Citrus Sinensis ID: 041600

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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
Protein Sequence
FCKKSIENVKEYLVQYCEERKQAGFMMLPDPLSDFYEAVCVGLVLDDNLTTDDYSQPPMTNSVQRERTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRLRSNDAEERANAQIEIQRLQEEMAAACAGLTR
Secondary Structure (PSIPRED)
cccccHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHcccccHHHHHHHccccHHHHHHHHHHHccccccccHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHHHccccc
Secondary Structure Prediction (SSPRO)
cccccHHHHHHHHHHHHHHHHHcccEEccccHHHHHHHHHccccccccccccccccccccccccccccccEcHHHHHHHHcccHHHHHHHccccHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHccccc
Coil and Loop (DISEMBL)
FCKKSIENVKEYLVQYCEERKQagfmmlpdplsdfYEAVCVGLVlddnlttddysqppmtnsvqrertgkltlRDLMIYFHLPIEEAARRMKLCPTVVKKicrrdglhrwphrkIKSIQRRMSVasgrlrsndAEERANAQIEIQRLQEEMAAACAGLTR
Flexible Loop (DISEMBL)
fckksienVKEYLVQYCEERKQAGFMMLPDPLSDFYEAVCVGLVLDDNLTtddysqppmtnsvqrertgkltLRDLMIYFHLPIEEAARRMKLCPTVVKkicrrdglhrwphrkiksiqrrmsvasgrlrsndaeeRANAQIEIQRLQEEMAAACAGLTR
Low Complexity Region (SEG)
FCKKSIENVKEYLVQYCEERKQAGFMMLPDPLSDFYEAVCVGLVLDDNLTTDDYSQPPMTNSVQRERTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRLRSNDAEERANAQIEIQRLQEEMAAACAGLTR
Disordered region (IsUnstruct)
*******NVKEYLVQYCEERKQAGFMMLPDPLSDFYEAVCVGLVLDDNLTT*****************GKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIK********************************************
Disordered Region (DISOPRED)
**********EYLVQYCEER******************************************************DLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPH*****************************************ACAG***
Disordered Region (DISEMBL)
FCKKSIENVKEYLVQYCEERKQAGFMMLPDPLSDFYEAVCVGLVLDDNLTTDDYSQPPMTNSVQRERTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRLRSNDAEERANAQIEIQRLQEEMA********
Disordered Region (DISPRO)
*CKKSIENVKEYLVQYCEERKQAGFMMLPDPLSDFYEAVCVGLVLD**********************GKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRLRSNDAEERANAQIEIQRLQEEMAAACAGLT*
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
FCKKSIENVKEYLVQYCEERKQAGFMMLPDPLSDFYEAVCVGLVLDDNLTTDDYSQPPMTNSVQRERTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRLxxxxxxxxxxxxxxxxxxxxxxxxxxxxLTR
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	160	2.2.26 [Sep-21-2011]
Q10S83	942	Protein NLP1 OS=Oryza sat	no	no	0.362	0.061	0.423	2e-08
O81791	370	Protein RKD5 OS=Arabidops	yes	no	0.312	0.135	0.54	2e-08
Q5NB82	938	Protein NLP3 OS=Oryza sat	no	no	0.418	0.071	0.376	3e-08
Q9M9U9	269	Protein RKD1 OS=Arabidops	no	no	0.331	0.197	0.433	4e-08
Q84TH9	959	Protein NLP7 OS=Arabidops	no	no	0.331	0.055	0.415	4e-08
Q0JC27	936	Protein NLP2 OS=Oryza sat	no	no	0.643	0.110	0.298	4e-08
Q8RWY4	841	Protein NLP6 OS=Arabidops	no	no	0.375	0.071	0.393	7e-08
Q9M1B0	894	Protein NLP9 OS=Arabidops	no	no	0.331	0.059	0.396	7e-08
Q9SFW8	808	Protein NLP5 OS=Arabidops	no	no	0.506	0.100	0.341	2e-07
Q9LE38	844	Protein NLP4 OS=Arabidops	no	no	0.325	0.061	0.423	2e-07

>sp|Q10S83|NLP1_ORYSJ Protein NLP1 OS=Oryza sativa subsp. japonica GN=NLP1 PE=2 SV=1

 Score = 58.5 bits (140), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 42/59 (71%), Gaps = 1/59 (1%)

Query: 65  RERTGK-LTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM 122
           R +T K ++L+DL  +F   ++EAA+ + +CPT +K+ICR+ G++RWP RKIK +   +
Sbjct: 616 RTKTEKTVSLQDLRKHFAGSLKEAAKNLGVCPTTLKRICRQHGINRWPSRKIKKVGHSL 674

Probable transcription factor.
Oryza sativa subsp. japonica (taxid: 39947)

>sp|O81791|RKD5_ARATH Protein RKD5 OS=Arabidopsis thaliana GN=RKD5 PE=3 SV=1

 Score = 58.2 bits (139), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 27/50 (54%), Positives = 36/50 (72%)

Query: 69  GKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI 118
            +L+L +L  YF L I EA+R +K+  TV+KK CR  G+ RWPHRKIKS+
Sbjct: 240 AELSLEELSKYFDLTIVEASRNLKVGLTVLKKKCREFGIPRWPHRKIKSL 289

Putative transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q5NB82|NLP3_ORYSJ Protein NLP3 OS=Oryza sativa subsp. japonica GN=NLP3 PE=3 SV=1

 Score = 57.8 bits (138), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 26/69 (37%), Positives = 43/69 (62%), Gaps = 2/69 (2%)

Query: 55  SQPPMTNSVQRERTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRK 114
           ++PP     + E+T  ++L  L  YF   ++ AA+ + +CPT +K+ICR+ G+ RWP RK
Sbjct: 585 NKPPERRRGKAEKT--ISLDVLQQYFSGSLKNAAKSLGVCPTTMKRICRQHGISRWPSRK 642

Query: 115 IKSIQRRMS 123
           I  + R +S
Sbjct: 643 INKVNRSLS 651

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9M9U9|RKD1_ARATH Protein RKD1 OS=Arabidopsis thaliana GN=RKD1 PE=3 SV=1

 Score = 57.4 bits (137), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 23/53 (43%), Positives = 38/53 (71%)

Query: 71  LTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123
           L+   + +YF++PI +AAR + +  T++KK CR  G+ RWPHRK+ S+Q+ +S
Sbjct: 128 LSKETISLYFYMPITQAARELNIGLTLLKKRCRELGIKRWPHRKLMSLQKLIS 180

Putative transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q84TH9|NLP7_ARATH Protein NLP7 OS=Arabidopsis thaliana GN=NLP7 PE=1 SV=2

 Score = 57.0 bits (136), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 22/53 (41%), Positives = 37/53 (69%)

Query: 71  LTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123
           ++L  L  YF   +++AA+ + +CPT +K+ICR+ G+ RWP RKIK + R ++
Sbjct: 592 ISLDVLQQYFTGSLKDAAKSLGVCPTTMKRICRQHGISRWPSRKIKKVNRSIT 644

Transcription factor involved in regulation of nitrate assimilation and in transduction of the nitrate signal.

