Citrus Sinensis ID: 019233

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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----
Protein Sequence
MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFIDSCCALHY
Secondary Structure (PSIPRED)
cccccEEccccccccccccccccccccccccccccccccccccccHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHccHHHHHHHHHHccccccccccccccccHHHcccccccccccccccccccHHHHHHHHHHHHHHHHHHccccccHHHHHHccccccHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHcccHHHHHHHHHHccccccHHHHHHHHHHccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEccEEccccccccccccccccccccccccEcccccEEEcccccccccccHHccccccEEEEccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHcHHHHHHHHHHHcccccccccccccccccccccccHHcccccEEEEccHHHHHHHHHHHccHHccccccccccccccccccccccHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHccccEEEEccccEccc
Coil and Loop (DISEMBL)
mgmgfrlnlkwvspvqshffttsscrlsstsvrgregsfnsARLSFLSTISedsasyfqdpvkayTCSFVntqtvendyseTEEIRQKstscigqdassrsDFRLLMENLDVlestfadsDALRLEREILQQLGKLGALKLFNSHLSRIvktsnvldlsdvhteeqkmndsrdyhmgkilvpskrkgkrklktaRVSEESIETSLlslpsealqeglkqptiFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEkesgkaasLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNyrglgipfsdllqVSRHALAFIDSCCALHY
Flexible Loop (DISEMBL)
MGMGFRLNLKWVSPVQSHFfttsscrlsstsvrgregsfNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEirqkstscigqdassRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRivktsnvldlsdvhteeqkmndsrdyhmgkilvpskrkgkrklktarvseesietsllslpsealqeglkqptifsaeralnsRGRRLtiarneaemskgvqvvaNLERIKTTLekesgkaasLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFIDSCCALHY
Low Complexity Region (SEG)
MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREIlqqlgklgalklFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVseesietsllslpseALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFIDSCCALHY
Disordered region (IsUnstruct)
****FRLNLKWVSPVQSHFFTTSSCR*****************LSFLSTISEDSASYFQDPVKAYTCSFVNTQTV***************************FRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDL******************************************************************************************VQVVANLERIKTTL*****KAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFIDSCCAL**
Disordered Region (DISOPRED)
**MGFRLNLKWVSPV****************************LS****************VK*YTCS*VNTQTVENDYSETEEIRQ**********SSRSDFRLLMENLDVLESTFAD*DALRLEREILQQLGKLGALKLFN***********************************************************************************RALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTL*******ASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFIDSCCALHY
Disordered Region (DISEMBL)
MGMGFRLNLKWVSPVQSHFFTTSS**************FNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVE********************ASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSK*******************SLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFIDSCCALHY
Disordered Region (DISPRO)
*GMGFRLNLKWVSPVQSHFFTTS*C*LSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVK*****************NDS***HMGKILVPSK************************************TIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFIDSCCALHY
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFIDSCCALHY
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	344	2.2.26 [Sep-21-2011]
O24621	571	RNA polymerase sigma fact	yes	no	0.822	0.495	0.424	3e-47
O22056	572	RNA polymerase sigma fact	no	no	0.270	0.162	0.397	1e-14
Q9LD95	547	RNA polymerase sigma fact	no	no	0.273	0.171	0.382	2e-11

>sp|O24621|SIGC_ARATH RNA polymerase sigma factor sigC OS=Arabidopsis thaliana GN=SIGC PE=2 SV=1

 Score =  189 bits (479), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 129/304 (42%), Positives = 188/304 (61%), Gaps = 21/304 (6%)

Query: 32  VRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVEND-YSETEEIRQKST 90
           VR    S  + R SFLS++ E+S  Y  D +KA  C+ V+  T +N+ Y E ++ ++   
Sbjct: 73  VRIPMTSVVATRWSFLSSVKEESRIYQNDSLKACGCASVSPYTAQNNVYVELKDPKEN-- 130

Query: 91  SCIGQDASSRS-------DFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFN 143
             IG  ++ RS        + LL +NL  LE TF   D++R+ER+I+ Q+GKLGA +LF 
Sbjct: 131 --IGVGSAERSYSSRSMLQYNLLAKNLLALEETFVALDSVRMERDIMLQMGKLGAAELFK 188

Query: 144 SHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIET 203
           + LSR   +S    LSD  TE      ++     ++ V S+RK K+K + + V+ E+ + 
Sbjct: 189 TCLSRYRGSSITSCLSDT-TELVDTTPNQ-----QVFVSSRRKVKKKARRSSVTAENGDQ 242

Query: 204 SLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLE 263
           S L +        +  P +    R    R +R  I+RNE EMS GV++VA++ERI+T LE
Sbjct: 243 SSLPIGLRTTWNNIDVPRV---RRPPKYRKKRERISRNETEMSTGVKIVADMERIRTQLE 299

Query: 264 KESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFS 323
           +ESGK ASL+CWA AAG++E++L ++L +GWYCR+EL+KSTR LVLFLARNYRGLGI   
Sbjct: 300 EESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLGIAHE 359

Query: 324 DLLQ 327
           DL+Q
Sbjct: 360 DLIQ 363

Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites and are then released.
Arabidopsis thaliana (taxid: 3702)

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

 Score = 80.9 bits (198), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 37/93 (39%), Positives = 60/93 (64%)

Query: 235 RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGW 294
           +L   R E E+S G+Q +  LER++T L + SG+  +   WA AAGV ++ L+Q +  G 
Sbjct: 271 KLLTVREEHELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGT 330

Query: 295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQ 327
            C++++IKS   LV+ +A+NY+G G+   DL+Q
Sbjct: 331 LCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQ 363

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 70.5 bits (171), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 36/94 (38%), Positives = 58/94 (61%)

Query: 234 RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG 293
           ++L  A+ EAE+   +Q +  LE++KT LE ++G   ++  WA+A G+S  VLK  +  G
Sbjct: 245 KQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRG 304

Query: 294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQ 327
              RE+LI +   LV+ +A+ Y+  G+ F DLLQ
Sbjct: 305 RSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQ 338

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

Arabidopsis thaliana (taxid: 3702)

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	344
225429414	561	PREDICTED: RNA polymerase sigma factor r	0.953	0.584	0.490	3e-87
147865632	611	hypothetical protein VITISV_036980 [Viti	0.866	0.487	0.48	1e-76
224088962	559	predicted protein [Populus trichocarpa]	0.959	0.590	0.457	3e-73
255550882	560	RNA polymerase sigma factor rpoD, putati	0.947	0.582	0.471	4e-67
39840783	548	sigma factor [Spinacia oleracea]	0.938	0.589	0.445	2e-64
449461399	559	PREDICTED: RNA polymerase sigma factor s	0.938	0.577	0.424	5e-63
356565804	551	PREDICTED: RNA polymerase sigma factor r	0.912	0.569	0.416	2e-54
7363220	567	sigma factor 3 [Sinapis alba]	0.793	0.481	0.426	2e-51
357436347	549	RNA polymerase sigma-B factor [Medicago	0.944	0.591	0.424	3e-50
297820128	568	predicted protein [Arabidopsis lyrata su	0.880	0.533	0.416	4e-46

>gi|225429414|ref|XP_002275831.1| PREDICTED: RNA polymerase sigma factor rpoD [Vitis vinifera] gi|296081598|emb|CBI20603.3| unnamed protein product [Vitis vinifera]

 Score =  328 bits (841), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 174/355 (49%), Positives = 231/355 (65%), Gaps = 27/355 (7%)

Query: 1   MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQD 60
           MGMGFRLNLKW  P+     T S  RL ++SV+G+E SF+S R SF S  SED  S ++D
Sbjct: 1   MGMGFRLNLKWDFPISCPTLTNSPSRLCTSSVQGKEASFDSTRFSFPSVTSEDCESLYKD 60

Query: 61  PVKAYTCSFVNTQTVENDYSETEEIRQKSTSC---------------IGQD--------- 96
           P K + CS    QT ENDYS  E ++ K   C               IG+D         
Sbjct: 61  PFKPFACSSGALQTFENDYSAMEAMKMKIGKCSHGDLFKIVNASQAPIGEDISASVAGLQ 120

Query: 97  ASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVL 156
           AS  S F LL+ENLD+LE  FADS+ +RLER+I+ QLG+LGALKLF   LSR +KTS   
Sbjct: 121 ASKASQFSLLLENLDILEEMFADSNMVRLERDIMVQLGRLGALKLFQICLSRTLKTSTSF 180

Query: 157 DLSDVHTE---EQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEAL 213
           DL    TE   E + N + D H+ K++V S +K +RK K  R  E++       LPS+ +
Sbjct: 181 DLFSAPTEHIRECQTNGTVDDHLDKVVVRSGKKEERKSKRERALEKADNIYAFPLPSKTI 240

Query: 214 QEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLN 273
           ++G  +P++ + +R LNSR +RL  A+NEAEMSKGV++VANLERI+ TLE+E G  ASL+
Sbjct: 241 RKGPGRPSVSTVKRTLNSRRKRLMNAKNEAEMSKGVKLVANLERIRATLEEEIGHVASLS 300

Query: 274 CWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQV 328
            WA+AAGV ++VL+Q L FGWYCR+EL++ST  LVL++ARNYRG+G+ F D+LQ 
Sbjct: 301 NWAEAAGVDKKVLQQQLQFGWYCRDELLRSTHSLVLYIARNYRGMGVAFEDILQA 355

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147865632|emb|CAN83254.1| hypothetical protein VITISV_036980 [Vitis vinifera]

 Score =  292 bits (748), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 156/325 (48%), Positives = 211/325 (64%), Gaps = 27/325 (8%)

Query: 32  VRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQKSTS 91
           ++G+E SF+S R SF S  SED  S ++DP K + CS    QT ENDYS  E ++ K   
Sbjct: 82  IQGKEASFDSTRFSFPSVTSEDCESLYKDPFKPFACSSGALQTFENDYSAMEAMKMKIGK 141

Query: 92  C---------------IGQD---------ASSRSDFRLLMENLDVLESTFADSDALRLER 127
           C               IG+D         AS  S F LL+ENLD+LE  FADS+ +RLER
Sbjct: 142 CSHGDLFKIVNASQAPIGEDISASVAGLQASKASQFSLLLENLDILEEMFADSNMVRLER 201

Query: 128 EILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTE---EQKMNDSRDYHMGKILVPSK 184
           +I+ QLG+LGALKLF   LSR +KTS   DL    TE   E + N + D H+ K++V S 
Sbjct: 202 DIMVQLGRLGALKLFQICLSRTLKTSTSFDLFSAPTEHIRECQTNGTVDDHLDKVVVRSG 261

Query: 185 RKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAE 244
           +K +RK K  R  E++       LPS+ +++G  +P++ + +R LNSR +RL  A+NEAE
Sbjct: 262 KKEERKSKRERALEKADNIYAFPLPSKTIRKGPGRPSVSTVKRTLNSRRKRLMNAKNEAE 321

Query: 245 MSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKST 304
           MSKGV++VANLERI+ TLE+E G  ASL+ WA+AAGV ++VL+Q L FGWYCR+EL++ST
Sbjct: 322 MSKGVKLVANLERIRATLEEEIGHVASLSNWAEAAGVDKKVLQQQLQFGWYCRDELLRST 381

Query: 305 RPLVLFLARNYRGLGIPFSDLLQVS 329
             LVL++ARNYRG+G+ F D+LQ  
Sbjct: 382 HSLVLYIARNYRGMGVAFEDILQAG 406

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224088962|ref|XP_002308586.1| predicted protein [Populus trichocarpa] gi|222854562|gb|EEE92109.1| predicted protein [Populus trichocarpa]

 Score =  281 bits (719), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 165/361 (45%), Positives = 223/361 (61%), Gaps = 31/361 (8%)

Query: 1   MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQD 60
           MG+GFRL  KW SP+QSH  T S+   SS S RG E S N ARLSFLS +SE+     + 
Sbjct: 1   MGVGFRLTPKWGSPMQSHSATNSTSMFSSFSARGMEASVNQARLSFLSVVSEEGDILNKH 60

Query: 61  PVKAYTCSFVNTQTVENDYSETEEIRQKS--------TSCIGQDASS------------- 99
             K++ CS    Q VEND  + E ++            + +G D  S             
Sbjct: 61  SFKSFACSSA-AQNVENDCLQMERLKMNVDKTSHVSINNMMGNDKVSVEEEISTSHTRLR 119

Query: 100 ---RSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVL 156
               S    L++NLD LE   AD DAL+LER+IL QLG+LGAL+ FN+ LSR ++TSNVL
Sbjct: 120 ERMTSRISFLLDNLDTLEKLVADLDALKLERDILLQLGRLGALEFFNACLSRTLQTSNVL 179

Query: 157 DLSDVHTE---EQKMNDSRDYHMGKILVPSKRKGKRKLKTARV-SEESIETSLLSLPSEA 212
           DLS V TE   E K +       GK +V + +K +RK +  R  S+   +T+ LSLPS+ 
Sbjct: 180 DLSAVPTENTGESKTDGMLGDLTGKTVVRTGKKEERKFRRERAASDNGKKTTSLSLPSKT 239

Query: 213 LQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASL 272
           +Q  L +PT    +R  +S  RR  IARNEA+M++GV+V ++LERI+TTLE+E+G+  SL
Sbjct: 240 VQNNLPKPTF--VKRTSSSSSRRSLIARNEAKMTRGVKVASDLERIRTTLEEETGQVVSL 297

Query: 273 NCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHA 332
           +CWA+A G+ ++VL+Q L FGWYCR+ELIK+T  LVL++ARNYRG+GI   DL+Q     
Sbjct: 298 SCWAEATGLDKKVLQQQLQFGWYCRDELIKNTHSLVLYIARNYRGMGIAMEDLIQAGNLG 357

Query: 333 L 333
           L
Sbjct: 358 L 358

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255550882|ref|XP_002516489.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis] gi|223544309|gb|EEF45830.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]

 Score =  261 bits (666), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 167/354 (47%), Positives = 233/354 (65%), Gaps = 28/354 (7%)

Query: 1   MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTS-VRGREGSFNSARLSFLSTISEDSASYFQ 59
           MG GFRLNLK   P  S    +      S+S VRGRE +   +RLSFLS ISE+     +
Sbjct: 1   MGFGFRLNLKLDFPFHSPNSPSRLSSSPSSSFVRGREATSYQSRLSFLSVISEEGDIAHR 60

Query: 60  DPVKAYTCSFVNTQTVENDYSETEEIRQK-------STSCIGQ-DASSRSD--------- 102
           DP+K Y  S+   QTVEN++S+ E  +           + IG  + S + D         
Sbjct: 61  DPLKTYAYSYA-VQTVENEHSQGEGFKVNFGKRSHFGLNIIGDAEVSLKEDIFVSPSSTK 119

Query: 103 -----FRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLD 157
                F LL+ENL++LE +FADSDA +LE +IL QLGKLGALKLFN+ L+R ++T+NVL+
Sbjct: 120 ERTSRFSLLLENLNILEQSFADSDASKLEEDILLQLGKLGALKLFNTCLTRTLETTNVLE 179

Query: 158 LSDVHTE---EQKMNDSRDYHMGKILVPSKRKGKRKLKTARVS-EESIETSLLSLPSEAL 213
           +SDVHTE   E  +N +   +  K++V + +K +RK +  R S  +  ++  L LPS  +
Sbjct: 180 VSDVHTEIIGECNINGTSINNQIKVVVHTAKKEERKSRRERASARKGHKSPSLPLPSRPI 239

Query: 214 QEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLN 273
           Q G ++PT+ S ++A  S+ RRL IARNEAEM++G++V+A+LE+I+TTLE+E+ +  SL+
Sbjct: 240 QSGSEKPTVSSGKKASKSKSRRLIIARNEAEMARGIKVLADLEKIRTTLEEETERVVSLS 299

