR 514
            +SRE VR+ E + + KL++  R D LR
Sbjct: 293 GLSRERVRQIEREVMSKLRNGERADRLR 320

Length = 324

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

 Score =  134 bits (340), Expect = 3e-34
 Identities = 104/283 (36%), Positives = 153/283 (54%), Gaps = 47/283 (16%)

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-----TVSSFTRVPFGLESTSI 363
           Q G  GLI A+++F+  + ++ STY  +WIR AI R+M     T+    R+P  +  T I
Sbjct: 303 QEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTI----RIPVHMVET-I 357

Query: 364 MQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMK-ASKPILSLHSRHGVTQ 422
            ++ G I+R   ELL EL R PT EE+ + +  +PE+ RE+ K   +PI SL    G  +
Sbjct: 358 NKL-GRIER---ELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPI-SLDKTIG--K 410

Query: 423 EE------FI---NGITDVDGVE-NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGL- 471
           E       FI     ++ VD V     Q Q       L +VL++L  +E+ VIR RFGL 
Sbjct: 411 EGDSQFGDFIEDSEAVSPVDAVSFTLLQDQ-------LQEVLETLSEREAGVIRMRFGLT 463

Query: 472 DGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 514
           DG+  +TL EI     ++RE +R+ E K L KL+HP+R   LR
Sbjct: 464 DGQ-PKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLR 505

Length = 509

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

 Score =  126 bits (318), Expect = 8e-31
 Identities = 97/259 (37%), Positives = 145/259 (55%), Gaps = 40/259 (15%)

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-----TVSSFTRVPFGLESTSIMQ-VRGEIQRAKLELLFELKRVP 385
           TY  +WIR AI RS+     T+    R+P  +  T I +  R  I R   ++L E+ R P
Sbjct: 435 TYATWWIRQAITRSIADQARTI----RIPVHMIET-INKLNR--ISR---QMLQEIGREP 484

Query: 386 TDEEIIQGVNISPERYREVMKASK-PILSLHSRHGVTQEE------FI---NGITDVDGV 435
           T EE+ + + +  ++ R+V+K +K PI SL +  G   +E      FI   N    +D  
Sbjct: 485 TPEELAERLGMPEDKVRKVLKIAKEPI-SLETPIG--DDEDSHLGDFIEDKNAELPIDAA 541

Query: 436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRK 495
             E+      LR A  DVL SL P+E+ V+R RFG+D   D TL E+    +++RE +R+
Sbjct: 542 IQES------LREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 595

Query: 496 HEVKGLMKLKHPTRVDYLR 514
            E K L KL+HP+R   LR
Sbjct: 596 IEAKALRKLRHPSRSRKLR 614

Length = 619

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

 Score =  114 bits (286), Expect = 2e-28
 Identities = 74/238 (31%), Positives = 123/238 (51%), Gaps = 16/238 (6%)

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-MTVSSFTRVPFGLESTSIMQVRGEIQ---RAKLELLFELKRVPTDEE 389
             +WIR  I R+ M  +   R+P        + V  E+    RA  +L  +L R P+ EE
Sbjct: 103 ATWWIRQTIERAIMNQARTIRLP--------VHVIKELNVYLRAARQLEKKLGREPSVEE 154

Query: 390 IIQGVNISPERYREVMKASKPILSLHSRHGV-TQEEFINGITDVDGVENENQRQPALLRL 448
           I + ++   E    V+  ++ I SL +     + +  ++ I D   ++ E+  Q   L+ 
Sbjct: 155 IAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQ 214

Query: 449 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506
            ++  L  L  ++  V+ +RFGL G    TL E+A  + ++RE VR+ +V+ L KL+ 
Sbjct: 215 LIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRR 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 =  101 bits (254), Expect = 2e-24
 Identities = 76/261 (29%), Positives = 119/261 (45%), Gaps = 28/261 (10%)

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 AGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGE 369
            G+ GLI AI+R++P +  + STY +  IR  I+  +  +   +VP      S+ ++   
Sbjct: 57  IGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKNDSVKVPR-----SLRELGRR 111

Query: 370 IQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA---SKPILSLHSRHGVTQEEFI 426
           I+ A  EL  EL R PTDEEI + + I  E Y E + A   S+ +           ++  
Sbjct: 112 IEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDDVD 171

Query: 427 NGITDV-DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGN 485
           + I +  DGVE E   +       L + ++ L  +E LV+  R+    K + T  EIA  
Sbjct: 172 DQIENPDDGVEKEELLE------ILKEAIEPLPEREKLVLVLRY----KEELTQKEIAEV 221

Query: 486 LNISREMVRKHEVKGLMKLKH 506
           L IS   V +   K + KL+ 
Sbjct: 222 LGISESRVSRLHKKAIKKLRK 242

Length = 247

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

 Score = 98.1 bits (245), Expect = 1e-22
 Identities = 71/236 (30%), Positives = 123/236 (52%), Gaps = 14/236 (5%)

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-MTVSSFTRVPFGLESTSIMQVR--GEIQRAKLELLFELKRVPTDEEI 390
             +WIR  I R+ M  +   R+P       +  V+      RA  EL  +L   P+ EEI
Sbjct: 143 ATWWIRQTIERAIMNQTRTIRLP-------VHVVKELNVYLRAARELEHKLDHEPSAEEI 195

Query: 391 IQGVNISPERYREVMKASKPILSLHSRHGV-TQEEFINGITDVDGVENENQRQPALLRLA 449
            + ++   +    ++  ++ I SL +  G   ++  ++ + D      E+  Q   ++ +
Sbjct: 196 AELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQS 255

Query: 450 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505
           +   L  L  K+  V+ +RFGL G    TL ++A  + ++RE VR+ +V+ L +L+
Sbjct: 256 IVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311

Length = 325

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

 Score = 93.4 bits (233), Expect = 1e-21
 Identities = 70/240 (29%), Positives = 113/240 (47%), Gaps = 25/240 (10%)

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-----RHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPT 386
           T+ +  I     R    R  T +   RVP       + ++  +I +A  EL   L R PT
Sbjct: 58  TFAVPTIMGEIKRF--FRDDTWA--VRVP-----RRLKELGVKINKATEELTQRLGRSPT 108

Query: 387 DEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV-ENENQRQPAL 445
             EI + + +S E   E ++A        S     +++  + I  +D + + ++  +   
Sbjct: 109 IAEIAERLGVSEEEVVEALEAGNA-YQALSLDASIEDDDGDPIALLDTLGDEDDALETVE 167

Query: 446 LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505
            RLAL  +L +L  +E  ++  RF      D+T  EIA  L IS+  V +   + L KL+
Sbjct: 168 DRLALKPLLAALPERERRILLLRF----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 = 92.1 bits (229), Expect = 3e-21
 Identities = 71/243 (29%), Positives = 120/243 (49%), Gaps = 18/243 (7%)

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 PKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKR 383
                + STY +  I   I R +      +V     S S+ ++  +I+  K EL  EL R
Sbjct: 58  LSYDVKFSTYAVPMIMGEIKRFLRDDGIIKV-----SRSLKELARKIRYMKEELSKELGR 112

Query: 384 VPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQP 443
            PT  E+ + + +SPE     +++++   SL+       ++  + I  +D + ++     
Sbjct: 113 EPTINELAEALGVSPEEIVMALESARSPQSLYD---TVHQDDGDPIYLLDQIADKGSEDS 169

Query: 444 ALL-RLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502
             L ++AL + +  L  +E  +I  R+      D+T  E+A  L IS+  V + E K L 
Sbjct: 170 DWLEKIALKEAISKLDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLK 225

Query: 503 KLK 505
           K+K
Sbjct: 226 KMK 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|180137 PRK05572, PRK05572, sporulation sigma factor SigF; Validated

 Score = 80.8 bits (200), Expect = 4e-17
 Identities = 72/256 (28%), Positives = 124/256 (48%), Gaps = 22/256 (8%)

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

Query: 310 AGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGE 369
            G  GL+ A+D+F+     + STY +  I   I R +      +V     S S+ +   +
Sbjct: 65  IGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDGTVKV-----SRSLKETANK 119

Query: 370 IQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGI 429
           I++ K EL  EL R PT EE+ + + ++PE   EV+ A +   S  S H    E   + I
Sbjct: 120 IRKDKDELSKELGREPTIEELAEYLGVTPE---EVVLAQEASRSPQSIHETVHENDGDPI 176

Query: 430 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNIS 489
           T +D +  +   +    ++AL + +  L  +E L++  R+      D+T  E+A  L IS
Sbjct: 177 TLLDQIA-DQSEEDWFDKIALKEAIRELDERERLIVYLRY----FKDKTQSEVAKRLGIS 231

Query: 490 REMVRKHEVKGLMKLK 505
           +  V + E K L ++K
Sbjct: 232 QVQVSRLEKKILKQMK 247

Length = 252

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

 Score = 79.0 bits (195), Expect = 1e-16
 Identities = 65/237 (27%), Positives = 94/237 (39%), Gaps = 66/237 (27%)

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

Query: 335 LFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGV 394
              I + I+  +               ++ + +GE+                        
Sbjct: 106 ARCIENEILMHL--------------RALKKTKGEV------------------------ 127

Query: 395 NISPERYREVMKASKPILSLHSRHGVTQEEFINGIT--DVDGVENENQRQPALLRLALDD 452
                             SL    GV +E   N I+  D+ G + ++  +   L L +  
Sbjct: 128 ------------------SLQDPIGVDKEG--NEISLIDILGSDGDSVIEQVELNLEIKK 167

Query: 453 V---LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506
           +   L  L  +E  VI  R+GL     +T  EIA  L ISR  V + E + LMKL  
Sbjct: 168 LYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYK 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|181296 PRK08215, PRK08215, sporulation sigma factor SigG; Reviewed

 Score = 73.8 bits (182), Expect = 9e-15
 Identities = 73/241 (30%), Positives = 111/241 (46%), Gaps = 30/241 (12%)

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 TYGLFWIRHAIIRSMTVSSFTRVPFGLESTS--IMQVRGEIQRAKLELLFELKRVPTDEE 389
           TY +  I   I R +  ++  RV   L   +   +QVR        +L+ E  + PT EE
Sbjct: 92  TYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVRE-------KLINENSKEPTVEE 144

Query: 390 IIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD----VDGVENE-NQRQPA 444
           I + + +  E     + A +  +SL        E   +   D    +D + +E N+ +  
Sbjct: 145 IAKELEVPREEVVFALDAIQDPVSL-------FEPIYHDGGDPIYVMDQISDEKNKDENW 197

Query: 445 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 504
           L  +AL + +  L  +E L++  RF   GK   T  E+A  + IS+  V + E   L  +
Sbjct: 198 LEEIALKEAMKKLNDREKLILNLRF-FQGK---TQMEVAEEIGISQAQVSRLEKAALKHM 253

Query: 505 K 505
           +
Sbjct: 254 R 254

Length = 258

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

 Score = 71.1 bits (175), Expect = 5e-14
 Identities = 57/226 (25%), Positives = 102/226 (45%), Gaps = 37/226 (16%)

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

Query: 339 RHAII---RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVN 395
           R A++   R +      R        S+ Q   +++RA  EL   L R PT+EEI + + 
Sbjct: 61  RGAMLDELRRLDW--VPR--------SLRQKARKLERAIRELEARLGREPTEEEIAEELG 110

Query: 396 ISPERYREVMKA--SKPILSLHSRHGVTQEEFINGITD-------VDGVENENQRQPAL- 445
           +  + YR+ +    +  ++SL        +E +    D       ++  ++E+  +    
Sbjct: 111 MDLKEYRQALNEINALSLVSL--------DELLESGDDGGSLIDRIEDDKSEDPEEELER 162

Query: 446 --LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNIS 489
             LR AL + ++SL  +E LV+   +      +  L EI   L ++
Sbjct: 163 EELREALAEAIESLSEREQLVLSLYY----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 = 66.2 bits (162), Expect = 5e-12
 Identities = 74/254 (29%), Positives = 113/254 (44%), Gaps = 39/254 (15%)

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----------IRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELK 382
           Y  +WIR +I          +R  T S+   + F L      ++R  + +A  EL     
Sbjct: 96  YATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLR-----RLRARLAQADEEL----- 145

Query: 383 RVPTDEEIIQGVNIS---PERYREVMKA--SKPILSLHSRHGVTQE---EFINGITDVDG 434
              T +EI + +  +        E+M A  S P  SL++      E   E ++ + D   
Sbjct: 146 ---TKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDFLVDDSP 202

Query: 435 VENENQRQP---ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISRE 491
           + +E           R  L   L +L  +E  +IR+R  L   G  TL  +   L IS+E
Sbjct: 203 LPDEQVESSIDGERRRRWLTQALQTLNERELRIIRER-RLREDG-ATLEALGEELGISKE 260

Query: 492 MVRKHEVKGLMKLK 505
            VR+ E + L KL+
Sbjct: 261 RVRQIEARALEKLR 274

Length = 289

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

 Score = 65.0 bits (158), Expect = 1e-11
 Identities = 65/240 (27%), Positives = 112/240 (46%), Gaps = 24/240 (10%)

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

Query: 336 FWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVN 395
           F I+ AII  +    +  VP      S+ Q   ++  A   L   L + PTD E+ + +N
Sbjct: 85  FLIKAAIIDDLRKQDW--VP-----RSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLN 137

Query: 396 ISPERYREVMKASKP--ILSLHSR--------HGVTQEEFINGITDVDGVENENQRQPAL 445
           IS +       +++P  ILSL+           G+  EE I       G +  ++++ + 
Sbjct: 138 ISQQELSGWFSSARPALILSLNEEFPCQSDDEAGLALEERIADERAETGYDVVDKKEFSS 197

Query: 446 LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505
           +   L + + +L+ KE    R+   L    +  L EI   L +S   V +   K L+KL+
Sbjct: 198 I---LAEAILALEEKE----RKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLR 250

Length = 257

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

 Score = 64.1 bits (156), Expect = 2e-11
 Identities = 70/236 (29%), Positives = 108/236 (45%), Gaps = 22/236 (9%)

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 YGLFWIRHAIIRSMTVSSFTRVPFGLESTS--IMQVRGEIQRAKLELLFELKRVPTDEEI 390
           Y +  I   I R +  ++  RV   L   +   +QVR        +L+ E  + PT  EI
Sbjct: 90  YAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVRD-------KLISENSKEPTVSEI 142

Query: 391 IQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALL-RLA 449
            + + +  E   EV+ A   I    S       +  + I  +D + +E  +    L  +A
Sbjct: 143 AKELKVPQE---EVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKNKDSQWLEGIA 199

Query: 450 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505
           L + +  L  +E +++  RF  +GK   T  E+A  + IS+  V + E   L  ++
Sbjct: 200 LKEAMKRLNEREKMILNMRF-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|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: 367 RGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EF 425
             +I+RA+ EL  EL R PT EEI + + IS E+ REV++A++  +SL    G  ++ E 
Sbjct: 3   LNKIKRAQRELEQELGREPTPEEIAEELGISEEKVREVLEAAREPVSLDLPVGEEEDGEL 62

Query: 426 INGITDVDGVENENQ 440
            + + 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|180965 PRK07408, PRK07408, RNA polymerase sigma factor SigF; Reviewed

 Score = 63.8 bits (156), Expect = 3e-11
 Identities = 75/243 (30%), Positives = 117/243 (48%), Gaps = 32/243 (13%)

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-----RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDE 388
            + +IR  I      +S TV    R+P         +++ + ++ + EL  EL R PTD+
Sbjct: 83  AIPYIRGEIQHYLRDKSPTV----RIP-----RRWQELQRQAKKVRQELRQELGRQPTDQ 133

Query: 389 EIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQEEFINGITDVDGVENENQR--QPA 444
           EI Q ++IS E ++E+  A   +  LSL +   V Q+E     +  D + +   R  Q A
Sbjct: 134 EIAQALDISLEEWQEIKLALQNRTPLSLDAP--VNQDED-GSTSLGDLLPDPRYRSFQLA 190

Query: 445 LL-RLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503
              R+ L   L  L+ +   V+   F      D T  E A  L IS   V +   KGL +
Sbjct: 191 QEDRIRLQQALAQLEERTREVLEFVF----LHDLTQKEAAERLGISPVTVSRRVKKGLDQ 246

Query: 504 LKH 506
           LK 
Sbjct: 247 LKK 249

Length = 256

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

 Score = 62.7 bits (153), Expect = 7e-11
 Identities = 65/250 (26%), Positives = 115/250 (46%), Gaps = 38/250 (15%)

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 GLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPT------D 387
            + WI+  I             + L +  +++V     +A+ +L F L+++        +
Sbjct: 92  AVHWIKAEIHE-----------YILRNWRLVKV--ATTKAQRKLFFNLRKMKKRLQGWLN 138

Query: 388 EEIIQGV----NISPERYREVMKA--SKPILSLHSRHGVTQEEFINGITD-VDGVEN--- 437
            E ++ +     +S    RE M++  S   +SL++     +++    I   VD   +   
Sbjct: 139 PEEVEAIAEELGVSEREVRE-MESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKRSDPED 197

Query: 438 --ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRK 495
             E ++   L R AL + L SL  +   +I  R+  D K   TL E+A    +S E +R+
Sbjct: 198 TLEEEQWEELQRQALANALGSLDARSRRIIEARWLDDDK--LTLQELAAEYGVSAERIRQ 255

Query: 496 HEVKGLMKLK 505
            E   + KLK
Sbjct: 256 IEKNAMKKLK 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 = 54.9 bits (133), 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 = 44/131 (33%), Positives = 61/131 (46%), Gaps = 7/131 (5%)

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

Query: 336 FWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVN 395
             IR AI   +   S   +P      S+ Q   +I+RA   L   L R P+DEEI   + 
Sbjct: 93  TRIRGAIFDEL--RSIDWIP-----RSVRQKARQIERAIAMLEARLGRTPSDEEIADELG 145

Query: 396 ISPERYREVMK 406
           IS E Y  ++ 
Sbjct: 146 ISLEEYNSLLS 156

Length = 268

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

 Score = 58.0 bits (141), Expect = 1e-09
 Identities = 33/107 (30%), Positives = 51/107 (47%), Gaps = 7/107 (6%)

Query: 405 MKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALD-----DVLDSLKP 459
           +K +K  +SL    GV +E   N I+ +D + +E       + L ++       +D L  
Sbjct: 121 LKKTKKEVSLQDPIGVDKEG--NEISLIDILGSEEDDVIEQVELKMEVEKLYKKIDILDE 178

Query: 460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506
           +E  VI  R+GL    ++T  EIA  L ISR  V + E + L KL  
Sbjct: 179 REKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFK 225

Length = 233

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

 Score = 58.0 bits (141), Expect = 2e-09
 Identities = 29/78 (37%), Positives = 44/78 (56%), Gaps = 7/78 (8%)

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

Query: 316 ITAIDRFEPKRRFRLSTY 333
           I AI+ F+  +  +L+TY
Sbjct: 88  IKAIESFDAGKGTKLATY 105

Length = 233

>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: 453 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506
            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 = 53.0 bits (127), Expect = 9e-08
 Identities = 62/258 (24%), Positives = 113/258 (43%), Gaps = 19/258 (7%)

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

Query: 310 AGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRG 368
            G+ GL+ AI R++         + +  I   I R +   +++  VP       I ++  
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSVHVP-----RRIKELGP 116

Query: 369 EIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING 428
           +I++A  EL   L+R P   EI   + +S E   E+M+  +   +L     +  +   + 
Sbjct: 117 KIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGST 176

Query: 429 ITDVDGV-ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN 487
           +  +D V E E+       R+ L+ +L  L  +E  +I   F  +    +  GE  G   
Sbjct: 177 VARLDSVGEVEDGYDQTERRMVLEKILPILSEREKSIIHCTF-EENLSQKETGERLG--- 232

Query: 488 ISREMVRKHEVKGLMKLK 505
           IS+  V + + + + KLK
Sbjct: 233 ISQMHVSRLQRQAISKLK 250

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

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

 Score = 50.8 bits (122), Expect = 4e-07
 Identities = 67/252 (26%), Positives = 109/252 (43%), Gaps = 40/252 (15%)

Query: 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPK--RRFRLST 332
           A+ KL+KH   LV  +  KY +        +DL Q G+ GL+ AI R++P   R F    
Sbjct: 30  AQEKLVKHYKNLVESLAYKYSK---GQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFE--- 83

Query: 333 YGLFWIRHAI------IRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPT 386
              F +   I      +R  T S    VP       I ++  +I++A  EL  EL+R P 
Sbjct: 84  --AFAVPTIIGEIKRYLRDKTWS--VHVP-----RRIKELGPKIKKAVDELTTELQRSPK 134

Query: 387 DEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD-------GVENEN 439
             EI   + +S E   E M+  K   +L   H +  +   + +T +D       G E   
Sbjct: 135 ISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGSTVTLLDIVGQQEDGYELTE 194

Query: 440 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499
           Q      R+ L+ +L  L  +E  +I+  F ++    +  GE  G   IS+  V + + +
Sbjct: 195 Q------RMILEKILPVLSDREKSIIQCTF-IENLSQKETGERLG---ISQMHVSRLQRQ 244

Query: 500 GLMKLKHPTRVD 511
            + KL+    +D
Sbjct: 245 AIKKLREAAFLD 256

Length = 257

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

 Score = 50.6 bits (121), Expect = 5e-07
 Identities = 57/233 (24%), Positives = 98/233 (42%), Gaps = 58/233 (24%)

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 YGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQ 392
           Y    I + I+  +  ++ TR     +    +   G       ELL     + TD +I+ 
Sbjct: 108 YASRCIENEILMYLRRNNKTRSEVSFDEPLNVDWDGN------ELLLS-DVLGTDSDIVY 160

Query: 393 GVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDD 452
              +  E  RE+++ +   L                          N R+  ++ L    
Sbjct: 161 KY-LEEEVDRELLRKALAKL--------------------------NDREKKIMEL---- 189

Query: 453 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505
                          RFGL G  ++T  E+A  L IS+  + + E + L +LK
Sbjct: 190 ---------------RFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLK 227

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

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

 Score = 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|235901 PRK06986, fliA, flagellar biosynthesis sigma factor; Validated

 Score = 48.7 bits (117), Expect = 2e-06
 Identities = 47/170 (27%), Positives = 78/170 (45%), Gaps = 26/170 (15%)

Query: 306 DLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI---IRSMTVSSFTRVPFGLESTS 362
           DL QAG+ GL+ A  R++ ++     TY    IR A+   +RS+       VP  +   +
Sbjct: 40  DLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLDW-----VPRSVRRNA 94

Query: 363 IMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK--PILSLHSRHGV 420
              V   I+    +L  EL R PTD E+ + + +S E YRE++  +    + S+    G 
Sbjct: 95  RE-VAQAIR----QLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGE 149

Query: 421 TQEEFINGITDVD-----GVENENQRQPALLRLALDDVLDSLKPKESLVI 465
             +  +      D      +E+E       LR AL + ++SL  +E LV+
Sbjct: 150 HGDSILVTEDHQDEDPLQQLEDEE------LREALVEAIESLPEREQLVL 193

Length = 236

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

 Score = 46.6 bits (111), Expect = 5e-06
 Identities = 36/155 (23%), Positives = 58/155 (37%), Gaps = 28/155 (18%)

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 GLFWIRHAII----RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEE 389
                R+ I+    R   +     +   L  +         Q  + E L E         
Sbjct: 56  LFRIARNLILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQEEEREALREA-------- 107

Query: 390 IIQGVNISPERYREVMKASKPILSLHSRHGVTQEE 424
               +   PER REV       L L    G++ +E
Sbjct: 108 ----LEKLPEREREV-------LVLRYLEGLSYKE 131

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

 Score = 43.1 bits (102), Expect = 6e-05
 Identities = 23/96 (23%), Positives = 38/96 (39%), Gaps = 5/96 (5%)

Query: 411 ILSLHSRHGVTQEEFINGITDVDGVEN-ENQRQPALLRLALDDVLDSLKPKESLVIRQRF 469
           IL    R    + E       +D   + E + +    R AL + L+ L  +E  V+  R+
Sbjct: 64  ILDYLRRKRRLRRELDLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRY 123

Query: 470 GLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505
                   +  EIA  L IS   V++   +   KL+
Sbjct: 124 L----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|181075 PRK07670, PRK07670, RNA polymerase sigma factor SigD; Validated

 Score = 44.3 bits (105), Expect = 7e-05
 Identities = 61/243 (25%), Positives = 98/243 (40%), Gaps = 25/243 (10%)

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

Query: 333 YGLFWIRHAIIRSMTVSSFTRVPFGLEST-----SIMQVRGEIQRAKLELLFELKRVPTD 387
           Y  F IR AII             GL        S+ +   +++ A  +L     R  T 
Sbjct: 81  YASFRIRGAIID------------GLRKEDWLPRSMREKTKKVEAAIEKLEQRYMRNVTP 128

Query: 388 EEIIQGVNISPERYREVMKAS--KPILSLHSR-HGVTQEEFIN-GITDVDGVENENQRQP 443
           +E+   + ++ E     M       +LS+  + H     E ++  I D      E +   
Sbjct: 129 KEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIRDDKTPTPEEKLLK 188

Query: 444 ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503
             L   L + +  L  KE LVI     L  K + TL EI   LN+S   + +   K L K
Sbjct: 189 EELIEELAEKIKQLSEKEQLVI----SLFYKEELTLTEIGQVLNLSTSRISQIHSKALFK 244

Query: 504 LKH 506
           LK 
Sbjct: 245 LKK 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: 447 RLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505
           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

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

 Score = 43.6 bits (104), Expect = 1e-04
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 10/72 (13%)

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 342
            ++ + WI+  I
Sbjct: 102 VSFAVHWIKAEI 113

Length = 284

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	518
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
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	100.0
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	100.0
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	100.0
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	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
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	100.0
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	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
PRK05572	252	sporulation sigma factor SigF; 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
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	99.91
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	99.91
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	99.89
PRK08295	208	RNA polymerase factor sigma-70; Validated	99.87
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	99.86
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	99.85
PRK12513	194	RNA polymerase sigma factor; Provisional	99.85
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	99.85
PRK05602	186	RNA polymerase sigma factor; Reviewed	99.85
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	99.85
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	99.85
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	99.84
PRK06759	154	RNA polymerase factor sigma-70; Validated	99.84
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	99.84
PRK11922	231	RNA polymerase sigma factor; Provisional	99.84
PRK06811	189	RNA polymerase factor sigma-70; Validated	99.83
PRK13919	186	putative RNA polymerase sigma E protein; Provision	99.83
PRK12519	194	RNA polymerase sigma factor; Provisional	99.83
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	99.82
PRK12514	179	RNA polymerase sigma factor; Provisional	99.82
PRK12524	196	RNA polymerase sigma factor; Provisional	99.82
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	99.82
PRK11924	179	RNA polymerase sigma factor; Provisional	99.82
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	99.82
PRK12537	182	RNA polymerase sigma factor; Provisional	99.81
PRK12534	187	RNA polymerase sigma factor; Provisional	99.81
PRK12538	233	RNA polymerase sigma factor; Provisional	99.81
PRK12531	194	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
PRK12542	185	RNA polymerase sigma factor; Provisional	99.8
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	99.8
PRK12526	206	RNA polymerase sigma factor; Provisional	99.8
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	99.8
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	99.79
PRK12543	179	RNA polymerase sigma factor; Provisional	99.79
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	99.79
PRK12536	181	RNA polymerase sigma factor; Provisional	99.79
PRK12512	184	RNA polymerase sigma factor; Provisional	99.78
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	99.78
PRK12522	173	RNA polymerase sigma factor; Provisional	99.78
PRK09415	179	RNA polymerase factor sigma C; Reviewed	99.77
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	99.77
PRK12539	184	RNA polymerase sigma factor; Provisional	99.77
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	99.77
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	99.77
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	99.77
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	99.77
PRK12518	175	RNA polymerase sigma factor; Provisional	99.76
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	99.76
PRK12520	191	RNA polymerase sigma factor; Provisional	99.76
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	99.75
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	99.75
PRK12529	178	RNA polymerase sigma factor; Provisional	99.75
PRK12533	216	RNA polymerase sigma factor; Provisional	99.75
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	99.74
PRK12523	172	RNA polymerase sigma factor; Reviewed	99.74
PRK12516	187	RNA polymerase sigma factor; Provisional	99.73
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	99.73
PRK12528	161	RNA polymerase sigma factor; Provisional	99.73
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	99.73
PRK12535	196	RNA polymerase sigma factor; Provisional	99.72
PRK12541	161	RNA polymerase sigma factor; Provisional	99.72
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	99.72
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	99.71
PRK08241	339	RNA polymerase factor sigma-70; Validated	99.71
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	99.71
PRK12547	164	RNA polymerase sigma factor; Provisional	99.71
PRK12532	195	RNA polymerase sigma factor; Provisional	99.71
PRK12545	201	RNA polymerase sigma factor; Provisional	99.7
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	99.7
PRK12530	189	RNA polymerase sigma factor; Provisional	99.7
PRK12544	206	RNA polymerase sigma factor; Provisional	99.69
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	99.68
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	99.68
PRK12540	182	RNA polymerase sigma factor; Provisional	99.67
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	99.67
PRK12517	188	RNA polymerase sigma factor; Provisional	99.67
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	99.66
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	99.66
PRK12527	159	RNA polymerase sigma factor; Reviewed	99.66
PRK12546	188	RNA polymerase sigma factor; Provisional	99.65
PRK12525	168	RNA polymerase sigma factor; Provisional	99.64
PRK12511	182	RNA polymerase sigma factor; Provisional	99.63
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	99.6
PRK09047	161	RNA polymerase factor sigma-70; Validated	99.59
PRK06704	228	RNA polymerase factor sigma-70; Validated	99.56
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	99.54
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	99.53
PRK09191	261	two-component response regulator; Provisional	99.43
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	99.41
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	99.38
PF07638	185	Sigma70_ECF: ECF sigma factor	99.31
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	99.19
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	99.12
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	98.93
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	98.89
PRK06930	170	positive control sigma-like factor; Validated	98.47
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	98.26
PRK00118	104	putative DNA-binding protein; Validated	98.19
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	98.15
PRK03975	141	tfx putative transcriptional regulator; Provisiona	98.04
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	97.97
PRK04217	110	hypothetical protein; Provisional	97.93
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	97.87
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	97.81
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	97.72
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	97.71
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	97.68
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	97.66
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	97.57
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	97.57
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	97.48
PRK15201	198	fimbriae regulatory protein FimW; Provisional	97.3
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	97.3
PRK10840	216	transcriptional regulator RcsB; Provisional	97.24
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	97.23
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	97.23
TIGR03020	247	EpsA transcriptional regulator EpsA. Proteins in t	97.23
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	97.21
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	97.18
COG4566	202	TtrR Response regulator [Signal transduction mecha	97.08
PRK13870	234	transcriptional regulator TraR; Provisional	97.06
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	97.05
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	97.04
COG2197	211	CitB Response regulator containing a CheY-like rec	97.0
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	96.98
PRK09483	217	response regulator; Provisional	96.83
COG3413	215	Predicted DNA binding protein [General function pr	96.79
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	96.74
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	96.73
PRK01381	99	Trp operon repressor; Provisional	96.69
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	96.69
PRK09390	202	fixJ response regulator FixJ; Provisional	96.63
PRK15369	211	two component system sensor kinase SsrB; Provision	96.53
PRK10651	216	transcriptional regulator NarL; Provisional	96.5
TIGR01637	132	phage_arpU phage transcriptional regulator, ArpU f	96.44
COG1356	143	tfx Transcriptional regulator [DNA replication, re	96.38
PF12645	65	HTH_16: Helix-turn-helix domain; InterPro: IPR0247	96.12
PRK10403	215	transcriptional regulator NarP; Provisional	96.04
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	95.96
PRK15320	251	transcriptional activator SprB; Provisional	95.93
COG1342	99	Predicted DNA-binding proteins [General function p	95.53
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	95.4
PRK09935	210	transcriptional regulator FimZ; Provisional	95.35
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	95.2
PRK13558	665	bacterio-opsin activator; Provisional	95.19
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	95.18
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	95.14
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	95.13
PRK04841	903	transcriptional regulator MalT; Provisional	95.09
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	94.98
COG4941	415	Predicted RNA polymerase sigma factor containing a	94.98
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	94.73
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	94.44
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	94.4
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	93.98
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	93.88
PRK15418	318	transcriptional regulator LsrR; Provisional	93.76
PRK05901	509	RNA polymerase sigma factor; Provisional	93.76
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	93.68
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	93.32
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	93.25
PRK07598	415	RNA polymerase sigma factor SigC; Validated	92.41
PF13518	52	HTH_28: Helix-turn-helix domain	92.39
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	92.31
PF06530	125	Phage_antitermQ: Phage antitermination protein Q;	92.09
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	92.06
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	92.06
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	92.05
PF10668	60	Phage_terminase: Phage terminase small subunit; In	92.04
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	91.81
PF13730	55	HTH_36: Helix-turn-helix domain	91.58
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	91.5
smart00351	125	PAX Paired Box domain.	90.91
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	90.89
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	90.36
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	90.2
PHA00675	78	hypothetical protein	89.85
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	89.84
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	89.66
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	89.63
PF02650	85	HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IP	89.48
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	89.48
PHA02591	83	hypothetical protein; Provisional	89.2
PRK00423	310	tfb transcription initiation factor IIB; Reviewed	88.46
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	88.16
PRK05949	327	RNA polymerase sigma factor; Validated	87.81
cd00131	128	PAX Paired Box domain	87.57
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	87.06
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	87.01
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	86.8
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	86.79
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	86.49
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	86.47
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	86.2
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	86.14
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	86.03
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	85.84
COG3355	126	Predicted transcriptional regulator [Transcription	85.82
PRK10046	225	dpiA two-component response regulator DpiA; Provis	85.7
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	85.67
PRK07405	317	RNA polymerase sigma factor SigD; Validated	85.62
COG3415	138	Transposase and inactivated derivatives [DNA repli	85.29
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	85.26
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	85.2
PHA02547	179	55 RNA polymerase sigma factor; Provisional	85.19
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	84.87
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	84.82
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	84.63
PF12728	51	HTH_17: Helix-turn-helix domain	84.63
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	84.43
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	84.26
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	84.26
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	84.1
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	84.0
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	83.82
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	83.56
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	83.11
PRK13413	200	mpi multiple promoter invertase; Provisional	82.99
PRK11083	228	DNA-binding response regulator CreB; Provisional	82.88
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	82.77
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	82.63
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	82.56
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	82.4
TIGR01764	49	excise DNA binding domain, excisionase family. An	82.34
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	82.12
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	82.02
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	81.7
PRK12423	202	LexA repressor; Provisional	81.41
PRK07670	251	RNA polymerase sigma factor SigD; Validated	81.22
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	80.93
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	80.82
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	80.69
PRK15479	221	transcriptional regulatory protein TctD; Provision	80.67
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	80.41
PF13551	112	HTH_29: Winged helix-turn helix	80.26
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	80.23

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=100.00  E-value=6.3e-64  Score=527.77  Aligned_cols=314  Identities=31%  Similarity=0.489  Sum_probs=290.6

Q ss_pred             hhcCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHH--------------------HHHHHHHHHHHhCCCCCHHHH
Q 010092          195 EYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKV--------------------FVQVKEQLQKDLGREPTDVEL  254 (518)
Q Consensus       195 ~~~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~--------------------l~~~~~~l~~~l~r~p~~~el  254 (518)
                      ....++|+|+.||++|+++|+||++||+.|+++||.++.                    |+++++.|+..+|++|+..||
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            346778999999999999999999999999999999998                    889999999999999999999


Q ss_pred             HHHcc----------------------CCHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHH
Q 010092          255 AEATN----------------------MSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV  312 (518)
Q Consensus       255 a~~~~----------------------~s~~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~  312 (518)
                      |.++|                      |+.++|.+.+..|..|+++||.+|+++|+++|++|.   ++|++++||||||+
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                      555566666677789999999999999999999998   78999999999999


Q ss_pred             HHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHH
Q 010092          313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEII  391 (518)
Q Consensus       313 IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA  391 (518)
                      +|||+|+++|||++|++|||||+||||++|.++++ ++++||+|.|+.+     .+++++++...|.+++||.||.+|||
T Consensus       211 iGL~ravekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e-----~l~~lrk~~r~L~~~lgR~pt~~EiA  285 (415)
T PRK07598        211 LGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITE-----KLNKIKKAQRKISQEKGRTPTIEDIA  285 (415)
T ss_pred             HHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            99999999999999999999999999999999999 8999999999999     99999999999999999999999999


Q ss_pred             HHhCCCHHHHHHHHHhcCCccccCCCcCCchhh-hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhc
Q 010092          392 QGVNISPERYREVMKASKPILSLHSRHGVTQEE-FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFG  470 (518)
Q Consensus       392 ~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ee-l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryG  470 (518)
                      +.+|+++++|+.++.....++|||.+++.+++. +.+.+. ++..+|++.+....+...|..+|..|||+|+.||.|+||
T Consensus       286 ~~l~is~~~vr~~l~~~~~~~SLd~~vg~~~d~~l~d~l~-~~~~~pee~~~~~~l~~~L~~~L~~L~~reR~VI~LRyg  364 (415)
T PRK07598        286 QELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLE-TDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFG  364 (415)
T ss_pred             HHhCCCHHHHHHHHHHccCCcccccccCCCccccHHHhcc-CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHh
Confidence            999999999999999999999999998766654 444443 344567888888889999999999999999999999999


Q ss_pred             CCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhhc
Q 010092          471 LDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  517 (518)
Q Consensus       471 L~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~y~  517 (518)
                      |+|++++|++|||+.||+|+++|++++++|++|||++.+...|++|+
T Consensus       365 l~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR~~~~~~~l~~y~  411 (415)
T PRK07598        365 LADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYL  411 (415)
T ss_pred             cCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999997

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=6.1e-60  Score=494.09  Aligned_cols=311  Identities=33%  Similarity=0.539  Sum_probs=292.1

Q ss_pred             CcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHH
Q 010092          199 STDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNK  278 (518)
Q Consensus       199 ~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~  278 (518)
                      ..|.+..||++|+++|+||++||..|++.++.+..++..+.+|+...|+.|+..+||.+.|++...|.+.+..|..|++.
T Consensus        61 ~~d~l~~Yl~~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~  140 (373)
T PRK07406         61 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEK  140 (373)
T ss_pred             CCCHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHHHH
Confidence            45889999999999999999999999999999999999999999999999999999999999999999999888999999


Q ss_pred             HHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccccc
Q 010092          279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFG  357 (518)
Q Consensus       279 LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~  357 (518)
                      ||.+|+++|+++|++|.   +++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+ ++++||+|.|
T Consensus       141 Li~~~l~lV~~iA~ry~---~~~~~~eDLiQEG~igL~~Ai~kFd~~kg~~FsTYA~wWIRqaI~~~I~~~~r~IRlP~~  217 (373)
T PRK07406        141 MVQSNLRLVVSIAKKYM---NRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH  217 (373)
T ss_pred             HHHHHHHHHHHHHHHHc---CCCCCHHHHHHHHHHHHHHHHHhcCCccCCCHHHHHHHHHHHHHHHHHHhcCCceeCCHH
Confidence            99999999999999999   7899999999999999999999999999999999999999999999999 8999999999


Q ss_pred             ccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCCCc
Q 010092          358 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVE  436 (518)
Q Consensus       358 ~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~~  436 (518)
                      +..     .+++++++...|.+++||.||.+|||+.+|+++++|..++.....++|||.+++.+++ .+.+.+.++ ..+
T Consensus       218 ~~~-----~~~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~~~~~~~~~~SLd~~i~~~~~~~l~d~l~d~-~~~  291 (373)
T PRK07406        218 LYE-----TISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEAD-GET  291 (373)
T ss_pred             HHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccCCCCCCCCcccHHHhcCCC-CCC
Confidence            998     9999999999999999999999999999999999999999988999999999765544 355555543 345


Q ss_pred             chhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhh
Q 010092          437 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQH  516 (518)
Q Consensus       437 ~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~y  516 (518)
                      |++.+....+...|..+|+.||++|+.||.+||||+|++++|++|||+.||||+++|||++.+|++|||++.....|..|
T Consensus       292 pee~~~~~~~~~~L~~aL~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~~~~~l~~~  371 (373)
T PRK07406        292 PEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEY  371 (373)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHHHHHHHH
Confidence            77777888889999999999999999999999999988899999999999999999999999999999999999999999


Q ss_pred             cC
Q 010092          517 MV  518 (518)
Q Consensus       517 ~~  518 (518)
                      +.
T Consensus       372 ~~  373 (373)
T PRK07406        372 IR  373 (373)
T ss_pred             hC
Confidence            74

>PRK05949 RNA polymerase sigma factor; Validated

Probab=100.00  E-value=1.1e-59  Score=486.15  Aligned_cols=309  Identities=33%  Similarity=0.541  Sum_probs=288.1

Q ss_pred             CCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHH
Q 010092          198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN  277 (518)
Q Consensus       198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e  277 (518)
                      .++|.+..||++|+++|+||++||..|++.++.+..+++.++.|+..+|++|+..+||.+++|+..++...+..|..|++
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            35799999999999999999999999999999999999999999999999999999999999999888888887789999


Q ss_pred             HHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccc
Q 010092          278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF  356 (518)
Q Consensus       278 ~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~  356 (518)
                      .||.+|+++|+++|++|.   +++.+++|||||||+|||+|+++|||++|++|||||+||||++|.+++. ++++||+|.
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            999999999999999999   7899999999999999999999999999999999999999999999999 899999999


Q ss_pred             cccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCCC
Q 010092          357 GLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGV  435 (518)
Q Consensus       357 ~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~  435 (518)
                      |+..     .+++++++...+..++||.||++|||+.+|+++++|..++.....++|||.+.+.+++ .+.+.+.++ ..
T Consensus       172 ~~~~-----~~~~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~l~d~-~~  245 (327)
T PRK05949        172 HITE-----KLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDE-GP  245 (327)
T ss_pred             HHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccccccCCCcCCCCCccHHhhcCCC-CC
Confidence            9999     9999999999999999999999999999999999999999999999999999865544 344545544 35


Q ss_pred             cchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhh
Q 010092          436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQ  515 (518)
Q Consensus       436 ~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~  515 (518)
                      +|++.+....+...|..+|+.||++|+.||.+||||+|++++|++|||+.||||+++|+|++.+|++|||+  ....|..
T Consensus       246 ~pe~~~~~~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~--~~~~l~~  323 (327)
T PRK05949        246 SPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR--RRANVKE  323 (327)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH--HHHHHHH
Confidence            67878888888999999999999999999999999999999999999999999999999999999999998  4567787


Q ss_pred             hc
Q 010092          516 HM  517 (518)
Q Consensus       516 y~  517 (518)
                      |+
T Consensus       324 ~~  325 (327)
T PRK05949        324 YL  325 (327)
T ss_pred             HH
Confidence            75

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

Probab=100.00  E-value=3.1e-58  Score=469.94  Aligned_cols=296  Identities=38%  Similarity=0.613  Sum_probs=276.5

Q ss_pred             ChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHHHH
Q 010092          201 DLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLI  280 (518)
Q Consensus       201 d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~LI  280 (518)
                      |.+..|+++|+.+|+||++||..|++.++.+..+++.+..|+...|++|+..+||+++|++...+...+..|..|+++||
T Consensus         1 ~~~~~yl~~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~~Lv   80 (298)
T TIGR02997         1 DLVRLYLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKEKMI   80 (298)
T ss_pred             CcHHHHHHHccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHHHHH
Confidence            46789999999999999999999999999999999999999999999999999999999999888888887799999999


Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccccccc
Q 010092          281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLE  359 (518)
Q Consensus       281 ~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~~~  359 (518)
                      .+|+++|+++|++|.   ++|.+++|||||||+|||+|+++|||++|++|+|||+||||++|.+++. ++++||+|.++.
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             chhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCCCcch
Q 010092          360 STSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENE  438 (518)
Q Consensus       360 e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~~~e  438 (518)
                      .     .+++++++...+...+|+.||.+|||+.+|+++++|..++.....++|||.+.+.+++ .+.+.+.+ ...+|+
T Consensus       158 ~-----~~~~~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~-~~~~pe  231 (298)
T TIGR02997       158 E-----KLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLED-DGESPE  231 (298)
T ss_pred             H-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHcccCcccCCCcCCCCcchHHHhccC-CCCCHH
Confidence            8     9999999999999999999999999999999999999999999999999998755443 34444444 345677


Q ss_pred             hhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092          439 NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  505 (518)
Q Consensus       439 e~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR  505 (518)
                      +.+...++...|..+|+.||++|+.||.+||||+|++++|++|||+.||||+++|||++++|++|||
T Consensus       232 ~~~~~~~~~~~L~~~L~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr  298 (298)
T TIGR02997       232 EQVERESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR  298 (298)
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            7788888889999999999999999999999999999999999999999999999999999999997

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=6.1e-58  Score=471.51  Aligned_cols=309  Identities=33%  Similarity=0.543  Sum_probs=286.9

Q ss_pred             CCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHH
Q 010092          198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN  277 (518)
Q Consensus       198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e  277 (518)
                      +++|.+..||++|+.+|+||++||..|++.++.+..+++.+..|++.+|++|+..+||.+++++...+...+.+|..|++
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            45789999999999999999999999999999999999999999999999999999999999999888888877789999


Q ss_pred             HHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccc
Q 010092          278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF  356 (518)
Q Consensus       278 ~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~  356 (518)
                      +||.+|+++|+++|++|.   +++.+++||+||||+|||+|+++|||++|++|+|||+||||++|.++|. ++++||+|.
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 899999999


Q ss_pred             cccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCCC
Q 010092          357 GLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGV  435 (518)
Q Consensus       357 ~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~  435 (518)
                      |+..     .+++++++...+...+|+.||.+|||+.+|++++++..++......+|||.+.+++++ .+.+.+.++ ..
T Consensus       162 ~~~~-----~~~~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~~~~~d~-~~  235 (317)
T PRK07405        162 HITE-----KLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDT-GA  235 (317)
T ss_pred             HHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCeeecCCCCCCCCccHHHhhcCC-CC
Confidence            9998     9999999999999999999999999999999999999999988899999998765544 344445443 35


Q ss_pred             cchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhh
Q 010092          436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQ  515 (518)
Q Consensus       436 ~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~  515 (518)
                      +|++.+....+...|..+|+.||++|+.||.+||||+|++++|++|||+.||||+++|||++.+|++|||+.  ...|..
T Consensus       236 ~pe~~~~~~~~~~~l~~al~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~--~~~l~~  313 (317)
T PRK07405        236 SPEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR--KANIQE  313 (317)
T ss_pred             CHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--HHHHHH
Confidence            678888888899999999999999999999999999999999999999999999999999999999999984  466777


Q ss_pred             hc
Q 010092          516 HM  517 (518)
Q Consensus       516 y~  517 (518)
                      |+
T Consensus       314 ~~  315 (317)
T PRK07405        314 YL  315 (317)
T ss_pred             HH
Confidence            65

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

Probab=100.00  E-value=2.1e-58  Score=472.31  Aligned_cols=314  Identities=35%  Similarity=0.532  Sum_probs=282.1

Q ss_pred             cCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHH-HhCCCCCHH---------------HHHHHccC
Q 010092          197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQK-DLGREPTDV---------------ELAEATNM  260 (518)
Q Consensus       197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~-~l~r~p~~~---------------ela~~~~~  260 (518)
                      ..++|.+..|+.+++..++++.+++..+.+.++....+......+.. .+++.|+..               +|+.....
T Consensus         5 ~~~~d~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~   84 (342)
T COG0568           5 RLSADAVRAYLDEIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTP   84 (342)
T ss_pred             ccchhHHHHHHHHhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccCh
Confidence            45789999999999999999999999999999888877666667665 666777764               33333222


Q ss_pred             CH-HHHH-HHHHH--cHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHH
Q 010092          261 SA-AQVK-KCLEV--GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLF  336 (518)
Q Consensus       261 s~-~~L~-~~~~g--d~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~  336 (518)
                      ++ ..+. ++..|  +..|+++||.+||+||++||++|.   ++|++|.||||||+||||+||++|||++||+|||||+|
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            22 2233 34456  678999999999999999999999   89999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccC
Q 010092          337 WIRHAIIRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLH  415 (518)
Q Consensus       337 wIRqaI~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD  415 (518)
                      ||||+|.++|. +.++||+|+|+.+     ..++++++.+.+.+++|++|+++|||+.+|+++++|+.++..+..++|||
T Consensus       162 WIrqaI~raI~~q~rtIRipvh~~e-----~~nkl~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~~~SLd  236 (342)
T COG0568         162 WIRQAITRAIADQARTIRIPVHQVE-----LINKLRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASEPISLD  236 (342)
T ss_pred             HHHHHHHHHHHHhcchhhHhHHHHH-----HHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhcccCcccC
Confidence            99999999999 9999999999999     99999999999999999999999999999999999999999999999999


Q ss_pred             CCcCCchh-hhhcccccCCCCcchhhhHHHHHHHHHHHHHhc-CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHH
Q 010092          416 SRHGVTQE-EFINGITDVDGVENENQRQPALLRLALDDVLDS-LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMV  493 (518)
Q Consensus       416 ~~~~~~~e-el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~-L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerV  493 (518)
                      .+++++++ .+.+.+.|+...+|++.+....+.+.+...|.. |+|+|+.||++||||+|+++.|++|||+.+|||+++|
T Consensus       237 ~~ig~ded~~l~d~leD~~~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~~~~~~TLeevg~~~~isrERv  316 (342)
T COG0568         237 TPIGDDEDSELGDFLEDDKSVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLDDGEPKTLEELGEEFGISRERV  316 (342)
T ss_pred             CcCCCCcccHHHHHhhcCCcCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccCCCCcchHHHHHHHhCCcHHHH
Confidence            99987765 477888888887899999999999999999999 9999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHh-CcchhhhhhhhcC
Q 010092          494 RKHEVKGLMKLK-HPTRVDYLRQHMV  518 (518)
Q Consensus       494 Rqie~rALkKLR-~~~~~~~L~~y~~  518 (518)
                      |||+.+|++||| ++.+...++.|+.
T Consensus       317 RQIE~kAl~KLr~~~~~~~~~~~~l~  342 (342)
T COG0568         317 RQIEAKALRKLRRHPERSALLRSYLD  342 (342)
T ss_pred             HHHHHHHHHHHHHhhhhhhHHHHhhC
Confidence            999999999999 7777777888863

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=100.00  E-value=1e-57  Score=491.32  Aligned_cols=303  Identities=32%  Similarity=0.478  Sum_probs=270.4

Q ss_pred             hhcCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHH
Q 010092          195 EYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRA  274 (518)
Q Consensus       195 ~~~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~  274 (518)
                      ..+...|.+..||++|+.+|+||++||..|++.++.+..+++.   +..       ..+|+..   ....+++.+..+..
T Consensus       205 ~~~~~~d~l~~YL~~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~~-------~~~~~~~---~~~~l~~~~~~g~~  271 (509)
T PRK05901        205 KLTATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEEL---LAE-------GEKLDPE---LRRDLQWIGRDGKR  271 (509)
T ss_pred             hccccccHHHHHHHHhccCCCCCHHHHHHHHHHHHhCCchhhh---hhh-------cccchhh---hhhhhhhhccchHH
Confidence            3466779999999999999999999999999999866433221   111       1123221   34557777888899


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcc
Q 010092          275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR  353 (518)
Q Consensus       275 A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iR  353 (518)
                      |+++||.+|+|||+++|++|.   ++|++++||||||+||||+|+++|||++|++|||||+||||++|.++|. +.++||
T Consensus       272 Ar~~LI~sNLrLVvsIAkrY~---~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IR  348 (509)
T PRK05901        272 AKNHLLEANLRLVVSLAKRYT---NRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIR  348 (509)
T ss_pred             HHHHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCcee
Confidence            999999999999999999998   7899999999999999999999999999999999999999999999999 899999


Q ss_pred             ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccC
Q 010092          354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDV  432 (518)
Q Consensus       354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~  432 (518)
                      +|.|+.+     .++++.++..+|.+.+||.||.+|||+.||+++++|..++.....++|||.+++.+++ .+.+.+.++
T Consensus       349 vP~~~~e-----~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~~~~~~~~~SLD~~i~~d~~~~l~d~l~D~  423 (509)
T PRK05901        349 IPVHMVE-----TINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDS  423 (509)
T ss_pred             cCHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCcccccccccCCcccHHHhccCC
Confidence            9999999     9999999999999999999999999999999999999999999999999999765544 466677777


Q ss_pred             CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      ....|++.+....+...|..+|..|+++|+.||.+||||++++++|+.|||+.||||+++||||+.+||.|||++.+...
T Consensus       424 ~~~~p~~~~~~~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~~~~~~  503 (509)
T PRK05901        424 EAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQV  503 (509)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            66678888888889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhcC
Q 010092          513 LRQHMV  518 (518)
Q Consensus       513 L~~y~~  518 (518)
                      |+.|+.
T Consensus       504 l~~~l~  509 (509)
T PRK05901        504 LRDFLD  509 (509)
T ss_pred             HHHhhC
Confidence            999973

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=100.00  E-value=5.2e-56  Score=457.89  Aligned_cols=299  Identities=31%  Similarity=0.438  Sum_probs=264.8

Q ss_pred             CCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHH
Q 010092          198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN  277 (518)
Q Consensus       198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e  277 (518)
                      ...|.+..||++|+.+|+||++||..|++.++.+..++..           |...+|+...  ....+...+..|..|++
T Consensus        23 ~~~~~~~~Yl~~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~A~~   89 (324)
T PRK07921         23 PAADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEAARR   89 (324)
T ss_pred             CCCChHHHHHHHhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHHHHH
Confidence            3458899999999999999999999999999866544332           1112221110  23456777788899999


Q ss_pred             HHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccc
Q 010092          278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF  356 (518)
Q Consensus       278 ~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~  356 (518)
                      +||.+|+++|+++|++|.   +++.+++||+|||++|||+|+++|||++|++|+|||+||||++|.++|+ ++++||+|.
T Consensus        90 ~Lv~~~~~lV~~iA~r~~---~~~~~~eDLvQEg~igL~~a~~~fdp~~G~rFsTYA~~wIr~aI~~~i~~~~r~vrlP~  166 (324)
T PRK07921         90 HLLEANLRLVVSLAKRYT---GRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPV  166 (324)
T ss_pred             HHHHHHHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHcCCccCCCHHHHHHHHHHHHHHHHHHHcCCCccCCH
Confidence            999999999999999999   7899999999999999999999999999999999999999999999999 889999999


Q ss_pred             cccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCCC
Q 010092          357 GLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGV  435 (518)
Q Consensus       357 ~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~  435 (518)
                      |+.+     .+++++++...|.+++|+.||.+|||+.+|+++++|..++.....++|||.+.+.+++ .+.+.+.++...
T Consensus       167 ~~~~-----~~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~~~~  241 (324)
T PRK07921        167 HLVE-----QVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEAT  241 (324)
T ss_pred             HHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHcCCCceecCCCCCCCCchHHHHhcCCCCC
Confidence            9998     9999999999999999999999999999999999999999988899999999765544 456666665556


Q ss_pred             cchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhh
Q 010092          436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQ  515 (518)
Q Consensus       436 ~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~  515 (518)
                      +|++.+....+...|..+|+.|+++|+.||.+||||+|++++|++|||+.||||+++||||+.+||+|||.......|..
T Consensus       242 ~pe~~~~~~~~~~~l~~~L~~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~~~~~~l~~  321 (324)
T PRK07921        242 SAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRS  321 (324)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence            67777788888999999999999999999999999998899999999999999999999999999999999999999998


Q ss_pred             hc
Q 010092          516 HM  517 (518)
Q Consensus       516 y~  517 (518)
                      |+
T Consensus       322 ~~  323 (324)
T PRK07921        322 YA  323 (324)
T ss_pred             hh
Confidence            86

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=7.4e-54  Score=449.29  Aligned_cols=273  Identities=34%  Similarity=0.557  Sum_probs=255.3

Q ss_pred             cCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHH
Q 010092          197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAAR  276 (518)
Q Consensus       197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~  276 (518)
                      ....|++.+||++|+.+|+||++||..|++.+                                        ..||..|+
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            44579999999999999999999999887655                                        35788999


Q ss_pred             HHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccc
Q 010092          277 NKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVP  355 (518)
Q Consensus       277 e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP  355 (518)
                      +.||..|+++|+++|++|.   +++.+++||+||||+|||+|+++|||++|++|+|||+||||++|.++|+ +.+++|+|
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            9999999999999999999   7899999999999999999999999999999999999999999999999 89999999


Q ss_pred             ccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCC
Q 010092          356 FGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDG  434 (518)
Q Consensus       356 ~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~  434 (518)
                      .|+.+     .++++.++.+.|..++||.||.+|||+.||+++++|+.++.....++|||.+.+.+++ .+.+.+.++..
T Consensus       209 ~~~~~-----~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~i~d~~~  283 (367)
T PRK09210        209 VHMVE-----TINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDA  283 (367)
T ss_pred             HHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCCcCCCCCCCCcchhhhhccCCCC
Confidence            99999     9999999999999999999999999999999999999999999899999999865543 46667777766


Q ss_pred             CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhh
Q 010092          435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR  514 (518)
Q Consensus       435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~  514 (518)
                      .+|++.+....++..|..+|..||++|+.||.+||||+|++++|++|||+.||||+++||||+.+||+|||++.+...|+
T Consensus       284 ~~p~~~~~~~~~~~~l~~~l~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~~~~~~l~  363 (367)
T PRK09210        284 TSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLK  363 (367)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhChHHHhHHH
Confidence            77888888889999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhc
Q 010092          515 QHM  517 (518)
Q Consensus       515 ~y~  517 (518)
                      .|+
T Consensus       364 ~~~  366 (367)
T PRK09210        364 DFL  366 (367)
T ss_pred             Hhh
Confidence            986

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=100.00  E-value=1.6e-50  Score=449.75  Aligned_cols=242  Identities=35%  Similarity=0.572  Sum_probs=226.4

Q ss_pred             HHHHc---HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092          268 CLEVG---RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (518)
Q Consensus       268 ~~~gd---~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r  344 (518)
                      +..|+   ..|+++||.+|+|||+++|++|.   ++|++++||||||+|||++|+++|||++|++|||||+||||++|.+
T Consensus       371 i~~g~~~~~~a~~~Li~~nlrlV~~iA~ky~---~~gl~~~DLiQeG~iGL~~Av~kfd~~~G~~FstYA~~wIr~aI~~  447 (619)
T PRK05658        371 ISKGEAKARRAKKEMVEANLRLVISIAKKYT---NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR  447 (619)
T ss_pred             HhccchhhhHHHHHHHHHHHHHHHHHHHHHh---hCCCCHHHHHHHHHHHHHHHHHhcCccCCCchHHHhHHHHHHHHHH
Confidence            34564   47899999999999999999998   7899999999999999999999999999999999999999999999


Q ss_pred             HHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092          345 SMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE  423 (518)
Q Consensus       345 aI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e  423 (518)
                      +|+ +.++||+|+|+.+     ..++++++...+.+++||.||++|||+.||+++++|+.++.....++|||.+++++++
T Consensus       448 ~i~~~~r~irip~~~~~-----~~~k~~~~~~~~~~~~gr~pt~~eiA~~l~~~~~~v~~~~~~~~~~~Sld~~i~~~~~  522 (619)
T PRK05658        448 SIADQARTIRIPVHMIE-----TINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDED  522 (619)
T ss_pred             HHHHcCCceecCHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCCCcCCCCCCCCCC
Confidence            999 8899999999999     9999999999999999999999999999999999999999999999999999765554


Q ss_pred             -hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          424 -EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       424 -el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                       .+.+.+.+....+|++.+....++..|..+|+.||++|+.||.+||||+++.++|++|||+.||||+++||||+.+||+
T Consensus       523 ~~l~d~i~d~~~~~p~~~~~~~~~~~~l~~~l~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~  602 (619)
T PRK05658        523 SHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR  602 (619)
T ss_pred             CchhhhcCCCCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHH
Confidence             4667777766667888888888999999999999999999999999999889999999999999999999999999999


Q ss_pred             HHhCcchhhhhhhhc
Q 010092          503 KLKHPTRVDYLRQHM  517 (518)
Q Consensus       503 KLR~~~~~~~L~~y~  517 (518)
                      |||++.+...|+.|+
T Consensus       603 kLr~~~~~~~l~~~~  617 (619)
T PRK05658        603 KLRHPSRSRKLRSFL  617 (619)
T ss_pred             HHhchHHHHHHHHHh
Confidence            999999999999997

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

Probab=100.00  E-value=1.2e-46  Score=372.64  Aligned_cols=235  Identities=34%  Similarity=0.570  Sum_probs=218.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcc
Q 010092          275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR  353 (518)
Q Consensus       275 A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iR  353 (518)
                      |+++||.+|+++|+++|++|.   +++.+++||+|||++||++|+++|||++|++|+|||+||||++|.+++. +.+.++
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             ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccC
Q 010092          354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDV  432 (518)
Q Consensus       354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~  432 (518)
                      +|.++.+     .++++.++...+..++|+.||.+|||+.+|+++++|..++......+|||.+.+.+++ .+.+.+.++
T Consensus        78 ip~~~~~-----~~~~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~~~~~~~~SLd~~~~~~~~~~l~d~l~d~  152 (238)
T TIGR02393        78 IPVHMVE-----TINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDT  152 (238)
T ss_pred             eCHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCCcCCCCCCCCcccHHHHhcCC
Confidence            9999888     9999999999999999999999999999999999999999888889999998765544 355666666


Q ss_pred             CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      ...+|++......+...|..+|+.||++|+.||.++|||++++++|++|||+.||||.++|+|++.+|++|||+....+.
T Consensus       153 ~~~~p~~~~~~~~~~~~l~~~l~~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~~~~~  232 (238)
T TIGR02393       153 SIESPDDYAAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKK  232 (238)
T ss_pred             CCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhHHHhH
Confidence            65667777778888999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhc
Q 010092          513 LRQHM  517 (518)
Q Consensus       513 L~~y~  517 (518)
                      |+.|+
T Consensus       233 ~~~~~  237 (238)
T TIGR02393       233 LKSFL  237 (238)
T ss_pred             HHHhh
Confidence            99886

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=5.3e-44  Score=369.21  Aligned_cols=270  Identities=29%  Similarity=0.443  Sum_probs=244.0

Q ss_pred             cCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHH
Q 010092          197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAAR  276 (518)
Q Consensus       197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~  276 (518)
                      ....|.+++|+++|+..|+||+++|..|...+                                        ..||..|+
T Consensus        49 ~~~~~~~~~y~~~~~~~~~l~~~ee~~li~~~----------------------------------------~~Gd~~A~   88 (325)
T PRK05657         49 QRVLDATQLYLNEIGYSPLLTAEEEVYFARRA----------------------------------------LRGDFAAR   88 (325)
T ss_pred             cccccHHHHHHHHHhcCCCCCHHHHHHHHHHH----------------------------------------HcCCHHHH
Confidence            35789999999999999999999998885544                                        56889999


Q ss_pred             HHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccc
Q 010092          277 NKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVP  355 (518)
Q Consensus       277 e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP  355 (518)
                      +.||..|.++|+++|++|.   +++.+++||+||||+|||+++++||+.+|++|+|||+||||++|.+++. +.+.+++|
T Consensus        89 ~~Li~~y~~~V~~~a~~~~---~~~~~aeDLvQE~fi~l~~ai~~fd~~rg~~Fstyatw~iR~ai~~~i~~~~r~ir~p  165 (325)
T PRK05657         89 QRMIESNLRLVVKIAKRYL---NRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLP  165 (325)
T ss_pred             HHHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCCccCCCHHHHHHHHHHHHHHHHHHHcCCccccC
Confidence            9999999999999999998   7889999999999999999999999999999999999999999999998 88999999


Q ss_pred             ccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCC
Q 010092          356 FGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDG  434 (518)
Q Consensus       356 ~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~  434 (518)
                      .++..     .++.+.++...|...+|+.||.+|||+.+|+++++|..++.......|||.+...+.. .+.+.+.+...
T Consensus       166 ~~~~~-----~l~~~~R~~~~l~~~l~r~~t~~eiA~~l~~~~~~v~~~l~~~~~~~sld~~~~~~~~~~l~d~l~d~~~  240 (325)
T PRK05657        166 VHVVK-----ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQE  240 (325)
T ss_pred             HHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhccCCcccCCCCCCCCCcchhhhccCCCC
Confidence            99877     7888888889999999999999999999999999999999988889999988654433 34555665555


Q ss_pred             CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhh
Q 010092          435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR  514 (518)
Q Consensus       435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~  514 (518)
                      .+|++.+...++...|..+|..||+++|.||.++|||.+.+++|++|||+.||||.++|++++++|+++||+.+....+.
T Consensus       241 ~~pe~~~~~~e~~~~L~~aL~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~~~~~~  320 (325)
T PRK05657        241 NGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGLS  320 (325)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhCccc
Confidence            56777788888889999999999999999999999999999999999999999999999999999999999877665554

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=1.8e-43  Score=359.96  Aligned_cols=267  Identities=25%  Similarity=0.270  Sum_probs=221.2

Q ss_pred             CCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHH
Q 010092          198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN  277 (518)
Q Consensus       198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e  277 (518)
                      ...++++.|++++..+|+||+++|..|++.++                                       ..||..|++
T Consensus         3 ~~~~~~~~y~~~~~~~~~l~~~~e~~L~~~~~---------------------------------------~~gd~~A~~   43 (289)
T PRK07500          3 ADASADRSMIRSAMKAPYLEREEEHALAYRWK---------------------------------------DHRDEDALH   43 (289)
T ss_pred             cchhHHHHHHHHHhcCCCCCHHHHHHHHHHHH---------------------------------------HCCCHHHHH
Confidence            45688999999999999999999998876541                                       247899999


Q ss_pred             HHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccc
Q 010092          278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF  356 (518)
Q Consensus       278 ~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~  356 (518)
                      .||..|+++|+++|++|.   +++.+++||+||||+|||+|+++|||.+|.+|+|||+||||++|.++++ +.+++|+|.
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   7899999999999999999999999999999999999999999999999 778999999


Q ss_pred             cccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHH-hcCCccccCCCcCCchh---hhhcccccC
Q 010092          357 GLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMK-ASKPILSLHSRHGVTQE---EFINGITDV  432 (518)
Q Consensus       357 ~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~-~~~~~~SLD~~~~~~~e---el~~~l~d~  432 (518)
                      +.....++..+.+++.....+...+|+.||.+|||+.||+++++|..+.. ....++|||.+.+++++   .+.+.+.++
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            86542222233333333333344789999999999999999999988753 45679999998765443   355556554


Q ss_pred             CCCcchhhhH----HHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          433 DGVENENQRQ----PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       433 ~~~~~ee~~~----~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      . .+|++.+.    ...+...|..+|+.||++|+.||.++||.  .+++|++|||+.||||+++|+|++++|+++||...
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  47899999999999999999999999999999765


Q ss_pred             h
Q 010092          509 R  509 (518)
Q Consensus       509 ~  509 (518)
                      .
T Consensus       278 ~  278 (289)
T PRK07500        278 L  278 (289)
T ss_pred             H
Confidence            4

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=100.00  E-value=1.7e-43  Score=359.19  Aligned_cols=261  Identities=23%  Similarity=0.283  Sum_probs=214.8

Q ss_pred             CcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHH
Q 010092          199 STDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNK  278 (518)
Q Consensus       199 ~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~  278 (518)
                      +.+.+..|++++...|+||.++|..|+...                                       ...||..|++.
T Consensus        12 ~~~~~~~y~~~~~~~~~l~~~~e~~l~~~~---------------------------------------~~~Gd~~a~~~   52 (284)
T PRK06596         12 PEGNLDAYIQAVNKIPMLTAEEEYMLAKRL---------------------------------------REHGDLEAAKQ   52 (284)
T ss_pred             CccHHHHHHHHHhccCCCCHHHHHHHHHHH---------------------------------------HHcCCHHHHHH
Confidence            448899999999999999999998886643                                       13588999999


Q ss_pred             HHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccccc
Q 010092          279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFG  357 (518)
Q Consensus       279 LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~  357 (518)
                      ||.+|+++|+++|++|.   +.+.+++||+|||++||++|+++|||++|++|+|||+|||+++|.++++ +.++|++|.+
T Consensus        53 Lv~~~~~lV~~ia~~~~---~~~~~~eDLvQeg~igL~~a~~~fd~~~~~~FstYA~~~Ir~~i~~~l~~~~~~vr~p~~  129 (284)
T PRK06596         53 LVLSHLRFVVHIARGYR---GYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATT  129 (284)
T ss_pred             HHHHhHHHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHHHHHHHHcCCeeeccch
Confidence            99999999999999998   7899999999999999999999999999999999999999999999999 6567899986


Q ss_pred             ccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh-cCCccccCCCcCCchh---hhhcccccCC
Q 010092          358 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA-SKPILSLHSRHGVTQE---EFINGITDVD  433 (518)
Q Consensus       358 ~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~-~~~~~SLD~~~~~~~e---el~~~l~d~~  433 (518)
                      ....   ....++.+...++.  .+++||.+|||+.||+++++|..++.. ....+|||.+.+++++   ++.+.+.+. 
T Consensus       130 ~~~~---~~~~~~~~~~~~l~--~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~~l~~~l~d~-  203 (284)
T PRK06596        130 KAQR---KLFFNLRKAKKRLG--WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEESGAPQDYLEDK-  203 (284)
T ss_pred             HHHH---HHHHHHHHHHHHhc--cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCcchHHHHcCCC-
Confidence            4320   02233333333332  349999999999999999999998763 4578999998754422   245555554 


Q ss_pred             CCcchhhhHHH----HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          434 GVENENQRQPA----LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       434 ~~~~ee~~~~~----~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                      ..+|++.++..    .+...|..+|+.||++|+.||.+|||.+  +++|++|||+.||||+++|+|++.+|++|||+...
T Consensus       204 ~~~p~~~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~~--~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~  281 (284)
T PRK06596        204 SSDPADVLEEDNWEDQRRALLADALEGLDERSRDIIEARWLDD--DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIE  281 (284)
T ss_pred             CCCchHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCC--CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            33455544432    4678899999999999999999999642  68999999999999999999999999999997654

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=100.00  E-value=1.9e-42  Score=349.05  Aligned_cols=257  Identities=25%  Similarity=0.311  Sum_probs=208.8

Q ss_pred             hHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHHHHH
Q 010092          202 LVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIK  281 (518)
Q Consensus       202 ~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~LI~  281 (518)
                      .+..|+++|+.+|+|++++|..|+..+                                       ...||..|++.||.
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             HHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccccccc
Q 010092          282 HNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLES  360 (518)
Q Consensus       282 ~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~~~e  360 (518)
                      +|+++|+++|++|.   +++.+++||+|||++|||+|+++|||++|++|+|||+|||+++|.++++ +.+++|+|.+...
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 6567899976332


Q ss_pred             hhhHHHHHHHHHHHHHHHHHhCCCC-CHHHHHHHhCCCHHHHHHHHHh-cCCccccCCCcCCchh---hhhcccccCCCC
Q 010092          361 TSIMQVRGEIQRAKLELLFELKRVP-TDEEIIQGVNISPERYREVMKA-SKPILSLHSRHGVTQE---EFINGITDVDGV  435 (518)
Q Consensus       361 ~~~~~~~~ki~ka~~eL~~elgR~P-T~eELA~~lgis~e~v~~~l~~-~~~~~SLD~~~~~~~e---el~~~l~d~~~~  435 (518)
                         .+...++.+....+.  .++.| +.+|||+.||+++++|..++.. ....+|||.+.+++++   .+.+.+.++. .
T Consensus       120 ---~~~~~~~~~~~~~~~--~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~l~d~~-~  193 (270)
T TIGR02392       120 ---RKLFFNLRKMKKRLQ--GWLNPEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDDEDDGGAPIAYLVDKT-S  193 (270)
T ss_pred             ---HHHHHHHHHHHHHHh--cCCCCCCHHHHHHHhCCCHHHHHHHHHHccCCCccCCCCCCCCCCccccHHHHhcCCC-C
Confidence               113334444443332  22566 6999999999999999998653 3458999998755432   2444555543 3


Q ss_pred             cchhhhHH----HHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          436 ENENQRQP----ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       436 ~~ee~~~~----~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      +|++.+..    ..+...|..+|..||++|+.||.++||.  .+++|++|||+.||||+++|+|++.+||+|||..+
T Consensus       194 ~pe~~~~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~--~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l  268 (270)
T TIGR02392       194 DPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLD--DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAAL  268 (270)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcC--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            45554433    3467889999999999999999999963  35899999999999999999999999999999754

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.