Arabidopsis thaliana (taxid: 3702)

>sp|Q0JC27|NLP2_ORYSJ Protein NLP2 OS=Oryza sativa subsp. japonica GN=NLP2 PE=2 SV=2

 Score = 57.0 bits (136), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 34/114 (29%), Positives = 58/114 (50%), Gaps = 11/114 (9%)

Query: 56  QPPMTNSVQRERTG---KLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPH 112
           QP      +++R+     ++L  L  YF   +++AA+ + +CPT +K+ICR  G+ RWP 
Sbjct: 550 QPSSIGHAEKKRSTAEKNISLDVLRKYFSGSLKDAAKSLGVCPTTLKRICRHHGISRWPS 609

Query: 113 RKI-------KSIQRRMSVASGRLRSNDAEERANAQIEIQRLQEEMA-AACAGL 158
           RKI       K IQ  ++   G  RS   +    + + +  L E++   +C GL
Sbjct: 610 RKINKVNRSLKKIQTVINSVHGVDRSLQYDPATGSLVPVVSLPEKLTFPSCDGL 663

Probable transcription factor.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q8RWY4|NLP6_ARATH Protein NLP6 OS=Arabidopsis thaliana GN=NLP6 PE=2 SV=2

 Score = 56.6 bits (135), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 41/61 (67%), Gaps = 1/61 (1%)

Query: 64  QRERTGK-LTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM 122
           +R +T K ++L  L  YF   +++AA+ + +CPT +K+ICR+ G+ RWP RKI  + R +
Sbjct: 549 KRGKTEKTISLEVLQQYFAGSLKDAAKSLGVCPTTMKRICRQHGISRWPSRKINKVNRSL 608

Query: 123 S 123
           +
Sbjct: 609 T 609

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M1B0|NLP9_ARATH Protein NLP9 OS=Arabidopsis thaliana GN=NLP9 PE=2 SV=1

 Score = 56.6 bits (135), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 21/53 (39%), Positives = 35/53 (66%)

Query: 70  KLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM 122
            ++L  L  YF   +++AA+ + +CPT +K+ICR+ G+ RWP RKI  + R +
Sbjct: 535 NVSLNVLQQYFSGSLKDAAKSLGVCPTTLKRICRQHGIMRWPSRKINKVNRSL 587

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SFW8|NLP5_ARATH Protein NLP5 OS=Arabidopsis thaliana GN=NLP5 PE=2 SV=1

 Score = 55.1 bits (131), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 47/82 (57%), Gaps = 1/82 (1%)

Query: 42  GLVLDDNLTTDDYSQPPMTNSVQRERTGK-LTLRDLMIYFHLPIEEAARRMKLCPTVVKK 100
           G+ +++N T    S        +R +  K +TL  L  YF   +++AA+ + +CPT +K+
Sbjct: 520 GVSVNENNTFSSASGFNRVTEKKRTKAEKNITLDVLRQYFAGSLKDAAKSIGVCPTTLKR 579

Query: 101 ICRRDGLHRWPHRKIKSIQRRM 122
           ICR+ G+ RWP RKIK +   +
Sbjct: 580 ICRQHGIQRWPSRKIKKVGHSL 601

Probable transcription factor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LE38|NLP4_ARATH Protein NLP4 OS=Arabidopsis thaliana GN=NLP4 PE=2 SV=1

 Score = 55.1 bits (131), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 22/52 (42%), Positives = 35/52 (67%)

Query: 71  LTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM 122
           +TL  L  YF   +++AA+ + +CPT +K+ICR+ G+ RWP RKIK +   +
Sbjct: 559 ITLDVLRQYFAGSLKDAAKNIGVCPTTLKRICRQHGIQRWPSRKIKKVGHSL 610

Probable transcription factor.

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	160
343887306	354	hypothetical protein [Citrus unshiu]	1.0	0.451	0.868	1e-85
224088770	381	predicted protein [Populus trichocarpa]	0.856	0.359	0.508	4e-40
357465807	498	RWP-RK domain-containing protein [Medica	0.981	0.315	0.420	1e-33
255550129	309	conserved hypothetical protein [Ricinus	0.743	0.385	0.496	3e-29
449447161	91	PREDICTED: protein RKD3-like [Cucumis sa	0.556	0.978	0.584	7e-23
168001367	539	predicted protein [Physcomitrella patens	0.862	0.256	0.405	9e-23
147797619	324	hypothetical protein VITISV_002228 [Viti	0.818	0.404	0.4	1e-21
90657580	89	hypothetical protein [Cleome spinosa]	0.456	0.820	0.636	3e-20
168064185	612	predicted protein [Physcomitrella patens	0.425	0.111	0.529	3e-15
302803869	65	hypothetical protein SELMODRAFT_118783 [	0.343	0.846	0.618	5e-14

>gi|343887306|dbj|BAK61852.1| hypothetical protein [Citrus unshiu]

 Score =  320 bits (821), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 159/183 (86%), Positives = 159/183 (86%), Gaps = 23/183 (12%)

Query: 1   FCKKSIENVKEYLVQYCEERKQAGFMMLPDPLSDFYEAVCVGLVLDDNLTTDDYSQPPMT 60
           FCKKSIENVKEYLVQYCEERKQAGFMMLPDPLSDFYEAVCVGLVLDDNLTTDDYSQPPMT
Sbjct: 172 FCKKSIENVKEYLVQYCEERKQAGFMMLPDPLSDFYEAVCVGLVLDDNLTTDDYSQPPMT 231

Query: 61  NS-----------------------VQRERTGKLTLRDLMIYFHLPIEEAARRMKLCPTV 97
           NS                        QRERTGKLTLRDLMIYFHLPIEEAARRMKLCPTV
Sbjct: 232 NSGENEMHQPDMENEAERTTRTSLSAQRERTGKLTLRDLMIYFHLPIEEAARRMKLCPTV 291

Query: 98  VKKICRRDGLHRWPHRKIKSIQRRMSVASGRLRSNDAEERANAQIEIQRLQEEMAAACAG 157
           VKKICRRDGLHRWPHRKIKSIQRRMSVASGRLRSNDAEERANAQIEIQRLQEEMAAACAG
Sbjct: 292 VKKICRRDGLHRWPHRKIKSIQRRMSVASGRLRSNDAEERANAQIEIQRLQEEMAAACAG 351