Query: 274 CWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQ 327
           CWA+AAG+  +VL+Q L+FGWYCR+ELIKSTR LVL+ ARNYRG GI   DLLQ
Sbjct: 300 CWAEAAGLDVKVLQQQLSFGWYCRDELIKSTRSLVLYFARNYRGTGIALEDLLQ 353

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|39840783|emb|CAD20832.1| sigma factor [Spinacia oleracea]

 Score =  252 bits (644), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 154/346 (44%), Positives = 215/346 (62%), Gaps = 23/346 (6%)

Query: 1   MGMGFRLNL-KWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQ 59
           MG G +LN+ + V P     FTT+S    STS RG+E  F SARLS L+   ++S +  +
Sbjct: 1   MGFGCKLNMMRCVLPSLRSPFTTNSSPPCSTSFRGKELDFGSARLSLLTIGFDESETLRK 60

Query: 60  DPVKAYTCSFVNTQTVENDYSETEE-IRQKSTSCIGQDASSRSD---------------- 102
           D ++ +  S     TVENDYS  E  I ++S   +  D    SD                
Sbjct: 61  DTLRPHAGSSSVPLTVENDYSNLETTISKRSCKDLISDTEVLSDRDVSVYVRSVQSCSAS 120

Query: 103 -FRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDV 161
            F  LM N+++LE+  +DS+ L+LE++IL QLG+LGAL+LF++ LSRI+  S   DL  +
Sbjct: 121 HFHTLMANINLLENKVSDSELLKLEKDILVQLGRLGALQLFHACLSRIIDMS---DLPGL 177

Query: 162 HTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPT 221
            TE+ K N  +D  + K LV SKRK +RKL+  R  + S  +   +  SE+  E      
Sbjct: 178 ITEDGKANVRKDNELKKKLVFSKRKEERKLRQERRLQAST-SKRCACKSESSIESSIHHV 236

Query: 222 IFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGV 281
           + +A +   +RGRR  IA+NEAEMS+G++VVA LE++K TLEKE+GKA SLNCWA+AAG+
Sbjct: 237 VSTAAKKTKARGRRAIIAKNEAEMSRGIKVVAQLEKVKLTLEKETGKAVSLNCWAEAAGI 296

Query: 282 SERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQ 327
            E+VL+  L FGWYCR+EL+KS R LVL+L+R YRGLG+   DL+Q
Sbjct: 297 DEKVLQHDLHFGWYCRDELLKSGRSLVLYLSRYYRGLGVAHEDLMQ 342

Source: Spinacia oleracea

Species: Spinacia oleracea

Genus: Spinacia

Family: Amaranthaceae

Order: Caryophyllales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449461399|ref|XP_004148429.1| PREDICTED: RNA polymerase sigma factor sigC-like [Cucumis sativus] gi|449507267|ref|XP_004162982.1| PREDICTED: RNA polymerase sigma factor sigC-like [Cucumis sativus]

 Score =  247 bits (631), Expect = 5e-63,   Method: Compositional matrix adjust.
 Identities = 152/358 (42%), Positives = 208/358 (58%), Gaps = 35/358 (9%)

Query: 1   MGMGFRLNLKWVSPVQSHFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASYFQD 60
           MG  FR NL+W   +Q+H    S  +LS  + +GRE +FNS RLSF S+I E+  S  ++
Sbjct: 1   MGTSFRPNLRWGFQIQTHSLKNSPSKLSPHASKGREAAFNSGRLSFFSSICEEGESIPRE 60

Query: 61  PVKAYTCSFVNTQTVENDYSETEEIRQKS------------------------TSCIGQD 96
            +K YTC     QT  ND    EEI   S                        +SC    
Sbjct: 61  TLKTYTCLSEAPQTSANDLLNLEEIEMNSGAKSLGPMHYGIKSTRPSKVEDNFSSCTSLP 120

Query: 97  ASSRSDFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVL 156
               S F +LMENLDVLE TF +S  L LER+I+ QL KLGAL+ FN+ LSR +KTS+  
Sbjct: 121 TGKASPFGILMENLDVLEETFTESGMLSLERDIVLQLTKLGALEFFNTCLSRTLKTSSFH 180

Query: 157 DLSDV-------HTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLP 209
           D S +       H   QK ND  D     + V S +K  R+    R  + + + +   L 
Sbjct: 181 DSSGLPIEGGEDHNVNQKTNDQND----NVTVYSAKKAGRRSVKKRAMDNADKIASRLLT 236

Query: 210 SEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKA 269
           + A++E + + T+FS +++ NS  RRL +A NEAEMS GV+VVANLERI+ TLEKESG+ 
Sbjct: 237 TRAVKEKIHRSTVFSRKKSSNSSKRRLIVAINEAEMSTGVKVVANLERIRETLEKESGRI 296

Query: 270 ASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQ 327
           AS++CWA+AA V  + L++ L FG +CR+EL++ST  LV+FLA+ YR  G+P  DL+Q
Sbjct: 297 ASMSCWAEAASVDIKDLQKQLQFGSFCRDELLRSTNSLVVFLAKKYRCSGLPMEDLVQ 354

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356565804|ref|XP_003551127.1| PREDICTED: RNA polymerase sigma factor rpoD-like [Glycine max]

 Score =  218 bits (556), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 148/355 (41%), Positives = 216/355 (60%), Gaps = 41/355 (11%)

Query: 1   MGMGFRLN--LKWVSPVQS-HFFTTSSCRLSSTSVRGREGSFNSARLSFLSTISEDSASY 57
           +G GF LN  L++   + + H FT S   LS +S   RE  FN  RLSF ST  E+  + 
Sbjct: 3   LGFGFGLNPRLRYCLLLHTPHSFTNSPLCLSPSSAGVRETCFNFTRLSFPSTFYEEGEAL 62

Query: 58  FQDPVKAYTCSFVNTQTVENDYSETEEIR----QKSTSCIGQ----------DASSRSD- 102
            +D  + +  S    +T+END    EE +    ++S S + +          + S+ S  
Sbjct: 63  QKDFGRVFAFSSSALETLENDSLGREETQVNKGKRSLSSVHKMIDNTQMPFGEVSTVSKK 122

Query: 103 --------FRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSN 154
                   FRLLMENL VLE TF DS+ALRLE+ I+ QLGKLGAL+LFN  LSR + TS 
Sbjct: 123 FESFRAQHFRLLMENLCVLEETFVDSEALRLEKAIILQLGKLGALELFNVCLSRSLGTSL 182

Query: 155 VLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSL--LSLPSEA 212
           V + +D      K++D +D    K++V S +K + K +  R   E + T++   SL  +A
Sbjct: 183 VSNYAD------KVDDYKD----KVVVQSSKKKENKTRRKR---EFVSTAVSSQSLTLKA 229

Query: 213 LQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASL 272
            QE L   +    +RA N++ +R+ +A+ EAEMSKGV+V+A LE+I+T +E+++ + ASL
Sbjct: 230 NQEDLLGFSASLVKRAPNTKNKRILVAKREAEMSKGVKVLAELEKIRTAIEEDTKRVASL 289

Query: 273 NCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQ 327
           + WA+A+GV E+VL++ L  G+YC++ELI+STR LVL+LAR YRG+GI   DLLQ
Sbjct: 290 STWAEASGVDEKVLQKLLHRGYYCQDELIRSTRSLVLYLARKYRGMGIALDDLLQ 344

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|7363220|emb|CAB83107.1| sigma factor 3 [Sinapis alba]

 Score =  209 bits (531), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 127/298 (42%), Positives = 185/298 (62%), Gaps = 25/298 (8%)

Query: 41  SARLSFLSTISEDSASYFQD-PVKAYTCSFVNTQTVENDYSETEEIRQKSTSCIGQDASS 99
           ++R SFLS+I E S S+ +D P+KA  C+   + T EN Y E ++ ++    C+  D  S
Sbjct: 76  ASRWSFLSSIKEGSRSHRRDHPLKACGCA---SATAENVYVELKDPKENIGMCLVGDQMS 132

Query: 100 RSD----------FRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRI 149
            ++          + LL +NL  LE TF   D+LR+ER+I+ Q+ KLGA +LFN+ LSR 
Sbjct: 133 SAEKAHLSRSMLQYNLLGKNLLALEQTFVALDSLRMERDIMLQMRKLGAAELFNTCLSRS 192

Query: 150 VKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLP 209
             +S    L D  T E   + +++    K  V S RK ++K +T    + S   S     
Sbjct: 193 RVSSATSCLPDTGTPELVDDTTQEQ---KTFVHSTRKLRKKARTGNGDQGSSTIS----- 244

Query: 210 SEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKA 269
           S    EG+  P +    +    R +R  I+RNEAEMS+GV++VA++ERI+T LE+E+GK 
Sbjct: 245 SRTTWEGIDVPRV---RKPSKYRKKRERISRNEAEMSQGVKIVADMERIRTKLEEETGKV 301

Query: 270 ASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQ 327
           AS++CWA+AAG+++++L  +L FGWYCR+EL+KSTR LVLFLARNYRGLGI   DL+Q
Sbjct: 302 ASMSCWAEAAGMNQKLLMHNLHFGWYCRDELVKSTRSLVLFLARNYRGLGIAHEDLIQ 359

Source: Sinapis alba

Species: Sinapis alba

Genus: Sinapis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357436347|ref|XP_003588449.1| RNA polymerase sigma-B factor [Medicago truncatula] gi|355477497|gb|AES58700.1| RNA polymerase sigma-B factor [Medicago truncatula]

 Score =  205 bits (521), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 149/351 (42%), Positives = 207/351 (58%), Gaps = 26/351 (7%)

Query: 1   MGM--GFRLNLKW-VSPVQSH----FFTTSSCRLSSTS-VRGREGSFNSARLSFLSTISE 52
           MG+  GFRLN K   S V  H    FF+ S   LSS+S   GRE  FN  RLS LST+ E
Sbjct: 1   MGLCFGFRLNTKLRYSTVPLHHSSPFFSNSHIFLSSSSSAGGRETLFNPVRLSLLSTVYE 60

Query: 53  DSASYFQDPVKAYTCSFVNTQTVENDYSETEEIRQ-----KSTSCIGQ--DAS----SRS 101
           +  +  +D  K +  S    +  E D  +  E+ +     +S S + +  D S      S
Sbjct: 61  EGETLQKDFRKTFAFSSA-LEAPEKDLLQGGELTKVNKGKRSLSSVHEMIDNSHLPFEES 119

Query: 102 DFRLLMENLDVLESTFADSDALRLEREILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDV 161
            F LLMENL VLE TFADS+ALRLE+ I+ QL KLGAL+LFN  L+    TS + + +  
Sbjct: 120 HFGLLMENLGVLEETFADSEALRLEKNIILQLEKLGALELFNVCLTTSFGTSCISNCTHK 179

Query: 162 ---HTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEG-L 217
                EE K N   D + GK++V S ++  ++ +  +    SI  S  SLP +  QE  L
Sbjct: 180 VLEQVEENKRNHKVDDYTGKVIVHSSKR--KENRRRKRGSVSIAPSSRSLPLDDNQEDPL 237

Query: 218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQ 277
           +       +RA N++ +R  IA+ E EMSKGV+V+A LE+I+T +E+++ +  SL+ WA+
Sbjct: 238 RSSPASFVKRASNTKNKRAVIAQREVEMSKGVKVLAELEKIRTAIEEDTKQVVSLSSWAE 297

Query: 278 AAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQV 328
            +GV E+VL+Q L  G+YCR+ELI+STR LVL+ AR YRG+GI   DLLQV
Sbjct: 298 TSGVDEKVLQQQLYHGYYCRDELIRSTRSLVLYFARKYRGMGIALEDLLQV 348

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297820128|ref|XP_002877947.1| predicted protein [Arabidopsis lyrata subsp. lyrata] gi|297323785|gb|EFH54206.1| predicted protein [Arabidopsis lyrata subsp. lyrata]

 Score =  191 bits (486), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 133/319 (41%), Positives = 194/319 (60%), Gaps = 16/319 (5%)

Query: 14  PVQSHFFTTSSCRLSSTS--VRGREGSFNSARLSFLSTISEDSASYFQDPVKAYTCSFVN 71
           P+  H+ +   C  +S    VR    SF + R SFLS++ E+S  Y +DP+KA  C+   
Sbjct: 53  PLIKHWLSLLRCDQTSFPIFVRIPVSSFVATRWSFLSSVKEESRIYQKDPLKA--CASSA 110

Query: 72  TQTVENDYSETEEIRQK-STSCIGQDASSRS--DFRLLMENLDVLESTFADSDALRLERE 128
             T EN + E ++ ++        +  SSRS   + LL +NL  LE TF   D+ R+ER+
Sbjct: 111 PYTAENVFLELKDPKENIGVGSAEKSCSSRSMLQYNLLAKNLLALEETFVALDSARMERD 170

Query: 129 ILQQLGKLGALKLFNSHLSRIVKTSNVLDLSDVHTEEQKMNDSRDYHMGKILVPSKRKGK 188
           I+ Q+GKLGA  LF + LSR   +S    LSD  TE      ++     ++ V S+RK K
Sbjct: 171 IMLQMGKLGAADLFKTCLSRSRGSSVASCLSDT-TELVGTTPNQ-----QVFVSSRRKLK 224

Query: 189 RKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIARNEAEMSKG 248
           +K + + V+ E+ +   L +        +  P +    R    R +R  I++NEAEMS G
Sbjct: 225 KKARRSTVTAENGDQGSLPMGLRTTWNNIDVPRV---RRPPKYRKKRERISKNEAEMSTG 281

Query: 249 VQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLV 308
           V++VA++ERI+T LE+ESGK ASL+CWA+AAG++E++L ++L +GWYCR+EL+KSTR LV
Sbjct: 282 VKIVADMERIRTQLEEESGKVASLSCWAEAAGMNEKLLMRNLHYGWYCRDELLKSTRSLV 341

Query: 309 LFLARNYRGLGIPFSDLLQ 327
           LFLARNYRGLGI   DL+Q
Sbjct: 342 LFLARNYRGLGIAHEDLIQ 360

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	344
TAIR|locus:2084420	571	SIGC "AT3G53920" [Arabidopsis	0.808	0.486	0.402	1.3e-45
TAIR|locus:2025650	572	SIG2 "AT1G08540" [Arabidopsis	0.290	0.174	0.396	4.4e-13
TAIR|locus:2057996	547	SIGF "AT2G36990" [Arabidopsis	0.273	0.171	0.382	4.5e-10
UNIPROTKB|Q84LK8	572	SIG6 "Sig6" [Oryza sativa Japo	0.258	0.155	0.325	2.5e-07

TAIR|locus:2084420 SIGC "AT3G53920" [Arabidopsis thaliana (taxid:3702)]

 Score = 479 (173.7 bits), Expect = 1.3e-45, P = 1.3e-45
 Identities = 117/291 (40%), Positives = 168/291 (57%)

Query:    41 SARLSFLSTISEDSASYFQDPVKAYTCSFVNTQTVEND-YSETEEIRQK-STSCIGQDAS 98
             + R SFLS++ E+S  Y  D +KA  C+ V+  T +N+ Y E ++ ++        +  S
Sbjct:    82 ATRWSFLSSVKEESRIYQNDSLKACGCASVSPYTAQNNVYVELKDPKENIGVGSAERSYS 141

Query:    99 SRS--DFRLLMENLDVLESTFADSDALRLEREIXXXXXXXXXXXXFNSHLSRIVKTSNVL 156
             SRS   + LL +NL  LE TF   D++R+ER+I            F + LSR   +S   
Sbjct:   142 SRSMLQYNLLAKNLLALEETFVALDSVRMERDIMLQMGKLGAAELFKTCLSRYRGSSITS 201