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=100.00  E-value=1.2e-42  Score=349.53  Aligned_cols=221  Identities=24%  Similarity=0.306  Sum_probs=194.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCC
Q 010092          273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSF  351 (518)
Q Consensus       273 ~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~  351 (518)
                      ..++++||.+|++||+++|++|.   ++|++++||||||+|||++|+++|||++|++|+|||+||||++|.++++ +.++
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             ccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCCcCCchhhhhccc
Q 010092          352 TRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEEFINGI  429 (518)
Q Consensus       352 iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLD~~~~~~~eel~~~l  429 (518)
                      ||+|.++.+     ..++++++..+|.+++|+.||.+|||+.||+++++|..++..  ...++|||.+.+.+++.. ..+
T Consensus       116 ir~Pr~~~~-----~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~-~~~  189 (264)
T PRK07122        116 VKVPRRLKE-----LHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAGSAYNTLSIDSGGGSGDDDA-RAI  189 (264)
T ss_pred             cccCHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhhcCCCCcccccccCCCCCc-ccc
Confidence            999999998     999999999999999999999999999999999999998865  457899999875432210 111


Q ss_pred             ccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          430 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       430 ~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      .+. ..+++..++.......|..+|+.||++|+.||.++|    .+++|++|||+.||+|.++|++++++|+++||..
T Consensus       190 ~d~-~~~~~~~~e~~~~~~~l~~~l~~L~~rer~vl~l~y----~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~  262 (264)
T PRK07122        190 ADT-LGDVDAGLDQIENREALRPLLAALPERERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTLARLRDQ  262 (264)
T ss_pred             hhc-cCCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHh----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            111 122344456667788899999999999999999999    4899999999999999999999999999999975

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=100.00  E-value=3.5e-40  Score=334.82  Aligned_cols=267  Identities=29%  Similarity=0.433  Sum_probs=238.2

Q ss_pred             CCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHH
Q 010092          198 YSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARN  277 (518)
Q Consensus       198 ~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e  277 (518)
                      .-.|++++||++|..+|.||.+++..|...+                                        .+|+..|++
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~~~~li~~~----------------------------------------~~gd~~a~~   49 (285)
T TIGR02394        10 RVADVTQLYLREIGFKPLLTAEEEIAYARRA----------------------------------------LAGDFEARK   49 (285)
T ss_pred             CcchHHHHHHHHHhccCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHH
Confidence            3569999999999999999999998775544                                        568899999


Q ss_pred             HHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccc
Q 010092          278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF  356 (518)
Q Consensus       278 ~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~  356 (518)
                      .||..|.++|+++|.+|.   +++.+++||+||||+|||+|+++||+..|++|+||++|||+.++++++. +.+.+++|.
T Consensus        50 ~L~~~y~~~v~~~a~~~~---~~~~~aeDLvQe~~i~l~~a~~~fd~~~g~~f~tya~w~i~~ain~~i~~~~~~~~~p~  126 (285)
T TIGR02394        50 VMIESNLRLVVSIAKHYV---NRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPV  126 (285)
T ss_pred             HHHHHhHHHHHHHHHHHh---cCCCCHHHHHHHHHHHHHHHHHHhCCCCCCCcHhhhHHHHHHHHHHHHHHcCCceeCcH
Confidence            999999999999999998   7899999999999999999999999999999999999999999999999 788999999


Q ss_pred             cccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCCC
Q 010092          357 GLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGV  435 (518)
Q Consensus       357 ~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~  435 (518)
                      ++..     .++.+.+....+...+|+.|+.+++|+.+|++++++..++......+|+|.+...+.. .+.+.+.++...
T Consensus       127 ~~~~-----~~~~~~r~~~~l~~~~~r~~~~~e~a~~l~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~  201 (285)
T TIGR02394       127 HVIK-----ELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSI  201 (285)
T ss_pred             HHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHhhcCCCcCCCCCCCCCCcchhhhhcCCCCC
Confidence            8887     8888888877788889999999999999999999999999988889999987543332 233444444445


Q ss_pred             cchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       436 ~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      +|++.+...+....|..+|..||+++|.||.|+|||.+.+++|++|||+.||+|.++|++++++|+++||..+....
T Consensus       202 ~pe~~~~~~e~~~~L~~al~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~~~  278 (285)
T TIGR02394       202 DPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDG  278 (285)
T ss_pred             CHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence            67777888888999999999999999999999999998999999999999999999999999999999998765433

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=3.8e-40  Score=329.95  Aligned_cols=227  Identities=29%  Similarity=0.377  Sum_probs=196.2

Q ss_pred             HHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-
Q 010092          269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-  347 (518)
Q Consensus       269 ~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-  347 (518)
                      ..|+..|+++||..|+++|+++|++|..  ..+.+++||+|||+||||+|+++|||++|++|+|||+|||+++|.++++ 
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            4678899999999999999999999973  2366799999999999999999999999999999999999999999999 


Q ss_pred             hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCCcCCchhh-
Q 010092          348 VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEE-  424 (518)
Q Consensus       348 ~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLD~~~~~~~ee-  424 (518)
                      +.++||+|.++.+     ..++++++...|.+++|++||.+|||+.||+++++|..++..  ....+|||.+...+++. 
T Consensus        98 ~~~~vr~pr~~~~-----~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~~  172 (256)
T PRK07408         98 KSPTVRIPRRWQE-----LQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRTPLSLDAPVNQDEDGS  172 (256)
T ss_pred             cCCeeeeCHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHhhccCCccccccCCCCCCCc
Confidence            7889999999988     999999999999999999999999999999999999998753  45688999986543332 


Q ss_pred             --hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          425 --FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       425 --l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                        +.+.+.++... +.  ....+....|..+|..||++++.||.++|    ++++|++|||+.||+|.++|++++.+|++
T Consensus       173 ~~l~d~~~d~~~~-~~--~~~~~~~~~l~~~l~~L~~~~r~vl~l~y----~~~~s~~eIA~~lgvs~~~V~~~~~ra~~  245 (256)
T PRK07408        173 TSLGDLLPDPRYR-SF--QLAQEDRIRLQQALAQLEERTREVLEFVF----LHDLTQKEAAERLGISPVTVSRRVKKGLD  245 (256)
T ss_pred             cccccccCCcccc-hh--hhhHHHHHHHHHHHHcCCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence              23333332211 11  12335567799999999999999999999    48999999999999999999999999999


Q ss_pred             HHhCcch
Q 010092          503 KLKHPTR  509 (518)
Q Consensus       503 KLR~~~~  509 (518)
                      +||..+.
T Consensus       246 kLr~~l~  252 (256)
T PRK07408        246 QLKKLLQ  252 (256)
T ss_pred             HHHHHhh
Confidence            9997654

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=100.00  E-value=5.8e-39  Score=320.72  Aligned_cols=241  Identities=27%  Similarity=0.353  Sum_probs=209.7

Q ss_pred             cCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHHHHHHHHHHHHH
Q 010092          210 MKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLF  289 (518)
Q Consensus       210 i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~LI~~nlrLV~s  289 (518)
                      ...+|+||++||..|+..+                                        ..||..|++.|+..|+++|++
T Consensus        10 ~~~~~~l~~~~~~~li~~~----------------------------------------~~gd~~a~~~L~~~~~~~v~~   49 (254)
T TIGR02850        10 TSKLPVLKNQEMRELFIRM----------------------------------------QSGDTTAREKLINGNLRLVLS   49 (254)
T ss_pred             ccCCCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHHHHHHHhHHHHHH
Confidence            4678999999887775443                                        357889999999999999999


Q ss_pred             HHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCccccccccchhhHHHHHH
Q 010092          290 VIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGE  369 (518)
Q Consensus       290 iAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRlP~~~~e~~~~~~~~k  369 (518)
                      +|++|.   +++.+++||+||||+|||+++++|||.+|.+|+||++|||++.|.+++++.+.+|+|.++.+     ..++
T Consensus        50 ~a~~~~---~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~tyl~~~irn~~~~~lr~~~~ir~p~~~~~-----~~~~  121 (254)
T TIGR02850        50 VIQRFN---NRGEYVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRD-----IAYK  121 (254)
T ss_pred             HHHHHh---CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHHhCCCccCchHHHH-----HHHH
Confidence            999998   77899999999999999999999999999999999999999999999996668999999888     8889


Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh---hhhcccccCCCCcchhhhHHHHH
Q 010092          370 IQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE---EFINGITDVDGVENENQRQPALL  446 (518)
Q Consensus       370 i~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e---el~~~l~d~~~~~~ee~~~~~~l  446 (518)
                      +.++...+..++|+.||.+|||+.||+++++|..++.....+.|||.+..++++   .+.+.+.++..  +.   .....
T Consensus       122 ~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~~~~~~~~Sld~~~~~~~~~~~~~~~~~~d~~~--~~---~~~~~  196 (254)
T TIGR02850       122 ALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKN--KD---SQWLE  196 (254)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCCcccCCCCCCCCCcchhhhhcCCccc--cH---HHHHh
Confidence            999999999999999999999999999999999999998889999988643332   23444444322  11   22345


Q ss_pred             HHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          447 RLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       447 ~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      ...|..+|+.|+++++.||.++|    .+++|++|||+.||+|.++|++++.+|+++||+.
T Consensus       197 ~~~l~~~l~~L~~rer~vi~~~~----~~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~~  253 (254)
T TIGR02850       197 GIALKEAMKRLNEREKMILNMRF----FEGKTQMEVAEEIGISQAQVSRLEKAALKHMRKY  253 (254)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence            56799999999999999999999    4789999999999999999999999999999964

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

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=100.00  E-value=2.7e-39  Score=324.05  Aligned_cols=228  Identities=26%  Similarity=0.355  Sum_probs=198.8

Q ss_pred             HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhc
Q 010092          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS  349 (518)
Q Consensus       270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~s  349 (518)
                      .|+..|+++||..|+++|+++|++|...+..+++++||+|||++|||+|+++|||++|++|+|||+||||++|.++++..
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            57889999999999999999999986433456789999999999999999999999999999999999999999999933


Q ss_pred             CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CccccCCCcCC--chh--
Q 010092          350 SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK--PILSLHSRHGV--TQE--  423 (518)
Q Consensus       350 r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~--~~~SLD~~~~~--~~e--  423 (518)
                      .  ++|.++.+     ..+++..+...|.+.+|+.||.+|||+.+|+++++|..++....  .++|||.+...  +++  
T Consensus        99 ~--~~pr~~~~-----~~~~l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~Sld~~~~~~~~~~~~  171 (257)
T PRK05911         99 D--WVPRSVHQ-----KANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSLNEEFPCQSDDEAG  171 (257)
T ss_pred             C--CCCHHHHH-----HHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHHhhccceeeccccCCCCCCCccc
Confidence            2  38998888     89999999999999999999999999999999999999987654  46899987532  111  


Q ss_pred             -hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          424 -EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       424 -el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                       .+.+.+.++....|++.....++...|..+|..||++|+.||.++|    ++++|++|||+.||+|.++|++++.+|++
T Consensus       172 ~~l~~~l~d~~~~~~~~~~~~~~~~~~l~~al~~L~~~er~vi~l~y----~e~~t~~EIA~~lgis~~~V~~~~~ral~  247 (257)
T PRK05911        172 LALEERIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKALL  247 (257)
T ss_pred             cchhhhccCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence             2445555555455667777778888999999999999999999999    48999999999999999999999999999


Q ss_pred             HHhCcc
Q 010092          503 KLKHPT  508 (518)
Q Consensus       503 KLR~~~  508 (518)
                      +||+.+
T Consensus       248 kLr~~l  253 (257)
T PRK05911        248 KLRATL  253 (257)
T ss_pred             HHHHHH
Confidence            999754

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

Probab=100.00  E-value=3.9e-38  Score=312.02  Aligned_cols=226  Identities=32%  Similarity=0.428  Sum_probs=198.6

Q ss_pred             HHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCC-CHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHH
Q 010092          267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGP-RFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS  345 (518)
Q Consensus       267 ~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~-~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ra  345 (518)
                      ....|+..++ .||+.|+|||.++|++|.   +++. +++||+|-|+|||++|+++|||++|.+|+|||...|+++|.++
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   4555 9999999999999999999999999999999999999999999


Q ss_pred             HHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CccccCCCcCCchh
Q 010092          346 MTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK--PILSLHSRHGVTQE  423 (518)
Q Consensus       346 I~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~--~~~SLD~~~~~~~e  423 (518)
                      ++....+++|..+.+     ..+++..+..+|..++||+||++|||+.||++.++|..++....  ..+|+|.....+++
T Consensus        93 LR~~~~v~vpR~~~~-----~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~~~sld~~~~~~~d  167 (247)
T COG1191          93 LRKNDSVKVPRSLRE-----LGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDD  167 (247)
T ss_pred             HHhCCCccCcHHHHH-----HHHHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHhccccccchhhhhccccc
Confidence            994449999998888     99999999999999999999999999999999999999998764  77888876543332


Q ss_pred             hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                      ..    .++...++++.++..++...|.+++..|+++|+.||.+||    ++++|++|||+.||||+++|+|++.+|+++
T Consensus       168 ~~----~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y----~eelt~kEI~~~LgISes~VSql~kkai~k  239 (247)
T COG1191         168 DD----VDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRY----KEELTQKEIAEVLGISESRVSRLHKKAIKK  239 (247)
T ss_pred             cc----hhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHH----HhccCHHHHHHHhCccHHHHHHHHHHHHHH
Confidence            21    2222334566677788888888898999999999999999    689999999999999999999999999999


Q ss_pred             HhCcch
Q 010092          504 LKHPTR  509 (518)
Q Consensus       504 LR~~~~  509 (518)
                      ||+.+.
T Consensus       240 Lr~~l~  245 (247)
T COG1191         240 LRKELN  245 (247)
T ss_pred             HHHHhc
Confidence            997643

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=100.00  E-value=1.9e-37  Score=310.33  Aligned_cols=222  Identities=28%  Similarity=0.377  Sum_probs=194.7

Q ss_pred             HHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh
Q 010092          269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV  348 (518)
Q Consensus       269 ~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~  348 (518)
                      ..||..|++.||..|+++|+++|++|.   +++.+++||+|||++|||+|+++||+.+|.+|+||++|||+++|.++++.
T Consensus        32 ~~gd~~a~~~l~~~~~~~v~~~a~~~~---~~~~~aeDlvQe~~i~l~~a~~~fd~~~~~~f~t~l~~~ir~~i~~~lr~  108 (258)
T PRK08215         32 QNGDKEAREKLINGNLRLVLSVIQRFN---NRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRD  108 (258)
T ss_pred             HcCCHHHHHHHHHHHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHHHHHHHHHHHHHHh
Confidence            357889999999999999999999998   78899999999999999999999999999999999999999999999996


Q ss_pred             cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhh---h
Q 010092          349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE---F  425 (518)
Q Consensus       349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ee---l  425 (518)
                      .+.+++|.++..     ...++.++..++..++|+.|+++|||+.+|+++++|..++.....+.|||.+...+++.   +
T Consensus       109 ~~~vrip~~~~~-----~~~~~~~~~~~l~~~~~r~p~~~eia~~l~v~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~  183 (258)
T PRK08215        109 NNPIRVSRSLRD-----IAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIYV  183 (258)
T ss_pred             CCceEecHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHhcCCCccccCCCCCCCCcchhh
Confidence            678899998887     88889999999999999999999999999999999999998888888999886543322   2


Q ss_pred             hcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092          426 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  505 (518)
Q Consensus       426 ~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR  505 (518)
                      .+.+.++..     ..........|..+|+.||++++.||.++|    ++++|+.|||+.||+|.++|++++++|+++||
T Consensus       184 ~~~~~~~~~-----~~~~~~~~~~l~~~l~~L~~~er~vi~~~~----~~~~t~~eIA~~lgis~~~V~~~~~~al~kLr  254 (258)
T PRK08215        184 MDQISDEKN-----KDENWLEEIALKEAMKKLNDREKLILNLRF----FQGKTQMEVAEEIGISQAQVSRLEKAALKHMR  254 (258)
T ss_pred             hhhccCccc-----cHHHHHhHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            333333221     122334556789999999999999999999    47899999999999999999999999999999


Q ss_pred             Cc
Q 010092          506 HP  507 (518)
Q Consensus       506 ~~  507 (518)
                      +.
T Consensus       255 ~~  256 (258)
T PRK08215        255 KY  256 (258)
T ss_pred             HH
Confidence            64

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=100.00  E-value=3.5e-36  Score=302.92  Aligned_cols=249  Identities=23%  Similarity=0.352  Sum_probs=213.7

Q ss_pred             CCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHHHHHHHHHHHHHH
Q 010092          211 KIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFV  290 (518)
Q Consensus       211 ~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~LI~~nlrLV~si  290 (518)
                      +.+|+||+++|..|+..++                                       ..||..|++.|+..|+++|+.+
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            6789999999998876652                                       3468899999999999999999


Q ss_pred             HHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCccccccccchhhHHHHHHH
Q 010092          291 IKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEI  370 (518)
Q Consensus       291 Akky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRlP~~~~e~~~~~~~~ki  370 (518)
                      |++|......+.+++||+||||+|||+|+++||+.+|++|+||++|||++.|.++++.  .+++|.++..     ..+++
T Consensus        48 a~~~~~~~~~~~~~eDl~Qeg~l~L~~a~~~fd~~~~~~f~ty~~~~ir~~i~d~~R~--~~~~p~~~~~-----~~~~i  120 (268)
T PRK06288         48 AGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRS--IDWIPRSVRQ-----KARQI  120 (268)
T ss_pred             HHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHcCcccCCCHHHHHHHHHHHHHHHHHHh--cCccCHHHHH-----HHHHH
Confidence            9998622235778999999999999999999999999999999999999999999983  3468888776     88899


Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCccccCCCcCCchh----hhhcccccCCCCcchhhhHHH
Q 010092          371 QRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQE----EFINGITDVDGVENENQRQPA  444 (518)
Q Consensus       371 ~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLD~~~~~~~e----el~~~l~d~~~~~~ee~~~~~  444 (518)
                      +++...|.+++|+.||.+|||+.+|++.+++..++...  ...+|||.....+++    ++.+.+.++...+|++.+...
T Consensus       121 ~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~l~~~~~~~~~~~pe~~~~~~  200 (268)
T PRK06288        121 ERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGDEVSLMDTLESPAALNPDEIAERE  200 (268)
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhcccccchhhhhccCCCcccchhhhhccCCCCCCHHHHHHHH
Confidence            99999999999999999999999999999999998753  467899887531111    244555555556677777888


Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          445 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       445 ~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                      +....|..+|..||++++.||.++|    .+++|++|||+.||+|.++|++++.+|+++||....
T Consensus       201 e~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~  261 (268)
T PRK06288        201 EIKRVIVEAIKTLPEREKKVLILYY----YEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLA  261 (268)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            8889999999999999999999999    589999999999999999999999999999998654

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=100.00  E-value=3.9e-36  Score=295.56  Aligned_cols=224  Identities=30%  Similarity=0.398  Sum_probs=196.9

Q ss_pred             HHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHH
Q 010092          267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM  346 (518)
Q Consensus       267 ~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI  346 (518)
                      +...||..|++.|+..|.++|+++|++|.   +++.+++||+|||++|||+++++|||..|.+|+||++|||++.|.+++
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   788999999999999999999999999999999999999999999999


Q ss_pred             HhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh---
Q 010092          347 TVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE---  423 (518)
Q Consensus       347 ~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e---  423 (518)
                      +....+++|.++..     ...++.++...+..++|+.||.+|||+.+|++++++..++.......|||.+...+++   
T Consensus        81 r~~~~i~~p~~~~~-----~~~~~~~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~  155 (231)
T TIGR02885        81 RDDGIIKVSRSLKE-----LARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPI  155 (231)
T ss_pred             HhCCCeECCHHHHH-----HHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHHHccCCcCcccCCCCCCCCcc
Confidence            95568999999888     9999999999999999999999999999999999999999888888999987654432   


Q ss_pred             hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                      .+++.+.++..  +   .........|..+|+.||++|+.||.++|+    +++|++|||+.||+|+++|++++++|+++
T Consensus       156 ~~~d~~~~~~~--~---~~~~~~~~~l~~~l~~L~~~e~~i~~~~~~----~~~t~~eIA~~lgis~~~V~~~~~~al~~  226 (231)
T TIGR02885       156 YLLDQIADKGS--E---DSDWLEKIALKEAISKLDERERQIIMLRYF----KDKTQTEVANMLGISQVQVSRLEKKVLKK  226 (231)
T ss_pred             hhhhhcCCCCc--c---HHhHHHHHHHHHHHHcCCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            23344433321  1   122345668899999999999999999994    78999999999999999999999999999


Q ss_pred             HhCc
Q 010092          504 LKHP  507 (518)
Q Consensus       504 LR~~  507 (518)
                      ||..
T Consensus       227 Lr~~  230 (231)
T TIGR02885       227 MKEK  230 (231)
T ss_pred             HHHh
Confidence            9964

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=3e-35  Score=293.76  Aligned_cols=225  Identities=25%  Similarity=0.301  Sum_probs=196.9

Q ss_pred             HcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hc
Q 010092          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VS  349 (518)
Q Consensus       271 gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~s  349 (518)
                      ||..|+++|+..|.++|+.+|++|.   +++.+++||+||||+|||+|+++||++.|.+|+||+++||++.|.++++ +.
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   7899999999999999999999999999999999999999999999999 67


Q ss_pred             CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCccccCCCcCCchhhhhc
Q 010092          350 SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQEEFIN  427 (518)
Q Consensus       350 r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLD~~~~~~~eel~~  427 (518)
                      +.+++|.++.+     ..++++++...+...+|+.||.+|||+.+|++.+++..++...  ....|||.++..+++.-..
T Consensus       103 ~~iri~~~~~~-----~~~~~~~~~~~l~~~~~r~p~~~eia~~l~i~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~  177 (255)
T TIGR02941       103 WSVHVPRRIKE-----LGPKIKKAIDELTDHLQRSPKIIEIADHLGLSEEEVLEIMEMGQSYRALSVDDVIEADSDGSTV  177 (255)
T ss_pred             CCcCCCHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHhccCCccccccccCCCCCccc
Confidence            78999998888     8999999999999999999999999999999999999988754  4678999886544332111


Q ss_pred             ccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          428 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       428 ~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      ...+. ..++++.....+....|..+|+.||+++|.||.++|    .+++|++|||+.||+|.++|++++++|+++||..
T Consensus       178 ~~~~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~ii~l~~----~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~  252 (255)
T TIGR02941       178 ARLDS-VGEVEDGYDQTERRMVLEKILPILSEREKSIIHCTF----EENLSQKETGERLGISQMHVSRLQRQAISKLKEA  252 (255)
T ss_pred             ccccc-cCCcchHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            11111 122455566677778899999999999999999999    5899999999999999999999999999999974


Q ss_pred             c
Q 010092          508 T  508 (518)
Q Consensus       508 ~  508 (518)
                      +
T Consensus       253 ~  253 (255)
T TIGR02941       253 A  253 (255)
T ss_pred             h
Confidence            3

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=7.2e-35  Score=285.67  Aligned_cols=222  Identities=31%  Similarity=0.396  Sum_probs=193.0

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcC
Q 010092          272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSS  350 (518)
Q Consensus       272 d~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr  350 (518)
                      |..|++.||..|.++|+++|++|.   +++.+++||+|||++|||+|+++||+++|.+|+||++|||++.|.++++ +.+
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            467999999999999999999998   7788999999999999999999999999999999999999999999999 667


Q ss_pred             CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCC--ccccCCCcCCchhhhhcc
Q 010092          351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKP--ILSLHSRHGVTQEEFING  428 (518)
Q Consensus       351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~--~~SLD~~~~~~~eel~~~  428 (518)
                      .+++|.++.+     ..++++++...+...+|+.|+.+|||+.+|++.+++..++.....  ..|||.+..++++. ...
T Consensus        78 ~~ri~~~~~~-----~~~~~~~~~~~l~~~~~~~p~~~ela~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~-~~~  151 (227)
T TIGR02980        78 AVRVPRRLKE-----LGLKINKATEELTQRLGRSPTIAEIAEELGVSEEEVVEALEAGNSYSALSLDAPIEDDDGD-PIA  151 (227)
T ss_pred             ceecCHHHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHhhccCCCeeccccCCCCCCC-Ccc
Confidence            9999998888     889999999999999999999999999999999999999887654  89999886522211 111


Q ss_pred             cccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          429 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       429 l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      +.+ ...+++...+..+....|..+|..||++++.||.++|    .+++|++|||+.||+|.++|++++++|+++||..
T Consensus       152 ~~d-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~y----~~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~  225 (227)
T TIGR02980       152 LLD-TLGDEDDALETVEDRLALKPLLAALPERERRILLLRF----FEDKTQSEIAERLGISQMHVSRLLRRALKKLREQ  225 (227)
T ss_pred             ccc-ccCCcchHHHhHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            111 1112344455567778899999999999999999999    4799999999999999999999999999999964

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=6.9e-34  Score=283.55  Aligned_cols=229  Identities=25%  Similarity=0.330  Sum_probs=197.3

Q ss_pred             HHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh
Q 010092          269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV  348 (518)
Q Consensus       269 ~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~  348 (518)
                      ..||..|++.||..|.++|+++|.+|..++.++.+.+||+||||+|||+++++||+.+|.+|+||++|||++.|.++++.
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            35689999999999999999999999743346889999999999999999999999999999999999999999999994


Q ss_pred             cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCCcCCchhh--
Q 010092          349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEE--  424 (518)
Q Consensus       349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLD~~~~~~~ee--  424 (518)
                      ..  ++|.++.+     .+++++++...+.+.+|+.|+.+|||+.+|++.++|..++..  ....+|||.+...+++.  
T Consensus        97 ~~--~~p~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~  169 (251)
T PRK07670         97 ED--WLPRSMRE-----KTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGEN  169 (251)
T ss_pred             cC--CCCHHHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcch
Confidence            32  58887777     888999999999999999999999999999999999999864  56789999886433332  


Q ss_pred             hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092          425 FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL  504 (518)
Q Consensus       425 l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL  504 (518)
                      +...+.++...++++.....+....|..+|+.||+++|.||.++|    .+++|++|||+.||+|.++|++++.+|+++|
T Consensus       170 ~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~EIA~~lgis~~tV~~~~~ra~~~L  245 (251)
T PRK07670        170 VSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKL  245 (251)
T ss_pred             hhhhhcCcCCCCHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            222333444445666667777788899999999999999999999    5899999999999999999999999999999


Q ss_pred             hCcc
Q 010092          505 KHPT  508 (518)
Q Consensus       505 R~~~  508 (518)
                      |...
T Consensus       246 r~~l  249 (251)
T PRK07670        246 KKLL  249 (251)
T ss_pred             HHHh
Confidence            9753

>PRK05572 sporulation sigma factor SigF; Validated

Probab=100.00  E-value=1.2e-33  Score=281.93  Aligned_cols=221  Identities=29%  Similarity=0.413  Sum_probs=193.5

Q ss_pred             HHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh
Q 010092          269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV  348 (518)
Q Consensus       269 ~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~  348 (518)
                      ..|+..|++.|+..|.++|+.+|++|.   +++.+++||+||||+++|+++++|++.+|.+|.||+++||++.|.++++.
T Consensus        27 ~~gd~~a~~~L~~~y~~~v~~~a~~~~---~~~~~aeDl~Qe~~l~l~~~~~~f~~~~~~~f~twl~~~i~~~i~~~lr~  103 (252)
T PRK05572         27 QDGDQEARDTLVEKNLRLVWSVVQRFL---NRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRD  103 (252)
T ss_pred             HcCCHHHHHHHHHHhHHHHHHHHHHHc---cCCCCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHh
Confidence            457889999999999999999999998   78899999999999999999999999988899999999999999999996


Q ss_pred             cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhh---h
Q 010092          349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE---F  425 (518)
Q Consensus       349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ee---l  425 (518)
                      .+.+++|.++..     ..++++++...+..++|+.|+++|+|+.+|++++++..++.......||+.+..+++.+   +
T Consensus       104 ~~~~r~~~~~~~-----~~~~~~~~~~~l~~~~~r~p~~~eia~~l~~~~~~v~~~~~~~~~~~sl~~~~~~~~~~~~~~  178 (252)
T PRK05572        104 DGTVKVSRSLKE-----TANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDGDPITL  178 (252)
T ss_pred             CCCCCCCHHHHH-----HHHHHHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHHHhcCCCcCcccCcccCCCCcchh
Confidence            678999998888     99999999999999999999999999999999999999988888889998876433221   1


Q ss_pred             hcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092          426 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  505 (518)
Q Consensus       426 ~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR  505 (518)
                      .+.+.++.       .........|..+|+.||++++.||.++|    .+++|++|||+.+|+|.++|++++++|+++||
T Consensus       179 ~d~~~~~~-------~~~~~~~~~l~~~l~~L~~~~~~v~~l~~----~~~~s~~eIA~~lgis~~~V~~~~~ral~kLr  247 (252)
T PRK05572        179 LDQIADQS-------EEDWFDKIALKEAIRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQMK  247 (252)
T ss_pred             hhhcCCCc-------hhhHHHHHHHHHHHHcCCHHHHHHHHHHH----hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            22222211       12234567899999999999999999999    47899999999999999999999999999999


Q ss_pred             Ccc
Q 010092          506 HPT  508 (518)
Q Consensus       506 ~~~  508 (518)
                      ..+
T Consensus       248 ~~l  250 (252)
T PRK05572        248 EKL  250 (252)
T ss_pred             HHh
Confidence            643

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=100.00  E-value=1.2e-33  Score=279.13  Aligned_cols=213  Identities=21%  Similarity=0.278  Sum_probs=178.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCcc
Q 010092          274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTR  353 (518)
Q Consensus       274 ~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iR  353 (518)
                      .....|+..|+|+|..+|++|......+.+.+||+|||++|||+|+++|||..| +|+|||+||||++|.++++...  .
T Consensus        15 ~~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a~~~fd~~~~-~F~tYa~~~Ir~~il~~lr~~~--~   91 (231)
T PRK12427         15 QEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILDELRELD--W   91 (231)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHhcCCCCC-ChHHHHHHHHHHHHHHHHHhcC--C
Confidence            345678999999999999999855456789999999999999999999998666 8999999999999999999321  2


Q ss_pred             ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCCcCCchhhhhccccc
Q 010092          354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVTQEEFINGITD  431 (518)
Q Consensus       354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLD~~~~~~~eel~~~l~d  431 (518)
                      +|.++..     ..++++++...+.+++|+.||.+|||+.||++.++|.+++..  .....|||.+.+++++.  +.+ +
T Consensus        92 ~~r~vr~-----~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~~~~~~~~~~SLd~~~~~~~~~--~~~-~  163 (231)
T PRK12427         92 RPRRLRQ-----KTHKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLLENAGTLESLDELLALEAHN--DIL-Q  163 (231)
T ss_pred             CCHHHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceeccCcccCCCcc--ccc-C
Confidence            5666655     889999999999999999999999999999999999999864  45789999986543321  111 1


Q ss_pred             CCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          432 VDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       432 ~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      .  .+++   +.......|..+|..||++++.||.++|    .+++|++|||+.||||.++|+|++.+|+++||.
T Consensus       164 ~--~~~~---~~~~~~~~l~~~l~~L~~~er~vi~l~~----~~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~  229 (231)
T PRK12427        164 S--RDLE---ENIIIEDNLKQALSQLDEREQLILHLYY----QHEMSLKEIALVLDLTEARICQLNKKIAQKIKS  229 (231)
T ss_pred             C--CCHH---HHHHHHHHHHHHHHcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence            1  1122   2233566789999999999999999999    589999999999999999999999999999985

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

Probab=100.00  E-value=1e-33  Score=277.32  Aligned_cols=218  Identities=28%  Similarity=0.415  Sum_probs=189.3

Q ss_pred             HHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCccccccc
Q 010092          279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGL  358 (518)
Q Consensus       279 LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRlP~~~  358 (518)
                      |+..|.++|+.+|++|..++.++.+++||+|||++|||+|+++|||++|++|+||+++||++.+.+++++.  .++|.++
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            58899999999999998543478999999999999999999999999999999999999999999999842  2578776


Q ss_pred             cchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHh--cCCccccCCCcCCc--hhhhhcccccCCC
Q 010092          359 ESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKA--SKPILSLHSRHGVT--QEEFINGITDVDG  434 (518)
Q Consensus       359 ~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~--~~~~~SLD~~~~~~--~eel~~~l~d~~~  434 (518)
                      ..     .++++.++..++.+.+|+.|+.+|||+.+|+++++|..++..  ....+|+|......  ...+.+.+.++..
T Consensus        79 ~~-----~~~~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~  153 (224)
T TIGR02479        79 RQ-----KARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKS  153 (224)
T ss_pred             HH-----HHHHHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHHHHHhcCCccccCCcccCCCccchhhhhcccccc
Confidence            66     899999999999999999999999999999999999999864  34677888765432  2234444554455


Q ss_pred             CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      .++++.+...+....|..+|+.||++++.||.++|    .+++|++|||+.||+|.++|++++++|+++||..
T Consensus       154 ~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~y----~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~  222 (224)
T TIGR02479       154 EDPEEELEREELREALAEAIESLSEREQLVLSLYY----YEELNLKEIGEVLGLTESRVSQIHSQALKKLRAK  222 (224)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            56777777888889999999999999999999999    5899999999999999999999999999999964

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.

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=100.00  E-value=4.1e-33  Score=278.68  Aligned_cols=227  Identities=25%  Similarity=0.299  Sum_probs=196.3

Q ss_pred             HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-h
Q 010092          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-V  348 (518)
Q Consensus       270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~  348 (518)
                      .||..|++.||..|.++|+++|++|.   +++.+++||+||||++||+++++||+..|.+|+||+++||++.|.++++ +
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            37899999999999999999999998   7888999999999999999999999999989999999999999999999 6


Q ss_pred             cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCccccCCCcCCchhhhh
Q 010092          349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQEEFI  426 (518)
Q Consensus       349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLD~~~~~~~eel~  426 (518)
                      ...+++|.++.+     ..++++++...+...+++.|+.+|+|+.+|++.+++..++...  ...+|+|.+.+.+.+...
T Consensus       102 ~~~~~i~r~~~~-----~~~~~~~~~~~~~~~~~r~~~~~e~a~~~~~~~~~~~~~~~~~~~~~~~sld~~~~~~~~~~~  176 (257)
T PRK08583        102 TWSVHVPRRIKE-----LGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDGST  176 (257)
T ss_pred             CCCcCCCHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHhccCCceecCccccCCCCCcc
Confidence            788999999888     8899999999999999999999999999999999998887754  367888887654333211


Q ss_pred             cccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          427 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       427 ~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      ..+.+ ...++++.....+....|..+|..||++++.||.++|    ++++|++|||+.||||.++|++++++|+++||.
T Consensus       177 ~~~~~-~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~  251 (257)
T PRK08583        177 VTLLD-IVGQQEDGYELTEQRMILEKILPVLSDREKSIIQCTF----IENLSQKETGERLGISQMHVSRLQRQAIKKLRE  251 (257)
T ss_pred             chHhh-hcCCcchhHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            11111 1123455566667778899999999999999999999    489999999999999999999999999999997


Q ss_pred             cch
Q 010092          507 PTR  509 (518)
Q Consensus       507 ~~~  509 (518)
                      ...
T Consensus       252 ~l~  254 (257)
T PRK08583        252 AAF  254 (257)
T ss_pred             Hhc
Confidence            553

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=100.00  E-value=1.6e-32  Score=271.16  Aligned_cols=226  Identities=24%  Similarity=0.358  Sum_probs=191.7

Q ss_pred             HcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC
Q 010092          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS  350 (518)
Q Consensus       271 gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr  350 (518)
                      .|.-+++.|+..|.++|+.+|.+|..+++++.+++||+||||+|||+++++|||+.|.+|+||+++||++.|.+++++..
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            45678999999999999999999974435788999999999999999999999999999999999999999999999432


Q ss_pred             CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCccccCCCcCCchhhhhcc
Q 010092          351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQEEFING  428 (518)
Q Consensus       351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLD~~~~~~~eel~~~  428 (518)
                        ++|.++..     ...++.++...+.+.+|+.||.+|||+.+|++.++|..++...  ...+|++...+.+++.+. .
T Consensus        85 --~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~-~  156 (236)
T PRK06986         85 --WVPRSVRR-----NAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSIL-V  156 (236)
T ss_pred             --CCCHHHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcccc-c
Confidence              25665555     6677888888999999999999999999999999999998863  456788887654444332 2


Q ss_pred             cccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          429 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       429 l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      ..++...++++.+...+....|..+|+.||++++.||.++|    .+++|++|||+.||+|.++|++++.+|+++||+..
T Consensus       157 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l  232 (236)
T PRK06986        157 TEDHQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYY----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARL  232 (236)
T ss_pred             ccCCCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHh----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            22233345666677777888999999999999999999999    58999999999999999999999999999999754

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=99.95  E-value=1.1e-26  Score=229.13  Aligned_cols=208  Identities=30%  Similarity=0.371  Sum_probs=164.1

Q ss_pred             hHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHHHHH
Q 010092          202 LVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIK  281 (518)
Q Consensus       202 ~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~LI~  281 (518)
                      ++..|+.++++.|.||+++|..|...+                                        ..||..|++.|+.
T Consensus        17 ~~~~~~~~~~~~~~~~~~~e~~l~~~~----------------------------------------~~gd~~a~~~l~~   56 (233)
T PRK05803         17 FLVSYVKNNSFPQPLSEEEERKYLELM----------------------------------------KEGDEEARNILIE   56 (233)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHHHH----------------------------------------HcCCHHHHHHHHH
Confidence            577899999999999999887764443                                        3578899999999


Q ss_pred             HHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCccccccccc
Q 010092          282 HNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRVPFGLES  360 (518)
Q Consensus       282 ~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~iRlP~~~~e  360 (518)
                      .|.++|+++|.+|.   +++.+++||+|||++++|+++++||+++|.+|.||+++|+++.+.+++++ .+..        
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            99999999999999   78999999999999999999999999988899999999999999998872 1110        


Q ss_pred             hhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCc--h--hhhhcccccCCCCc
Q 010092          361 TSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVT--Q--EEFINGITDVDGVE  436 (518)
Q Consensus       361 ~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~--~--eel~~~l~d~~~~~  436 (518)
                                                                       ...+++.....+  +  ..+.+...+ ...+
T Consensus       126 -------------------------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~  155 (233)
T PRK05803        126 -------------------------------------------------KEVSLQDPIGVDKEGNEISLIDILGS-EEDD  155 (233)
T ss_pred             -------------------------------------------------cCCCccccccCCCCcCcccHHHHccC-CCCC
Confidence                                                             000111110000  0  011111111 1223


Q ss_pred             chhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          437 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       437 ~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      +++..........|..+|+.||+++|.||.++|++.+.+++|++|||+.||+|.++|++++++|+++||..+..
T Consensus       156 ~~~~~~~~~~~~~l~~~l~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l~~  229 (233)
T PRK05803        156 VIEQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYR  229 (233)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            45555666677789999999999999999999988777899999999999999999999999999999986543

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=99.91  E-value=4.4e-23  Score=203.31  Aligned_cols=182  Identities=25%  Similarity=0.398  Sum_probs=138.5

Q ss_pred             HHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHH
Q 010092          266 KKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS  345 (518)
Q Consensus       266 ~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ra  345 (518)
                      .++..||..|++.|+..|.++|+.+|.+|.   +++.+++|++||+|+++|+++++|++..+++|.||+++++++.+.++
T Consensus        44 ~~~~~gd~~af~~l~~~y~~~l~~~a~~~~---~~~~~AeDlvQevfl~l~~~~~~f~~~~~~~f~twl~~iarn~~~d~  120 (234)
T PRK08301         44 NKLPKGDEAVRSLLIERNLRLVVYIARKFE---NTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMY  120 (234)
T ss_pred             HHHHccCHHHHHHHHHHhHHHHHHHHHHhh---cCCCCHHHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHH
Confidence            334578999999999999999999999998   77889999999999999999999999888899999999999999999


Q ss_pred             HH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCC--ch
Q 010092          346 MT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV--TQ  422 (518)
Q Consensus       346 I~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~--~~  422 (518)
                      ++ +.+..                                                         ...+++.+...  +.
T Consensus       121 lRk~~~~~---------------------------------------------------------~~~~~~~~~~~~~~~  143 (234)
T PRK08301        121 LRRNNKVK---------------------------------------------------------AEVSFDEPLNIDWDG  143 (234)
T ss_pred             HHHHhccc---------------------------------------------------------cccccccccccccCC
Confidence            98 32110                                                         00011111000  00


Q ss_pred             h-h-hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          423 E-E-FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       423 e-e-l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      . . ..+...+. ...++...........|..+|+.||+++|.||.|+|||...+++|++|||+.||+|.++|++++++|
T Consensus       144 ~~~~~~~~~~~~-~~~~~~~~~~~~~~~~l~~al~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA  222 (234)
T PRK08301        144 NELLLSDVLGTD-NDIIYKDIEDEVDRKLLKKALKKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRI  222 (234)
T ss_pred             CcccHHHhccCc-ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            0 0 00111111 1112223334445667999999999999999999997766689999999999999999999999999


Q ss_pred             HHHHhCcc
Q 010092          501 LMKLKHPT  508 (518)
Q Consensus       501 LkKLR~~~  508 (518)
                      +++||+..
T Consensus       223 ~~~Lr~~l  230 (234)
T PRK08301        223 IKRLKKEI  230 (234)
T ss_pred             HHHHHHHH
Confidence            99999753

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=99.91  E-value=5e-23  Score=202.57  Aligned_cols=183  Identities=33%  Similarity=0.429  Sum_probs=138.1

Q ss_pred             HHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHH
Q 010092          267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM  346 (518)
Q Consensus       267 ~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI  346 (518)
                      ++..|+..|++.|+..|.++|+++|.+|.   ++..+++||+||+|+++|+++++|+++.+..|.||+++++++.+.+++
T Consensus        41 ~~~~gd~~af~~l~~~y~~~v~~~~~~~~---~~~~dAEDlvQevfi~l~~~~~~~~~~~~~~f~twl~~i~rN~~~d~~  117 (227)
T TIGR02846        41 RLKEGDEEARNVLIERNLRLVAHIVKKFS---NTGEDVDDLISIGTIGLIKAIDSFDPDKGTRLATYAARCIENEILMHL  117 (227)
T ss_pred             HHHcCCHHHHHHHHHHhHHHHHHHHHHhc---CCCCCHHHHHHHHHHHHHHHHHhCCcccCCChHHHHHHHHHHHHHHHH
Confidence            34578899999999999999999999998   678899999999999999999999999888899999999999999988


Q ss_pred             Hh-cCCc-cccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhh
Q 010092          347 TV-SSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE  424 (518)
Q Consensus       347 ~~-sr~i-RlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ee  424 (518)
                      ++ .+.. +.+.                                                    ....+.+...  ....
T Consensus       118 Rk~~r~~~~~~~----------------------------------------------------~~~~~~~~~~--~~~~  143 (227)
T TIGR02846       118 RALKKTKGEVSL----------------------------------------------------QDPIGVDKEG--NEIS  143 (227)
T ss_pred             HHHhccccceec----------------------------------------------------cccccCCccc--Cccc
Confidence            83 2110 0000                                                    0000000000  0000


Q ss_pred             hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092          425 FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL  504 (518)
Q Consensus       425 l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL  504 (518)
                      ..+... +....+++.....+....|..+|+.||+++|.||.++|.++..+++|++|||+.||+|.++|++++++|+++|
T Consensus       144 ~~~~~~-~~~~~~~~~~~~~~~~~~l~~~i~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~L  222 (227)
T TIGR02846       144 LIDILG-SDGDSVIEQVELNLEIKKLYKKLSVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKL  222 (227)
T ss_pred             HHHHhc-CCCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            111111 1122244444555566779999999999999999999965445899999999999999999999999999999


Q ss_pred             hCc
Q 010092          505 KHP  507 (518)
Q Consensus       505 R~~  507 (518)
                      |+.
T Consensus       223 r~~  225 (227)
T TIGR02846       223 YKE  225 (227)
T ss_pred             HHH
Confidence            964

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=99.89  E-value=8.8e-22  Score=194.57  Aligned_cols=184  Identities=26%  Similarity=0.401  Sum_probs=139.1

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r  344 (518)
                      +..+..||..|++.|+..|.+.|+++|.+|.   +++.+++||+||+|+++|+++++|++..+++|.||++.++++.+.+
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            4445678999999999999999999999998   7888999999999999999999999988888999999999999999


Q ss_pred             HHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcC---C
Q 010092          345 SMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHG---V  420 (518)
Q Consensus       345 aI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~---~  420 (518)
                      ++++ .+.. .                                                        ..+++....   .
T Consensus       120 ~~Rk~~r~~-~--------------------------------------------------------~~~~~~~~~~~~~  142 (234)
T TIGR02835       120 YLRRNNKTR-S--------------------------------------------------------EVSFDEPLNVDWD  142 (234)
T ss_pred             HHHHhcccc-C--------------------------------------------------------cccccccccCCCC
Confidence            9983 2110 0                                                        001111000   0


Q ss_pred             chhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          421 TQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       421 ~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +.........+.+...+++..........|..+|+.||+++|.||.++|.|.+++++|++|||+.||+|..+|++.+++|
T Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~ai~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra  222 (234)
T TIGR02835       143 GNELLLSDVLGTDSDIVYKYLEEEVDRELLRKALAKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRI  222 (234)
T ss_pred             CCcchHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            00000001111111112223334455667999999999999999999997655589999999999999999999999999


Q ss_pred             HHHHhCcc
Q 010092          501 LMKLKHPT  508 (518)
Q Consensus       501 LkKLR~~~  508 (518)
                      +++||+..
T Consensus       223 ~~~LR~~l  230 (234)
T TIGR02835       223 LKRLKKEI  230 (234)
T ss_pred             HHHHHHHh
Confidence            99999754

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=8.3e-21  Score=182.78  Aligned_cols=187  Identities=18%  Similarity=0.222  Sum_probs=137.8

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      .+..+..|+..|++.|+..|.++|+.+|.+|.   ++..+++||+||+|++||+++.+|++.+|.+|.||++.++++.+.
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   788999999999999999999999998877999999999999998


Q ss_pred             HHHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092          344 RSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ  422 (518)
Q Consensus       344 raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~  422 (518)
                      ++++. .+..+.+.                                                    ....|++.....+.
T Consensus        91 d~~r~~~r~~~~~~----------------------------------------------------~~~~s~~~~~~~~~  118 (208)
T PRK08295         91 TAIKTANRQKHIPL----------------------------------------------------NSYVSLDKPIYDEE  118 (208)
T ss_pred             HHHHHhhhhccccc----------------------------------------------------cceeecCCcccCCc
Confidence            88872 11101110                                                    00112222111000


Q ss_pred             --hhhhcccccCCCCcchhhhHHHHHHHHH-HHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          423 --EEFINGITDVDGVENENQRQPALLRLAL-DDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       423 --eel~~~l~d~~~~~~ee~~~~~~l~~~L-~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                        ..+.+.+.++...+|++.+...+....+ ..+++.||+.++.||.+ |    .+++|++|||+.||+|.++|+..+.|
T Consensus       119 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~~r~vl~l-~----~e~~s~~EIA~~lgis~~tV~~~l~r  193 (208)
T PRK08295        119 SDRTLLDVISEAKVTDPEELIISKEELEDIEEKIEELLSELEKEVLEL-Y----LDGKSYQEIAEELNRHVKSIDNALQR  193 (208)
T ss_pred             cchhHHHHhcCcccCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHH-H----HccCCHHHHHHHHCCCHHHHHHHHHH
Confidence              0111212222223355544444444455 45679999999999999 6    48999999999999999999999999


Q ss_pred             HHHHHhCcchh
Q 010092          500 GLMKLKHPTRV  510 (518)
Q Consensus       500 ALkKLR~~~~~  510 (518)
                      |+++||.....
T Consensus       194 ar~~Lr~~l~~  204 (208)
T PRK08295        194 VKRKLEKYLEN  204 (208)
T ss_pred             HHHHHHHHHHh
Confidence            99999986543

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=99.86  E-value=2.9e-20  Score=176.92  Aligned_cols=171  Identities=17%  Similarity=0.168  Sum_probs=133.7

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhcc-CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDF-ANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~-~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      +.....|+..|++.|+..|.+.|+.+|.++..+. +...+++|++||+|++||+++.+|++. +..|.+|++..+++.+.
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            5567789999999999999999999999987311 124689999999999999999999864 45799999999999999


Q ss_pred             HHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092          344 RSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ  422 (518)
Q Consensus       344 raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~  422 (518)
                      ++++ +.+....+                                                          .+       
T Consensus        94 d~~r~~~r~~~~~----------------------------------------------------------~~-------  108 (189)
T PRK09648         94 DAHRAAGRDKAVP----------------------------------------------------------TE-------  108 (189)
T ss_pred             HHHHHhCCCcccc----------------------------------------------------------cc-------
Confidence            8887 32110000                                                          00       


Q ss_pred             hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                       .+.+.. + ...++++.....+....|..+|..||+++|.||.++|    .+++|++|||+.||+|..+|++.++||++
T Consensus       109 -~~~~~~-~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~  181 (189)
T PRK09648        109 -EVPERP-S-DDAGPEERALRSESSNRMRELLDTLPEKQREILILRV----VVGLSAEETAEAVGSTPGAVRVAQHRALA  181 (189)
T ss_pred             -cccccc-c-cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence             000000 0 1123455555666777899999999999999999999    58999999999999999999999999999


Q ss_pred             HHhCcc
Q 010092          503 KLKHPT  508 (518)
Q Consensus       503 KLR~~~  508 (518)
                      +||+..
T Consensus       182 ~Lr~~l  187 (189)
T PRK09648        182 RLRAEI  187 (189)
T ss_pred             HHHHHh
Confidence            999753

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=99.85  E-value=3e-20  Score=177.39  Aligned_cols=185  Identities=18%  Similarity=0.237  Sum_probs=136.3

Q ss_pred             HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (518)
Q Consensus       263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI  342 (518)
                      ..+..+..||..|++.|+..|.+.|+.+|.++.   ++..+++||+||+|+.+|+++.+|++..+..|.||++.+|++.+
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            345556789999999999999999999999998   67889999999999999999999999887799999999999988


Q ss_pred             HHHHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCC-
Q 010092          343 IRSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV-  420 (518)
Q Consensus       343 ~raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~-  420 (518)
                      .++++. .+..+.+.                                                    ....|++.+... 
T Consensus        85 ~~~~r~~~~~~~~~~----------------------------------------------------~~~~~~~~~~~~~  112 (198)
T TIGR02859        85 ITAIKTATRQKHIPL----------------------------------------------------NSYVSLNKPIYDE  112 (198)
T ss_pred             HHHHHHHHHhcccch----------------------------------------------------hhhcCcccccccc
Confidence            877762 11000000                                                    011222222111 


Q ss_pred             -chhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhc-CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          421 -TQEEFINGITDVDGVENENQRQPALLRLALDDVLDS-LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       421 -~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~-L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                       .++++.+.+.+....++++.....+....|.++|+. |++.++.|+.. |    .+++|++|||+.||+|.++|+..++
T Consensus       113 ~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~Ll~~~~~~i~~~-~----~~~~s~~eIA~~l~~s~~tV~~~l~  187 (198)
T TIGR02859       113 ESDRTLLDVISGAKVTDPEELIISQEEYGDIESKMNELLSDLEWKVLQS-Y----LDGKSYQEIACDLNRHVKSIDNALQ  187 (198)
T ss_pred             cccchHHHHhhccccCCHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHH-H----HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence             111122222222223456666666777789999999 46667777654 5    4899999999999999999999999


Q ss_pred             HHHHHHhCc
Q 010092          499 KGLMKLKHP  507 (518)
Q Consensus       499 rALkKLR~~  507 (518)
                      +|+++||..
T Consensus       188 r~r~~L~~~  196 (198)
T TIGR02859       188 RVKRKLEKY  196 (198)
T ss_pred             HHHHHHHHh
Confidence            999999974

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=99.85  E-value=1.6e-20  Score=179.36  Aligned_cols=177  Identities=20%  Similarity=0.189  Sum_probs=140.1

Q ss_pred             HHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHH
Q 010092          262 AAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHA  341 (518)
Q Consensus       262 ~~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqa  341 (518)
                      ...+..+..||..|++.|+..|.+.|+++|.++.   ++..+++|++||+|+++|++.++|++..  .|.+|++..+++.
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            3456677889999999999999999999999998   7788999999999999999999999743  6999999999999


Q ss_pred             HHHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCC
Q 010092          342 IIRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV  420 (518)
Q Consensus       342 I~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~  420 (518)
                      +.++++ ..+....+.                                                          +.    
T Consensus        89 ~~~~~R~~~~~~~~~~----------------------------------------------------------~~----  106 (194)
T PRK12513         89 LIDHWRRHGARQAPSL----------------------------------------------------------DA----  106 (194)
T ss_pred             HHHHHHHhcccccccc----------------------------------------------------------cc----
Confidence            998887 322111000                                                          00    


Q ss_pred             chhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          421 TQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       421 ~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                       +... .... ....+++...+..+....|..+|+.||++++.||.++|    .+++|++|||+.||+|.++|++.+.||
T Consensus       107 -~~~~-~~~~-~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~ra  179 (194)
T PRK12513        107 -DEQL-HALA-DDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLRE----HGDLELEEIAELTGVPEETVKSRLRYA  179 (194)
T ss_pred             -chhh-hhcC-CCCCCHHHHHHHHHHHHHHHHHHHhCCHhHhhheeeeh----ccCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence             0000 0001 11223455555666778899999999999999999998    589999999999999999999999999


Q ss_pred             HHHHhCcchhhh
Q 010092          501 LMKLKHPTRVDY  512 (518)
Q Consensus       501 LkKLR~~~~~~~  512 (518)
                      +++||.......
T Consensus       180 ~~~Lr~~l~~~~  191 (194)
T PRK12513        180 LQKLRELLAEEV  191 (194)
T ss_pred             HHHHHHHHHHhh
Confidence            999998766544

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=99.85  E-value=2.1e-20  Score=174.80  Aligned_cols=174  Identities=16%  Similarity=0.118  Sum_probs=134.7

Q ss_pred             HHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHH
Q 010092          267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM  346 (518)
Q Consensus       267 ~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI  346 (518)
                      ++.+||..|++.|+..|.++|+.++++|.   +++.+.+|++||++++||++++.|+  .+.+|.+|++..+++.+.+.+
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            45789999999999999999999999998   6788999999999999999999999  445899999999999999888


Q ss_pred             Hh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhh
Q 010092          347 TV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEF  425 (518)
Q Consensus       347 ~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel  425 (518)
                      +. .+....+    .                                                   .+.+..   +....
T Consensus        78 r~~~~~~~~~----~---------------------------------------------------~~~~~~---~~~~~   99 (182)
T PRK09652         78 RKQGRRPPAS----D---------------------------------------------------VDAEEA---EDFDL   99 (182)
T ss_pred             HcccCCCCcc----c---------------------------------------------------cccccc---ccccc
Confidence            73 2210000    0                                                   000000   00000


Q ss_pred             hcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092          426 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  505 (518)
Q Consensus       426 ~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR  505 (518)
                      .+.. + ...++++.+...+....+..+|..|||+++.||.++|    ..++|++|||+.||+|..+|++.+++|+++||
T Consensus       100 ~~~~-~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr  173 (182)
T PRK09652        100 ADAL-R-DISTPENELLSAELEQRVRAAIESLPEELRTAITLRE----IEGLSYEEIAEIMGCPIGTVRSRIFRAREALR  173 (182)
T ss_pred             cccc-c-cccChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            0111 1 1123555555666778899999999999999999998    47999999999999999999999999999999


Q ss_pred             Ccch
Q 010092          506 HPTR  509 (518)
Q Consensus       506 ~~~~  509 (518)
                      +.+.
T Consensus       174 ~~l~  177 (182)
T PRK09652        174 AKLQ  177 (182)
T ss_pred             HHHH
Confidence            7553

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=99.85  E-value=3e-20  Score=176.41  Aligned_cols=169  Identities=12%  Similarity=0.131  Sum_probs=135.1

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      .+..+..|+..|++.|+..|.++|+.+|.+|.   +++.+++|++||+|+++|+++.+|+++ +..|.+|++..+++.+.
T Consensus        10 l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeDlvQe~fi~l~~~~~~~~~~-~~~f~~wl~~ia~n~~~   85 (186)
T PRK05602         10 LLARVAAGDPAAFRVLVARKLPRLLALATRML---GDPAEAEDVAQETFLRIWKQAPSWRPG-EARFDTWLHRVVLNLCY   85 (186)
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHHHHHhhhcCCC-CCcHHHHHHHHHHHHHH
Confidence            45567889999999999999999999999998   788899999999999999999999986 45799999999999888


Q ss_pred             HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092          344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE  423 (518)
Q Consensus       344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e  423 (518)
                      ++++..+..  +                                                          .+.     ..
T Consensus        86 d~~R~~~~~--~----------------------------------------------------------~~~-----~~  100 (186)
T PRK05602         86 DRLRRRREV--P----------------------------------------------------------VED-----AP  100 (186)
T ss_pred             HHHHhcCCC--C----------------------------------------------------------ccc-----cc
Confidence            877621100  0                                                          000     00


Q ss_pred             hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                      +    ..+ ....++..+...+....+..+|..||++++.||.++|    .+++|++|||+.||+|..+|++.++||+++
T Consensus       101 ~----~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~  171 (186)
T PRK05602        101 D----VPD-PAPGPDAGLEARQRARRVEQALAALPERQREAIVLQY----YQGLSNIEAAAVMDISVDALESLLARGRRA  171 (186)
T ss_pred             c----cCC-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHH----hcCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence            0    000 1112344444455667899999999999999999998    589999999999999999999999999999


Q ss_pred             HhCcchh
Q 010092          504 LKHPTRV  510 (518)
Q Consensus       504 LR~~~~~  510 (518)
                      ||+....
T Consensus       172 Lr~~l~~  178 (186)
T PRK05602        172 LRAQLAD  178 (186)
T ss_pred             HHHHHHh
Confidence            9986654

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=99.85  E-value=4.6e-20  Score=176.74  Aligned_cols=170  Identities=15%  Similarity=0.180  Sum_probs=133.2

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r  344 (518)
                      +.....|+..|++.|+..|.++|+.+|.+|.   ++..+++|++||+|+++|+++++||+..| .|.+|++..+++.+.+
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   78899999999999999999999998766 6999999999999988


Q ss_pred             HHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092          345 SMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE  423 (518)
Q Consensus       345 aI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e  423 (518)
                      +++ +.+..+.-.                                                        +..      ..
T Consensus        97 ~~r~~~~~~~~~~--------------------------------------------------------~~~------~~  114 (194)
T PRK09646         97 RVRSEQAASQREV--------------------------------------------------------RYG------AR  114 (194)
T ss_pred             HHHhhcccccccc--------------------------------------------------------ccc------cc
Confidence            887 221000000                                                        000      00


Q ss_pred             hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                         +  .+.....+++.....+....|..+|..||++++.||.|+|    .+++|++|||+.||+|..+|++.++||+++
T Consensus       115 ---~--~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~  185 (194)
T PRK09646        115 ---N--VDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAY----YGGLTYREVAERLAVPLGTVKTRMRDGLIR  185 (194)
T ss_pred             ---c--ccccccchHHHHHHHhHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCChHhHHHHHHHHHHH
Confidence               0  0000011223333345567899999999999999999998    589999999999999999999999999999


Q ss_pred             HhCcch
Q 010092          504 LKHPTR  509 (518)
Q Consensus       504 LR~~~~  509 (518)
                      ||....
T Consensus       186 Lr~~l~  191 (194)
T PRK09646        186 LRDCLG  191 (194)
T ss_pred             HHHHhc
Confidence            997653

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

Probab=99.85  E-value=6.6e-20  Score=170.50  Aligned_cols=167  Identities=18%  Similarity=0.196  Sum_probs=133.5