Query: 158 LTR 160
           LTR
Sbjct: 352 LTR 354

Source: Citrus unshiu

Species: Citrus unshiu

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224088770|ref|XP_002308532.1| predicted protein [Populus trichocarpa] gi|222854508|gb|EEE92055.1| predicted protein [Populus trichocarpa]

 Score =  169 bits (427), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 86/169 (50%), Positives = 107/169 (63%), Gaps = 32/169 (18%)

Query: 1   FCKKSIENVKEYLVQYCEERKQAGFMMLPDPLSDFYEAVCVGLVLDDNLTTDDYSQPPMT 60
           FCKKS+ENVKE+L +YC++R+QAGF+M+ DP S FYEA+CVG    D+L  D++  P   
Sbjct: 203 FCKKSLENVKEFLQKYCDDRRQAGFIMVQDPHSFFYEALCVGYEWTDDLHFDEFHDPSPP 262

Query: 61  NS--------------------------------VQRERTGKLTLRDLMIYFHLPIEEAA 88
           NS                                +QRER G+LTL D   YFHLPIE+AA
Sbjct: 263 NSDLQAGTLTGERQATNHGEGEIETERTTRSNLALQRERAGRLTLDDFRQYFHLPIEDAA 322

Query: 89  RRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRLRSNDAEER 137
           RR+ LCPTVVKKICR+ G+ RWPHRKIKSI R+++     L SNDAEER
Sbjct: 323 RRLHLCPTVVKKICRKFGMTRWPHRKIKSIHRQLTDLQVLLNSNDAEER 371

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357465807|ref|XP_003603188.1| RWP-RK domain-containing protein [Medicago truncatula] gi|355492236|gb|AES73439.1| RWP-RK domain-containing protein [Medicago truncatula]

 Score =  147 bits (372), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 74/176 (42%), Positives = 107/176 (60%), Gaps = 19/176 (10%)

Query: 1   FCKKSIENVKEYLVQYCEERKQAGFMMLPDPLSDFYEAVCVGL----------VLDDNLT 50
           FC KS+  +K +L QYC ER  AG++++ DP+S+FYE +C GL          ++ +N  
Sbjct: 308 FCGKSLGEIKIFLAQYCVERHLAGYILMQDPMSEFYETLCTGLDWFSDINMDGLIQNNSD 367

Query: 51  TDDYSQPPMTN-------SVQRERTGKLTLRDLMIYFHLPIEEAA--RRMKLCPTVVKKI 101
             +  Q  M +       S QR+++ KL L DL  YFHLPI+EAA   ++KLCPTV+KK 
Sbjct: 368 EVEQEQEQMGDNGTLRNLSEQRKKSAKLKLSDLCDYFHLPIDEAADHEKVKLCPTVLKKT 427

Query: 102 CRRDGLHRWPHRKIKSIQRRMSVASGRLRSNDAEERANAQIEIQRLQEEMAAACAG 157
           CR+ GL RWPHRK+KS+ +++ + + +    D E RA  + EI+ LQ EM   C G
Sbjct: 428 CRKAGLPRWPHRKVKSLLKQIKLLAKQWEGQDPEARARTEREIKSLQTEMIKHCGG 483

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255550129|ref|XP_002516115.1| conserved hypothetical protein [Ricinus communis] gi|223544601|gb|EEF46117.1| conserved hypothetical protein [Ricinus communis]

 Score =  132 bits (333), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 70/141 (49%), Positives = 91/141 (64%), Gaps = 22/141 (15%)

Query: 38  AVCVGLVLDDNLTTDDYSQPPMTN----------------------SVQRERTGKLTLRD 75
           A+ VG+  ++NL  DD   P  ++                      + QRERTGKLTL+D
Sbjct: 165 ALSVGIEWEENLDNDDIFDPSPSSWARQWDLTGGGNDAERVMKTALAQQRERTGKLTLKD 224

Query: 76  LMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRLRSNDAE 135
              YF LPIEEAA+RM LCPTVVKKICRR G++RWPHRKIKS++R+M+     +RSN++E
Sbjct: 225 FTAYFDLPIEEAAKRMSLCPTVVKKICRRYGMNRWPHRKIKSMRRQMAKIRHFVRSNNSE 284

Query: 136 ERANAQIEIQRLQEEMAAACA 156
           E+A A  EIQRLQ+E+A  C 
Sbjct: 285 EKARALAEIQRLQQEIANICT 305

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449447161|ref|XP_004141337.1| PREDICTED: protein RKD3-like [Cucumis sativus] gi|449486703|ref|XP_004157374.1| PREDICTED: protein RKD3-like [Cucumis sativus]

 Score =  112 bits (279), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 52/89 (58%), Positives = 66/89 (74%)

Query: 71  LTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRLR 130
           +T+ DL  Y HLPI EAA++M LC TVVKKICRR GL RWP+RK+KS QR+M     RLR
Sbjct: 1   MTVNDLKEYLHLPISEAAKKMNLCLTVVKKICRRSGLRRWPYRKVKSYQRKMGALGTRLR 60

Query: 131 SNDAEERANAQIEIQRLQEEMAAACAGLT 159
           S DA  RA A+ E++RL++E+A  CAG+ 
Sbjct: 61  SRDAGTRARAEAEMERLRQELAQFCAGIV 89

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168001367|ref|XP_001753386.1| predicted protein [Physcomitrella patens subsp. patens] gi|162695265|gb|EDQ81609.1| predicted protein [Physcomitrella patens subsp. patens]

 Score =  111 bits (278), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 64/158 (40%), Positives = 93/158 (58%), Gaps = 20/158 (12%)

Query: 21  KQAGFMMLPDPL---SDFYEAVCV---GLVLDDNL-------TTDDY------SQPPMTN 61
           K  G ++LPD L   SDF ++ C    G +  + L       +TD+       ++PP +N
Sbjct: 378 KSMGHIILPDVLCTSSDFSKSGCAYGKGGLGQNKLHHCGSIDSTDNADMTIGPAKPPKSN 437

Query: 62  SV-QRERTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQR 120
           +  QRERTGKL + DL  +FHLPI  AA+ + +CPTV+KKICRR+G+ RWPHRKIKSI+R
Sbjct: 438 AAAQRERTGKLKMTDLAQHFHLPINAAAKELGICPTVLKKICRRNGMRRWPHRKIKSIER 497

Query: 121 RMSVASGRLRSNDAEERANAQIEIQRLQEEMAAACAGL 158
            ++     +     +   + ++EI  L+ E A  CAG 
Sbjct: 498 IIATLEQTIAEGAGQGDESIRMEIAMLRNERAQLCAGF 535

Source: Physcomitrella patens subsp. patens

Species: Physcomitrella patens

Genus: Physcomitrella

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147797619|emb|CAN62943.1| hypothetical protein VITISV_002228 [Vitis vinifera]