Query:   157 DLSDVHTEEQKMNDSRDYHMGKILVPSKRKGKRKLKTARVXXXXXXXXXXXXXXXALQEG 216
              LSD  TE   + D+      ++ V S+RK K+K + + V                    
Sbjct:   202 CLSDT-TE---LVDTTPNQ--QVFVSSRRKVKKKARRSSVTAENGDQSSLPIGLRTTWNN 255

Query:   217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWA 276
             +  P +    R    R +R  I+RNE EMS GV++VA++ERI+T LE+ESGK ASL+CWA
Sbjct:   256 IDVPRV---RRPPKYRKKRERISRNETEMSTGVKIVADMERIRTQLEEESGKVASLSCWA 312

Query:   277 QAAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQ 327
              AAG++E++L ++L +GWYCR+EL+KSTR LVLFLARNYRGLGI   DL+Q
Sbjct:   313 AAAGMNEKLLMRNLHYGWYCRDELVKSTRSLVLFLARNYRGLGIAHEDLIQ 363

GO:0003677 "DNA binding" evidence=ISS

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

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

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

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0019685 "photosynthesis, dark reaction" evidence=NAS

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

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

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

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

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 197 (74.4 bits), Expect = 4.4e-13, P = 4.4e-13
 Identities = 40/101 (39%), Positives = 64/101 (63%)

Query:   227 RALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVL 286
             R   S  + LT+ R E E+S G+Q +  LER++T L + SG+  +   WA AAGV ++ L
Sbjct:   264 RMTTSSSKLLTV-REEHELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSL 322

Query:   287 KQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQ 327
             +Q +  G  C++++IKS   LV+ +A+NY+G G+   DL+Q
Sbjct:   323 RQRIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQ 363

GO:0003677 "DNA binding" evidence=ISS

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

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

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

GO:0009507 "chloroplast" evidence=ISM;IDA

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

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

GO:0009658 "chloroplast organization" evidence=IMP

GO:0006399 "tRNA metabolic process" evidence=IMP

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

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

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

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

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

GO:0006364 "rRNA processing" evidence=RCA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

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

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

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

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0016987 "sigma factor activity" evidence=ISS

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

 Score = 171 (65.3 bits), Expect = 4.5e-10, P = 4.5e-10
 Identities = 36/94 (38%), Positives = 58/94 (61%)

Query:   234 RRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG 293
             ++L  A+ EAE+   +Q +  LE++KT LE ++G   ++  WA+A G+S  VLK  +  G
Sbjct:   245 KQLLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRG 304

Query:   294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQ 327
                RE+LI +   LV+ +A+ Y+  G+ F DLLQ
Sbjct:   305 RSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQ 338

GO:0003677 "DNA binding" evidence=ISS

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0009507 "chloroplast" evidence=IDA

GO:0009536 "plastid" evidence=IDA

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

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

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

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

GO:0090351 "seedling development" evidence=IMP

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

GO:0005515 "protein binding" evidence=IPI

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0009965 "leaf morphogenesis" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0016117 "carotenoid biosynthetic process" evidence=RCA

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

GO:0030154 "cell differentiation" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

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

 Score = 147 (56.8 bits), Expect = 2.5e-07, P = 2.5e-07
 Identities = 29/89 (32%), Positives = 50/89 (56%)

Query:   239 ARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCRE 298
             A+ E  +   +Q++  +E     LE + G+  +L  WA+A G+S + L+  +  G  CRE
Sbjct:   276 AKEERHLFSKIQILMKIEEAHRKLEVQCGREPTLAEWAEAVGMSSKELQSSIRTGRRCRE 335

Query:   299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQ 327
             ++ +S   LV+ +AR Y G G+   DL+Q
Sbjct:   336 KMARSNFRLVIHVARKYEGYGLDIQDLVQ 364


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.318   0.130   0.369    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      344       317   0.00083  116 3  11 22  0.38    34
                                                     33  0.45    37


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  4
  No. of states in DFA:  608 (65 KB)
  Total size of DFA:  199 KB (2113 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  24.05u 0.10s 24.15t   Elapsed:  00:00:01
  Total cpu time:  24.05u 0.10s 24.15t   Elapsed:  00:00:01
  Start:  Sat May 11 04:45:04 2013   End:  Sat May 11 04:45:05 2013

GO:0009536 "plastid" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	344
TIGR02997	298	TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma f	2e-07
PRK05949	327	PRK05949, PRK05949, RNA polymerase sigma factor; V	8e-06
PRK07406	373	PRK07406, PRK07406, RNA polymerase sigma factor Rp	2e-05
PRK07405	317	PRK07405, PRK07405, RNA polymerase sigma factor Si	3e-05

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

 Score = 51.5 bits (124), Expect = 2e-07
 Identities = 36/100 (36%), Positives = 57/100 (57%), Gaps = 1/100 (1%)

Query: 229 LNSRGR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLK 287
           L   GR  L     E E+++ VQ +  LE ++  LE++ G+  S   WA AAG+SE  L+
Sbjct: 7   LQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELR 66

Query: 288 QHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQ 327
           Q L  G   +E++IK+   LV+ +A+ Y+  G+   DL+Q
Sbjct: 67  QRLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQ 106

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

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

 Score = 46.8 bits (111), Expect = 8e-06
 Identities = 29/81 (35%), Positives = 47/81 (58%)

Query: 247 KGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRP 306
           K VQ + +L   K  L K+ G+  SL  WA+A  +SE  LKQ L  G   ++++I++   
Sbjct: 43  KQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMIEANLR 102

Query: 307 LVLFLARNYRGLGIPFSDLLQ 327
           LV+ +A+ Y+   + F DL+Q
Sbjct: 103 LVVAIAKKYQKRNMEFLDLIQ 123

Length = 327

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

 Score = 45.9 bits (109), Expect = 2e-05
 Identities = 27/96 (28%), Positives = 49/96 (51%), Gaps = 1/96 (1%)

Query: 233 GR-RLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLA 291
           GR RL     E E+++ +  +  LE ++   E E G+  S   WA+   +     ++ L 
Sbjct: 73  GRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLM 132

Query: 292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQ 327
            G   +E++++S   LV+ +A+ Y   G+ F DL+Q
Sbjct: 133 LGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQ 168

Length = 373

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

 Score = 44.8 bits (106), Expect = 3e-05
 Identities = 25/86 (29%), Positives = 46/86 (53%)

Query: 242 EAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELI 301
           E    K VQ +  L+ I+  L +E G+  +   WA+AA +SE  L+  +A G   + +++
Sbjct: 28  EILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMV 87

Query: 302 KSTRPLVLFLARNYRGLGIPFSDLLQ 327
           ++   LV+ +A+ Y    +   DL+Q
Sbjct: 88  EANLRLVVSVAKKYLKRNVDLLDLIQ 113

Length = 317

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	344
PRK07598	415	RNA polymerase sigma factor SigC; Validated	99.93
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	99.91
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	99.88
PRK05949	327	RNA polymerase sigma factor; Validated	99.87
PRK07405	317	RNA polymerase sigma factor SigD; Validated	99.87
PRK05901	509	RNA polymerase sigma factor; Provisional	99.78
COG0568	342	RpoD DNA-directed RNA polymerase, sigma subunit (s	99.73
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	99.66
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	99.36
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	99.34
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	99.17
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	99.16
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	99.1
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	99.08
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	98.78
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	98.66
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	98.66
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	98.65
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	98.6
PRK08215	258	sporulation sigma factor SigG; Reviewed	98.6
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	98.4
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	98.36
PRK05803	233	sporulation sigma factor SigK; Reviewed	98.22
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	98.14
PF00140	37	Sigma70_r1_2: Sigma-70 factor, region 1.2; InterPr	98.01
PRK08583	257	RNA polymerase sigma factor SigB; Validated	98.0
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	97.86
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	97.84
PRK05572	252	sporulation sigma factor SigF; Validated	97.77
PRK07670	251	RNA polymerase sigma factor SigD; Validated	97.37
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	96.97
PF04542	71	Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR00762	96.68
PRK08301	234	sporulation sigma factor SigE; Reviewed	96.63
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	96.61
PRK05658	619	RNA polymerase sigma factor RpoD; Validated	96.56
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	96.43
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	96.05
PRK05602	186	RNA polymerase sigma factor; Reviewed	95.94
PRK08295	208	RNA polymerase factor sigma-70; Validated	95.88
PRK11922	231	RNA polymerase sigma factor; Provisional	95.75
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	95.65
PRK08311	237	putative RNA polymerase sigma factor SigI; Reviewe	95.45
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	95.44
PRK12513	194	RNA polymerase sigma factor; Provisional	95.27
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	95.26
PRK13919	186	putative RNA polymerase sigma E protein; Provision	95.02
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	94.8
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	94.73
PRK12519	194	RNA polymerase sigma factor; Provisional	94.32
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	94.22
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	93.93
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	93.88
PRK06811	189	RNA polymerase factor sigma-70; Validated	93.83
PRK11924	179	RNA polymerase sigma factor; Provisional	93.59
PRK12524	196	RNA polymerase sigma factor; Provisional	93.47
PRK12534	187	RNA polymerase sigma factor; Provisional	93.11
PRK12514	179	RNA polymerase sigma factor; Provisional	92.97
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	92.01
PRK06759	154	RNA polymerase factor sigma-70; Validated	91.34
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	90.49
PRK12512	184	RNA polymerase sigma factor; Provisional	89.7
PRK12531	194	RNA polymerase sigma factor; Provisional	89.33
PRK12515	189	RNA polymerase sigma factor; Provisional	88.97
PRK12538	233	RNA polymerase sigma factor; Provisional	88.94
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	88.86
PRK12537	182	RNA polymerase sigma factor; Provisional	87.98
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	86.81
PRK12539	184	RNA polymerase sigma factor; Provisional	85.49
PRK12526	206	RNA polymerase sigma factor; Provisional	84.63
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	84.43
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	83.22
PRK12536	181	RNA polymerase sigma factor; Provisional	83.1
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	82.61
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	82.38
PRK12518	175	RNA polymerase sigma factor; Provisional	82.31
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	81.1
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	80.75
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	80.22
PRK07921	324	RNA polymerase sigma factor SigB; Reviewed	80.17
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	80.08

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=99.93  E-value=2e-25  Score=222.93  Aligned_cols=117  Identities=26%  Similarity=0.299  Sum_probs=107.3

Q ss_pred             CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHH--------------------HHHHHHHHHHHhCCCCchHHHH
Q 019233          217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVAN--------------------LERIKTTLEKESGKAASLNCWA  276 (344)
Q Consensus       217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~--------------------LE~ir~~Lee~lGrePT~~eWA  276 (344)
                      -.|++..||+   +|+++||||++||++|+++||.+++                    |++++..|++++|++||..|||
T Consensus        58 ~~d~v~~yl~---~igr~~lL~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~ewa  134 (415)
T PRK07598         58 STDLVRLYLQ---EIGRVRLLGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLERWA  134 (415)
T ss_pred             CCChHHHHHH---hcccccCCCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHHHHH
Confidence            3689999999   9999999999999999999999999                    8999999999999999999999


Q ss_pred             HHcCCCHHHHHH----------------------HhhhhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHh
Q 019233          277 QAAGVSERVLKQ----------------------HLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALA  334 (344)
Q Consensus       277 ~aaGld~~eL~~----------------------~l~~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLm  334 (344)
                      .++|+++.+|+.                      .+..|..|+++||.+|++||++||++|.++|+.++||||||++|||
T Consensus       135 ~~~~~~~~~l~~~l~~~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g~~~eDLiQEG~iGL~  214 (415)
T PRK07598        135 KTADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLE  214 (415)
T ss_pred             HHhCCcHHHHHHhhhhhhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHH
Confidence            776665555554                      4567889999999999999999999999999999999999999999


Q ss_pred             hh
Q 019233          335 FI  336 (344)
Q Consensus       335 ka  336 (344)
                      ++
T Consensus       215 ra  216 (415)
T PRK07598        215 RA  216 (415)
T ss_pred             HH
Confidence            94

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

Probab=99.91  E-value=2.5e-24  Score=204.02  Aligned_cols=115  Identities=30%  Similarity=0.416  Sum_probs=111.8

Q ss_pred             chHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHH
Q 019233          219 QPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCRE  298 (344)
Q Consensus       219 dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARd  298 (344)
                      |++..||+   +++++|+||++||++|++.|+.+..+++++.+|+++.|++||..+||+++|++..+|...+..|..|++
T Consensus         1 ~~~~~yl~---~~~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~~   77 (298)
T TIGR02997         1 DLVRLYLQ---EIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAELRQRLRQGQRAKE   77 (298)
T ss_pred             CcHHHHHH---HccccCCCCHHHHHHHHHHHHHHhHHHHHHHHHHHhhcCCCcHHHHHHhccCCHHHHHHHHhccHHHHH
Confidence            46788999   999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          299 ELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       299 rLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      +||.+|+|+|++||++|.++|.+++||||||++|||+|
T Consensus        78 ~Lv~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~~a  115 (298)
T TIGR02997        78 KMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERA  115 (298)
T ss_pred             HHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999994

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

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=99.88  E-value=1.6e-22  Score=199.62  Aligned_cols=116  Identities=22%  Similarity=0.373  Sum_probs=113.4

Q ss_pred             CchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHH
Q 019233          218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCR  297 (344)
Q Consensus       218 ~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~AR  297 (344)
                      .|++..||+   +++++||||++||++|+++|+.++.+++++.+|+++.|++|+.++||.++|++..+|++++..|..|+
T Consensus        62 ~d~l~~Yl~---~i~~~~lLt~eEE~~La~~i~~~~~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~l~~~~~~g~~A~  138 (373)
T PRK07406         62 EDSIRVYLQ---EIGRIRLLRPDEEIELARKIADLLELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAK  138 (373)
T ss_pred             CCHHHHHHH---HhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccchhhHhhhccccHHHHHHHHhcCHHHH
Confidence            578899999   99999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       298 drLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      ++||..|+++|++||++|.++|++++||||||++|||++
T Consensus       139 ~~Li~~~l~lV~~iA~ry~~~~~~~eDLiQEG~igL~~A  177 (373)
T PRK07406        139 EKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRA  177 (373)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999994

>PRK05949 RNA polymerase sigma factor; Validated

Probab=99.87  E-value=9.4e-22  Score=190.41  Aligned_cols=117  Identities=27%  Similarity=0.301  Sum_probs=113.8

Q ss_pred             CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHH
Q 019233          217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYC  296 (344)
Q Consensus       217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~A  296 (344)
                      .+|++..||+   +++++||||++||++|++.||.++.+++.++.|+..+|++|+..+||.+++++..+|...+..|..|
T Consensus        16 ~~d~~~~yl~---~i~~~~lLt~eeE~~l~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~eL~~~~~~g~~A   92 (327)
T PRK05949         16 SADMVRTYLH---EIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRA   92 (327)
T ss_pred             CCCHHHHHHH---HcCCccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCchHHHHHhccCCHHHHHHHHHccHHH
Confidence            4689999999   9999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       297 RdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      +++||..|+++|+++|++|.+.|.+++||||||++||+++
T Consensus        93 ~~~Li~~~~~~V~~iA~~y~~~~~~~eDLvQEg~igL~~a  132 (327)
T PRK05949         93 KQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERG  132 (327)
T ss_pred             HHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999994

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=99.87  E-value=1e-21  Score=188.94  Aligned_cols=116  Identities=22%  Similarity=0.260  Sum_probs=113.1