Q ss_pred             HHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHH
Q 010092          266 KKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS  345 (518)
Q Consensus       266 ~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ra  345 (518)
                      .+..+||..|++.|+..|.+.+++++.++.   ++..+++|++||+|+.+|++.++|+...+ .|.+|++..+++.+.++
T Consensus         3 ~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~vQe~~l~l~~~~~~~~~~~~-~~~~wl~~i~~n~~~d~   78 (170)
T TIGR02952         3 ERAQDREEDAFARIYETYSDRVYRYIYYRV---GCKYTAEDLTSEVFERVLRKIDSFKEQKN-SFEAWLFTIARNVVNDY   78 (170)
T ss_pred             HHHHccCHHHHHHHHHHHHHHHHHHHHHHH---CChhhHHHHHHHHHHHHHHhHHhcccccc-cHHHHHHHHHHHHHHHH
Confidence            456789999999999999999999999887   67789999999999999999999997555 79999999999999999


Q ss_pred             HHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhh
Q 010092          346 MTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEF  425 (518)
Q Consensus       346 I~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel  425 (518)
                      +++....  +.                                                       .+++        ..
T Consensus        79 ~R~~~~~--~~-------------------------------------------------------~~~~--------~~   93 (170)
T TIGR02952        79 FRGSKRH--PL-------------------------------------------------------FSLD--------VF   93 (170)
T ss_pred             HHhcCCC--CC-------------------------------------------------------CcHH--------HH
Confidence            8832110  00                                                       0000        00


Q ss_pred             hcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092          426 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  505 (518)
Q Consensus       426 ~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR  505 (518)
                      .+...  ...++++.....+....+..+|..|||+++.||.++|    .+++|++|||+.||+|..+|++.++||+++||
T Consensus        94 ~~~~~--~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr  167 (170)
T TIGR02952        94 KELLS--NEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRF----GQNLPIAEVARILGKTEGAVKILQFRAIKKLA  167 (170)
T ss_pred             hhcCC--CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            00000  1112445555556677899999999999999999998    58999999999999999999999999999999


Q ss_pred             Cc
Q 010092          506 HP  507 (518)
Q Consensus       506 ~~  507 (518)
                      +.
T Consensus       168 ~~  169 (170)
T TIGR02952       168 RQ  169 (170)
T ss_pred             Hh
Confidence            64

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

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=99.84  E-value=5.5e-20  Score=173.80  Aligned_cols=177  Identities=18%  Similarity=0.202  Sum_probs=135.8

Q ss_pred             HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (518)
Q Consensus       263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI  342 (518)
                      ..+....+|+..|+..|+..|.++|+.+|.+|.   +++.+++|++||+|+++|+++..|++..  .|.+|++..+++.+
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            346667889999999999999999999999998   7788999999999999999999999865  69999999999999


Q ss_pred             HHHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcC-Cc
Q 010092          343 IRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHG-VT  421 (518)
Q Consensus       343 ~raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~-~~  421 (518)
                      .++++..+. ..                                                          .++.... .+
T Consensus        82 ~~~~rk~~~-~~----------------------------------------------------------~~~~~~~~~~  102 (187)
T TIGR02948        82 IDRLRKRKP-DF----------------------------------------------------------YLDDEVQGTD  102 (187)
T ss_pred             HHHHHhhcc-cc----------------------------------------------------------cccccccCcc
Confidence            888772110 00                                                          0000000 00


Q ss_pred             hhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          422 QEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       422 ~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      .....+...+ ....+++.....+....+..+|+.|||+++.||.++|    .+++|++|||+.||+|.++|++.++||+
T Consensus       103 ~~~~~~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Rar  177 (187)
T TIGR02948       103 GLTMESQLAA-DEAPPEDQVISLELRDTIQQEIQALPPKYRMVIVLKY----MEDLSLKEISEILDLPVGTVKTRIHRGR  177 (187)
T ss_pred             cccccccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            0000011111 1123445555556667799999999999999999988    4899999999999999999999999999


Q ss_pred             HHHhCcc
Q 010092          502 MKLKHPT  508 (518)
Q Consensus       502 kKLR~~~  508 (518)
                      ++||...
T Consensus       178 ~~Lr~~l  184 (187)
T TIGR02948       178 EALRKQL  184 (187)
T ss_pred             HHHHHHh
Confidence            9999754

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

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=99.84  E-value=6.5e-20  Score=168.25  Aligned_cols=152  Identities=22%  Similarity=0.274  Sum_probs=121.5

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCC
Q 010092          272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSF  351 (518)
Q Consensus       272 d~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~  351 (518)
                      +..|++.|+..|.++|+.+++++.    ...+++|++||+++++|++++.|++..| .|.+|++..+++.+.+++++.. 
T Consensus         2 ~~~af~~l~~~y~~~l~~~~~~~~----~~~~aeDi~Qe~~l~l~~~~~~~~~~~~-~f~~wl~~i~~n~~ld~~rk~~-   75 (154)
T PRK06759          2 KPATFTEAVVLYEGLIVNQIKKLG----IYQDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEF-   75 (154)
T ss_pred             CcccHHHHHHHHHHHHHHHHHHhC----CcccHHHHHHHHHHHHHHHHHHhCccCC-chHHHHHHHHHHHHHHHHHHHH-
Confidence            457899999999999999998864    4568999999999999999999998776 6999999999999998887210 


Q ss_pred             ccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhccccc
Q 010092          352 TRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD  431 (518)
Q Consensus       352 iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d  431 (518)
                                       .   ..     .                             . .+                .+
T Consensus        76 -----------------~---~~-----~-----------------------------~-~~----------------~~   84 (154)
T PRK06759         76 -----------------A---VQ-----E-----------------------------K-CV----------------CV   84 (154)
T ss_pred             -----------------h---hc-----c-----------------------------c-cc----------------cc
Confidence                             0   00     0                             0 00                00


Q ss_pred             CCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          432 VDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       432 ~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                         ..+++.....+....|..+|..||++++.||.++|    .+++|++|||+.||+|..+|++++.||+++||+.
T Consensus        85 ---~~~~~~~~~~~~~~~l~~~l~~L~~~~r~ii~l~~----~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~  153 (154)
T PRK06759         85 ---GEYEDHFHFEDVEMKVKDFMSVLDEKEKYIIFERF----FVGKTMGEIALETEMTYYQVRWIYRQALEKMRNS  153 (154)
T ss_pred             ---CCCcccccHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence               00111222234456799999999999999999999    5899999999999999999999999999999963

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=99.84  E-value=1.6e-19  Score=170.74  Aligned_cols=176  Identities=16%  Similarity=0.170  Sum_probs=135.9

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      .+.....|+..|++.|+..|.++|+.+|.++.   ++..+++|++||++++||++..+|++..  .|.+|++..+++.+.
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            35566789999999999999999999999998   7888999999999999999999999853  699999999999999


Q ss_pred             HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCC-ch
Q 010092          344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV-TQ  422 (518)
Q Consensus       344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~-~~  422 (518)
                      +++++.+..   .                                                        +++..... +.
T Consensus        83 d~~R~~~~~---~--------------------------------------------------------~~~~~~~~~~~  103 (187)
T PRK09641         83 DRLRKRKPD---Y--------------------------------------------------------YLDAEVAGTEG  103 (187)
T ss_pred             HHHHhcCcc---c--------------------------------------------------------cccccccCCcc
Confidence            888732100   0                                                        00000000 00


Q ss_pred             hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                      ....+.+.+ ...++++.....+....|..+|+.||++++.||.++|    .+++|++|||+.||+|.++|++.++||++
T Consensus       104 ~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~----~~~~s~~eIA~~lgis~~~v~~~l~Rar~  178 (187)
T PRK09641        104 LTMYSQLAA-DDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKY----IEDLSLKEISEILDLPVGTVKTRIHRGRE  178 (187)
T ss_pred             hhhhccccc-CcCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----hhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            001111111 1223455555566677899999999999999999998    58999999999999999999999999999


Q ss_pred             HHhCcc
Q 010092          503 KLKHPT  508 (518)
Q Consensus       503 KLR~~~  508 (518)
                      +||...
T Consensus       179 ~Lr~~l  184 (187)
T PRK09641        179 ALRKQL  184 (187)
T ss_pred             HHHHHH
Confidence            999754

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=99.84  E-value=1.2e-19  Score=178.89  Aligned_cols=175  Identities=15%  Similarity=0.127  Sum_probs=134.5

Q ss_pred             HHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH
Q 010092          268 CLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT  347 (518)
Q Consensus       268 ~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~  347 (518)
                      ...||..|++.|+..|.++|+.+|.++.   ++..+++||+||+|++||++++.|++.  ..|.+|++..+++.+.++++
T Consensus        24 ~~~gd~~a~~~l~~~y~~~l~~~a~~~~---~~~~~AEDlvQE~fi~l~~~~~~~~~~--~~~~~wL~~iarn~~~d~~R   98 (231)
T PRK11922         24 VLAGDEAAFEALMRRHNRRLYRTARAIL---RNDAEAEDVVQEAYLRAFRALGTFRGD--ASLSTWLSRIVLNEALGRLR   98 (231)
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHHHHHHh---CChhhHHHHHHHHHHHHHHHHHhcCCC--chhHHHHHHHHHHHHHHHHH
Confidence            4568899999999999999999999998   678899999999999999999999986  36999999999999988887


Q ss_pred             -hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhh
Q 010092          348 -VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFI  426 (518)
Q Consensus       348 -~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~  426 (518)
                       ..+...++.                                 .                      ..+.   ...++..
T Consensus        99 k~~r~~~~~~---------------------------------~----------------------~~~~---~~~~~~~  120 (231)
T PRK11922         99 RRRRLVNLAE---------------------------------M----------------------VMAS---TIAGGER  120 (231)
T ss_pred             hhcccccchh---------------------------------c----------------------cccc---ccccccc
Confidence             221100000                                 0                      0000   0000000


Q ss_pred             cccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          427 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       427 ~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                       ........++++.....+..+.|..+|+.||+++++||.++|    .+++|++|||+.||+|.++|++.+.+|+++||+
T Consensus       121 -~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~  195 (231)
T PRK11922        121 -TPLADPAEDPERAAARREIRALLERAIDALPDAFRAVFVLRV----VEELSVEETAQALGLPEETVKTRLHRARRLLRE  195 (231)
T ss_pred             -cccCcccCChHHHHHHHHHHHHHHHHHHhCCHHHhhhheeeh----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence             000111223555566667778899999999999999999988    589999999999999999999999999999998


Q ss_pred             cchh
Q 010092          507 PTRV  510 (518)
Q Consensus       507 ~~~~  510 (518)
                      ....
T Consensus       196 ~l~~  199 (231)
T PRK11922        196 SLAR  199 (231)
T ss_pred             HHHH
Confidence            6653

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=99.83  E-value=1.7e-19  Score=172.20  Aligned_cols=175  Identities=13%  Similarity=0.118  Sum_probs=135.9

Q ss_pred             HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (518)
Q Consensus       263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI  342 (518)
                      ..+.+...|+..|++.|+..|.++|+.++.++..+.....+++|++||++++||+++++|+++.+ .|.+|++..+++.+
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            34566778999999999999999999999999832112357999999999999999999997655 79999999999999


Q ss_pred             HHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCc
Q 010092          343 IRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVT  421 (518)
Q Consensus       343 ~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~  421 (518)
                      .++++ +.+....                                                         .+.+.     
T Consensus        86 ~d~~rk~~~~~~~---------------------------------------------------------~~~~~-----  103 (189)
T PRK06811         86 IDYKRKLTKNNEI---------------------------------------------------------DSIDE-----  103 (189)
T ss_pred             HHHHHHhcccccc---------------------------------------------------------ccchh-----
Confidence            99887 3211000                                                         00000     


Q ss_pred             hhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          422 QEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       422 ~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                        ..    .+ ...++++.....+....|..+|..|||+++.||.++|    .+++|++|||+.||+|..+|++.+.||+
T Consensus       104 --~~----~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIAe~lgis~~~V~~~l~Ra~  172 (189)
T PRK06811        104 --FI----LI-SEESIENEIILKENKEEILKLINDLEKLDREIFIRRY----LLGEKIEEIAKKLGLTRSAIDNRLSRGR  172 (189)
T ss_pred             --hh----hc-ccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence              00    00 0122444455556667799999999999999999988    4899999999999999999999999999


Q ss_pred             HHHhCcchhh
Q 010092          502 MKLKHPTRVD  511 (518)
Q Consensus       502 kKLR~~~~~~  511 (518)
                      ++||....+-
T Consensus       173 ~~Lr~~~~~~  182 (189)
T PRK06811        173 KKLQKNKLNI  182 (189)
T ss_pred             HHHHHcccCc
Confidence            9999865543

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=99.83  E-value=2.3e-19  Score=169.99  Aligned_cols=171  Identities=19%  Similarity=0.199  Sum_probs=129.8

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      .+.....||..|++.|+..|.+.|+.++++|.   +++.+++|++||+|+.+|+++++|++..+ .|.+|++..+++.+.
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            34556789999999999999999999999998   67889999999999999999999987643 699999999999999


Q ss_pred             HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092          344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE  423 (518)
Q Consensus       344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e  423 (518)
                      +++++....  +..                                                        ++.    ...
T Consensus        89 d~~rk~~~~--~~~--------------------------------------------------------~~~----~~~  106 (186)
T PRK13919         89 DHVRRRAAR--PQP--------------------------------------------------------LEP----DER  106 (186)
T ss_pred             HHHHhhhcc--ccc--------------------------------------------------------ccc----ccc
Confidence            888731100  000                                                        000    000


Q ss_pred             hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                      +. .. .+.  .+++...........|..+|+.||++++.||.++|    .+++|++|||+.||+|..+|+..++||+++
T Consensus       107 ~~-~~-~~~--~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~~V~~~l~ra~~~  178 (186)
T PRK13919        107 EP-EA-FDL--PGPGLDEEGHLDRTRLGRALKALSPEERRVIEVLY----YQGYTHREAAQLLGLPLGTLKTRARRALSR  178 (186)
T ss_pred             cc-cc-ccC--CCccccHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            00 00 000  00111112233456789999999999999999998    589999999999999999999999999999


Q ss_pred             HhCcc
Q 010092          504 LKHPT  508 (518)
Q Consensus       504 LR~~~  508 (518)
                      ||...
T Consensus       179 Lr~~l  183 (186)
T PRK13919        179 LKEVL  183 (186)
T ss_pred             HHHHh
Confidence            99643

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=99.83  E-value=2.2e-19  Score=171.44  Aligned_cols=171  Identities=22%  Similarity=0.208  Sum_probs=132.0

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      .+.+...||..|++.|+..|.+.|+.++.++.   ++..+++|++||+|+++|+. ..|++..+ .|.||++..+++.+.
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            35556789999999999999999999999998   67789999999999999976 67887655 799999999999999


Q ss_pred             HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092          344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE  423 (518)
Q Consensus       344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e  423 (518)
                      +++++.+..  .. ...               ..                                            ..
T Consensus        94 d~~Rk~~~~--~~-~~~---------------~~--------------------------------------------~~  111 (194)
T PRK12519         94 DRLRSRRSR--QR-LLE---------------RW--------------------------------------------QQ  111 (194)
T ss_pred             HHHHhcccc--cc-hhh---------------hh--------------------------------------------hh
Confidence            988731100  00 000               00                                            00


Q ss_pred             hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                      ...   .+....++++.+...+....|..+|..||++++.||.++|    .+++|++|||+.||+|.++|++++.||+++
T Consensus       112 ~~~---~~~~~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~  184 (194)
T PRK12519        112 ELL---GEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAY----YEGLSQSEIAKRLGIPLGTVKARARQGLLK  184 (194)
T ss_pred             hhc---ccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhhh----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            000   0001112344444455566789999999999999999998    589999999999999999999999999999


Q ss_pred             HhCcc
Q 010092          504 LKHPT  508 (518)
Q Consensus       504 LR~~~  508 (518)
                      ||...
T Consensus       185 Lr~~l  189 (194)
T PRK12519        185 LRELL  189 (194)
T ss_pred             HHHHH
Confidence            99754

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=99.82  E-value=5.3e-19  Score=167.52  Aligned_cols=177  Identities=12%  Similarity=0.086  Sum_probs=134.6

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      .+.....||..|+..|+..|.+.|+.+|.++.   ++..+++||+||+|++||+++.+|++.  ..|.+|++...++.+.
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            35556789999999999999999999999998   788899999999999999999999975  3699999999988888


Q ss_pred             HHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092          344 RSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ  422 (518)
Q Consensus       344 raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~  422 (518)
                      ++++ ..+......                                                       .+.+.     .
T Consensus        85 ~~~r~~~r~~~~~~-------------------------------------------------------~~~~~-----~  104 (190)
T TIGR02939        85 NHLVAQGRRPPTSD-------------------------------------------------------VEIED-----A  104 (190)
T ss_pred             HHHHHhccCCCccc-------------------------------------------------------ccccc-----h
Confidence            7776 221100000                                                       00000     0


Q ss_pred             hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                      +............++++.....+....|..+|..||++++.||.++|    .+++|++|||+.||+|..+|++.++||++
T Consensus       105 ~~~~~~~~~~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~lgis~~tv~~~l~rar~  180 (190)
T TIGR02939       105 EHFEGADRLREIDTPERLLLSRELEQTVMRAVEALPEDLRTAITLRE----LEGLSYEDIARIMDCPVGTVRSRIFRARE  180 (190)
T ss_pred             hhhcccccccccCChHHHHHHHHHHHHHHHHHHcCCHHHhhhhhhhh----hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            00000000001123455555566777899999999999999999998    58999999999999999999999999999


Q ss_pred             HHhCcch
Q 010092          503 KLKHPTR  509 (518)
Q Consensus       503 KLR~~~~  509 (518)
                      +||+..+
T Consensus       181 ~Lr~~l~  187 (190)
T TIGR02939       181 AIAIRLR  187 (190)
T ss_pred             HHHHHhh
Confidence            9997653

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.

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=4.2e-19  Score=167.37  Aligned_cols=168  Identities=14%  Similarity=0.153  Sum_probs=131.7

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r  344 (518)
                      +.....|+..|+..|+..|.+.|+.+|.+|.   ++..+++|++||+|+.+|+++++|++..+ .|.+|++..+++.+.+
T Consensus        10 i~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~fl~~~~~~~~~~~~~~-~~~~wl~~ia~n~~~d   85 (179)
T PRK12514         10 IVRVSLGDRDAFSSLYDATSAKLFGICLRVL---KDRSEAEEALQDVYVKIWTKADRFAVSGL-SPMTWLITIARNHAID   85 (179)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHH---cCHHHHHHHHHHHHHHHHHhHHhcCcccc-cHHHHHHHHHHHHHHH
Confidence            5556789999999999999999999999998   78889999999999999999999997543 6999999999999988


Q ss_pred             HHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhh
Q 010092          345 SMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE  424 (518)
Q Consensus       345 aI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ee  424 (518)
                      ++++.+....+  .                                                        +.     ..+
T Consensus        86 ~~R~~~~~~~~--~--------------------------------------------------------~~-----~~~  102 (179)
T PRK12514         86 RLRARKAVAVD--I--------------------------------------------------------DE-----AHD  102 (179)
T ss_pred             HHHhcCCcccc--c--------------------------------------------------------cc-----chh
Confidence            88731100000  0                                                        00     000


Q ss_pred             hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092          425 FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL  504 (518)
Q Consensus       425 l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL  504 (518)
                          ..+ ...++++.+........|..+|..||++++.||.++|    .+++|++|||+.||+|..+|++.+.||+++|
T Consensus       103 ----~~~-~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~L  173 (179)
T PRK12514        103 ----LAD-PSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAY----LEGLSYKELAERHDVPLNTMRTWLRRSLLKL  173 (179)
T ss_pred             ----ccc-cCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCChHHHHHHHHHHHHHH
Confidence                000 0112344443344456788999999999999999999    5899999999999999999999999999999


Q ss_pred             hCcc
Q 010092          505 KHPT  508 (518)
Q Consensus       505 R~~~  508 (518)
                      |+..
T Consensus       174 r~~l  177 (179)
T PRK12514        174 RECL  177 (179)
T ss_pred             HHHh
Confidence            9754

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=4.7e-19  Score=170.03  Aligned_cols=171  Identities=17%  Similarity=0.095  Sum_probs=135.2

Q ss_pred             HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (518)
Q Consensus       263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI  342 (518)
                      ..+.+...||..|++.|+..|.+.|+.+|.++.   ++..+++|++||+++.+|+....|++.. ..|.+|++..+++.+
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            445667789999999999999999999999998   7889999999999999999999998533 469999999999988


Q ss_pred             HHHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092          343 IRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ  422 (518)
Q Consensus       343 ~raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~  422 (518)
                      .+.+++.+...                                                          ..++..     
T Consensus        91 ~d~~Rk~~~~~----------------------------------------------------------~~~~~~-----  107 (196)
T PRK12524         91 TDRLRRRRRAS----------------------------------------------------------VDLDDA-----  107 (196)
T ss_pred             HHHHHhhcCCC----------------------------------------------------------CCcccc-----
Confidence            88777211000                                                          000000     


Q ss_pred             hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                      .   + ..+ ....+++.....+....|..+|+.||++++.||.|+|    .+++|++|||+.||+|..+|++.++||++
T Consensus       108 ~---~-~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~L~~----~~g~s~~eIA~~lgis~~tV~~~l~Ra~~  178 (196)
T PRK12524        108 P---E-PAD-AAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRH----IEGLSNPEIAEVMEIGVEAVESLTARGKR  178 (196)
T ss_pred             c---c-ccc-cCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            0   0 000 1112344455556677899999999999999999998    58999999999999999999999999999


Q ss_pred             HHhCcch
Q 010092          503 KLKHPTR  509 (518)
Q Consensus       503 KLR~~~~  509 (518)
                      +||....
T Consensus       179 ~Lr~~l~  185 (196)
T PRK12524        179 ALAALLA  185 (196)
T ss_pred             HHHHHHH
Confidence            9997654

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=99.82  E-value=7.3e-19  Score=167.70  Aligned_cols=177  Identities=11%  Similarity=0.062  Sum_probs=134.7

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      .+..+..||..|++.|+..|.+.|+.++.++.   ++..+++|++||+|+.+|+++.+|++..  .|.+|++...++.+.
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            35556788999999999999999999999998   6788999999999999999999999864  589999988888888


Q ss_pred             HHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092          344 RSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ  422 (518)
Q Consensus       344 raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~  422 (518)
                      ++++ +.+.....                                                       ..+++......+
T Consensus        85 d~~rk~~~~~~~~-------------------------------------------------------~~~~~~~~~~~~  109 (193)
T PRK11923         85 NHLVSRGRRPPDS-------------------------------------------------------DVSSEDAEFYDG  109 (193)
T ss_pred             HHHHHhcCCCccc-------------------------------------------------------cccccchhhhcc
Confidence            8776 32210000                                                       000000000000


Q ss_pred             hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                      ..   .+.  +...|++.....+....+..+|..||++++.||.++|    .+++|++|||+.||+|..+|++...||++
T Consensus       110 ~~---~~~--~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Rar~  180 (193)
T PRK11923        110 DH---ALK--DIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLRE----FDGLSYEDIASVMQCPVGTVRSRIFRARE  180 (193)
T ss_pred             cc---ccc--CcCCHHHHHHHHHHHHHHHHHHHhCCHHHhHHHhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            00   000  1123455555667778899999999999999999988    58999999999999999999999999999


Q ss_pred             HHhCcch
Q 010092          503 KLKHPTR  509 (518)
Q Consensus       503 KLR~~~~  509 (518)
                      +||....
T Consensus       181 ~Lr~~l~  187 (193)
T PRK11923        181 AIDKALQ  187 (193)
T ss_pred             HHHHHHH
Confidence            9997543

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=99.82  E-value=7.7e-19  Score=163.76  Aligned_cols=170  Identities=15%  Similarity=0.041  Sum_probs=136.2

Q ss_pred             HHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHH
Q 010092          266 KKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS  345 (518)
Q Consensus       266 ~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ra  345 (518)
                      .....|+..|++.|+..|.+.|+.+|+++.   ++..+.+|++||+++.||.+.+.|+  .+..|.+|++..+++.+.++
T Consensus         5 ~~~~~~~~~a~~~l~~~y~~~l~~~~~~~~---~~~~~aeDl~qe~~~~l~~~~~~~~--~~~~~~~~l~~i~~~~~~d~   79 (179)
T PRK11924          5 PVDATGDKEAFSELFRPHAPDLLRYARRQL---GDRALAEDAVQEAFLRAWRKADLFN--GKGSARTWLLTIARNVCYDL   79 (179)
T ss_pred             HHHHccCHHHHHHHHHHHHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHHHhhcC--CcchHHHHHHHHHHHHHHHH
Confidence            345789999999999999999999999998   7888999999999999999999998  34579999999999999888


Q ss_pred             HHhc-CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhh
Q 010092          346 MTVS-SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE  424 (518)
Q Consensus       346 I~~s-r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ee  424 (518)
                      +++. +.....                                                          .+.     .. 
T Consensus        80 ~r~~~~~~~~~----------------------------------------------------------~~~-----~~-   95 (179)
T PRK11924         80 LRRRRREKAVL----------------------------------------------------------SDD-----AL-   95 (179)
T ss_pred             HHhcccccccC----------------------------------------------------------ccc-----cc-
Confidence            8731 110000                                                          000     00 


Q ss_pred             hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092          425 FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL  504 (518)
Q Consensus       425 l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL  504 (518)
                        ....+....++++.+...+....|..+|..||++++.||.++|    .+++|+.|||+.||+|+.+|++.+.+|+++|
T Consensus        96 --~~~~~~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~~~~~~eIA~~lgis~~tv~~~~~ra~~~l  169 (179)
T PRK11924         96 --EPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRY----VEGLSYREIAEILGVPVGTVKSRLRRARQLL  169 (179)
T ss_pred             --ccccCCccCCHHHHHhhHHHHHHHHHHHHhCCHHHHHHhhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence              0000002234566677777888999999999999999999998    4799999999999999999999999999999


Q ss_pred             hCcchh
Q 010092          505 KHPTRV  510 (518)
Q Consensus       505 R~~~~~  510 (518)
                      |+....
T Consensus       170 r~~l~~  175 (179)
T PRK11924        170 RECLEA  175 (179)
T ss_pred             HHHHHH
Confidence            976543

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=99.82  E-value=3.5e-19  Score=169.74  Aligned_cols=160  Identities=18%  Similarity=0.223  Sum_probs=125.3

Q ss_pred             HcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC
Q 010092          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS  350 (518)
Q Consensus       271 gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr  350 (518)
                      ||..|++.|+..|.+.|+.+|.+|.   ++..+++|++||+|+.+|+++++|++.  ..|.+|++.++++.+.++++...
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            6999999999999999999999999   788899999999999999999999863  37999999999999998887311


Q ss_pred             CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccc
Q 010092          351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT  430 (518)
Q Consensus       351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~  430 (518)
                      .....   ..                                                      +        ...+...
T Consensus        98 ~~~~~---~~------------------------------------------------------~--------~~~~~~~  112 (188)
T PRK09640         98 RKRRL---MD------------------------------------------------------A--------LSLDPLE  112 (188)
T ss_pred             ccccC---cc------------------------------------------------------h--------hhhcccc
Confidence            00000   00                                                      0        0000000


Q ss_pred             cCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          431 DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       431 d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      +..    ++.....+....|..+|+.||++++.||.++|    .+++|++|||+.||||..+|+..+.||+++||...
T Consensus       113 ~~~----~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l  182 (188)
T PRK09640        113 EAS----EEKAPKPEERGGLDRWLVHVNPIDREILVLRF----VAELEFQEIADIMHMGLSATKMRYKRALDKLREKF  182 (188)
T ss_pred             ccc----ccccccHHHHHHHHHHHHhcChhheeeeeeHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            000    01111224456799999999999999999999    58999999999999999999999999999999754

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=5.6e-19  Score=167.47  Aligned_cols=168  Identities=15%  Similarity=0.128  Sum_probs=131.8

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      .+..+..|+..|++.|+..|.+.++.++.++.   ++..+.+|++||+|+.+|+..++|++..+ .|.+|++..+++.+.
T Consensus        13 l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDivQe~fl~l~~~~~~~~~~~~-~~~~wL~~iarn~~~   88 (182)
T PRK12537         13 CLLACARGDRRALQALYQQESARLLGVARRIV---RDRALAEDIVHDAFIKIWTGAASFDPARG-SARGWIYSVTRHLAL   88 (182)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHhccccCCcccc-cHHHHHHHHHHHHHH
Confidence            45667789999999999999999999999998   78889999999999999999999986443 699999999999998


Q ss_pred             HHHHhcC-CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092          344 RSMTVSS-FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ  422 (518)
Q Consensus       344 raI~~sr-~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~  422 (518)
                      ++++..+ ...                                                            .+..    .
T Consensus        89 d~~r~~~~~~~------------------------------------------------------------~~~~----~  104 (182)
T PRK12537         89 NVLRDTRREVV------------------------------------------------------------LDDD----A  104 (182)
T ss_pred             HHHHhccccCc------------------------------------------------------------cccc----h
Confidence            8887311 000                                                            0000    0


Q ss_pred             hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                         .+...+  ..++++..........|..+|+.||++++.||.++|    .+++|++|||+.||+|..+|+..++||++
T Consensus       105 ---~~~~~~--~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~~~s~~eIA~~lgis~~tV~~~l~ra~~  175 (182)
T PRK12537        105 ---EETAQT--LHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAY----VDGCSHAEIAQRLGAPLGTVKAWIKRSLK  175 (182)
T ss_pred             ---hhhccc--ccchHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCChhhHHHHHHHHHH
Confidence               000000  011222233334556789999999999999999998    58999999999999999999999999999


Q ss_pred             HHhCcc
Q 010092          503 KLKHPT  508 (518)
Q Consensus       503 KLR~~~  508 (518)
                      +||...
T Consensus       176 ~Lr~~l  181 (182)
T PRK12537        176 ALRECM  181 (182)
T ss_pred             HHHHHh
Confidence            999753

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=6e-19  Score=167.47  Aligned_cols=170  Identities=19%  Similarity=0.183  Sum_probs=132.3

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r  344 (518)
                      +.....|+..+++.|+..|.++|+++|.++.   ++..+++|++||+|+.+|++.++|++..+ .|.+|++..+++.+.+
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            4455678999999999999999999999998   77889999999999999999999998654 5889999999999888


Q ss_pred             HHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhh
Q 010092          345 SMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE  424 (518)
Q Consensus       345 aI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ee  424 (518)
                      ++++....+..                                                        .+++.        
T Consensus        92 ~~R~~~~~~~~--------------------------------------------------------~~~~~--------  107 (187)
T PRK12534         92 HLRANAPQRRN--------------------------------------------------------VALDD--------  107 (187)
T ss_pred             HHHhccccccc--------------------------------------------------------ccccc--------
Confidence            87731100000                                                        00000        


Q ss_pred             hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092          425 FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL  504 (518)
Q Consensus       425 l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL  504 (518)
                      .... .+ ...++++.....+....|..+|..||++++.||.++|    .+++|++|||+.||+|..+|++.++||+++|
T Consensus       108 ~~~~-~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Rar~~L  181 (187)
T PRK12534        108 AGEL-RA-ADASPLERTERASTRRRIDHCLAELEPPRSELIRTAF----FEGITYEELAARTDTPIGTVKSWIRRGLAKL  181 (187)
T ss_pred             hhhh-cc-ccCChhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCChhHHHHHHHHHHHHH
Confidence            0000 00 0111233334456677899999999999999999999    5899999999999999999999999999999


Q ss_pred             hCcc
Q 010092          505 KHPT  508 (518)
Q Consensus       505 R~~~  508 (518)
                      |...
T Consensus       182 r~~l  185 (187)
T PRK12534        182 KACL  185 (187)
T ss_pred             HHHH
Confidence            9753

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=8.2e-19  Score=173.75  Aligned_cols=169  Identities=14%  Similarity=0.156  Sum_probs=133.6

Q ss_pred             HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (518)
Q Consensus       263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI  342 (518)
                      ..+..+..||..|++.|+..|.+.|+.++.++.   ++..+.+|++||+|+.+|+..++|++..+ .|.+|++..+++.+
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            345567789999999999999999999999998   77789999999999999999999987544 69999999999888


Q ss_pred             HHHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092          343 IRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ  422 (518)
Q Consensus       343 ~raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~  422 (518)
                      .+++++.+..       .                                                     ++.     .
T Consensus       128 id~~Rk~~~~-------~-----------------------------------------------------~~~-----~  142 (233)
T PRK12538        128 IDLRRKPRTE-------N-----------------------------------------------------VDA-----V  142 (233)
T ss_pred             HHHHHhhccc-------c-----------------------------------------------------ccc-----c
Confidence            8777621100       0                                                     000     0


Q ss_pred             hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                      .   +. .+ ...++++.....+....|..+|..||+++|.||.|+|    .+++|++|||+.||+|.++|++.++||++
T Consensus       143 ~---~~-~~-~~~~~~~~~~~~e~~~~l~~~L~~Lp~~~R~v~~L~~----~eg~s~~EIA~~Lgis~~tVk~~l~RAr~  213 (233)
T PRK12538        143 P---EV-AD-GKPDAVSVIERNELSDLLEAAMQRLPEQQRIAVILSY----HENMSNGEIAEVMDTTVAAVESLLKRGRQ  213 (233)
T ss_pred             c---cc-cc-CCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            0   00 00 0112233344456667899999999999999999999    68999999999999999999999999999


Q ss_pred             HHhCcch
Q 010092          503 KLKHPTR  509 (518)
Q Consensus       503 KLR~~~~  509 (518)
                      +||+...
T Consensus       214 kLr~~l~  220 (233)
T PRK12538        214 QLRDLLR  220 (233)
T ss_pred             HHHHHHH
Confidence            9998654

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=9.4e-19  Score=167.70  Aligned_cols=175  Identities=14%  Similarity=0.130  Sum_probs=132.6

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r  344 (518)
                      +.+...||..|++.|+..|.+.|+.+|.++.   ++..+++|++||+|+.+|+...+|++..+ .|.+|++..+++.+.+
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            6667889999999999999999999999998   67788999999999999999999997554 6999999999999998


Q ss_pred             HHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092          345 SMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE  423 (518)
Q Consensus       345 aI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e  423 (518)
                      ++++ .+... ..  ..                                                      +...  ..+
T Consensus        94 ~~Rk~~~~~~-~~--~~------------------------------------------------------~~~~--~~~  114 (194)
T PRK12531         94 LLRKQKGKDL-HI--HA------------------------------------------------------DDIW--PSD  114 (194)
T ss_pred             HHHHhccccc-cc--ch------------------------------------------------------hhcc--ccc
Confidence            8873 21000 00  00                                                      0000  000


Q ss_pred             hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                      .......  ....++    .......+..+|..||++++.||.++|    .+++|++|||+.||+|..+|+..+++|+++
T Consensus       115 ~~~~~~~--~~~~~e----~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~eg~s~~EIA~~lgis~~tVk~rl~ra~~~  184 (194)
T PRK12531        115 YYPPDLV--DHYSPE----QDMLKEQVMKFLDRLPKAQRDVLQAVY----LEELPHQQVAEMFDIPLGTVKSRLRLAVEK  184 (194)
T ss_pred             ccccccc--cccCHH----HHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence            0000000  001111    123346788999999999999999998    589999999999999999999999999999


Q ss_pred             HhCcchhhh
Q 010092          504 LKHPTRVDY  512 (518)
Q Consensus       504 LR~~~~~~~  512 (518)
                      ||.....+.
T Consensus       185 Lr~~l~~~~  193 (194)
T PRK12531        185 LRHSMDAES  193 (194)
T ss_pred             HHHHhhhcc
Confidence            998766544

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=99.81  E-value=9.8e-19  Score=166.60  Aligned_cols=173  Identities=16%  Similarity=0.140  Sum_probs=136.5

Q ss_pred             HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (518)
Q Consensus       263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI  342 (518)
                      ..+.....||..|++.|+..|.+.++.++.++.   ++..+.+|++||+|+.+|++.+.|++.  ..|.+|++..+++.+
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            445667889999999999999999999999998   778899999999999999999999964  379999999999998


Q ss_pred             HHHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092          343 IRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ  422 (518)
Q Consensus       343 ~raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~  422 (518)
                      .+++++.+..  +.                                                          ..      
T Consensus        86 ~d~~r~~~~~--~~----------------------------------------------------------~~------   99 (189)
T PRK12515         86 LSALRRRKHE--EI----------------------------------------------------------DD------   99 (189)
T ss_pred             HHHHHccCCC--CC----------------------------------------------------------cc------
Confidence            8887721100  00                                                          00      


Q ss_pred             hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                       +......+ ...++++.....++...+..+|+.||++++.||.++|    .+++|++|||+.||+|..+|++.+.||++
T Consensus       100 -~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~~~s~~eIA~~lgis~~tV~~~l~Rar~  173 (189)
T PRK12515        100 -EAAAAIED-GADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVY----YHEKSVEEVGEIVGIPESTVKTRMFYARK  173 (189)
T ss_pred             -ccccccCC-CCCCHHHHHHhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence             00000011 1122444444556667899999999999999999998    58999999999999999999999999999


Q ss_pred             HHhCcchhhh
Q 010092          503 KLKHPTRVDY  512 (518)
Q Consensus       503 KLR~~~~~~~  512 (518)
                      +||+......
T Consensus       174 ~Lr~~l~~~~  183 (189)
T PRK12515        174 KLAELLKAAG  183 (189)
T ss_pred             HHHHHHHHhc
Confidence            9998765543

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

Probab=99.80  E-value=1.6e-18  Score=155.47  Aligned_cols=155  Identities=23%  Similarity=0.286  Sum_probs=125.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcc
Q 010092          275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR  353 (518)
Q Consensus       275 A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iR  353 (518)
                      |++.|+..|.++|.++++++.   .++.+.+|++|||+++||++++.|++.  ..|.+|+.+++++.+.++++ +.+   
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  58999999999999999988 322   


Q ss_pred             ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCC
Q 010092          354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD  433 (518)
Q Consensus       354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~  433 (518)
                      .+..+..                                                             ..    .. ...
T Consensus        74 ~~~~~~~-------------------------------------------------------------~~----~~-~~~   87 (158)
T TIGR02937        74 LRRELDL-------------------------------------------------------------LE----EL-LDS   87 (158)
T ss_pred             CCcchhh-------------------------------------------------------------hh----hc-ccc
Confidence            1100000                                                             00    00 001


Q ss_pred             CCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          434 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       434 ~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      ...+++..........|..+|+.||+.++.||.++|    ..++|..|||+.||+|+.+|+++..+++++||+.
T Consensus        88 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~~~ii~~~~----~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~  157 (158)
T TIGR02937        88 DPSPEEELEQEEEREALREALEKLPEREREVLVLRY----LEGLSYKEIAEILGISVGTVKRRLKRARKKLREL  157 (158)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            112444455566777899999999999999999998    4789999999999999999999999999999963

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.

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=4.1e-19  Score=168.62  Aligned_cols=171  Identities=17%  Similarity=0.149  Sum_probs=130.3

Q ss_pred             HHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh
Q 010092          269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV  348 (518)
Q Consensus       269 ~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~  348 (518)
                      ..||..|+..|+..|.+.++.+|.++.   ++..+++|++||.|+.+|++.++|++..+..|.||++..+++.+.+++++
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            468999999999999999999999999   67788999999999999999999987544579999999999999888872


Q ss_pred             cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcc
Q 010092          349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING  428 (518)
Q Consensus       349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~  428 (518)
                      ...                      ...+...                                 .+       ..   .
T Consensus        81 ~~~----------------------~~~~~~~---------------------------------~~-------~~---~   95 (185)
T PRK12542         81 NKR----------------------HETFLEE---------------------------------YE-------RE---S   95 (185)
T ss_pred             hhh----------------------hhhhhhh---------------------------------cc-------cc---c
Confidence            110                      0000000                                 00       00   0


Q ss_pred             cccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          429 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       429 l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      .... ...+++.....+....|..+|..|||++++||.|+|    .+++|++|||+.||+|..+|+..+.||+++||...
T Consensus        96 ~~~~-~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l  170 (185)
T PRK12542         96 IEAV-DENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKV----FYNLTYQEISSVMGITEANVRKQFERARKRVQNMI  170 (185)
T ss_pred             hhhh-hccHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            0000 011222222333446789999999999999999998    58999999999999999999999999999999866


Q ss_pred             hhhh
Q 010092          509 RVDY  512 (518)
Q Consensus       509 ~~~~  512 (518)
                      ....
T Consensus       171 ~~~~  174 (185)
T PRK12542        171 GGIQ  174 (185)
T ss_pred             cccc
Confidence            5443

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

Probab=99.80  E-value=1.5e-18  Score=164.04  Aligned_cols=182  Identities=15%  Similarity=0.138  Sum_probs=133.8

Q ss_pred             HHcHHHHHHHHHHHHHHHHHHHHHhhhc-cCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh
Q 010092          270 EVGRAARNKLIKHNLRLVLFVIKKYFQD-FANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV  348 (518)
Q Consensus       270 ~gd~~A~e~LI~~nlrLV~siAkky~~~-~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~  348 (518)
                      .|+..|++.|+..|.+.|+.+|++|... +++..+++|++||+++.+|+++..|+...+..|.+|++..+++.+.+++++
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            5789999999999999999999997531 235678999999999999999999997666689999999999999888762


Q ss_pred             cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCC--chhhhh
Q 010092          349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGV--TQEEFI  426 (518)
Q Consensus       349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~--~~eel~  426 (518)
                      ..                ...    .+.        +                       ....+++.....  ....+.
T Consensus        83 ~~----------------~~~----~r~--------~-----------------------~~~~~~~~~~~~~~~~~~~~  111 (189)
T TIGR02984        83 HL----------------GAQ----KRD--------I-----------------------RREQSLDAGGRLDESSVRLA  111 (189)
T ss_pred             HH----------------HHH----hhh--------c-----------------------ccccCCCcccccCCcchhHH
Confidence            10                000    000        0                       000112211100  011122


Q ss_pred             cccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          427 NGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       427 ~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      +.+.+ ...++++.....+....|..+|..|||+++.||.++|    ..++|++|||+.||||.++|++.++||+++||+
T Consensus       112 ~~~~~-~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vi~l~~----~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~  186 (189)
T TIGR02984       112 AQLAA-DGPSPSQVAARREAAVRLAQALAKLPEDYREVILLRH----LEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ  186 (189)
T ss_pred             HHccC-CCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            22222 2223555555566667899999999999999999999    489999999999999999999999999999996


Q ss_pred             c
Q 010092          507 P  507 (518)
Q Consensus       507 ~  507 (518)
                      .
T Consensus       187 ~  187 (189)
T TIGR02984       187 I  187 (189)
T ss_pred             H
Confidence            4

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).

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=99.80  E-value=1.9e-18  Score=167.42  Aligned_cols=173  Identities=12%  Similarity=0.153  Sum_probs=131.4

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r  344 (518)
                      +.....|+..|++.|+..|.+.|+.++.++.   ++..+++|++||+|+.+|+++..|++.++ .|.+|++.++++.+.+
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            3345679999999999999999999999998   67788999999999999999999997665 5999999999999999


Q ss_pred             HHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092          345 SMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE  423 (518)
Q Consensus       345 aI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e  423 (518)
                      +++ +.+.....                              ..++                     ..+          
T Consensus       105 ~~Rk~~~~~~~~------------------------------~~~~---------------------~~~----------  123 (206)
T PRK12526        105 MLRKIKAKKEQN------------------------------LGDD---------------------IWP----------  123 (206)
T ss_pred             HHHHhccccccc------------------------------cccc---------------------cch----------
Confidence            887 32110000                              0000                     000          


Q ss_pred             hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                       ..+.+.+.. . .............|..+|..||++++.||.++|    .+++|++|||+.||+|..+|+..+++|+++
T Consensus       124 -~~~~~~~~~-~-~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~  196 (206)
T PRK12526        124 -IEQALAESQ-S-ESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVY----FQELSQEQLAQQLNVPLGTVKSRLRLALAK  196 (206)
T ss_pred             -hhhhccccc-C-chHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence             000001110 1 111222333456799999999999999999999    589999999999999999999999999999


Q ss_pred             HhCcch
Q 010092          504 LKHPTR  509 (518)
Q Consensus       504 LR~~~~  509 (518)
                      ||....
T Consensus       197 Lr~~l~  202 (206)
T PRK12526        197 LKVQMG  202 (206)
T ss_pred             HHHHHh
Confidence            997654

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=99.80  E-value=3.6e-18  Score=167.48  Aligned_cols=186  Identities=13%  Similarity=0.175  Sum_probs=134.4

Q ss_pred             HHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHH
Q 010092          267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM  346 (518)
Q Consensus       267 ~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI  346 (518)
                      .+.+||.. ++.||..|.|+|.++|.+|..+. .+.+.+|++|+|++|||+|+++|||++|.+|.|||.+||++.|.+++
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            35678877 99999999999999999997321 13589999999999999999999999999999999999999999999


Q ss_pred             H-hc---CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHh------CCCHHHHHHHHHhcCCccccCC
Q 010092          347 T-VS---SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGV------NISPERYREVMKASKPILSLHS  416 (518)
Q Consensus       347 ~-~s---r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~l------gis~e~v~~~l~~~~~~~SLD~  416 (518)
                      + ..   ..+++|....+     ....+..+..++..++++.|+.+||+..-      |+|.+++-+             
T Consensus        81 Rk~~k~~~~v~~~~~~~e-----~~~~~~~~~~~~~~~~~~~~~~eEI~~~~~~L~~~gi~~~dLv~-------------  142 (218)
T TIGR02895        81 RKNQKYQNLLYLDEDYDE-----NPLEFNKSMEEYRNEIENENRRLEILEYKKLLKQFGIEFVELVK-------------  142 (218)
T ss_pred             HhcccccCeeeCCchHHH-----HHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCcHHHHhh-------------
Confidence            9 44   46688865554     56677777888999999999999998542      444443211             


Q ss_pred             CcCCchhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHH
Q 010092          417 RHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH  496 (518)
Q Consensus       417 ~~~~~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqi  496 (518)
                                     .   +|-+ -+.....-.+...+.    ....++..-+.   ...+.++||+..++||+.++.+.
T Consensus       143 ---------------~---sPkh-~d~r~~~i~ia~~~~----~~~~l~~~l~~---kk~LP~k~l~~~~~v~rktier~  196 (218)
T TIGR02895       143 ---------------V---SPKH-RDTRKKAIKIAKVIV----ENEELLEYLIR---KKKLPIKEIEERVRISRKTIERY  196 (218)
T ss_pred             ---------------c---CCCC-HHHHHHHHHHHHHHh----cCHHHHHHHHH---hCCCCHHHHHHHcCCCHHHHHHh
Confidence                           0   1111 111122222322222    12222322221   35789999999999999999875


Q ss_pred             HH
Q 010092          497 EV  498 (518)
Q Consensus       497 e~  498 (518)
                      ..
T Consensus       197 rk  198 (218)
T TIGR02895       197 RK  198 (218)
T ss_pred             hH
Confidence            44

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).

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

Probab=99.79  E-value=4.6e-18  Score=155.60  Aligned_cols=160  Identities=16%  Similarity=0.184  Sum_probs=124.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCcc
Q 010092          274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTR  353 (518)
Q Consensus       274 ~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iR  353 (518)
                      .|++.|+..|.+.|+.+++++.   ++..+.+|++||+++++|+++.+|++..  +|.+|++.++++.+.++++...   
T Consensus         1 ~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~~~~~~~~~~~~~~~~--~~~~wl~~i~r~~~~d~~r~~~---   72 (161)
T TIGR02985         1 KAFEQLYRRYYPKLCAFAYRYV---KDEEEAEDIVQDVFVKLWENRETLEEVE--SFKAYLFTIVKNRSLNYLRHKQ---   72 (161)
T ss_pred             ChHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhccccc--cHHHHHHHHHHHHHHHHHHHHH---
Confidence            3789999999999999999998   6788899999999999999999998643  7999999999999998887211   


Q ss_pred             ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCC
Q 010092          354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD  433 (518)
Q Consensus       354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~  433 (518)
                                     ........+...                                  +             .....
T Consensus        73 ---------------~~~~~~~~~~~~----------------------------------~-------------~~~~~   90 (161)
T TIGR02985        73 ---------------VEEKYQEEILEI----------------------------------E-------------VDELS   90 (161)
T ss_pred             ---------------hHhHHHHHHHhh----------------------------------c-------------ccccC
Confidence                           000000000000                                  0             00001


Q ss_pred             CCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          434 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       434 ~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      ..++++.+...++...|..+|..||++++.||.++|    .+++|..|||+.||+|+++|++.+.+|+++||+.
T Consensus        91 ~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~il~l~~----~~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~  160 (161)
T TIGR02985        91 ENDPEEELEAKELQLIIYKAIEKLPEQCRKIFILSR----FEGKSYKEIAEELGISVKTVEYHISKALKELRKE  160 (161)
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            112444455566777899999999999999999988    4899999999999999999999999999999964

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.

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=99.79  E-value=4e-18  Score=161.21  Aligned_cols=165  Identities=16%  Similarity=0.093  Sum_probs=128.6

Q ss_pred             HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhc
Q 010092          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS  349 (518)
Q Consensus       270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~s  349 (518)
                      .|+..|+..|+..|.+.|+.++..|.   ++..+.+|++||+|+.+|+++.+|++..  .|.+|++..+++.+.++++..
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  699999988888887766521


Q ss_pred             CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhccc
Q 010092          350 SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGI  429 (518)
Q Consensus       350 r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l  429 (518)
                      ..-..                                                          .++..     .+..+. 
T Consensus        78 ~~~~~----------------------------------------------------------~~~~~-----~~~~~~-   93 (179)
T PRK12543         78 WRRFR----------------------------------------------------------IFEKA-----EEQRKP-   93 (179)
T ss_pred             ccccc----------------------------------------------------------ccccc-----cccccc-
Confidence            10000                                                          00000     000000 


Q ss_pred             ccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          430 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       430 ~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                        .....++. ....+....|..+|..|||++|.||.|+|    .+++|++|||+.||+|..+|+..+++|+++||+.+.
T Consensus        94 --~~~~~~~~-~~~~~~~~~l~~~l~~Lp~~~r~i~~l~~----~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~  166 (179)
T PRK12543         94 --VSIDFSED-VLSKESNQELIELIHKLPYKLRQVIILRY----LHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ  166 (179)
T ss_pred             --ccccChHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence              00112333 45556677899999999999999999998    589999999999999999999999999999998665


Q ss_pred             h
Q 010092          510 V  510 (518)
Q Consensus       510 ~  510 (518)
                      .
T Consensus       167 ~  167 (179)
T PRK12543        167 I  167 (179)
T ss_pred             H
Confidence            4

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=99.79  E-value=6e-18  Score=162.15  Aligned_cols=167  Identities=13%  Similarity=0.101  Sum_probs=133.2

Q ss_pred             HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (518)
Q Consensus       263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI  342 (518)
                      ..+.....|+..+++.|+..|.+.|++++.++.   ++..+++|++||+|+.+|++.++|++..  .|.+|++..+++.+
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            345567789999999999999999999999998   7888999999999999999999999753  69999999999999


Q ss_pred             HHHHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCc
Q 010092          343 IRSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVT  421 (518)
Q Consensus       343 ~raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~  421 (518)
                      .+++++ .+....                                                          +++.     
T Consensus        91 ~d~~Rk~~~~~~~----------------------------------------------------------~~~~-----  107 (192)
T PRK09643         91 LDRLRRAKARPTV----------------------------------------------------------PLDD-----  107 (192)
T ss_pred             HHHHHccccCCCC----------------------------------------------------------Cccc-----
Confidence            998883 211000                                                          0000     


Q ss_pred             hhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          422 QEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       422 ~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      ..    ....    .+++.....+....|..+|+.||++++.||.|+|    .+++|++|||+.||+|..+|+..+.+|+
T Consensus       108 ~~----~~~~----~~~~~~~~~e~~~~l~~~l~~Lp~~~r~i~~l~~----~~g~s~~EIA~~lg~s~~tV~~rl~rar  175 (192)
T PRK09643        108 VY----PVAQ----LERDPTARVETALAVQRALMRLPVEQRAALVAVD----MQGYSVADAARMLGVAEGTVKSRCARGR  175 (192)
T ss_pred             cc----cccC----CcccHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            00    0000    1122233445567799999999999999999998    5899999999999999999999999999


Q ss_pred             HHHhCcch
Q 010092          502 MKLKHPTR  509 (518)
Q Consensus       502 kKLR~~~~  509 (518)
                      ++||....
T Consensus       176 ~~Lr~~l~  183 (192)
T PRK09643        176 ARLAELLG  183 (192)
T ss_pred             HHHHHHHH
Confidence            99997654

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=99.79  E-value=5e-18  Score=160.79  Aligned_cols=168  Identities=15%  Similarity=0.112  Sum_probs=129.2

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      .+.....||..|++.|+..|.+.|+.++.++..  +...+++|++||+|+.||+..+.|++.  ..|.+|++..+++.+.
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            356778899999999999999999999988652  346799999999999999999999974  3699999999999999


Q ss_pred             HHHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092          344 RSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ  422 (518)
Q Consensus       344 raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~  422 (518)
                      +++++ .+..  +.+                                                      .+++       
T Consensus        87 d~~Rk~~~~~--~~~------------------------------------------------------~~~~-------  103 (181)
T PRK12536         87 DFLRSRARRE--ALH------------------------------------------------------DPLD-------  103 (181)
T ss_pred             HHHHHHhccc--ccc------------------------------------------------------CCcc-------
Confidence            88873 1110  000                                                      0000       


Q ss_pred             hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                       +..+...+. .  ++    ..+....+..+|..||++++.||.++|    .+++|++|||+.||+|.++|+..+++|++
T Consensus       104 -~~~~~~~~~-~--~~----~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~l~is~~tV~~~l~rar~  171 (181)
T PRK12536        104 -DESELFATS-D--DE----AAEARRDLGKLLEQLPDRQRLPIVHVK----LEGLSVAETAQLTGLSESAVKVGIHRGLK  171 (181)
T ss_pred             -chhhhcCCC-C--cc----hHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence             000000000 0  11    123445689999999999999999998    58999999999999999999999999999


Q ss_pred             HHhCcchh
Q 010092          503 KLKHPTRV  510 (518)
Q Consensus       503 KLR~~~~~  510 (518)
                      +||+.+..
T Consensus       172 ~Lr~~l~~  179 (181)
T PRK12536        172 ALAAKIRG  179 (181)
T ss_pred             HHHHHhcC
Confidence            99986543

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=7.6e-18  Score=159.49  Aligned_cols=167  Identities=16%  Similarity=0.187  Sum_probs=127.6

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccC-CCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFA-NGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~-~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      +.....||..|++.|+..|.+.|+.+|.++..+.+ +..+++|++||+++.+|...+.|+..  ..|.+|++..+++.+.
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            44567799999999999999999999999874211 34689999999999999999999864  3699999999999998


Q ss_pred             HHHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092          344 RSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ  422 (518)
Q Consensus       344 raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~  422 (518)
                      +++++ .+...+                                                          +++       
T Consensus        91 d~~Rr~~~~~~~----------------------------------------------------------~~~-------  105 (184)
T PRK12512         91 DALRRRGRRVFV----------------------------------------------------------DID-------  105 (184)
T ss_pred             HHHHhhcccccC----------------------------------------------------------Cch-------
Confidence            88872 111000                                                          000       


Q ss_pred             hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                       ++.+.+.+..   ..    .......+..+|+.||+++++||.++|    .+++|++|||+.||+|..+|+..+++|++
T Consensus       106 -~~~~~~~~~~---~~----~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~l~is~~tV~~~l~ra~~  173 (184)
T PRK12512        106 -DFAETLPAEP---AT----ETLPAGDVGRHLETLPPRQRDVVQSIS----VEGASIKETAAKLSMSEGAVRVALHRGLA  173 (184)
T ss_pred             -hccccccccc---hh----hHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence             0000000100   00    112345688899999999999999998    58999999999999999999999999999


Q ss_pred             HHhCcchh
Q 010092          503 KLKHPTRV  510 (518)
Q Consensus       503 KLR~~~~~  510 (518)
                      +||...++
T Consensus       174 ~Lr~~l~~  181 (184)
T PRK12512        174 ALAAKFRS  181 (184)
T ss_pred             HHHHHhhc
Confidence            99976654

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=99.78  E-value=3.5e-18  Score=160.39  Aligned_cols=167  Identities=16%  Similarity=0.126  Sum_probs=129.1

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      .+....+||..|++.|+..|.+.|+.+|.+|.   ++..+++|++||+|+++|++++.|++.  .+|.+|++..+++.+.
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            34566789999999999999999999999998   778889999999999999999999864  3799999999999999


Q ss_pred             HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092          344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE  423 (518)
Q Consensus       344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e  423 (518)
                      ++++..+.. .+                     ..         +.                       ..+        
T Consensus        83 d~~r~~~~~-~~---------------------~~---------~~-----------------------~~~--------  100 (176)
T PRK09638         83 DHLRKQKRE-KL---------------------RL---------QR-----------------------AKE--------  100 (176)
T ss_pred             HHHHHhccc-cc---------------------hh---------hh-----------------------ccc--------
Confidence            888731100 00                     00         00                       000        


Q ss_pred             hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                          ...+..  .. +..........|..+|..||++++.||.++|    .+++|++|||+.||+|..+|++.+.||+++
T Consensus       101 ----~~~~~~--~~-~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~l~is~~~V~~~l~ra~~~  169 (176)
T PRK09638        101 ----ETLRKE--KW-EAAIKGAEWSEMLDALSKLDPEFRAPVILKH----YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQ  169 (176)
T ss_pred             ----ccCCcc--ch-HHHHHhhhHHHHHHHHHcCCHHHhheeeehh----hcCCCHHHHHHHHCCChhHHHHHHHHHHHH
Confidence                000000  00 1112223445688999999999999999988    579999999999999999999999999999


Q ss_pred             HhCcc
Q 010092          504 LKHPT  508 (518)
Q Consensus       504 LR~~~  508 (518)
                      ||+..
T Consensus       170 l~~~l  174 (176)
T PRK09638        170 LRKEW  174 (176)
T ss_pred             HHHHh
Confidence            99743

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=9.4e-18  Score=157.51  Aligned_cols=164  Identities=12%  Similarity=0.013  Sum_probs=125.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCc
Q 010092          274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFT  352 (518)
Q Consensus       274 ~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~i  352 (518)
                      ..++.|+..|.++|+.+|.+|.   ++..+++|++||+++.||++.+.|++..  +|.+|++..+++.+.++++ +.+..
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            4689999999999999999998   7889999999999999999999999754  7999999999999999888 32210


Q ss_pred             cccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccC
Q 010092          353 RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV  432 (518)
Q Consensus       353 RlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~  432 (518)
                      ..+....                                                       +      .+...+.....
T Consensus        78 ~~~~~~~-------------------------------------------------------~------~~~~~~~~~~~   96 (173)
T PRK12522         78 DRILDLF-------------------------------------------------------H------KEDGGEIEFAD   96 (173)
T ss_pred             ccccccc-------------------------------------------------------c------hhhhhhhcccc
Confidence            0000000                                                       0      00000000000


Q ss_pred             CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      ....++. ....+..+.|..+|..||++++.||.|+|    .+++|++|||+.||+|..+|+..+.||+++||+..
T Consensus        97 ~~~~~~~-~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l  167 (173)
T PRK12522         97 DVNISEE-FIQKVEAEMIREVIQLLNEKYKTVLVLYY----YEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHL  167 (173)
T ss_pred             CCCChHH-HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence            1111222 34455677899999999999999999999    68999999999999999999999999999999654

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=99.77  E-value=9.1e-18  Score=158.91  Aligned_cols=163  Identities=15%  Similarity=0.060  Sum_probs=129.3

Q ss_pred             HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhc
Q 010092          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS  349 (518)
Q Consensus       270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~s  349 (518)
                      ..+..|++.|+..|.+.|+.+|.++.   ++..+++|++||+|+.||++..+|+..  ..|.+|++..+++.+.+++++.
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            45689999999999999999999998   778899999999999999999999864  3699999999999998888731


Q ss_pred             -CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcc
Q 010092          350 -SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING  428 (518)
Q Consensus       350 -r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~  428 (518)
                       +....+                                                          .+.        ..+.
T Consensus        87 ~~~~~~~----------------------------------------------------------~~~--------~~~~  100 (179)
T PRK09415         87 HNKKVIV----------------------------------------------------------TED--------IFTY  100 (179)
T ss_pred             ccccccc----------------------------------------------------------ccc--------cccc
Confidence             100000                                                          000        0000


Q ss_pred             cccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          429 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       429 l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      .. ....++++.....+....|..+|+.||+++++||.++|    .+++|++|||+.||+|..+|++.+.||+++||...
T Consensus       101 ~~-~~~~~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l  175 (179)
T PRK09415        101 ME-SQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFY----YEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL  175 (179)
T ss_pred             cc-ccccCcHHHHHHHHHHHHHHHHHHhCCHHHhhHhHhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            00 01123445555566777899999999999999999998    58999999999999999999999999999999754

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

Probab=99.77  E-value=9.9e-18  Score=156.61  Aligned_cols=162  Identities=25%  Similarity=0.226  Sum_probs=127.5

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      .+..+..||..|++.|+..|.+.+++++.++.   ++..+++|++||+++.+|+..+.|++..  .|.+|++..+++.+.
T Consensus         6 l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~~l~~~~~~~~~~~~~--~~~~wl~~i~~n~~~   80 (169)
T TIGR02954         6 LVKKAKRGNKPAFESLIKKHKEKLYKTAFIYV---KNEHDALDVIQETVYKAYLSIDKLKHPK--YFNTWLTRILINECI   80 (169)
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHHhccCcc--ccHHHHHHHHHHHHH
Confidence            35567789999999999999999999999999   7888999999999999999999999753  699999999999999


Q ss_pred             HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092          344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE  423 (518)
Q Consensus       344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e  423 (518)
                      ++++.... ..|                                                          ++....    
T Consensus        81 d~~R~~~~-~~~----------------------------------------------------------~~~~~~----   97 (169)
T TIGR02954        81 DLLKKKKK-VIP----------------------------------------------------------FDPNTS----   97 (169)
T ss_pred             HHHHhcCC-cCc----------------------------------------------------------cccccc----
Confidence            88873110 000                                                          000000    


Q ss_pred             hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                           ..+.   .++.  + ......|..+|+.||+++++||.++|    .+++|++|||+.||+|..+|+..+.||+++
T Consensus        98 -----~~~~---~~~~--~-~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~  162 (169)
T TIGR02954        98 -----IEKG---ECET--H-ADSRLDLYKAIDTLNDKYQTAIILRY----YHDLTIKEIAEVMNKPEGTVKTYLHRALKK  162 (169)
T ss_pred             -----cccc---hhhh--c-hHHHHHHHHHHHhCCHHHhHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                 0000   0000  0 01123788999999999999999998    589999999999999999999999999999


Q ss_pred             HhCcc
Q 010092          504 LKHPT  508 (518)
Q Consensus       504 LR~~~  508 (518)
                      ||..+
T Consensus       163 Lr~~l  167 (169)
T TIGR02954       163 LKKRL  167 (169)
T ss_pred             HHHHh
Confidence            99754

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.