 Score =  107 bits (268), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 64/160 (40%), Positives = 88/160 (55%), Gaps = 29/160 (18%)

Query: 1   FCKKSIENVKEYLVQYCEERKQAGFMMLPDPLSDFYEAVCVGLVLDDNLTTDDYSQ--PP 58
           FCKKSIE VK++L QYC+ER+QAGF ML DPLS FYEA+CVGL  ++++  D++ Q  P 
Sbjct: 180 FCKKSIEGVKQFLQQYCKERRQAGFAMLKDPLSLFYEAICVGLDYEESMNADEFFQRSPS 239

Query: 59  MTNSVQRERTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI 118
            +   Q            + +     E  + R +  P                  ++KSI
Sbjct: 240 HSGGCQ------------INHPETEAENRSERTQKIPLAA---------------QVKSI 272

Query: 119 QRRMSVASGRLRSNDAEERANAQIEIQRLQEEMAAACAGL 158
           QR+M      LRS DA ERA AQ E++RL++EM  AC G+
Sbjct: 273 QRQMVRLKPSLRSKDAAERARAQTEMERLKQEMTNACGGI 312

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|90657580|gb|ABD96880.1| hypothetical protein [Cleome spinosa]

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 49/77 (63%), Positives = 60/77 (77%), Gaps = 4/77 (5%)

Query: 64  QRERTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123
           QRERTG+LTL+D+  YFHLP+EEAAR MK+CPTVVKKICRR GL RWPHRKI+SI+R++S
Sbjct: 15  QRERTGRLTLKDIGKYFHLPVEEAARIMKVCPTVVKKICRRGGLARWPHRKIRSIERKIS 74

Query: 124 VASGRLRSNDAEERANA 140
               + +S   E R   
Sbjct: 75  ----KWKSVGQESRGKG 87

Source: Cleome spinosa

Species: Cleome spinosa

Genus: Cleome

Family: Cleomaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168064185|ref|XP_001784045.1| predicted protein [Physcomitrella patens subsp. patens] gi|162664431|gb|EDQ51151.1| predicted protein [Physcomitrella patens subsp. patens]

 Score = 86.7 bits (213), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 36/68 (52%), Positives = 49/68 (72%)

Query: 62  SVQRERTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRR 121
           + QRERTGKL + DL  +FHLPI  AA+ + +CPTV+KKICRR+G+ RWPHRK+  +   
Sbjct: 461 AAQRERTGKLKMIDLAQHFHLPINAAAKELGICPTVLKKICRRNGMRRWPHRKVGVLFNM 520

Query: 122 MSVASGRL 129
             ++SG  
Sbjct: 521 NYLSSGAF 528

Source: Physcomitrella patens subsp. patens

Species: Physcomitrella patens

Genus: Physcomitrella

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|302803869|ref|XP_002983687.1| hypothetical protein SELMODRAFT_118783 [Selaginella moellendorffii] gi|302814670|ref|XP_002989018.1| hypothetical protein SELMODRAFT_129268 [Selaginella moellendorffii] gi|300143119|gb|EFJ09812.1| hypothetical protein SELMODRAFT_129268 [Selaginella moellendorffii] gi|300148524|gb|EFJ15183.1| hypothetical protein SELMODRAFT_118783 [Selaginella moellendorffii]

 Score = 82.4 bits (202), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 34/55 (61%), Positives = 44/55 (80%)

Query: 64  QRERTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI 118
           QRERTGKL + DL  +FHLPI  AA+ + +CPTV+KKICRR+G+ RWPHRK+  +
Sbjct: 1   QRERTGKLKMSDLAQHFHLPINAAAKELGICPTVLKKICRRNGMRRWPHRKVSDV 55

Source: Selaginella moellendorffii

Species: Selaginella moellendorffii

Genus: Selaginella

Family: Selaginellaceae

Order: Selaginellales

Class: Isoetopsida

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	160
DICTYBASE|DDB_G0274295	548	DDB_G0274295 "RWP-RK domain-co	0.512	0.149	0.397	1.1e-11
TAIR|locus:2035000	269	RKD1 "RWP-RK domain containing	0.493	0.293	0.345	1.9e-09
TAIR|locus:2127908	370	RKD5 "RWP-RK domain-containing	0.506	0.218	0.390	7.5e-09
TAIR|locus:2168412	256	RKD4 "RWP-RK domain-containing	0.356	0.222	0.403	1.8e-08
TAIR|locus:2059692	909	AT2G17150 [Arabidopsis thalian	0.343	0.060	0.428	6.8e-08
TAIR|locus:2019424	841	AT1G64530 [Arabidopsis thalian	0.568	0.108	0.340	9.2e-08
TAIR|locus:2134941	959	NLP7 "NIN like protein 7" [Ara	0.375	0.062	0.409	1.4e-07
TAIR|locus:2014624	808	AT1G76350 [Arabidopsis thalian	0.481	0.095	0.358	1.4e-07
TAIR|locus:2030397	844	AT1G20640 [Arabidopsis thalian	0.462	0.087	0.346	1.5e-07
TAIR|locus:2019175	298	RKD2 "RWP-RK domain containing	0.443	0.238	0.356	3.4e-07

DICTYBASE|DDB_G0274295 DDB_G0274295 "RWP-RK domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 168 (64.2 bits), Expect = 1.1e-11, P = 1.1e-11
 Identities = 33/83 (39%), Positives = 51/83 (61%)

Query:    68 TGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASG 127
             T ++ L  L  YFH+PI   A+ + +C TV+KK+CRR+G+ RWPHRKIKS+ + +S    
Sbjct:     5 TLEIDLEYLSKYFHMPINSVAKEIGVCATVLKKVCRRNGIPRWPHRKIKSLDKMISNLEN 64

Query:   128 RLRSNDAEERANAQIEIQRLQEE 150
              +     EE    Q EI  ++++
Sbjct:    65 -MTPKTKEEEIKIQNEIAIIKKK 86

GO:0005615 "extracellular space" evidence=IDA

TAIR|locus:2035000 RKD1 "RWP-RK domain containing 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 141 (54.7 bits), Expect = 1.9e-09, P = 1.9e-09
 Identities = 28/81 (34%), Positives = 51/81 (62%)

Query:    71 LTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRLR 130
             L+   + +YF++PI +AAR + +  T++KK CR  G+ RWPHRK+ S+Q+ +S     L 
Sbjct:   128 LSKETISLYFYMPITQAARELNIGLTLLKKRCRELGIKRWPHRKLMSLQKLISNVK-ELE 186