Q ss_pred             CchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHH
Q 019233          218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCR  297 (344)
Q Consensus       218 ~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~AR  297 (344)
                      +|++..||+   +++++||||++||++|+++|+.++.+++++..|++++|++|+..+||++++++..+|...+..|..|+
T Consensus         7 ~~~~~~yl~---~i~~~~lLt~eeE~~La~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~L~~~~~~g~~A~   83 (317)
T PRK07405          7 TDLVRTYLR---EIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAK   83 (317)
T ss_pred             CcHHHHHHH---HccccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhcccccchHHHhhhccCCHHHHHHHHhccHHHH
Confidence            578999999   99999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          298 EELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       298 drLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      ++||..|+++|+++|++|.+.|.+.+||||||++||+++
T Consensus        84 ~~L~~~~~~~V~~~a~~~~~~~~~~eDLvQEg~i~L~~a  122 (317)
T PRK07405         84 RKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRG  122 (317)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999993

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=99.78  E-value=2.9e-19  Score=182.80  Aligned_cols=104  Identities=22%  Similarity=0.216  Sum_probs=88.4

Q ss_pred             CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHH
Q 019233          217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYC  296 (344)
Q Consensus       217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~A  296 (344)
                      ..|++..||+   .++++|+||++||++|+++|+.+..++..   +.       ...+|+.+   ...+|++++..|..|
T Consensus       209 ~~d~l~~YL~---~i~~~~lLt~eEE~~La~~i~~g~~~~~~---~~-------~~~~~~~~---~~~~l~~~~~~g~~A  272 (509)
T PRK05901        209 TADPVKAYLK---QIGKVKLLNAEEEVELAKRIEAGLYAEEL---LA-------EGEKLDPE---LRRDLQWIGRDGKRA  272 (509)
T ss_pred             cccHHHHHHH---HhccCCCCCHHHHHHHHHHHHhCCchhhh---hh-------hcccchhh---hhhhhhhhccchHHH
Confidence            3688999999   99999999999999999999987544331   11       11234422   467899999999999


Q ss_pred             HHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       297 RdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      |++||.+|||||++||++|.++|++++|||||||||||+|
T Consensus       273 r~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikA  312 (509)
T PRK05901        273 KNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKA  312 (509)
T ss_pred             HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999995

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

Probab=99.73  E-value=5.6e-18  Score=166.21  Aligned_cols=116  Identities=23%  Similarity=0.281  Sum_probs=100.6

Q ss_pred             CchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHH-HhCCCCchH---------------HHHHHcCC
Q 019233          218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEK-ESGKAASLN---------------CWAQAAGV  281 (344)
Q Consensus       218 ~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee-~lGrePT~~---------------eWA~aaGl  281 (344)
                      .|.+..|+.   +++..+++++++|.++...++....+......|.. ..++.|+..               +|+..+..
T Consensus         8 ~d~~~~~l~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~   84 (342)
T COG0568           8 ADAVRAYLD---EIGRIPLLVREAEVELAKQLEDEQLLVELGEDLTDLKLGREPSERARRPAGRLSFYIRAIEAAPLLTP   84 (342)
T ss_pred             hhHHHHHHH---HhcchhhhhHHHHHHHHHHHhHhhhhhHHHHHHHhcccccccchhhhhhhhhHHHHHHHHhhhcccCh
Confidence            467788998   89999999999999999999998877777777776 567888876               55555555


Q ss_pred             CH-HHHHHHhhhhHH---HHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          282 SE-RVLKQHLAFGWY---CREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       282 d~-~eL~~~l~~g~~---ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      ++ ..|..++..|..   |+.+||.+|||||++|||+|.|+|++|.|||||||||||+|
T Consensus        85 ~Ee~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkA  143 (342)
T COG0568          85 EEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKA  143 (342)
T ss_pred             HHHHHHHHHHHcCCccHHHHHHHHHHHHHHHHHHHHHhhcCCCcHHHHHhcccHHHHHH
Confidence            54 788888888754   99999999999999999999999999999999999999996

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=99.66  E-value=2.6e-16  Score=152.71  Aligned_cols=105  Identities=23%  Similarity=0.239  Sum_probs=89.6

Q ss_pred             CCCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHH
Q 019233          216 GLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY  295 (344)
Q Consensus       216 ~~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~  295 (344)
                      +-+|++..||+   +++++|+||++||++|+++|+.+..++..           |+..+|+...  ...+|...+..|..
T Consensus        23 ~~~~~~~~Yl~---~i~~~~lLt~eeE~~La~~~~~g~~~~~~-----------~~~~~~~~~~--~~~~l~~~~~~~~~   86 (324)
T PRK07921         23 PAADLVRVYLN---GIGKTALLTAADEVELAKRIEAGLYAEHL-----------LETRKRLSEA--RKRDLAAVVRDGEA   86 (324)
T ss_pred             CCCChHHHHHH---HhcccCCCCHHHHHHHHHHHHhhhhhhhh-----------hccccccchh--HHHHHHHHHhcCHH
Confidence            34688999999   99999999999999999999988766543           2233332111  45688999999999


Q ss_pred             HHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       296 ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      |+++||..|+++|+++|++|.++|++++||||||+|||+++
T Consensus        87 A~~~Lv~~~~~lV~~iA~r~~~~~~~~eDLvQEg~igL~~a  127 (324)
T PRK07921         87 ARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRA  127 (324)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999994

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=99.36  E-value=1.9e-12  Score=127.21  Aligned_cols=78  Identities=23%  Similarity=0.299  Sum_probs=72.0

Q ss_pred             CCCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHH
Q 019233          216 GLKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWY  295 (344)
Q Consensus       216 ~~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~  295 (344)
                      ..+|++..||+   ++++.|+||++||.+|++.++.+                                        +..
T Consensus        93 ~~~d~~~~yl~---~i~~~~~l~~~ee~~L~~~~~~G----------------------------------------d~~  129 (367)
T PRK09210         93 KINDPVRMYLK---EIGRVPLLTAEEEIELAKRIEEG----------------------------------------DEE  129 (367)
T ss_pred             ccCcHHHHHHH---HhhccCCCCHHHHHHHHHHHHhh----------------------------------------HHH
Confidence            34789999999   99999999999999999988764                                        257


Q ss_pred             HHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          296 CREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       296 ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      |+++||..|+++|++||++|.++|.+++||||||++|||+|
T Consensus       130 A~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a  170 (367)
T PRK09210        130 AKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKA  170 (367)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence            89999999999999999999999999999999999999995

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=99.34  E-value=1e-12  Score=136.85  Aligned_cols=60  Identities=25%  Similarity=0.455  Sum_probs=49.0

Q ss_pred             HHcCCCHHHHH---HHhhhh----HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          277 QAAGVSERVLK---QHLAFG----WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       277 ~aaGld~~eL~---~~l~~g----~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      ...+++.+++.   +.+..|    ..|+++||.+|||||++||++|.++|++++|||||||||||+|
T Consensus       355 ~~~~Ls~eElk~l~~~i~~g~~~~~~a~~~Li~~nlrlV~~iA~ky~~~gl~~~DLiQeG~iGL~~A  421 (619)
T PRK05658        355 EETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA  421 (619)
T ss_pred             HHhCCCHHHHHHHHHHHhccchhhhHHHHHHHHHHHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHH
Confidence            34455554443   334444    3789999999999999999999999999999999999999995

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=99.17  E-value=8.5e-11  Score=111.66  Aligned_cols=78  Identities=22%  Similarity=0.235  Sum_probs=69.0

Q ss_pred             CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHH
Q 019233          217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYC  296 (344)
Q Consensus       217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~A  296 (344)
                      +.+++..|++   ++.+.|+|+.++|.+|...++.                                       ..+..+
T Consensus        12 ~~~~~~~y~~---~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~Gd~~a   49 (284)
T PRK06596         12 PEGNLDAYIQ---AVNKIPMLTAEEEYMLAKRLRE---------------------------------------HGDLEA   49 (284)
T ss_pred             CccHHHHHHH---HHhccCCCCHHHHHHHHHHHHH---------------------------------------cCCHHH
Confidence            3468899999   8999999999999999887532                                       014679


Q ss_pred             HHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       297 RdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      +++||..|+++|.+||++|.+.|++++||||+|++||++|
T Consensus        50 ~~~Lv~~~~~lV~~ia~~~~~~~~~~eDLvQeg~igL~~a   89 (284)
T PRK06596         50 AKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKA   89 (284)
T ss_pred             HHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999994

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=99.16  E-value=8.2e-11  Score=110.43  Aligned_cols=75  Identities=21%  Similarity=0.244  Sum_probs=66.7

Q ss_pred             hHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHHH
Q 019233          220 PTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREE  299 (344)
Q Consensus       220 pl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARdr  299 (344)
                      ++..||+   ++++.|+|+.++|.+|...+..                                       ..+..|+++
T Consensus         2 ~~~~yl~---~~~~~~~l~~~~e~~l~~~~~~---------------------------------------~gd~~a~~~   39 (270)
T TIGR02392         2 SLDAYIR---AVNRIPMLTPEEEYQLAKRLRE---------------------------------------HGDLDAAKK   39 (270)
T ss_pred             hHHHHHH---HHhcCCCCCHHHHHHHHHHHHH---------------------------------------CCCHHHHHH
Confidence            5678999   9999999999999999886431                                       024679999


Q ss_pred             HHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          300 LIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       300 LI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      ||..|+++|.++|++|.+.|.+.+||||+|++||+++
T Consensus        40 Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~igl~~a   76 (270)
T TIGR02392        40 LVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKA   76 (270)
T ss_pred             HHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999993

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=99.10  E-value=6.9e-11  Score=111.19  Aligned_cols=43  Identities=33%  Similarity=0.473  Sum_probs=41.4

Q ss_pred             HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       294 ~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      ..+|++||.+|+|||++||++|.++|++++||||+|+||||+|
T Consensus        39 ~~~r~~Lv~~~l~LV~~iA~~y~~~g~~~~DLiQeG~iGLi~A   81 (264)
T PRK07122         39 QRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNA   81 (264)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHH
Confidence            5699999999999999999999999999999999999999995

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=99.08  E-value=3.4e-10  Score=107.95  Aligned_cols=75  Identities=16%  Similarity=0.133  Sum_probs=67.5

Q ss_pred             hHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHHH
Q 019233          220 PTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREE  299 (344)
Q Consensus       220 pl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARdr  299 (344)
                      -+..||+   ++.+.|+||+++|.+|.+.++..                                       .+..|+++
T Consensus         7 ~~~~y~~---~~~~~~~l~~~~e~~L~~~~~~~---------------------------------------gd~~A~~~   44 (289)
T PRK07500          7 ADRSMIR---SAMKAPYLEREEEHALAYRWKDH---------------------------------------RDEDALHR   44 (289)
T ss_pred             HHHHHHH---HHhcCCCCCHHHHHHHHHHHHHC---------------------------------------CCHHHHHH
Confidence            4578999   99999999999999999887531                                       24689999


Q ss_pred             HHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          300 LIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       300 LI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      ||..|+++|.++|++|.+.|.+.+||+|||++||+++
T Consensus        45 Lv~~~~~lV~~~a~~~~~~~~~~eDLvQeg~i~L~~a   81 (289)
T PRK07500         45 IISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEA   81 (289)
T ss_pred             HHHHhHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999993

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=98.78  E-value=1.6e-08  Score=98.34  Aligned_cols=77  Identities=19%  Similarity=0.229  Sum_probs=70.2

Q ss_pred             CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHH
Q 019233          217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYC  296 (344)
Q Consensus       217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~A  296 (344)
                      ..|.+..|+.   +++..|+||+++|.+|...++.+                                        +..|
T Consensus        51 ~~~~~~~y~~---~~~~~~~l~~~ee~~li~~~~~G----------------------------------------d~~A   87 (325)
T PRK05657         51 VLDATQLYLN---EIGYSPLLTAEEEVYFARRALRG----------------------------------------DFAA   87 (325)
T ss_pred             cccHHHHHHH---HHhcCCCCCHHHHHHHHHHHHcC----------------------------------------CHHH
Confidence            4678899999   99999999999999998887752                                        4678


Q ss_pred             HHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       297 RdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      .++||..|.++|.++|++|.+.+.+.+||+|+|++||+++
T Consensus        88 ~~~Li~~y~~~V~~~a~~~~~~~~~aeDLvQE~fi~l~~a  127 (325)
T PRK05657         88 RQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRA  127 (325)
T ss_pred             HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999984

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=98.66  E-value=5.3e-08  Score=90.52  Aligned_cols=67  Identities=24%  Similarity=0.193  Sum_probs=59.5

Q ss_pred             cCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHHHHHHhchHHHH
Q 019233          230 NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVL  309 (344)
Q Consensus       230 ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARdrLI~sNLRLVv  309 (344)
                      +..++|+||+++|.+|...++.+                                        +..+.++|+..|+++|.
T Consensus         9 ~~~~~~~l~~~~~~~li~~~~~g----------------------------------------d~~a~~~L~~~~~~~v~   48 (254)
T TIGR02850         9 NTSKLPVLKNQEMRELFIRMQSG----------------------------------------DTTAREKLINGNLRLVL   48 (254)
T ss_pred             cccCCCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHHHHHHhHHHHH
Confidence            45788999999998887776642                                        35789999999999999


Q ss_pred             HHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          310 FLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       310 sIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      ++|++|.+.+.+.+||+|+|++||+++
T Consensus        49 ~~a~~~~~~~~~aeDlvQe~~i~l~~a   75 (254)
T TIGR02850        49 SVIQRFNNRGEYVDDLFQVGCIGLMKS   75 (254)
T ss_pred             HHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence            999999999999999999999999993

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

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

Probab=98.66  E-value=2.6e-08  Score=94.58  Aligned_cols=50  Identities=32%  Similarity=0.381  Sum_probs=43.7

Q ss_pred             HHHHhhhh-HHHHHHHHHhchHHHHHHHHhcCCCCC-ChhhHHHHHHHHHhhh
Q 019233          286 LKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGI-PFSDLLQVSRHALAFI  336 (344)
Q Consensus       286 L~~~l~~g-~~ARdrLI~sNLRLVvsIAKrY~grGl-s~eDLIQEG~iGLmka  336 (344)
                      +...++.| ..+| +||+.|+|||.+||++|.++|. .++||||.|+||||+|
T Consensus        14 ~~~~~~~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~A   65 (247)
T COG1191          14 LLEYYAEGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKA   65 (247)
T ss_pred             HHHHHHhcCHHHH-HHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHH
Confidence            33444444 7788 9999999999999999999998 9999999999999995

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=98.65  E-value=7.3e-08  Score=91.14  Aligned_cols=77  Identities=21%  Similarity=0.279  Sum_probs=69.9

Q ss_pred             CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHH
Q 019233          217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYC  296 (344)
Q Consensus       217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~A  296 (344)
                      ..|.+..||.   +|...|.|+.++|.+|...++.+                                        ...|
T Consensus        11 ~~~~~~~~~~---~~~~~~~~~~~~~~~li~~~~~g----------------------------------------d~~a   47 (285)
T TIGR02394        11 VADVTQLYLR---EIGFKPLLTAEEEIAYARRALAG----------------------------------------DFEA   47 (285)
T ss_pred             cchHHHHHHH---HHhccCCCCHHHHHHHHHHHHcC----------------------------------------CHHH
Confidence            3578899999   99999999999999998887753                                        3678


Q ss_pred             HHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          297 REELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       297 RdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      .+.||..+.++|..+|.+|.+.+...+||+|+|++||+++
T Consensus        48 ~~~L~~~y~~~v~~~a~~~~~~~~~aeDLvQe~~i~l~~a   87 (285)
T TIGR02394        48 RKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHA   87 (285)
T ss_pred             HHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999983

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=98.60  E-value=7e-08  Score=90.24  Aligned_cols=44  Identities=25%  Similarity=0.270  Sum_probs=40.5

Q ss_pred             hHHHHHHHHHhchHHHHHHHHhcCCC-CCChhhHHHHHHHHHhhh
Q 019233          293 GWYCREELIKSTRPLVLFLARNYRGL-GIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       293 g~~ARdrLI~sNLRLVvsIAKrY~gr-Gls~eDLIQEG~iGLmka  336 (344)
                      +..++++||..|++||.+||++|.++ +.+++||||+|+||||+|
T Consensus        23 d~~a~~~Lv~~~~~lV~~ia~~~~~~~~~~~eDL~Qeg~igL~~a   67 (256)
T PRK07408         23 SIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRA   67 (256)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHH
Confidence            36899999999999999999999876 778999999999999994