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=99.77  E-value=1.5e-17  Score=157.91  Aligned_cols=168  Identities=16%  Similarity=0.181  Sum_probs=127.7

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhcc-CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDF-ANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~-~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      +.+...||..|++.|+..|.+.|+.+|.+...++ ++..+.+|++||+++.+|++.+.|++..  .|.+|++..+++.+.
T Consensus        12 ~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~~~~~~~~~~--~f~~wl~~i~~n~~~   89 (184)
T PRK12539         12 MLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTPWVYAIARYKLI   89 (184)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHHHHhhcCCCC--ChHHHHHHHHHHHHH
Confidence            4567789999999999999999999987533211 5778999999999999999999999753  699999999999998


Q ss_pred             HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092          344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE  423 (518)
Q Consensus       344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e  423 (518)
                      ++++.......+                                                        .+++.     . 
T Consensus        90 d~~R~~~~~~~~--------------------------------------------------------~~~~~-----~-  107 (184)
T PRK12539         90 DHLRRTRASLAD--------------------------------------------------------VPIDD-----A-  107 (184)
T ss_pred             HHHHHHhccccc--------------------------------------------------------cChhh-----h-
Confidence            888721100000                                                        00000     0 


Q ss_pred             hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                         +...      +.+.....+....|..+|..||++++.||.|+|    .+++|++|||+.||+|..+|++.+++|+++
T Consensus       108 ---~~~~------~~~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~  174 (184)
T PRK12539        108 ---DELV------AHDDHAAVESTLDLGRLLARLPEKMRLAIQAVK----LEGLSVAEAATRSGMSESAVKVSVHRGLKA  174 (184)
T ss_pred             ---cccc------CCcHHhhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCcHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence               0000      001112223456799999999999999999998    589999999999999999999999999999


Q ss_pred             HhCcch
Q 010092          504 LKHPTR  509 (518)
Q Consensus       504 LR~~~~  509 (518)
                      ||+...
T Consensus       175 Lr~~l~  180 (184)
T PRK12539        175 LAALIG  180 (184)
T ss_pred             HHHHHh
Confidence            997543

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=99.77  E-value=1.2e-17  Score=156.47  Aligned_cols=163  Identities=15%  Similarity=0.166  Sum_probs=126.2

Q ss_pred             HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhc
Q 010092          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS  349 (518)
Q Consensus       270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~s  349 (518)
                      .++..+++.|+..|.+.|+.+|.++.   ++..+++|++||.|+.+|+..++|++.. ..|.+|++..+++.+.+++++.
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   6778999999999999999999997533 3699999999999999888731


Q ss_pred             CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhccc
Q 010092          350 SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGI  429 (518)
Q Consensus       350 r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l  429 (518)
                      +..  +..  .                                                     .+        +... .
T Consensus        81 ~~~--~~~--~-----------------------------------------------------~~--------~~~~-~   94 (173)
T PRK09645         81 RAR--PVE--G-----------------------------------------------------GD--------DVLG-V   94 (173)
T ss_pred             ccc--ccc--c-----------------------------------------------------cc--------cccc-C
Confidence            100  000  0                                                     00        0000 0


Q ss_pred             ccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          430 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       430 ~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                      .+   ..+++..........|..+|+.||+++++||.|+|    .+++|++|||+.||+|..+|+..++||+++||+.+.
T Consensus        95 ~~---~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~L~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~  167 (173)
T PRK09645         95 PE---QSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSY----YRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQ  167 (173)
T ss_pred             CC---CCCchHHHHHhHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence            00   01122233334455789999999999999999999    589999999999999999999999999999998654

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=99.77  E-value=1e-17  Score=159.68  Aligned_cols=168  Identities=16%  Similarity=0.118  Sum_probs=128.5

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r  344 (518)
                      +.++..|+..|++.|+..|.+.++.++. +.   ++..+++|++||.|+.+|+..++|++.  ..|.+|++..+++.+.+
T Consensus        15 ~~~~~~gd~~af~~l~~~~~~~l~~~~~-~~---~~~~~AeDivQe~flkl~~~~~~~~~~--~~~~~Wl~~Iarn~~~d   88 (185)
T PRK09649         15 ALSAAKGNGRALEAFIKATQQDVWRFVA-YL---SDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAIARHVVAD   88 (185)
T ss_pred             HHHHHccCHHHHHHHHHHHHHHHHHHHH-Hh---CCHHHHHHHHHHHHHHHHHhccccCcc--chHHHHHHHHHHHHHHH
Confidence            5567789999999999999999999995 55   677899999999999999999999864  36999999999999998


Q ss_pred             HHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092          345 SMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE  423 (518)
Q Consensus       345 aI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e  423 (518)
                      ++++ .+..+..                                                          .+.    ..+
T Consensus        89 ~~Rk~~~~~~~~----------------------------------------------------------~~~----~~~  106 (185)
T PRK09649         89 HIRHVRSRPRTT----------------------------------------------------------RGA----RPE  106 (185)
T ss_pred             HHHHhccccccc----------------------------------------------------------ccc----chh
Confidence            8872 1100000                                                          000    000


Q ss_pred             hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                          ...+     ++......+....|..+|+.||+++|.||.|+|    .+++|++|||+.||+|.++|++.+.||+++
T Consensus       107 ----~~~~-----~~~~~~~~e~~~~l~~~l~~Lp~~~r~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~  173 (185)
T PRK09649        107 ----HLID-----GDRHARGFEDLVEVTTMIADLTTDQREALLLTQ----LLGLSYADAAAVCGCPVGTIRSRVARARDA  173 (185)
T ss_pred             ----hccC-----hhhhhhhHHHHHHHHHHHHhCCHHHhHHhhhHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence                0000     000011112234588899999999999999999    589999999999999999999999999999


Q ss_pred             HhCcchhhhh
Q 010092          504 LKHPTRVDYL  513 (518)
Q Consensus       504 LR~~~~~~~L  513 (518)
                      ||+....+.|
T Consensus       174 Lr~~~~~~~~  183 (185)
T PRK09649        174 LLADAEPDDL  183 (185)
T ss_pred             HHhhCCcccc
Confidence            9987665544

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

Probab=99.77  E-value=1.3e-17  Score=153.61  Aligned_cols=157  Identities=14%  Similarity=0.194  Sum_probs=121.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCc
Q 010092          274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFT  352 (518)
Q Consensus       274 ~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~i  352 (518)
                      +|++.++..|.+.|+.+|+++.   ++..+.+|++||+++.+|+++++|++..  .|.+|++..+++.+.+++++ .+..
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  69999999999999998883 2110


Q ss_pred             cccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccC
Q 010092          353 RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV  432 (518)
Q Consensus       353 RlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~  432 (518)
                       .+   ..                           ++.                                   .+.+.+.
T Consensus        76 -~~---~~---------------------------~~~-----------------------------------~~~~~~~   89 (159)
T TIGR02989        76 -LV---FD---------------------------DEL-----------------------------------LEALAAE   89 (159)
T ss_pred             -cc---cC---------------------------HHH-----------------------------------HHHHHhh
Confidence             00   00                           000                                   0000000


Q ss_pred             CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                        .++.+..........|..+|+.||++++.||.++|    .+++|.+|||+.||+|..+|+...+||+++||..
T Consensus        90 --~~~~~~~~~~~~~~~l~~~i~~L~~~~r~v~~l~~----~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~~  158 (159)
T TIGR02989        90 --AEATEADRSEDELQALEGCLEKLPERQRELLQLRY----QRGVSLTALAEQLGRTVNAVYKALSRLRVRLRDC  158 (159)
T ss_pred             --cccchHhhHHHHHHHHHHHHHHCCHHHHHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhc
Confidence              00111122233456789999999999999999988    5899999999999999999999999999999974

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).

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

Probab=99.77  E-value=1.4e-17  Score=166.06  Aligned_cols=178  Identities=16%  Similarity=0.155  Sum_probs=136.0

Q ss_pred             HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHH-------HHHhcCCCCCCccchHHH
Q 010092          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLIT-------AIDRFEPKRRFRLSTYGL  335 (518)
Q Consensus       263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLir-------AvekFDp~rG~kFSTYA~  335 (518)
                      ..+..+..||..|+..|+..|.+.|+.++.++.   ++..+++|++||.|+.+|.       ++.+|++.  ..|.||++
T Consensus        28 ~Li~~~~~gd~~Af~~L~~~y~~~l~~~~~~~~---~~~~dAEDivQEvFlkl~~~~~~~~~~~~~~~~~--~~~~tWL~  102 (244)
T TIGR03001        28 YLACACAQGEPAALAALERHVLSKVPARLAGLR---PPTAFVDEVLQRLRQRLLVPRAERPPRIAEYSGR--GPLLSWVR  102 (244)
T ss_pred             HHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhccchhhhhhccCCC--CchHhHHH
Confidence            455567789999999999999999999999997   6788999999999999994       78889864  36999999


Q ss_pred             HHHHHHHHHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCcccc
Q 010092          336 FWIRHAIIRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSL  414 (518)
Q Consensus       336 ~wIRqaI~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SL  414 (518)
                      ..+++.+.++++ +.+...+                                                            
T Consensus       103 ~Ia~N~~id~lRk~~r~~~~------------------------------------------------------------  122 (244)
T TIGR03001       103 IVATRIALELQAQERRHSPV------------------------------------------------------------  122 (244)
T ss_pred             HHHHHHHHHHHHHhcccCcc------------------------------------------------------------
Confidence            999999988887 2110000                                                            


Q ss_pred             CCCcCCchhhhhcccccCCCCcchhhhHH----HHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCH
Q 010092          415 HSRHGVTQEEFINGITDVDGVENENQRQP----ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISR  490 (518)
Q Consensus       415 D~~~~~~~eel~~~l~d~~~~~~ee~~~~----~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISr  490 (518)
                      +.     .+...+ ..+. ..++++....    .+....|..+|+.||+++|+||.|+|    .+++|++|||++||||.
T Consensus       123 ~~-----~~~~~~-~~~~-~~~~e~~~~~~e~~~e~~~~l~~aL~~Lp~~~R~v~~L~~----~eg~S~~EIA~~Lgis~  191 (244)
T TIGR03001       123 EE-----PTELAA-LPAP-GSDPELDLLRERYRQDFRQALREALAALSERERHLLRLHF----VDGLSMDRIGAMYQVHR  191 (244)
T ss_pred             cc-----cccccc-ccCC-CCCHHHHHHHHhhHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCH
Confidence            00     000000 0001 1122322221    34567799999999999999999999    68999999999999999


Q ss_pred             HHHHHHHHHHHHHHhCcchhhhhhhh
Q 010092          491 EMVRKHEVKGLMKLKHPTRVDYLRQH  516 (518)
Q Consensus       491 erVRqie~rALkKLR~~~~~~~L~~y  516 (518)
                      ++|+..+.+|+++||+....+-...|
T Consensus       192 ~TVk~rl~RAr~~Lr~~l~~~~~~~~  217 (244)
T TIGR03001       192 STVSRWVAQARERLLERTRRRLAERL  217 (244)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999998776655544

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.

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=99.76  E-value=1e-17  Score=157.03  Aligned_cols=168  Identities=13%  Similarity=0.061  Sum_probs=126.6

Q ss_pred             HHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHH
Q 010092          266 KKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS  345 (518)
Q Consensus       266 ~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ra  345 (518)
                      ..+..||..|++.|+..|.+.|+.++.++.   + ..+++|++||+|+.+|+..+.|++.  ..|.+|++..+++.+.++
T Consensus         3 ~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~-~~~aeDivQe~~l~l~~~~~~~~~~--~~~~~wl~~ia~n~~~d~   76 (175)
T PRK12518          3 LRCQRGDRQSFRQLYRRYQQKVRSTLYQLC---G-RELLDDLVQEVFLRVWKGLPKLRNP--AYFSTWLYRITWNVATDA   76 (175)
T ss_pred             hHHHcCCHHHHHHHHHHHHHHHHHHHHHHc---C-HhHHHHHHHHHHHHHHHhHHhhCCc--ccHHHHHHHHHHHHHHHH
Confidence            446789999999999999999999999976   3 4689999999999999999999974  369999999999998888


Q ss_pred             HHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhh
Q 010092          346 MTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEF  425 (518)
Q Consensus       346 I~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel  425 (518)
                      +++....  +...                                                        +.     ... 
T Consensus        77 ~R~~~~~--~~~~--------------------------------------------------------~~-----~~~-   92 (175)
T PRK12518         77 RRQFAQR--PSRI--------------------------------------------------------QD-----DSL-   92 (175)
T ss_pred             HHHhhcc--ccch--------------------------------------------------------hc-----ccc-
Confidence            7621100  0000                                                        00     000 


Q ss_pred             hcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092          426 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  505 (518)
Q Consensus       426 ~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR  505 (518)
                      ... ...  ..+++..........+..+|+.||++++.||.|+|    .+++|++|||+.||+|..+|++.+.||+++||
T Consensus        93 ~~~-~~~--~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~  165 (175)
T PRK12518         93 NDQ-PSR--PSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHD----LEDLPQKEIAEILNIPVGTVKSRLFYARRQLR  165 (175)
T ss_pred             ccc-ccC--CCCcHHHHHHHHHHHHHHHHHhCCHHHeeeeeehH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            000 000  01111122223445688999999999999999998    58999999999999999999999999999999


Q ss_pred             Ccchh
Q 010092          506 HPTRV  510 (518)
Q Consensus       506 ~~~~~  510 (518)
                      .....
T Consensus       166 ~~l~~  170 (175)
T PRK12518        166 KFLQQ  170 (175)
T ss_pred             HHHHh
Confidence            86543

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

Probab=99.76  E-value=1.9e-17  Score=156.32  Aligned_cols=167  Identities=15%  Similarity=0.107  Sum_probs=120.9

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCC-----CHHHHHHHHHHHHHH-HHHhcCCCCCCccchHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGP-----RFQDLCQAGVKGLIT-AIDRFEPKRRFRLSTYGLFWI  338 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~-----~~eDLIQEG~IGLir-AvekFDp~rG~kFSTYA~~wI  338 (518)
                      +..+..||..|+..|+..|.+.++.+|.+|.   ++..     +++|++||+|+.+|+ ...+|++.  ..|.+|++.++
T Consensus         8 i~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~~~--~~~~~wl~~i~   82 (183)
T TIGR02999         8 LQQWQNGDAAARDQLFPQLYQELRRIARRQL---RRERSGQTLQTTALVHEAYLRLSDQDEQKWDDR--AHFFAAAAKAM   82 (183)
T ss_pred             HHHHHcCCHHHHHHHHHHHHHHHHHHHHHHh---hcccccccchHHHHHHHHHHHHhhcccCCCCch--HHHHHHHHHHH
Confidence            4556789999999999999999999999998   5555     899999999999998 78888754  36999999999


Q ss_pred             HHHHHHHHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCC
Q 010092          339 RHAIIRSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSR  417 (518)
Q Consensus       339 RqaI~raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~  417 (518)
                      ++.+.+.+++ .+..+...                                                    .....++  
T Consensus        83 ~n~~~d~~R~~~~~~~~~~----------------------------------------------------~~~~~~~--  108 (183)
T TIGR02999        83 RRILVDHARRRRAQKRGGG----------------------------------------------------AVRVPLD--  108 (183)
T ss_pred             HHHHHHHHHHHHHHhccCC----------------------------------------------------ccccccc--
Confidence            9999888762 11000000                                                    0000000  


Q ss_pred             cCCchhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 010092          418 HGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHE  497 (518)
Q Consensus       418 ~~~~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie  497 (518)
                                ......  .++. .+.......+...|+.||+++|.||.|+|    .+++|++|||+.||+|..+|+..+
T Consensus       109 ----------~~~~~~--~~~~-~~~~~~l~~~~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tVk~~l  171 (183)
T TIGR02999       109 ----------EVLPDA--EADL-DEELLDLDDALDKLAQVDPRQAEVVELRF----FAGLTVEEIAELLGVSVRTVERDW  171 (183)
T ss_pred             ----------cccCCC--CccH-HHHHHHHHHHHHHhhcCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHH
Confidence                      000000  0111 11111122334456779999999999999    589999999999999999999999


Q ss_pred             HHHHHHHhCc
Q 010092          498 VKGLMKLKHP  507 (518)
Q Consensus       498 ~rALkKLR~~  507 (518)
                      .||+++||+.
T Consensus       172 ~Rar~~Lr~~  181 (183)
T TIGR02999       172 RFARAWLADE  181 (183)
T ss_pred             HHHHHHHHHH
Confidence            9999999964

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=1.8e-17  Score=158.09  Aligned_cols=180  Identities=14%  Similarity=0.143  Sum_probs=130.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcc
Q 010092          275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTR  353 (518)
Q Consensus       275 A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iR  353 (518)
                      +++.|+..|.+.|+.+|.++.   ++..+++|++||.|+.+|+.+++|+...  .|.+|++..+++.+.++++ +.+...
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            689999999999999999998   7788999999999999999999998543  6999999999999999888 322111


Q ss_pred             ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCC
Q 010092          354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD  433 (518)
Q Consensus       354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~  433 (518)
                      .+.....                       .....++                       ++...  +.+.......+ .
T Consensus        78 ~~~~~~~-----------------------~~~~~~~-----------------------~~~~~--~~~~~~~~~~~-~  108 (191)
T PRK12520         78 LSLDDAD-----------------------EQSDDDL-----------------------FDALF--AADGHYREPPS-D  108 (191)
T ss_pred             ccccccc-----------------------cchhhhh-----------------------hhhhc--ccccccccCcc-c
Confidence            1100000                       0000000                       00000  00000000111 1


Q ss_pred             CCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          434 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       434 ~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      ..++++.....+....|..+|..||+++|.||.|+|    .+++|++|||+.||+|.++|++.+.||+++||+......
T Consensus       109 ~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~  183 (191)
T PRK12520        109 WGDPDAALSRREFFEVLQACVDRLPPRTGRVFMMRE----WLELETEEICQELQITATNAWVLLYRARMRLRECLDLHW  183 (191)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            123555555666677899999999999999999999    589999999999999999999999999999998766543

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

Probab=99.75  E-value=6.9e-17  Score=153.27  Aligned_cols=170  Identities=18%  Similarity=0.148  Sum_probs=132.5

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r  344 (518)
                      +.....++..+++.++..|.+.++.++.++.   ++..+.+||+||+|+.+|+++..| .. +..|.||++..+++.+.+
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            3445688999999999999999999999999   666699999999999999999999 33 347999999999999999


Q ss_pred             HHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092          345 SMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE  423 (518)
Q Consensus       345 aI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e  423 (518)
                      .++ +.+.... .  .                                                              ..
T Consensus        81 ~~R~~~r~~~~-~--~--------------------------------------------------------------~~   95 (182)
T COG1595          81 RLRKRKRRRAR-V--E--------------------------------------------------------------EA   95 (182)
T ss_pred             HHHHhcccccc-c--c--------------------------------------------------------------cc
Confidence            988 3221110 0  0                                                              00


Q ss_pred             hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                      +......+...... +.....+....|..+|..||+++|.+|.|+|    .+++|++|||+.||||.++|+..+++|+.+
T Consensus        96 ~~~~~~~~~~~~~~-~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~----~~gls~~EIA~~l~i~~~tVks~l~ra~~~  170 (182)
T COG1595          96 DLLPEEADPAPDLA-ELLLAEEELERLRRALARLPPRQREAFLLRY----LEGLSYEEIAEILGISVGTVKSRLHRARKK  170 (182)
T ss_pred             cccccccCcccccc-hHHHHHHHHHHHHHHHHhCCHHHhHHhhhHh----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            00000000000000 2345567778899999999999999999999    689999999999999999999999999999


Q ss_pred             HhCcch
Q 010092          504 LKHPTR  509 (518)
Q Consensus       504 LR~~~~  509 (518)
                      |+....
T Consensus       171 l~~~l~  176 (182)
T COG1595         171 LREQLE  176 (182)
T ss_pred             HHHHHh
Confidence            997654

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=99.75  E-value=4.7e-17  Score=157.83  Aligned_cols=164  Identities=17%  Similarity=0.200  Sum_probs=130.5

Q ss_pred             HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhc
Q 010092          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS  349 (518)
Q Consensus       270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~s  349 (518)
                      .|+..+++.|+..|.+.++.++.++.   ++..+.+|++||+|+.+|+...+|++  + .|.+|++..+++.+.+++++.
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            47899999999999999999999999   77789999999999999999999985  3 699999999999999988832


Q ss_pred             CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhccc
Q 010092          350 SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGI  429 (518)
Q Consensus       350 r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l  429 (518)
                      ...+..    .                                                     ++       +++ +..
T Consensus        98 ~~~~~~----~-----------------------------------------------------~~-------~~~-~~~  112 (203)
T PRK09647         98 ARIRME----A-----------------------------------------------------LP-------EDY-DRV  112 (203)
T ss_pred             ccCccc----c-----------------------------------------------------cc-------ccc-ccc
Confidence            111000    0                                                     00       000 000


Q ss_pred             ccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          430 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       430 ~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                      . ....+++.......+...|..+|..||++++.||.|+|    .+++|++|||+.||+|..+|++.+.||+++||+...
T Consensus       113 ~-~~~~~~~~~~~~~~~~~~l~~~L~~L~~~~r~v~~L~~----~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~  187 (203)
T PRK09647        113 P-GDEPNPEQIYHDARLDPDLQAALDSLPPEFRAAVVLCD----IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALA  187 (203)
T ss_pred             C-CCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            1 11223444455666777899999999999999999998    589999999999999999999999999999997554

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=5.5e-17  Score=153.53  Aligned_cols=166  Identities=14%  Similarity=0.070  Sum_probs=126.8

Q ss_pred             HHHHcHHHHHHHHHHHHHHHHHHHHHhhhccC--CCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHH
Q 010092          268 CLEVGRAARNKLIKHNLRLVLFVIKKYFQDFA--NGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRS  345 (518)
Q Consensus       268 ~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~--~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~ra  345 (518)
                      ...||..++..|+..|.+.|+.++..+.   +  +..+++|++||.|+.+|+..+.|+......|.||++...++.+.++
T Consensus         7 ~~~~d~~af~~ly~~~~~~l~~~~~~~~---~~~~~~~AeDivQevFl~~~~~~~~~~~~~~~~~~~wL~~ia~n~~~d~   83 (178)
T PRK12529          7 CLSADRDKVATLYRENHAWLRNWLAYRL---RSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVSW   83 (178)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHh---CCCChHHHHHHHHHHHHHHHhcccccccccccCHHHHHHHHHHHHHHHH
Confidence            4578999999999999999999876665   3  3568999999999999999999985444579999999999988877


Q ss_pred             HHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhh
Q 010092          346 MTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEF  425 (518)
Q Consensus       346 I~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel  425 (518)
                      +++.+                     ......                                     +        .+
T Consensus        84 ~Rk~~---------------------~~~~~~-------------------------------------~--------~~   97 (178)
T PRK12529         84 RRRQS---------------------LELAWL-------------------------------------E--------AL   97 (178)
T ss_pred             HHHHH---------------------HHhhhh-------------------------------------h--------Hh
Confidence            66210                     000000                                     0        00


Q ss_pred             hcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092          426 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  505 (518)
Q Consensus       426 ~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR  505 (518)
                      .. .......++++.....+....|..+|..||+++|.||.|+|    .+++|++|||+.||+|.++|+..+++|+.+|+
T Consensus        98 ~~-~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~  172 (178)
T PRK12529         98 AT-LPEPLHPSPEQQSVILETLHEIDALLDTLRPRVKQAFLMAT----LDGMKQKDIAQALDIALPTVKKYIHQAYVTCL  172 (178)
T ss_pred             hh-ccCcCCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            00 00011123444444555567899999999999999999998    58999999999999999999999999999998


Q ss_pred             Cc
Q 010092          506 HP  507 (518)
Q Consensus       506 ~~  507 (518)
                      ..
T Consensus       173 ~~  174 (178)
T PRK12529        173 SL  174 (178)
T ss_pred             Hh
Confidence            65

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=99.75  E-value=6.1e-17  Score=158.71  Aligned_cols=169  Identities=14%  Similarity=0.089  Sum_probs=130.0

Q ss_pred             HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-
Q 010092          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-  348 (518)
Q Consensus       270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-  348 (518)
                      .....++..|+..|.+.++.++.++.   ++..+.+|++||.|+.+|+.+++|++.   .|.+|++..+++.+.+++++ 
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            45578999999999999999999998   778899999999999999999999853   48999999999999888772 


Q ss_pred             cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcc
Q 010092          349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING  428 (518)
Q Consensus       349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~  428 (518)
                      .+......  .+                                                    .++      .+...+.
T Consensus        88 ~~~~~~~~--~~----------------------------------------------------~~~------~~~~~~~  107 (216)
T PRK12533         88 ANAHEVAA--PD----------------------------------------------------TLD------DADSLDD  107 (216)
T ss_pred             cccccccc--cc----------------------------------------------------ccc------ccccccc
Confidence            21100000  00                                                    000      0000000


Q ss_pred             cccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          429 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       429 l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      . ++...++++.+...+....|..+|+.||++++.||.|+|    .+++|++|||+.||||.++|+++++||+++||+.+
T Consensus       108 ~-~~~~~~~e~~~~~~e~~~~l~~al~~Lp~~~R~v~~L~y----~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l  182 (216)
T PRK12533        108 W-QPAGEDPLALLLRAEDVRLVNAALAKLPVEYREVLVLRE----LEDMSYREIAAIADVPVGTVMSRLARARRRLAALL  182 (216)
T ss_pred             c-ccCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHhHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            0 111123555566667778899999999999999999999    58999999999999999999999999999999865


Q ss_pred             h
Q 010092          509 R  509 (518)
Q Consensus       509 ~  509 (518)
                      .
T Consensus       183 ~  183 (216)
T PRK12533        183 G  183 (216)
T ss_pred             c
Confidence            4

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

Probab=99.74  E-value=5.7e-17  Score=150.15  Aligned_cols=157  Identities=16%  Similarity=0.147  Sum_probs=124.2

Q ss_pred             HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhc
Q 010092          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS  349 (518)
Q Consensus       270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~s  349 (518)
                      .|+..+++.|+..|.+.|+.+|..+.   ++..+.+|++||+|+.+|++.++|+.  ...|.+|++..+++.+.+++++.
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  34799999999999888877621


Q ss_pred             CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhccc
Q 010092          350 SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGI  429 (518)
Q Consensus       350 r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l  429 (518)
                      ....+                                                          . +.       +.    
T Consensus        77 ~~~~~----------------------------------------------------------~-~~-------~~----   86 (162)
T TIGR02983        77 RLLEL----------------------------------------------------------P-TR-------EL----   86 (162)
T ss_pred             ccccc----------------------------------------------------------c-cc-------cc----
Confidence            10000                                                          0 00       00    


Q ss_pred             ccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          430 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       430 ~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      ....   +++..........|..+|..||++++.||.|+|    .+++|.+|||+.||+|..+|++.+.||+++||+..
T Consensus        87 ~~~~---~~~~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l  158 (162)
T TIGR02983        87 PDAA---APDPAPDVALRAALARALRRLPARQRAVVVLRY----YEDLSEAQVAEALGISVGTVKSRLSRALARLRELL  158 (162)
T ss_pred             Cccc---CCccchhHHHHHHHHHHHHhCCHHHHHHhhhHH----HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            0000   011112334556789999999999999999999    58999999999999999999999999999999754

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.

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=99.74  E-value=9.5e-17  Score=150.70  Aligned_cols=164  Identities=16%  Similarity=0.088  Sum_probs=124.4

Q ss_pred             HHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh
Q 010092          269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV  348 (518)
Q Consensus       269 ~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~  348 (518)
                      ..|+..|+..|+..|.+.|+.++.++.   ++..+++|++||.|+.+|+. ..|...  ..|.+|++..+++.+.+++++
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   77889999999999999986 445543  369999999999999988872


Q ss_pred             cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcc
Q 010092          349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING  428 (518)
Q Consensus       349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~  428 (518)
                      ..                  +  .. ... .         ++                                   .. 
T Consensus        79 ~~------------------~--~~-~~~-~---------~~-----------------------------------~~-   91 (172)
T PRK12523         79 AA------------------L--EQ-AYL-A---------EL-----------------------------------AL-   91 (172)
T ss_pred             HH------------------H--HH-HHH-H---------HH-----------------------------------hh-
Confidence            10                  0  00 000 0         00                                   00 


Q ss_pred             cccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          429 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       429 l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      ........++......+....|..+|+.||++++.||.|+|    .+++|++|||+.||+|..+|++.+.+|+++||..+
T Consensus        92 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~L~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l  167 (172)
T PRK12523         92 VPEAEQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNR----LDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIAL  167 (172)
T ss_pred             cccccCCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence            00000112333333334446799999999999999999998    58999999999999999999999999999998654


Q ss_pred             h
Q 010092          509 R  509 (518)
Q Consensus       509 ~  509 (518)
                      .
T Consensus       168 ~  168 (172)
T PRK12523        168 Y  168 (172)
T ss_pred             c
Confidence            3

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=99.73  E-value=8.1e-17  Score=154.00  Aligned_cols=160  Identities=13%  Similarity=0.083  Sum_probs=123.9

Q ss_pred             HcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC
Q 010092          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS  350 (518)
Q Consensus       271 gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr  350 (518)
                      +|..++..|+..|.+.++.+|.++.   ++..+++|++||.|+.+|+..++|+...  .|.+|++..+++.+.+++++.+
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            5688999999999999999999999   7788999999999999999999998643  5999999999999988887311


Q ss_pred             CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccc
Q 010092          351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT  430 (518)
Q Consensus       351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~  430 (518)
                      ..  +.   .                                                     .+       +.+.+.. 
T Consensus        82 ~~--~~---~-----------------------------------------------------~~-------~~~~~~~-   95 (187)
T PRK12516         82 RE--VQ---D-----------------------------------------------------TD-------GMFTEQL-   95 (187)
T ss_pred             CC--cc---c-----------------------------------------------------cc-------ccccccc-
Confidence            00  00   0                                                     00       0000000 


Q ss_pred             cCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          431 DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       431 d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      +.   .++.  ........|..+|..||++++.||.|+|    .+++|++|||+.||+|.++|+..+.+|+++||+.+..
T Consensus        96 ~~---~~~~--~~~~~~~~l~~~L~~Lp~~~r~i~~L~~----~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~  166 (187)
T PRK12516         96 AV---HPSQ--YGTLDLQDFRAALDQLPDDQREAIILVG----ASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQI  166 (187)
T ss_pred             CC---Ccch--hhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            00   0110  1112235688999999999999999998    5899999999999999999999999999999986654

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

Probab=99.73  E-value=4.6e-17  Score=155.58  Aligned_cols=173  Identities=14%  Similarity=0.076  Sum_probs=127.0

Q ss_pred             HHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-
Q 010092          270 EVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-  348 (518)
Q Consensus       270 ~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-  348 (518)
                      .++..+|+.|+..|.+.|+.+|.++.   ++..+++|++||.|+.+|+....|++.  ..|.+|++..+++.+.+++++ 
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  369999999999999988873 


Q ss_pred             cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcc
Q 010092          349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING  428 (518)
Q Consensus       349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~  428 (518)
                      .+.....   ..                           +++.           ..        .+..    .     ..
T Consensus        82 ~~~~~~~---~~---------------------------~~~~-----------~~--------~~~~----~-----~~  103 (193)
T TIGR02947        82 QRRPQQS---DD---------------------------DDIE-----------DW--------QLAK----A-----AS  103 (193)
T ss_pred             cCCcccc---cc---------------------------hhhh-----------hh--------hhcc----c-----cc
Confidence            2110000   00                           0000           00        0000    0     00


Q ss_pred             cccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          429 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       429 l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      ........++...........|..+|+.||++++.||.|+|    .+++|++|||+.||+|..+|+..+.||+++||+..
T Consensus       104 ~~~~~~~~~e~~~~~~~~~~~l~~~l~~Lp~~~r~i~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l  179 (193)
T TIGR02947       104 HTSNGLRSAELEALDGLPDQDIKDALQGLPEEFRQAVYLAD----VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL  179 (193)
T ss_pred             cccccccchhHHHHhhhhHHHHHHHHHhCCHHHhhheeehh----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            00000011222222334456788999999999999999999    68999999999999999999999999999999765


Q ss_pred             h
Q 010092          509 R  509 (518)
Q Consensus       509 ~  509 (518)
                      .
T Consensus       180 ~  180 (193)
T TIGR02947       180 V  180 (193)
T ss_pred             H
Confidence            4

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.

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=99.73  E-value=2.7e-16  Score=145.76  Aligned_cols=158  Identities=17%  Similarity=0.133  Sum_probs=120.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCc
Q 010092          273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT  352 (518)
Q Consensus       273 ~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~i  352 (518)
                      ..|++.|+..|.+.|+.++.++.   ++..+.+|++||.|+.+|+..+.|++.   .|.+|.+.++++.+.++++...  
T Consensus         3 ~~a~~~l~~~~~~~l~~~~~~~~---~~~~~AeDivQe~flk~~~~~~~~~~~---~~~~wl~~i~~n~~~d~~R~~~--   74 (161)
T PRK12528          3 SATVEGLYSAHHHWLTGWLRRRL---GCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRVLCNHYRRQD--   74 (161)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHc---CCcccHHHHHHHHHHHHHhcccccccc---CHHHHHHHHHHHHHHHHHHHHH--
Confidence            36899999999999999999999   677899999999999999998887642   5899999999999988876210  


Q ss_pred             cccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccC
Q 010092          353 RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV  432 (518)
Q Consensus       353 RlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~  432 (518)
                                    .   ...   ..         +++                                    ....+.
T Consensus        75 --------------~---~~~---~~---------~~~------------------------------------~~~~~~   89 (161)
T PRK12528         75 --------------L---ERA---YL---------EAL------------------------------------AQLPER   89 (161)
T ss_pred             --------------H---HHh---hH---------HHh------------------------------------hccccc
Confidence                          0   000   00         000                                    000000


Q ss_pred             CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      ....++......+....|..+|..||++++.||.|+|    .+++|++|||+.||+|.++|+..+.+|+++||..
T Consensus        90 ~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~----~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~  160 (161)
T PRK12528         90 VAPSEEERAIILETLVELDQLLDGLPPLVKRAFLLAQ----VDGLGYGEIATELGISLATVKRYLNKAAMRCYFA  160 (161)
T ss_pred             cCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhc
Confidence            0111222233334456799999999999999999999    5899999999999999999999999999999854

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=99.73  E-value=6e-17  Score=149.83  Aligned_cols=154  Identities=14%  Similarity=0.090  Sum_probs=119.3

Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCcccccccc
Q 010092          281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRVPFGLE  359 (518)
Q Consensus       281 ~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~iRlP~~~~  359 (518)
                      +.|.+.|+.+|.++.   ++..+++|++||+|+.+|++.++|++.   .|.+|++..+++.+.+++++ .+....     
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            568999999999998   778899999999999999999999863   49999999999999988872 210000     


Q ss_pred             chhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchh
Q 010092          360 STSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN  439 (518)
Q Consensus       360 e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee  439 (518)
                                                                          .++..    ..   .+...  ...++++
T Consensus        71 ----------------------------------------------------~~~~~----~~---~~~~~--~~~~~~~   89 (160)
T PRK09642         71 ----------------------------------------------------LSLCK----ET---EENIK--SSHNIED   89 (160)
T ss_pred             ----------------------------------------------------cccch----hh---hhhcc--CCCChHH
Confidence                                                                00000    00   00000  1112344


Q ss_pred             hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          440 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       440 ~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      .....+....|..+|+.||+.++.||.|+|    .+++|++|||+.||+|..+|++.+.||+++||.....
T Consensus        90 ~~~~~e~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~  156 (160)
T PRK09642         90 LLLTKEQKLLIAQKLRELPENYRDVVLAHY----LEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKE  156 (160)
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhh
Confidence            455556677899999999999999999999    5899999999999999999999999999999986643

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=99.72  E-value=2.1e-16  Score=152.35  Aligned_cols=167  Identities=16%  Similarity=0.127  Sum_probs=126.4

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      .+.+...|+..|++.|+..|.+.++.++. +.   ++..+++|++||.|+.+|+..++|++.  ..|.+|++..+++.+.
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            35567789999999999999999999975 45   577899999999999999999999864  3699999999999999


Q ss_pred             HHHHh-cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092          344 RSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ  422 (518)
Q Consensus       344 raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~  422 (518)
                      +++++ .+..+..    .                                                      +.     .
T Consensus        89 d~~Rk~~~~~~~~----~------------------------------------------------------~~-----~  105 (196)
T PRK12535         89 DNIRHDMARPRKS----A------------------------------------------------------TE-----Y  105 (196)
T ss_pred             HHHHhhccCCCcc----c------------------------------------------------------cc-----c
Confidence            88883 2110000    0                                                      00     0


Q ss_pred             hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                      ...    .+ ....++... .......|..+|+.||+++++||.|+|    .+++|++|||+.||+|..+|++.++||++
T Consensus       106 ~~~----~~-~~~~~~~~~-~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIAe~lgis~~tV~~~l~Rar~  175 (196)
T PRK12535        106 EDA----AA-TTASNETTG-SWSEWIDVRTLIDALPPERREALILTQ----VLGYTYEEAAKIADVRVGTIRSRVARARA  175 (196)
T ss_pred             ccc----cc-ccCCcchhH-HHHHHHHHHHHHHcCCHHHHHHhhhHH----HhCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            000    00 000111111 112234788999999999999999999    68999999999999999999999999999


Q ss_pred             HHhCcch
Q 010092          503 KLKHPTR  509 (518)
Q Consensus       503 KLR~~~~  509 (518)
                      +||+.+.
T Consensus       176 ~Lr~~l~  182 (196)
T PRK12535        176 DLIAATA  182 (196)
T ss_pred             HHHHHhc
Confidence            9997543

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=99.72  E-value=2e-16  Score=146.64  Aligned_cols=158  Identities=15%  Similarity=0.059  Sum_probs=120.5

Q ss_pred             HcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC
Q 010092          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS  350 (518)
Q Consensus       271 gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr  350 (518)
                      ++..|+..++..|.+.|+.++.++.   ++..+++|++||+++.+|+..++|++.   .|.||++..+++.+.+++++.+
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            4578999999999999999999998   778899999999999999999999863   5999999999999998887311


Q ss_pred             CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccc
Q 010092          351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT  430 (518)
Q Consensus       351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~  430 (518)
                      .. ...   .                                                     .        ++.. .  
T Consensus        76 ~~-~~~---~-----------------------------------------------------~--------~~~~-~--   87 (161)
T PRK12541         76 KY-KTT---T-----------------------------------------------------I--------EEFH-L--   87 (161)
T ss_pred             cc-ccc---c-----------------------------------------------------h--------hhhh-c--
Confidence            00 000   0                                                     0        0000 0  


Q ss_pred             cCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          431 DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       431 d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      +.....+++.....+. ..+..+|..||++++.||.|+|    .+++|++|||+.||+|..+|++.++||+++||+.
T Consensus        88 ~~~~~~~~~~~~~~~~-~~~~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~  159 (161)
T PRK12541         88 PNVPSTEHEYFIKHEI-ASWLDSLSSLPLERRNVLLLRD----YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI  159 (161)
T ss_pred             cCCCCcHHHHHHHhHH-HHHHHHHHHCCHHHHHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            0000001122222222 3455789999999999999999    5899999999999999999999999999999964

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=99.72  E-value=2.2e-16  Score=146.61  Aligned_cols=158  Identities=14%  Similarity=0.091  Sum_probs=123.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC-C
Q 010092          273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS-F  351 (518)
Q Consensus       273 ~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr-~  351 (518)
                      ..+++.|+..|.+.|+.+|.++.   ++..+++|++||+|+.+|++  .|+.  +..|.+|++..+++.+.++++..+ .
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            46899999999999999999998   77889999999999999999  6764  347999999999999998887311 0


Q ss_pred             ccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhccccc
Q 010092          352 TRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD  431 (518)
Q Consensus       352 iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d  431 (518)
                      .+...   .                                                             ..+..+ +  
T Consensus        75 ~~~~~---~-------------------------------------------------------------~~~~~~-~--   87 (166)
T PRK09639         75 RARIL---G-------------------------------------------------------------EFQWQE-V--   87 (166)
T ss_pred             ccccc---c-------------------------------------------------------------hhhhhh-c--
Confidence            00000   0                                                             000000 0  


Q ss_pred             CCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          432 VDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       432 ~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                      +....+++.....+....|..+|..||++++.||.++|     +++|++|||+.||+|..+|+..+.+|+++||..+.
T Consensus        88 ~~~~~~e~~~~~~~~~~~l~~~l~~L~~~~r~il~l~~-----~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~  160 (166)
T PRK09639         88 DNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-----SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIYE  160 (166)
T ss_pred             cCCCChHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            11223455555556667789999999999999999999     58999999999999999999999999999998654

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

Probab=99.71  E-value=2.9e-16  Score=161.52  Aligned_cols=182  Identities=17%  Similarity=0.110  Sum_probs=129.2

Q ss_pred             HcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC
Q 010092          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS  350 (518)
Q Consensus       271 gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr  350 (518)
                      ||..|++.|+..|.+.++.+|.++.   ++..+.+|++||.|+.+|+...+|+..  ..|.+|++..+++.+.+++++.+
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  36999999999999999888321


Q ss_pred             CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccc
Q 010092          351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT  430 (518)
Q Consensus       351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~  430 (518)
                      ....+.  ..                    ..                          ..................+.+.
T Consensus        77 ~~~~~~--~~--------------------~~--------------------------~~~~~~~~~~~~~~~~~~~~~~  108 (324)
T TIGR02960        77 RRPRPV--GL--------------------GA--------------------------PSADGTAAASEAAEVTWLEPLP  108 (324)
T ss_pred             CCcCcc--cc--------------------CC--------------------------CCCcccccccccccccccCCCC
Confidence            100000  00                    00                          0000000000000000000000


Q ss_pred             -------cCCCCcchhhhHHHH-HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          431 -------DVDGVENENQRQPAL-LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       431 -------d~~~~~~ee~~~~~~-l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                             .....++++.....+ +...+..+|+.||+++|.||.|+|    .+++|++|||+.||+|..+|+++++||++
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~  184 (324)
T TIGR02960       109 DLTLDLDDPAAADPSVAAGSRESVRLAFVAAIQYLPPRQRAVLLLRD----VLGWRAAETAELLGTSTASVNSALQRARA  184 (324)
T ss_pred             ccccccccCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHhhHhhhHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                   011123444333333 456788999999999999999999    58999999999999999999999999999


Q ss_pred             HHhCcch
Q 010092          503 KLKHPTR  509 (518)
Q Consensus       503 KLR~~~~  509 (518)
                      +||+...
T Consensus       185 ~Lr~~l~  191 (324)
T TIGR02960       185 TLDEVGP  191 (324)
T ss_pred             HHHHhcc
Confidence            9998654

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.

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=99.71  E-value=3e-16  Score=162.76  Aligned_cols=188  Identities=18%  Similarity=0.175  Sum_probs=133.8

Q ss_pred             HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (518)
Q Consensus       263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI  342 (518)
                      +.+.++..||..|++.|+..|.+.|+.+|.++.   ++..+.+|++||.|+.+|+.+++|++.  ..|.+|++...++.+
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            456678899999999999999999999999998   677899999999999999999999853  369999999999999


Q ss_pred             HHHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092          343 IRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ  422 (518)
Q Consensus       343 ~raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~  422 (518)
                      .+++++.+....+.....                        +..++.                   .  .+.   ....
T Consensus        83 ~d~~Rk~~~~~~~~~~~~------------------------~~~~~~-------------------~--~~~---~~~~  114 (339)
T PRK08241         83 LDALEGRARRPLPTDLGA------------------------PAADPV-------------------D--ELV---ERPE  114 (339)
T ss_pred             HHHHHhhccccCccccCC------------------------CcCccc-------------------c--ccc---cccc
Confidence            988873111000000000                        000000                   0  000   0000


Q ss_pred             hhhhcccccC----CCCcchhhhHHHH-HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 010092          423 EEFINGITDV----DGVENENQRQPAL-LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHE  497 (518)
Q Consensus       423 eel~~~l~d~----~~~~~ee~~~~~~-l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie  497 (518)
                      ....+.+.+.    ...++++.....+ +...|..+|+.||+++|.||.|+|    .+++|++|||+.||+|..+|++.+
T Consensus       115 ~~~~~~~~~~~~~~~~~~~e~~~~~~e~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l  190 (339)
T PRK08241        115 VPWLEPYPDALLDPAAADPAARVVARESVRLAFVAALQHLPPRQRAVLILRD----VLGWSAAEVAELLDTSVAAVNSAL  190 (339)
T ss_pred             ccccCCCCcccccccCCChHHHHHHHHHHHHHHHHHHHhCCHHHhhhhhhHH----hhCCCHHHHHHHhCCCHHHHHHHH
Confidence            0001111110    0123444333333 455688999999999999999999    589999999999999999999999


Q ss_pred             HHHHHHHhCc
Q 010092          498 VKGLMKLKHP  507 (518)
Q Consensus       498 ~rALkKLR~~  507 (518)
                      .||+++||+.
T Consensus       191 ~RAr~~Lr~~  200 (339)
T PRK08241        191 QRARATLAER  200 (339)
T ss_pred             HHHHHHHhhc
Confidence            9999999983

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=99.71  E-value=2.1e-16  Score=147.22  Aligned_cols=155  Identities=15%  Similarity=0.113  Sum_probs=123.5

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhc-CCccc
Q 010092          276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS-SFTRV  354 (518)
Q Consensus       276 ~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~s-r~iRl  354 (518)
                      ++.|+..|.+.|+.+|.++.   ++..+++|++||.|+.+|++++.|++.   .|.+|++..+++.+.+++++. +...+
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            67899999999999999998   778899999999999999999999863   599999999999999888731 10000


Q ss_pred             cccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCC
Q 010092          355 PFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG  434 (518)
Q Consensus       355 P~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~  434 (518)
                                                     +.++                                    .+.+..   
T Consensus        77 -------------------------------~~~~------------------------------------~~~~~~---   86 (165)
T PRK09644         77 -------------------------------GTDE------------------------------------IEAIQA---   86 (165)
T ss_pred             -------------------------------chhH------------------------------------Hhhhcc---
Confidence                                           0000                                    000000   


Q ss_pred             CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      .++++.....+....|..+|..||+++++||.++|    .+++|++|||+.||+|..+|+..+.||+++||+....
T Consensus        87 ~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~  158 (165)
T PRK09644         87 ESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCD----VHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE  158 (165)
T ss_pred             cChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            12344444555667899999999999999999998    5899999999999999999999999999999986543

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=99.71  E-value=3e-16  Score=146.37  Aligned_cols=156  Identities=12%  Similarity=0.046  Sum_probs=121.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCC
Q 010092          273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSF  351 (518)
Q Consensus       273 ~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~  351 (518)
                      ...+..++..|.+.|+.+|.++.   ++..+++|++||+|+.+|+..+.|++..  .|.+|++..+++.+.+.++. .+.
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            56899999999999999999998   7888999999999999999999998543  59999999999999988872 110


Q ss_pred             ccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhccccc
Q 010092          352 TRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD  431 (518)
Q Consensus       352 iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d  431 (518)
                         +.. ..                                                              ...... .+
T Consensus        80 ---~~~-~~--------------------------------------------------------------~~~~~~-~~   92 (164)
T PRK12547         80 ---VQD-SD--------------------------------------------------------------GVFTAR-VA   92 (164)
T ss_pred             ---ccc-cc--------------------------------------------------------------cccccc-CC
Confidence               000 00                                                              000000 00


Q ss_pred             CCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          432 VDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       432 ~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                         ..++.  ........|..+|..||+++++||.|+|    .+++|++|||+.||+|..+|++.+.||+++||....
T Consensus        93 ---~~~~~--~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~  161 (164)
T PRK12547         93 ---VHPAQ--YGSLDLQDFKKALNLLSADQREAIILIG----ASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLK  161 (164)
T ss_pred             ---CCchh--hhHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence               00111  1122345688999999999999999998    589999999999999999999999999999997654

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=99.71  E-value=2.9e-16  Score=150.30  Aligned_cols=180  Identities=14%  Similarity=0.114  Sum_probs=126.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhhccCCCCC-HHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCccc
Q 010092          277 NKLIKHNLRLVLFVIKKYFQDFANGPR-FQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRV  354 (518)
Q Consensus       277 e~LI~~nlrLV~siAkky~~~~~~g~~-~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~iRl  354 (518)
                      +..+..|.+.|+.+|.++.   ++..+ ++|++||+|+.+|++.++|+..  ..|.+|++..+++.+.+++++ .+....
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            3566778999999999998   66777 9999999999999999999864  379999999999999998883 221100


Q ss_pred             cccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCC
Q 010092          355 PFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG  434 (518)
Q Consensus       355 P~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~  434 (518)
                      ......                        ....+..                    .+....    +............
T Consensus        83 ~~~~~~------------------------~~~~~~~--------------------~~~~~~----~~~~~~~~~~~~~  114 (195)
T PRK12532         83 FTLLDD------------------------ELLDEAF--------------------ESHFSQ----NGHWTPEGQPQHW  114 (195)
T ss_pred             cccccc------------------------cccchhh--------------------hhhhcc----ccccccccCcccc
Confidence            000000                        0000000                    000000    0000000000111


Q ss_pred             CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010092          435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  513 (518)
Q Consensus       435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L  513 (518)
                      .++++.....+....+..+|..||++++.||.|+|    .+++|++|||+.||+|..+|++.++||+++||+......+
T Consensus       115 ~~~e~~~~~~e~~~~l~~~l~~L~~~~r~i~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~  189 (195)
T PRK12532        115 NTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKE----ILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWF  189 (195)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhhHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            23555555666777899999999999999999998    5899999999999999999999999999999987765543

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=99.70  E-value=3.9e-16  Score=150.76  Aligned_cols=177  Identities=12%  Similarity=0.070  Sum_probs=123.0

Q ss_pred             HHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccccc
Q 010092          279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFG  357 (518)
Q Consensus       279 LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~  357 (518)
                      ++..|.+.++.+|.++.   ++..+++|++||.|+.+|+..++|++..  .|.+|++..+++.+.++++ +.+...++..
T Consensus        13 ~~~~~~~~l~~~~~~~~---~d~~~AEDivQe~fl~~~~~~~~~~~~~--~~~~WL~~IarN~~~d~~Rk~~r~~~~~~~   87 (201)
T PRK12545         13 YLAQLRHDLLRFARLQL---RDADAAEDAVQEALAAAWSQAGRFAGQS--AHKTWVFGILRNKLIDTLRARQRTVNLSAL   87 (201)
T ss_pred             HHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhhhhccccc--hHHHHHHHHHHHHHHHHHHhhccccccccc
Confidence            47889999999999999   7778999999999999999999999753  6999999999999999888 3221101000


Q ss_pred             ccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcc
Q 010092          358 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN  437 (518)
Q Consensus       358 ~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~  437 (518)
                       ..                            ++.      ..            ..++.........+......+...++
T Consensus        88 -~~----------------------------~~~------~~------------~~~~~~~~~~~~~~~~~~~~~~~~~~  120 (201)
T PRK12545         88 -DA----------------------------ELD------GE------------ALLDRELFKDNGHWAAHAKPRPWPKP  120 (201)
T ss_pred             -cc----------------------------ccc------hh------------hhhhhhhhcccccccccccCcCCCCH
Confidence             00                            000      00            00000000000000000001111223


Q ss_pred             hhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092          438 ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  511 (518)
Q Consensus       438 ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~  511 (518)
                      ++.....+....|..+|..||+++|.||.|+|    .+++|++|||+.||+|.++|+..+.||+++||+.....
T Consensus       121 ~~~~~~~~~~~~l~~~L~~Lp~~~r~v~~L~~----~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~  190 (201)
T PRK12545        121 ETILQQQQFWTLFETCLDHLPEQIGRVFMMRE----FLDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEK  190 (201)
T ss_pred             HHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence            44444455566789999999999999999999    58999999999999999999999999999999876543

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

Probab=99.70  E-value=4.5e-16  Score=148.78  Aligned_cols=178  Identities=15%  Similarity=0.124  Sum_probs=127.1

Q ss_pred             HHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccc
Q 010092          277 NKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVP  355 (518)
Q Consensus       277 e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP  355 (518)
                      .+.+..|.+.|+.+|.++.   ++..+++|++||+|+.+|+..+.|++.  .+|.+|++..+++.+.++++ +.+....+
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            3567789999999999999   778899999999999999999999865  37999999999999999888 32211111


Q ss_pred             ccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCC
Q 010092          356 FGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV  435 (518)
Q Consensus       356 ~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~  435 (518)
                      . +..                            +.      ...             .++... .+.+............
T Consensus        80 ~-~~~----------------------------~~------~~~-------------~~~~~~-~~~~~~~~~~~~~~~~  110 (188)
T TIGR02943        80 D-LDD----------------------------EL------DDE-------------AFNALF-TQNGHWAQHGQPQHWN  110 (188)
T ss_pred             c-ccc----------------------------cc------ccc-------------hhhhhh-ccccchhccccccccC
Confidence            0 000                            00      000             000000 0000000001111112


Q ss_pred             cchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       436 ~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      .++..+...+....|..+|..||++++.||.++|    .+++|++|||+.||+|.++|++.+.||+++||+......
T Consensus       111 ~~e~~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~  183 (188)
T TIGR02943       111 TPEKQLENKEFWEVFEACLYHLPEQTARVFMMRE----VLGFESDEICQELEISTSNCHVLLYRARLSLRACLSINW  183 (188)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3455556666677899999999999999999998    589999999999999999999999999999998766443

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.

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=99.70  E-value=4.5e-16  Score=148.81  Aligned_cols=174  Identities=15%  Similarity=0.088  Sum_probs=123.7

Q ss_pred             HHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccc
Q 010092          277 NKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVP  355 (518)
Q Consensus       277 e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP  355 (518)
                      +..|..|.+.++.+|.++.   ++..+++|++||.|+.+|+..+.|++..  +|.+|++...++.+.++++ +.+.....
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            3456778889999999998   6778999999999999999999998653  6999999999999998888 32211000


Q ss_pred             ccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCC
Q 010092          356 FGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV  435 (518)
Q Consensus       356 ~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~  435 (518)
                       ....                            +                   ..........   .....+........
T Consensus        85 -~~~~----------------------------~-------------------~~~~~~~~~~---~~~~~~~~~~~~~~  113 (189)
T PRK12530         85 -ELIE----------------------------E-------------------DSPNSFFDEK---GHWKPEYYEPSEWQ  113 (189)
T ss_pred             -cccc----------------------------c-------------------ccchhhhccc---ccccccccCCcccc
Confidence             0000                            0                   0000000000   00000000011112


Q ss_pred             cchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       436 ~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      ++++.....+....|..+|+.||+++|+||.|+|    .+++|++|||+.||+|.++|+..++||+++||+.+..
T Consensus       114 ~~~~~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~  184 (189)
T PRK12530        114 EVENTVYKEEFWLIFEACLNHLPAQQARVFMMRE----YLELSSEQICQECDISTSNLHVLLYRARLQLQACLSK  184 (189)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhCCHHHHHHHhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence            3444555567777899999999999999999999    5899999999999999999999999999999986543

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=99.69  E-value=6.2e-16  Score=150.32  Aligned_cols=181  Identities=13%  Similarity=0.136  Sum_probs=128.8

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccc
Q 010092          276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRV  354 (518)
Q Consensus       276 ~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRl  354 (518)
                      -..++..|.+.|+.+|.++.   ++..+++|++||+|+.+|+.+..|+..  .+|.+|++..+++.+.++++ ..+....
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            46788999999999999999   788899999999999999999999864  36999999999999999998 3321111


Q ss_pred             cccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCC
Q 010092          355 PFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG  434 (518)
Q Consensus       355 P~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~  434 (518)
                      +.....                         ...         ...+..+...              .............
T Consensus        95 ~~~~~~-------------------------~~~---------~~~~~~~~~~--------------~~~~~~~~~~~~~  126 (206)
T PRK12544         95 SSLLRD-------------------------EEE---------EEDFEELFDE--------------SGHWQKDERPQAW  126 (206)
T ss_pred             cccccc-------------------------cch---------hhHHHHhhcc--------------ccccccccccccc
Confidence            100000                         000         0000000000              0000000001111


Q ss_pred             CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010092          435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  513 (518)
Q Consensus       435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L  513 (518)
                      ..+++.....+....+..+|..||++++.||.|+|    .+++|++|||+.||+|..+|++.++||+++||+....+.+
T Consensus       127 ~~~e~~~~~~e~~~~l~~~L~~L~~~~r~v~~L~~----~~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~~  201 (206)
T PRK12544        127 GNPEESLEQEQFWRIFEACLDGLPAKYARVFMMRE----FIELETNEICHAVDLSVSNLNVLLYRARLRLRECLENKWF  201 (206)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            23455555566667889999999999999999999    5899999999999999999999999999999987765443

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=99.68  E-value=2.5e-16  Score=144.28  Aligned_cols=150  Identities=15%  Similarity=0.083  Sum_probs=116.0

Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCcccccccc
Q 010092          281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLE  359 (518)
Q Consensus       281 ~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~~~  359 (518)
                      ..|.+.|+.++.++.   ++..+++|++||+++.+|+++++|++   .+|.+|++..+++.+.++++ +.+....     
T Consensus         2 ~~~~~~l~~~~~~~~---~~~~~aeD~~Qe~~~~l~~~~~~~~~---~~f~~wl~~i~~~~~~d~~r~~~~~~~~-----   70 (154)
T TIGR02950         2 REYMHDVFRYLYRLT---KDKHLAEDLLQETFLKAYIHLHSFKD---SSIKPWLFRIARNAFIDWYRKDKKIQTI-----   70 (154)
T ss_pred             chHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHHhcC---CchHHHHHHHHHHHHHHHHHHhhhhccc-----
Confidence            568999999999998   67789999999999999999999997   37999999999999988887 2110000     


Q ss_pred             chhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchh
Q 010092          360 STSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN  439 (518)
Q Consensus       360 e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee  439 (518)
                      .                           .+                                  .+.+... +....+++
T Consensus        71 ~---------------------------~~----------------------------------~~~~~~~-~~~~~~~~   88 (154)
T TIGR02950        71 D---------------------------DD----------------------------------AIGDLEQ-HPVESPEH   88 (154)
T ss_pred             c---------------------------Hh----------------------------------hhhhccc-cccCChhH
Confidence            0                           00                                  0000000 01112344


Q ss_pred             hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          440 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       440 ~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      .....+....|..+|+.||+.++.||.++|    .+++|++|||+.||+|..+|++.++||+++||+.
T Consensus        89 ~~~~~~~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~  152 (154)
T TIGR02950        89 HLLIKIEQEEITHHLSRLPENYRTVLILRE----FKEFSYKEIAELLNLSLAKVKSNLFRARKELKKL  152 (154)
T ss_pred             HHHHHHHHHHHHHHHHhCCHhheeeeeehh----hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            444455667799999999999999999998    4899999999999999999999999999999964

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.

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=99.68  E-value=1.2e-15  Score=145.00  Aligned_cols=152  Identities=16%  Similarity=0.152  Sum_probs=121.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC-Cccc
Q 010092          276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS-FTRV  354 (518)
Q Consensus       276 ~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr-~iRl  354 (518)
                      ++.|+..|.+.|+.+|.++.   ++..+++|++||.++.+|+.+..|++.  ..|.+|++..+++.+.+++++.+ ...+
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            67899999999999999998   788999999999999999999999853  37999999999999998887321 1000


Q ss_pred             cccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCC
Q 010092          355 PFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG  434 (518)
Q Consensus       355 P~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~  434 (518)
                      +                                                                  .+..   ..+   
T Consensus        78 ~------------------------------------------------------------------~~~~---~~~---   85 (181)
T PRK09637         78 P------------------------------------------------------------------DDLL---FED---   85 (181)
T ss_pred             c------------------------------------------------------------------hhhh---ccC---
Confidence            0                                                                  0000   000   


Q ss_pred             CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                       .+++.....+....+..+|+.||++++.||.|+|    .+++++.|||+.||+|..+|+..+.||+++||+...
T Consensus        86 -~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~  155 (181)
T PRK09637         86 -EEREENAKKELAPCLRPFIDALPEKYAEALRLTE----LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE  155 (181)
T ss_pred             -CChhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence             0111223344567899999999999999999998    589999999999999999999999999999997544

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=99.67  E-value=1.4e-15  Score=144.83  Aligned_cols=158  Identities=14%  Similarity=0.091  Sum_probs=121.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCc
Q 010092          274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFT  352 (518)
Q Consensus       274 ~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~i  352 (518)
                      .++..++..|.+.|+.+|.++.   ++..+++|++||.|+.+|+..++|++..  .|.+|++..+++.+.+.+++ .+..
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   7788999999999999999999998654  68999999999998887762 1100


Q ss_pred             cccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccC
Q 010092          353 RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV  432 (518)
Q Consensus       353 RlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~  432 (518)
                        ..  .                                                              .+...+.. +.
T Consensus        80 --~~--~--------------------------------------------------------------~~~~~~~~-~~   92 (182)
T PRK12540         80 --ED--A--------------------------------------------------------------DGSYAKTL-KS   92 (182)
T ss_pred             --cc--c--------------------------------------------------------------cccccccc-cC
Confidence              00  0                                                              00000000 00


Q ss_pred             CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                         .++..  .......|..+|+.||++++.||.|+|    .+++|++|||+.||+|..+|++.++||+++||+.+....
T Consensus        93 ---~~~~~--~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~  163 (182)
T PRK12540         93 ---QPGQN--AHLEFEEFRAALDKLPQDQREALILVG----ASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDG  163 (182)
T ss_pred             ---CCchH--HHHHHHHHHHHHHhCCHHHHHHhhHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence               01111  112234689999999999999999999    589999999999999999999999999999998766544

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=99.67  E-value=1.5e-15  Score=140.76  Aligned_cols=156  Identities=14%  Similarity=0.127  Sum_probs=117.5

Q ss_pred             HHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccc
Q 010092          278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPF  356 (518)
Q Consensus       278 ~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~  356 (518)
                      .++..|.+.++.+|.++.   ++..+++|++||+++.+|+....|++.   .|.+|++..+++.+.++++ +.....  .
T Consensus         2 ~~~~~~~~~l~~~~~~~~---~~~~~aeDivQe~~l~l~~~~~~~~~~---~~~~wl~~iarn~~~d~~R~~~~~~~--~   73 (163)
T PRK07037          2 DVFVDNRSMLVKIAARIV---GCRSRAEDVVQDAFVKLVEAPNQDAVK---QPVAYLFRIVRNLAIDHYRRQALENK--Y   73 (163)
T ss_pred             hHHHHHHHHHHHHHHHHc---CCHhHHHHHHHHHHHHHHhccccCCcc---cHHHHHHHHHHHHHHHHHHhhccccc--c
Confidence            367788999999999998   778899999999999999988877653   4789999999998888887 211000  0


Q ss_pred             cccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCc
Q 010092          357 GLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVE  436 (518)
Q Consensus       357 ~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~  436 (518)
                                                                              +      ...+.... .... ..+
T Consensus        74 --------------------------------------------------------~------~~~~~~~~-~~~~-~~~   89 (163)
T PRK07037         74 --------------------------------------------------------H------GDEEDGLD-VPSP-EAS   89 (163)
T ss_pred             --------------------------------------------------------c------cccccccc-cCCC-CCC
Confidence                                                                    0      00000000 0011 122


Q ss_pred             chhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          437 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       437 ~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                      ++......+..+.|..+|+.|||+++.||.++|    .+++|.+|||+.||+|..+|++.+.+|+++||....
T Consensus        90 ~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l~  158 (163)
T PRK07037         90 PEAALINRDTLRHVADALSELPARTRYAFEMYR----LHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLD  158 (163)
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence            444444555667789999999999999999998    589999999999999999999999999999997543

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=99.67  E-value=2.1e-15  Score=144.23  Aligned_cols=162  Identities=14%  Similarity=0.132  Sum_probs=122.8

Q ss_pred             HHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH
Q 010092          268 CLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT  347 (518)
Q Consensus       268 ~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~  347 (518)
                      -..++..+++.++..|.+.|+.+|.++.   ++..+++|++||.|+.+|+.+..|++..  .|.+|++..+++.+.+..+
T Consensus        17 ~~~~~~~~f~~l~~~y~~~l~~~~~~~~---~~~~~AeDlvQdvflkl~~~~~~~~~~~--~~~~wL~~Iarn~~~~~~r   91 (188)
T PRK12517         17 DMLSKQRRYEALVKALHADIYRYAYWLC---KDKHIAEDLVQETFLRAWRSLDSLKDEK--AAKAWLITILRRENARRFE   91 (188)
T ss_pred             hhhccHHHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHhHHhhcCcc--chHHHHHHHHHHHHHHHHH
Confidence            3567899999999999999999999999   7888999999999999999999998653  6899998888886544333


Q ss_pred             hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhc
Q 010092          348 VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN  427 (518)
Q Consensus       348 ~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~  427 (518)
                      +...                                                          ...+.+      ..    
T Consensus        92 ~~~~----------------------------------------------------------~~~~~~------~~----  103 (188)
T PRK12517         92 RKQF----------------------------------------------------------DLVDIE------DD----  103 (188)
T ss_pred             Hhcc----------------------------------------------------------CccCcc------cc----
Confidence            1000                                                          000000      00    


Q ss_pred             ccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          428 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       428 ~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      ...+....+++.    ......|..+|..||++++.||.++|    .+++|++|||+.||+|..+|+..+.||+++||..
T Consensus       104 ~~~~~~~~~~e~----~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~  175 (188)
T PRK12517        104 SIEDDASHSSEE----EMEQEWLRRQIAKLDPEYREPLLLQV----IGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEA  175 (188)
T ss_pred             cccCccccChhH----HHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            000110111221    22335689999999999999999999    5899999999999999999999999999999986


Q ss_pred             chh
Q 010092          508 TRV  510 (518)
Q Consensus       508 ~~~  510 (518)
                      ...
T Consensus       176 l~~  178 (188)
T PRK12517        176 LEK  178 (188)
T ss_pred             HHH
Confidence            653

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=99.66  E-value=4.4e-15  Score=139.67  Aligned_cols=160  Identities=14%  Similarity=0.094  Sum_probs=120.1

Q ss_pred             HcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcC
Q 010092          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS  350 (518)
Q Consensus       271 gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr  350 (518)
                      .+..|++.++..|.+.++.++.++.   ++..+++||+||.|+.+|+. ..|++-.  .|.+|++..+++.+.+++++..
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   77889999999999999987 3454332  5889999888888887776210


Q ss_pred             CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccc
Q 010092          351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT  430 (518)
Q Consensus       351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~  430 (518)
                                        + .....            +.+                                .    .+.
T Consensus        81 ------------------~-~~~~~------------~~~--------------------------------~----~~~   93 (172)
T PRK09651         81 ------------------L-EKAYL------------EML--------------------------------A----LMP   93 (172)
T ss_pred             ------------------H-Hhhhh------------hHH--------------------------------h----hcc
Confidence                              0 00000            000                                0    000


Q ss_pred             cCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          431 DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       431 d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      +....+++......+....|..+|..||++++.||.++|    .+++|++|||+.||+|..+|+..++||+++|+..
T Consensus        94 ~~~~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~i~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~  166 (172)
T PRK09651         94 EGGAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQ----LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLF  166 (172)
T ss_pred             ccCCCChHHHHHHHHHHHHHHHHHHhCCHHHhHHhhhhh----ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            001112333333344556789999999999999999999    5899999999999999999999999999999854

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=99.66  E-value=1.7e-15  Score=142.42  Aligned_cols=147  Identities=17%  Similarity=0.152  Sum_probs=115.6

Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCcccccccc
Q 010092          281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRVPFGLE  359 (518)
Q Consensus       281 ~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~iRlP~~~~  359 (518)
                      ..|.+.++.++.++.   ++..+++|++||+|+.+|+++..|++.  .+|.+|++..+++.+.++++. .+...++    
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            457888999999998   788899999999999999999999963  479999999999999998883 2110000    


Q ss_pred             chhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchh
Q 010092          360 STSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENEN  439 (518)
Q Consensus       360 e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee  439 (518)
                                                                                     +...    ...  ++++
T Consensus        73 ---------------------------------------------------------------~~~~----~~~--~~~~   83 (170)
T TIGR02959        73 ---------------------------------------------------------------ESLL----AAD--SARE   83 (170)
T ss_pred             ---------------------------------------------------------------hhhc----ccC--CccH
Confidence                                                                           0000    000  1112


Q ss_pred             hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          440 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       440 ~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                      .....+....|..+|..||++++.||.++|    .+++|++|||+.||+|..+|++.+.||+++||....
T Consensus        84 ~~~~~e~~~~l~~~l~~L~~~~r~v~~l~~----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~  149 (170)
T TIGR02959        84 ETFVKELSQCIPPMIKELPDEYREAIRLTE----LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE  149 (170)
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence            223344566799999999999999999998    589999999999999999999999999999997543

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).