Query:   131 SNDAEERANA-QIEIQRLQEE 150
               + EE  +  +  +++L++E
Sbjct:   187 KMEGEENEDKLRNALEKLEKE 207

GO:0005634 "nucleus" evidence=ISM

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

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

GO:0051302 "regulation of cell division" evidence=IMP

TAIR|locus:2127908 RKD5 "RWP-RK domain-containing 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 139 (54.0 bits), Expect = 7.5e-09, P = 7.5e-09
 Identities = 32/82 (39%), Positives = 48/82 (58%)

Query:    70 KLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRL 129
             +L+L +L  YF L I EA+R +K+  TV+KK CR  G+ RWPHRKIKS+   +     R 
Sbjct:   241 ELSLEELSKYFDLTIVEASRNLKVGLTVLKKKCREFGIPRWPHRKIKSLDCLIHDLQ-RE 299

Query:   130 RSNDAEERANAQIEIQRLQEEM 151
                  E+   A + + + QE++
Sbjct:   300 AEKQQEKNEAAAMAVAKKQEKL 321

GO:0005634 "nucleus" evidence=ISM

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

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

TAIR|locus:2168412 RKD4 "RWP-RK domain-containing 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 132 (51.5 bits), Expect = 1.8e-08, P = 1.8e-08
 Identities = 23/57 (40%), Positives = 41/57 (71%)

Query:    62 SVQRERTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI 118
             +++++R  KL + ++  +F  PI +AA+ + +  TV+KK CR  G++RWPHRK+KS+
Sbjct:   139 NLKKKRQDKLEMSEIKQFFDRPIMKAAKELNVGLTVLKKRCRELGIYRWPHRKLKSL 195

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009790 "embryo development" evidence=IMP

TAIR|locus:2059692 AT2G17150 [Arabidopsis thaliana (taxid:3702)]

 Score = 124 (48.7 bits), Expect = 6.8e-08, Sum P(2) = 6.8e-08
 Identities = 24/56 (42%), Positives = 38/56 (67%)

Query:    64 QRERTGK-LTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI 118
             +R +T K + L  L  YF   +++AA+ + +CPT +K+ICR+ G+ RWP RKIK +
Sbjct:   601 KRAKTEKTIGLEVLRQYFAGSLKDAAKSIGVCPTTLKRICRQHGIMRWPSRKIKKV 656

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2019424 AT1G64530 [Arabidopsis thaliana (taxid:3702)]

 Score = 134 (52.2 bits), Expect = 9.2e-08, P = 9.2e-08
 Identities = 32/94 (34%), Positives = 52/94 (55%)

Query:    33 SDFYEAVCVGLVLDDNLTTDDYSQPPMTNSVQRER--TGK-LTLRDLMIYFHLPIEEAAR 89
             SDF E   V   ++   T D   +       +R+R  T K ++L  L  YF   +++AA+
Sbjct:   516 SDFMENNEVDDGVERFQTLDPIPEAKTVKKSERKRGKTEKTISLEVLQQYFAGSLKDAAK 575

Query:    90 RMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS 123
              + +CPT +K+ICR+ G+ RWP RKI  + R ++
Sbjct:   576 SLGVCPTTMKRICRQHGISRWPSRKINKVNRSLT 609

GO:0005634 "nucleus" evidence=ISM

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

TAIR|locus:2134941 NLP7 "NIN like protein 7" [Arabidopsis thaliana (taxid:3702)]

 Score = 133 (51.9 bits), Expect = 1.4e-07, P = 1.4e-07
 Identities = 25/61 (40%), Positives = 42/61 (68%)

Query:    64 QRERTGK-LTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM 122
             +R +T K ++L  L  YF   +++AA+ + +CPT +K+ICR+ G+ RWP RKIK + R +
Sbjct:   584 KRGKTEKTISLDVLQQYFTGSLKDAAKSLGVCPTTMKRICRQHGISRWPSRKIKKVNRSI 643

Query:   123 S 123
             +
Sbjct:   644 T 644

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009414 "response to water deprivation" evidence=IMP

GO:0010118 "stomatal movement" evidence=IMP

GO:0010167 "response to nitrate" evidence=IMP

GO:0042128 "nitrate assimilation" evidence=IMP

TAIR|locus:2014624 AT1G76350 [Arabidopsis thaliana (taxid:3702)]

 Score = 132 (51.5 bits), Expect = 1.4e-07, P = 1.4e-07
 Identities = 28/78 (35%), Positives = 46/78 (58%)

Query:    42 GLVLDDNLTTDDYSQPPMTNSVQRERTGK-LTLRDLMIYFHLPIEEAARRMKLCPTVVKK 100
             G+ +++N T    S        +R +  K +TL  L  YF   +++AA+ + +CPT +K+
Sbjct:   520 GVSVNENNTFSSASGFNRVTEKKRTKAEKNITLDVLRQYFAGSLKDAAKSIGVCPTTLKR 579

Query:   101 ICRRDGLHRWPHRKIKSI 118
             ICR+ G+ RWP RKIK +
Sbjct:   580 ICRQHGIQRWPSRKIKKV 597

GO:0005634 "nucleus" evidence=ISM

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

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

TAIR|locus:2030397 AT1G20640 [Arabidopsis thaliana (taxid:3702)]

 Score = 132 (51.5 bits), Expect = 1.5e-07, P = 1.5e-07
 Identities = 27/78 (34%), Positives = 47/78 (60%)

Query:    45 LDDNLT-TDDYSQPPMTNSVQRERTGK---LTLRDLMIYFHLPIEEAARRMKLCPTVVKK 100
             +D N+  +  +S    +   +++RT     +TL  L  YF   +++AA+ + +CPT +K+
Sbjct:   529 MDSNVNESSTFSSGGFSMMAEKKRTKADKTITLDVLRQYFAGSLKDAAKNIGVCPTTLKR 588

Query:   101 ICRRDGLHRWPHRKIKSI 118
             ICR+ G+ RWP RKIK +
Sbjct:   589 ICRQHGIQRWPSRKIKKV 606

GO:0005634 "nucleus" evidence=ISM

GO:0009877 "nodulation" evidence=ISS

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

TAIR|locus:2019175 RKD2 "RWP-RK domain containing 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 122 (48.0 bits), Expect = 3.4e-07, P = 3.4e-07
 Identities = 26/73 (35%), Positives = 44/73 (60%)

Query:    79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRLRSNDAEERA 138
             YF++PI +AA  + +  T++K+ CR  G+ RWPHRK+ S+   +S     L+  + EE A
Sbjct:   143 YFYMPITQAAIALNVGLTLLKRRCRELGIRRWPHRKLMSLNTLISNVK-ELQKMEGEENA 201

Query:   139 NA-QIEIQRLQEE 150
                Q  ++ L++E
Sbjct:   202 EKLQDALEMLEKE 214