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=98.60  E-value=1.1e-07  Score=88.59  Aligned_cols=67  Identities=24%  Similarity=0.210  Sum_probs=58.9

Q ss_pred             cCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHHHHHHhchHHHH
Q 019233          230 NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVL  309 (344)
Q Consensus       230 ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARdrLI~sNLRLVv  309 (344)
                      +..+.|+|+++|+..|...++.+                                        +..++++||..|+++|.
T Consensus        12 ~~~~~~~l~~~~~~~l~~~~~~g----------------------------------------d~~a~~~l~~~~~~~v~   51 (258)
T PRK08215         12 NTSKLPVLKNEEMRELFERMQNG----------------------------------------DKEAREKLINGNLRLVL   51 (258)
T ss_pred             cCCCCCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHHHHHHHHHHHH
Confidence            44677899999998887776632                                        46789999999999999


Q ss_pred             HHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          310 FLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       310 sIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      .+|++|.+.+.+.+||+|+|++||+++
T Consensus        52 ~~a~~~~~~~~~aeDlvQe~~i~l~~a   78 (258)
T PRK08215         52 SVIQRFNNRGENVDDLFQVGCIGLMKA   78 (258)
T ss_pred             HHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence            999999999999999999999999993

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=98.40  E-value=5e-07  Score=84.73  Aligned_cols=44  Identities=23%  Similarity=0.144  Sum_probs=39.2

Q ss_pred             hHHHHHHHHHhchHHHHHHHHhcCC---CCCChhhHHHHHHHHHhhh
Q 019233          293 GWYCREELIKSTRPLVLFLARNYRG---LGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       293 g~~ARdrLI~sNLRLVvsIAKrY~g---rGls~eDLIQEG~iGLmka  336 (344)
                      +..||++||..|++||.+||++|.+   .+++++||+|+|+|||++|
T Consensus        21 ~~~ar~~Li~~~~~lV~~ia~~~~~~~~~~~~~eDL~QeG~igL~~a   67 (257)
T PRK05911         21 EIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRA   67 (257)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence            4679999999999999999999862   3567999999999999994

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=98.36  E-value=1e-06  Score=82.56  Aligned_cols=67  Identities=24%  Similarity=0.209  Sum_probs=57.6

Q ss_pred             CCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHHHHHHhchHHHHH
Q 019233          231 SRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVLF  310 (344)
Q Consensus       231 i~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARdrLI~sNLRLVvs  310 (344)
                      .++.|+||.++|.+|...++..                                       .+..+.+.++..|++||..
T Consensus         6 ~~~~~~~~~~~e~~l~~~~~~~---------------------------------------~d~~a~~~l~~~y~~lv~~   46 (268)
T PRK06288          6 SGKIPKYAQQDETELWREYKKT---------------------------------------GDPKIREYLILKYSPLVKY   46 (268)
T ss_pred             cCCCccccchHHHHHHHHHHHc---------------------------------------CCHHHHHHHHHHHHHHHHH
Confidence            4789999999999998877642                                       1467899999999999999


Q ss_pred             HHHhcC-C--CCCChhhHHHHHHHHHhhh
Q 019233          311 LARNYR-G--LGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       311 IAKrY~-g--rGls~eDLIQEG~iGLmka  336 (344)
                      +|++|. +  .+.+.+||+|+|++||+++
T Consensus        47 ~a~~~~~~~~~~~~~eDl~Qeg~l~L~~a   75 (268)
T PRK06288         47 VAGRIAVGMPQNVEFDDLVSYGVFGLIDA   75 (268)
T ss_pred             HHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence            999986 2  5678999999999999993

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=98.22  E-value=4.5e-06  Score=76.49  Aligned_cols=74  Identities=15%  Similarity=0.107  Sum_probs=64.1

Q ss_pred             hHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHHH
Q 019233          220 PTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREE  299 (344)
Q Consensus       220 pl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARdr  299 (344)
                      .+.+|+.   ++++.|+||+++|..|...++.+                                        +..+.+.
T Consensus        17 ~~~~~~~---~~~~~~~~~~~~e~~l~~~~~~g----------------------------------------d~~a~~~   53 (233)
T PRK05803         17 FLVSYVK---NNSFPQPLSEEEERKYLELMKEG----------------------------------------DEEARNI   53 (233)
T ss_pred             HHHHHHH---HhcccCCCCHHHHHHHHHHHHcC----------------------------------------CHHHHHH
Confidence            3578888   88888999999988876665531                                        4678999


Q ss_pred             HHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          300 LIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       300 LI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      |+..+.++|..+|.+|.+.+.+.+||+|||.+||+++
T Consensus        54 l~~~y~~~l~~~a~~~~~~~~daeDlvQE~fi~l~~~   90 (233)
T PRK05803         54 LIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKA   90 (233)
T ss_pred             HHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999995

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=98.14  E-value=5.7e-06  Score=76.66  Aligned_cols=42  Identities=29%  Similarity=0.242  Sum_probs=40.7

Q ss_pred             HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          294 WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       294 ~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      ..|.++|+..|.++|..+|++|.+.+...+||+|+|++||++
T Consensus        28 ~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~   69 (255)
T TIGR02941        28 GEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLG   69 (255)
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHH
Confidence            678999999999999999999999999999999999999998

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

>PF00140 Sigma70_r1_2: Sigma-70 factor, region 1

Probab=98.01  E-value=2.1e-06  Score=59.62  Aligned_cols=35  Identities=11%  Similarity=0.088  Sum_probs=30.9

Q ss_pred             CchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHH
Q 019233          218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANL  255 (344)
Q Consensus       218 ~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~L  255 (344)
                      +|++..||+   +++++||||++||++|+++|+.+...
T Consensus         1 ~D~l~~Yl~---ei~~~~LLt~eeE~~LA~~i~~g~~~   35 (37)
T PF00140_consen    1 SDSLRLYLK---EIGRYPLLTAEEEIELARRIRKGDEA   35 (37)
T ss_dssp             HHHHHHHHH---HHHHS-EETTHHHHHHHHHHHHHHHH
T ss_pred             CcHHHHHHH---HHcCCCCCCHHHHHHHHHHHHHhHHh
Confidence            378999999   99999999999999999999998654

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 ....

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=98.00  E-value=1.8e-05  Score=73.49  Aligned_cols=44  Identities=30%  Similarity=0.199  Sum_probs=41.3

Q ss_pred             hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      +..|.++|+..|.++|..+|++|.+.+...+||+|+|++||+++
T Consensus        27 d~~a~~~l~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~l~l~~~   70 (257)
T PRK08583         27 DEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGA   70 (257)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence            36789999999999999999999999999999999999999983

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=97.86  E-value=1.6e-05  Score=73.74  Aligned_cols=42  Identities=19%  Similarity=0.081  Sum_probs=37.5

Q ss_pred             HHHHHHHHhchHHHHHHHHhcCCC---CCChhhHHHHHHHHHhhh
Q 019233          295 YCREELIKSTRPLVLFLARNYRGL---GIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       295 ~ARdrLI~sNLRLVvsIAKrY~gr---Gls~eDLIQEG~iGLmka  336 (344)
                      .-+..+|..|+|||.++|++|.++   +++.+||||+|++||++|
T Consensus        15 ~~~~~lv~~y~~lV~~la~~~~~~~~~~~~~eDLvQeg~igL~~a   59 (231)
T PRK12427         15 QEEGKYLNAYLPLVKKVVRQLAFQADSVIDREDMEQIALMGLLEA   59 (231)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHH
Confidence            456789999999999999999854   579999999999999994

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=97.84  E-value=2.7e-05  Score=70.92  Aligned_cols=45  Identities=22%  Similarity=0.226  Sum_probs=42.4

Q ss_pred             hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       292 ~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      .+..+.++|+..|.++|.++|++|.+.+.+.+||+|+|.+||+++
T Consensus         8 gd~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDl~Qe~~i~l~~a   52 (231)
T TIGR02885         8 GDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKA   52 (231)
T ss_pred             CCHHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence            357899999999999999999999999999999999999999994

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.

>PRK05572 sporulation sigma factor SigF; Validated

Probab=97.77  E-value=7.5e-05  Score=69.39  Aligned_cols=67  Identities=19%  Similarity=0.176  Sum_probs=57.7

Q ss_pred             cCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhhHHHHHHHHHhchHHHH
Q 019233          230 NSRGRRLTIARNEAEMSKGVQVVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFGWYCREELIKSTRPLVL  309 (344)
Q Consensus       230 ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g~~ARdrLI~sNLRLVv  309 (344)
                      +-...|.||.+++.+|...++.                                        .+..+.++|+..|.++|.
T Consensus         7 ~~~~~~~l~~~~~~~li~~~~~----------------------------------------gd~~a~~~L~~~y~~~v~   46 (252)
T PRK05572          7 NKKKKPQLKDEENKELIKKSQD----------------------------------------GDQEARDTLVEKNLRLVW   46 (252)
T ss_pred             cCcCCCCCCHHHHHHHHHHHHc----------------------------------------CCHHHHHHHHHHhHHHHH
Confidence            5577899999988887655442                                        135789999999999999


Q ss_pred             HHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          310 FLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       310 sIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      .+|.+|.+.+...+||+|||.++|+++
T Consensus        47 ~~a~~~~~~~~~aeDl~Qe~~l~l~~~   73 (252)
T PRK05572         47 SVVQRFLNRGYEPDDLFQIGCIGLLKA   73 (252)
T ss_pred             HHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence            999999999999999999999999983

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=97.37  E-value=0.0003  Score=65.39  Aligned_cols=52  Identities=19%  Similarity=0.120  Sum_probs=44.0

Q ss_pred             HHHHHHhhh--hHHHHHHHHHhchHHHHHHHHhcCC---CCCChhhHHHHHHHHHhh
Q 019233          284 RVLKQHLAF--GWYCREELIKSTRPLVLFLARNYRG---LGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       284 ~eL~~~l~~--g~~ARdrLI~sNLRLVvsIAKrY~g---rGls~eDLIQEG~iGLmk  335 (344)
                      .+|.+++..  +..|.++|+..|.++|..+|.+|.+   .+...+||+|+|++||++
T Consensus         9 ~~l~~~~~~~~d~~a~~~L~~~y~~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~   65 (251)
T PRK07670          9 QKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYD   65 (251)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHH
Confidence            445555332  4789999999999999999999965   678999999999999999

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=96.97  E-value=0.0035  Score=57.48  Aligned_cols=44  Identities=20%  Similarity=0.277  Sum_probs=40.8

Q ss_pred             hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      +..+-+.|+..|.++|..+|.+|.+...+.+||+||+.++++++
T Consensus        46 d~~af~~l~~~y~~~v~~~~~~~~~~~~dAEDlvQevfi~l~~~   89 (227)
T TIGR02846        46 DEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKA   89 (227)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHH
Confidence            46788999999999999999999999999999999999999983

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.

>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=96.68  E-value=0.0023  Score=46.87  Aligned_cols=36  Identities=31%  Similarity=0.234  Sum_probs=34.6

Q ss_pred             HHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          300 LIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       300 LI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      |++.+.++|..+|.+|.+.+.+.+|++||+.++|++
T Consensus         1 L~~~~~~~l~~~~~~~~~~~~~~eD~~qe~~~~l~~   36 (71)
T PF04542_consen    1 LYERYYPLLYRYARRYTGDPEDAEDLVQEAFIKLWR   36 (71)
T ss_dssp             HHHHTHHHHHHHHHTCTTCSSHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHhCCHhhHHHHhhHHHHHHHh
Confidence            688999999999999999999999999999999997

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 ....

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=96.63  E-value=0.0088  Score=54.68  Aligned_cols=43  Identities=28%  Similarity=0.434  Sum_probs=40.7

Q ss_pred             hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      +..+.+.|+..+.++|..+|.+|.+.+..-+||+||+.+++++
T Consensus        50 d~~af~~l~~~y~~~l~~~a~~~~~~~~~AeDlvQevfl~l~~   92 (234)
T PRK08301         50 DEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIK   92 (234)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHH
Confidence            4678999999999999999999999999999999999999998

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=96.61  E-value=0.0051  Score=47.29  Aligned_cols=40  Identities=25%  Similarity=0.367  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhh
Q 019233          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF  292 (344)
Q Consensus       253 ~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~  292 (344)
                      .++.+++.+|+..+||+||.+|+|+.+|++.+++...+..
T Consensus         4 ~~i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~   43 (78)
T PF04539_consen    4 RKIERARRELEQELGREPTDEEIAEELGISVEEVRELLQA   43 (78)
T ss_dssp             HHHHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHh
Confidence            4567788899999999999999999999999988766653

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 ....

>PRK05658 RNA polymerase sigma factor RpoD; Validated

Probab=96.56  E-value=0.0022  Score=67.63  Aligned_cols=35  Identities=17%  Similarity=0.192  Sum_probs=32.7

Q ss_pred             CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHH
Q 019233          217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVAN  254 (344)
Q Consensus       217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~  254 (344)
                      -+|||.+|||   +|+..||||+|+|++||++|..|.+
T Consensus       102 t~DPVRMYLR---EMG~V~LLTREgEIeIAKRIE~G~~  136 (619)
T PRK05658        102 TDDPVRMYLR---EMGTVELLTREGEIEIAKRIEAGEN  136 (619)
T ss_pred             CCChHHHHHH---HhccCcCCCcHHHHHHHHHHHHHHH
Confidence            4799999999   9999999999999999999998764

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=96.43  E-value=0.011  Score=54.41  Aligned_cols=44  Identities=25%  Similarity=0.416  Sum_probs=41.4

Q ss_pred             hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      +..+.+.++..+.+.|..+|.+|.+.+.+-+||+||+.+++++.
T Consensus        50 d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AEDlvQE~fl~l~~~   93 (234)
T TIGR02835        50 DESAKSTLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGLIKA   93 (234)
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHH
Confidence            47899999999999999999999999999999999999999983

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.

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=96.05  E-value=0.01  Score=51.38  Aligned_cols=52  Identities=13%  Similarity=-0.048  Sum_probs=44.7

Q ss_pred             HHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          285 VLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       285 eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      .|...+.. ...+-++++..+.++|..+|.+|.+...+.+|++|++.++|++.
T Consensus         7 ~li~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~~l~l~~~   59 (187)
T PRK09641          7 RLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVN   59 (187)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            34444443 47789999999999999999999999999999999999999984

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=95.94  E-value=0.012  Score=51.44  Aligned_cols=54  Identities=19%  Similarity=0.030  Sum_probs=46.2

Q ss_pred             CHHHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          282 SERVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       282 d~~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      +.+.|...+. .+..+-+.|+..+.++|..+|.+|.+.+.+-+|++||+.++|++
T Consensus         6 ~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~   60 (186)
T PRK05602          6 PDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWK   60 (186)
T ss_pred             cHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Confidence            3444544444 45889999999999999999999999999999999999999997

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=95.88  E-value=0.022  Score=50.33  Aligned_cols=54  Identities=22%  Similarity=0.103  Sum_probs=46.1

Q ss_pred             CHHHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          282 SERVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       282 d~~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      +...|...+. .+..+-+.|+..+.++|..+|.+|.+.....+||+|++.++|++
T Consensus        10 ~~~~l~~~~~~~d~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~   64 (208)
T PRK08295         10 EDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYK   64 (208)
T ss_pred             ChHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHH
Confidence            3444554444 44789999999999999999999999999999999999999987

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=95.75  E-value=0.02  Score=52.50  Aligned_cols=44  Identities=14%  Similarity=-0.053  Sum_probs=40.7

Q ss_pred             hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      +..+-+.|+..|.++|..+|.+|.+.+..-+||+||+.++|++.
T Consensus        28 d~~a~~~l~~~y~~~l~~~a~~~~~~~~~AEDlvQE~fi~l~~~   71 (231)
T PRK11922         28 DEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRA   71 (231)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHHHHHHH
Confidence            46788899999999999999999999999999999999999983

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=95.65  E-value=0.032  Score=48.88  Aligned_cols=55  Identities=22%  Similarity=0.166  Sum_probs=47.3

Q ss_pred             CCHHHHHHHhhhh-HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       281 ld~~eL~~~l~~g-~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      |+.++|...+..| ..+-++|+..+.+.|..+|.+|.+...+.+||+||+.+.+.+
T Consensus         4 ~~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~a~~~~~~~~~aeDlvQe~fl~~~~   59 (198)
T TIGR02859         4 LEDEEIVELARQGNTHALEYLINKYKNFVRAKARSYFLIGADKEDIIQEGMIGLYK   59 (198)
T ss_pred             cchHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHccccCcHHHHHHHHHHHHHH
Confidence            3445555665554 789999999999999999999999999999999999999988

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.