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=99.66  E-value=1.4e-15  Score=140.62  Aligned_cols=153  Identities=13%  Similarity=0.103  Sum_probs=116.5

Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCccccccccc
Q 010092          281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLES  360 (518)
Q Consensus       281 ~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRlP~~~~e  360 (518)
                      ..|.+.++.++.++.   ++..+++|++||.|+.+|+..+.|++.   +|.||++..+++.+.++++......       
T Consensus         2 ~~~~~~l~~~~~~~~---~~~~~aeDi~Qevf~~l~~~~~~~~~~---~~~~wL~~ia~n~~~d~~R~~~~~~-------   68 (159)
T PRK12527          2 ENYYRELVRFLSARL---GNRQAAEDVAHDAYLRVLERSSSAQIE---HPRAFLYRTALNLVVDRHRRHRVRQ-------   68 (159)
T ss_pred             hhHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHhcccccccc---chHHHHHHHHHHHHHHHHHHHhccc-------
Confidence            467888889999998   677889999999999999999998753   6899999999999988877211000       


Q ss_pred             hhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchhh
Q 010092          361 TSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQ  440 (518)
Q Consensus       361 ~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee~  440 (518)
                                     .                                   .+++.        +.+. ......++++.
T Consensus        69 ---------------~-----------------------------------~~~~~--------~~~~-~~~~~~~~~~~   89 (159)
T PRK12527         69 ---------------A-----------------------------------EPLEV--------LDEE-ERLHSPSPQTR   89 (159)
T ss_pred             ---------------c-----------------------------------cchhh--------hhcc-ccccCCCHHHH
Confidence                           0                                   00000        0000 00011234555


Q ss_pred             hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          441 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       441 ~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                      ....+....|..+|..||++++.||.|+|    .+++|++|||+.||+|.++|+..+.||+++||....
T Consensus        90 ~~~~~~~~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~  154 (159)
T PRK12527         90 LDLGQRLALLQRALAELPPACRDSFLLRK----LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR  154 (159)
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence            55556667899999999999999999999    589999999999999999999999999999997654

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=99.65  E-value=4.1e-15  Score=142.54  Aligned_cols=157  Identities=12%  Similarity=0.075  Sum_probs=117.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCc
Q 010092          273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT  352 (518)
Q Consensus       273 ~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~i  352 (518)
                      ..+++.|.. |.+.|+++|..+.   ++..+++|++||.|+.+|+.+..|+..  ..|.+|++..+++.+.+++++... 
T Consensus         7 ~~~~~~l~~-~~~~l~~~a~~~l---~~~~~AEDivQevfl~l~~~~~~~~~~--~~~~awL~~ia~n~~~d~~Rk~~r-   79 (188)
T PRK12546          7 RDPRDELVE-HLPALRAFAISLT---RNVAVADDLVQDTIVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSDRRKHKR-   79 (188)
T ss_pred             hhHHHHHHH-HHHHHHHHHHHHc---CChhhHHHHHHHHHHHHHHHHhccCCC--cchHHHHHHHHHHHHHHHHHHhcc-
Confidence            456667766 6799999999998   788999999999999999999999864  369999999999999887773110 


Q ss_pred             cccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccC
Q 010092          353 RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV  432 (518)
Q Consensus       353 RlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~  432 (518)
                       .+.   .                                                     .+       +...+...++
T Consensus        80 -~~~---~-----------------------------------------------------~~-------~~~~~~~~~~   95 (188)
T PRK12546         80 -EVP---D-----------------------------------------------------PE-------GVHAASLAVK   95 (188)
T ss_pred             -ccc---C-----------------------------------------------------cc-------cccccccccC
Confidence             000   0                                                     00       0000000000


Q ss_pred             CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                          +..  ........+..+|+.||++++.||.|+|    .+++|.+|||+.||+|..+|++.+.||+++||+....
T Consensus        96 ----~~~--~~~~~~~~l~~~L~~Lp~~~r~v~~L~~----~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~  163 (188)
T PRK12546         96 ----PAH--DGRLAMSDFRAAFAQLPDEQREALILVG----ASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQL  163 (188)
T ss_pred             ----Ccc--hhHHHHHHHHHHHHhCCHHHhHHhhhHH----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence                000  1122235688999999999999999998    5899999999999999999999999999999976543

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=99.64  E-value=1.5e-14  Score=135.37  Aligned_cols=159  Identities=14%  Similarity=0.076  Sum_probs=120.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCc
Q 010092          273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT  352 (518)
Q Consensus       273 ~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~i  352 (518)
                      ..++.+++..|.+.++.+|.++.   ++..+.+|++||.|+.+|+..+.++.   ..|.+|++..+++.+.++++..+  
T Consensus         8 ~~~~~~~~~~~~~~l~~~~~~~~---~~~~~aeDlvQevf~~l~~~~~~~~~---~~~~~wl~~Iarn~~~d~~Rr~~--   79 (168)
T PRK12525          8 NTLIGQMFQQDYDWLCKKLSRQL---GCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEGWRRQD--   79 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHc---CCcCcHHHHHHHHHHHHHhCCCcccc---cCHHHHHHHHHHHHHHHHHHHHH--
Confidence            46889999999999999999998   67789999999999999986555542   26899999888888887766210  


Q ss_pred             cccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccC
Q 010092          353 RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDV  432 (518)
Q Consensus       353 RlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~  432 (518)
                                       ..+.   ....                                 +           .+ ....
T Consensus        80 -----------------~~~~---~~~~---------------------------------~-----------~~-~~~~   94 (168)
T PRK12525         80 -----------------LERA---YLQS---------------------------------L-----------AE-APEA   94 (168)
T ss_pred             -----------------HHHH---HHHH---------------------------------H-----------hc-cccc
Confidence                             0000   0000                                 0           00 0000


Q ss_pred             CCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          433 DGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       433 ~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      ...++++..........|..+|+.||++++.||.|+|    .+++|++|||+.||+|..+|+..+.+|+++|+...
T Consensus        95 ~~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~v~~L~~----~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~~  166 (168)
T PRK12525         95 VQPSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQ----LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQGF  166 (168)
T ss_pred             ccCChHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhh
Confidence            1122444444555667899999999999999999998    58999999999999999999999999999999653

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=99.63  E-value=9.3e-15  Score=139.31  Aligned_cols=154  Identities=12%  Similarity=0.091  Sum_probs=116.2

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCccc
Q 010092          276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRV  354 (518)
Q Consensus       276 ~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~iRl  354 (518)
                      ....+..+++.|+.+|.++.   ++..+.+|++||.|+.+|+....|+...  .|.+|++..+++.+.+++++ .+....
T Consensus         6 ~~~~~~~~~~~l~~~~~~~~---~~~~dAEDivQe~flkl~~~~~~~~~~~--~~~~WL~~Iarn~~id~~Rk~~~~~~~   80 (182)
T PRK12511          6 KRFDVLDQLVPLRRYARSLT---RDSAEAEDLVHDALVRALERRASFRSGG--NLRTWLMSILHNAFIDELRRRRVEARR   80 (182)
T ss_pred             hhhhHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHHHHHHhhcccccc
Confidence            34457788999999999998   7788999999999999999999998643  69999999999999988873 111000


Q ss_pred             cccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCC
Q 010092          355 PFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG  434 (518)
Q Consensus       355 P~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~  434 (518)
                                                      .+++                                ..    ..+...
T Consensus        81 --------------------------------~~~~--------------------------------~~----~~~~~~   92 (182)
T PRK12511         81 --------------------------------ADEL--------------------------------AV----LADASL   92 (182)
T ss_pred             --------------------------------ccch--------------------------------hh----ccccCC
Confidence                                            0000                                00    000000


Q ss_pred             CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                      ..+.   ........|..+|..||++++.||.|+|    .+++|++|||+.||+|.++|++.+.||+++||....
T Consensus        93 ~~~~---~~~~~~~~l~~~l~~Lp~~~R~v~~L~~----~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~  160 (182)
T PRK12511         93 PAAQ---EHAVRLAQIRDAFFDLPEEQRAALHLVA----IEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEE  160 (182)
T ss_pred             Ccch---HHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence            0011   1122345688999999999999999998    589999999999999999999999999999997543

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=99.60  E-value=1.4e-14  Score=147.76  Aligned_cols=159  Identities=15%  Similarity=0.051  Sum_probs=118.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCcc
Q 010092          274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTR  353 (518)
Q Consensus       274 ~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iR  353 (518)
                      .....++..|.+.++.+|+++.   ++..+++|++||.|+. |.....|+.   ..|.+|++..+++.+.+++++.+..+
T Consensus         4 ~~~~~l~~~~~~~l~~~a~~~~---~~~~dAEDlvQe~fl~-~~~~~~~~~---~~~~~WL~~Ia~n~~~d~lR~~~~~~   76 (293)
T PRK09636          4 ADAAAEFEPLRPHLLSVAYRML---GSVADAEDIVQEAWLR-WNNADRAQI---RDPRAWLTRVVTRLCLDRLRSARHRR   76 (293)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHc---CCHHHHHHHHHHHHHH-HHhcccccc---cCHHHHHHHHHHHHHHHHHHhhhccc
Confidence            4577899999999999999998   7788999999999999 556677752   46999999999999988887211000


Q ss_pred             ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCC
Q 010092          354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD  433 (518)
Q Consensus       354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~  433 (518)
                       ...  .                                                ..  .+.           +...+..
T Consensus        77 -~~~--~------------------------------------------------~~--~~~-----------e~~~~~~   92 (293)
T PRK09636         77 -ETY--V------------------------------------------------GP--WLP-----------EPVVEEL   92 (293)
T ss_pred             -ccc--c------------------------------------------------CC--cCC-----------cCCCCCC
Confidence             000  0                                                00  000           0001111


Q ss_pred             CCcchh-hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          434 GVENEN-QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       434 ~~~~ee-~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                       .++++ ......+...+..+|+.|||++|.||.|+|    ..++|++|||+.||+|..+|++.++||+++||+..
T Consensus        93 -~~~~~~~~~~~~~~~~l~~~l~~L~~~~R~v~~L~~----~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~  163 (293)
T PRK09636         93 -DDPLEAVVAAEDLSLALMLALERLSPLERAAFLLHD----VFGVPFDEIASTLGRSPAACRQLASRARKHVRAAR  163 (293)
T ss_pred             -CChHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence             11322 233445566789999999999999999999    58999999999999999999999999999999853

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=99.59  E-value=1.5e-14  Score=133.38  Aligned_cols=152  Identities=11%  Similarity=0.078  Sum_probs=105.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh-cCCccccccccchhhHHHHHHHHHHHHHH
Q 010092          299 ANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV-SSFTRVPFGLESTSIMQVRGEIQRAKLEL  377 (518)
Q Consensus       299 ~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~-sr~iRlP~~~~e~~~~~~~~ki~ka~~eL  377 (518)
                      ++..+++|++||+|+.+|+....+ +  +..|.+|++..+++.+.+++++ .+.......                    
T Consensus         2 ~~~~~AeDivQe~fl~~~~~~~~~-~--~~~~~~wl~~ia~n~~~d~~Rk~~~~~~~~~~--------------------   58 (161)
T PRK09047          2 RDDDAALDIVQDAMIKLAEKYGDR-P--AAEWPPLFQRILQNRIHDWFRRQKVRNTWVSL--------------------   58 (161)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhhc-c--cCchHHHHHHHHHHHHHHHHHhhccccccccc--------------------
Confidence            345679999999999999988863 3  3469999999999999998873 211000000                    


Q ss_pred             HHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCC--CCcchhhhHHHHHHHHHHHHHh
Q 010092          378 LFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD--GVENENQRQPALLRLALDDVLD  455 (518)
Q Consensus       378 ~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~--~~~~ee~~~~~~l~~~L~~~L~  455 (518)
                                                       ..++......+..+..+.+.+..  ..++++.....+....|..+|.
T Consensus        59 ---------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~  105 (161)
T PRK09047         59 ---------------------------------FSSFSDDDDDDDFDPLETLDSADEGAESPADKLERAQVLQLIEEAIQ  105 (161)
T ss_pred             ---------------------------------ccccccccccccccHHHHhccccccCCCHHHHHHHHHHHHHHHHHHH
Confidence                                             00000000000011111111111  1235555666677788999999


Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      .||++++.||.|+|    .+++|++|||+.||+|..+|+..+.+|+++||.....
T Consensus       106 ~Lp~~~r~v~~l~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~  156 (161)
T PRK09047        106 KLPARQREAFLLRY----WEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEA  156 (161)
T ss_pred             hCCHHHHHHHHHHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999    5899999999999999999999999999999976654

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=99.56  E-value=6.1e-14  Score=138.70  Aligned_cols=158  Identities=18%  Similarity=0.119  Sum_probs=119.7

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      .+.+...++..+++.+++.| +.++.+|.++.   ++..+.+||+||.|+.+|+.   |+..  ..|.+|++...++.+.
T Consensus         8 ~~~~~~~~~~~~~~~l~~~y-~~L~r~~~~~~---~d~~dAEDlvQE~flk~~~~---~~~~--~~~~~WL~~IarN~~i   78 (228)
T PRK06704          8 ILKNHIDMNHSNINFLIEQY-GELKRYCTFLT---KNKWDGEDLAQETVCKVLQK---YSNK--DICMTLVYKIARNRWL   78 (228)
T ss_pred             HHhcccCCCHHHHHHHHHHH-HHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHH---cCcc--ccHHHHHHHHHHHHHH
Confidence            46667788899999888888 78999999998   77889999999999999986   5543  2489999999999888


Q ss_pred             HHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh
Q 010092          344 RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE  423 (518)
Q Consensus       344 raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e  423 (518)
                      +.+++....       .               .+                                    .+.       
T Consensus        79 d~~Rk~k~~-------~---------------~~------------------------------------~~~-------   93 (228)
T PRK06704         79 DQIKSKSVH-------E---------------KI------------------------------------RDQ-------   93 (228)
T ss_pred             HHHhccccc-------c---------------cc------------------------------------ccc-------
Confidence            877621100       0               00                                    000       


Q ss_pred             hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          424 EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       424 el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                           ....   .+++.  .......+..+|+.||+++|.||.|+|    .+++|++|||+.||+|.++|++.+.||+++
T Consensus        94 -----~~~~---~~~~~--~~~~~~~l~~~L~~Lp~~~R~v~lL~~----~eg~S~~EIAe~LgiS~~tVksrL~Rark~  159 (228)
T PRK06704         94 -----ITFE---EPHEK--IADLHEMVGKVLSSLNVQQSAILLLKD----VFQYSIADIAKVCSVSEGAVKASLFRSRNR  159 (228)
T ss_pred             -----cccC---ChHHH--HHHHHHHHHHHHHhCCHHHhhHhhhHH----hhCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence                 0000   01111  122345688999999999999999998    589999999999999999999999999999


Q ss_pred             HhCcch
Q 010092          504 LKHPTR  509 (518)
Q Consensus       504 LR~~~~  509 (518)
                      ||....
T Consensus       160 Lr~~l~  165 (228)
T PRK06704        160 LKTVSE  165 (228)
T ss_pred             HHHHHH
Confidence            997543

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

Probab=99.54  E-value=1.1e-13  Score=140.51  Aligned_cols=155  Identities=15%  Similarity=0.075  Sum_probs=113.7

Q ss_pred             HHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCcccccc
Q 010092          278 KLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFG  357 (518)
Q Consensus       278 ~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRlP~~  357 (518)
                      +++..|.+.++.+|+++.   ++..+.+|++||+|+.+++.  .|+.  ...|.+|++..+++.+.++++..+..+ .  
T Consensus         1 ~l~~~~~~~l~~~a~r~l---g~~~dAEDvvQE~flk~~~~--~~~~--~~~~~awL~~Ia~n~~ld~lR~~~~~~-~--   70 (281)
T TIGR02957         1 EEFEALRPLLFSLAYRML---GSVADAEDIVQETFLRWQEA--DRAQ--IENPKAYLTKVVTRRCIDVLRSARARR-E--   70 (281)
T ss_pred             ChHHHHHHHHHHHHHHHh---CCHhHHHHHHHHHHHHHHhC--Cccc--ccCHHHHHHHHHHHHHHHHHHHhhhcc-c--
Confidence            368899999999999998   77889999999999997775  4543  236999999999999998887211000 0  


Q ss_pred             ccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcc
Q 010092          358 LESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN  437 (518)
Q Consensus       358 ~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~  437 (518)
                                        .+                              ...  -+..           ...+ ...++
T Consensus        71 ------------------~~------------------------------~~~--~~~e-----------~~~~-~~~~~   88 (281)
T TIGR02957        71 ------------------VY------------------------------VGP--WLPE-----------PLLT-TSADP   88 (281)
T ss_pred             ------------------cc------------------------------CCC--CCCc-----------ccCC-CCCCh
Confidence                              00                              000  0000           0000 01123


Q ss_pred             hhhhH-HHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          438 ENQRQ-PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       438 ee~~~-~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      ++... ...+...+..+|+.|||+||.||.|+|    ..++|++|||+.||+|..+|++.++||+++||+..
T Consensus        89 ~~~~~~~e~~~~~l~~~l~~L~~~~R~v~~L~~----~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~  156 (281)
T TIGR02957        89 AESVELAESLSMAYLLLLERLSPLERAVFVLRE----VFDYPYEEIASIVGKSEANCRQLVSRARRHLDARR  156 (281)
T ss_pred             HHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence            33332 334556788999999999999999998    58999999999999999999999999999999743

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=99.53  E-value=1.6e-13  Score=140.38  Aligned_cols=160  Identities=13%  Similarity=0.068  Sum_probs=118.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCcc
Q 010092          274 AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTR  353 (518)
Q Consensus       274 ~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iR  353 (518)
                      ..+..++..|.+.++.+|.++.   ++..+++|++||.|+.+|++...+ .   ..|.+|++...++.+.++++..+..+
T Consensus         5 ~~~~~l~~~~~~~L~~~a~r~l---gs~~dAEDvvQE~flr~~~~~~~~-~---~~~~aWL~~Ia~n~~id~lRk~~~rr   77 (290)
T PRK09635          5 DPVSAAWRAHRAYLVDLAFRMV---GDIGVAEDMVQEAFSRLLRAPVGD-I---DDERGWLIVVTSRLCLDHIKSASTRR   77 (290)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHhcCccc-c---ccHHHHHHHHHHHHHHHHHhhhhccC
Confidence            5678999999999999999999   788899999999999999986543 1   25899999999999988887311100


Q ss_pred             ccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCC
Q 010092          354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD  433 (518)
Q Consensus       354 lP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~  433 (518)
                      ...                                                       ...+...   .+   +...  .
T Consensus        78 ~~~-------------------------------------------------------~~~~~~~---~~---~~~~--~   94 (290)
T PRK09635         78 ERP-------------------------------------------------------QDIAAWH---DG---DASV--S   94 (290)
T ss_pred             cCc-------------------------------------------------------ccccccC---cc---ccCC--C
Confidence            000                                                       0000000   00   0000  1


Q ss_pred             CCcchh-hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          434 GVENEN-QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       434 ~~~~ee-~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      ..++++ .....+....+..+|..|||++|.||.|+|    ..++|++|||+.||+|..+|+++++||+++||..
T Consensus        95 ~~~~~~~~~~~~e~~~al~~~L~~L~p~~R~vf~L~~----~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~  165 (290)
T PRK09635         95 SVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHE----IFGLPYQQIATTIGSQASTCRQLAHRARRKINES  165 (290)
T ss_pred             CCCcHHHHHHHHHHHHHHHHHHHhCCHHHHHHhhHHH----HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence            112222 233455667899999999999999999999    5799999999999999999999999999999974

>PRK09191 two-component response regulator; Provisional

Probab=99.43  E-value=1.6e-12  Score=128.33  Aligned_cols=136  Identities=8%  Similarity=-0.040  Sum_probs=108.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCccc
Q 010092          275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRV  354 (518)
Q Consensus       275 A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRl  354 (518)
                      ++..|+..|.+.++.+|.++.   ++..+.+|++||+|+.+|+....|++..  .|.+|++.++++.....         
T Consensus         2 ~~~~l~~~~~~~l~~~~~~~~---~~~~~aeDi~qd~~~~~~~~~~~~~~~~--~~~~wl~~~~~~~~~~~---------   67 (261)
T PRK09191          2 SLSQRIAPHLPYLRRYARALT---GSQSSGDAYVAATLEALLADPSIFPEAS--SPRVGLYRLFHRLWSSA---------   67 (261)
T ss_pred             chHHHHHHHhHHHHHHHHHhc---CChhhHHHHHHHHHHHHHHhHHhcCCCc--chhhHHHHHHHHHhccc---------
Confidence            578999999999999999998   7788999999999999999999998643  58888886654321000         


Q ss_pred             cccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCC
Q 010092          355 PFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDG  434 (518)
Q Consensus       355 P~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~  434 (518)
                                                                                    ..  ..      ....  
T Consensus        68 --------------------------------------------------------------~~--~~------~~~~--   75 (261)
T PRK09191         68 --------------------------------------------------------------GA--ND------PEPG--   75 (261)
T ss_pred             --------------------------------------------------------------cc--cC------CCCC--
Confidence                                                                          00  00      0000  


Q ss_pred             CcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          435 VENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       435 ~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                       .+..        ..+..+|+.||+++|.||.|+|    .+++|++|||+.||+|.++|+....+|+++|+....
T Consensus        76 -~~~~--------~~l~~~l~~L~~~~r~v~~l~~----~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~  137 (261)
T PRK09191         76 -SPFE--------ARAERRLAGLTPLPRQAFLLTA----LEGFSVEEAAEILGVDPAEAEALLDDARAEIARQVA  137 (261)
T ss_pred             -CCch--------HHHHHHHHhCCHHHhHHHHHHH----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence             0110        1688999999999999999998    589999999999999999999999999999997654

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=99.41  E-value=1.6e-11  Score=122.18  Aligned_cols=80  Identities=15%  Similarity=0.207  Sum_probs=73.5

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCC--CHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGP--RFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAI  342 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~--~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI  342 (518)
                      +..+..||..|++.|+..|.++|+++|.++.   ++..  +.+|++|||++++|+++++|++++|..|.+|++.+|++.+
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  5899999999999999999999998889999999999999


Q ss_pred             HHHHH
Q 010092          343 IRSMT  347 (518)
Q Consensus       343 ~raI~  347 (518)
                      .++++
T Consensus        86 iDylR   90 (237)
T PRK08311         86 IDYFR   90 (237)
T ss_pred             HHHHH
Confidence            99999

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=99.38  E-value=6.9e-12  Score=113.99  Aligned_cols=136  Identities=18%  Similarity=0.220  Sum_probs=96.4

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHh-----cCCCCCCccchHHHHHHHHHHHHHHHhcC
Q 010092          276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDR-----FEPKRRFRLSTYGLFWIRHAIIRSMTVSS  350 (518)
Q Consensus       276 ~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvek-----FDp~rG~kFSTYA~~wIRqaI~raI~~sr  350 (518)
                      ++.++..|.++++.+|++|.   .    .+| +||.++.+|....+     |++.  ..|.||++..+++.+.++++...
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            46799999999999999997   2    234 49999999999875     5432  46999999999999998887210


Q ss_pred             CccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccc
Q 010092          351 FTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGIT  430 (518)
Q Consensus       351 ~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~  430 (518)
                                      ..  .... .   .       .+                        ++               
T Consensus        71 ----------------~~--~~~~-~---~-------~~------------------------~~---------------   82 (142)
T TIGR03209        71 ----------------RD--KKII-Y---N-------SE------------------------IT---------------   82 (142)
T ss_pred             ----------------hh--hhhh-h---h-------hh------------------------hh---------------
Confidence                            00  0000 0   0       00                        00               


Q ss_pred             cCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHH
Q 010092          431 DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVR  494 (518)
Q Consensus       431 d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVR  494 (518)
                      +.. ..+++.....+....|..+|+.||+.+|.||.|+|    .+++|++|||+.||+|.++|+
T Consensus        83 ~~~-~~~~~~~~~~~~~~~l~~~l~~Lp~~~r~v~~l~~----~~~~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209        83 DIK-LSLINVYSSNDLEFEFNDLISILPNKQKKIIYMKF----FEDMKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             ccc-cchhHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHhhc
Confidence            000 00111222334456688999999999999999998    589999999999999999997

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

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=99.31  E-value=6e-11  Score=113.48  Aligned_cols=175  Identities=19%  Similarity=0.164  Sum_probs=115.9

Q ss_pred             HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHH--HHHHHHHHHHHHHhcCCCCCCccchHHHHHHHH
Q 010092          263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDL--CQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRH  340 (518)
Q Consensus       263 ~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDL--IQEG~IGLirAvekFDp~rG~kFSTYA~~wIRq  340 (518)
                      +.|.++.+||..|.+.|+..|++-++.+|.++......+.+.+|.  ++|.|+.++..-...+.+.-..|..|+...+++
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            347778999999999999999999999999877543344555554  667777776633322333333577777777777


Q ss_pred             HHHHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcC
Q 010092          341 AIIRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHG  419 (518)
Q Consensus       341 aI~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~  419 (518)
                      .+.+.++ +....|-..                                                    ....+||... 
T Consensus        86 ~lid~~R~~~a~KRg~~----------------------------------------------------~~~~~l~~~~-  112 (185)
T PF07638_consen   86 KLIDHARRRQAQKRGGD----------------------------------------------------QVRVELDERA-  112 (185)
T ss_pred             HHHHHHHHHHHHhcCCC----------------------------------------------------Ccccchhhhh-
Confidence            7777666 211110000                                                    0001111110 


Q ss_pred             CchhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          420 VTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       420 ~~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                                .+.+...++..   .++.+.+..+.. |+|++..+|.++|    ..|+|.+|||+.||||..+|++....
T Consensus       113 ----------~~~~~~~~~~~---~~l~e~l~~L~~-l~~~~~~~v~l~~----~~Gls~~EIA~~lgiS~~tV~r~l~~  174 (185)
T PF07638_consen  113 ----------DSGDEPSPEEL---LELEEALERLLA-LDPRQRRVVELRF----FEGLSVEEIAERLGISERTVRRRLRR  174 (185)
T ss_pred             ----------ccccCCCHHHH---HHHHHHHHHHHc-cCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence                      00011122222   244555555555 9999999999988    58999999999999999999999999


Q ss_pred             HHHHHhCcc
Q 010092          500 GLMKLKHPT  508 (518)
Q Consensus       500 ALkKLR~~~  508 (518)
                      |..+|+..+
T Consensus       175 aR~~l~~~l  183 (185)
T PF07638_consen  175 ARAWLRREL  183 (185)
T ss_pred             HHHHHHHHh
Confidence            999998654

>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=4.1e-11  Score=90.65  Aligned_cols=50  Identities=46%  Similarity=0.587  Sum_probs=45.8

Q ss_pred             HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          453 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       453 ~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      +|+.|||+|+.||.++|    ++++|+.|||+.||+|.++|++++.+|+++||+
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            58899999999999999    589999999999999999999999999999984

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=99.12  E-value=1.9e-10  Score=91.60  Aligned_cols=66  Identities=21%  Similarity=0.312  Sum_probs=63.4

Q ss_pred             HHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH
Q 010092          279 LIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT  347 (518)
Q Consensus       279 LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~  347 (518)
                      |++.|.++|+.+|.+|.   +++.+.+|++||++++||+++++||++.|..|.+|++..+++.+.+.++
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            68999999999999998   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=98.93  E-value=2.3e-09  Score=88.17  Aligned_cols=75  Identities=37%  Similarity=0.421  Sum_probs=60.5

Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhcccccCCCCcchhh
Q 010092          366 VRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQ  440 (518)
Q Consensus       366 ~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~~~ee~  440 (518)
                      .+++|.++..+|.+++||.||.+|||+.|||++++|+.++.+...++||+.+...+++ .+.+.+.|+...+|++.
T Consensus         2 ~l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~~~~~~~~~l~~~i~d~~~~~P~e~   77 (78)
T PF04539_consen    2 KLRKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLPVGDEDDSTLGDFIEDDDAPSPEEE   77 (78)
T ss_dssp             HHHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHCCSSSSSEEGGGSSB-SSS--HHHH
T ss_pred             hHHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeeeecCCCCCchhheecCCCCCChhhc
Confidence            6789999999999999999999999999999999999999999999999998876644 56677777777777653

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=98.89  E-value=5.6e-09  Score=79.93  Aligned_cols=54  Identities=28%  Similarity=0.329  Sum_probs=46.1

Q ss_pred             HHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092          447 RLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL  504 (518)
Q Consensus       447 ~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL  504 (518)
                      ++.|..+|..|||+++.||.++|    .+++|+.|||+.+|+|.++|++.+.+|+++|
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            35789999999999999999999    5899999999999999999999999999987

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=4.7e-07  Score=86.01  Aligned_cols=66  Identities=20%  Similarity=0.185  Sum_probs=58.7

Q ss_pred             hhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          440 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       440 ~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                      ..........|..+|+.||++++.||.++|    .+++|++|||+.||+|.++|++++.+|+++|+....
T Consensus        98 ~~~~~e~~~~l~~al~~L~~rer~V~~L~~----~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~  163 (170)
T PRK06930         98 SVISEWDKIRIEDALSVLTEREKEVYLMHR----GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQIN  163 (170)
T ss_pred             HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence            334455677899999999999999999988    489999999999999999999999999999997654

>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=98.26  E-value=3.4e-06  Score=62.53  Aligned_cols=54  Identities=39%  Similarity=0.467  Sum_probs=49.7

Q ss_pred             HHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092          448 LALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  505 (518)
Q Consensus       448 ~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR  505 (518)
                      ..+..++..|++.++.++.++|    .+++|..+||+.+|+|..+|+++..++..+|+
T Consensus         2 ~~~~~~~~~l~~~~~~~~~~~~----~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~   55 (55)
T cd06171           2 ERLEEALDKLPEREREVILLRF----GEGLSYEEIAEILGISRSTVRQRLHRALKKLR   55 (55)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence            3578889999999999999999    47899999999999999999999999998875

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=98.19  E-value=5e-06  Score=72.77  Aligned_cols=59  Identities=25%  Similarity=0.238  Sum_probs=52.1

Q ss_pred             HHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          448 LALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       448 ~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      ..++-....||++++.|+.++|    .+++|..|||+.+|+|+.+|++++.+|+++||+....
T Consensus         9 ~l~d~~~~~L~ekqRevl~L~y----~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~   67 (104)
T PRK00118          9 LLFDFYGSLLTEKQRNYMELYY----LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEK   67 (104)
T ss_pred             HHHHHHhccCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            3445566789999999999999    5899999999999999999999999999999986544

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=98.15  E-value=4.3e-06  Score=76.62  Aligned_cols=55  Identities=18%  Similarity=0.170  Sum_probs=48.3

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhh
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQ  515 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~  515 (518)
                      -||++|+.||.+++     +++|++|||+.||+|+++|++++++|+++|+.....-.|..
T Consensus         6 ~Lte~qr~VL~Lr~-----~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~   60 (137)
T TIGR00721         6 FLTERQIKVLELRE-----KGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVK   60 (137)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHH
Confidence            59999999999976     79999999999999999999999999999997655444433

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=98.04  E-value=7.9e-06  Score=75.26  Aligned_cols=50  Identities=26%  Similarity=0.213  Sum_probs=46.1

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                      ..|+|+|++||.+++     +++|++|||+.||+|+.+|++++++|+++||+...
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            469999999999976     79999999999999999999999999999997654

>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=97.97  E-value=3.2e-05  Score=67.22  Aligned_cols=55  Identities=29%  Similarity=0.330  Sum_probs=43.7

Q ss_pred             HHHHHHhc-CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          449 ALDDVLDS-LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       449 ~L~~~L~~-L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      .|.+.... |+++|+.++.++|    .+++|+.|||+.+|||+.+|...+.||.++|...
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            44555544 8999999999999    6899999999999999999999999999999754

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=70.63  Aligned_cols=55  Identities=15%  Similarity=-0.040  Sum_probs=49.4

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  513 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L  513 (518)
                      ..|++.|++||.++|    .+++|++|||+.||||+.+|++++.+|.++|+.......+
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            479999999999998    5899999999999999999999999999999987665443

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=97.87  E-value=4e-05  Score=57.74  Aligned_cols=50  Identities=36%  Similarity=0.358  Sum_probs=44.5

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                      ..|++.|+.|+.+.+     .++|..|||+.||+|+.+|+++..+++.+|.-...
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            468999999998755     68999999999999999999999999999986554

lux regulon (activates the bioluminescence operon

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=97.81  E-value=6.3e-05  Score=68.70  Aligned_cols=61  Identities=18%  Similarity=0.194  Sum_probs=53.6

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          445 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       445 ~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      .....|..+|+.|++.++.||.++|+ . ...+|..+||..||+|+.+|+++..+|+.+|...
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            45678999999999999999999994 1 1236999999999999999999999999999864

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.

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=97.72  E-value=1.3e-05  Score=57.22  Aligned_cols=33  Identities=21%  Similarity=0.245  Sum_probs=29.1

Q ss_pred             cChHHHHHHhcCCCCCCChHHHHHHHHHHhHhH
Q 010092          200 TDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMK  232 (518)
Q Consensus       200 ~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~  232 (518)
                      +|+++.||++|+.+|+||++||..|++.|+.+.
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            478999999999999999999999999997654

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 ....

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=97.71  E-value=0.00014  Score=54.86  Aligned_cols=49  Identities=35%  Similarity=0.366  Sum_probs=43.9

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      |+++|+.|+.+.+     .++|.+|||+.||+|..+|+++..+++++|......
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            6899999998865     689999999999999999999999999999986543

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

>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=97.68  E-value=0.00012  Score=56.88  Aligned_cols=52  Identities=31%  Similarity=0.319  Sum_probs=44.6

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  511 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~  511 (518)
                      +.|+++|.+||.+..     .|+|.+|||..+|+|..+|+.+..++++||.-..+.+
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            479999999999887     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 ....

>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19

Probab=97.66  E-value=0.00018  Score=62.41  Aligned_cols=56  Identities=32%  Similarity=0.481  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHhcC-CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092          445 LLRLALDDVLDSL-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL  504 (518)
Q Consensus       445 ~l~~~L~~~L~~L-~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKL  504 (518)
                      ..+..|..+++.| ++.+|.||.++|    ...++..+||+.||+|+.++..+..+|++.|
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            4456688889898 489999999999    4789999999999999999999999999876

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.

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=97.57  E-value=0.00027  Score=54.51  Aligned_cols=48  Identities=27%  Similarity=0.373  Sum_probs=41.3

Q ss_pred             CCHHHHHHHhHHh--cCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092          457 LKPKESLVIRQRF--GLDGK-GDRTLGEIAGNLNISREMVRKHEVKGLMKL  504 (518)
Q Consensus       457 L~~rEr~VL~lry--GL~~~-e~~Tl~EIA~~LgISrerVRqie~rALkKL  504 (518)
                      |+++|+++|..-|  |..+. ..-|+.|||+.||||.+++..++.+|.+||
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            7899999998755  44343 368999999999999999999999999987

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=97.57  E-value=9.7e-05  Score=63.36  Aligned_cols=51  Identities=20%  Similarity=0.248  Sum_probs=43.6

Q ss_pred             HHHHHHHh-cCCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          448 LALDDVLD-SLKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       448 ~~L~~~L~-~L~~rEr~VL~lryGL~~---~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      +.+..+|. -|+|+|+.+|.+||||.+   ..++|+.|||+.+|||+.+|.+..+
T Consensus        23 ~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn   77 (94)
T TIGR01321        23 DDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSN   77 (94)
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHh
Confidence            34666674 499999999999999987   6789999999999999999986643

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.

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=97.48  E-value=0.00023  Score=58.41  Aligned_cols=48  Identities=21%  Similarity=0.192  Sum_probs=41.5

Q ss_pred             HHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          449 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       449 ~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .+.+-|+.||++.+.++.|.+-   .+++|+.|||+.||+|..+|++++++
T Consensus         8 ~~~~~l~~l~~~~r~af~L~R~---~eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879         8 KLAERLTWVDSLAEAAAALARE---EAGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             hHHHHHhcCCHHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            4566788999999999999531   48999999999999999999999874

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.

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=97.30  E-value=0.00058  Score=64.96  Aligned_cols=51  Identities=20%  Similarity=0.164  Sum_probs=47.0

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  511 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~  511 (518)
                      .|+++|++||.+.-     +|+|.+|||+.|++|..||+....++++||.-..+.+
T Consensus       133 ~LSpRErEVLrLLA-----qGkTnKEIAe~L~IS~rTVkth~srImkKLgV~SRaE  183 (198)
T PRK15201        133 HFSVTERHLLKLIA-----SGYHLSETAALLSLSEEQTKSLRRSIMRKLHVKTEQQ  183 (198)
T ss_pred             CCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence            59999999999887     8999999999999999999999999999998766654

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=97.30  E-value=0.00043  Score=67.46  Aligned_cols=50  Identities=24%  Similarity=0.268  Sum_probs=46.1

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      .|+++|++||.+.-     +|+|.+|||+.||+|..||+.+..+.++||.-..+.
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            59999999999887     799999999999999999999999999999865553

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=97.24  E-value=0.00052  Score=66.20  Aligned_cols=52  Identities=31%  Similarity=0.328  Sum_probs=46.5

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  511 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~  511 (518)
                      ..|++||++|+.+.-     +|+|.+|||+.|++|..||+.+..+.++||--..+.+
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            359999999999887     7999999999999999999999999999997654443

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=97.23  E-value=0.00052  Score=67.13  Aligned_cols=52  Identities=21%  Similarity=0.279  Sum_probs=46.9

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  511 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~  511 (518)
                      ..|++||++||.+.-     +|+|.+|||+.|++|..||+.+..+.++||--..+.+
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            469999999999887     7999999999999999999999999999997655443

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=97.23  E-value=0.00066  Score=67.36  Aligned_cols=54  Identities=26%  Similarity=0.187  Sum_probs=48.3

Q ss_pred             HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       454 L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      ...||++|++||.+..     +++|..|||+.||||..+|+.++.+|++||.-..+.+.
T Consensus       169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~~~a  222 (232)
T TIGR03541       169 AGVLSEREREVLAWTA-----LGRRQADIAAILGISERTVENHLRSARRKLGVATTAQA  222 (232)
T ss_pred             hccCCHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHHH
Confidence            3479999999999976     79999999999999999999999999999997766543

Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.

>TIGR03020 EpsA transcriptional regulator EpsA

Probab=97.23  E-value=0.00063  Score=68.48  Aligned_cols=54  Identities=24%  Similarity=0.202  Sum_probs=49.0

Q ss_pred             HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       454 L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      +..||++|++||.+..     +++|.+|||+.||||..||+.+..++++||.-..+.+.
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     79999999999999999999999999999998776654

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.

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=97.21  E-value=0.00077  Score=66.22  Aligned_cols=56  Identities=14%  Similarity=-0.043  Sum_probs=50.4

Q ss_pred             HHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092          451 DDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  511 (518)
Q Consensus       451 ~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~  511 (518)
                      .++...|+|+|++||.+.-     +|+|.+|||+.|++|..||+.+..+.++||--..+.+
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            4566789999999999887     7999999999999999999999999999998766654

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=97.18  E-value=0.00076  Score=66.37  Aligned_cols=52  Identities=23%  Similarity=0.210  Sum_probs=47.8

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  511 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~  511 (518)
                      ..|+++|++|+.+.+     +|+|.+|||+.|++|..||+.+..++++||.-..+.+
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

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=97.08  E-value=0.002  Score=62.01  Aligned_cols=67  Identities=24%  Similarity=0.255  Sum_probs=58.1

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhh
Q 010092          444 ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQ  515 (518)
Q Consensus       444 ~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~  515 (518)
                      ......+...+.+|+||||+|+...-     .++..++||..||||..||..+-...+.||+.....+-++-
T Consensus       130 ~~~~~~~~~~l~tLT~RERqVl~~vV-----~G~~NKqIA~dLgiS~rTVe~HRanvM~Km~a~SlaeLvr~  196 (202)
T COG4566         130 ADRQAAIRARLATLTPRERQVLDLVV-----RGLMNKQIAFDLGISERTVELHRANVMEKMQARSLAELVRM  196 (202)
T ss_pred             HHHHHHHHHHHHhcCHHHHHHHHHHH-----cCcccHHHHHHcCCchhhHHHHHHHHHHHHhhccHHHHHHH
Confidence            34556788899999999999999876     78999999999999999999999999999998766555443

>PRK13870 transcriptional regulator TraR; Provisional

Probab=97.06  E-value=0.001  Score=66.34  Aligned_cols=52  Identities=21%  Similarity=0.240  Sum_probs=47.1

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      .|++||++||.+-=     +|+|..|||.+||||..||..+++.|.+||--..+.+.
T Consensus       173 ~LT~RE~E~L~W~A-----~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga~nr~qA  224 (234)
T PRK13870        173 WLDPKEATYLRWIA-----VGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHL  224 (234)
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHHH
Confidence            49999999999886     89999999999999999999999999999987665543

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=97.05  E-value=0.0025  Score=49.62  Aligned_cols=54  Identities=31%  Similarity=0.359  Sum_probs=47.5

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  513 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L  513 (518)
                      ..|+++|.+|+.+.-     .++|..|||..+|+|..+|+.+..++.+||.-..+.+.+
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            369999999998876     579999999999999999999999999999877665443

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=97.04  E-value=0.00085  Score=49.60  Aligned_cols=41  Identities=27%  Similarity=0.328  Sum_probs=24.5

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      ..|++.|+..|...+    ..++|..+||+.||+|++||+..+.|
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            468999999999888    68899999999999999999998876

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=97.00  E-value=0.0015  Score=64.04  Aligned_cols=53  Identities=32%  Similarity=0.339  Sum_probs=47.6

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      ..|++||++|+++.-     +|+|.+|||+.|++|..||+.+..+.++||.-..+.+-
T Consensus       147 ~~LT~RE~eVL~lla-----~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~~Rtea  199 (211)
T COG2197         147 ELLTPRELEVLRLLA-----EGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRNRTEA  199 (211)
T ss_pred             CCCCHHHHHHHHHHH-----CCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCCCCHHHH
Confidence            469999999999876     79999999999999999999999999999987665543

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=96.98  E-value=0.0016  Score=65.13  Aligned_cols=52  Identities=23%  Similarity=0.288  Sum_probs=47.2

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      .|+++|++||.+-.     +|+|..|||.+||||..||+.++..+++||--..+.+.
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            59999999999987     79999999999999999999999999999987665543

>PRK09483 response regulator; Provisional

Probab=96.83  E-value=0.0021  Score=60.91  Aligned_cols=51  Identities=24%  Similarity=0.255  Sum_probs=45.2

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      ..|+++|++||.+..     .++|.+|||+.|++|..||+.+..+.++||--..+.
T Consensus       147 ~~Lt~rE~~vl~~~~-----~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v~~~~  197 (217)
T PRK09483        147 ASLSERELQIMLMIT-----KGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDV  197 (217)
T ss_pred             cccCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHH
Confidence            469999999998765     789999999999999999999999999999654443

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=96.79  E-value=0.0028  Score=62.17  Aligned_cols=51  Identities=24%  Similarity=0.310  Sum_probs=43.8

Q ss_pred             cCCHHHHHHHhHHh--cCCCC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          456 SLKPKESLVIRQRF--GLDGK-GDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       456 ~L~~rEr~VL~lry--GL~~~-e~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      .|+++|++||..-|  |..+. ...+++|||+.||||.+++.+++.+|.+||=.
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            69999999999855  54443 35899999999999999999999999999853

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.74  E-value=0.005  Score=53.30  Aligned_cols=47  Identities=23%  Similarity=0.285  Sum_probs=42.7

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      -|+.+|+..+.++|    ..++|+.|||+.++||+++|...++|.-+.|-.
T Consensus        17 LLT~KQ~~Y~~lyy----~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~   63 (105)
T COG2739          17 LLTKKQKNYLELYY----LDDLSLSEIAEEFNVSRQAIYDNIKRTEKILED   63 (105)
T ss_pred             HHhHHHHHHHHHHH----HhhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence            38999999999999    589999999999999999999999999777654

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=96.73  E-value=0.0035  Score=70.92  Aligned_cols=38  Identities=16%  Similarity=0.156  Sum_probs=34.2

Q ss_pred             hhcCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhH
Q 010092          195 EYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMK  232 (518)
Q Consensus       195 ~~~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~  232 (518)
                      +.+.++|+|+|||++||.+||||.|+|+.+++.|+.+.
T Consensus        98 ~~~rt~DPVRMYLREMG~V~LLTREgEIeIAKRIE~G~  135 (619)
T PRK05658         98 EIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGE  135 (619)
T ss_pred             ccCCCCChHHHHHHHhccCcCCCcHHHHHHHHHHHHHH
Confidence            34568999999999999999999999999999997654

>PRK01381 Trp operon repressor; Provisional

Probab=96.69  E-value=0.0014  Score=56.69  Aligned_cols=50  Identities=18%  Similarity=0.224  Sum_probs=41.7

Q ss_pred             HHHHHHHHHhc-CCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHH
Q 010092          446 LRLALDDVLDS-LKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRK  495 (518)
Q Consensus       446 l~~~L~~~L~~-L~~rEr~VL~lryGL~~---~e~~Tl~EIA~~LgISrerVRq  495 (518)
                      ....+..+|.. |+|.|+..|..||++..   ..++|+.|||+.+|||..+|.+
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 89999999999999976   4579999999999999988873

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=96.69  E-value=0.0033  Score=55.25  Aligned_cols=49  Identities=18%  Similarity=0.081  Sum_probs=44.8

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      .|+..|-+.|+|.+    ++++|.+|-|+.||||+.|+..++..|.+|+-..+
T Consensus        41 ~L~~dElEAiRL~D----~egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~AL   89 (106)
T PF02001_consen   41 VLTVDELEAIRLVD----YEGLSQEEAAERMGVSRPTFQRILESARKKIADAL   89 (106)
T ss_pred             EeeHHHHHHHHHHH----HcCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHH
Confidence            58889999999988    58999999999999999999999999999997644

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=96.63  E-value=0.0073  Score=55.51  Aligned_cols=59  Identities=19%  Similarity=0.195  Sum_probs=51.1

Q ss_pred             HHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          449 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       449 ~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      .+...+..|+++|+.||.+.+     .+++.++||+.+|+|..+|+.+..++++||+...+.+-
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            455667789999999999755     57899999999999999999999999999987766553

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=96.53  E-value=0.0069  Score=55.96  Aligned_cols=51  Identities=25%  Similarity=0.285  Sum_probs=45.3

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      ..|+++|++||.+.-     +++|.+|||+.|++|..||+.+..++++||.-..+.
T Consensus       148 ~~lt~~e~~vl~l~~-----~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~~  198 (211)
T PRK15369        148 PLLTPRERQILKLIT-----EGYTNRDIAEQLSISIKTVETHRLNMMRKLDVHKVA  198 (211)
T ss_pred             cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHH
Confidence            359999999999843     789999999999999999999999999999865543

>PRK10651 transcriptional regulator NarL; Provisional

Probab=96.50  E-value=0.0061  Score=57.03  Aligned_cols=52  Identities=27%  Similarity=0.337  Sum_probs=46.5

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  511 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~  511 (518)
                      ..|+++|++|+.+..     ++++.++||+.+++|..||+.+..+.++||.-..+.+
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            359999999999866     7899999999999999999999999999998665544

>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family

Probab=96.44  E-value=0.016  Score=52.51  Aligned_cols=60  Identities=10%  Similarity=0.146  Sum_probs=50.7

Q ss_pred             HHHHHHHHH-hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          446 LRLALDDVL-DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       446 l~~~L~~~L-~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      ....+..++ +.|++.+|.||.++|. + .++++..+|+..||+|+.+...+.++|+.++-..
T Consensus        68 ~~~~i~~ai~~~l~~~~r~Il~~~Yl-~-~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~  128 (132)
T TIGR01637        68 EARAIVNAIVNQLDEISRQILYDKYL-E-PDQKYDYQIMMELGYSHRQYYRIKKRALLRFATL  128 (132)
T ss_pred             HHHHHHHHHHHhCCHHHHHHHHHHHc-C-ccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHH
Confidence            345677777 8999999999999994 1 1278999999999999999999999999988644

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.

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=96.38  E-value=0.0023  Score=57.44  Aligned_cols=50  Identities=24%  Similarity=0.199  Sum_probs=45.7

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      -|+++|-.||.||-     .|+|.+|||++||-|+..|+-|+.+|+.++.+..+.
T Consensus         8 flte~qikvl~lRe-----kG~tQ~eIA~~L~TTraNvSaIEkrA~enIekarnT   57 (143)
T COG1356           8 FLTEQQIKVLVLRE-----KGLTQSEIARILKTTRANVSAIEKRALENIEKARNT   57 (143)
T ss_pred             eeehhheeeeehhh-----ccccHHHHHHHHccchhhHHHHHHHHHHHHHHHHHH
Confidence            38999999999997     899999999999999999999999999999876543

>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=96.12  E-value=0.02  Score=45.97  Aligned_cols=60  Identities=25%  Similarity=0.230  Sum_probs=48.9

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhc-c--CCCCCHHHHHHHHHHHHHHHHHhcC
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQD-F--ANGPRFQDLCQAGVKGLITAIDRFE  323 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~-~--~~g~~~eDLIQEG~IGLirAvekFD  323 (518)
                      .|.++.+||..|.++++.+|-|++.+.+.+-..+ .  ..+.-=+||-|+-...|++++-+|+
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            4677899999999999999999999988862211 0  1244459999999999999999996

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

>PRK10403 transcriptional regulator NarP; Provisional

Probab=96.04  E-value=0.015  Score=54.15  Aligned_cols=54  Identities=30%  Similarity=0.241  Sum_probs=47.4

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  513 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L  513 (518)
                      ..|+++|.+|+.+..     +++|.++||+.+|+|..||+.+..+.++||.-..+.+-.
T Consensus       152 ~~Lt~~e~~vl~~~~-----~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~~~~~~  205 (215)
T PRK10403        152 SVLTERELDVLHELA-----QGLSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVAAT  205 (215)
T ss_pred             ccCCHHHHHHHHHHH-----CCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHHHH
Confidence            359999999998776     689999999999999999999999999999776665543

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=95.96  E-value=0.021  Score=53.11  Aligned_cols=57  Identities=26%  Similarity=0.310  Sum_probs=49.1

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQH  516 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~y  516 (518)
                      ..|+++|.+|+.+..     +++|.++||+.|++|..+|+.+..+.++||.-..+.+-...|
T Consensus       136 ~~Lt~~E~~il~~l~-----~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~~~~~l~~~~  192 (196)
T PRK10360        136 DPLTKRERQVAEKLA-----QGMAVKEIAAELGLSPKTVHVHRANLMEKLGVSNDVELARRM  192 (196)
T ss_pred             cCCCHHHHHHHHHHH-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence            369999999999876     579999999999999999999999999999877666544433

>PRK15320 transcriptional activator SprB; Provisional

Probab=95.93  E-value=0.014  Score=56.59  Aligned_cols=51  Identities=10%  Similarity=0.068  Sum_probs=45.6

Q ss_pred             HHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          452 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       452 ~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      .+--.|+++|.+|+.+--     .|+|.+|||+.|++|..+|+...++.+.||.-.
T Consensus       160 ~~~~~LSdREIEVL~LLA-----kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgAk  210 (251)
T PRK15320        160 NLPPGVTQAKYALLILLS-----SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGMD  210 (251)
T ss_pred             cCCCCCCHHHHHHHHHHH-----cCCCHHHHHHHhccchhhHHHHHHHHHHHcCCC
Confidence            334579999999998876     799999999999999999999999999999754

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=95.53  E-value=0.026  Score=48.47  Aligned_cols=48  Identities=21%  Similarity=0.067  Sum_probs=43.4

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      .|+..|-+.|+|..    ++++|.+|-|..||||+.|+-+.++.|.+|.-..
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            47778889999988    6899999999999999999999999999998654

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=95.40  E-value=0.058  Score=49.20  Aligned_cols=58  Identities=26%  Similarity=0.334  Sum_probs=48.4

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092          446 LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  505 (518)
Q Consensus       446 l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR  505 (518)
                      ....|..+++.|.+.++.||.+||+  +..++|..+||..|++|..+++.+...-...++
T Consensus        71 ~k~~id~~~~~l~de~k~Ii~lry~--~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i~  128 (130)
T PF05263_consen   71 QKEAIDRWLETLIDEEKRIIKLRYD--RRSRRTWYQIAQKLHISERTARRWRDRFKNDIY  128 (130)
T ss_pred             HHHHHHHHHHhhCHHHHHHHHHHHc--ccccchHHHHHHHhCccHHHHHHHHHHHHHHhc
Confidence            4567888899999999999999996  234699999999999999999988776555443

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=95.35  E-value=0.039  Score=51.53  Aligned_cols=49  Identities=24%  Similarity=0.209  Sum_probs=43.3

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                      .|+++|..|+.+..     +++|.+|||+.|++|..||+.+..++++||.-..+
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            48999999998654     67999999999999999999999999999975544

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=95.20  E-value=0.042  Score=46.84  Aligned_cols=39  Identities=15%  Similarity=0.193  Sum_probs=32.2

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +.|++| ..|+.+.-     .++|..+||+.+|+|+.||.++. ++
T Consensus        35 ~~Ls~R-~~I~~ll~-----~G~S~~eIA~~LgISrsTIyRi~-R~   73 (88)
T TIGR02531        35 QSLAQR-LQVAKMLK-----QGKTYSDIEAETGASTATISRVK-RC   73 (88)
T ss_pred             HhhhHH-HHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHH-Hh
Confidence            458899 78877765     57999999999999999999944 44

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.

>PRK13558 bacterio-opsin activator; Provisional

Probab=95.19  E-value=0.035  Score=62.79  Aligned_cols=52  Identities=17%  Similarity=0.153  Sum_probs=43.4

Q ss_pred             HhcCCHHHHHHHhHHhcCC--CC-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092          454 LDSLKPKESLVIRQRFGLD--GK-GDRTLGEIAGNLNISREMVRKHEVKGLMKLK  505 (518)
Q Consensus       454 L~~L~~rEr~VL~lryGL~--~~-e~~Tl~EIA~~LgISrerVRqie~rALkKLR  505 (518)
                      ...|+++|+++|..-|-.+  +. .+-|++|||+.||||++++.+++.+|.+||=
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            3579999999999977321  11 2359999999999999999999999999984

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=95.18  E-value=0.047  Score=51.03  Aligned_cols=50  Identities=26%  Similarity=0.285  Sum_probs=44.7

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                      ..|+++|.+|+.+..     .+.|.++||+.+++|..||+.+..+..+||.-..+
T Consensus       142 ~~lt~~E~~vl~~l~-----~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~~~~  191 (204)
T PRK09958        142 DSLSKQEISVMRYIL-----DGKDNNDIAEKMFISNKTVSTYKSRLMEKLECKSL  191 (204)
T ss_pred             ccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCH
Confidence            469999999998877     67899999999999999999999999999965443

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=95.14  E-value=0.046  Score=41.82  Aligned_cols=48  Identities=17%  Similarity=0.168  Sum_probs=42.2

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      +|+..++.++.+.|-   ..+.|++.+|..+|||+++|+++.+..+.-|-.
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            588899999888774   678999999999999999999999998877754

>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=95.13  E-value=0.046  Score=44.57  Aligned_cols=39  Identities=36%  Similarity=0.674  Sum_probs=30.8

Q ss_pred             hHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092          231 MKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (518)
Q Consensus       231 ~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~  269 (518)
                      +..+.++..+|+..+||.|+..|+|..+|++.+.+..++
T Consensus         3 l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l   41 (78)
T PF04539_consen    3 LRKIERARRELEQELGREPTDEEIAEELGISVEEVRELL   41 (78)
T ss_dssp             HHHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHH
Confidence            345677888999999999999999999999998887655

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 ....

>PRK04841 transcriptional regulator MalT; Provisional

Probab=95.09  E-value=0.042  Score=64.14  Aligned_cols=53  Identities=21%  Similarity=0.277  Sum_probs=47.8

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      ..|+++|.+|+.+..     +++|.+|||..|+||..||+.++++...||.-..+.+.
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

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=94.98  E-value=0.022  Score=42.50  Aligned_cols=33  Identities=27%  Similarity=0.256  Sum_probs=23.2

Q ss_pred             HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          463 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       463 ~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .||.+..     +++|..+||+.||||+.+|+++.++-
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            4555555     58999999999999999999997764

>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]

Probab=94.98  E-value=0.59  Score=49.05  Aligned_cols=57  Identities=19%  Similarity=0.339  Sum_probs=48.8

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          446 LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       446 l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      ++...--+--.|++.+|.-|.+|.    ..++|..|||..|=|+..++-|.+.||.++++.
T Consensus       110 LRLiFvccHPal~~~~riALtLR~----v~GLs~~eIArAFLv~e~am~QRivRAK~ri~~  166 (415)
T COG4941         110 LRLIFVCCHPALPPEQRIALTLRL----VGGLSTAEIARAFLVPEAAMAQRIVRAKARIRE  166 (415)
T ss_pred             HHhhhhhcCCCCChhhHHHHHHHH----HcCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHh
Confidence            333333333459999999999998    679999999999999999999999999999996

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=94.73  E-value=0.28  Score=52.15  Aligned_cols=129  Identities=22%  Similarity=0.286  Sum_probs=71.8

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHH
Q 010092          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV  312 (518)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~  312 (518)
                      .+......|...+|++|+..|+|..+|++.+.+..++....            -.+++-...    +.+   +|      
T Consensus       217 ~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~~~~------------~~~SLd~~~----~~~---~~------  271 (367)
T PRK09210        217 KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQ------------EPVSLETPI----GEE---DD------  271 (367)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhc------------CCCCcCCCC----CCC---Cc------
Confidence            44566677888999999999999999999988876542210            001110000    000   01      


Q ss_pred             HHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHH--hCCCCCHHHH
Q 010092          313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFE--LKRVPTDEEI  390 (518)
Q Consensus       313 IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~e--lgR~PT~eEL  390 (518)
                      ..|...+.  |+.............++..+..++..     +|.             -.+..-.+..-  .|.+-|.+||
T Consensus       272 ~~l~d~i~--d~~~~~p~~~~~~~~~~~~l~~~l~~-----L~~-------------rEr~Vl~lrygl~~~~~~tl~EI  331 (367)
T PRK09210        272 SHLGDFIE--DQDATSPADHAAYELLKEQLEDVLDT-----LTD-------------REENVLRLRFGLDDGRTRTLEEV  331 (367)
T ss_pred             chhhhhcc--CCCCCCHHHHHHHHHHHHHHHHHHHh-----CCH-------------HHHHHHHHHhccCCCCCccHHHH
Confidence            01111111  11112223344555666677666651     222             11111122221  2377899999


Q ss_pred             HHHhCCCHHHHHHHHH
Q 010092          391 IQGVNISPERYREVMK  406 (518)
Q Consensus       391 A~~lgis~e~v~~~l~  406 (518)
                      |+.+|+|.++|+.+..
T Consensus       332 a~~lgvs~erVrQi~~  347 (367)
T PRK09210        332 GKVFGVTRERIRQIEA  347 (367)
T ss_pred             HHHHCCCHHHHHHHHH
Confidence            9999999999998854

>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=94.44  E-value=0.066  Score=39.56  Aligned_cols=33  Identities=18%  Similarity=0.118  Sum_probs=24.1

Q ss_pred             HHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          461 ESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       461 Er~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      ...|+.|+-     +++|..+||+.+|||+.||.+++.
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            355666665     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 ....

>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=94.40  E-value=0.11  Score=38.53  Aligned_cols=41  Identities=24%  Similarity=0.167  Sum_probs=30.1

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      |++.++.||..-+=   .++.|..|||+.+|+|..+|++++++-
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            56788888876552   456999999999999999999877654

...

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=93.98  E-value=0.058  Score=37.38  Aligned_cols=26  Identities=38%  Similarity=0.431  Sum_probs=18.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092          476 DRTLGEIAGNLNISREMVRKHEVKGLMKLK  505 (518)
Q Consensus       476 ~~Tl~EIA~~LgISrerVRqie~rALkKLR  505 (518)
                      ++|.+|||+.+|+|+++|++    ++++|+
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            47899999999999999995    455554

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 ....

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=93.88  E-value=0.7  Score=48.47  Aligned_cols=36  Identities=33%  Similarity=0.593  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC  268 (518)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~  268 (518)
                      .+......|...+|++|+..|+|..+|++.+.+..+
T Consensus       174 ~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~  209 (324)
T PRK07921        174 KLARIKRELHQQLGREATDEELAEESGIPEEKIADL  209 (324)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence            445667778889999999999999999998777654

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=93.76  E-value=0.084  Score=55.13  Aligned_cols=36  Identities=22%  Similarity=0.204  Sum_probs=32.2

Q ss_pred             HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          463 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       463 ~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                      .|-.|||    .+++|.+|||++||+||.+|.+++.+|.+
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            4566788    68999999999999999999999999965

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=93.76  E-value=0.73  Score=51.20  Aligned_cols=36  Identities=31%  Similarity=0.556  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC  268 (518)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~  268 (518)
                      .+...+.+|...+|++|+..|+|..+|++.+.+..+
T Consensus       359 kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~  394 (509)
T PRK05901        359 KLGRIERELLQELGREPTPEELAKEMGFTPEKVREI  394 (509)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            445667788889999999999999999998877654

>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=93.68  E-value=0.13  Score=33.91  Aligned_cols=36  Identities=25%  Similarity=0.385  Sum_probs=27.6

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH  496 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqi  496 (518)
                      +++.++..+...|    ..+.|..+||+.+|+|+.+|.++
T Consensus         6 ~~~~~~~~i~~~~----~~~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569           6 LTPEQIEEARRLL----AAGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             CCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHh
Confidence            4555565555555    35679999999999999999875

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

>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=93.32  E-value=0.11  Score=41.64  Aligned_cols=46  Identities=20%  Similarity=0.255  Sum_probs=28.6

Q ss_pred             HhcCCHHHHHHHhH--HhcCCCCCCCCHHHHHHHhCCC-HHHHHHHHHH
Q 010092          454 LDSLKPKESLVIRQ--RFGLDGKGDRTLGEIAGNLNIS-REMVRKHEVK  499 (518)
Q Consensus       454 L~~L~~rEr~VL~l--ryGL~~~e~~Tl~EIA~~LgIS-rerVRqie~r  499 (518)
                      |..|+++|++||..  .|--..+-+-|+.|||+.||++ .++|.+++..
T Consensus         1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~   49 (65)
T PF01726_consen    1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA   49 (65)
T ss_dssp             -----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence            45799999999876  2222223467999999999997 9999877643

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.

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

Probab=93.25  E-value=0.94  Score=44.92  Aligned_cols=36  Identities=44%  Similarity=0.712  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC  268 (518)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~  268 (518)
                      .+......+...+|++|+.+|+|..+|++.+.+..+
T Consensus        88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~  123 (238)
T TIGR02393        88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVREI  123 (238)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            344566778889999999999999999998877654

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.

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=92.41  E-value=0.94  Score=49.11  Aligned_cols=39  Identities=18%  Similarity=0.162  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Q 010092          367 RGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVM  405 (518)
Q Consensus       367 ~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l  405 (518)
                      ...+.+....|..++|++||.+|.|..+|+++.+++..+
T Consensus       110 ~~~l~~~~~~l~~~~g~~pt~~ewa~~~~~~~~~l~~~l  148 (415)
T PRK07598        110 YLRLIEVRERLTSELGHRPSLERWAKTADISLADLKPTL  148 (415)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCCcHHHHHHhh
Confidence            345566778899999999999999988887766665544

>PF13518 HTH_28: Helix-turn-helix domain

Probab=92.39  E-value=0.28  Score=36.50  Aligned_cols=27  Identities=26%  Similarity=0.254  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          475 GDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       475 e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      ++.|+.+||..+|||+.+|+++..+-.
T Consensus        11 ~g~s~~~~a~~~gis~~tv~~w~~~y~   37 (52)
T PF13518_consen   11 EGESVREIAREFGISRSTVYRWIKRYR   37 (52)
T ss_pred             cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence            456999999999999999999887653

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=92.31  E-value=0.32  Score=43.33  Aligned_cols=50  Identities=28%  Similarity=0.256  Sum_probs=42.9

Q ss_pred             HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          453 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       453 ~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      .+..|++.+..-|..+.    ...=+++|+++.||||..|||..+.+.+.+|-.
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            35689998888887665    234589999999999999999999999999986

>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ

Probab=92.09  E-value=0.7  Score=41.75  Aligned_cols=50  Identities=18%  Similarity=0.110  Sum_probs=44.9

Q ss_pred             HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       454 L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      |..-.|.+-.+|.++|    ..++|...||..+++|...||+.+.+|-.-+...
T Consensus        60 L~~~~~~~~~ll~~~Y----v~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~  109 (125)
T PF06530_consen   60 LKKRDPEEYDLLILYY----VYGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGC  109 (125)
T ss_pred             HHccCHHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhh
Confidence            4457999999999999    4799999999999999999999999998888765

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

>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=92.06  E-value=0.4  Score=35.12  Aligned_cols=39  Identities=23%  Similarity=0.368  Sum_probs=26.7

Q ss_pred             CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          458 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       458 ~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      ++-.+.||..--.   ....|+.+||+.+|+|..+|.+...+
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            4456666665442   35799999999999999999977654

...

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

Probab=92.06  E-value=2.4  Score=42.90  Aligned_cols=38  Identities=32%  Similarity=0.561  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092          232 KVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (518)
Q Consensus       232 ~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~  269 (518)
                      ..+..+.+.|+.++||+||+.|+|...|++.+++...+
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            44567788899999999999999999999987765544

>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []

Probab=92.05  E-value=0.3  Score=38.37  Aligned_cols=26  Identities=23%  Similarity=0.270  Sum_probs=24.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          475 GDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       475 e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .+++..|||+.||+++.+|.+...+-
T Consensus        12 ~G~~~~eIA~~Lg~~~~TV~~W~~r~   37 (58)
T PF06056_consen   12 QGWSIKEIAEELGVPRSTVYSWKDRY   37 (58)
T ss_pred             cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence            79999999999999999999998775

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>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=92.04  E-value=0.25  Score=39.20  Aligned_cols=26  Identities=31%  Similarity=0.519  Sum_probs=23.2

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          474 KGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       474 ~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      ...+++.+||+.||||..+||....+
T Consensus        20 ~g~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   20 NGKIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHhhh
Confidence            45899999999999999999988764

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 [].

>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=91.81  E-value=0.17  Score=38.88  Aligned_cols=40  Identities=28%  Similarity=0.322  Sum_probs=27.8

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .|+..|+.=|.-+|    ..+.+..+||..|||+.+||+.|...
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            46666666555566    36779999999999999999999875

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.