GO:0005634 "nucleus" evidence=ISM

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

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

---

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

Your Input: fgenesh4_pg.C_LG_VI001512 hypothetical protein (381 aa) (Populus trichocarpa)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	160
pfam02042	52	pfam02042, RWP-RK, RWP-RK domain	2e-23

>gnl|CDD|190197 pfam02042, RWP-RK, RWP-RK domain

 Score = 86.5 bits (215), Expect = 2e-23
 Identities = 30/52 (57%), Positives = 41/52 (78%)

Query: 67  RTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI 118
            T +LTL DL  YFHLPI++AA+ + +  TV+K+ICR+ G+ RWPHRKIKS+
Sbjct: 1   ATKELTLEDLSKYFHLPIKDAAKELGVGLTVLKRICRQLGIPRWPHRKIKSL 52

This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development. Length = 52

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	160
PF02042	52	RWP-RK: RWP-RK domain; InterPro: IPR003035 This do	99.95
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	96.7
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	96.0
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	95.95
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	95.92
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	95.77
cd01106	103	HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain	95.63
TIGR01764	49	excise DNA binding domain, excisionase family. An	95.62
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	95.1
PRK09413	121	IS2 repressor TnpA; Reviewed	95.08
PF12728	51	HTH_17: Helix-turn-helix domain	94.83
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	94.76
PRK11302	284	DNA-binding transcriptional regulator HexR; Provis	94.67
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	94.63
PRK15482	285	transcriptional regulator MurR; Provisional	94.63
cd04789	102	HTH_Cfa Helix-Turn-Helix DNA binding domain of the	94.54
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	94.49
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	94.21
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	94.1
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	94.06
COG1342	99	Predicted DNA-binding proteins [General function p	94.0
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	94.0
PRK00430	95	fis global DNA-binding transcriptional dual regula	93.93
cd01107	108	HTH_BmrR Helix-Turn-Helix DNA binding domain of th	93.91
PRK11557	278	putative DNA-binding transcriptional regulator; Pr	93.85
COG1737	281	RpiR Transcriptional regulators [Transcription]	93.77
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	93.67
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	93.57
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	93.55
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	93.48
cd04788	96	HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain	93.47
PRK11337	292	DNA-binding transcriptional repressor RpiR; Provis	93.44
PRK13182	175	racA polar chromosome segregation protein; Reviewe	93.39
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	93.36
cd04774	96	HTH_YfmP Helix-Turn-Helix DNA binding domain of th	93.27
PRK00118	104	putative DNA-binding protein; Validated	93.15
cd04782	97	HTH_BltR Helix-Turn-Helix DNA binding domain of th	93.06
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	93.03
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	92.93
cd01110	139	HTH_SoxR Helix-Turn-Helix DNA binding domain of th	92.47
PRK04217	110	hypothetical protein; Provisional	92.44
cd01282	112	HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding dom	92.4
PRK01905	77	DNA-binding protein Fis; Provisional	92.39
PRK09706	135	transcriptional repressor DicA; Reviewed	92.34
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	92.24
cd04775	102	HTH_Cfa-like Helix-Turn-Helix DNA binding domain o	92.08
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	92.07
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	91.83
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	91.75
cd01109	113	HTH_YyaN Helix-Turn-Helix DNA binding domain of th	91.73
PRK10219	107	DNA-binding transcriptional regulator SoxS; Provis	91.69
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	91.61
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	91.4
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	91.4
PRK12536	181	RNA polymerase sigma factor; Provisional	91.36
PRK13413	200	mpi multiple promoter invertase; Provisional	91.31
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	91.28
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	91.12
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	91.11
PRK11608	326	pspF phage shock protein operon transcriptional ac	91.07
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	91.02
cd04773	108	HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding	91.02
PRK12532	195	RNA polymerase sigma factor; Provisional	90.91
PRK09047	161	RNA polymerase factor sigma-70; Validated	90.78
PRK15115	444	response regulator GlrR; Provisional	90.78
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	90.74
cd04790	172	HTH_Cfa-like_unk Helix-Turn-Helix DNA binding doma	90.73
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	90.72
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	90.72
cd04787	133	HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain	90.68
PRK12513	194	RNA polymerase sigma factor; Provisional	90.65
PRK12515	189	RNA polymerase sigma factor; Provisional	90.64
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	90.61
PRK12522	173	RNA polymerase sigma factor; Provisional	90.6
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	90.55
PRK12543	179	RNA polymerase sigma factor; Provisional	90.36
PRK05602	186	RNA polymerase sigma factor; Reviewed	90.35
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	90.29
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	90.28
cd00592	100	HTH_MerR-like Helix-Turn-Helix DNA binding domain	90.28
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	90.22
PRK12511	182	RNA polymerase sigma factor; Provisional	90.2
cd04772	99	HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding d	90.2
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	90.15
PRK12527	159	RNA polymerase sigma factor; Reviewed	90.14
PF13518	52	HTH_28: Helix-turn-helix domain	90.12
PRK05022	509	anaerobic nitric oxide reductase transcription reg	89.97
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	89.95
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	89.92
PRK12520	191	RNA polymerase sigma factor; Provisional	89.78
PRK12530	189	RNA polymerase sigma factor; Provisional	89.68
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	89.62
PRK12542	185	RNA polymerase sigma factor; Provisional	89.59
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	89.59
PRK12516	187	RNA polymerase sigma factor; Provisional	89.59
COG1522	154	Lrp Transcriptional regulators [Transcription]	89.39
PRK12538	233	RNA polymerase sigma factor; Provisional	89.28
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	89.25
PF12844	64	HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_	89.24
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	89.22
TIGR02044	127	CueR Cu(I)-responsive transcriptional regulator. T	89.13
PRK12519	194	RNA polymerase sigma factor; Provisional	89.12
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	89.1
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	89.07
PRK12545	201	RNA polymerase sigma factor; Provisional	89.03
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	89.03
PRK12533	216	RNA polymerase sigma factor; Provisional	88.92
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	88.89
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	88.85
TIGR02051	124	MerR Hg(II)-responsive transcriptional regulator.	88.84
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	88.81
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	88.8
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	88.79
PRK12535	196	RNA polymerase sigma factor; Provisional	88.73
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	88.66
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	88.64
COG1476	68	Predicted transcriptional regulators [Transcriptio	88.51
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	88.47
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	88.33
PRK12531	194	RNA polymerase sigma factor; Provisional	88.32
cd04781	120	HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding dom	88.32
PRK12539	184	RNA polymerase sigma factor; Provisional	88.29
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	88.23
PRK14101	638	bifunctional glucokinase/RpiR family transcription	88.18
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	88.08
PRK12547	164	RNA polymerase sigma factor; Provisional	88.05
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	87.99
PRK12524	196	RNA polymerase sigma factor; Provisional	87.76
PRK12515	189	RNA polymerase sigma factor; Provisional	87.74
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	87.63
TIGR02047	127	CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional	87.61
PRK09415	179	RNA polymerase factor sigma C; Reviewed	87.61
PHA01976	67	helix-turn-helix protein	87.6
PRK08295	208	RNA polymerase factor sigma-70; Validated	87.44
PRK12540	182	RNA polymerase sigma factor; Provisional	87.28
cd04770	123	HTH_HMRTR Helix-Turn-Helix DNA binding domain of H	87.19
PF07453	37	NUMOD1: NUMOD1 domain; InterPro: IPR010896 This he	87.1
TIGR01950	142	SoxR redox-sensitive transcriptional activator Sox	87.08
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	87.01
cd01108	127	HTH_CueR Helix-Turn-Helix DNA binding domain of Cu	86.96
PRK08301	234	sporulation sigma factor SigE; Reviewed	86.93
cd04776	118	HTH_GnyR Helix-Turn-Helix DNA binding domain of th	86.78
PRK09726	88	antitoxin HipB; Provisional	86.63
PRK12514	179	RNA polymerase sigma factor; Provisional	86.51
smart00497	53	IENR1 Intron encoded nuclease repeat motif. Repeat	86.46
PRK12541	161	RNA polymerase sigma factor; Provisional	86.4
PRK10072	96	putative transcriptional regulator; Provisional	86.33
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	86.26
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	86.18
PF03374	111	ANT: Phage antirepressor protein KilAC domain; Int	86.0
cd04783	126	HTH_MerR1 Helix-Turn-Helix DNA binding domain of t	85.97
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	85.84
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	85.76
PRK15002	154	redox-sensitivie transcriptional activator SoxR; P	85.69
TIGR03830	127	CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he	85.65
PRK11303	328	DNA-binding transcriptional regulator FruR; Provis	85.6
PRK12537	182	RNA polymerase sigma factor; Provisional	85.52
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	85.5
PRK12529	178	RNA polymerase sigma factor; Provisional	85.46
cd04784	127	HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain	85.43
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	85.43
PRK11511	127	DNA-binding transcriptional activator MarA; Provis	85.38
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	85.28
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	85.2
PRK09413	121	IS2 repressor TnpA; Reviewed	85.08
PRK12518	175	RNA polymerase sigma factor; Provisional	85.08
PF08535	93	KorB: KorB domain; InterPro: IPR013741 This entry	85.02
PRK12546	188	RNA polymerase sigma factor; Provisional	84.9
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	84.84
PRK13919	186	putative RNA polymerase sigma E protein; Provision	84.75
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	84.67
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	84.5
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	84.33
PRK12517	188	RNA polymerase sigma factor; Provisional	84.32
PRK12544	206	RNA polymerase sigma factor; Provisional	84.29
PRK12526	206	RNA polymerase sigma factor; Provisional	84.29
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	84.28
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	84.28
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	84.25
PRK03975	141	tfx putative transcriptional regulator; Provisiona	84.2
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	84.18
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	84.09
PRK12512	184	RNA polymerase sigma factor; Provisional	83.99
PF10668	60	Phage_terminase: Phage terminase small subunit; In	83.89
PRK06704	228	RNA polymerase factor sigma-70; Validated	83.88
PRK11924	179	RNA polymerase sigma factor; Provisional	83.8
smart00354	70	HTH_LACI helix_turn _helix lactose operon represso	83.8
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	83.61
PRK09514	140	zntR zinc-responsive transcriptional regulator; Pr	83.5
PRK12523	172	RNA polymerase sigma factor; Reviewed	83.41
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	83.25
PF07638	185	Sigma70_ECF: ECF sigma factor	83.25
PF03683	76	UPF0175: Uncharacterised protein family (UPF0175);	83.11
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	82.96
PRK09393	322	ftrA transcriptional activator FtrA; Provisional	82.81
TIGR02607	78	antidote_HigA addiction module antidote protein, H	82.74
cd00093	58	HTH_XRE Helix-turn-helix XRE-family like proteins.	82.7
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	82.67
PRK08241	339	RNA polymerase factor sigma-70; Validated	82.54
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	82.5
PRK11169	164	leucine-responsive transcriptional regulator; Prov	82.42
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	82.41
TIGR02043	131	ZntR Zn(II)-responsive transcriptional regulator.	82.39
TIGR02040	442	PpsR-CrtJ transcriptional regulator PpsR. This mod	81.97
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	81.91
cd04785	126	HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding do	81.9
PRK15043	243	transcriptional regulator MirA; Provisional	81.89
PRK09685	302	DNA-binding transcriptional activator FeaR; Provis	81.86
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	81.83
PRK12534	187	RNA polymerase sigma factor; Provisional	81.74
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	81.66
PHA00542	82	putative Cro-like protein	81.58
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	81.23
PRK10339	327	DNA-binding transcriptional repressor EbgR; Provis	81.2
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	80.97
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	80.9
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	80.84
TIGR02054	120	MerD mercuric resistence transcriptional repressor	80.74
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	80.69
cd04786	131	HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding dom	80.67
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	80.64
cd01111	107	HTH_MerD Helix-Turn-Helix DNA binding domain of th	80.5
PRK11922	231	RNA polymerase sigma factor; Provisional	80.41
KOG0251	491	consensus Clathrin assembly protein AP180 and rela	80.17
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	80.05