>PRK08311 putative RNA polymerase sigma factor SigI; Reviewed

Probab=95.45  E-value=0.034  Score=52.57  Aligned_cols=53  Identities=23%  Similarity=0.212  Sum_probs=44.0

Q ss_pred             HHHHHHhhhh-HHHHHHHHHhchHHHHHHHHhcCCCCC--ChhhHHHHHHHHHhhh
Q 019233          284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGI--PFSDLLQVSRHALAFI  336 (344)
Q Consensus       284 ~eL~~~l~~g-~~ARdrLI~sNLRLVvsIAKrY~grGl--s~eDLIQEG~iGLmka  336 (344)
                      ..|...+..| ..|.++|+..+.++|..+|.+|.++..  ..+|++|+|.++++++
T Consensus         6 ~~Li~~~~~gD~~AfeeLi~~Y~p~I~~~a~~~~~~~~~~eaeDlvQe~fi~l~ea   61 (237)
T PRK08311          6 EDILEKIKNGDEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEA   61 (237)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCCchHHHHHHHHHHHHH
Confidence            3444444444 779999999999999999999988776  4899999999999984

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=95.44  E-value=0.021  Score=49.50  Aligned_cols=45  Identities=11%  Similarity=-0.112  Sum_probs=41.8

Q ss_pred             hhhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          291 AFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       291 ~~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      .....+-.+|+..+.++|..+|.+|.+.+.+.+|++|++.+++++
T Consensus        14 ~gd~~a~~~l~~~y~~~v~~~~~~~~~~~~~aeDlvQe~~l~l~~   58 (187)
T TIGR02948        14 KGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYT   58 (187)
T ss_pred             cCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence            345778999999999999999999999999999999999999998

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

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=95.27  E-value=0.028  Score=49.53  Aligned_cols=54  Identities=11%  Similarity=-0.057  Sum_probs=46.4

Q ss_pred             HHHHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          283 ERVLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       283 ~~eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      ...|...+.. +..+.+.|+..+.+.|..+|.+|.+...+.+|++|++.++|++.
T Consensus        13 ~~~l~~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~fi~l~~~   67 (194)
T PRK12513         13 DEALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRA   67 (194)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence            4445555554 48899999999999999999999999889999999999999984

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=95.26  E-value=0.056  Score=47.45  Aligned_cols=52  Identities=23%  Similarity=0.210  Sum_probs=42.4

Q ss_pred             HHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCC----CCChhhHHHHHHHHHhhh
Q 019233          285 VLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGL----GIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       285 eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~gr----Gls~eDLIQEG~iGLmka  336 (344)
                      .|...+.. ...+-++|+..+.+.|..+|.+|.+.    +.+.+|++||+.++|++.
T Consensus        13 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDlvQe~fi~l~~~   69 (189)
T PRK09648         13 ALVAEAVAGDRRALREVLEIIRPLVVRYCRARLGGVERPGLSADDVAQEVCLAVITA   69 (189)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHHHH
Confidence            34444444 47899999999999999999988643    468999999999999984

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=95.02  E-value=0.043  Score=47.80  Aligned_cols=55  Identities=20%  Similarity=0.001  Sum_probs=46.6

Q ss_pred             CHHHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          282 SERVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       282 d~~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      +.++|...+. ....+-+.++..+.+.|..+|++|.+.+..-+|++||+.+.|.+.
T Consensus         9 ~~~~l~~~~~~~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~~i~l~~~   64 (186)
T PRK13919          9 SDEALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKK   64 (186)
T ss_pred             CHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHh
Confidence            3455555553 447899999999999999999999999999999999999999874

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=94.80  E-value=0.066  Score=47.15  Aligned_cols=55  Identities=15%  Similarity=0.154  Sum_probs=48.5

Q ss_pred             CCHHHHHHHhhh----hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          281 VSERVLKQHLAF----GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       281 ld~~eL~~~l~~----g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      ++.+.|...++.    +..+-+.|+..+.+.|..+|.+|.+....-+|++|++.+.|++
T Consensus         8 ~~~~~li~~~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~f~~l~~   66 (188)
T PRK09640          8 LNDEELVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLY   66 (188)
T ss_pred             CCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHH
Confidence            455666666663    5889999999999999999999999999999999999999987

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=94.73  E-value=0.07  Score=45.97  Aligned_cols=54  Identities=13%  Similarity=-0.111  Sum_probs=45.4

Q ss_pred             CHHHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          282 SERVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       282 d~~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      +...+..... .+..+-+.|+..+.+.|..+|.+|.+....-+|++||+.+.+++
T Consensus         4 ~~~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~   58 (176)
T PRK09638          4 DEKELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIE   58 (176)
T ss_pred             cHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHcCCHhHHHHHHHHHHHHHHH
Confidence            3444444443 34789999999999999999999999888999999999999987

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=94.32  E-value=0.075  Score=46.72  Aligned_cols=54  Identities=22%  Similarity=-0.040  Sum_probs=45.6

Q ss_pred             HHHHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          283 ERVLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       283 ~~eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      ..+|..++.. +..+-+.|+..+.+.|..+|++|.+....-+|++|++.+++++.
T Consensus        16 ~~~l~~~~~~gd~~a~~~L~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~l~~~   70 (194)
T PRK12519         16 DAELFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRK   70 (194)
T ss_pred             HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHh
Confidence            3445554444 47899999999999999999999998888999999999999863

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=94.22  E-value=0.097  Score=45.99  Aligned_cols=51  Identities=12%  Similarity=-0.086  Sum_probs=43.7

Q ss_pred             HHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          285 VLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       285 eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      .|...+.. ...+-++|+..|.+.|..+|++|.+.....+|++|++.+.+++
T Consensus         9 ~ll~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~daeDlvQe~~i~l~~   60 (193)
T PRK11923          9 QLVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYR   60 (193)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHH
Confidence            34444444 4789999999999999999999998888999999999999988

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=93.93  E-value=0.11  Score=45.09  Aligned_cols=51  Identities=14%  Similarity=-0.003  Sum_probs=44.0

Q ss_pred             HHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          285 VLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       285 eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      .|...+.. +..+-+.|+..+.+.|..+|.++.+....-+||+||+.++|.+
T Consensus         9 ~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDlvQe~fi~l~~   60 (190)
T TIGR02939         9 ELVERVQRGEKQAFDLLVRKYQHKVVALVGRYVRDSSEVEDVAQEAFVKAYR   60 (190)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHH
Confidence            34444443 4778999999999999999999999889999999999999987

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.

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=93.88  E-value=0.11  Score=46.15  Aligned_cols=52  Identities=17%  Similarity=-0.107  Sum_probs=45.2

Q ss_pred             HHHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          284 RVLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       284 ~eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      ..|...+.. +..+-++|+..|-++|..+|.+|.+....-+|++||+.+.+.+
T Consensus        18 ~~li~~~~~g~~~a~~~l~~~y~~~l~~~~~~~~~~~~dAeDivQe~fi~l~~   70 (194)
T PRK09646         18 DALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWR   70 (194)
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence            444444444 4789999999999999999999999999999999999999987

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=93.83  E-value=0.17  Score=44.75  Aligned_cols=56  Identities=11%  Similarity=-0.044  Sum_probs=45.9

Q ss_pred             CCHHHHHHHhhhh-HHHHHHHHHhchHHHHHHHHhcCCCC---CChhhHHHHHHHHHhhh
Q 019233          281 VSERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLG---IPFSDLLQVSRHALAFI  336 (344)
Q Consensus       281 ld~~eL~~~l~~g-~~ARdrLI~sNLRLVvsIAKrY~grG---ls~eDLIQEG~iGLmka  336 (344)
                      ++.+.|...+..| ..+-++|+..+.++|..+|.+|.+.+   ..-+|++|++.++|++.
T Consensus         3 ~~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~~~daeDi~Qe~~i~l~~~   62 (189)
T PRK06811          3 INEDNFIKELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIEECVNDIFLSIWNN   62 (189)
T ss_pred             CcHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHcccCchhHHHHHHHHHHHHHHHh
Confidence            4455666666554 77999999999999999999998754   35799999999999984

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=93.59  E-value=0.13  Score=43.67  Aligned_cols=45  Identities=20%  Similarity=-0.038  Sum_probs=41.7

Q ss_pred             hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       292 ~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      .+..+-+.++..+.+.|..+|+++.+...+-+||+|++.+.|+..
T Consensus        10 ~~~~a~~~l~~~y~~~l~~~~~~~~~~~~~aeDl~qe~~~~l~~~   54 (179)
T PRK11924         10 GDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRK   54 (179)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHHH
Confidence            457899999999999999999999999999999999999999874

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=93.47  E-value=0.14  Score=45.40  Aligned_cols=54  Identities=22%  Similarity=0.055  Sum_probs=47.0

Q ss_pred             CHHHHHHHhhhh-HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          282 SERVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       282 d~~eL~~~l~~g-~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      +...|...+..| ..+-+.|+..+-+.|..+|.+|.+....-+|++||+.+.|.+
T Consensus        12 ~~~~li~~~~~gd~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQe~~l~l~~   66 (196)
T PRK12524         12 SDEALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWR   66 (196)
T ss_pred             CHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence            445566666554 789999999999999999999999999999999999999987

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=93.11  E-value=0.14  Score=44.78  Aligned_cols=47  Identities=13%  Similarity=-0.042  Sum_probs=42.4

Q ss_pred             hhhhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          290 LAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       290 l~~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      ...+..+-+.|+..+.++|..+|.+|.+....-+|++||..+.+++.
T Consensus        20 ~~~~~~~~~~l~~~y~~~l~~~~~~~~~~~~~aeDlvQe~fl~~~~~   66 (187)
T PRK12534         20 AGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHK   66 (187)
T ss_pred             HcCCHHHHHHHHHHhhHHHHHHHHHHhcCHHHHHHHHHHHHHHHHhc
Confidence            33457899999999999999999999999899999999999999983

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=92.97  E-value=0.16  Score=44.06  Aligned_cols=52  Identities=10%  Similarity=-0.128  Sum_probs=44.2

Q ss_pred             HHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          284 RVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       284 ~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      ..|..... .+..+-++|+..+.+.|..+|.+|.+....-+|++||+.+.+.+
T Consensus         7 ~~li~~~~~g~~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~fl~~~~   59 (179)
T PRK12514          7 EKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWT   59 (179)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHHH
Confidence            33444433 34789999999999999999999999989999999999999987

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

Probab=92.01  E-value=0.31  Score=41.93  Aligned_cols=52  Identities=17%  Similarity=-0.030  Sum_probs=44.3

Q ss_pred             HHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          284 RVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       284 ~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      ++|...+. .+..+-+.++..+.+.+..+|.+|.+...+-+|++||..+-+.+
T Consensus         4 ~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~~Qe~~l~~~~   56 (169)
T TIGR02954         4 EELVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYL   56 (169)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence            34444443 45789999999999999999999999999999999999999886

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.

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=91.34  E-value=0.34  Score=40.72  Aligned_cols=41  Identities=10%  Similarity=-0.045  Sum_probs=35.2

Q ss_pred             HHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          295 YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       295 ~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      .+-+.|+..+.++|..+++++.+ ..+.+|++||+.++++++
T Consensus         4 ~af~~l~~~y~~~l~~~~~~~~~-~~~aeDi~Qe~~l~l~~~   44 (154)
T PRK06759          4 ATFTEAVVLYEGLIVNQIKKLGI-YQDYEEYYQCGLIGLWHA   44 (154)
T ss_pred             ccHHHHHHHHHHHHHHHHHHhCC-cccHHHHHHHHHHHHHHH
Confidence            45567999999999999999854 468899999999999984

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=90.49  E-value=0.52  Score=41.94  Aligned_cols=54  Identities=20%  Similarity=0.087  Sum_probs=46.2

Q ss_pred             CHHHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          282 SERVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       282 d~~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      +.+.+...+. .+..+-+.++..+.+.|..+|.++.+....-+|++||..+-+++
T Consensus        13 ~~~~l~~~~~~gd~~~~~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQEvfl~l~~   67 (192)
T PRK09643         13 SDAELLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHR   67 (192)
T ss_pred             CHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHcCCHhhHHHHHHHHHHHHHH
Confidence            3455555554 45889999999999999999999999988999999999999997

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=89.70  E-value=0.94  Score=39.47  Aligned_cols=44  Identities=18%  Similarity=0.067  Sum_probs=38.2

Q ss_pred             hhHHHHHHHHHhchHHHHHHHHhcCCC----CCChhhHHHHHHHHHhh
Q 019233          292 FGWYCREELIKSTRPLVLFLARNYRGL----GIPFSDLLQVSRHALAF  335 (344)
Q Consensus       292 ~g~~ARdrLI~sNLRLVvsIAKrY~gr----Gls~eDLIQEG~iGLmk  335 (344)
                      .+..+.++|+..+-+.|..+|.+|.++    ...-+|++||+.+.+..
T Consensus        19 gd~~a~~~l~~~y~~~l~~~~~~~l~~~~~~~~~aeDlvQe~fl~l~~   66 (184)
T PRK12512         19 GDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHL   66 (184)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHHHHHH
Confidence            458899999999999999999988652    35799999999999875

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=89.33  E-value=0.67  Score=41.11  Aligned_cols=51  Identities=8%  Similarity=-0.096  Sum_probs=43.5

Q ss_pred             HHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          285 VLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       285 eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      +|..++. .+..+-+.|+..+.+.|..+|.+|.+....-+|++||..+.+.+
T Consensus        16 ~li~~~~~~d~~af~~l~~~y~~~l~~~~~~~~~~~~~AeDlvQev~l~l~~   67 (194)
T PRK12531         16 ECMEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQ   67 (194)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence            3444444 34778999999999999999999998888899999999999988

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=88.97  E-value=0.52  Score=41.46  Aligned_cols=54  Identities=11%  Similarity=-0.057  Sum_probs=46.0

Q ss_pred             CHHHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          282 SERVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       282 d~~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      +...|...+. .+..+-+.|+..+.+.+..+|.+|.+....-+|++||+.+.+++
T Consensus         8 ~~~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~l~~   62 (189)
T PRK12515          8 TDEMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWR   62 (189)
T ss_pred             CHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence            4455555555 45779999999999999999999998888999999999999987

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=88.94  E-value=0.73  Score=42.95  Aligned_cols=52  Identities=15%  Similarity=-0.022  Sum_probs=44.2

Q ss_pred             HHHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          284 RVLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       284 ~eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      .+|...+.. +..+-++|+..+.+.|..++.+|.+....-+|++||..+.+++
T Consensus        51 ~~Li~~~~~gd~~af~~L~~~y~~~l~~~~~~~~~d~~dAEDivQEvfl~l~~  103 (233)
T PRK12538         51 EELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWT  103 (233)
T ss_pred             HHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Confidence            344444444 4779999999999999999999998888899999999999987

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

Probab=88.86  E-value=0.82  Score=38.82  Aligned_cols=44  Identities=9%  Similarity=-0.158  Sum_probs=40.0

Q ss_pred             hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       292 ~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      .+..+-+.|+..+.+.+..++.++.+....-+|++||+.+.+++
T Consensus         8 ~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~~l~l~~   51 (170)
T TIGR02952         8 REEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLR   51 (170)
T ss_pred             cCHHHHHHHHHHHHHHHHHHHHHHHCChhhHHHHHHHHHHHHHH
Confidence            35788999999999999999988888888999999999999998

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.