>PF13730 HTH_36: Helix-turn-helix domain

Probab=91.58  E-value=0.56  Score=35.54  Aligned_cols=46  Identities=24%  Similarity=0.362  Sum_probs=32.8

Q ss_pred             cCCHHHHHHHhHHhcCCCCCC---CCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092          456 SLKPKESLVIRQRFGLDGKGD---RTLGEIAGNLNISREMVRKHEVKGLMKLK  505 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~---~Tl~EIA~~LgISrerVRqie~rALkKLR  505 (518)
                      .|++.++.|+..-.-+.+..+   .|.+.||+.+|+|+.+|++    +++.|.
T Consensus         2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~----~i~~L~   50 (55)
T PF13730_consen    2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQR----AIKELE   50 (55)
T ss_pred             CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHH----HHHHHH
Confidence            588888888766443322222   3899999999999999984    555554

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=91.50  E-value=0.36  Score=47.33  Aligned_cols=47  Identities=23%  Similarity=0.164  Sum_probs=36.8

Q ss_pred             cCCHHHHHHHhHHh-cCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRF-GLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       456 ~L~~rEr~VL~lry-GL~~~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                      .|+++|.+++.... +. ..+++|.+|||+.||+|..||+.+..++...
T Consensus       158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~  205 (239)
T PRK10430        158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIWLVNC  205 (239)
T ss_pred             CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHHHHhC
Confidence            48899977764433 11 1378999999999999999999999988554

>smart00351 PAX Paired Box domain

Probab=90.91  E-value=0.54  Score=42.37  Aligned_cols=42  Identities=19%  Similarity=0.059  Sum_probs=32.7

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                      |+..+|.-|...|    .++.|..+||+.||||+.+|.++.++...
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            4555555555555    36789999999999999999999998753

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=90.89  E-value=2  Score=45.95  Aligned_cols=36  Identities=25%  Similarity=0.501  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHH
Q 010092          232 KVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKK  267 (518)
Q Consensus       232 ~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~  267 (518)
                      ..+......|...+|+.|+..|+|..+|++.+.+..
T Consensus       223 ~~i~~a~~~l~~~lgr~Pt~~EIA~~lg~~~e~v~~  258 (373)
T PRK07406        223 SRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRF  258 (373)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHH
Confidence            344556677888999999999999999999877754

>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=90.36  E-value=0.43  Score=36.15  Aligned_cols=39  Identities=21%  Similarity=0.332  Sum_probs=27.6

Q ss_pred             HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       460 rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      |+..||.+-+  ...++.|.+|||+.||||+.+|++.+..-
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            4556665542  22345999999999999999999776654

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 ....

>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=90.20  E-value=0.59  Score=35.97  Aligned_cols=44  Identities=25%  Similarity=0.246  Sum_probs=32.7

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .|++.|..||..-+.-++ .+.|..|||+.+++++.+|.++.++-
T Consensus         2 glt~~q~~vL~~l~~~~~-~~~t~~~la~~l~~~~~~vs~~v~~L   45 (62)
T PF12802_consen    2 GLTPSQFRVLMALARHPG-EELTQSELAERLGISKSTVSRIVKRL   45 (62)
T ss_dssp             TSTHHHHHHHHHHHHSTT-SGEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHCCC-CCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            378888888887664221 23899999999999999999776654

...

>PHA00675 hypothetical protein

Probab=89.85  E-value=0.65  Score=38.49  Aligned_cols=40  Identities=18%  Similarity=0.105  Sum_probs=30.5

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      .|++-+-+.|+..+-   ..+.|+.+||..||||+++|.+|.+
T Consensus        22 KLt~~qV~~IR~l~~---r~G~s~~~IA~~fGVsrstV~~I~~   61 (78)
T PHA00675         22 KLTDAEVERIRELHE---VEGMSYAVLAEKFEQSKGAIAKICR   61 (78)
T ss_pred             ccCHHHHHHHHHHHH---hcCccHHHHHHHhCCCHHHHHHHHc
Confidence            566666665555441   2577999999999999999999875

>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=89.84  E-value=0.65  Score=34.41  Aligned_cols=37  Identities=27%  Similarity=0.391  Sum_probs=27.9

Q ss_pred             HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      |.-..||.+-.    ..+++..||++.+|+|+++|++++..
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            44455665554    36899999999999999999988754

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 ....

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=89.66  E-value=1.3  Score=44.70  Aligned_cols=36  Identities=33%  Similarity=0.589  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC  268 (518)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~  268 (518)
                      .+..+..+|...+|++|+..|+|..+|++.+.+..+
T Consensus       114 ~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~  149 (256)
T PRK07408        114 QAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI  149 (256)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence            445667788889999999999999999998877554

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=89.63  E-value=0.49  Score=49.61  Aligned_cols=35  Identities=29%  Similarity=0.203  Sum_probs=30.6

Q ss_pred             HHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          464 VIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       464 VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                      +-.+||    .+++|..|||++||||+.+|++++.+|.+
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            345677    68999999999999999999999999864

>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA

Probab=89.48  E-value=0.72  Score=39.10  Aligned_cols=44  Identities=30%  Similarity=0.240  Sum_probs=34.0

Q ss_pred             HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh--CCCHHHHHHHHHHH
Q 010092          454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNL--NISREMVRKHEVKG  500 (518)
Q Consensus       454 L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~L--gISrerVRqie~rA  500 (518)
                      ++.||+..+++..+|.-   ..+.|+.|+|+.|  .||++.|..+..+-
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            47899999999999874   5789999999999  99999998877664

It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=89.48  E-value=0.48  Score=54.96  Aligned_cols=51  Identities=27%  Similarity=0.159  Sum_probs=46.5

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      ||.||.+|+.+.|     .|+|.+|||+++.||-.||+.+...--.||.-..+.+.
T Consensus       832 Ls~RE~eVL~Lia-----~G~SN~eIa~~L~isl~TVKtH~rniy~KLgV~~RtqA  882 (894)
T COG2909         832 LSQRELEVLGLIA-----QGLSNEEIAQELFISLTTVKTHIRNIYQKLGVANRTQA  882 (894)
T ss_pred             ccHHHHHHHHHHH-----ccCCHHHHHHHHHHHHHHHHHHHHHHHHHhCcchHHHH
Confidence            8999999999999     79999999999999999999999999999976655443

>PHA02591 hypothetical protein; Provisional

Probab=89.20  E-value=0.46  Score=39.46  Aligned_cols=24  Identities=29%  Similarity=0.209  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          475 GDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       475 e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      .|+|.++||+.||+|.++|+++..
T Consensus        58 qGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         58 KGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHh
Confidence            589999999999999999999875

>PRK00423 tfb transcription initiation factor IIB; Reviewed

Probab=88.46  E-value=15  Score=38.22  Aligned_cols=176  Identities=14%  Similarity=0.015  Sum_probs=89.8

Q ss_pred             HHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCccccccccc
Q 010092          281 KHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLES  360 (518)
Q Consensus       281 ~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRlP~~~~e  360 (518)
                      ...+..+-.++...        .+.+-+.|...-+++.+.....-+|.....++.-.|.-++.                 
T Consensus       123 ~~a~~~I~~~~~~L--------~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR-----------------  177 (310)
T PRK00423        123 AFALSELDRIASQL--------GLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACR-----------------  177 (310)
T ss_pred             HHHHHHHHHHHHHc--------CCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHH-----------------
Confidence            33445555555544        34466777777788877666767787665555434333332                 


Q ss_pred             hhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchhh
Q 010092          361 TSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQ  440 (518)
Q Consensus       361 ~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee~  440 (518)
                                         ..|-+-|..||++.++++..++....+.-...+.++.+.. +..+++..+.+.-..+ .+.
T Consensus       178 -------------------~~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~-~p~~~i~r~~~~L~L~-~~v  236 (310)
T PRK00423        178 -------------------RCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPPT-DPIDYVPRFASELGLS-GEV  236 (310)
T ss_pred             -------------------HcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCC-CHHHHHHHHHHHcCCC-HHH
Confidence                               1234456777888888888777655443322222322221 1223332222211111 111


Q ss_pred             hHHHHHHHHHHHHHh-cC----CHHH--HHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092          441 RQPALLRLALDDVLD-SL----KPKE--SLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  505 (518)
Q Consensus       441 ~~~~~l~~~L~~~L~-~L----~~rE--r~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR  505 (518)
                      ..  .-...+..+.+ .|    +|.-  ..+|.+-.-+. +.+.|++|||...|||..+|++....-.+.|.
T Consensus       237 ~~--~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~-g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~  305 (310)
T PRK00423        237 QK--KAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLL-GERRTQREVAEVAGVTEVTVRNRYKELAEKLD  305 (310)
T ss_pred             HH--HHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHh-CCCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence            10  11112222221 11    1211  11222211112 36799999999999999999988777766654

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=88.16  E-value=1.6  Score=34.02  Aligned_cols=39  Identities=31%  Similarity=0.388  Sum_probs=29.3

Q ss_pred             CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          458 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       458 ~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      +|.-..||.+-.+   .+++|..|||+.+|++.++|+.++..
T Consensus         9 ~p~R~~Il~~L~~---~~~~t~~ela~~l~~~~~t~s~hL~~   47 (61)
T PF12840_consen    9 DPTRLRILRLLAS---NGPMTVSELAEELGISQSTVSYHLKK   47 (61)
T ss_dssp             SHHHHHHHHHHHH---CSTBEHHHHHHHHTS-HHHHHHHHHH
T ss_pred             CHHHHHHHHHHhc---CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            3666667666522   57999999999999999999977643

...

>PRK05949 RNA polymerase sigma factor; Validated

Probab=87.81  E-value=4.5  Score=42.48  Aligned_cols=36  Identities=22%  Similarity=0.462  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC  268 (518)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~  268 (518)
                      .+......+...+|++|+..|+|..+|++.+.+..+
T Consensus       179 ~l~k~~~~l~~~lgr~pt~~eiA~~l~i~~~~v~~~  214 (327)
T PRK05949        179 KIKKTQRELSQKLGRSATPAEIAKELELEPSQIREY  214 (327)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence            344555667788999999999999999998777654

>cd00131 PAX Paired Box domain

Probab=87.57  E-value=1.3  Score=40.13  Aligned_cols=42  Identities=17%  Similarity=0.022  Sum_probs=31.8

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                      |+...|.-|...|    .+++|..+||+.||||+.+|..+.++-..
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            4444444444445    36899999999999999999999988653

>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=87.06  E-value=1.9  Score=34.58  Aligned_cols=42  Identities=21%  Similarity=0.198  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCC-HHHHHHHHHh
Q 010092          366 VRGEIQRAKLELLFELKRVPTDEEIIQGVNIS-PERYREVMKA  407 (518)
Q Consensus       366 ~~~ki~ka~~eL~~elgR~PT~eELA~~lgis-~e~v~~~l~~  407 (518)
                      .-.++-....+...+.|..||..|||+.+|++ ...|...|..
T Consensus         7 rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~   49 (65)
T PF01726_consen    7 RQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKA   49 (65)
T ss_dssp             HHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence            33445556667778899999999999999997 8888777654

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.

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=87.01  E-value=13  Score=37.54  Aligned_cols=36  Identities=25%  Similarity=0.393  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC  268 (518)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~  268 (518)
                      .+......|+..+|++|+..|+|..+|++.+.+..+
T Consensus       119 ~i~~~~~~l~~~~~~~pt~~eia~~lg~~~~~v~~~  154 (268)
T PRK06288        119 QIERAIAMLEARLGRTPSDEEIADELGISLEEYNSL  154 (268)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHH
Confidence            445556678889999999999999999998766543

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=86.80  E-value=5.6  Score=40.08  Aligned_cols=36  Identities=33%  Similarity=0.559  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092          234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (518)
Q Consensus       234 l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~  269 (518)
                      +......+...+|++|+..|+|..+|++.+.+....
T Consensus       112 l~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~  147 (257)
T PRK05911        112 LADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWF  147 (257)
T ss_pred             HHHHHHHHHHHHCcCCCHHHHHHHhCcCHHHHHHHH
Confidence            344556677889999999999999999987775543

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=86.79  E-value=1.5  Score=32.71  Aligned_cols=25  Identities=24%  Similarity=0.320  Sum_probs=22.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          476 DRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       476 ~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      ..|+++||+.+|||-.+|..+..+.
T Consensus        27 ~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   27 SRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            4699999999999999999998764

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=86.49  E-value=4.3  Score=39.83  Aligned_cols=33  Identities=48%  Similarity=0.636  Sum_probs=27.0

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092          236 QVKEQLQKDLGREPTDVELAEATNMSAAQVKKC  268 (518)
Q Consensus       236 ~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~  268 (518)
                      ...+.+...+|+.|+..|+|..+|++.+.+...
T Consensus       101 ~~~~~l~~~~~r~pt~~ela~~l~~~~~~v~~~  133 (231)
T TIGR02885       101 YMKEELSKELGREPTINELAEALGVSPEEIVMA  133 (231)
T ss_pred             HHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHH
Confidence            445667788999999999999999998776544

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.

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=86.47  E-value=1.6  Score=35.07  Aligned_cols=24  Identities=21%  Similarity=0.230  Sum_probs=20.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          476 DRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       476 ~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      +.|..|||+.+|++..+|++++.+
T Consensus        22 ~~ta~eLa~~lgl~~~~v~r~L~~   45 (68)
T smart00550       22 TSTALQLAKNLGLPKKEVNRVLYS   45 (68)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHH
Confidence            599999999999999999866543

Helix-turn-helix-containing domain. Also known as Zab.

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=86.20  E-value=1.2  Score=34.06  Aligned_cols=42  Identities=29%  Similarity=0.352  Sum_probs=31.4

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      |+..|-.||..-+-   .++.|..+||+.+++++.+|.++..+-.
T Consensus         1 lt~~q~~iL~~l~~---~~~~~~~~la~~~~~~~~~~t~~i~~L~   42 (59)
T PF01047_consen    1 LTPSQFRILRILYE---NGGITQSELAEKLGISRSTVTRIIKRLE   42 (59)
T ss_dssp             STHHHHHHHHHHHH---HSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence            46667777766553   4579999999999999999997766543

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 ....

>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=86.14  E-value=1.4  Score=34.43  Aligned_cols=43  Identities=26%  Similarity=0.219  Sum_probs=28.1

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      |+..|..||..-.  ....++|..+||+.++++..+|.+.+++-.
T Consensus         1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~   43 (68)
T PF13463_consen    1 LTRPQWQVLRALA--HSDGPMTQSDLAERLGISKSTVSRIIKKLE   43 (68)
T ss_dssp             --HHHHHHHHHHT----TS-BEHHHHHHHTT--HHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH--ccCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            5667777776555  235789999999999999999996655543

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=86.03  E-value=1.6  Score=37.54  Aligned_cols=41  Identities=15%  Similarity=0.191  Sum_probs=31.7

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      |++.++.||....-   ....|+.+||+.+|+|+.+|++...+-
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            46677888766442   246999999999999999999776554

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=85.84  E-value=7.8  Score=39.27  Aligned_cols=36  Identities=33%  Similarity=0.478  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092          234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (518)
Q Consensus       234 l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~  269 (518)
                      +......+...+|+.|+..|+|..+|++.+.+..++
T Consensus       129 i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~  164 (264)
T PRK07122        129 LGRATAELSQRLGRAPTASELAAELGMDREEVVEGL  164 (264)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence            344566777889999999999999999988776543

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=85.82  E-value=2.8  Score=38.16  Aligned_cols=51  Identities=25%  Similarity=0.270  Sum_probs=38.5

Q ss_pred             HHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092          449 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  505 (518)
Q Consensus       449 ~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR  505 (518)
                      .+-.+.-.|++.+-+|+..-.  .-..++|..|||+.+|+|+++|.    |||++|=
T Consensus        17 dvl~c~~GLs~~Dv~v~~~LL--~~~~~~tvdelae~lnr~rStv~----rsl~~L~   67 (126)
T COG3355          17 DVLKCVYGLSELDVEVYKALL--EENGPLTVDELAEILNRSRSTVY----RSLQNLL   67 (126)
T ss_pred             HHHHHHhCCcHHHHHHHHHHH--hhcCCcCHHHHHHHHCccHHHHH----HHHHHHH
Confidence            455566679999988876544  12468999999999999999997    5666653

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=85.70  E-value=0.82  Score=44.44  Aligned_cols=40  Identities=23%  Similarity=0.114  Sum_probs=29.8

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .|+++  +|+.+.-  .|..++|.+|||+.||+|+.||+.+...
T Consensus       161 ~Lt~r--~Vl~~~~--~g~~g~s~~eIa~~l~iS~~Tv~~~~~~  200 (225)
T PRK10046        161 PLTLN--AVRKLFK--EPGVQHTAETVAQALTISRTTARRYLEY  200 (225)
T ss_pred             HHHHH--HHHHHHH--cCCCCcCHHHHHHHhCccHHHHHHHHHH
Confidence            35565  5665543  2234799999999999999999998853

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=85.67  E-value=0.8  Score=34.27  Aligned_cols=22  Identities=23%  Similarity=0.271  Sum_probs=19.8

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHH
Q 010092          478 TLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       478 Tl~EIA~~LgISrerVRqie~r  499 (518)
                      |+++||+..|||..+|+..++.
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            7899999999999999987764

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 ....

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=85.62  E-value=6.7  Score=40.91  Aligned_cols=36  Identities=33%  Similarity=0.448  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC  268 (518)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~  268 (518)
                      .+......+...+|+.|+..|+|..+|++.+.+...
T Consensus       169 ~l~~~~~~l~~~~gr~pt~~eiA~~~~~~~~~v~~~  204 (317)
T PRK07405        169 KIKKAQRQLSQQLGRAATIGELAEELELTPKQVREY  204 (317)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHH
Confidence            345566677788999999999999999987766543

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=85.29  E-value=1.2  Score=41.08  Aligned_cols=37  Identities=16%  Similarity=-0.000  Sum_probs=29.2

Q ss_pred             HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       460 rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      +.+.++...+     +++|..|||++||||.++|..+.++.-
T Consensus        10 R~~~~~~~~~-----~G~S~re~Ak~~gvs~sTvy~wv~r~~   46 (138)
T COG3415          10 RERVVDAVVG-----EGLSCREAAKRFGVSISTVYRWVRRYR   46 (138)
T ss_pred             HHHHHHHHHH-----cCccHHHHHHHhCccHHHHHHHHHHhc
Confidence            4444444444     799999999999999999999988754

>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=85.26  E-value=1.1  Score=35.23  Aligned_cols=42  Identities=21%  Similarity=0.227  Sum_probs=29.1

Q ss_pred             CCHHHHHHHhHHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLD-GKGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       457 L~~rEr~VL~lryGL~-~~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      |++....-|...|-|. +++..+..+||+.||+|+.+|....+
T Consensus         2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~   44 (60)
T PF01325_consen    2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLK   44 (60)
T ss_dssp             CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHH
Confidence            4555555555555443 34679999999999999999985443

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=85.20  E-value=0.59  Score=37.13  Aligned_cols=41  Identities=32%  Similarity=0.303  Sum_probs=30.9

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .|++.|..|+..-.   ..++.|..|||+.+|+|+.+|+..+++
T Consensus         5 gLs~~E~~vy~~Ll---~~~~~t~~eIa~~l~i~~~~v~~~L~~   45 (68)
T PF01978_consen    5 GLSENEAKVYLALL---KNGPATAEEIAEELGISRSTVYRALKS   45 (68)
T ss_dssp             CHHHHHHHHHHHHH---HHCHEEHHHHHHHHTSSHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            36777888875432   135899999999999999999865543

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.

>PHA02547 55 RNA polymerase sigma factor; Provisional

Probab=85.19  E-value=6.8  Score=37.39  Aligned_cols=62  Identities=11%  Similarity=0.160  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHHhhhccCCCCC---HHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH
Q 010092          283 NLRLVLFVIKKYFQDFANGPR---FQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT  347 (518)
Q Consensus       283 nlrLV~siAkky~~~~~~g~~---~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~  347 (518)
                      .+..+..++++|.   -.+..   -+|+|.+|.-..++.+..|||++...+-.|.+..+-++..+-|.
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            4445555555554   23444   58999999999999999999999877777666665555554443

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=84.87  E-value=9.5  Score=38.20  Aligned_cols=35  Identities=29%  Similarity=0.434  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092          235 VQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (518)
Q Consensus       235 ~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~  269 (518)
                      ......+..++|++|+.+|+|..+|++.+.+..++
T Consensus       123 ~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~  157 (254)
T TIGR02850       123 LQVRDKLISENSKEPTVSEIAKELKVPQEEVVFAL  157 (254)
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34456677889999999999999999988876554

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.

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=84.82  E-value=10  Score=38.84  Aligned_cols=107  Identities=19%  Similarity=0.187  Sum_probs=59.3

Q ss_pred             CCCCCHHHHHHHhC--CCHHHHHHHHHhcC--CccccCCCcCCchhhhhcccccCCCCcchhh-hHHHHHHHHHHHHHhc
Q 010092          382 KRVPTDEEIIQGVN--ISPERYREVMKASK--PILSLHSRHGVTQEEFINGITDVDGVENENQ-RQPALLRLALDDVLDS  456 (518)
Q Consensus       382 gR~PT~eELA~~lg--is~e~v~~~l~~~~--~~~SLD~~~~~~~eel~~~l~d~~~~~~ee~-~~~~~l~~~L~~~L~~  456 (518)
                      +..+++++||+.++  ||.+++++.+..-.  ..+--+.....  ......+.......+... -.+.++.+.-.++|+.
T Consensus       135 ~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g~y--~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al~~  212 (271)
T TIGR02147       135 PFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDGFY--KQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEALDA  212 (271)
T ss_pred             CCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCCcE--EeecceeecCCccchHHHHHHHHHHHHHHHHHHHh
Confidence            44567889999999  99999999887421  22222211000  000011111111112111 1122333444667888


Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMV  493 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerV  493 (518)
                      .|+.+|.+=.+-+|+   ..-++++|.+.+.--+..|
T Consensus       213 ~p~~eR~~S~lT~~i---~~~~~~~i~~~i~~fRk~i  246 (271)
T TIGR02147       213 LPPSERDVSTVTFGI---SEEAYKEIVKKIQEFRKEV  246 (271)
T ss_pred             CCccccccceeeEec---CHHHHHHHHHHHHHHHHHH
Confidence            999999998888875   4557777777764433333

This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.

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

Probab=84.63  E-value=9.3  Score=39.31  Aligned_cols=35  Identities=34%  Similarity=0.641  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHH
Q 010092          234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC  268 (518)
Q Consensus       234 l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~  268 (518)
                      +......+...+|+.|+..|+|..+|++.+.+..+
T Consensus       163 ~rk~~~~l~~~~~~~pt~~eia~~l~~~~~~v~~~  197 (298)
T TIGR02997       163 IKKVQRELSQKLGRTPSEAEIAEALELEPEQVREL  197 (298)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence            34455667778999999999999999998877654

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).

>PF12728 HTH_17: Helix-turn-helix domain

Probab=84.63  E-value=1  Score=33.60  Aligned_cols=24  Identities=38%  Similarity=0.338  Sum_probs=21.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          477 RTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       477 ~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +|.+|+|+.||||+.+|+++..+.
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

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=84.43  E-value=1.7  Score=35.61  Aligned_cols=52  Identities=15%  Similarity=0.146  Sum_probs=35.5

Q ss_pred             HHHHHHHHhcCCHHHHHHHhHHhc-CCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          447 RLALDDVLDSLKPKESLVIRQRFG-LDGKGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       447 ~~~L~~~L~~L~~rEr~VL~lryG-L~~~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      ...|......|++.|+.|.....- .+....+|..|||+..|||..+|.+..+
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            456777788999999998854331 0112469999999999999999986654

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.

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=84.26  E-value=2  Score=32.85  Aligned_cols=39  Identities=23%  Similarity=0.211  Sum_probs=25.6

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      .|++-|+.-|-...    ..++++.|||..+|-|+..|+..++
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            46777777666665    3589999999999999999998753

>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=84.26  E-value=2.3  Score=35.54  Aligned_cols=43  Identities=14%  Similarity=0.163  Sum_probs=34.2

Q ss_pred             cCCHHHHHHHhHHhc--CCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFG--LDGKGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       456 ~L~~rEr~VL~lryG--L~~~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      .|+++++.||..---  ...+++-.-++||+.+++|..+||+.+.
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            388999999876321  2345788999999999999999998764

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

>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=84.10  E-value=1.2  Score=37.85  Aligned_cols=46  Identities=20%  Similarity=0.265  Sum_probs=31.4

Q ss_pred             CCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRKHEVKGLMK  503 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~---~e~~Tl~EIA~~LgISrerVRqie~rALkK  503 (518)
                      |+|.|..-|..|+-+-.   .+++|+.||++.+|+|..+|.+. +++|+.
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            56666665555542211   25899999999999999999753 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 ....

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=84.00  E-value=9.8  Score=39.10  Aligned_cols=25  Identities=28%  Similarity=0.262  Sum_probs=21.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHh
Q 010092          383 RVPTDEEIIQGVNISPERYREVMKA  407 (518)
Q Consensus       383 R~PT~eELA~~lgis~e~v~~~l~~  407 (518)
                      ..-|.+|||+.||+|..+|+.++..
T Consensus       244 ~~~t~~EIa~~lgvs~~~V~q~~~~  268 (289)
T PRK07500        244 DGATLEALGEELGISKERVRQIEAR  268 (289)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4669999999999999999888654

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=83.82  E-value=2.4  Score=35.94  Aligned_cols=43  Identities=19%  Similarity=0.236  Sum_probs=37.0

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      .|+|.-+..|..+.-   .++++..++|+.||||+.+++++..|-.
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            589999988888762   3579999999999999999999988754

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

Probab=83.56  E-value=14  Score=36.01  Aligned_cols=37  Identities=32%  Similarity=0.530  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (518)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~  269 (518)
                      .+......+...+|++|+..|+|+.+|++.+.+..+.
T Consensus        84 ~l~~~~~~l~~~~~~~~~~~ela~~l~~~~~~v~~~~  120 (224)
T TIGR02479        84 KLERAIRELEARLGREPTEEEIAEELGMDLKEYRQAL  120 (224)
T ss_pred             HHHHHHHHHHHHHCcCCCHHHHHHHhCCCHHHHHHHH
Confidence            4455667788889999999999999999987776543

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.

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=83.11  E-value=1.6  Score=32.96  Aligned_cols=27  Identities=30%  Similarity=0.393  Sum_probs=21.9

Q ss_pred             CCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          472 DGKGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       472 ~~~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      ....++|+.|||+.+|+++++|.+++.
T Consensus        14 ~~~~~~t~~eia~~~gl~~stv~r~L~   40 (52)
T PF09339_consen   14 ESGGPLTLSEIARALGLPKSTVHRLLQ   40 (52)
T ss_dssp             CTBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             cCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            334668999999999999999997765

One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=82.99  E-value=2  Score=41.44  Aligned_cols=35  Identities=23%  Similarity=0.209  Sum_probs=28.3

Q ss_pred             HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       460 rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .++.|..++.     .++|+.+||+.||||++||.++.+.
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            3456666654     5799999999999999999998863

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=82.88  E-value=1.7  Score=41.00  Aligned_cols=50  Identities=14%  Similarity=0.018  Sum_probs=42.5

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCC-----HHHHHHHHHHHHHHHhC
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNIS-----REMVRKHEVKGLMKLKH  506 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgIS-----rerVRqie~rALkKLR~  506 (518)
                      .|+++|.+||.+..- +.+..+|.++|++.++.+     ..+|+.+..+.++||..
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            599999999987662 223469999999999986     78999999999999974

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=82.77  E-value=1.5  Score=31.44  Aligned_cols=25  Identities=28%  Similarity=0.244  Sum_probs=22.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          477 RTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       477 ~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      +|..|+|+.||||+.+|+++.....
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.

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=82.63  E-value=1.7  Score=40.76  Aligned_cols=50  Identities=22%  Similarity=0.154  Sum_probs=41.7

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhC
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~Lg-----ISrerVRqie~rALkKLR~  506 (518)
                      .|+++|.+||.+.. -+.+..+|.++|++.+.     +|..+|+.+..+..+||..
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            49999999998655 12234589999999996     9999999999999999963

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=82.56  E-value=17  Score=28.60  Aligned_cols=74  Identities=18%  Similarity=0.157  Sum_probs=45.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHH
Q 010092          384 VPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESL  463 (518)
Q Consensus       384 ~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~  463 (518)
                      ++++++||+.+|++...+..++.....                        .++.+...    ...+.           .
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            368899999999999988877653210                        01111110    01111           2


Q ss_pred             HHhHHhcCCCCCCCCHHHHHHHhCC-CHHHHHHHHHHH
Q 010092          464 VIRQRFGLDGKGDRTLGEIAGNLNI-SREMVRKHEVKG  500 (518)
Q Consensus       464 VL~lryGL~~~e~~Tl~EIA~~LgI-SrerVRqie~rA  500 (518)
                      ++.+..    ..+.++.+||..+|+ |.....+...+.
T Consensus        42 a~~~l~----~~~~~~~~ia~~~g~~s~~~f~r~Fk~~   75 (84)
T smart00342       42 ARRLLR----DTDLSVTEIALRVGFSSQSYFSRAFKKL   75 (84)
T ss_pred             HHHHHH----cCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence            222222    127899999999999 988887766543

>TIGR00498 lexA SOS regulatory protein LexA

Probab=82.40  E-value=1.9  Score=41.43  Aligned_cols=45  Identities=13%  Similarity=0.072  Sum_probs=33.8

Q ss_pred             hcCCHHHHHHHhHHh--cCCCCCCCCHHHHHHHhCCC-HHHHHHHHHH
Q 010092          455 DSLKPKESLVIRQRF--GLDGKGDRTLGEIAGNLNIS-REMVRKHEVK  499 (518)
Q Consensus       455 ~~L~~rEr~VL~lry--GL~~~e~~Tl~EIA~~LgIS-rerVRqie~r  499 (518)
                      ..|+++|+.||.+-.  ...++.+.|..|||+.+|++ +++|+.++.+
T Consensus         2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~   49 (199)
T TIGR00498         2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKA   49 (199)
T ss_pred             CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHH
Confidence            358999999987744  12234568999999999998 9999865543

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.

>TIGR01764 excise DNA binding domain, excisionase family

Probab=82.34  E-value=1.5  Score=31.57  Aligned_cols=24  Identities=29%  Similarity=0.339  Sum_probs=21.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          477 RTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       477 ~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +|.+|+|+.||||+.+|+++.+..
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g   25 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEG   25 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcC
Confidence            589999999999999999998765

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).

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=82.12  E-value=2  Score=40.97  Aligned_cols=50  Identities=14%  Similarity=0.131  Sum_probs=43.5

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhC
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~Lg-----ISrerVRqie~rALkKLR~  506 (518)
                      .|+++|.+|+.+... +.+...|.++|++.+.     +|..+|..+..+.++||..
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            599999999998763 3345799999999998     9999999999999999974

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=82.02  E-value=5.3  Score=34.18  Aligned_cols=48  Identities=23%  Similarity=0.245  Sum_probs=35.2

Q ss_pred             hcCCHHHHHHHhHH----hcCC-CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          455 DSLKPKESLVIRQR----FGLD-GKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       455 ~~L~~rEr~VL~lr----yGL~-~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      ..|++++..+|...    ||.. .....|..|||+.+|+|+++|+    ++|++|.+
T Consensus        21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVs----r~L~~Le~   73 (95)
T TIGR01610        21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVS----DAIKSLAR   73 (95)
T ss_pred             CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHH----HHHHHHHH
Confidence            56899999977632    4422 2357999999999999999988    45555543

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=81.70  E-value=2.5  Score=31.75  Aligned_cols=29  Identities=31%  Similarity=0.440  Sum_probs=22.6

Q ss_pred             CCCC-CHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          474 KGDR-TLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       474 ~e~~-Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      +... |..|||+.+|+|+.+|++    ++++|.+
T Consensus        17 ~~~l~s~~~la~~~~vs~~tv~~----~l~~L~~   46 (60)
T smart00345       17 GDKLPSERELAAQLGVSRTTVRE----ALSRLEA   46 (60)
T ss_pred             CCcCcCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence            3456 899999999999999985    5555554

>PRK12423 LexA repressor; Provisional

Probab=81.41  E-value=2.3  Score=41.42  Aligned_cols=48  Identities=27%  Similarity=0.350  Sum_probs=33.5

Q ss_pred             hcCCHHHHHHHhHHhc--CCCCCCCCHHHHHHHhC-CCHHHHHHHHHHHHHHHhC
Q 010092          455 DSLKPKESLVIRQRFG--LDGKGDRTLGEIAGNLN-ISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       455 ~~L~~rEr~VL~lryG--L~~~e~~Tl~EIA~~Lg-ISrerVRqie~rALkKLR~  506 (518)
                      ..|++++++|+..---  ..++-.-|..|||+.|| .|+.+|+.    +|+.|.+
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            3489999999875321  11223469999999999 59999995    4455544

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=81.22  E-value=17  Score=36.34  Aligned_cols=37  Identities=22%  Similarity=0.250  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092          233 VFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (518)
Q Consensus       233 ~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~  269 (518)
                      .+.+....+...+|++|+..|+|...|++.+.+..+.
T Consensus       110 ~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~  146 (251)
T PRK07670        110 KVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATM  146 (251)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHH
Confidence            3444556677889999999999999999988776544

>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=80.93  E-value=2.3  Score=32.90  Aligned_cols=25  Identities=24%  Similarity=0.412  Sum_probs=21.8

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          474 KGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       474 ~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      ....|.+|+|+.||||..|||+-+.
T Consensus        12 ~~~~s~~ela~~~~VS~~TiRRDl~   36 (57)
T PF08220_consen   12 KGKVSVKELAEEFGVSEMTIRRDLN   36 (57)
T ss_pred             cCCEEHHHHHHHHCcCHHHHHHHHH
Confidence            3578999999999999999997654

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

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=80.82  E-value=3.3  Score=38.34  Aligned_cols=41  Identities=10%  Similarity=0.169  Sum_probs=32.3

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .|++.++.||..---   ....|+.+||+.+|+|+.+|+....+
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            377788888876441   24699999999999999999976654

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=80.69  E-value=6.6  Score=34.42  Aligned_cols=49  Identities=14%  Similarity=0.171  Sum_probs=36.3

Q ss_pred             HHHHHHH--hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          448 LALDDVL--DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       448 ~~L~~~L--~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      ..+...+  ..|++.+..||..-+.   .++.|..|||+.+|+++.+|.++..+
T Consensus        15 ~~~~~~l~~~~lt~~q~~iL~~l~~---~~~~t~~ela~~~~~~~~tvs~~l~~   65 (118)
T TIGR02337        15 SFFRPILAQHGLTEQQWRILRILAE---QGSMEFTQLANQACILRPSLTGILAR   65 (118)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHH---cCCcCHHHHHHHhCCCchhHHHHHHH
Confidence            3344444  2589999988876552   45799999999999999999755544

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.

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=80.67  E-value=2.7  Score=39.31  Aligned_cols=50  Identities=14%  Similarity=0.094  Sum_probs=41.5

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhC
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~Lg-----ISrerVRqie~rALkKLR~  506 (518)
                      .|+++|.+|+.+..- +.+...|.++|++.+.     +|..+|..+..+.++||..
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

>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=80.41  E-value=2.4  Score=30.75  Aligned_cols=38  Identities=26%  Similarity=0.269  Sum_probs=25.1

Q ss_pred             HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      +-|+.+|.-.+-   ..+.+..+.|+.||||+.+++..+.+
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            345566555442   23568899999999999999876653

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 ....

>PF13551 HTH_29: Winged helix-turn helix

Probab=80.26  E-value=3.1  Score=35.47  Aligned_cols=26  Identities=35%  Similarity=0.325  Sum_probs=23.2

Q ss_pred             CCC-CHHHHHHHhCCCHHHHHHHHHHH
Q 010092          475 GDR-TLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       475 e~~-Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      ++. |..+||+.+|+|+.+|+++.++-
T Consensus        10 ~g~~~~~~ia~~lg~s~~Tv~r~~~~~   36 (112)
T PF13551_consen   10 EGVSTIAEIARRLGISRRTVYRWLKRY   36 (112)
T ss_pred             cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence            567 59999999999999999998873

>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily

Probab=80.23  E-value=1.3  Score=32.29  Aligned_cols=25  Identities=36%  Similarity=0.404  Sum_probs=22.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          477 RTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       477 ~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      +|..|+|+.+|||..+|+.++.+.+
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~~~g~   25 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYERIGL   25 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHCCC
Confidence            5889999999999999999988875

Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	518
3iyd_F	613	Three-Dimensional Em Structure Of An Intact Activat		1e-29
4igc_X	613	X-ray Crystal Structure Of Escherichia Coli Sigma70		2e-29
1l9z_H	438	Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Jun		2e-25
1l9u_H	332	Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A		4e-25
3dxj_F	423	Crystal Structure Of Thermus Thermophilus Rna Polym		7e-25
1iw7_F	423	Crystal Structure Of The Rna Polymerase Holoenzyme		7e-25
4g7h_F	443	Crystal Structure Of Thermus Thermophilus Transcrip		9e-25
3ugo_A	245	Crystal Structure Of Rna-Polymerase Sigma Subunit D		9e-18
1ku2_A	241	Crystal Structure Of Thermus Aquaticus Rna Polymera		1e-17
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		4e-10
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 =  127 bits (320), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 86/280 (30%), Positives = 149/280 (53%), Gaps = 29/280 (10%)
Query: 253 ELAEATNMSAAQVKKC---LEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQ 305
           ++ E T ++  QVK     + +G A    A+ ++++ NLRLV+ + KKY      G +F 
Sbjct: 346 QIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN---RGLQFL 402
Query: 306 DLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIM 364
           DL Q G  GL+ A+D+FE +R ++ STY  +WIR AI RS+   + T R+P  +     +
Sbjct: 403 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM-----I 457
Query: 365 QVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE- 423
           +   ++ R   ++L E+ R PT EE+ + + +  ++ R+V+K +K  +S+ +  G  ++ 
Sbjct: 458 ETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 517
Query: 424 ---EFINGIT---DVDGVENENQRQPAXXXXXXXXXXXXXKPKESLVIRQRFGLDGKGDR 477
              +FI   T    +D    E+ R                  +E+ V+R RFG+D   D 
Sbjct: 518 HLGDFIEDTTLELPLDSATTESLRAATHDVLAGLT------AREAKVLRMRFGIDMNTDH 571
Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
           TL E+    +++RE +R+ E K L KL+HP+R + LR  +
Sbjct: 572 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 611

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

Iteration: 1
 Score =  127 bits (319), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 86/280 (30%), Positives = 149/280 (53%), Gaps = 29/280 (10%)
Query: 253 ELAEATNMSAAQVKKC---LEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQ 305
           ++ E T ++  QVK     + +G A    A+ ++++ NLRLV+ + KKY      G +F 
Sbjct: 346 QIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN---RGLQFL 402
Query: 306 DLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIM 364
           DL Q G  GL+ A+D+FE +R ++ STY  +WIR AI RS+   + T R+P  +     +
Sbjct: 403 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM-----I 457
Query: 365 QVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE- 423
           +   ++ R   ++L E+ R PT EE+ + + +  ++ R+V+K +K  +S+ +  G  ++ 
Sbjct: 458 ETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 517
Query: 424 ---EFINGIT---DVDGVENENQRQPAXXXXXXXXXXXXXKPKESLVIRQRFGLDGKGDR 477
              +FI   T    +D    E+ R                  +E+ V+R RFG+D   D 
Sbjct: 518 HLGDFIEDTTLELPLDSATTESLRAATHDVLAGLT------AREAKVLRMRFGIDMNTDY 571
Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
           TL E+    +++RE +R+ E K L KL+HP+R + LR  +
Sbjct: 572 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 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 =  114 bits (284), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 87/267 (32%), Positives = 135/267 (50%), Gaps = 26/267 (9%)
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-RVPFGLESTSIMQVRGEIQRAKLELLF 379
           +FE KRRF+ STY  +WIR AI R++   + T R+P       +++   ++ R   +L  
Sbjct: 241 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIP-----VHMVETINKLSRTARQLQQ 295
Query: 380 ELKRVPTDEEIIQ--GVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN 437
           EL R P+ EEI +  G     +R  E +K ++  +SL +  G  ++ F       D + +
Sbjct: 296 ELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYG-----DFIPD 350
Query: 438 ENQRQPAXXXXXXXXXXXXXKP------KESLVIRQRFGLDGKGDRTLGEIAGNLNISRE 491
           EN   P              K       +E++V++ R GL    + TL E+     ++RE
Sbjct: 351 ENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRE 410
Query: 492 MVRKHEVKGLMKLK-HPTRVDYLRQHM 517
            +R+ E K L KLK H +R   LR  +
Sbjct: 411 RIRQIENKALRKLKYHESRTRKLRDFL 437

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

Iteration: 1
 Score =  112 bits (281), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 87/267 (32%), Positives = 135/267 (50%), Gaps = 26/267 (9%)
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-RVPFGLESTSIMQVRGEIQRAKLELLF 379
           +FE KRRF+ STY  +WIR AI R++   + T R+P       +++   ++ R   +L  
Sbjct: 135 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIP-----VHMVETINKLSRTARQLQQ 189
Query: 380 ELKRVPTDEEIIQ--GVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN 437
           EL R P+ EEI +  G     +R  E +K ++  +SL +  G  ++ F       D + +
Sbjct: 190 ELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYG-----DFIPD 244
Query: 438 ENQRQPAXXXXXXXXXXXXXKP------KESLVIRQRFGLDGKGDRTLGEIAGNLNISRE 491
           EN   P              K       +E++V++ R GL    + TL E+     ++RE
Sbjct: 245 ENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRE 304
Query: 492 MVRKHEVKGLMKLK-HPTRVDYLRQHM 517
            +R+ E K L KLK H +R   LR  +
Sbjct: 305 RIRQIENKALRKLKYHESRTRKLRDFL 331

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

Iteration: 1
 Score =  112 bits (279), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 85/256 (33%), Positives = 129/256 (50%), Gaps = 23/256 (8%)
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-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEI 390
           TY  +WIR AI R++   + T R+P       +++   ++ R   +L  EL R PT EEI
Sbjct: 237 TYATWWIRQAINRAIADQARTIRIP-----VHMVETINKLSRTARQLQQELGREPTYEEI 291
Query: 391 IQ--GVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXXXX 448
            +  G     +R  E +K ++  +SL +  G  ++ F       D + +E+   P     
Sbjct: 292 AEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYG-----DFIPDEHLPSPVDAAT 346
Query: 449 XXXXXXXXXKP------KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502
                    K       +E++V++ R GL    + TL E+     ++RE +R+ E K L 
Sbjct: 347 QSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALR 406
Query: 503 KLK-HPTRVDYLRQHM 517
           KLK H +R   LR  +
Sbjct: 407 KLKYHESRTRKLRDFL 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 =  112 bits (279), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 85/256 (33%), Positives = 129/256 (50%), Gaps = 23/256 (8%)
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-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEI 390
           TY  +WIR AI R++   + T R+P       +++   ++ R   +L  EL R PT EEI
Sbjct: 237 TYATWWIRQAINRAIADQARTIRIP-----VHMVETINKLSRTARQLQQELGREPTYEEI 291
Query: 391 IQ--GVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXXXX 448
            +  G     +R  E +K ++  +SL +  G  ++ F       D + +E+   P     
Sbjct: 292 AEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYG-----DFIPDEHLPSPVDAAT 346
Query: 449 XXXXXXXXXKP------KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502
                    K       +E++V++ R GL    + TL E+     ++RE +R+ E K L 
Sbjct: 347 QSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALR 406
Query: 503 KLK-HPTRVDYLRQHM 517
           KLK H +R   LR  +
Sbjct: 407 KLKYHESRTRKLRDFL 422

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

Iteration: 1
 Score =  111 bits (278), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 85/256 (33%), Positives = 129/256 (50%), Gaps = 23/256 (8%)
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-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEI 390
           TY  +WIR AI R++   + T R+P       +++   ++ R   +L  EL R PT EEI
Sbjct: 257 TYATWWIRQAINRAIADQARTIRIP-----VHMVETINKLSRTARQLQQELGREPTYEEI 311
Query: 391 IQ--GVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPAXXXX 448
            +  G     +R  E +K ++  +SL +  G  ++ F       D + +E+   P     
Sbjct: 312 AEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYG-----DFIPDEHLPSPVDAAT 366
Query: 449 XXXXXXXXXKP------KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502
                    K       +E++V++ R GL    + TL E+     ++RE +R+ E K L 
Sbjct: 367 QSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALR 426
Query: 503 KLK-HPTRVDYLRQHM 517
           KLK H +R   LR  +
Sbjct: 427 KLKYHESRTRKLRDFL 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 = 88.2 bits (217), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 59/157 (37%), Positives = 89/157 (56%), Gaps = 14/157 (8%)
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-RVPFGLESTSIMQVRGEIQRAKLELLF 379
           +FE KRRF+ STY  +WIR AI R++   + T R+P       +++   ++ R   +L  
Sbjct: 154 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIP-----VHMVETINKLSRTARQLQQ 208
Query: 380 ELKRVPTDEEIIQ--GVNISPERYREVMKASKPILSL 414
           EL R P+ EEI +  G     +R  E +K ++  +SL
Sbjct: 209 ELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 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 = 88.2 bits (217), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 59/157 (37%), Positives = 89/157 (56%), Gaps = 14/157 (8%)
Query: 264 QVKKCLEV---GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAID 320
           ++K+ L +   G AAR  LI+ NLRLV+ + KKY      G  F DL Q G +GLI A++
Sbjct: 93  ELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYT---GRGLSFLDLIQEGNQGLIRAVE 149
Query: 321 RFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLF 379
           +FE KRRF+ STY  +WIR AI R++   + T R+P       +++   ++ R   +L  
Sbjct: 150 KFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIP-----VHMVETINKLSRTARQLQQ 204
Query: 380 ELKRVPTDEEIIQ--GVNISPERYREVMKASKPILSL 414
           EL R P+ EEI +  G     +R  E +K ++  +SL
Sbjct: 205 ELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL 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 = 62.8 bits (151), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 112/241 (46%), Gaps = 16/241 (6%)
Query: 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEP 324
           +++  E  + AR+++I+ N+RLV  V++++      G    DL Q G  GL+ ++D+F+ 
Sbjct: 19  IRRSQEGDQEARDEIIEKNMRLVWSVVQRFLN---RGYEADDLFQIGCIGLLKSVDKFDL 75
Query: 325 KRRFRLSTYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRV 384
               + STY +  I   I R +      +V     S S+ ++  +I++AK EL     R 
Sbjct: 76  SYDVKFSTYAVPMIIGEIQRFLRDDGTVKV-----SRSLKEMGNKIRKAKDELSKTRGRA 130
Query: 385 PTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA 444
           PT  EI   + ISPE   +V+ A + +    S H    E   + IT +D + + ++    
Sbjct: 131 PTVTEIADHLGISPE---DVVLAQEAVRLPTSIHETVYENDGDPITLLDQIADADE-ASW 186
Query: 445 XXXXXXXXXXXXXKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 504
                          +E L++  R+      D+T  E+A  L IS+  + + E K L  +
Sbjct: 187 FDKIALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLEKKILQHI 242
Query: 505 K 505
           K
Sbjct: 243 K 243

>pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga Maritima Length = 87

Iteration: 1
 Score = 56.2 bits (134), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 28/57 (49%), Positives = 42/57 (73%), Gaps = 2/57 (3%)
Query: 459 PKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 514
           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: 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
            +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 = 53.5 bits (127), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 24/59 (40%), Positives = 38/59 (64%)
Query: 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
            +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: 459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLR 514
            +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: 460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
           +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: 460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507
           +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 = 43.1 bits (100), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 39/59 (66%), Gaps = 2/59 (3%)
Query: 460 KESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
           +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	518
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	5e-43
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	3e-05
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	2e-41
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	2e-40
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	8e-40
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	8e-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-22
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	4e-15
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	6e-15
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	4e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-07
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04

>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 =  151 bits (385), Expect = 5e-43
 Identities = 64/234 (27%), Positives = 112/234 (47%), Gaps = 18/234 (7%)

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 TYGLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEII 391
           TY +  I   I R +      +V       S+ ++  +I++AK EL     R PT  EI 
Sbjct: 83  TYAVPMIIGEIQRFLRDDGTVKVS-----RSLKEMGNKIRKAKDELSKTRGRAPTVTEIA 137

Query: 392 QGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALD 451
             + ISPE      +A +   S+H        +    IT +D + + ++      ++AL 
Sbjct: 138 DHLGISPEDVVLAQEAVRLPTSIHETVYENDGDP---ITLLDQIADADEASW-FDKIALK 193

Query: 452 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505
             ++ L  +E L++  R+      D+T  E+A  L IS+  + + E K L  +K
Sbjct: 194 KAIEELDERERLIVYLRYYK----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 =  155 bits (394), Expect = 2e-41
 Identities = 93/306 (30%), Positives = 160/306 (52%), Gaps = 18/306 (5%)

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-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEE 389
           STY  +WIR AI RS+   + T R+P       +++   ++ R   ++L E+ R PT EE
Sbjct: 428 STYATWWIRQAITRSIADQARTIRIP-----VHMIETINKLNRISRQMLQEMGREPTPEE 482

Query: 390 IIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQRQPALLRL 448
           + + + +  ++ R+V+K +K  +S+ +  G  ++    + I D       +      LR 
Sbjct: 483 LAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA 542

Query: 449 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT 508
           A  DVL  L  +E+ V+R RFG+D   D TL E+    +++RE +R+ E K L KL+HP+
Sbjct: 543 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 509 RVDYLR 514
           R + LR
Sbjct: 603 RSEVLR 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 =  150 bits (381), Expect = 2e-40
 Identities = 105/391 (26%), Positives = 170/391 (43%), Gaps = 29/391 (7%)

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-RVPFGLESTSIMQVRGE 369
           G +GLI A+++FE KRRF+ STY  +WIR AI R++   + T R+P  +  T     R  
Sbjct: 231 GNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSR-- 288

Query: 370 IQRAKLELLFELKRVPTDEEIIQ--GVNISPERYREVMKASKPILSLHSRHGVTQEE--- 424
             R   +L  EL R P+ EEI +  G     +R  E +K ++  +SL +  G   E+   
Sbjct: 289 TAR---QLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIG--DEKDSF 343

Query: 425 FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAG 484
           + + I D +          +LL   L+  L  L  +E++V++ R GL    + TL E+  
Sbjct: 344 YGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGA 403

Query: 485 NLNISREMVRKHEVKGLMKLK-HPTRVDYLR 514
              ++RE +R+ E K L KLK H +R   LR
Sbjct: 404 YFGVTRERIRQIENKALRKLKYHESRTRKLR 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 =  148 bits (375), Expect = 8e-40
 Identities = 105/384 (27%), Positives = 164/384 (42%), Gaps = 37/384 (9%)

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-RVPFGLESTSIMQVRGEIQRAKLE 376
           A+++FE KRRF+ STY  +WIR AI R++   + T R+P  +  T     R    R   +
Sbjct: 223 AVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSR--TAR---Q 277

Query: 377 LLFELKRVPTDEEIIQ--GVNISPERYREVMKASKPILSLHSRHGVTQEE---FINGITD 431
           L  EL R PT EEI +  G     +R  E +K ++  +SL +  G   E+   + + I D
Sbjct: 278 LQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIG--DEKDSFYGDFIPD 335

Query: 432 VDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISRE 491
                  +    +LL   L+  L  L  +E++V++ R GL    + TL E+     ++RE
Sbjct: 336 EHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRE 395

Query: 492 MVRKHEVKGLMKLK-HPTRVDYLR 514
            +R+ E K L KLK H +R   LR
Sbjct: 396 RIRQIENKALRKLKYHESRTRKLR 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 =  135 bits (342), Expect = 8e-37
 Identities = 57/239 (23%), Positives = 91/239 (38%), Gaps = 21/239 (8%)

Query: 272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLS 331
            +  R +LI   L LV  +     +        +DL   GV GLI A+D    +   R  
Sbjct: 10  NQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAE 69

Query: 332 TYGLFWIRHAII---RSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDE 388
            Y    I+ AI    RS+                + +    I+    +L  +L R PTDE
Sbjct: 70  AYIKLRIKGAIYDYLRSL-----DFGS-----RQVREKERRIKEVVEKLKEKLGREPTDE 119

Query: 389 EIIQGVNISPERYREVMKASKP--ILSLHSRHGVTQEEFINGITDVDGVENENQRQPALL 446
           E+ + + IS E   + +       ILSL         ++   I     VE E  ++   L
Sbjct: 120 EVAKELGISTEELFKTLDKINFSYILSLEEVFRDFARDYSELIPSSTNVEEEVIKR--EL 177

Query: 447 RLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505
              + + +  L  +E LVI+  F      +    E+A  L  S   V + + K L +L+
Sbjct: 178 TEKVKEAVSKLPEREKLVIQLIFYE----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 = 94.6 bits (235), Expect = 4e-22
 Identities = 61/192 (31%), Positives = 92/192 (47%), Gaps = 11/192 (5%)

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-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQ--GVNISPERYR 402
           +   + T R+P  +  T     R    R   +L  EL R P+ EEI +  G     +R  
Sbjct: 179 IADQARTIRIPVHMVETINKLSR--TAR---QLQQELGREPSYEEIAEAMGPGWDAKRVE 233

Query: 403 EVMKASKPILSL 414
           E +K ++  +SL
Sbjct: 234 ETLKIAQEPVSL 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: 444 ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503
             LR A  DVL  L  +E+ V+R RFG+D   D TL E+    +++RE +R+ E K L K
Sbjct: 7   ESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRK 66

Query: 504 LKHPTRVDYLR 514
           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 = 73.6 bits (181), Expect = 2e-16
 Identities = 31/71 (43%), Positives = 48/71 (67%)

Query: 444 ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503
            L+R  L+ VL +L P+E++V+R R+GL     +TL E+    N++RE +R+ EVK L K
Sbjct: 6   MLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRK 65

Query: 504 LKHPTRVDYLR 514
           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 = 4e-15
 Identities = 28/63 (44%), Positives = 41/63 (65%)

Query: 452 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 511
           DVL  L  +E+ V+R RFG+D   D TL E+    +++RE +R+ E K L KL+HP+R +
Sbjct: 1   DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 60

Query: 512 YLR 514
            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 = 75.3 bits (185), 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 = 63.5 bits (155), Expect = 4e-13
 Identities = 24/67 (35%), Positives = 37/67 (55%), Gaps = 1/67 (1%)

Query: 449 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK-HP 507
            L+  L  L  +E++V++ R GL    + TL E+     ++RE +R+ E K L KLK H 
Sbjct: 3   ELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHE 62

Query: 508 TRVDYLR 514
           +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 = 64.9 bits (157), Expect = 4e-11
 Identities = 77/566 (13%), Positives = 155/566 (27%), Gaps = 148/566 (26%)

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 GLFWIRHAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKL-ELLFELKRVPTDE---- 388
            L W        M V +       L   S+++ + +     +  +  ELK    +E    
Sbjct: 393 SLIWFDVIKSDVMVVVN------KLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALH 446

Query: 389 -EIIQGVNISPERYREVMKASKPI--------LSLH---SRHGVTQEEFINGITDVDGVE 436
             I+   NI P+ + +      P         +  H     H      F     D   +E
Sbjct: 447 RSIVDHYNI-PKTF-DSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLE 504

Query: 437 N--ENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVR 494
               +         ++ + L  LK  +  +       D K +R +  I   L    E + 
Sbjct: 505 QKIRHDSTAWNASGSILNTLQQLKFYKPYICDN----DPKYERLVNAILDFLPKIEENLI 560

Query: 495 KHEVKGLMK--LKHPTRVDYL---RQ 515
             +   L++  L       +    +Q
Sbjct: 561 CSKYTDLLRIALMAEDEAIFEEAHKQ 586

>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 = 51.0 bits (121), Expect = 7e-07
 Identities = 60/393 (15%), Positives = 113/393 (28%), Gaps = 132/393 (33%)

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-------HAIIRSMTVSSFTRVPFGLESTSIMQ---V 366
                ++ + +     + +FW+          ++  +    +   P     +       +
Sbjct: 169 DVCLSYKVQCKM---DFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKL 225

Query: 367 RGEIQRAKLELLFELKRVPT---------DEEIIQGVNIS-----PERYREVM-----KA 407
           R    +A+L  L + K             + +     N+S       R+++V        
Sbjct: 226 RIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAAT 285

Query: 408 SKPILSLHSRHGVTQEE-------FIN-GITDV--------------------DGVE-NE 438
           +  I   H    +T +E       +++    D+                    DG+   +
Sbjct: 286 TTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD 345

Query: 439 NQRQPALLRL--ALDDVLDSLKPKESLVIRQRF 469
           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 = 42.1 bits (98), Expect = 4e-04
 Identities = 69/460 (15%), Positives = 120/460 (26%), Gaps = 171/460 (37%)

Query: 38  KSNNQALFSPQEQIPLPIETPKRHQKRRENSRKRLERVKGVFSDEASPCTLDVD--YNEA 95
             N  +       I L I + +  + RR    K  E            C L +    N  
Sbjct: 210 DPNWTSRSDHSSNIKLRIHSIQ-AELRRLLKSKPYEN-----------CLLVLLNVQNAK 257

Query: 96  AAKLENIY-KLSPAVTTSEVKYADGVVKRGRQRRKRIGEVEK-----------------K 137
           A    N+  K+   +TT   +  D  +         +                      +
Sbjct: 258 AWNAFNLSCKI--LLTTRFKQVTD-FLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCR 314

Query: 138 SDD-----VSGKPVV--------RNQVKRP---KRLSLDK--RI-----------ELRK- 167
             D     ++  P          R+ +      K ++ DK   I           E RK 
Sbjct: 315 PQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKM 374

Query: 168 -------NEDEKVVTKT-----RKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPV 215
                       + T             D    + KL + YS    LV    K+  I   
Sbjct: 375 FDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHK-YS----LVEKQPKESTI--- 426

Query: 216 LSSTEHTWLFKLMQPM-------KVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKC 268
              +  +   +L   +       +  V   +        +  D+                
Sbjct: 427 ---SIPSIYLELKVKLENEYALHRSIV---DHYNIPKTFDSDDLIPPYLDQYF------Y 474

Query: 269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRF--QDLCQAGV-------------- 312
             +G   +N  I+H  R+ LF  +  F DF    RF  Q +                   
Sbjct: 475 SHIGHHLKN--IEHPERMTLF--RMVFLDF----RFLEQKIRHDSTAWNASGSILNTLQQ 526

Query: 313 ----KGLITAIDRFEPKRRFRLSTYGLFWIRHA--IIRSMTVSSFTRVPFGLESTSIMQV 366
               K  I   D   PK    ++    F  +    +I S             + T +++ 
Sbjct: 527 LKFYKPYICDND---PKYERLVNAILDFLPKIEENLICS-------------KYTDLLR- 569

Query: 367 RGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMK 406
                   + L+ E      DE I +      E +++V +
Sbjct: 570 --------IALMAE------DEAIFE------EAHKQVQR 589

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	518
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	99.85
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	99.81
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	99.62
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	99.61
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	99.52
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.48
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	99.31
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	99.31
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	99.3
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	99.16
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	98.9
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	98.73
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	98.68
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
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	98.57
3c57_A	95	Two component transcriptional regulatory protein;	98.55
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	98.49
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	98.47
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	98.45
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	98.29
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	98.07
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	97.98
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	97.91
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	97.89
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	97.21
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	97.13
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.84
1yio_A	208	Response regulatory protein; transcription regulat	96.71
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	96.57
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	96.31
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	96.19
3c3w_A	225	Two component transcriptional regulatory protein;	95.78
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	95.23
3p7n_A	258	Sensor histidine kinase; LOV domain, light-activat	95.18
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	94.77
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	92.81
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	92.79
2gwr_A	238	DNA-binding response regulator MTRA; two-component	92.31
2oqr_A	230	Sensory transduction protein REGX3; response regul	91.95
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	91.87
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	91.58
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	91.21
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	91.06
1ys7_A	233	Transcriptional regulatory protein PRRA; response	90.97
1u78_A	141	TC3 transposase, transposable element TC3 transpos	90.81
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	90.48
3q9s_A	249	DNA-binding response regulator; DNA binding protei	89.19
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	89.13
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	88.97
2hqr_A	223	Putative transcriptional regulator; phosporylation	88.88
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	88.62
3r0a_A	123	Putative transcriptional regulator; structural gen	88.27
1sfx_A	109	Conserved hypothetical protein AF2008; structural	88.18
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	87.44
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	87.43
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	87.38
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	87.35
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	87.26
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	87.09
3r0j_A	250	Possible two component system response transcript	87.02
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	87.0
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	86.51
2w25_A	150	Probable transcriptional regulatory protein; trans	86.23
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	86.12
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	86.05
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	85.9
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	85.78
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	85.72
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	85.64
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	85.62
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	85.38
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	85.25
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	85.2
1ku9_A	152	Hypothetical protein MJ223; putative transcription	84.81
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	84.41
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	84.36
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	84.33
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	84.23
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	84.2
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	83.97
2gxg_A	146	146AA long hypothetical transcriptional regulator;	83.92
2nnn_A	140	Probable transcriptional regulator; structural gen	83.81
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	83.8
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	83.76
3nqo_A	189	MARR-family transcriptional regulator; structural	83.71
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	83.64
3jth_A	98	Transcription activator HLYU; transcription factor	83.58
1y0u_A	96	Arsenical resistance operon repressor, putative; s	83.52
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	83.5
1u78_A	141	TC3 transposase, transposable element TC3 transpos	83.25
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	83.24
3frw_A	107	Putative Trp repressor protein; structural genomic	83.24
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	83.22
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	83.17
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	83.1
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	82.91
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	82.87
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	82.75
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	82.73
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	82.64
3sqn_A	485	Conserved domain protein; structural genomics, PSI	82.49
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	82.17
2k27_A	159	Paired box protein PAX-8; paired domain, solution	82.12
2pex_A	153	Transcriptional regulator OHRR; transcription regu	82.06
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	81.98
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	81.97
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	81.87
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	81.86
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	81.65
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	81.61
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	81.53
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	81.5
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	81.04
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	80.89
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	80.8
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	80.76
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	80.51
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	80.5
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	80.26
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	80.23
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	80.19
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	80.16
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	80.03

>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=4.5e-53  Score=449.61  Aligned_cols=313  Identities=29%  Similarity=0.411  Sum_probs=274.3

Q ss_pred             cCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHH------------------HHHHHhCCCCCHHHHHH--
Q 010092          197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKE------------------QLQKDLGREPTDVELAE--  256 (518)
Q Consensus       197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~------------------~l~~~l~r~p~~~ela~--  256 (518)
                      ..+.|.+++||++|+++|+||++||+.|++.++.+..+.+...                  .....+++.|+..+|+.  
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                  11224566777776632  


Q ss_pred             ----------HccCCHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCC
Q 010092          257 ----------ATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKR  326 (518)
Q Consensus       257 ----------~~~~s~~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~r  326 (518)
                                ..+++...|.....+|..|+++||.+|+++|+++|++|.   ++|.+++|||||||||||+|+++|||++
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                      124555677777788999999999999999999999999   7899999999999999999999999999


Q ss_pred             CCccchHHHHHHHHHHHHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhC--CCHHHHHH
Q 010092          327 RFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVN--ISPERYRE  403 (518)
Q Consensus       327 G~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lg--is~e~v~~  403 (518)
                      |++|+|||+||||++|.++|+ +.+.+++|.|+..     .+++++++...+.+.+||.|+.+|||+.+|  +++++|..
T Consensus       247 G~rFsTYA~~wIR~~I~~~i~~~~R~irlp~~~~~-----~l~~lrr~~r~l~~~lgr~pt~eeiA~~l~~~v~~e~V~~  321 (438)
T 1l9z_H          247 RFKFSTYATWWIRQAINRAIADQARTIRIPVHMVE-----TINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEE  321 (438)
T ss_pred             CCChHHHHHHHHHHHHHHHHHHhcchhccchHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHH
Confidence            999999999999999999999 8899999999998     999999999999999999999999999999  99999999


Q ss_pred             HHHhcCCccccCCCcCCchh-hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHH
Q 010092          404 VMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEI  482 (518)
Q Consensus       404 ~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EI  482 (518)
                      +++.....+|||.+.+++++ .+.+.+.+....+|++.+....+...|..+|+.||++||.||.+||||+|++++|++||
T Consensus       322 ~~~~~~~~~SLd~~~~~d~d~~l~d~l~d~~~~~pee~~~~~~~~~~L~~aL~~L~ereR~VI~LRygL~~~e~~TleEI  401 (438)
T 1l9z_H          322 TLKIAQEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEV  401 (438)
T ss_pred             HHHhcccccccccccccccchhhhhhhcccccCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHhccCCCCCCHHHH
Confidence            99999999999998765443 34455555444557777777788899999999999999999999999999899999999


Q ss_pred             HHHhCCCHHHHHHHHHHHHHHHh-Ccchhhhhhhhc
Q 010092          483 AGNLNISREMVRKHEVKGLMKLK-HPTRVDYLRQHM  517 (518)
Q Consensus       483 A~~LgISrerVRqie~rALkKLR-~~~~~~~L~~y~  517 (518)
                      |+.||||+++|||++++|++||| ++.+...|++|+
T Consensus       402 Ae~LgIS~erVRqi~~RAlkKLR~~~~~~~~l~~yl  437 (438)
T 1l9z_H          402 GAYFGVTRERIRQIENKALRKLKYHESRTRKLRDFL  437 (438)
T ss_pred             HHHHCcCHHHHHHHHHHHHHHHHHhHhhHHHHHHhh
Confidence            99999999999999999999999 888999999997

>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=3.5e-53  Score=450.37  Aligned_cols=313  Identities=30%  Similarity=0.415  Sum_probs=265.3

Q ss_pred             cCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHH------------------HHHHhCCCCCHHH-----
Q 010092          197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQ------------------LQKDLGREPTDVE-----  253 (518)
Q Consensus       197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~------------------l~~~l~r~p~~~e-----  253 (518)
                      ...+|.+++||++|+.+|+||++||.+|++.++.+..+......                  ....+++.|+..+     
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            45679999999999999999999999999999886433221111                  0012234555333     


Q ss_pred             ----HHH---HccCCHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCC
Q 010092          254 ----LAE---ATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKR  326 (518)
Q Consensus       254 ----la~---~~~~s~~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~r  326 (518)
                          |+.   +++++...|.....+|..|+++||.+|+++|+++|++|.   ++|.+++|||||||+|||+|+++|||++
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                221   234555666666777899999999999999999999999   7899999999999999999999999999