>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain

Probab=99.95  E-value=2.3e-28  Score=164.06  Aligned_cols=51  Identities=55%  Similarity=0.946  Sum_probs=49.3

Q ss_pred             cCCCCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhH
Q 041600           68 TGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI  118 (160)
Q Consensus        68 ~~~lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl  118 (160)
                      +++||++||++|||+|++|||++||||+|+|||+||++||.||||||++||
T Consensus         2 ~~~lt~~~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR~~GI~RWP~Rkl~Sl   52 (52)
T PF02042_consen    2 TKSLTLEDLSQYFHLPIKEAAKELGVSVTTLKRRCRRLGIPRWPYRKLKSL   52 (52)
T ss_pred             CCccCHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHcCCCCCCchhhccC
Confidence            468999999999999999999999999999999999999999999999986

The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=96.70  E-value=0.0026  Score=44.46  Aligned_cols=40  Identities=18%  Similarity=0.408  Sum_probs=31.1

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChh
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPH  112 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPy  112 (160)
                      ++.....-.+++.|.|+.+|||++++=|.|+++|...|+-
T Consensus        26 l~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf~e   65 (77)
T PF01418_consen   26 LENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSGFKE   65 (77)
T ss_dssp             HH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCHHH
T ss_pred             HhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCHHH
Confidence            4444566689999999999999999999999999988773

Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=96.00  E-value=0.019  Score=43.66  Aligned_cols=49  Identities=29%  Similarity=0.289  Sum_probs=36.3