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=87.98  E-value=1.1  Score=39.29  Aligned_cols=52  Identities=12%  Similarity=-0.090  Sum_probs=44.7

Q ss_pred             HHHHHHhh-hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          284 RVLKQHLA-FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       284 ~eL~~~l~-~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      .+|..... .+..+-+.|+..+-+.+..+|.++.+....-+|++||..+.+++
T Consensus        11 ~~l~~~~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~   63 (182)
T PRK12537         11 EACLLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWT   63 (182)
T ss_pred             HHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhCCHhHHHHHHHHHHHHHHh
Confidence            34444444 45889999999999999999999999988999999999999987

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

Probab=86.81  E-value=1.4  Score=42.52  Aligned_cols=41  Identities=20%  Similarity=0.204  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhhh
Q 019233          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAFG  293 (344)
Q Consensus       253 ~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~g  293 (344)
                      .+++.+..+|+.++||+||..|+|+..|++.+++...+..+
T Consensus       110 ~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~  150 (247)
T COG1191         110 RRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAI  150 (247)
T ss_pred             HHHHHHHHHHHHHhCCCCcHHHHHHHhCCCHHHHHHHHHHh
Confidence            34556778899999999999999999999988776655443

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=85.49  E-value=2.4  Score=37.14  Aligned_cols=51  Identities=12%  Similarity=-0.073  Sum_probs=41.2

Q ss_pred             HHHHHhhh-hHHHHHHHHHhchHHHHHHHH----hcCCCCCChhhHHHHHHHHHhh
Q 019233          285 VLKQHLAF-GWYCREELIKSTRPLVLFLAR----NYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       285 eL~~~l~~-g~~ARdrLI~sNLRLVvsIAK----rY~grGls~eDLIQEG~iGLmk  335 (344)
                      .|..+... +..+-+.|+..+.+.|..+|.    +|.+...+-+|++|+..+.|++
T Consensus        10 ~l~~~~~~gd~~af~~l~~~~~~~l~~~~~~~~~~~~~~~~~AeDlvQe~~l~l~~   65 (184)
T PRK12539         10 ALMLASLDGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHT   65 (184)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHhccCCcchHHHHHHHHHHHHHH
Confidence            34444443 367899999999999999876    5667778899999999999998

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=84.63  E-value=1.4  Score=39.68  Aligned_cols=44  Identities=11%  Similarity=-0.039  Sum_probs=40.5

Q ss_pred             hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       292 ~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      .+..+-++|+..+.++|..+|.+|.+....-+|++|++.+.+++
T Consensus        35 ~d~~a~~~l~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~l~~   78 (206)
T PRK12526         35 RDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWR   78 (206)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHhCCHhhHHHHHHHHHHHHHH
Confidence            45778899999999999999999988878899999999999988

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=84.43  E-value=2.7  Score=39.63  Aligned_cols=37  Identities=19%  Similarity=0.240  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHH
Q 019233          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQH  289 (344)
Q Consensus       253 ~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~  289 (344)
                      .++.+.+.+|...+|++||.++.|+.+|++++++...
T Consensus       113 ~~~~~~~~~l~~~lgr~pt~~elA~~lgi~~~~v~~~  149 (256)
T PRK07408        113 RQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI  149 (256)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence            3455667788899999999999999999998887664

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=83.22  E-value=1.2  Score=41.96  Aligned_cols=17  Identities=18%  Similarity=0.024  Sum_probs=15.6

Q ss_pred             CChhhHHHHHHHHHhhh
Q 019233          320 IPFSDLLQVSRHALAFI  336 (344)
Q Consensus       320 ls~eDLIQEG~iGLmka  336 (344)
                      .+.+||+|+|++||++|
T Consensus        36 ~e~dDlvQ~glial~eA   52 (218)
T TIGR02895        36 TKSDDELSIGLIAFNEA   52 (218)
T ss_pred             CChhHHHHHHHHHHHHH
Confidence            57999999999999994

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).

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=83.10  E-value=3.1  Score=36.39  Aligned_cols=47  Identities=17%  Similarity=-0.027  Sum_probs=39.8

Q ss_pred             HhhhhHHHHHHHHHhchHHHHHHHHhcC-CCCCChhhHHHHHHHHHhh
Q 019233          289 HLAFGWYCREELIKSTRPLVLFLARNYR-GLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       289 ~l~~g~~ARdrLI~sNLRLVvsIAKrY~-grGls~eDLIQEG~iGLmk  335 (344)
                      ....+..+-++|+..+-+.|..+|.++. +....-+||+||+.+.|++
T Consensus        15 ~~~~d~~a~~~l~~~~~~~l~~~~~~~~~~~~~~aeDlvQevfl~l~~   62 (181)
T PRK12536         15 GLAGDAAAYRQFLSELAAHLRGFLRRRLPQLPDEVEDLVQEILLAVHN   62 (181)
T ss_pred             HHcCCHHHHHHHHHHHHHHHHHHHHHHcCCChhhHHHHHHHHHHHHHH
Confidence            3344577889999999999999998765 4577899999999999987

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=82.61  E-value=3.4  Score=38.66  Aligned_cols=37  Identities=16%  Similarity=0.179  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL  290 (344)
Q Consensus       254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l  290 (344)
                      ++.+...++..++|++||.+|.|+.+|++++.+...+
T Consensus       121 ~~~~~~~~l~~~l~~~pt~~elA~~l~~~~e~v~~~~  157 (254)
T TIGR02850       121 KALQVRDKLISENSKEPTVSEIAKELKVPQEEVVFAL  157 (254)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            3445567788889999999999999999988776544

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.

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

Probab=82.38  E-value=3.8  Score=37.92  Aligned_cols=37  Identities=16%  Similarity=0.256  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL  290 (344)
Q Consensus       254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l  290 (344)
                      ++.++...|...+|++||.+|.|+.+|++.+.+....
T Consensus        88 ~~~~~~~~l~~~~g~~pt~~eia~~l~~~~~~v~~~~  124 (238)
T TIGR02393        88 KLIKAERQLTQELGREPTDEELAERMGMPAEKVREIK  124 (238)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence            4455667888889999999999999999988776643

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.

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=82.31  E-value=2.4  Score=36.43  Aligned_cols=43  Identities=14%  Similarity=-0.093  Sum_probs=37.7

Q ss_pred             hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       292 ~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      .+..+-+.++..+.+.|..+|.+|.+. .+-+|++||..+.+.+
T Consensus         8 gd~~a~~~l~~~~~~~l~~~~~~~~~~-~~aeDivQe~~l~l~~   50 (175)
T PRK12518          8 GDRQSFRQLYRRYQQKVRSTLYQLCGR-ELLDDLVQEVFLRVWK   50 (175)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHcCH-hHHHHHHHHHHHHHHH
Confidence            347788999999999999999998754 5779999999999987

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=81.10  E-value=4.2  Score=38.66  Aligned_cols=37  Identities=22%  Similarity=0.312  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL  290 (344)
Q Consensus       254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l  290 (344)
                      ++.+...+|...+|++||.+|.|+.+|++++++...+
T Consensus       128 ~i~~~~~~l~~~lg~~pt~~eiA~~lg~~~~~v~~~~  164 (264)
T PRK07122        128 RLGRATAELSQRLGRAPTASELAAELGMDREEVVEGL  164 (264)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHH
Confidence            3445567788889999999999999999988876644

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

Probab=80.75  E-value=4.4  Score=35.08  Aligned_cols=51  Identities=16%  Similarity=0.002  Sum_probs=42.1

Q ss_pred             HHHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCC-----ChhhHHHHHHHHHhh
Q 019233          285 VLKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGI-----PFSDLLQVSRHALAF  335 (344)
Q Consensus       285 eL~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGl-----s~eDLIQEG~iGLmk  335 (344)
                      .|...+.. +..+-+.|+..+.+.+..+|.+|.+...     .-+|++||..+.+.+
T Consensus         6 ~li~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~   62 (183)
T TIGR02999         6 ELLQQWQNGDAAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSD   62 (183)
T ss_pred             HHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhh
Confidence            34444443 4678999999999999999999987766     789999999999986

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.

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

Probab=80.22  E-value=2.4  Score=35.93  Aligned_cols=43  Identities=16%  Similarity=-0.045  Sum_probs=39.5

Q ss_pred             hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      +..+-+.|+..+.+.|..+|.++.+....-+|++|+..+-+..
T Consensus         4 ~~~~~~~l~~~~~~~l~~~~~~~~~~~~~aeDivQe~f~~~~~   46 (162)
T TIGR02983         4 TEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYV   46 (162)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHH
Confidence            4678889999999999999999999888999999999999877

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.

>PRK07921 RNA polymerase sigma factor SigB; Reviewed

Probab=80.17  E-value=4.4  Score=40.14  Aligned_cols=39  Identities=31%  Similarity=0.466  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233          252 VANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL  290 (344)
Q Consensus       252 l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l  290 (344)
                      ..++.+++.+|...+|++||.+|.|+.+|++.+.+...+
T Consensus       172 ~~~l~~~~~~l~~~lgr~pt~~EiA~~lgi~~~~v~~~~  210 (324)
T PRK07921        172 VNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLL  210 (324)
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHH
Confidence            334566777888899999999999999999987776543

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=80.08  E-value=4.2  Score=37.86  Aligned_cols=37  Identities=8%  Similarity=0.134  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHh
Q 019233          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHL  290 (344)
Q Consensus       254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l  290 (344)
                      ++.+....|...+|++||.+|.|+.+|++++++...+
T Consensus       102 ~i~~~~~~l~~~~g~~pt~~eiA~~lg~~~~~v~~~~  138 (231)
T PRK12427        102 KTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYL  138 (231)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHhCCCHHHHHHHH
Confidence            3445567888889999999999999999988876554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	344
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-04

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

 Score = 40.6 bits (94), Expect = 7e-04
 Identities = 40/215 (18%), Positives = 70/215 (32%), Gaps = 51/215 (23%)

Query: 74  TVENDYSETEEIRQKSTSC--IGQDASSRSDF----RLLMENL-DVLESTFADSD---AL 123
            ++N  S    +         I  + +SRSD     +L + ++   L            L
Sbjct: 188 NLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCL 247

Query: 124 RLEREILQQLGKLGALKLFNSHLSRIVKTS---NVLD-LSDVHTEEQKMNDSRDYHMGKI 179
            L   +L  +    A   FN    +I+ T+    V D LS   T    ++     H    
Sbjct: 248 -L---VLLNVQNAKAWNAFNLS-CKILLTTRFKQVTDFLSAATTTHISLD-----HHSMT 297

Query: 180 LVPSKRKGKRKLKTARVSEESIETSLLSLPSEALQEGLKQPTIFSAERALNSRGRRLTIA 239
           L P +           +  + ++     LP E L      P      R L+     +   
Sbjct: 298 LTPDE--------VKSLLLKYLDCRPQDLPREVLTTN---P------RRLSIIAESI--- 337

Query: 240 RNEAEMSKGVQVVANLERIKTTLEKESGKAASLNC 274
           R+        + V N +++ T +E      +SLN 
Sbjct: 338 RDGLATWDNWKHV-NCDKLTTIIE------SSLNV 365

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	344
3ugo_A	245	RNA polymerase sigma factor; protein-DNA complex,	99.75
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	99.74
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	99.71
1sig_A	339	Sigma70, RNA polymerase primary sigma factor; RNA	98.29
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	97.83
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	97.01
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	96.98
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	95.62
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	95.42
3iyd_F	613	RNA polymerase sigma factor RPOD; transcription, i	94.42
2o7g_A	112	Probable RNA polymerase sigma-C factor; sigma fact	90.98
1h3l_A	87	RNA polymerase sigma factor; transcription, DNA-bi	87.87

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

Probab=99.75  E-value=3.9e-18  Score=157.26  Aligned_cols=116  Identities=19%  Similarity=0.184  Sum_probs=97.9

Q ss_pred             CchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHH-HHHHHH------H--HHH-----------------hCCCCc
Q 019233          218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANL-ERIKTT------L--EKE-----------------SGKAAS  271 (344)
Q Consensus       218 ~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~L-E~ir~~------L--ee~-----------------lGrePT  271 (344)
                      .||+..||+   +|+++||||++||++|+++|+.++.. +.+...      +  +..                 .+.+|+
T Consensus         6 ~d~~~~yl~---~i~~~~llt~~~e~~la~~i~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~g~~~~~~~~   82 (245)
T 3ugo_A            6 SDPVRQYLH---EIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPK   82 (245)
T ss_dssp             CHHHHHHHH---HHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHTTGGGCSCCCCTTCCCCCCHH
T ss_pred             CCcHHHHHH---HcccccCCCHHHHHHHHHHHHHHHHHHHHHHhccCCcHHHHHHhhhhhhhccchhcccccccccccch
Confidence            689999999   99999999999999999999998863 333221      1  000                 146899


Q ss_pred             hHHHHHHcCCCH----HHHHHHhhhhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          272 LNCWAQAAGVSE----RVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       272 ~~eWA~aaGld~----~eL~~~l~~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      ..+||.+.|++.    +.|.+....+..|+++||..|+++|.++|++|.+.+.+.+||+|||++||+++
T Consensus        83 ~~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~L~~~y~~lV~~ia~r~~~~~~~aeDLvQegfi~L~~a  151 (245)
T 3ugo_A           83 TVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRA  151 (245)
T ss_dssp             HHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHGGGTTSSSCHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHhhccchHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHcCCCCcHHHHHHHHHHHHHHH
Confidence            999999998853    45666677889999999999999999999999999999999999999999994

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

Probab=99.74  E-value=5.2e-18  Score=169.19  Aligned_cols=116  Identities=18%  Similarity=0.158  Sum_probs=97.8

Q ss_pred             CchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHH------------------HHHHHhCCCCchHHHHHH-
Q 019233          218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKT------------------TLEKESGKAASLNCWAQA-  278 (344)
Q Consensus       218 ~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~------------------~Lee~lGrePT~~eWA~a-  278 (344)
                      .|++..||+   +|+++||||++||++|+++|+.+..++....                  +.....++.|+..+|+.. 
T Consensus        93 ~d~~~~Yl~---ei~~~pLLt~eEE~~La~~i~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  169 (438)
T 1l9z_H           93 SDPVRQYLH---EIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPK  169 (438)
T ss_pred             CChHHHHHH---HhccCCCCCHHHHHHHHHHHHHhhhHHHHHHhhhccchhhhhhhhhhhhhhcccccccccccccccch
Confidence            578999999   9999999999999999999999865443221                  112235678888887532 


Q ss_pred             -----------cCCCHHHHHHHhhhhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          279 -----------AGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       279 -----------aGld~~eL~~~l~~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                                 .+++..+|...+..+..|+++||.+|+|+|++||++|.++|++++||||||+||||+|
T Consensus       170 ~~~~~~~~~~~~~~~~~eLi~~~~~d~~A~~~Li~~nlrlVv~iA~ry~~~g~~aeDLIQEg~IgL~kA  238 (438)
T 1l9z_H          170 TVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRA  238 (438)
T ss_pred             hhhhhhhhhhcccchHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence                       3556788888888889999999999999999999999999999999999999999995