Q ss_pred             CCccchHHHHHHHHHHHHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhC--CCHHHHHH
Q 010092          327 RFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVN--ISPERYRE  403 (518)
Q Consensus       327 G~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lg--is~e~v~~  403 (518)
                      |++|+|||+||||++|.++|+ +.+++++|.|+.+     .+++++++...+.+.+||.|+.+|||+.+|  +++++|..
T Consensus       232 g~~FstYa~~wIr~~i~~~i~~~~r~ir~p~~~~~-----~~~~lrr~~~~l~~~~~r~p~~~eiA~~l~~~~~~~~v~~  306 (423)
T 2a6h_F          232 RFKFSTYATWWIRQAINRAIADQARTIRIPVHMVE-----TINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEE  306 (423)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHSSSSCCCHHHHH-----HHHHHHHHHHHHHHHHSSCCCHHHHHHHHCTTCCHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHccceeeccHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCCCHHHHHH
Confidence            999999999999999999999 8899999999998     999999999999999999999999999999  99999999


Q ss_pred             HHHhcCCccccCCCcCCchh-hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHH
Q 010092          404 VMKASKPILSLHSRHGVTQE-EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEI  482 (518)
Q Consensus       404 ~l~~~~~~~SLD~~~~~~~e-el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EI  482 (518)
                      ++......+|||.+.+++++ .+.+.+.+....+|++.+....+...|..+|+.||++|+.||.+||||+|++++|++||
T Consensus       307 ~~~~~~~~~Sld~~~~~~~~~~l~d~l~d~~~~~pe~~~~~~~~~~~L~~aL~~L~~rer~Vl~lr~~L~~~e~~Tl~EI  386 (423)
T 2a6h_F          307 TLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEV  386 (423)
T ss_dssp             HHHHHSCCEESSCBCSSSSSCBGGGSSCCSSSCCHHHHHHHHHHHHHHHHHHHSSCHHHHHHHHHHHHTTCC-----CHH
T ss_pred             HHHhccCCcccccccCCCCccchhhhhccccCCCHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhccCCCCCCCHHHH
Confidence            99999999999998765433 35555555545567777777888899999999999999999999999999999999999


Q ss_pred             HHHhCCCHHHHHHHHHHHHHHHh-Ccchhhhhhhhc
Q 010092          483 AGNLNISREMVRKHEVKGLMKLK-HPTRVDYLRQHM  517 (518)
Q Consensus       483 A~~LgISrerVRqie~rALkKLR-~~~~~~~L~~y~  517 (518)
                      |+.||||+++|||++++|++||| ++.+...|+.|+
T Consensus       387 A~~lgiS~erVrqi~~rAl~kLR~~~~~~~~l~~~l  422 (423)
T 2a6h_F          387 GAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFL  422 (423)
T ss_dssp             HHSSSSCHHHHHHHHHHHHHHHHHHHHHTTSSSSCC
T ss_pred             HHHHCcCHHHHHHHHHHHHHHHHhhhhhhHHHHHhh
Confidence            99999999999999999999999 888888999987

>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=2.8e-41  Score=374.06  Aligned_cols=246  Identities=33%  Similarity=0.539  Sum_probs=226.6

Q ss_pred             HHHHHHHHcHHH---HHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHH
Q 010092          264 QVKKCLEVGRAA---RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRH  340 (518)
Q Consensus       264 ~L~~~~~gd~~A---~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRq  340 (518)
                      .+.++..|+..|   ++.||..|+++|+++|++|.   +++.+++||+||||+|||+++++||+.+|++|+||++||||+
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            455678899887   99999999999999999999   789999999999999999999999999999999999999999


Q ss_pred             HHHHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcC
Q 010092          341 AIIRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHG  419 (518)
Q Consensus       341 aI~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~  419 (518)
                      +|.++++ +.+++|+|.|+.+     .+++++++...+.+++||.||++|||+.+|+++++++.++.....++||+.+.+
T Consensus       438 ~i~~~lr~~~r~~rip~~~~~-----~~~k~~r~~~~l~~~~gr~pt~eela~~l~~~~~~v~~~~~~~~~~~sld~~~~  512 (613)
T 3iyd_F          438 AITRSIADQARTIRIPVHMIE-----TINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIG  512 (613)
T ss_dssp             HHHHHTTTSCSSSCCCSHHHH-----TTTTTTTTTTTTTTTTCSCCCTTTTTTTSSCCSSHHHHHHHHSCCCCCSSCCCS
T ss_pred             HHHHHHHhcCcceeCcHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhccCCcccCCCCC
Confidence            9999999 8899999999998     899999999999999999999999999999999999999999999999999876


Q ss_pred             Cchh-hhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          420 VTQE-EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       420 ~~~e-el~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      .+.+ .+.+.+.+....+|++.+...++...|..+|+.||++++.||.|+||+++++++|++|||+.||||++||+++++
T Consensus       513 ~~~~~~l~d~i~d~~~~~p~~~~~~~e~~~~l~~aL~~Lp~~er~Vl~Lr~~~~~~e~~s~~EIA~~lgis~~tVk~~~~  592 (613)
T 3iyd_F          513 DDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA  592 (613)
T ss_dssp             SSSSCCGGGSCCCSSSCCHHHHHHHHTTSSSHHHHTTSSCHHHHHHHHHHHTSSSCCCCSTTGGGTTTSSCSSHHHHHHH
T ss_pred             CCCCccHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhccCCCCCcCHHHHHHHhCCCHHHHHHHHH
Confidence            5544 355556655555677777777778889999999999999999999999888999999999999999999999999


Q ss_pred             HHHHHHhCcchhhhhhhhc
Q 010092          499 KGLMKLKHPTRVDYLRQHM  517 (518)
Q Consensus       499 rALkKLR~~~~~~~L~~y~  517 (518)
                      +|+++||++.+...|+.|+
T Consensus       593 rAl~kLR~~~~~~~l~~~l  611 (613)
T 3iyd_F          593 KALRKLRHPSRSEVLRSFL  611 (613)
T ss_dssp             HHHTTTTSCSSSCSSTTCC
T ss_pred             HHHHHhhCcchhhHHHHHh
Confidence            9999999999999999886

>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=5.1e-36  Score=297.11  Aligned_cols=210  Identities=31%  Similarity=0.464  Sum_probs=129.2

Q ss_pred             cCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHH-HHHHHH--HHH-----------------------hCCCCC
Q 010092          197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFV-QVKEQL--QKD-----------------------LGREPT  250 (518)
Q Consensus       197 ~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~-~~~~~l--~~~-----------------------l~r~p~  250 (518)
                      ..++|+|++||++|+++||||++||++|++.|+.+.... .+....  +..                       ...+|+
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 221110  000                       135788


Q ss_pred             HHHHHHHccCCH----HHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCC
Q 010092          251 DVELAEATNMSA----AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKR  326 (518)
Q Consensus       251 ~~ela~~~~~s~----~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~r  326 (518)
                      ..+||.+.+++.    ..|.+...||..|++.||..|+++|+++|++|.   +++.+++||+||||+|||+|+++|||++
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    356667889999999999999999999999999   7899999999999999999999999999


Q ss_pred             CCccchHHHHHHHHHHHHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhC--CCHHHHHH
Q 010092          327 RFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVN--ISPERYRE  403 (518)
Q Consensus       327 G~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lg--is~e~v~~  403 (518)
                      |++|+||++||||++|+++++ +.+.+++|.++.+     .++++.++...|...+|+.||.+|||+.||  ||+.+|..
T Consensus       160 g~~F~tya~~~ir~~i~~~ir~~~r~~r~p~~l~e-----~i~~l~~~~~~L~~~~~~~ps~~EIAe~Lg~~is~~tVk~  234 (245)
T 3ugo_A          160 RFKFSTYATWWIRQAINRAIADQARTIRIPVHMVE-----TINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEE  234 (245)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHHTC-------------------------------------------------------
T ss_pred             CCcHHHHHHHHHHHHHHHHHHHhcccccccHHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHH
Confidence            999999999999999999999 8889999999999     999999999999999999999999999999  99999999


Q ss_pred             HHHhcCCcccc
Q 010092          404 VMKASKPILSL  414 (518)
Q Consensus       404 ~l~~~~~~~SL  414 (518)
                      .+..+...+||
T Consensus       235 ~l~~ar~~lsl  245 (245)
T 3ugo_A          235 TLKIAQEPVSL  245 (245)
T ss_dssp             -----------
T ss_pred             HHHHHhhccCC
Confidence            99988887775

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

Probab=99.97  E-value=1.4e-30  Score=250.87  Aligned_cols=224  Identities=23%  Similarity=0.249  Sum_probs=185.8

Q ss_pred             cHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCC
Q 010092          272 GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSF  351 (518)
Q Consensus       272 d~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~  351 (518)
                      +..|++.|+..|.++|+.+|++|.++++++.+++||+|||+++||+++++||+.+|.+|+||+++||++.+.+++++.. 
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            3458999999999999999999974334678999999999999999999999999999999999999999999999432 


Q ss_pred             ccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcC--CccccCCCcCCchhhhhccc
Q 010092          352 TRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK--PILSLHSRHGVTQEEFINGI  429 (518)
Q Consensus       352 iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~--~~~SLD~~~~~~~eel~~~l  429 (518)
                       +.|.+...     ...++.++...+...+|+.|+.+++|+.+|++++++..++....  ...|+|.+...+++...+. 
T Consensus        89 -~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~~~~-  161 (239)
T 1rp3_A           89 -FGSRQVRE-----KERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSLEEVFRDFARDYSEL-  161 (239)
T ss_dssp             -TTCHHHHH-----HHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-
T ss_pred             -ccchHHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHhccCCCccccccccCCCcccccc-
Confidence             45655555     78889999999999999999999999999999999998876542  3355655432222111221 


Q ss_pred             ccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          430 TDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       430 ~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      .++ ..+|++.+...+....|..+|+.||++++.||.++|    .+++|++|||+.||||.++|++++++|+++||+.+
T Consensus       162 ~~~-~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~~V~~~~~ra~~~Lr~~l  235 (239)
T 1rp3_A          162 IPS-STNVEEEVIKRELTEKVKEAVSKLPEREKLVIQLIF----YEELPAKEVAKILETSVSRVSQLKAKALERLREML  235 (239)
T ss_dssp             GGG-SCHHHHHHHHHHHHHHHHHHHTTSCHHHHHHHHHHH----TSCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCC-CCCHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence            222 344666677777888999999999999999999999    48999999999999999999999999999999754

>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=8.2e-31  Score=252.36  Aligned_cols=222  Identities=27%  Similarity=0.408  Sum_probs=51.5

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r  344 (518)
                      +.++.+||..|++.|+..|.++|+.+|++|.   ++..+++||+||||++||+++++||+.+|..|+||+++|+++.+.+
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            4445678999999999999999999999998   6778999999999999999999999999889999999999999999


Q ss_pred             HHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhh
Q 010092          345 SMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEE  424 (518)
Q Consensus       345 aI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~ee  424 (518)
                      ++++...+++|.++..     ...+++++...+....|+.|+.++++..+|++.+++...+.......|++.+..+++++
T Consensus        96 ~~r~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~  170 (243)
T 1l0o_C           96 FLRDDGTVKVSRSLKE-----MGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGD  170 (243)
T ss_dssp             ----CCCCTTHHHHHH-----HHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHHHC--------------
T ss_pred             HHHhcCCccCcHHHHH-----HHHHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHhccccCccccccccCCc
Confidence            9995557899988777     88999999999999999999999999999999999998888777778888764322211


Q ss_pred             ---hhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          425 ---FINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       425 ---l~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                         +.+.+       +++.....+....|..+|..||++++.||.++|    .+++|++|||+.||||.++|++++++|+
T Consensus       171 ~~~~~~~~-------~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~~~ra~  239 (243)
T 1l0o_C          171 PITLLDQI-------ADADEASWFDKIALKKAIEELDERERLIVYLRY----YKDQTQSEVASRLGISQVQMSRLEKKIL  239 (243)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             ccchhhcc-------CcchhHHHHHHHHHHHHHHhCCHHHHHHHHHHH----hcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence               11111       222333445667889999999999999999999    4899999999999999999999999999


Q ss_pred             HHHh
Q 010092          502 MKLK  505 (518)
Q Consensus       502 kKLR  505 (518)
                      ++||
T Consensus       240 ~~Lr  243 (243)
T 1l0o_C          240 QHIK  243 (243)
T ss_dssp             ----
T ss_pred             HHcC
Confidence            9997

>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=2.2e-21  Score=181.63  Aligned_cols=175  Identities=15%  Similarity=0.124  Sum_probs=133.1

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHH
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAII  343 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~  343 (518)
                      .+.++..||..|++.|+..|.+.|+.+|.+|.   + ..+++|++||+|+.+|+++++|++..  .|.+|++.++++.+.
T Consensus        13 l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~---~-~~~aeDl~Qe~~l~~~~~~~~~~~~~--~~~~~l~~i~~n~~~   86 (194)
T 1or7_A           13 LVERVQKGDQKAFNLLVVRYQHKVASLVSRYV---P-SGDVPDVVQEAFIKAYRALDSFRGDS--AFYTWLYRIAVNTAK   86 (194)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTS---C-GGGHHHHHHHHHHHHHHHGGGCCSSS--CHHHHHHHHHHHHHH
T ss_pred             HHHHHHccCHHHHHHHHHHHHHHHHHHHHHHc---C-HHhHHHHHHHHHHHHHHhHHhcCCcc--chHHHHHHHHHHHHH
Confidence            45667889999999999999999999999998   7 88999999999999999999999875  599999999999999


Q ss_pred             HHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCch
Q 010092          344 RSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQ  422 (518)
Q Consensus       344 raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~  422 (518)
                      ++++ ..+....                                 .++.           ...     ...++..     
T Consensus        87 d~~R~~~~~~~~---------------------------------~~~~-----------~~~-----~~~~~~~-----  112 (194)
T 1or7_A           87 NYLVAQGRRPPS---------------------------------SDVD-----------AIE-----AENFESG-----  112 (194)
T ss_dssp             HHHHHHTTCCTH---------------------------------HHHH-----------HHH-----HHSCCSS-----
T ss_pred             HHHHHHhccCcc---------------------------------cccc-----------ccc-----ccccccc-----
Confidence            9988 3221100                                 0000           000     0000100     


Q ss_pred             hhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          423 EEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       423 eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                          ..+.+  ..+|++.....+....|..+|..||++++.||.|+|    .+++|++|||+.||+|..+|++++.+|++
T Consensus       113 ----~~~~~--~~~~~~~~~~~e~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgis~~tV~~~l~ra~~  182 (194)
T 1or7_A          113 ----GALKE--ISNPENLMLSEELRQIVFRTIESLPEDLRMAITLRE----LDGLSYEEIAAIMDCPVGTVRSRIFRARE  182 (194)
T ss_dssp             ----CC----------CEEEHHHHHHHHHHHHHHSCHHHHHHHHHHH----TTCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             ----ccccC--CCChHHHHHHHHHHHHHHHHHHhCCHHHHHHhHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence                00011  122344444456677889999999999999999999    58999999999999999999999999999


Q ss_pred             HHhCcc
Q 010092          503 KLKHPT  508 (518)
Q Consensus       503 KLR~~~  508 (518)
                      +||+..
T Consensus       183 ~Lr~~l  188 (194)
T 1or7_A          183 AIDNKV  188 (194)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            999654

>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=99.81  E-value=1.2e-19  Score=164.23  Aligned_cols=152  Identities=14%  Similarity=0.136  Sum_probs=102.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH-hcCCccccccccchhhHHHHHHHHHHHHHHHH
Q 010092          301 GPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT-VSSFTRVPFGLESTSIMQVRGEIQRAKLELLF  379 (518)
Q Consensus       301 g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~-~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~  379 (518)
                      |.+++|++||||++||+++.+||+.+ .+|.||+++++++.+.++++ +.+..+.+..                      
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 68999999999999999998 3322111110                      


Q ss_pred             HhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchh-hhhc---ccccCCCCcchhhhHHHHHHHHHHHHHh
Q 010092          380 ELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFIN---GITDVDGVENENQRQPALLRLALDDVLD  455 (518)
Q Consensus       380 elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~e-el~~---~l~d~~~~~~ee~~~~~~l~~~L~~~L~  455 (518)
                                                    ..++++.....+.. ++.+   ........++++.+...+....|..+|.
T Consensus        58 ------------------------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l~~~l~  107 (164)
T 3mzy_A           58 ------------------------------EALKTNAILEDSAYFDDEGHNINNYKSSESNPEEAYLLKEEIEEFKKFSE  107 (164)
T ss_dssp             --------------------------------------------------------------CHHHHHHHHHHHHHHHHH
T ss_pred             ------------------------------HHhhhhhhhccCCCCCcccchhhhhcccCCCHHHHHHHHHHHHHHHHHHH
Confidence                                          00011110000000 0000   0011222345666777778888999999


Q ss_pred             -cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          456 -SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       456 -~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                       .||++++.||. +|    .+++|++|||+.||+|.++|++++++|+++||+.+..
T Consensus       108 ~~L~~~~r~v~~-~~----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l~~  158 (164)
T 3mzy_A          108 NNFSKFEKEVLT-YL----IRGYSYREIATILSKNLKSIDNTIQRIRKKSEEWIKE  158 (164)
T ss_dssp             HHSCHHHHHHHH-HH----TTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHH-HH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence             99999999999 66    4899999999999999999999999999999976654

>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=1.1e-15  Score=157.35  Aligned_cols=81  Identities=40%  Similarity=0.686  Sum_probs=76.7

Q ss_pred             HHHHHHHHcH---HHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHH
Q 010092          264 QVKKCLEVGR---AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRH  340 (518)
Q Consensus       264 ~L~~~~~gd~---~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRq  340 (518)
                      .+.++..|+.   .|++.||..|+++|+++|++|.   +++.+++||+||||+|||+++++|++.+|++|+||++|||++
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            3566778998   9999999999999999999999   789999999999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q 010092          341 AIIRSMT  347 (518)
Q Consensus       341 aI~raI~  347 (518)
                      .|.++++
T Consensus       329 ~~~~~lr  335 (339)
T 1sig_A          329 AITRSIA  335 (339)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9999998

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=99.61  E-value=1.7e-17  Score=152.14  Aligned_cols=141  Identities=10%  Similarity=0.041  Sum_probs=114.3

Q ss_pred             HHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHhcCCcccc
Q 010092          276 RNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFTRVP  355 (518)
Q Consensus       276 ~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~sr~iRlP  355 (518)
                      ++.|+..|.+.|+.+|.++.   ++..+++|++||+|+.+|++.++|++..  .|.+|++..+++.+.++++...     
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   6788999999999999999999999763  6999999999998887765200     


Q ss_pred             ccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCC
Q 010092          356 FGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV  435 (518)
Q Consensus       356 ~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~  435 (518)
                          .                                                 .    +.+            .+ .  
T Consensus        73 ----~-------------------------------------------------~----~~~------------~e-~--   80 (157)
T 2lfw_A           73 ----A-------------------------------------------------Q----TSQ------------SD-A--   80 (157)
T ss_dssp             ----C-------------------------------------------------C----CCC------------CS-C--
T ss_pred             ----c-------------------------------------------------c----cCC------------cc-h--
Confidence                0                                                 0    000            00 0  


Q ss_pred             cchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       436 ~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                       .       +....|..+|..||++++.||.|+|    .+++|++|||+.||||..+|++.+.+|+++||+....
T Consensus        81 -~-------~~~~~l~~~l~~Lp~~~r~vl~L~~----~~g~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l~~  143 (157)
T 2lfw_A           81 -E-------GTEAVARARLARMTPLSRQALLLTA----MEGFSPEDAAYLIEVDTSEVETLVTEALAEIEKQTRA  143 (157)
T ss_dssp             -S-------SSSSTTTTTTTTSCTTHHHHHTTTS----SSCCCHHHHHHTTTSCHHHHHHHHHHHHHHHHTTSSC
T ss_pred             -H-------HHHHHHHHHHHhCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence             0       0112466788999999999999998    5899999999999999999999999999999986543

>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=99.52  E-value=2.9e-14  Score=122.23  Aligned_cols=77  Identities=40%  Similarity=0.625  Sum_probs=72.6

Q ss_pred             hHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhhc
Q 010092          441 RQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  517 (518)
Q Consensus       441 ~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~y~  517 (518)
                      +...++...|..+|+.|||+|+.||.++||++|.+++|++|||+.||+|.++|++++.+|+++||...+...|+.|+
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            45567888999999999999999999999999889999999999999999999999999999999999999999986

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.48  E-value=2.2e-14  Score=144.28  Aligned_cols=145  Identities=8%  Similarity=-0.079  Sum_probs=115.8

Q ss_pred             HHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHHh
Q 010092          269 LEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTV  348 (518)
Q Consensus       269 ~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~~  348 (518)
                      .+|+..+|+.|+..|.+.++.+|.+|.   ++..+++|++||.|+.+|+...+|++.  ..|.+|++..+++.+.++++.
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            467888999999999999999999999   778899999999999999999999975  369999998888876544321


Q ss_pred             cCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcc
Q 010092          349 SSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING  428 (518)
Q Consensus       349 sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~  428 (518)
                      ..                                                                 ...          
T Consensus        91 ~~-----------------------------------------------------------------~~~----------   95 (286)
T 3n0r_A           91 LE-----------------------------------------------------------------VGH----------   95 (286)
T ss_dssp             --------------------------------------------------------------------CC----------
T ss_pred             cc-----------------------------------------------------------------cCC----------
Confidence            00                                                                 000          


Q ss_pred             cccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          429 ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       429 l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                       ....    +       ....|..+|+.||+++|.||.|+|    .+++|++|||+.+|+|..+|+....+|+..|+...
T Consensus        96 -~~~~----~-------~~~~l~~al~~Lp~~~R~v~~L~~----~eg~s~~EIA~~lgis~~tVks~l~rA~~~Lr~~l  159 (286)
T 3n0r_A           96 -DQGL----H-------AGDDAAQRLMRIAPRSRQAFLLTA----LEGFTPTEAAQILDCDFGEVERLIGDAQAEIDAEL  159 (286)
T ss_dssp             -CCCC----C-------TTSHHHHHHHHHSCHHHHHHHHHH----TTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHTSC
T ss_pred             -Cccc----c-------hHHHHHHHHHhCCHHHeeEEEEEe----eCCCCHHHHHHHhCcCHHHHHHHHHHHHhhhhccC
Confidence             0000    0       012488899999999999999999    68999999999999999999999999999999764


Q ss_pred             h
Q 010092          509 R  509 (518)
Q Consensus       509 ~  509 (518)
                      .
T Consensus       160 ~  160 (286)
T 3n0r_A          160 A  160 (286)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.31  E-value=2.2e-12  Score=102.12  Aligned_cols=65  Identities=42%  Similarity=0.711  Sum_probs=61.4

Q ss_pred             HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhhc
Q 010092          453 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  517 (518)
Q Consensus       453 ~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~y~  517 (518)
                      +|+.||++|+.||.++|||+|.+++|++|||+.||+|.++|++++.+|+++||.......+..|+
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            36789999999999999998889999999999999999999999999999999999999888875

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=99.31  E-value=5.2e-12  Score=105.03  Aligned_cols=70  Identities=41%  Similarity=0.735  Sum_probs=64.9

Q ss_pred             HHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhhc
Q 010092          448 LALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  517 (518)
Q Consensus       448 ~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~y~  517 (518)
                      ..|..+|+.||++++.||.++|+|+|.+++|++|||+.||+|.++|++++.+|+++||.......+..|+
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            4588899999999999999999988889999999999999999999999999999999998888877764

>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=99.30  E-value=1.3e-12  Score=104.86  Aligned_cols=68  Identities=35%  Similarity=0.565  Sum_probs=55.6

Q ss_pred             HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh-Ccchhhhhhhhc
Q 010092          450 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK-HPTRVDYLRQHM  517 (518)
Q Consensus       450 L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR-~~~~~~~L~~y~  517 (518)
                      |..+|+.||++|+.||.++|+|+|.+++|++|||+.||+|.++|++++.+|+++|| .......|+.|+
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            45667899999999999999988888999999999999999999999999999999 998888888885

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=99.16  E-value=8.9e-11  Score=98.28  Aligned_cols=73  Identities=21%  Similarity=0.271  Sum_probs=66.3

Q ss_pred             CCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          434 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       434 ~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      ..++++.+...+....|..+|..||++++.||.|+|    .+++|++|||+.||||..+|++++.+|+++||..+..
T Consensus        15 ~~~~~~~~~~~~~~~~l~~~l~~L~~~~r~vl~l~~----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~   87 (92)
T 3hug_A           15 EQSTPDEVNAALDRLLIADALAQLSAEHRAVIQRSY----YRGWSTAQIATDLGIAEGTVKSRLHYAVRALRLTLQE   87 (92)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHTSCHHHHHHHHHHH----TSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCchHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            345777788888999999999999999999999998    5899999999999999999999999999999976554

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=98.90  E-value=2.8e-09  Score=83.65  Aligned_cols=64  Identities=8%  Similarity=-0.021  Sum_probs=53.9

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          445 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       445 ~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      +....|..+|+.||++++.||.++|    .+++|++|||+.||+|..+|+++.++|+++|+.......
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            3456788899999999999999998    478999999999999999999999999999998776544

>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=1.1e-08  Score=83.73  Aligned_cols=75  Identities=13%  Similarity=0.060  Sum_probs=68.6

Q ss_pred             HHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH
Q 010092          268 CLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT  347 (518)
Q Consensus       268 ~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~  347 (518)
                      +..|+..|++.|+..|.+.++.+|.++.   ++..+++|++||+|+.+|+..+.|++.  ..|.+|++..+++.+.++++
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            4578999999999999999999999998   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=98.68  E-value=4.5e-08  Score=85.43  Aligned_cols=66  Identities=21%  Similarity=0.135  Sum_probs=58.5

Q ss_pred             hHHHHHHHHHHHHH-hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          441 RQPALLRLALDDVL-DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       441 ~~~~~l~~~L~~~L-~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      ++..+....+..+| ..||++++.||.++|    .+++|++|||+.||+|..+|+++.++|+++||.....
T Consensus         9 ~e~~~~~~~l~~~l~~~L~~~~r~vl~l~~----~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~   75 (113)
T 1xsv_A            9 LVKTLRMNYLFDFYQSLLTNKQRNYLELFY----LEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKK   75 (113)
T ss_dssp             HHHHHHHHHHHHHHGGGSCHHHHHHHHHHH----TSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence            44456667888999 999999999999998    5899999999999999999999999999999976543

>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=3.8e-08  Score=84.29  Aligned_cols=77  Identities=21%  Similarity=0.160  Sum_probs=68.8

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r  344 (518)
                      +..+..|+..|++.|+..|.+.++.+|.++ .   +..+++|++||+|+.+|+.+.+|++.  ..|.+|++..+++.+.+
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            455678999999999999999999999987 3   56789999999999999999999964  36999999999999998


Q ss_pred             HHH
Q 010092          345 SMT  347 (518)
Q Consensus       345 aI~  347 (518)
                      +++
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=3.2e-08  Score=82.47  Aligned_cols=64  Identities=19%  Similarity=0.128  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          444 ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       444 ~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      ......+..++..|+++|+.||.+++     +++|.+|||+.||+|..+|+.+..++++||+...+.+.
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            34456688889999999999999965     78999999999999999999999999999998766553

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=98.57  E-value=1.2e-07  Score=76.17  Aligned_cols=61  Identities=21%  Similarity=0.229  Sum_probs=54.1

Q ss_pred             HHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010092          448 LALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  513 (518)
Q Consensus       448 ~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L  513 (518)
                      ..|..++..||++|+.||.+++     +++|.+|||+.||+|..+|+++..++++||+...+.+.+
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            4577888999999999999954     789999999999999999999999999999987765543

>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=98.55  E-value=1e-07  Score=80.34  Aligned_cols=63  Identities=19%  Similarity=0.143  Sum_probs=47.5

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          445 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       445 ~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      +....|..+|..|+++|++||.+++     +++|.+|||+.||+|..+|+.++.++++||+...+.+.
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            3455688889999999999999975     78999999999999999999999999999998766543

>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=98.49  E-value=2.3e-07  Score=81.01  Aligned_cols=61  Identities=23%  Similarity=0.165  Sum_probs=54.3

Q ss_pred             HHHHHHHHH-hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          446 LRLALDDVL-DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       446 l~~~L~~~L-~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      ....+..++ ..|||+++.||.++|    .+++|++|||+.||+|..+|+++.++|+++||.....
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            345677788 899999999999998    4899999999999999999999999999999976543

>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=7.6e-08  Score=82.45  Aligned_cols=64  Identities=16%  Similarity=0.144  Sum_probs=54.0

Q ss_pred             HHHHHHHHHH-hcCCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcch
Q 010092          445 LLRLALDDVL-DSLKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR  509 (518)
Q Consensus       445 ~l~~~L~~~L-~~L~~rEr~VL~lryGL~~---~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~  509 (518)
                      ...+.+..++ +.|+++|+.+|.+||||.+   ..++|+.|||+.+|+|+++|+++ +++|++|....+
T Consensus        23 ~~~~~l~~~l~~lLT~~Er~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L~~l~~~~k   90 (101)
T 1jhg_A           23 YQNDLHLPLLNLMLTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSLKAAPVELR   90 (101)
T ss_dssp             HHTTCHHHHHHHHSCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHHHHSCHHHH
T ss_pred             CCHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHHHHccHHHH
Confidence            3344566777 5699999999999999975   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=98.45  E-value=2.1e-07  Score=76.22  Aligned_cols=60  Identities=23%  Similarity=0.277  Sum_probs=51.3

Q ss_pred             HHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010092          449 ALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  513 (518)
Q Consensus       449 ~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L  513 (518)
                      .+..++..|+++|++||.+++     +++|.+|||+.||+|..+|+.+..++++||+...+.+..
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            356677899999999999954     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=1e-06  Score=69.58  Aligned_cols=59  Identities=29%  Similarity=0.241  Sum_probs=49.9

Q ss_pred             HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010092          450 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  513 (518)
Q Consensus       450 L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L  513 (518)
                      +...+..|+++|+.||.+.+     +++|.+|||+.||+|..+|+++..+++++|+...+.+.+
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            34456789999999999954     789999999999999999999999999999987765543

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=98.07  E-value=5.5e-06  Score=81.52  Aligned_cols=159  Identities=10%  Similarity=-0.000  Sum_probs=110.6

Q ss_pred             HHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHH----HHHHHHHHHHHHhcCCCCCCccchHHHHHHH
Q 010092          264 QVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLC----QAGVKGLITAIDRFEPKRRFRLSTYGLFWIR  339 (518)
Q Consensus       264 ~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLI----QEG~IGLirAvekFDp~rG~kFSTYA~~wIR  339 (518)
                      .+.++-.+|..+++.+...+.+++..+.....   .......|+.    ||.++.+|+....|++..  .|.+|++..++
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            34445467788999999999999999988765   4566778886    999999999999998654  68888764333


Q ss_pred             HHHHHHHHhcCCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcC
Q 010092          340 HAIIRSMTVSSFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHG  419 (518)
Q Consensus       340 qaI~raI~~sr~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~  419 (518)
                      +.+.+..+.           .                                                    .+..   
T Consensus       162 n~~~d~~r~-----------~----------------------------------------------------~~~~---  175 (258)
T 3clo_A          162 SLSADQRPE-----------Q----------------------------------------------------GIYA---  175 (258)
T ss_dssp             EECSCCCCC-----------S----------------------------------------------------SCCC---
T ss_pred             HHHcchhhh-----------h----------------------------------------------------HHHH---
Confidence            322111000           0                                                    0000   


Q ss_pred             CchhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          420 VTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       420 ~~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                          .+... .....  ....        .+..++..||+++++||.|++     +++|.+|||+.||+|..||+.+.+|
T Consensus       176 ----~~~~~-~~~~~--~~~~--------~~~~~~~~L~~~erevl~L~~-----~G~s~~EIA~~L~iS~~TVk~~l~r  235 (258)
T 3clo_A          176 ----TITQM-ERGEV--ETLS--------LSEEHRNILSEREKEILRCIR-----KGLSSKEIAATLYISVNTVNRHRQN  235 (258)
T ss_dssp             ----EEEET-TTTEE--EECC--------CHHHHTTSSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             ----HHHhh-ccccc--ccch--------hhHHHHccCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence                00000 00000  0000        145667899999999999986     7999999999999999999999999


Q ss_pred             HHHHHhCcchhhhh
Q 010092          500 GLMKLKHPTRVDYL  513 (518)
Q Consensus       500 ALkKLR~~~~~~~L  513 (518)
                      |++|||...+.+..
T Consensus       236 a~~kL~~~~~~~~~  249 (258)
T 3clo_A          236 ILEKLSVGNSIEAC  249 (258)
T ss_dssp             HHHHTTCSSHHHHH
T ss_pred             HHHHHcCCCHHHHH
Confidence            99999987665443

>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=97.98  E-value=1.4e-05  Score=66.64  Aligned_cols=55  Identities=25%  Similarity=0.283  Sum_probs=47.6

Q ss_pred             HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          453 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       453 ~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      ....|+++|++||.+.+     +++|.+|||+.||||..+|+.+..++++||.-..+.+-
T Consensus        26 ~~~~Lt~rE~~Vl~l~~-----~G~s~~eIA~~L~iS~~TV~~~~~~i~~Klgv~~r~~l   80 (90)
T 3ulq_B           26 EQDVLTPRECLILQEVE-----KGFTNQEIADALHLSKRSIEYSLTSIFNKLNVGSRTEA   80 (90)
T ss_dssp             ---CCCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCSSHHHH
T ss_pred             cccCCCHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHHH
Confidence            45689999999999988     78999999999999999999999999999987665543

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=97.91  E-value=1.5e-05  Score=60.67  Aligned_cols=49  Identities=22%  Similarity=0.198  Sum_probs=43.6

Q ss_pred             HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      |+|++|+.+.+     +++|.+|||+.||+|..+|+.+..++++||+...+.+-
T Consensus         1 ~re~~vl~l~~-----~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~~~~~l   49 (61)
T 2jpc_A            1 LRERQVLKLID-----EGYTNHGISEKLHISIKTVETHRMNMMRKLQVHKVTEL   49 (61)
T ss_dssp             CHHHHHHHHHH-----TSCCSHHHHHHTCSCHHHHHHHHHHHHHHHTCSSHHHH
T ss_pred             CHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHCCCCHHHH
Confidence            47999999943     79999999999999999999999999999998766543

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=97.89  E-value=2.1e-05  Score=66.95  Aligned_cols=53  Identities=30%  Similarity=0.321  Sum_probs=47.7

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      ..|+++|++||.+.+     +++|.+|||+.||||..+|+....++++||.-..+.+-
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     68999999999999999999999999999987766543

>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=0.00031  Score=67.85  Aligned_cols=52  Identities=21%  Similarity=0.138  Sum_probs=47.2

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      .|+++|++||.+.+     +++|.+|||+.||||..||+.+..++++||.-..+.+.
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            59999999999966     79999999999999999999999999999987766543

>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=0.00035  Score=67.37  Aligned_cols=52  Identities=21%  Similarity=0.240  Sum_probs=46.9

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      .||++|++||.+.+     +++|.+|||+.||+|..||+.++.++++||.-..+.+.
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     79999999999999999999999999999987666543

>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=97.21  E-value=0.00048  Score=66.81  Aligned_cols=53  Identities=25%  Similarity=0.330  Sum_probs=47.5

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      ..||++|++||.+..     +++|.+|||+.||||..||+.+..++++||.-..+.+-
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            369999999999976     79999999999999999999999999999987665543

>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=97.13  E-value=0.00061  Score=67.39  Aligned_cols=51  Identities=29%  Similarity=0.245  Sum_probs=47.0

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  511 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~  511 (518)
                      .|+++|++||.+..     +++|.+|||+.||||..||+.++.++++||.-..+.+
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=96.84  E-value=0.0013  Score=46.60  Aligned_cols=40  Identities=18%  Similarity=0.116  Sum_probs=32.6

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .|++.++..+...|    .+++|..+||+.||||+.+|+.++.+
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            47888886655555    36899999999999999999988754

>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=96.71  E-value=0.006  Score=56.21  Aligned_cols=58  Identities=24%  Similarity=0.330  Sum_probs=49.6

Q ss_pred             HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          450 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       450 L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      +...+..|+++|++|+.+..     .++|.++||+.||+|..+|+.+..++++||....+.+.
T Consensus       136 ~~~~~~~Lt~rE~~vl~~l~-----~g~s~~~Ia~~l~is~~TV~~~~~~i~~Kl~~~~~~~~  193 (208)
T 1yio_A          136 LEQLFSSLTGREQQVLQLTI-----RGLMNKQIAGELGIAEVTVKVHRHNIMQKLNVRSLANL  193 (208)
T ss_dssp             HHHHHHTSCHHHHHHHHHHT-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCSSHHHH
T ss_pred             HHHHHHhcCHHHHHHHHHHH-----cCCcHHHHHHHcCCCHHHHHHHHHHHHHHhCCCCHHHH
Confidence            34455689999999998765     67999999999999999999999999999987655543

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=96.57  E-value=0.0049  Score=52.60  Aligned_cols=46  Identities=11%  Similarity=0.143  Sum_probs=42.4

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK  505 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR  505 (518)
                      .+++.-..|-.++|    .+++|..|||+.||+|+.+|.+++.+|...+-
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    68999999999999999999999999998763

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=96.31  E-value=0.0023  Score=47.39  Aligned_cols=39  Identities=21%  Similarity=0.064  Sum_probs=30.0

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +++..+.|+.++.     .++|..|||+.||||+.+|++++.+|
T Consensus        17 ~~~~~~~i~~l~~-----~g~s~~eIA~~lgis~~TV~~~l~~a   55 (55)
T 2x48_A           17 EDDLVSVAHELAK-----MGYTVQQIANALGVSERKVRRYLESC   55 (55)
T ss_dssp             HHHHHHHHHHHHH-----TTCCHHHHHHHHTSCHHHHHHHHTC-
T ss_pred             CHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHhC
Confidence            3445566666643     68899999999999999999987654

>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=96.19  E-value=0.01  Score=55.06  Aligned_cols=52  Identities=27%  Similarity=0.337  Sum_probs=46.6

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  511 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~  511 (518)
                      ..|+++|.+|+.+..     +++|.+|||+.+++|..||+.+..+.++||.-..+.+
T Consensus       153 ~~Lt~rE~~vl~~l~-----~g~s~~~Ia~~l~is~~TV~~hi~~i~~Kl~~~~r~~  204 (215)
T 1a04_A          153 NQLTPRERDILKLIA-----QGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVE  204 (215)
T ss_dssp             GGSCHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCCSHHH
T ss_pred             cCCCHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence            369999999998876     6889999999999999999999999999998766554

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=95.78  E-value=0.015  Score=54.65  Aligned_cols=52  Identities=19%  Similarity=0.172  Sum_probs=45.9

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  511 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~  511 (518)
                      ..|+++|.+||.+-.     +++|.+|||+.+++|..||+.+..+.++||.-..+.+
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=95.23  E-value=0.022  Score=53.33  Aligned_cols=52  Identities=23%  Similarity=0.255  Sum_probs=45.9

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  511 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~  511 (518)
                      ..|+++|.+||.+..     .++|.++||+.+++|..||+.+..+.++||.-..+.+
T Consensus       158 ~~Lt~rE~~vL~~l~-----~g~s~~~Ia~~l~~s~~Tv~~~i~~l~~KL~~~~~~~  209 (225)
T 3klo_A          158 AKLTKREQQIIKLLG-----SGASNIEIADKLFVSENTVKTHLHNVFKKINAKNRLQ  209 (225)
T ss_dssp             HTSCHHHHHHHHHHT-----TTCCHHHHHHHTTCCHHHHHHHHHHHTTTSCCSSHHH
T ss_pred             ccCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence            469999999998854     6899999999999999999999999999997665543

>3p7n_A Sensor histidine kinase; LOV domain, light-activated transcription factor, DNA bindin; HET: FMN; 2.10A {Erythrobacter litoralis}

Probab=95.18  E-value=0.068  Score=50.63  Aligned_cols=64  Identities=23%  Similarity=0.244  Sum_probs=55.0

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhh
Q 010092          445 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL  513 (518)
Q Consensus       445 ~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L  513 (518)
                      .........+..|+++++.|+.+..     .+++..+||..||+|..+|+....++++||.-..+.+-+
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            3445677888999999999999876     578999999999999999999999999999877665443

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

Probab=94.77  E-value=0.008  Score=66.37  Aligned_cols=38  Identities=18%  Similarity=0.129  Sum_probs=13.0

Q ss_pred             hhcCCcChHHHHHHhcCCCCCCChHHHHHHHHHHhHhH
Q 010092          195 EYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMK  232 (518)
Q Consensus       195 ~~~~~~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~  232 (518)
                      +.+..+|+|+|||++||.+||||+++|+.|++.|+.+.
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            34578999999999999999999999999999997553

>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=92.81  E-value=0.079  Score=37.58  Aligned_cols=25  Identities=8%  Similarity=-0.065  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          475 GDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       475 e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .+.|..+||+.||||+.+|++++.+
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=92.79  E-value=0.091  Score=48.66  Aligned_cols=51  Identities=12%  Similarity=-0.019  Sum_probs=43.0

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC---CCHHHHHHHHHHHHHHHhCc
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN---ISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~Lg---ISrerVRqie~rALkKLR~~  507 (518)
                      .|+++|.+||.+..- +.+..+|.+|||+.++   +|..+|+.+..+.++||...
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            599999999986551 1123499999999999   99999999999999999753

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=92.31  E-value=0.13  Score=48.38  Aligned_cols=51  Identities=16%  Similarity=0.066  Sum_probs=42.1

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHhCc
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNL-----NISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~L-----gISrerVRqie~rALkKLR~~  507 (518)
                      .|+++|.+||.+..- +.+..+|.+|||+.+     ++|..+|+.+..+.++||...
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 112349999999999     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=91.95  E-value=0.12  Score=48.07  Aligned_cols=51  Identities=14%  Similarity=0.063  Sum_probs=43.2

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHhCc
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNL-----NISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~L-----gISrerVRqie~rALkKLR~~  507 (518)
                      .|+++|.+||.+-.- +.+..+|.+|||+.+     ++|..+|+.+..+.++||...
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            599999999987551 123459999999999     999999999999999999753

>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=91.87  E-value=0.14  Score=41.13  Aligned_cols=42  Identities=12%  Similarity=0.145  Sum_probs=29.6

Q ss_pred             HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +.++.||.+-.-...+...|..|||+.||||+.+|++++.+-
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L   55 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSL   55 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            345666655443322347899999999999999998775543

>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=91.58  E-value=0.11  Score=47.99  Aligned_cols=52  Identities=17%  Similarity=0.109  Sum_probs=43.1

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhCcc
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~Lg-----ISrerVRqie~rALkKLR~~~  508 (518)
                      .|+++|.+||.+..- +.+..+|.+|||+.++     +|..+|+.+..+.++||....
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            599999999987541 1123499999999998     999999999999999997543

>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=91.21  E-value=0.29  Score=39.74  Aligned_cols=40  Identities=13%  Similarity=0.194  Sum_probs=27.7

Q ss_pred             HHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          460 KESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       460 rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .++.||.+-.-...+...|..|||+.||||+.+|++.+.+
T Consensus        11 ~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~   50 (81)
T 1qbj_A           11 QEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYS   50 (81)
T ss_dssp             HHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            3555665544322345799999999999999888855443

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=91.06  E-value=0.18  Score=44.09  Aligned_cols=36  Identities=17%  Similarity=0.106  Sum_probs=28.8

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHH
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH  496 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqi  496 (518)
                      ..|+.| .+|+.+-.     +++|+.|||+.+|+|..||.+.
T Consensus        60 ~aLs~R-~eV~klL~-----~G~syreIA~~~g~S~aTIsRv   95 (119)
T 3kor_A           60 QSLSQR-LQVAKMIK-----QGYTYATIEQESGASTATISRV   95 (119)
T ss_dssp             HHHHHH-HHHHHHHH-----HTCCHHHHHHHHCCCHHHHHHH
T ss_pred             HHHHHH-HHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHH
Confidence            345566 67777755     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=90.97  E-value=0.11  Score=48.37  Aligned_cols=51  Identities=10%  Similarity=-0.089  Sum_probs=42.0

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhCc
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~Lg-----ISrerVRqie~rALkKLR~~  507 (518)
                      .|+++|.+||.+..- +.+..+|.++||+.++     +|..+|+.+..+.++||...
T Consensus       159 ~Lt~rE~~vL~~l~~-g~~~~~s~~~Ia~~l~~~~~~~s~~tv~~hi~~l~~Kl~~~  214 (233)
T 1ys7_A          159 DLTKREFDLLAVLAE-HKTAVLSRAQLLELVWGYDFAADTNVVDVFIGYLRRKLEAG  214 (233)
T ss_dssp             CCCHHHHHHHHHHHH-TTTCCBCHHHHHHHHHCCCCC-CCCHHHHHHHHHHHHHHCC
T ss_pred             ccCHHHHHHHHHHHh-CCCCeEcHHHHHHHhcCcccCCCccCHHHHHHHHHHHhccC
Confidence            599999999987651 1123399999999998     99999999999999999864

>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=90.81  E-value=0.24  Score=42.69  Aligned_cols=41  Identities=17%  Similarity=0.101  Sum_probs=33.1

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .|++.++..|...+    ..++|..+||+.||+|+.+|+.+..+.
T Consensus         6 ~~s~~~r~~i~~~~----~~G~s~~~ia~~lgis~~Tv~r~~~~~   46 (141)
T 1u78_A            6 ALSDTERAQLDVMK----LLNVSLHEMSRKISRSRHCIRVYLKDP   46 (141)
T ss_dssp             CCCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHSG
T ss_pred             cCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHcc
Confidence            46777776666655    367999999999999999999988653

>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=90.48  E-value=0.36  Score=40.51  Aligned_cols=42  Identities=19%  Similarity=0.029  Sum_probs=32.1

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      .+++.++.-|...|    ..++|..+||+.||||+.+|+++..+..
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            45555555544444    2578999999999999999999998754

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=89.19  E-value=0.2  Score=47.92  Aligned_cols=54  Identities=20%  Similarity=0.121  Sum_probs=44.5

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHH-----HhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAG-----NLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~-----~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      .|+++|.+||.+..- +.+..+|.+|||+     .+++|..+|+.+..+.++||....+.
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

>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=89.13  E-value=0.073  Score=51.97  Aligned_cols=50  Identities=14%  Similarity=0.219  Sum_probs=0.0

Q ss_pred             HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC--CCHHHHHHHHHHHHHHH
Q 010092          450 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN--ISREMVRKHEVKGLMKL  504 (518)
Q Consensus       450 L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~Lg--ISrerVRqie~rALkKL  504 (518)
                      +...+..|++.++. |...||    .+.|.+|||+.||  ||.++|+.++.+|++.|
T Consensus       192 l~e~i~~l~~~~~~-L~~~~~----~~ps~~EIAe~Lg~~is~~tVk~~l~~ar~~l  243 (245)
T 3ugo_A          192 MVETINKLSRTARQ-LQQELG----REPSYEEIAEAMGPGWDAKRVEETLKIAQEPV  243 (245)
T ss_dssp             ---------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHH-HHHHhC----CCCCHHHHHHHHCCCCCHHHHHHHHHHHhhcc
Confidence            45556677777777 444563    6789999999999  99999999999998776

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=88.97  E-value=0.43  Score=45.06  Aligned_cols=28  Identities=14%  Similarity=0.121  Sum_probs=25.5

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          474 KGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       474 ~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      ..++|..|||+.||||+.+|++++..|.
T Consensus        22 ~~g~tQ~eIA~~lGiSr~~VSR~L~~A~   49 (192)
T 1zx4_A           22 NDGMSQKDIAAKEGLSQAKVTRALQAAS   49 (192)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHHHHhc
Confidence            3679999999999999999999998874

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=88.88  E-value=0.11  Score=48.09  Aligned_cols=51  Identities=10%  Similarity=0.049  Sum_probs=42.5

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhC-----CCHHHHHHHHHHHHHHHhCc
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN-----ISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~Lg-----ISrerVRqie~rALkKLR~~  507 (518)
                      .|+++|.+||.+-.- +.+..+|.+|||+.++     +|..+|+.+..+.++||...
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            599999999987651 0112399999999999     99999999999999999753

>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=88.62  E-value=0.57  Score=41.21  Aligned_cols=43  Identities=16%  Similarity=-0.006  Sum_probs=33.0

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                      .++..++.-|...+    ..++|..+||+.||||+.+|+++..+...
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            45666665555555    25789999999999999999999987543

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=88.27  E-value=0.8  Score=39.46  Aligned_cols=45  Identities=11%  Similarity=0.118  Sum_probs=34.7

Q ss_pred             HHhcCCHHHHHHHhHHhcCCCCCC-CCHHHHHHHhCCCHHHHHHHHHH
Q 010092          453 VLDSLKPKESLVIRQRFGLDGKGD-RTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       453 ~L~~L~~rEr~VL~lryGL~~~e~-~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      ..-.|++.+..|+..-..  ...+ +|..|||+.+|+|+++|.+.+.+
T Consensus        20 ~~~gLt~~e~~il~~L~~--~~~~~~t~~eLa~~l~~s~sTV~r~L~~   65 (123)
T 3r0a_A           20 CALNLTKADLNVMKSFLN--EPDRWIDTDALSKSLKLDVSTVQRSVKK   65 (123)
T ss_dssp             HHHTCCHHHHHHHHHHHH--STTCCEEHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHH--CCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            345799999999876553  1234 89999999999999999865544

>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=88.18  E-value=1.1  Score=36.37  Aligned_cols=42  Identities=26%  Similarity=0.358  Sum_probs=33.6

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .|++.+..||..-.-   ..+.|..|||+.+|+|+.+|++++.+-
T Consensus        17 ~l~~~~~~il~~l~~---~~~~s~~ela~~l~is~~tv~~~l~~L   58 (109)
T 1sfx_A           17 SFKPSDVRIYSLLLE---RGGMRVSEIARELDLSARFVRDRLKVL   58 (109)
T ss_dssp             CCCHHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            478999888876542   257999999999999999999766543

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=87.44  E-value=1.1  Score=39.64  Aligned_cols=43  Identities=19%  Similarity=0.157  Sum_probs=33.6

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      ..|++.++.||.+-..   ....|+.|||+.+|+|+.+|++..++-
T Consensus         5 ~~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~L   47 (151)
T 2dbb_A            5 RKLDRVDMQLVKILSE---NSRLTYRELADILNTTRQRIARRIDKL   47 (151)
T ss_dssp             -CCCHHHHHHHHHHHH---CTTCCHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3588999998875432   357999999999999999998766543

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=87.43  E-value=0.81  Score=36.97  Aligned_cols=27  Identities=7%  Similarity=0.126  Sum_probs=23.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          475 GDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       475 e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      .+.|..+||+.||||+.+|+++..+..
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

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=87.38  E-value=0.49  Score=38.67  Aligned_cols=25  Identities=20%  Similarity=0.215  Sum_probs=22.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          476 DRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       476 ~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +.|..|||+.||||+++|++++.+-
T Consensus        30 g~sa~eLAk~LgiSk~aVr~~L~~L   54 (82)
T 1oyi_A           30 GATAAQLTRQLNMEKREVNKALYDL   54 (82)
T ss_dssp             TEEHHHHHHHSSSCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3999999999999999999887653

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=87.35  E-value=0.87  Score=40.04  Aligned_cols=42  Identities=12%  Similarity=0.120  Sum_probs=33.0

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .|++.++.||.+-..   ....|+.|||+.+|+|+++|++.+++-
T Consensus         2 ~ld~~d~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~L   43 (144)
T 2cfx_A            2 KLDQIDLNIIEELKK---DSRLSMRELGRKIKLSPPSVTERVRQL   43 (144)
T ss_dssp             CCCHHHHHHHHHHHH---CSCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            378888888876432   356999999999999999998766543

>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=87.26  E-value=1.1  Score=36.26  Aligned_cols=44  Identities=16%  Similarity=0.099  Sum_probs=33.8

Q ss_pred             HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       454 L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      ...|++.+..+|...+.  ...+.|..|||+.+|+|+.+|++++..
T Consensus        16 ~~~l~~~~~~~l~~l~~--~~~~~t~~ela~~l~is~~tv~~~l~~   59 (109)
T 2d1h_A           16 CYKITDTDVAVLLKMVE--IEKPITSEELADIFKLSKTTVENSLKK   59 (109)
T ss_dssp             HHTCCHHHHHHHHHHHH--HCSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hhcCCHHHHHHHHHHHH--cCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            35789988888765441  125799999999999999999866544

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=87.09  E-value=0.63  Score=35.98  Aligned_cols=40  Identities=5%  Similarity=0.043  Sum_probs=26.9

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      +++....||.+.--  +..++|..|||+.+|+|+++|.+++.
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  12579999999999999988886544

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=87.02  E-value=0.86  Score=43.11  Aligned_cols=50  Identities=16%  Similarity=0.086  Sum_probs=43.3

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh-----CCCHHHHHHHHHHHHHHHhC
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNL-----NISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~L-----gISrerVRqie~rALkKLR~  506 (518)
                      .|+++|.+||.+.. .+.+...|.++|++.+     ++|..+|+.+..+..+||..
T Consensus       176 ~LT~rE~~iL~~l~-~~~~~~~s~~~i~~~lw~~~~~~~~~tv~~~i~~lr~KL~~  230 (250)
T 3r0j_A          176 SLSPTEFTLLRYFV-INAGTVLSKPKILDHVWRYDFGGDVNVVESYVSYLRRKIDT  230 (250)
T ss_dssp             CCCHHHHHHHHHHH-HTTTCCBCHHHHHHHHTTTSCCSCTHHHHHHHHHHHHHHCC
T ss_pred             ecCHHHHHHHHHHH-HCCCceEcHHHHHHHHcCCCCCCCccCHHHHHHHHHHhhcC
Confidence            59999999998765 2224679999999999     78999999999999999975

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=87.00  E-value=0.71  Score=46.22  Aligned_cols=36  Identities=22%  Similarity=0.287  Sum_probs=31.1

Q ss_pred             HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          463 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       463 ~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                      .|..++|    .+++|..|||+.||||+.+||+.+..+.+
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            4666777    57899999999999999999999988755

>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=86.51  E-value=0.61  Score=43.37  Aligned_cols=43  Identities=16%  Similarity=0.112  Sum_probs=33.0

Q ss_pred             cCCHHHHHHHhHHhcC--CCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGL--DGKGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL--~~~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      .|+++|++||.+-.-+  ..+.+.|..|||+.||+|..+|++++.
T Consensus         2 ~lt~~q~~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~l~   46 (196)
T 3k2z_A            2 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHLI   46 (196)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHHHH
Confidence            5899999999774321  123578999999999999998876653

>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=86.23  E-value=1.1  Score=39.61  Aligned_cols=42  Identities=21%  Similarity=0.305  Sum_probs=33.5

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .|++.++.||.+-..   ....|+.|||+.+|+|+++|++++.+-
T Consensus         4 ~ld~~~~~iL~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~L   45 (150)
T 2w25_A            4 ALDDIDRILVRELAA---DGRATLSELATRAGLSVSAVQSRVRRL   45 (150)
T ss_dssp             CCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            488889888876431   347999999999999999998776553

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=86.12  E-value=1.1  Score=39.68  Aligned_cols=42  Identities=17%  Similarity=0.192  Sum_probs=33.2

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .|++.++.||.+-..   ....|+.|||+.+|+|+.+|++.+.+-
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            478888888875431   247999999999999999999776554

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=86.05  E-value=1.9  Score=36.48  Aligned_cols=52  Identities=10%  Similarity=0.105  Sum_probs=39.5

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          446 LRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       446 l~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +...+...+.  .|++.+..||..-+.   .++.|..|||+.+|+|+.+|.++..+-
T Consensus        14 ~~~~~~~~~~~~~l~~~~~~iL~~l~~---~~~~~~~ela~~l~~s~~tvs~~l~~L   67 (138)
T 3bpv_A           14 HRVFIGRELGHLNLTDAQVACLLRIHR---EPGIKQDELATFFHVDKGTIARTLRRL   67 (138)
T ss_dssp             HHHHHHHHSGGGTCCHHHHHHHHHHHH---STTCBHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3344555554  489999999887653   367999999999999999999766553

>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=85.90  E-value=2  Score=35.70  Aligned_cols=47  Identities=15%  Similarity=0.237  Sum_probs=33.7

Q ss_pred             HHHHHHhcCC-HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          449 ALDDVLDSLK-PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       449 ~L~~~L~~L~-~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .+..++..|. +....||.+-.    ..++|..|||+.+|+|+++|+++++.
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            4455555554 55566666543    25789999999999999999977654

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=85.78  E-value=1.1  Score=40.08  Aligned_cols=42  Identities=12%  Similarity=0.080  Sum_probs=33.4

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .|++.++.||.+-..   ....|+.|||+.+|+|+.+|++++.+-
T Consensus         7 ~ld~~~~~il~~L~~---~~~~s~~ela~~lg~s~~tv~~~l~~L   48 (162)
T 2p5v_A            7 TLDKTDIKILQVLQE---NGRLTNVELSERVALSPSPCLRRLKQL   48 (162)
T ss_dssp             CCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            478888888876442   346899999999999999999776553

>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=85.72  E-value=1.6  Score=37.47  Aligned_cols=52  Identities=13%  Similarity=0.237  Sum_probs=38.0

Q ss_pred             HHHHHHHHHhc----CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          446 LRLALDDVLDS----LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       446 l~~~L~~~L~~----L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +...+...+..    |++.|..||..-+.   .++.|..|||+.+|+|+++|.++..+-
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    99999999987663   357999999999999999999776654

>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=85.64  E-value=1.8  Score=36.84  Aligned_cols=50  Identities=18%  Similarity=0.142  Sum_probs=39.2

Q ss_pred             HHHHHHHHhcCCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          447 RLALDDVLDSLKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       447 ~~~L~~~L~~L~~rEr~VL~lryGL~~---~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      ...|...+..|++.|+.|..+..  ..   ...+|..|||+..|+|..+|.+.-+
T Consensus         9 ~~~i~~~~~~ls~~e~~ia~yil--~~~~~~~~~si~elA~~~~vS~aTv~Rf~k   61 (111)
T 2o3f_A            9 LAIIQSMXHXLPPSERKLADYIL--AHPHXAIESTVNEISALANSSDAAVIRLCX   61 (111)
T ss_dssp             HHHHHHHGGGSCHHHHHHHHHHH--HCHHHHHTCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHhccCCHHHHHHHHHHH--HChHHHHhcCHHHHHHHHCCCHHHHHHHHH
Confidence            34577778899999999986554  21   1369999999999999999987654

>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=85.62  E-value=0.95  Score=39.26  Aligned_cols=41  Identities=22%  Similarity=0.272  Sum_probs=31.3

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      |++.++.||..-..   ....|+.|||+.+|+|+.+|++.+.+-
T Consensus         2 ld~~~~~il~~L~~---~~~~~~~ela~~lg~s~~tv~~~l~~L   42 (141)
T 1i1g_A            2 IDERDKIILEILEK---DARTPFTEIAKKLGISETAVRKRVKAL   42 (141)
T ss_dssp             CCSHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            66777888765431   246899999999999999998765543

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=85.38  E-value=1.2  Score=39.36  Aligned_cols=42  Identities=14%  Similarity=0.216  Sum_probs=33.3

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .|++.++.||.+-.-   ....|+.|||+.+|+|+++|++.+++-
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            478888888875431   357999999999999999999776554

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=85.25  E-value=1.3  Score=38.89  Aligned_cols=41  Identities=15%  Similarity=0.137  Sum_probs=31.3

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      |++.+..||.+--   .....|+.|||+.+|+|+++|++.+.+-
T Consensus         1 ld~~~~~il~~L~---~~~~~~~~ela~~lg~s~~tv~~~l~~L   41 (150)
T 2pn6_A            1 MDEIDLRILKILQ---YNAKYSLDEIAREIRIPKATLSYRIKKL   41 (150)
T ss_dssp             CCHHHHHHHHHHT---TCTTSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CChHHHHHHHHHH---HcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            5677778876543   1346999999999999999998766543

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=85.20  E-value=1.3  Score=35.63  Aligned_cols=45  Identities=20%  Similarity=0.347  Sum_probs=32.1

Q ss_pred             HHHhcC-CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          452 DVLDSL-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       452 ~~L~~L-~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .++..| ++.+..||..-.   .+.+.|..|||+.+|+|+.+|++++.+
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            333333 466667775543   235799999999999999999976654

>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=84.81  E-value=2.2  Score=36.45  Aligned_cols=50  Identities=20%  Similarity=0.210  Sum_probs=37.1

Q ss_pred             HHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          448 LALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       448 ~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      ..+...+.  .|++.+..|+.+-+ +. .++.|..|||+.+|+|+++|.++..+
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  48999999987664 22 25799999999999999999876654

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=84.41  E-value=1.5  Score=35.70  Aligned_cols=40  Identities=18%  Similarity=0.157  Sum_probs=29.3

Q ss_pred             CCHHHHHH-HhHHhcCCCCC-CCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          457 LKPKESLV-IRQRFGLDGKG-DRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       457 L~~rEr~V-L~lryGL~~~e-~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .++..+.- +.++.    .. +.|+.+||..+|||+.+|+++..+.
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            45555543 43443    23 6899999999999999999998654

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=84.36  E-value=1.6  Score=37.38  Aligned_cols=41  Identities=22%  Similarity=0.160  Sum_probs=32.8

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .|++.+..||..-+.   .+ .|..|||+.+|+|+++|+++..+-
T Consensus        35 ~lt~~~~~iL~~l~~---~~-~t~~eLa~~l~~s~~tvs~~l~~L   75 (146)
T 3tgn_A           35 ALTNTQEHILMLLSE---ES-LTNSELARRLNVSQAAVTKAIKSL   75 (146)
T ss_dssp             CCCHHHHHHHHHHTT---CC-CCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh---CC-CCHHHHHHHHCCCHHHHHHHHHHH
Confidence            478888888876652   33 999999999999999999766553

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=84.33  E-value=1.4  Score=38.01  Aligned_cols=47  Identities=17%  Similarity=0.133  Sum_probs=33.6

Q ss_pred             HhcCCHHHHHHHhHHhcC-CCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          454 LDSLKPKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       454 L~~L~~rEr~VL~lryGL-~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +-.|++.+..+|...+-+ ....+.|..+||+.+|+|+.+|++++++-
T Consensus         8 ~~~lt~~~~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~~~l~~L   55 (139)
T 2x4h_A            8 MSNLSRREFSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVFEEVSHL   55 (139)
T ss_dssp             ---CCHHHHHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HhhcCHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHHHHHHHH
Confidence            346888888887765432 22357899999999999999999766543

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=84.23  E-value=1.5  Score=39.38  Aligned_cols=40  Identities=10%  Similarity=0.154  Sum_probs=31.3

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      |++.++.||.+---   ....|+.|||+.+|+|+.+|++.+.+
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            56677888765431   34689999999999999999977655

>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=84.20  E-value=3.4  Score=35.05  Aligned_cols=54  Identities=7%  Similarity=0.009  Sum_probs=39.6

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          446 LRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       446 l~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +...+...+.  .|++.|..||..-+.- ++.+.|..+||+.+|+|+.+|.++..+-
T Consensus        19 ~~~~~~~~~~~~~lt~~~~~iL~~l~~~-~~~~~~~~ela~~l~~~~~tvs~~l~~L   74 (141)
T 3bro_A           19 MSTRFDIFAKKYDLTGTQMTIIDYLSRN-KNKEVLQRDLESEFSIKSSTATVLLQRM   74 (141)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHT-TTSCCBHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHC-CCCCcCHHHHHHHHCCCcchHHHHHHHH
Confidence            3444555554  4899999998876642 1237999999999999999998766554

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=83.97  E-value=3.1  Score=36.07  Aligned_cols=52  Identities=10%  Similarity=0.022  Sum_probs=39.3

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          446 LRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       446 l~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +...+...+.  .|++.+..||..-+.   .++.|..+||+.+|+++.+|.+++.+-
T Consensus        28 ~~~~~~~~l~~~~lt~~~~~iL~~l~~---~~~~t~~ela~~l~i~~~tvs~~l~~L   81 (155)
T 3cdh_A           28 ASAQFHDHIRAQGLRVPEWRVLACLVD---NDAMMITRLAKLSLMEQSRMTRIVDQM   81 (155)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHSS---CSCBCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHH---CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3344555553  499999999877652   357999999999999999999776554

>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=83.92  E-value=3.3  Score=35.31  Aligned_cols=48  Identities=21%  Similarity=0.254  Sum_probs=37.4

Q ss_pred             HHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          449 ALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       449 ~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .+...+.  .|++.+..||..-+    .++.|..|||+.+|+|+++|++++.+-
T Consensus        25 ~~~~~~~~~~l~~~~~~iL~~l~----~~~~~~~ela~~l~~s~~tvs~~l~~L   74 (146)
T 2gxg_A           25 ELNRRLGELNLSYLDFLVLRATS----DGPKTMAYLANRYFVTQSAITASVDKL   74 (146)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHHHT----TSCBCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHh----cCCcCHHHHHHHhCCCchhHHHHHHHH
Confidence            3444443  48999999987765    357999999999999999998766554

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=83.81  E-value=2  Score=36.42  Aligned_cols=50  Identities=6%  Similarity=0.041  Sum_probs=38.0

Q ss_pred             HHHHHHHh-cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          448 LALDDVLD-SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       448 ~~L~~~L~-~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      ..+...+. .|++.+..||..-+.   .++.|..+||+.+|+|+.+|.+++.+-
T Consensus        26 ~~~~~~~~~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~tvs~~l~~L   76 (140)
T 2nnn_A           26 ALFANGIGNGLTPTQWAALVRLGE---TGPCPQNQLGRLTAMDAATIKGVVERL   76 (140)
T ss_dssp             HHHHHHCSSCCCHHHHHHHHHHHH---HSSBCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            34444443 699999999877652   247999999999999999998766553

>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=83.80  E-value=2.8  Score=35.49  Aligned_cols=54  Identities=11%  Similarity=-0.014  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          445 LLRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       445 ~l~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      .+...+...+.  .|++.|..||..-+.   .++.|..+||+.+|+|+++|.++..+-.
T Consensus        18 ~~~~~~~~~~~~~~lt~~~~~iL~~l~~---~~~~~~~~la~~l~~~~~tvs~~l~~L~   73 (138)
T 1jgs_A           18 KKDRLLNEYLSPLDITAAQFKVLCSIRC---AACITPVELKKVLSVDLGALTRMLDRLV   73 (138)
T ss_dssp             HHHHHHHHHHTTTTSCHHHHHHHHHHHH---HSSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhcCCCHHHHHHHHHHHh---cCCCCHHHHHHHHCCChHHHHHHHHHHH
Confidence            34455666664  389999999887653   3578999999999999999997766543

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=83.76  E-value=2.9  Score=36.23  Aligned_cols=52  Identities=15%  Similarity=0.169  Sum_probs=39.5

Q ss_pred             HHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          447 RLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       447 ~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      ...+...+.  .|++.|..||..-+.   .++.|..+||+.+|+++.+|.++..+-.
T Consensus        27 ~~~~~~~~~~~~lt~~q~~iL~~l~~---~~~~~~~eLa~~l~~~~~~vs~~l~~L~   80 (149)
T 4hbl_A           27 AQFYEKKLKQFGITYSQYLVMLTLWE---ENPQTLNSIGRHLDLSSNTLTPMLKRLE   80 (149)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHH---SSSEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            334444443  489999999887653   3679999999999999999997766543

>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=83.71  E-value=2.6  Score=38.46  Aligned_cols=55  Identities=16%  Similarity=0.250  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          445 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       445 ~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .+...+...+..|++.|..||..-+-.. .++.|..+||+.+|+|+++|.+++.+-
T Consensus        27 ~~~~~~~~~~~~lt~~q~~vL~~L~~~~-~~~~t~~eLa~~l~is~~tvs~~l~~L   81 (189)
T 3nqo_A           27 KIQIEGDKYFGILTSRQYMTILSILHLP-EEETTLNNIARKMGTSKQNINRLVANL   81 (189)
T ss_dssp             HHHHHHHHHHCSSCHHHHHHHHHHHHSC-GGGCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHccCCHHHHHHHHHHHhcc-CCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3445566666779999999998766211 247999999999999999999766553

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=83.64  E-value=2.7  Score=34.36  Aligned_cols=47  Identities=15%  Similarity=0.367  Sum_probs=32.1

Q ss_pred             HHHHHHhcC-CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          449 ALDDVLDSL-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       449 ~L~~~L~~L-~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .+..++..| +|....||.+-.    ..++|..|||+.+|+|+.+|++++..
T Consensus        12 ~~~~~~~~l~~~~r~~Il~~L~----~~~~~~~ela~~l~is~~tvs~~L~~   59 (102)
T 3pqk_A           12 EVANLLKTLSHPVRLMLVCTLV----EGEFSVGELEQQIGIGQPTLSQQLGV   59 (102)
T ss_dssp             HHHHHHHHHCSHHHHHHHHHHH----TCCBCHHHHHHHHTCCTTHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHH----hCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            344455555 445555555443    24699999999999999999876543

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=83.58  E-value=1.6  Score=35.40  Aligned_cols=47  Identities=13%  Similarity=0.246  Sum_probs=31.9

Q ss_pred             HHHHHHhcC-CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          449 ALDDVLDSL-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       449 ~L~~~L~~L-~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .+..++..| ++....||.+-.   . .++|..|||+.+|+|+++|++++..
T Consensus        12 ~~~~~~~~l~~~~r~~Il~~L~---~-~~~~~~ela~~l~is~~tvs~~L~~   59 (98)
T 3jth_A           12 KAVVLLKAMANERRLQILCMLH---N-QELSVGELCAKLQLSQSALSQHLAW   59 (98)
T ss_dssp             HHHHHHHHHCSHHHHHHHHHTT---T-SCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHHHHh---c-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            344445555 455555554432   2 5799999999999999999866543

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=83.52  E-value=4.2  Score=32.92  Aligned_cols=37  Identities=22%  Similarity=0.251  Sum_probs=28.5

Q ss_pred             CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          458 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       458 ~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      ++....||.+-.     .++|..|||+.+|+|+.+|++++..
T Consensus        30 ~~~r~~Il~~L~-----~~~~~~eLa~~l~is~~tv~~~L~~   66 (96)
T 1y0u_A           30 NPVRRKILRMLD-----KGRSEEEIMQTLSLSKKQLDYHLKV   66 (96)
T ss_dssp             CHHHHHHHHHHH-----TTCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHc-----CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            556666665541     4699999999999999999976553

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=83.50  E-value=2.7  Score=35.58  Aligned_cols=42  Identities=12%  Similarity=0.094  Sum_probs=34.8

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .|++.+..||..-+.   .++.|..+||+.+|+|+.+|+++..+-
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   357999999999999999999766554

>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=83.25  E-value=6.3  Score=33.47  Aligned_cols=78  Identities=15%  Similarity=0.124  Sum_probs=48.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchhhhHHHHHHHHHHHHHhcCCHHHH-H
Q 010092          385 PTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKES-L  463 (518)
Q Consensus       385 PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee~~~~~~l~~~L~~~L~~L~~rEr-~  463 (518)
                      -+..+||+.+|++...|...++.....-..               .. ... +                 ..|++.+. .
T Consensus        23 ~s~~~ia~~lgis~~Tv~r~~~~~~~~g~~---------------~~-~gr-~-----------------~~l~~~~~~~   68 (141)
T 1u78_A           23 VSLHEMSRKISRSRHCIRVYLKDPVSYGTS---------------KR-APR-R-----------------KALSVRDERN   68 (141)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHSGGGTTCC---------------CC-CCC-C-----------------CSSCHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcccccCCc---------------CC-CCC-C-----------------CcCCHHHHHH
Confidence            478999999999999999888653211000               00 000 0                 01222222 2


Q ss_pred             HHhHHhcCCCCCCCCHHHHHHHhC--CCHHHHHHHHHHH
Q 010092          464 VIRQRFGLDGKGDRTLGEIAGNLN--ISREMVRKHEVKG  500 (518)
Q Consensus       464 VL~lryGL~~~e~~Tl~EIA~~Lg--ISrerVRqie~rA  500 (518)
                      |+.+.-    ....|..+|+..||  +|.++|++++.+.
T Consensus        69 i~~~~~----~~~~s~~~i~~~lg~~~s~~tV~r~l~~~  103 (141)
T 1u78_A           69 VIRAAS----NSCKTARDIRNELQLSASKRTILNVIKRS  103 (141)
T ss_dssp             HHHHHH----HCCCCHHHHHHHTTCCSCHHHHHHHHHHT
T ss_pred             HHHHHh----CCCCCHHHHHHHHCCCccHHHHHHHHHHC
Confidence            222211    24589999999999  8999999998763

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=83.24  E-value=3  Score=35.85  Aligned_cols=52  Identities=13%  Similarity=0.257  Sum_probs=39.7

Q ss_pred             HHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          447 RLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       447 ~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      ...+...+.  .|++.|..||..-+.   .++.|..+||+.+|+|+.+|.+++.+-.
T Consensus        28 ~~~~~~~~~~~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~tvs~~l~~Le   81 (150)
T 2rdp_A           28 KQRGREILTNYPITPPQFVALQWLLE---EGDLTVGELSNKMYLACSTTTDLVDRME   81 (150)
T ss_dssp             HHHHHHHHTTSSSCHHHHHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCchhHHHHHHHHH
Confidence            344555554  489999999877653   3579999999999999999997766543

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=83.24  E-value=1.5  Score=37.47  Aligned_cols=40  Identities=23%  Similarity=0.272  Sum_probs=28.5

Q ss_pred             CCHHHHHHHhHHhcCCC--CCCCCHHHHHHHhCCCHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDG--KGDRTLGEIAGNLNISREMVRKH  496 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~--~e~~Tl~EIA~~LgISrerVRqi  496 (518)
                      |++.|+.-|..|+-+-.  ..++|+.+|++.+|+|..+|.+.
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            56666665554442210  25799999999999999999864

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=83.22  E-value=1.7  Score=34.27  Aligned_cols=25  Identities=20%  Similarity=0.127  Sum_probs=21.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          475 GDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       475 e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .+.|..|||+.+|+|+.+|++.+..
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            4699999999999999999876654

>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=83.17  E-value=2.2  Score=36.57  Aligned_cols=53  Identities=8%  Similarity=-0.005  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          445 LLRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       445 ~l~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .+...+...+.  .|++.|..||..-+.   .++.|..|||+.+|+++++|.++..+-
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  499999988876552   467999999999999999999776654

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=83.10  E-value=3.4  Score=34.66  Aligned_cols=48  Identities=13%  Similarity=0.221  Sum_probs=35.2

Q ss_pred             HHHHHHhc-CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          449 ALDDVLDS-LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       449 ~L~~~L~~-L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .+..++.. .++.+..||.+-.    ..+.|+.|||+.+|+|+.+|++++.+-
T Consensus        21 ~~~~~~~~l~~~~~~~il~~L~----~~~~s~~ela~~l~is~stvsr~l~~L   69 (119)
T 2lkp_A           21 QVASTLQALATPSRLMILTQLR----NGPLPVTDLAEAIGMEQSAVSHQLRVL   69 (119)
T ss_dssp             HHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH----HCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            34444444 3577777777655    247999999999999999999877653

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=82.91  E-value=4.2  Score=35.47  Aligned_cols=52  Identities=13%  Similarity=0.034  Sum_probs=39.7

Q ss_pred             HHHHHHHH---hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          447 RLALDDVL---DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       447 ~~~L~~~L---~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      ...+...+   ..|++.|..||..-+.   .++.|..+||+.+|+|+.+|.+++.+-.
T Consensus        34 ~~~~~~~l~~~~~lt~~~~~iL~~l~~---~~~~t~~ela~~l~is~~tvs~~l~~Le   88 (162)
T 2fa5_A           34 SGNIAKVYGDRYGMAIPEWRVITILAL---YPGSSASEVSDRTAMDKVAVSRAVARLL   88 (162)
T ss_dssp             HHHHHHHHHHHHCCCHHHHHHHHHHHH---STTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            33444444   2599999999887663   3579999999999999999997766543

>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=82.75  E-value=3.2  Score=35.25  Aligned_cols=55  Identities=13%  Similarity=0.114  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          445 LLRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       445 ~l~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .+...+...+.  .|++.|..||..-+.- +.++.|..|||+.+|+|+.+|.++..+-
T Consensus        15 ~~~~~~~~~~~~~~lt~~~~~vL~~l~~~-~~~~~t~~ela~~l~~~~~tvs~~l~~L   71 (139)
T 3eco_A           15 EMKQKADQKLEQFDITNEQGHTLGYLYAH-QQDGLTQNDIAKALQRTGPTVSNLLRNL   71 (139)
T ss_dssp             HHHHHHHHHHGGGTCCHHHHHHHHHHHHS-TTTCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHhc-CCCCcCHHHHHHHhCCCcccHHHHHHHH
Confidence            34445555554  3899999999876631 1248999999999999999999766554

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=82.73  E-value=2.9  Score=35.85  Aligned_cols=51  Identities=16%  Similarity=0.090  Sum_probs=38.6

Q ss_pred             HHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          447 RLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       447 ~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      ...+...+.  .|++.|..||..-+.   .++.|..+||+.+|+++.+|.++..+-
T Consensus        17 ~~~~~~~~~~~~lt~~q~~iL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L   69 (145)
T 3g3z_A           17 CNVFDKWIGQQDLNYNLFAVLYTLAT---EGSRTQKHIGEKWSLPKQTVSGVCKTL   69 (145)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            334445553  489999999887653   346999999999999999999766554

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=82.64  E-value=2.6  Score=35.97  Aligned_cols=53  Identities=19%  Similarity=0.142  Sum_probs=39.1

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          446 LRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       446 l~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +...+...+.  .|++.+..||..-+.  ..++.|..+||+.+|+|+.+|.++..+-
T Consensus        22 ~~~~~~~~~~~~~l~~~~~~iL~~l~~--~~~~~t~~~la~~l~~s~~~vs~~l~~L   76 (146)
T 2fbh_A           22 WRAELDRRLSHLGLSQARWLVLLHLAR--HRDSPTQRELAQSVGVEGPTLARLLDGL   76 (146)
T ss_dssp             HHHHHHHHTGGGCCTTTHHHHHHHHHH--CSSCCBHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHH--cCCCCCHHHHHHHhCCChhhHHHHHHHH
Confidence            3344555554  489999998877622  1457999999999999999999766554

>3sqn_A Conserved domain protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MGA family; 2.31A {Enterococcus faecalis}

Probab=82.49  E-value=1.5  Score=46.72  Aligned_cols=119  Identities=12%  Similarity=0.042  Sum_probs=67.2

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhcCCccccCCCcCCchhhhhcccccCCCCcchhhhHHHHHHHH
Q 010092          370 IQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLA  449 (518)
Q Consensus       370 i~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~~~~~SLD~~~~~~~eel~~~l~d~~~~~~ee~~~~~~l~~~  449 (518)
                      ..+....|..  +..-|..+||+.+|+|...++.-+..-...+.-.......+..+  .+..++.    ....      .
T Consensus        20 ~~~IL~~L~~--~~~it~~eLA~~L~VS~RTIr~dI~~In~~L~~~~~I~~~~~Gy--~L~~~~~----~~~~------~   85 (485)
T 3sqn_A           20 QIRLLEQLLN--VPQLTAKRLAAQIQTTERTVFSDLQYIRSQLPADWSIETDSSGI--RLRNQGN----AQTN------E   85 (485)
T ss_dssp             HHHHHHHHHH--CCSCBCGGGHHHHTSCHHHHHHHHHHHHTTCCTTEEEEEETTEE--EEEEC-------CTH------H
T ss_pred             HHHHHHHHHh--CCCcCHHHHHHHhCCCHHHHHHHHHHHHHhcccCcEEEEcCCEE--EEecCcH----HHHH------H
Confidence            3344444543  44579999999999999999988765433321000000000000  0111100    0010      1


Q ss_pred             HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          450 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       450 L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      +   ...+++.+|....+.+.|. .+..|+.++|+.|.||++||.+.+.+.-..|..
T Consensus        86 ~---~~~~~~~eR~~~Il~~LL~-~~~isi~~Lae~l~VS~sTi~~DLk~i~~~L~~  138 (485)
T 3sqn_A           86 L---WSLFLPQSISIQLLKELLF-TKELVTTSFLSTSGVSYETLKRHIKKMNQALRD  138 (485)
T ss_dssp             H---HHHHGGGSHHHHHHHHHHH-CSEEEHHHHHHHHTCCHHHHHHHHHHHHHHHGG
T ss_pred             H---HHhcCHHHHHHHHHHHHHh-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            1   1123344444433433333 348999999999999999999999998888865

>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=82.17  E-value=3.2  Score=35.79  Aligned_cols=51  Identities=8%  Similarity=0.039  Sum_probs=38.6

Q ss_pred             HHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          447 RLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       447 ~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      ...+...+.  .|++.+..||..-+.   .++.|..+||+.+|+|+.+|.+++.+-
T Consensus        26 ~~~~~~~~~~~~lt~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~~vs~~l~~L   78 (152)
T 3bj6_A           26 TAAVERGTLREGVTVGQRAILEGLSL---TPGATAPQLGAALQMKRQYISRILQEV   78 (152)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHH---STTEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            334444443  489999999887653   357999999999999999998766554

>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=82.12  E-value=0.63  Score=41.49  Aligned_cols=40  Identities=18%  Similarity=0.038  Sum_probs=30.0

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .++..++.-|...+    ..++|..+||+.||||+.+|+++..+
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            35555555444444    25789999999999999999999865

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=82.06  E-value=2.8  Score=36.32  Aligned_cols=53  Identities=15%  Similarity=0.184  Sum_probs=39.9

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          446 LRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       446 l~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      +...+...+.  .|++.+..||..-+.   .++.|..+||+.+|+|+.+|.+++.+-.
T Consensus        32 ~~~~~~~~~~~~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~s~~tvs~~l~~Le   86 (153)
T 2pex_A           32 MHKLYRGLLKALDLTYPQYLVMLVLWE---TDERSVSEIGERLYLDSATLTPLLKRLQ   86 (153)
T ss_dssp             HHHHHHHHTTTTTCCHHHHHHHHHHHH---SCSEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHh---CCCcCHHHHHHHhCCCcccHHHHHHHHH
Confidence            3444455553  489999999877653   3579999999999999999997766543

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=81.98  E-value=1.6  Score=35.88  Aligned_cols=39  Identities=15%  Similarity=0.279  Sum_probs=29.0

Q ss_pred             CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          458 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       458 ~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      +|....||..-..   .+++|..|||+.+|+|+++|++++..
T Consensus        26 ~~~Rl~IL~~l~~---~~~~~~~ela~~l~is~stvs~hL~~   64 (99)
T 2zkz_A           26 HPMRLKIVNELYK---HKALNVTQIIQILKLPQSTVSQHLCK   64 (99)
T ss_dssp             SHHHHHHHHHHHH---HSCEEHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH---CCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            5666677733221   24799999999999999999977653

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=81.97  E-value=3.2  Score=35.62  Aligned_cols=46  Identities=15%  Similarity=0.301  Sum_probs=32.5

Q ss_pred             HHHHHhcC-CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          450 LDDVLDSL-KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       450 L~~~L~~L-~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      +..++..| ++....||.+-.    ..+++..|||+.+|+|+++|++++..
T Consensus        36 ~~~~~kaL~~~~rl~IL~~L~----~~~~s~~ela~~lgis~stvs~~L~~   82 (122)
T 1r1t_A           36 LAEFFAVLADPNRLRLLSLLA----RSELCVGDLAQAIGVSESAVSHQLRS   82 (122)
T ss_dssp             HHHHHHHHCCHHHHHHHHHHT----TCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHhCCHHHHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            33334333 555666776544    24799999999999999999977654

>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=81.87  E-value=1.1  Score=34.60  Aligned_cols=23  Identities=26%  Similarity=0.101  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q 010092          477 RTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       477 ~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      +|+.|||+.+|||+.+|+++++.
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

>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=81.86  E-value=2.3  Score=34.13  Aligned_cols=27  Identities=15%  Similarity=0.159  Sum_probs=21.3

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          474 KGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       474 ~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      ++..|..+||+.||+|+..|.+++.+-
T Consensus        27 ~~~~Ta~~IAkkLg~sK~~vNr~LY~L   53 (75)
T 1sfu_A           27 NDYTTAISLSNRLKINKKKINQQLYKL   53 (75)
T ss_dssp             TCEECHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CcchHHHHHHHHHCCCHHHHHHHHHHH
Confidence            345899999999999987777665543

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=81.65  E-value=3.3  Score=35.78  Aligned_cols=50  Identities=10%  Similarity=0.072  Sum_probs=38.3

Q ss_pred             HHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          449 ALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       449 ~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      .+...+.  .|++.|..||..-+-   .++.|..+||+.+|+|+++|.++..+-.
T Consensus        29 ~~~~~~~~~~lt~~~~~iL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~Le   80 (154)
T 2qww_A           29 YADQNAASLGLTIQQLAMINVIYS---TPGISVADLTKRLIITGSSAAANVDGLI   80 (154)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHHHHH---STTEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3444443  499999999887653   3579999999999999999997766543

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=81.61  E-value=1.6  Score=32.53  Aligned_cols=25  Identities=24%  Similarity=0.199  Sum_probs=21.9

Q ss_pred             CCC----HHHHHHHhCCCHHHHHHHHHHH
Q 010092          476 DRT----LGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       476 ~~T----l~EIA~~LgISrerVRqie~rA  500 (518)
                      +.|    ..+||..|||++++|+++....
T Consensus        21 g~s~~~~~~~vA~~~gIs~~tl~~W~~~~   49 (59)
T 2glo_A           21 DNDCKGNQRATARKYNIHRRQIQKWLQCE   49 (59)
T ss_dssp             CTTTTTCHHHHHHHTTSCHHHHHHHHTTH
T ss_pred             CCCcchHHHHHHHHHCcCHHHHHHHHHHH
Confidence            567    9999999999999999997643

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=81.53  E-value=2.1  Score=39.01  Aligned_cols=42  Identities=14%  Similarity=0.114  Sum_probs=32.5

Q ss_pred             hcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          455 DSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       455 ~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      ..|++.++.||.+-.-   ....|+.|||+.+|+|+.+|++.+.+
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            3578888888776431   24699999999999999999977654

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=81.50  E-value=2.7  Score=34.78  Aligned_cols=46  Identities=22%  Similarity=0.317  Sum_probs=32.7

Q ss_pred             HHHHHhcCC-HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          450 LDDVLDSLK-PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       450 L~~~L~~L~-~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      +..++..|. +....||..-.    ..+.|..|||+.+|+|+.+|++++.+
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            444455553 55666665432    34799999999999999999977654

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=81.04  E-value=3.2  Score=36.36  Aligned_cols=55  Identities=15%  Similarity=0.062  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHhc--CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          445 LLRLALDDVLDS--LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       445 ~l~~~L~~~L~~--L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .+...+...|..  |+..|-.||.+-+.- ...+.|..+||+.+++++++|.++..+-
T Consensus        19 ~l~~~~~~~l~~~gLt~~q~~vL~~L~~~-~~~~~t~~eLa~~l~~~~~tvs~~v~~L   75 (147)
T 4b8x_A           19 ILLGEVDAVVKPYGLTFARYEALVLLTFS-KSGELPMSKIGERLMVHPTSVTNTVDRL   75 (147)
T ss_dssp             HHHHHHHHHHGGGTCCHHHHHHHHHHHTS-GGGEEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHHC-CCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            344556666653  999999998876531 1246899999999999999999776654

>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=80.89  E-value=3.4  Score=36.34  Aligned_cols=53  Identities=11%  Similarity=0.023  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          445 LLRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       445 ~l~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .+...+...+.  .|++.|..||..-+.   .++.|..|||+.+|+++.+|.+++.+-
T Consensus        30 ~~~~~~~~~l~~~glt~~q~~iL~~l~~---~~~~t~~eLa~~l~~~~~tvs~~l~~L   84 (162)
T 3k0l_A           30 IISKYLTEHLSALEISLPQFTALSVLAA---KPNLSNAKLAERSFIKPQSANKILQDL   84 (162)
T ss_dssp             HHHHHHHHHHHTTTCCHHHHHHHHHHHH---CTTCCHHHHHHHHTSCGGGHHHHHHHH
T ss_pred             HHHHHHHHHhhhcCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            34445555554  499999999987653   357999999999999999999776653

>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=80.80  E-value=2.5  Score=36.63  Aligned_cols=51  Identities=14%  Similarity=0.221  Sum_probs=38.6

Q ss_pred             HHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          447 RLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       447 ~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      ...+...+.  .|++.+..||..-+.   .++.|..+||+.+|+|+.+|.+++.+-
T Consensus        23 ~~~~~~~~~~~~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~s~~tvs~~l~~L   75 (155)
T 1s3j_A           23 QPEMLESMEKQGVTPAQLFVLASLKK---HGSLKVSEIAERMEVKPSAVTLMADRL   75 (155)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHHHHH---HSEEEHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcCCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            334444443  699999999877652   247899999999999999999766554

>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=80.76  E-value=2.9  Score=35.65  Aligned_cols=42  Identities=14%  Similarity=0.261  Sum_probs=34.7

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .|++.+..||..-+.   .++.|..+||+.+|+|+.+|.+++.+-
T Consensus        30 ~l~~~~~~iL~~l~~---~~~~~~~~la~~l~~s~~tvs~~l~~L   71 (145)
T 2a61_A           30 GITPAQFDILQKIYF---EGPKRPGELSVLLGVAKSTVTGLVKRL   71 (145)
T ss_dssp             TCCHHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH---cCCCCHHHHHHHHCCCchhHHHHHHHH
Confidence            499999999887653   357999999999999999998766554

>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=80.51  E-value=2.5  Score=36.04  Aligned_cols=53  Identities=13%  Similarity=0.033  Sum_probs=39.4

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          446 LRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       446 l~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      +...+...+.  .|++.+..||..-+.   .++.|..+||+.+|+|+.+|.++..+-.
T Consensus        14 ~~~~~~~~~~~~~lt~~~~~iL~~l~~---~~~~t~~~la~~l~~s~~~vs~~l~~Le   68 (144)
T 1lj9_A           14 LDSISNIEFKELSLTRGQYLYLVRVCE---NPGIIQEKIAELIKVDRTTAARAIKRLE   68 (144)
T ss_dssp             HHHHHHHHTGGGTCTTTHHHHHHHHHH---STTEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHH---CcCcCHHHHHHHHCCCHhHHHHHHHHHH
Confidence            3444555554  489999988877653   3578999999999999999997665543

>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=80.50  E-value=1.7  Score=36.21  Aligned_cols=40  Identities=33%  Similarity=0.211  Sum_probs=29.2

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      +.+....||...+-  .++..|..|||+.+|+|+.+|++.+.
T Consensus        16 ~~~~~l~Il~~l~~--~g~~~s~~eLa~~lgvs~~tV~~~L~   55 (110)
T 1q1h_A           16 LGDDVIDVLRILLD--KGTEMTDEEIANQLNIKVNDVRKKLN   55 (110)
T ss_dssp             SCSTTHHHHHHHHH--HCSCBCHHHHHHTTTSCHHHHHHHHH
T ss_pred             cChHHHHHHHHHHH--cCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45666677765431  23468999999999999999995443

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=80.26  E-value=1.5  Score=35.66  Aligned_cols=45  Identities=20%  Similarity=0.082  Sum_probs=33.7

Q ss_pred             cCCHHHHHHHhHHhcCC-CCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLD-GKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~-~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .|+.++..||...+... ++...|..+||+.+|+++++|.+++.+-
T Consensus         9 ~l~~~~~~iL~~l~~~~~~~~~~t~~eLa~~l~i~~~tvs~~l~~L   54 (95)
T 2qvo_A            9 LFKEKALEILMTIYYESLGGNDVYIQYIASKVNSPHSYVWLIIKKF   54 (95)
T ss_dssp             HSCHHHHHHHHHHHHHHHTTCCEEHHHHHHHSSSCHHHHHHHHHHH
T ss_pred             CCchhHHHHHHHHHHccCCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            47888888887654321 2233899999999999999999876554

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=80.23  E-value=1.4  Score=36.70  Aligned_cols=38  Identities=16%  Similarity=0.190  Sum_probs=28.3

Q ss_pred             HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +|...|+.+..    ..+.|+.+||+.+|||..||+..++.-
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            35555555443    234899999999999999999988753

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=80.19  E-value=2.5  Score=36.39  Aligned_cols=43  Identities=16%  Similarity=0.117  Sum_probs=35.0

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      .|++.+..||..-+.   .++.|..|||+.+|+|+++|.++..+-.
T Consensus        37 ~l~~~~~~iL~~l~~---~~~~t~~ela~~l~~~~~tvs~~l~~Le   79 (148)
T 3nrv_A           37 GIGMTEWRIISVLSS---ASDCSVQKISDILGLDKAAVSRTVKKLE   79 (148)
T ss_dssp             TCCHHHHHHHHHHHH---SSSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHc---CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            488888888877653   3589999999999999999997766543

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=80.16  E-value=2.8  Score=36.74  Aligned_cols=42  Identities=7%  Similarity=-0.019  Sum_probs=34.9

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .|++.+..||..-+.   .++.|..+||+.+|+|+.+|.+++.+-
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            499999999887663   357999999999999999999776554

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=80.03  E-value=2.9  Score=35.78  Aligned_cols=52  Identities=15%  Similarity=0.017  Sum_probs=39.5

Q ss_pred             HHHHHHHHHh--cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          446 LRLALDDVLD--SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       446 l~~~L~~~L~--~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +...+...+.  .|++.|..||..-+.   .++.|..|||+.+|+|+++|.++..+-
T Consensus        22 ~~~~~~~~~~~~~lt~~~~~iL~~l~~---~~~~t~~eLa~~l~~~~~~vs~~l~~L   75 (143)
T 3oop_A           22 MHLFLMRSIASYDVTPEQWSVLEGIEA---NEPISQKEIALWTKKDTPTVNRIVDVL   75 (143)
T ss_dssp             HHHHHHHHTTTSSSCHHHHHHHHHHHH---HSSEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhhhCCCCHHHHHHHHHHHH---cCCcCHHHHHHHHCCCHhhHHHHHHHH
Confidence            3444555554  389999999887653   358999999999999999999766554

---

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	518
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	4e-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	4e-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) {	9e-06
d1l0oc_	57	a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus	1e-04
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	8e-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: 445 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 504
           L+R  L+ VL +L P+E++V+R R+GL     +TL E+    N++RE +R+ EVK L KL
Sbjct: 7   LMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKL 66

Query: 505 KHPTRVDYLRQHM 517
           +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 = 67.8 bits (166), Expect = 4e-15
 Identities = 28/66 (42%), Positives = 42/66 (63%)

Query: 452 DVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD 511
           DVL  L  +E+ V+R RFG+D   D TL E+    +++RE +R+ E K L KL+HP+R +
Sbjct: 1   DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 60

Query: 512 YLRQHM 517
            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: 450 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507
           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 = 4e-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 = 41.7 bits (98), Expect = 9e-06
 Identities = 17/57 (29%), Positives = 27/57 (47%), Gaps = 2/57 (3%)

Query: 360 STSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKP--ILSL 414
           S  + +    I+    +L  +L R PTDEE+ + + IS E   + +       ILSL
Sbjct: 2   SRQVREKERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLDKINFSYILSL 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 = 38.1 bits (89), Expect = 1e-04
 Identities = 17/50 (34%), Positives = 26/50 (52%)

Query: 360 STSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK 409
           S S+ ++  +I++AK EL     R PT  EI   + ISPE      +A +
Sbjct: 7   SRSLKEMGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAVR 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: 446 LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLK 505
           L   + + +  L  +E LVI+  F  +        E+A  L  S   V + + K L +L+
Sbjct: 11  LTEKVKEAVSKLPEREKLVIQLIFYEE----LPAKEVAKILETSVSRVSQLKAKALERLR 66

Query: 506 H 506
            
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 = 8e-04
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 370 IQRAKLELLFELKRVPTDEEIIQ--GVNISPERYREVMKASKPILSL 414
           + 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	518
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	99.78
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	99.66
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	99.65
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	99.55
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	99.25
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.08
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.04
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	99.04
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	98.9
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.66
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	98.65
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	98.61
d1h3la_	75	Sigma factor SigR {Streptomyces coelicolor a3(2) [	98.42
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	98.26
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	98.05
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	97.87
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	97.81
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	97.5
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	95.9
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	95.75
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	94.84
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	94.62
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	93.84
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	92.68
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	91.47
d1hlva1	66	DNA-binding domain of centromere binding protein B	91.3
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	91.04
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.9
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	89.24
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	89.03
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	87.65
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	87.4
d1nr3a_	122	DNA-binding protein Tfx {Archaeon Methanobacterium	87.3
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	86.71
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	86.65
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	86.53
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	86.35
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	85.57
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	85.51
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	84.89
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	84.88
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	83.94
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	83.59
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	83.53
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	83.16
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	82.96
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	82.7
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	82.69
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	82.49
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	82.32
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	82.14
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	81.97
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	81.49
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	81.17
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	80.93
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	80.84
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	80.72
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	80.62
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	80.46

>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=261.62  Aligned_cols=149  Identities=32%  Similarity=0.442  Sum_probs=119.1

Q ss_pred             cChHHHHHHhcCCCCCCChHHHHHHHHHHhHhHHHHHHHHHHH------------------HHhCCCCCHHH--------
Q 010092          200 TDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQ------------------KDLGREPTDVE--------  253 (518)
Q Consensus       200 ~d~~~~yl~~i~~~plLt~eEE~~L~~~iq~~~~l~~~~~~l~------------------~~l~r~p~~~e--------  253 (518)
                      ||+|++||++|+.+||||++||+.|++.|+.+..+.....+..                  ......|...+        
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            6999999999999999999999999999998765544322221                  01222232222        


Q ss_pred             -HHHHccCC---HHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCc
Q 010092          254 -LAEATNMS---AAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFR  329 (518)
Q Consensus       254 -la~~~~~s---~~~L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~k  329 (518)
                       +.......   ...+.+....+..|+++||.+|++||+++|++|.   +.|++++||||||+||||+|+++|||++|++
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             22222221   2345566778899999999999999999999998   7899999999999999999999999999999


Q ss_pred             cchHHHHHHHHHHHHHHH-hcCC
Q 010092          330 LSTYGLFWIRHAIIRSMT-VSSF  351 (518)
Q Consensus       330 FSTYA~~wIRqaI~raI~-~sr~  351 (518)
                      |||||+|||+++|.++++ ++++
T Consensus       158 f~tya~~~i~~~i~~~~~~~~rt  180 (180)
T d1ku2a2         158 FSTYATWWIRQAINRAIADQART  180 (180)
T ss_dssp             HHHHHHHHHHHHHHHHHTTSCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCC
Confidence            999999999999999998 6653

>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=1.6e-21  Score=197.16  Aligned_cols=80  Identities=41%  Similarity=0.725  Sum_probs=74.2

Q ss_pred             HHHHHHHcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHH
Q 010092          265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR  344 (518)
Q Consensus       265 L~~~~~gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~r  344 (518)
                      +.+.......|+++||.+|++||++||++|.   ++|++++||||+|++||++|+++|||.+|++|||||+||||++|.|
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            3334455678999999999999999999998   7899999999999999999999999999999999999999999999


Q ss_pred             HHH
Q 010092          345 SMT  347 (518)
Q Consensus       345 aI~  347 (518)
                      +|+
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=99.78  E-value=1.4e-19  Score=149.82  Aligned_cols=75  Identities=27%  Similarity=0.353  Sum_probs=70.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHHH
Q 010092          273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMT  347 (518)
Q Consensus       273 ~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI~  347 (518)
                      +..+++||..|++||.++|++|..+++.+++++||+|+|++||++|+++|||++|.+|+|||.+|||++|.++++
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            446799999999999999999986666789999999999999999999999999999999999999999999998

>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=99.66  E-value=2.7e-17  Score=129.60  Aligned_cols=65  Identities=42%  Similarity=0.711  Sum_probs=62.9

Q ss_pred             HHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhhc
Q 010092          453 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  517 (518)
Q Consensus       453 ~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~y~  517 (518)
                      +|+.|+|+|+.||.+||||+|++++|++|||+.||||+++|||++.+|++|||++...+.|+.|+
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            46889999999999999999999999999999999999999999999999999999999999997

>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=99.65  E-value=7.9e-17  Score=132.85  Aligned_cols=72  Identities=42%  Similarity=0.749  Sum_probs=68.7

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhhhhhhc
Q 010092          446 LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM  517 (518)
Q Consensus       446 l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~L~~y~  517 (518)
                      +++.|..+|+.|+|+|+.||.+||||+|++++|+.|||+.||||+++|||++.+|++|||.+.....|+.|+
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            456789999999999999999999999999999999999999999999999999999999999999999986

>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=7.4e-16  Score=118.85  Aligned_cols=59  Identities=34%  Similarity=0.510  Sum_probs=55.0

Q ss_pred             HHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          450 LDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       450 L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      |..+|+.|+++|+.||.+||||++++++|+.|||+.||||+++|||++.+|++|||+..
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            34568899999999999999999999999999999999999999999999999999753

>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=99.25  E-value=5.9e-12  Score=98.65  Aligned_cols=68  Identities=24%  Similarity=0.241  Sum_probs=62.8

Q ss_pred             chhhhHHHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          437 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       437 ~ee~~~~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      +++.+...++...|..+|+.|||+++.||.++|    .+++|++|||+.||+|.++|+++..+|+++||+..
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            566677788899999999999999999999999    58999999999999999999999999999999654

>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=99.08  E-value=5.2e-11  Score=90.96  Aligned_cols=58  Identities=28%  Similarity=0.413  Sum_probs=54.9

Q ss_pred             ccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhC--CCHHHHHHHHHhcCCcccc
Q 010092          352 TRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVN--ISPERYREVMKASKPILSL  414 (518)
Q Consensus       352 iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lg--is~e~v~~~l~~~~~~~SL  414 (518)
                      ||+|+|+.+     .+++++++.++|.+++||+||.+|||+.+|  +++++|+.+++.++.++||
T Consensus         1 IRlPvH~~e-----~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~~~~~p~SL   60 (60)
T d1ku2a1           1 IRIPVHMVE-----TINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLKIAQEPVSL   60 (60)
T ss_dssp             CCCCHHHHH-----HHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGGGSSSCCCC
T ss_pred             CccchhHHH-----HHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHHHccCCCCC
Confidence            799999999     999999999999999999999999999997  5588999999999999887

>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=99.04  E-value=2.3e-10  Score=89.06  Aligned_cols=62  Identities=18%  Similarity=0.157  Sum_probs=57.4

Q ss_pred             HHHHHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          443 PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       443 ~~~l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      ..++...|..+|+.||++++.||.++|    .+++|++|||+.||+|.++|++...+|+++||...
T Consensus         5 ~~e~~~~l~~~l~~Lp~~~r~v~~l~~----~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l   66 (68)
T d1or7a1           5 SEELRQIVFRTIESLPEDLRMAITLRE----LDGLSYEEIAAIMDCPVGTVRSRIFRAREAIDNKV   66 (68)
T ss_dssp             HHHHHHHHHHHHHHSCHHHHHHHHHHH----TTCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCHHHHHHHHHHH----HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHc
Confidence            456778899999999999999999999    68999999999999999999999999999999643

>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=98.90  E-value=5.3e-10  Score=84.38  Aligned_cols=54  Identities=31%  Similarity=0.319  Sum_probs=51.5

Q ss_pred             CCccccccccchhhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc
Q 010092          350 SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS  408 (518)
Q Consensus       350 r~iRlP~~~~e~~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~  408 (518)
                      ++||+|.|+.+     ..++++++..+|.+++||+||.+|||+.||+|+++|..++.++
T Consensus         2 g~IrvPr~~~e-----~~~ki~~~~~~l~q~lgRePT~~EiA~~l~~~~e~V~~~l~a~   55 (57)
T d1l0oc_           2 GTVKVSRSLKE-----MGNKIRKAKDELSKTRGRAPTVTEIADHLGISPEDVVLAQEAV   55 (57)
T ss_dssp             CCCTTHHHHHH-----HHHHHHHHHHHHHHHHTSCCBHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCEeCcHHHHH-----HHHHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHh
Confidence            57999999999     9999999999999999999999999999999999999998764

>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=98.66  E-value=3.9e-09  Score=83.97  Aligned_cols=69  Identities=25%  Similarity=0.272  Sum_probs=56.7

Q ss_pred             hhHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHhc--CCccccCCCcCCchhhhhcccc
Q 010092          362 SIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS--KPILSLHSRHGVTQEEFINGIT  430 (518)
Q Consensus       362 ~~~~~~~ki~ka~~eL~~elgR~PT~eELA~~lgis~e~v~~~l~~~--~~~~SLD~~~~~~~eel~~~l~  430 (518)
                      .+++..+++.++...|.+++||.||.+|||++|||++++|+.++...  ..++|||.+..++++++.+.++
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            35568999999999999999999999999999999999999998753  4678999876554445554443

>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=98.65  E-value=3.1e-08  Score=83.64  Aligned_cols=56  Identities=25%  Similarity=0.220  Sum_probs=49.0

Q ss_pred             HHHHHHhc-CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcc
Q 010092          449 ALDDVLDS-LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPT  508 (518)
Q Consensus       449 ~L~~~L~~-L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~  508 (518)
                      .|.+.... |||+||.||.++|    .+++|+.|||+.||||+++|+++++||+++||+..
T Consensus        10 ~L~d~y~~LLpe~QR~vl~L~~----~e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~L~~ye   66 (106)
T d1xsva_          10 YLFDFYQSLLTNKQRNYLELFY----LEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYE   66 (106)
T ss_dssp             HHHHHHGGGSCHHHHHHHHHHH----TSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH----HhCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            34344333 9999999999999    69999999999999999999999999999999743

>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=98.61  E-value=3.1e-08  Score=83.67  Aligned_cols=48  Identities=25%  Similarity=0.250  Sum_probs=45.7

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP  507 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~  507 (518)
                      -|||++|.||.|+|    .+++|++|||+.||||+++|+++++||+++|+..
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            49999999999999    5899999999999999999999999999999974

>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=98.42  E-value=1.5e-07  Score=73.78  Aligned_cols=71  Identities=14%  Similarity=0.069  Sum_probs=63.3

Q ss_pred             HcHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCHHHHHHHHHHHHHHHHHhcCCCCCCccchHHHHHHHHHHHHHH
Q 010092          271 VGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSM  346 (518)
Q Consensus       271 gd~~A~e~LI~~nlrLV~siAkky~~~~~~g~~~eDLIQEG~IGLirAvekFDp~rG~kFSTYA~~wIRqaI~raI  346 (518)
                      +...++++++..|.+.++.+|.++.   ++..+++|++||.++-+|+..+.|++.  .+|.+|++..+++.+.+++
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  3699999999999887654

>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=98.26  E-value=1.7e-06  Score=67.17  Aligned_cols=61  Identities=23%  Similarity=0.292  Sum_probs=53.9

Q ss_pred             HHHHHHHHHhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092          446 LRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  511 (518)
Q Consensus       446 l~~~L~~~L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~  511 (518)
                      ..+.+...++.|+|+|.+|+.+..     .|+|..|||..||+|..||+.+..++++||--..+.+
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            346678888899999999999876     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=98.05  E-value=4.4e-06  Score=64.14  Aligned_cols=53  Identities=26%  Similarity=0.342  Sum_probs=48.1

Q ss_pred             HhcCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092          454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  511 (518)
Q Consensus       454 L~~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~  511 (518)
                      ++.|+|+|.+|+.+.-     +|+|..|||+.||||..||+++..+++.||.-..+.+
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            5689999999999887     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=97.87  E-value=1.6e-05  Score=60.57  Aligned_cols=51  Identities=22%  Similarity=0.244  Sum_probs=46.4

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhh
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVD  511 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~  511 (518)
                      .|+++|++||.+.-     +++|.+|||+.||+|..+|+.+..+++.||.-..+.+
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            69999999998876     7999999999999999999999999999998766544

>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=97.81  E-value=2.4e-05  Score=59.76  Aligned_cols=52  Identities=33%  Similarity=0.327  Sum_probs=46.6

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchhhh
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY  512 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~~~  512 (518)
                      .|+++|++|+.+.-     +|+|.+|||..||+|..||+.+..+.++||--..+.+-
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            49999999998865     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=97.50  E-value=8.9e-05  Score=59.54  Aligned_cols=50  Identities=32%  Similarity=0.339  Sum_probs=45.8

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      .|+++|.+|+.+..     .|++.+|||+.|++|..+|+.+..++++||.-..+.
T Consensus        22 ~LT~rE~~vl~ll~-----~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~~~~~~   71 (87)
T d1p4wa_          22 RLSPKESEVLRLFA-----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDI   71 (87)
T ss_dssp             SCCHHHHHHHHHHH-----HTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHH
T ss_pred             CCCHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHH
Confidence            59999999999887     799999999999999999999999999999765544

>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=95.90  E-value=0.0094  Score=43.59  Aligned_cols=40  Identities=30%  Similarity=0.409  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHHHH
Q 010092          232 KVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEV  271 (518)
Q Consensus       232 ~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~~g  271 (518)
                      ..+.++..+|..++||+||.+|+|..+|++.+.+..++..
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            3556778889999999999999999999999999877654

>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=95.75  E-value=0.0083  Score=46.23  Aligned_cols=40  Identities=38%  Similarity=0.544  Sum_probs=34.6

Q ss_pred             HhHHHHHHHHHHHHHhCCCCCHHHHHHHccCCHHHHHHHH
Q 010092          230 PMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCL  269 (518)
Q Consensus       230 ~~~~l~~~~~~l~~~l~r~p~~~ela~~~~~s~~~L~~~~  269 (518)
                      ....+.++...|+.++||+|+..|+|..+||+.+.+.+++
T Consensus         8 ~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l   47 (77)
T d1rp3a1           8 KERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTL   47 (77)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHH
Confidence            3456778888999999999999999999999998887654

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=94.84  E-value=0.015  Score=40.99  Aligned_cols=38  Identities=11%  Similarity=0.069  Sum_probs=31.4

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHE  497 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie  497 (518)
                      .|++.+.+-++-.+    ..+.|..+||..||||+.||.+++
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            47777777777666    368999999999999999998764

>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=94.62  E-value=0.016  Score=44.08  Aligned_cols=44  Identities=20%  Similarity=0.125  Sum_probs=35.0

Q ss_pred             cCCHHHHHHHhH--HhcCCCCCCCCHHHHHHHhCC-CHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQ--RFGLDGKGDRTLGEIAGNLNI-SREMVRKHEVK  499 (518)
Q Consensus       456 ~L~~rEr~VL~l--ryGL~~~e~~Tl~EIA~~LgI-SrerVRqie~r  499 (518)
                      .|+++|+.||..  .|-...+-+-|+.|||+.||+ |.++|+.++..
T Consensus         2 ~LT~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~   48 (71)
T d1jhfa1           2 ALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKA   48 (71)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHH
Confidence            599999999876  333333467899999999999 89999988643

>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=93.84  E-value=0.057  Score=39.70  Aligned_cols=40  Identities=38%  Similarity=0.567  Sum_probs=31.6

Q ss_pred             HhHHHHHHHHHHHHHhCCCCCHHHHHHHcc--CCHHHHHHHH
Q 010092          230 PMKVFVQVKEQLQKDLGREPTDVELAEATN--MSAAQVKKCL  269 (518)
Q Consensus       230 ~~~~l~~~~~~l~~~l~r~p~~~ela~~~~--~s~~~L~~~~  269 (518)
                      .+..+.++..+|..++||+||.+|+|+++|  ++.+.+..++
T Consensus        10 ~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l   51 (60)
T d1ku2a1          10 TINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETL   51 (60)
T ss_dssp             HHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHG
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHH
Confidence            344566778889999999999999999987  4566776654

>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=92.68  E-value=0.049  Score=37.40  Aligned_cols=32  Identities=22%  Similarity=0.159  Sum_probs=27.4

Q ss_pred             HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          463 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       463 ~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .|..|+-     ++++-.+||+.|||++.+|.++++.
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     8999999999999999999988764

>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=91.47  E-value=0.17  Score=37.11  Aligned_cols=41  Identities=15%  Similarity=0.238  Sum_probs=33.3

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      |++.++.||..--.   ...+|+.|||+.+|+|..+|+....+=
T Consensus         3 lD~~D~~IL~~L~~---~~r~s~~eiA~~l~ls~~~v~~Ri~rL   43 (63)
T d2cg4a1           3 IDNLDRGILEALMG---NARTAYAELAKQFGVSPETIHVRVEKM   43 (63)
T ss_dssp             CCHHHHHHHHHHHH---CTTSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            67788888877552   357999999999999999999776553

>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=91.30  E-value=0.16  Score=38.07  Aligned_cols=45  Identities=24%  Similarity=0.191  Sum_probs=33.4

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM  502 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rALk  502 (518)
                      .|+..|+.=|..+|  +.++.++..|||..|||++++|+.|+..-=+
T Consensus         7 ~LT~~eK~~ii~~~--e~g~k~sq~eIA~~fGv~~STvs~IlKnK~k   51 (66)
T d1hlva1           7 QLTFREKSRIIQEV--EENPDLRKGEIARRFNIPPSTLSTILKNKRA   51 (66)
T ss_dssp             CCCHHHHHHHHHHH--HHCTTSCHHHHHHHHTCCHHHHHHHHHTHHH
T ss_pred             cCCHHHHHHHHHHH--HcCCcchHHHHHHHhCCChhHHHHHHHHHHH
Confidence            36667766555555  1234478999999999999999999876433

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=91.04  E-value=0.21  Score=36.64  Aligned_cols=41  Identities=12%  Similarity=0.159  Sum_probs=32.5

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .|++.++.||..--.   ....|+.|||+.+|+|+++|.+...+
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            367788888876542   35789999999999999999977654

>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=90.90  E-value=0.16  Score=36.89  Aligned_cols=41  Identities=22%  Similarity=0.272  Sum_probs=31.6

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      |++.++.||.+---   ....|+.|||+.+|+|+++|.+.+.+=
T Consensus         1 lD~~D~kIl~~L~~---n~r~s~~~lA~~~gls~~~v~~Ri~~L   41 (60)
T d1i1ga1           1 IDERDKIILEILEK---DARTPFTEIAKKLGISETAVRKRVKAL   41 (60)
T ss_dssp             CCSHHHHHHHHHHH---CTTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            45667778776442   356899999999999999999776553

>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=89.24  E-value=0.42  Score=35.79  Aligned_cols=42  Identities=26%  Similarity=0.265  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCC-CHHHHHHHHHh
Q 010092          366 VRGEIQRAKLELLFELKRVPTDEEIIQGVNI-SPERYREVMKA  407 (518)
Q Consensus       366 ~~~ki~ka~~eL~~elgR~PT~eELA~~lgi-s~e~v~~~l~~  407 (518)
                      .-.++-.....+..+.|..||..|||+.+|+ |...+...+..
T Consensus         6 rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~   48 (71)
T d1jhfa1           6 RQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKA   48 (71)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHH
Confidence            3445566667777889999999999999999 78888887764

>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=89.03  E-value=0.38  Score=34.68  Aligned_cols=41  Identities=17%  Similarity=0.194  Sum_probs=30.8

Q ss_pred             CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          457 LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       457 L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      |++.++.||..---   ....|+.|||+.+|+|..+|....++=
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            45566777765431   356899999999999999999776553

>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=87.65  E-value=0.5  Score=34.47  Aligned_cols=39  Identities=15%  Similarity=0.095  Sum_probs=28.3

Q ss_pred             CHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          458 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       458 ~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      +.....||.+--   +....|.+|+|+.||||+.+|++.+..
T Consensus         4 ~~~~~~iL~~L~---~~~~~s~~eLa~~l~vS~~ti~r~i~~   42 (63)
T d1biaa1           4 NTVPLKLIALLA---NGEFHSGEQLGETLGMSRAAINKHIQT   42 (63)
T ss_dssp             CHHHHHHHHHHT---TSSCBCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             cHHHHHHHHHHH---HCCcCCHHHHHHHHCcCHHHHHHHHHH
Confidence            344555555432   346689999999999999999976543

>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=87.40  E-value=0.36  Score=40.05  Aligned_cols=26  Identities=19%  Similarity=0.036  Sum_probs=24.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          475 GDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       475 e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      ++++..+||+.||||+.+|+++..+=
T Consensus        31 ~G~s~r~iA~~~~VS~~tV~k~l~r~   56 (123)
T d1pdnc_          31 DGIRPCVISRQLRVSHGCVSKILNRY   56 (123)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            68999999999999999999998774

>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=87.30  E-value=0.0085  Score=50.45  Aligned_cols=36  Identities=19%  Similarity=0.245  Sum_probs=32.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCcchh
Q 010092          475 GDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRV  510 (518)
Q Consensus       475 e~~Tl~EIA~~LgISrerVRqie~rALkKLR~~~~~  510 (518)
                      .|+|++|||++||.|+..|+.++.+|+.++++..+.
T Consensus         4 kGltQ~eIA~~LgTSraNIs~IEk~A~eNIekAr~T   39 (122)
T d1nr3a_           4 RGWSQKKIARELKTTRQNVSAIERKAMENIEKSRNT   39 (122)
T ss_dssp             CSCSSCSTHHHHHHCCSSSCCHHHHHHTTCSSSSCH
T ss_pred             ccCCHHHHHHHHCccHHHHHHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999876543

>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=86.71  E-value=0.21  Score=36.37  Aligned_cols=25  Identities=20%  Similarity=0.132  Sum_probs=22.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          475 GDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       475 e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .++|.+|+|+.+|||+.+|+++++-
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            3689999999999999999999973

>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=86.65  E-value=0.56  Score=37.22  Aligned_cols=47  Identities=15%  Similarity=0.296  Sum_probs=33.2

Q ss_pred             HHHHHHhcCC-HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          449 ALDDVLDSLK-PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       449 ~L~~~L~~L~-~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .+.+++..|. |.-..||.+-.    ..++|..|||+.+|+|+++|++++..
T Consensus        12 ~la~~~kaL~~p~Rl~Il~~L~----~~~~~v~ela~~l~is~stvS~HL~~   59 (98)
T d1r1ta_          12 SLAEFFAVLADPNRLRLLSLLA----RSELCVGDLAQAIGVSESAVSHQLRS   59 (98)
T ss_dssp             HHHHHHHHHCCHHHHHHHHHHT----TCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHHHH----cCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            4555555554 44445554433    35799999999999999999988653

>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=86.53  E-value=0.49  Score=34.89  Aligned_cols=26  Identities=19%  Similarity=0.072  Sum_probs=23.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          475 GDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       475 e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +++|..+||++|+||.++|.++.++-
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

>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=86.35  E-value=0.39  Score=37.28  Aligned_cols=35  Identities=20%  Similarity=0.213  Sum_probs=27.8

Q ss_pred             HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          463 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       463 ~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      ++|.+..=   .+++|..+||+.||||..+|+++..+.
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            45555540   137999999999999999999998875

>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=85.57  E-value=0.67  Score=37.12  Aligned_cols=41  Identities=27%  Similarity=0.403  Sum_probs=33.4

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      .|++.|-.|+..-+-   ..+.|..|||+.+|+++.+|..++.+
T Consensus        17 Glt~~e~~v~~~L~~---~g~~t~~eia~~~~i~~~~v~~~l~~   57 (109)
T d1sfxa_          17 SFKPSDVRIYSLLLE---RGGMRVSEIARELDLSARFVRDRLKV   57 (109)
T ss_dssp             CCCHHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh---cCCCCHHHHHHHhCCCcchHHHHHHH
Confidence            489999999766542   35899999999999999999966554

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=85.51  E-value=0.75  Score=35.43  Aligned_cols=50  Identities=20%  Similarity=0.143  Sum_probs=39.5

Q ss_pred             HHHHHHHhcCCHHHHHHHhHHhcCCC---CCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          448 LALDDVLDSLKPKESLVIRQRFGLDG---KGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       448 ~~L~~~L~~L~~rEr~VL~lryGL~~---~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      ..|...+..|++.|+.|..+.  +++   ...+|..|||+..|||..+|-+.-++
T Consensus         7 ~~i~~~~~~Ls~~e~~ia~yi--l~~~~~~~~~si~~lA~~~~vS~sTi~Rf~kk   59 (83)
T d2o3fa1           7 AIIQSMKHKLPPSERKLADYI--LAHPHKAIESTVNEISALANSSDAAVIRLCKS   59 (83)
T ss_dssp             HHHHHHGGGSCHHHHHHHHHH--HHCHHHHHTCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             HHHHHHHhhCCHHHHHHHHHH--HcCHHHHHHccHHHHHHHHCCCHHHHHHHHHH
Confidence            467788899999999988543  332   23599999999999999999876543

>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=84.89  E-value=0.41  Score=37.52  Aligned_cols=43  Identities=14%  Similarity=0.083  Sum_probs=33.6

Q ss_pred             cCCHHHHHHHhHH--hcCCCCCCCCHHHHHHHhC--CCHHHHHHHHH
Q 010092          456 SLKPKESLVIRQR--FGLDGKGDRTLGEIAGNLN--ISREMVRKHEV  498 (518)
Q Consensus       456 ~L~~rEr~VL~lr--yGL~~~e~~Tl~EIA~~Lg--ISrerVRqie~  498 (518)
                      +|++|+++||...  +-+..+.+-+.++|++.+|  +|..+||..+.
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            4899999998752  1244568999999999966  58999998875

>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=84.88  E-value=0.85  Score=37.91  Aligned_cols=53  Identities=17%  Similarity=0.107  Sum_probs=39.8

Q ss_pred             HHHHHHHHHhc--CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          446 LRLALDDVLDS--LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       446 l~~~L~~~L~~--L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      +.+.+...+..  |++.+-.|+.+-|. . ++++|..|||+.+|+|+++|++..++=
T Consensus        11 ~~~~~~~~~~~~Gl~~~~~~i~~~L~~-~-~~plt~~ela~~l~vsk~~vs~~l~~L   65 (151)
T d1ku9a_          11 IIELFSELAKIHGLNKSVGAVYAILYL-S-DKPLTISDIMEELKISKGNVSMSLKKL   65 (151)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHHHHH-C-SSCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHh-C-CCCcCHHHHHHHhCCCcchHHHHHHHH
Confidence            34445555544  79999999988762 3 356999999999999999999666543

>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=83.94  E-value=0.56  Score=33.06  Aligned_cols=49  Identities=20%  Similarity=0.229  Sum_probs=39.1

Q ss_pred             cCCHHHHHHHhHHhcCCCCCC-CCHHHHHHHhCCCHHHHHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGD-RTLGEIAGNLNISREMVRKHEVKGLMKL  504 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~-~Tl~EIA~~LgISrerVRqie~rALkKL  504 (518)
                      .|+|.+..||.-.|-.+.+.. ....+||..+|+|...|..+...-..+.
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            589999999999997654432 4678999999999999999887655443

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=83.59  E-value=0.38  Score=35.47  Aligned_cols=27  Identities=33%  Similarity=0.250  Sum_probs=21.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          476 DRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       476 ~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      ++|.+|||..+|+|+++|.+    .|++|++
T Consensus        29 ~lt~~~lA~~~G~sRetvsr----~L~~l~~   55 (69)
T d1i5za1          29 KITRQEIGQIVGCSRETVGR----ILKMLED   55 (69)
T ss_dssp             ECCHHHHHHHHTCCHHHHHH----HHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHH----HHHHHHH
Confidence            48999999999999999985    4555553

>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=83.53  E-value=0.54  Score=37.49  Aligned_cols=43  Identities=16%  Similarity=0.157  Sum_probs=34.3

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKG  500 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rA  500 (518)
                      .|++.+..||..-+--  .+++|..|||+.+|+++.+|++++.+-
T Consensus        18 gLs~~~~~iL~~L~~~--~~~~t~~eLa~~~~i~~~tvs~~l~~L   60 (109)
T d2d1ha1          18 KITDTDVAVLLKMVEI--EKPITSEELADIFKLSKTTVENSLKKL   60 (109)
T ss_dssp             TCCHHHHHHHHHHHHH--CSCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHc--CCCCCHHHHHHHHCccHhHHHHHHHHH
Confidence            5999999998654321  246999999999999999999776654

>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=83.16  E-value=1.8  Score=35.15  Aligned_cols=53  Identities=8%  Similarity=0.028  Sum_probs=38.8

Q ss_pred             HHHHHHHHHhc--CCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          446 LRLALDDVLDS--LKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       446 l~~~L~~~L~~--L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      +...+...+..  |++.|-.||..-+.. ++++.|..|||+.++++.++|..+.++
T Consensus        14 ~~~~~~~~l~~~glt~~q~~vL~~l~~~-~~~~it~~ela~~~~~~~~~vs~~l~~   68 (135)
T d3broa1          14 MSTRFDIFAKKYDLTGTQMTIIDYLSRN-KNKEVLQRDLESEFSIKSSTATVLLQR   68 (135)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHHHHHT-TTSCCBHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHHHHc-CCCCCCHHHHHHHHCcCHhHHHHHHHH
Confidence            34445555544  899999998776632 235699999999999999999854443

>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=82.96  E-value=0.76  Score=34.41  Aligned_cols=43  Identities=9%  Similarity=0.098  Sum_probs=37.5

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHh-CCCHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNL-NISREMVRKHEV  498 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~L-gISrerVRqie~  498 (518)
                      -|++.++.|+.+.-.-.+.+|.+..||+..| |+|...|++...
T Consensus         3 GLs~~q~~V~~~i~s~~~~eGi~~~el~~~l~~~~~~~i~~aid   46 (69)
T d1dpua_           3 GLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVD   46 (69)
T ss_dssp             CSCHHHHHHHHHHHHCCCTTTEEHHHHHHHSTTSCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhCCCccCcCHHHHHHHccCCCHHHHHHHHH
Confidence            5899999999998877777899999999999 899999886543

>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=82.70  E-value=0.8  Score=33.80  Aligned_cols=37  Identities=11%  Similarity=0.037  Sum_probs=28.4

Q ss_pred             HHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Q 010092          462 SLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL  501 (518)
Q Consensus       462 r~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~rAL  501 (518)
                      ..||.+-+-   ..+.|-.|||+.+|+|+.+|+++...-+
T Consensus         9 ~~Il~~l~~---~g~~sr~eLa~~~glS~~Tv~~~l~~L~   45 (71)
T d1z05a1           9 GRVYKLIDQ---KGPISRIDLSKESELAPASITKITRELI   45 (71)
T ss_dssp             HHHHHHHHH---HCSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHH---cCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            345555442   3589999999999999999999887643

>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=82.69  E-value=0.66  Score=37.55  Aligned_cols=40  Identities=25%  Similarity=0.351  Sum_probs=32.5

Q ss_pred             cCCHHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          456 SLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      .|+|-|.-.-.-++ +  ..++|.++||+.+|.|+.+|++++.
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            48888887766655 2  2478999999999999999998865

>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=82.49  E-value=0.7  Score=33.98  Aligned_cols=31  Identities=13%  Similarity=-0.040  Sum_probs=26.5

Q ss_pred             HHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          464 VIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       464 VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      |-.+|.    ..++|..|+|+.+|||+.+|+++++
T Consensus        11 i~~~r~----~~gltq~elA~~~gv~~~~is~ie~   41 (69)
T d2a6ca1          11 LQEHLR----NSGLTQFKAAELLGVTQPRVSDLMR   41 (69)
T ss_dssp             HHHHHH----TTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHH----HcCCCHHHHHHHHHcCHhHHHHHHc
Confidence            344555    5789999999999999999999986

>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=82.32  E-value=0.91  Score=33.71  Aligned_cols=24  Identities=33%  Similarity=0.342  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          475 GDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       475 e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      .++|..|+|+.||||+.+|.++++
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            478999999999999999999986

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=82.14  E-value=1.3  Score=34.81  Aligned_cols=48  Identities=15%  Similarity=0.224  Sum_probs=34.7

Q ss_pred             HHHHHHHhcCCHHHH-HHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          448 LALDDVLDSLKPKES-LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       448 ~~L~~~L~~L~~rEr-~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      +.+.+++..|+..-| .||.+-.    .++++..||++.+|+|+++|++++..
T Consensus         6 e~~a~~fkaL~d~~Rl~Il~~L~----~~~~~v~el~~~l~~s~~~vS~HL~~   54 (94)
T d1r1ua_           6 ERVTEIFKALGDYNRIRIMELLS----VSEASVGHISHQLNLSQSNVSHQLKL   54 (94)
T ss_dssp             HHHHHHHHHTCSHHHHHHHHHHH----HCCBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHH----cCCccHHHHHHHHCCCHHHHHHHHHH
Confidence            456666777755555 4444333    35799999999999999999987643

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=81.97  E-value=0.56  Score=35.46  Aligned_cols=27  Identities=33%  Similarity=0.330  Sum_probs=22.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          476 DRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       476 ~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      ++|.+|||..+|+|+++|.    ++|++|++
T Consensus        30 ~~t~~eiA~~lG~sretvs----r~l~~l~~   56 (80)
T d1ft9a1          30 DFTVEEIANLIGSSRQTTS----TALNSLIK   56 (80)
T ss_dssp             CCCHHHHHHHHCSCHHHHH----HHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            6899999999999999998    55666664

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.49  E-value=1.9  Score=30.88  Aligned_cols=51  Identities=18%  Similarity=0.081  Sum_probs=42.3

Q ss_pred             cCCHHHHHHHhHHhcCCCCC-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          456 SLKPKESLVIRQRFGLDGKG-DRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e-~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      .+++.+..+|...|..+.+. .....+||..+|+|...|..+......+.|.
T Consensus         7 ~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr   58 (60)
T d1yz8p1           7 HFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK   58 (60)
T ss_dssp             CCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHh
Confidence            36888999999999766553 3678999999999999999999887777763

>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=81.17  E-value=0.78  Score=33.46  Aligned_cols=39  Identities=15%  Similarity=0.183  Sum_probs=28.5

Q ss_pred             HHHHHHHhHHhcCCCCCCCCHHHHHHHhCCCHHHHHHHHHH
Q 010092          459 PKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK  499 (518)
Q Consensus       459 ~rEr~VL~lryGL~~~e~~Tl~EIA~~LgISrerVRqie~r  499 (518)
                      +|...||.+-.  ......|..|+|+.||||+.||++-+..
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            45556665433  1123579999999999999999987754

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=80.93  E-value=1.2  Score=31.84  Aligned_cols=51  Identities=20%  Similarity=0.285  Sum_probs=42.0

Q ss_pred             cCCHHHHHHHhHHhcCCCCCC-CCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          456 SLKPKESLVIRQRFGLDGKGD-RTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       456 ~L~~rEr~VL~lryGL~~~e~-~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      .+++.+..+|...|-.+.+.. ....+||..+|+|...|+.+...-..+.|+
T Consensus         5 ~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr   56 (58)
T d1au7a1           5 TISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR   56 (58)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTS
T ss_pred             CCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHh
Confidence            367889999999997654433 567899999999999999999988888775

>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=80.84  E-value=0.61  Score=33.92  Aligned_cols=25  Identities=28%  Similarity=0.332  Sum_probs=23.0

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          474 KGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       474 ~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      ..++|..|+|+.+|||+++|.++++
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            3579999999999999999999986

>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=80.72  E-value=0.67  Score=35.96  Aligned_cols=25  Identities=16%  Similarity=0.155  Sum_probs=23.4

Q ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHH
Q 010092          474 KGDRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       474 ~e~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      ..++|..++|+.+|+|+.+|.++++
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            4689999999999999999999997

>d1vz0a1 a.4.14.1 (A:116-208) Putative partitioning protein ParB/Spo0J {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Putative partitioning protein ParB/Spo0J
species: Thermus thermophilus [TaxId: 274]

Probab=80.62  E-value=1.1  Score=35.32  Aligned_cols=23  Identities=22%  Similarity=0.146  Sum_probs=20.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Q 010092          476 DRTLGEIAGNLNISREMVRKHEV  498 (518)
Q Consensus       476 ~~Tl~EIA~~LgISrerVRqie~  498 (518)
                      ++|..+||+.+|.|+++|.+.+.
T Consensus        19 g~t~~~iA~~~Gks~~~V~~~Lr   41 (93)
T d1vz0a1          19 GLTQEEVARRVGKARSTVANALR   41 (93)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHccchHHHHHHHH
Confidence            58999999999999999998764

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=80.46  E-value=0.69  Score=34.88  Aligned_cols=27  Identities=19%  Similarity=0.137  Sum_probs=22.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Q 010092          476 DRTLGEIAGNLNISREMVRKHEVKGLMKLKH  506 (518)
Q Consensus       476 ~~Tl~EIA~~LgISrerVRqie~rALkKLR~  506 (518)
                      ++|.+|||..+|+|+++|.    +++++|++
T Consensus        30 ~lt~~elA~~~g~sretvs----r~l~~l~~   56 (80)
T d3e5ua1          30 PLSQKSIGEITGVHHVTVS----RVLASLKR   56 (80)
T ss_dssp             CCCHHHHHHHHTCCHHHHH----HHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHH----HHHHHHHH
Confidence            5899999999999999998    55666664