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

Probab=99.71  E-value=5.5e-18  Score=167.12  Aligned_cols=117  Identities=19%  Similarity=0.190  Sum_probs=95.0

Q ss_pred             CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHH------------------HHHhCCCCchHHHH--
Q 019233          217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTL------------------EKESGKAASLNCWA--  276 (344)
Q Consensus       217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~L------------------ee~lGrePT~~eWA--  276 (344)
                      ..|++..||+   ++++.||||++||++|+++|+.+..+.......                  ....++.|+..+|+  
T Consensus        77 ~~d~~~~Yl~---ei~~~plLt~eEE~~La~ri~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (423)
T 2a6h_F           77 TSDPVRQYLH---EIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDP  153 (423)
T ss_dssp             THHHHHHHHH---HHHHCCCCTTHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHTTSCSSSCTT
T ss_pred             CCcHHHHHHH---HhcccCCCCHHHHHHHHHHHHhchhHHHHHHHhhccchhhhhhhHhhhhhhhhhcccccchhhhhhh
Confidence            3579999999   999999999999999999999986543321110                  11234567655543  


Q ss_pred             -------H---HcCCCHHHHHHHhhhhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          277 -------Q---AAGVSERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       277 -------~---aaGld~~eL~~~l~~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                             .   +++++..+|...+..+..|+++||.+|+|+|++||++|.++|++++||||||++|||+|
T Consensus       154 ~~~~~~~~~~~~~~~~~~~L~~~~~~d~~A~~~Li~~~lrlV~~iA~~y~~~~~~~eDLiQEg~igL~ka  223 (423)
T 2a6h_F          154 KTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRA  223 (423)
T ss_dssp             HHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTTCTTTSCHHHHHHHHHHHHHHH
T ss_pred             hhhhhhhhhhhcccccHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence                   2   34667788888888889999999999999999999999999999999999999999995

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

Probab=98.29  E-value=1.7e-06  Score=81.91  Aligned_cols=53  Identities=23%  Similarity=0.452  Sum_probs=46.6

Q ss_pred             HHHHHHhhhh-H---HHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          284 RVLKQHLAFG-W---YCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       284 ~eL~~~l~~g-~---~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      ..|..++..| .   .|.+.|+..|+++|.++|++|.+++...+||+|+|++||+++
T Consensus       250 ~~l~~~~~~gd~~~~~A~~~L~~~~~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a  306 (339)
T 1sig_A          250 KDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA  306 (339)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccccchhhhHHHHHHHHHHHHHHHHHHhcCCCCHhHHHHHHHHHHHHH
Confidence            3455555555 4   799999999999999999999999999999999999999994

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

Probab=97.83  E-value=9.2e-06  Score=83.38  Aligned_cols=54  Identities=22%  Similarity=0.430  Sum_probs=47.1

Q ss_pred             HHHHHHHhhhh-HHH---HHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          283 ERVLKQHLAFG-WYC---REELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       283 ~~eL~~~l~~g-~~A---RdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      ...|..++..| ..|   .++||..|+++|.++|++|.+++..++||+|+|++||+++
T Consensus       358 ~~~Li~~~~~Gd~~A~~A~~~L~~~y~~~v~~ia~r~~~~~~~aeDlvQE~fi~l~~a  415 (613)
T 3iyd_F          358 VKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA  415 (613)
T ss_dssp             HHHHHHTHHHHHHHHHHHHTTTTTTTTHHHHHGGGSSSTTSSCSTTTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence            35566666666 344   9999999999999999999999999999999999999994

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

Probab=97.01  E-value=0.0001  Score=63.27  Aligned_cols=44  Identities=23%  Similarity=0.268  Sum_probs=0.0

Q ss_pred             hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      +..+.+.|+..|.++|..+|.+|.+.....+||+|+|.++|+++
T Consensus        26 d~~a~~~l~~~~~~~v~~~~~~~~~~~~~aeDl~Qe~~l~l~~~   69 (243)
T 1l0o_C           26 DQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKS   69 (243)
T ss_dssp             --------------------------------------------
T ss_pred             CHHHHHHHHHHhHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHH
Confidence            36789999999999999999999999999999999999999984

>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=96.98  E-value=0.00069  Score=58.23  Aligned_cols=43  Identities=30%  Similarity=0.266  Sum_probs=39.5

Q ss_pred             HHHHHHHHHhchHHHHHHHHhcC---CCCCChhhHHHHHHHHHhhh
Q 019233          294 WYCREELIKSTRPLVLFLARNYR---GLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       294 ~~ARdrLI~sNLRLVvsIAKrY~---grGls~eDLIQEG~iGLmka  336 (344)
                      ..+.++|+..|.++|..+|++|.   +.+...+||+|+|.+||+++
T Consensus        11 ~~a~~~l~~~~~~~v~~~a~~~~~~~~~~~~aeDl~Qe~~l~l~~~   56 (239)
T 1rp3_A           11 QIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKA   56 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHH
Confidence            45799999999999999999998   67889999999999999984

>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=95.62  E-value=0.011  Score=49.43  Aligned_cols=52  Identities=17%  Similarity=0.048  Sum_probs=44.8

Q ss_pred             HHHHHHhhhh-HHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          284 RVLKQHLAFG-WYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       284 ~eL~~~l~~g-~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      .+|...+..| ..+-+.|+..+.+.|..+|.+|.+ ....+|++|++.+.+++.
T Consensus        11 ~~l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~~~-~~~aeDl~Qe~~l~~~~~   63 (194)
T 1or7_A           11 QVLVERVQKGDQKAFNLLVVRYQHKVASLVSRYVP-SGDVPDVVQEAFIKAYRA   63 (194)
T ss_dssp             HHHHHHHHTTCHHHHHHHHHHHHHHHHHHHTTTSC-GGGHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHcC-HHhHHHHHHHHHHHHHHh
Confidence            3455555444 789999999999999999999999 889999999999999983

>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=94.42  E-value=0.0041  Score=63.89  Aligned_cols=35  Identities=14%  Similarity=0.148  Sum_probs=14.7

Q ss_pred             CCchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHH
Q 019233          217 LKQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVAN  254 (344)
Q Consensus       217 ~~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~  254 (344)
                      .+||+.+|||   +|++.||||+++|++||++|..|.+
T Consensus        94 ~~dpvrmyl~---emg~~~ll~~~~e~~~ak~ie~g~~  128 (613)
T 3iyd_F           94 TTDPVRMYMR---EMGTVELLTREGEIDIAKRIEDGIN  128 (613)
T ss_dssp             --------------C--------CSSSTTTHHHHHHHH
T ss_pred             CCCcHHHHHH---HhcccccCCchhHHHHHHHHHHhHH
Confidence            5899999999   9999999999999999999998864

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

Probab=90.98  E-value=0.25  Score=38.42  Aligned_cols=49  Identities=20%  Similarity=-0.066  Sum_probs=41.4

Q ss_pred             HHHHhhh-hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          286 LKQHLAF-GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       286 L~~~l~~-g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      |...+.. ...+-+.|+..+.+.+..+|.++ +....-+|++|+..+.+.+
T Consensus        14 l~~~~~~gd~~a~~~l~~~~~~~l~~~~~~~-~~~~~aeD~vQe~fl~~~~   63 (112)
T 2o7g_A           14 LALSAAKGNGRALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIG   63 (112)
T ss_dssp             HHHHHHTTCHHHHHHHHHHHHHHHHHHHHHH-SCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHHHH
Confidence            3334443 46788999999999999999999 8778899999999999987

>1h3l_A RNA polymerase sigma factor; transcription, DNA-binding, transcription regulation; 2.37A {Streptomyces coelicolor A3} SCOP: a.177.1.1

Probab=87.87  E-value=0.34  Score=35.93  Aligned_cols=43  Identities=12%  Similarity=-0.219  Sum_probs=39.7

Q ss_pred             hHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhh
Q 019233          293 GWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAF  335 (344)
Q Consensus       293 g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmk  335 (344)
                      ...+-+.|+..+.+.+..+|.++.+....-+|++||..+.+.+
T Consensus        10 ~~~af~~l~~~~~~~l~~~~~~~~~~~~~aeD~vQe~fl~~~~   52 (87)
T 1h3l_A           10 RSARFERDALEFLDQMYSAALRMTRNPADAEDLVQETYAKAYA   52 (87)
T ss_dssp             HHHHHHHHHHHTHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Confidence            4678889999999999999999998888899999999999987

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	344
d1ku2a2	180	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	99.89
d1siga_	334	Sigma70 {Escherichia coli [TaxId: 562]}	99.39
d1rp3a3	87	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	98.88
d1rp3a1	77	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	96.93
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	96.84
d1ku2a1	60	Sigma factor SigA {Thermus aquaticus [TaxId: 271]}	95.91
d1or7a2	113	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	94.41
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	80.02

>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=99.89  E-value=6.7e-24  Score=183.14  Aligned_cols=116  Identities=19%  Similarity=0.189  Sum_probs=92.2

Q ss_pred             CchHHHHHHHhhcCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHH------------------HHhCCCCchHHHHHHc
Q 019233          218 KQPTIFSAERALNSRGRRLTIARNEAEMSKGVQVVANLERIKTTLE------------------KESGKAASLNCWAQAA  279 (344)
Q Consensus       218 ~dpl~~YLk~~~ei~~~~LLTaEEE~eLs~~Iq~l~~LE~ir~~Le------------------e~lGrePT~~eWA~aa  279 (344)
                      .||+..||+   +|+++||||++||++|+++|+.+..+.+...+..                  ...+..|...+|+...
T Consensus         1 tDpVr~YLr---eig~v~LLT~EEEieLAr~Ie~g~~~~~~~~e~~~~~~~l~~e~~~~~~~~~~~~~~~~~~~e~~~~~   77 (180)
T d1ku2a2           1 SDPVRQYLH---EIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPK   77 (180)
T ss_dssp             CHHHHHHHH---HHTTSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHTTCSSCCCTTSCCSSCTT
T ss_pred             CCcHHHHHH---HhcCcCCCCHHHHHHHHHHHHHHHHHHHHHHHhhhccHHHHHHHHHHHhhhHHHHhcchhhHHHhhHH
Confidence            489999999   9999999999999999999999887654432211                  0123445555554332


Q ss_pred             CC------------CHHHHHHHhhhhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          280 GV------------SERVLKQHLAFGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       280 Gl------------d~~eL~~~l~~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      .+            ..+.+.+....+..||++||.+|+|||++||++|.++|++++||||||+||||+|
T Consensus        78 ~~~~~~~~~~~~~~el~~l~~~~~~~~~a~~~li~~~~~lv~~~a~~~~~~~~~~~dl~q~g~~gl~~a  146 (180)
T d1ku2a2          78 TVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRA  146 (180)
T ss_dssp             THHHHHHHHHSCCHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHTTCSSSSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHHH
Confidence            22            2355667777889999999999999999999999999999999999999999995

>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=99.39  E-value=1.9e-13  Score=125.29  Aligned_cols=45  Identities=24%  Similarity=0.400  Sum_probs=42.9

Q ss_pred             hhHHHHHHHHHhchHHHHHHHHhcCCCCCChhhHHHHHHHHHhhh
Q 019233          292 FGWYCREELIKSTRPLVLFLARNYRGLGIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       292 ~g~~ARdrLI~sNLRLVvsIAKrY~grGls~eDLIQEG~iGLmka  336 (344)
                      ....||++||++|||||++||++|.++|++|+||||+|++|||+|
T Consensus       259 ~~~~ak~~~~~~~~~lv~~~~~~~~~~~~~~~dl~~~~~~~l~~~  303 (334)
T d1siga_         259 KARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA  303 (334)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHHTTSTTSSSCHHHHHHHHHHHHHHH
T ss_pred             hccchHHHHHHhHHHHHHHHHHhccCCCCCHHHHHHhhHHHHHHH
Confidence            347899999999999999999999999999999999999999996

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

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

Probab=98.88  E-value=6.7e-10  Score=86.54  Aligned_cols=43  Identities=30%  Similarity=0.277  Sum_probs=39.2

Q ss_pred             HHHHHHHHHhchHHHHHHHHhcCCC---CCChhhHHHHHHHHHhhh
Q 019233          294 WYCREELIKSTRPLVLFLARNYRGL---GIPFSDLLQVSRHALAFI  336 (344)
Q Consensus       294 ~~ARdrLI~sNLRLVvsIAKrY~gr---Gls~eDLIQEG~iGLmka  336 (344)
                      ...|++||..|++||.+||++|.++   +++++||+|+|++||++|
T Consensus         9 ~~~re~li~~~~~LV~~ia~~~~~~~~~~~e~eDL~q~G~igL~~A   54 (87)
T d1rp3a3           9 QIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKA   54 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSCTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhHHHHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHH
Confidence            4568999999999999999999765   899999999999999995

>d1rp3a1 a.4.13.1 (A:87-163) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma3 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.93  E-value=0.00092  Score=49.27  Aligned_cols=41  Identities=17%  Similarity=0.233  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhh
Q 019233          251 VVANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLA  291 (344)
Q Consensus       251 ~l~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~  291 (344)
                      ...+++++...|..++||+||.+|+|..+||+.+++.+.+.
T Consensus         8 ~~~ki~~a~~~L~~~lGR~Pt~~EiA~~lg~s~~e~~~~l~   48 (77)
T d1rp3a1           8 KERRIKEVVEKLKEKLGREPTDEEVAKELGISTEELFKTLD   48 (77)
T ss_dssp             HHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34467888999999999999999999999999988876654

>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=96.84  E-value=0.0014  Score=46.44  Aligned_cols=40  Identities=20%  Similarity=0.258  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhh
Q 019233          253 ANLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF  292 (344)
Q Consensus       253 ~~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~  292 (344)
                      .++.++..+|..++||+||.+|+|+++|++++++...+..
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            3466778899999999999999999999999988777654

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

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

Probab=95.91  E-value=0.0087  Score=42.88  Aligned_cols=41  Identities=24%  Similarity=0.383  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHHhCCCCchHHHHHHcC--CCHHHHHHHhh
Q 019233          251 VVANLERIKTTLEKESGKAASLNCWAQAAG--VSERVLKQHLA  291 (344)
Q Consensus       251 ~l~~LE~ir~~Lee~lGrePT~~eWA~aaG--ld~~eL~~~l~  291 (344)
                      ..-++.++..+|..++||+||.+|.|+++|  ++++.+...+.
T Consensus        10 ~i~rv~r~~~~l~qe~gRePt~eEiA~~l~~~l~~ekV~~~l~   52 (60)
T d1ku2a1          10 TINKLSRTARQLQQELGREPSYEEIAEAMGPGWDAKRVEETLK   52 (60)
T ss_dssp             HHHHHHHHHHHHHHHHTSCCCHHHHHHHHCSSCCHHHHHHHGG
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHCCCCCHHHHHHHHH
Confidence            344566778899999999999999999997  45666666554

>d1bl0a1 a.4.1.8 (A:9-62) MarA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: MarA
species: Escherichia coli [TaxId: 562]

Probab=80.02  E-value=0.98  Score=29.93  Aligned_cols=39  Identities=18%  Similarity=0.176  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHhCCCCchHHHHHHcCCCHHHHHHHhhh
Q 019233          254 NLERIKTTLEKESGKAASLNCWAQAAGVSERVLKQHLAF  292 (344)
Q Consensus       254 ~LE~ir~~Lee~lGrePT~~eWA~aaGld~~eL~~~l~~  292 (344)
                      .++++..-+++....++|.+++|+.+|++...+.+..+.
T Consensus         4 ~i~~v~~yI~~~~~~~~tl~~lA~~~~~s~~~l~r~Fk~   42 (54)
T d1bl0a1           4 TIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK   42 (54)
T ss_dssp             HHHHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            355666777888899999999999999999888776654