Q ss_pred             CCCCCCCCchhhhhccCCCCHHHHH-----hhcCCcHHHHHHHcCCChhHHHHH
Q 041600           53 DYSQPPMTNSVQRERTGKLTLRDLM-----IYFHLPIEEAARRMKLCPTVVKKI  101 (160)
Q Consensus        53 ~~~~ps~s~s~~r~r~~~lt~~~L~-----~yF~lP~~eAA~~Lgv~~T~LKr~  101 (160)
                      ..+.|.....+.....-.|++|++.     .|.+|++.|||..+|||.+|+-++
T Consensus        24 ~~F~P~g~~~~~~~~~V~L~~dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ri   77 (106)
T PF02001_consen   24 RCFKPAGPGSELEKEPVVLTVDELEAIRLVDYEGLSQEEAAERMGVSRPTFQRI   77 (106)
T ss_pred             CEEeCCCCCCCCCcceEEeeHHHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHH
Confidence            3445544222223345678999876     778999999999999999999888

>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators

Probab=95.95  E-value=0.049  Score=40.06  Aligned_cols=74  Identities=18%  Similarity=0.197  Sum_probs=50.6

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCC---C-------ChhHH------HhhH-H---HHHHHHhhhccC--CcHHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLH---R-------WPHRK------IKSI-Q---RRMSVASGRLRS--NDAEERAN  139 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~---R-------WPyRk------ikSl-~---~~i~~L~~~~~~--~~~eerar  139 (160)
                      +++.|+|+.+|||+++|+...++.|+.   |       |....      |+++ +   -.|+.+..+++.  +....++.
T Consensus         1 yti~EvA~~~gVs~~tLR~ye~~~gli~p~r~~~g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~~~~~~~~~~   80 (99)
T cd04765           1 FSIGEVAEILGLPPHVLRYWETEFPQLKPVKRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDGAAAIREEE   80 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHcCCCCCcCCCCCCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhccccccchhh
Confidence            468999999999999999999886642   2       33222      3332 1   124555666653  23356778


Q ss_pred             HHHHHHHHHHHHHHHh
Q 041600          140 AQIEIQRLQEEMAAAC  155 (160)
Q Consensus       140 ~~~eIerL~~Em~~~c  155 (160)
                      +..++.++..|+..+.
T Consensus        81 ~~~~~~~~~~~~~~l~   96 (99)
T cd04765          81 AEERLPSIRAELLDLR   96 (99)
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            8888999999988764

Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=95.92  E-value=0.012  Score=37.48  Aligned_cols=32  Identities=13%  Similarity=0.342  Sum_probs=23.2

Q ss_pred             HHHHHhhc--CCcHHHHHHHcCCChhHHHHHHHH
Q 041600           73 LRDLMIYF--HLPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        73 ~~~L~~yF--~lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      ++++...+  ++|+.++|+.+|||.+|+.|+.++
T Consensus        11 ~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~~   44 (45)
T PF02796_consen   11 IEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLNK   44 (45)
T ss_dssp             HHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHCC
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            45555555  599999999999999999998653

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator

Probab=95.77  E-value=0.06  Score=38.44  Aligned_cols=73  Identities=21%  Similarity=0.263  Sum_probs=46.7

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCCC----------ChhHHHhhHHHHHHHHhhhcc--CCcHHHHHHHHHHHHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLHR----------WPHRKIKSIQRRMSVASGRLR--SNDAEERANAQIEIQRLQE  149 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~R----------WPyRkikSl~~~i~~L~~~~~--~~~~eerar~~~eIerL~~  149 (160)
                      +++.++|+.+||++++|+...+ .|+-.          .+...+..+.. |..|.....  -.+-.+-.....+++.|++
T Consensus         2 ~~i~e~A~~~gvs~~tLr~ye~-~Gli~p~r~~~g~R~y~~~dv~~l~~-i~~L~~d~g~~l~~i~~~l~l~~~~~~l~~   79 (91)
T cd04766           2 YVISVAAELSGMHPQTLRLYER-LGLLSPSRTDGGTRRYSERDIERLRR-IQRLTQELGVNLAGVKRILELEEELAELRA   79 (91)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH-CCCcCCCcCCCCCeeECHHHHHHHHH-HHHHHHHcCCCHHHHHHHHHHHHHHHHHHH
Confidence            6899999999999999998876 46433          23334444443 444444221  1233334456688888888


Q ss_pred             HHHHHhc
Q 041600          150 EMAAACA  156 (160)
Q Consensus       150 Em~~~c~  156 (160)
                      |+..+-.
T Consensus        80 ~l~~l~~   86 (91)
T cd04766          80 ELDELRA   86 (91)
T ss_pred             HHHHHHH
Confidence            8887653

Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA

Probab=95.63  E-value=0.05  Score=39.62  Aligned_cols=72  Identities=14%  Similarity=0.107  Sum_probs=46.2

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC----CCCh--hHH--------------HhhHHHHHHHHhhhccCCcHHHHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL----HRWP--HRK--------------IKSIQRRMSVASGRLRSNDAEERANAQ  141 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI----~RWP--yRk--------------ikSl~~~i~~L~~~~~~~~~eerar~~  141 (160)
                      +.+.|+|+.+||++++|+...+ .|+    .|.|  ||.              ++.+.--|+.++..+...+++..+...
T Consensus         1 ~ti~eva~~~gvs~~tlR~ye~-~Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~~~~~~~~~l~   79 (103)
T cd01106           1 YTVGEVAKLTGVSVRTLHYYDE-IGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSEDLLEALR   79 (103)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHcCcHHHHHHHH
Confidence            4688999999999999997764 454    2344  221              222223355566666654455566666


Q ss_pred             HHHHHHHHHHHHH
Q 041600          142 IEIQRLQEEMAAA  154 (160)
Q Consensus       142 ~eIerL~~Em~~~  154 (160)
                      .++..|++++.++
T Consensus        80 ~~~~~l~~~i~~l   92 (103)
T cd01106          80 EQKELLEEKKERL   92 (103)
T ss_pred             HHHHHHHHHHHHH
Confidence            7777777777665

Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip

>TIGR01764 excise DNA binding domain, excisionase family

Probab=95.62  E-value=0.015  Score=35.44  Aligned_cols=28  Identities=25%  Similarity=0.348  Sum_probs=24.8

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLHR  109 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~R  109 (160)
                      |.+.|||+.||||.+++.+.+++..|+.
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g~i~~   29 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEGELPA   29 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcCCCCe
Confidence            6789999999999999999998876753

An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).

>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators

Probab=95.10  E-value=0.099  Score=37.88  Aligned_cols=73  Identities=16%  Similarity=0.125  Sum_probs=49.4

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCC---CC-h--hHH--------------HhhHHHHHHHHhhhccCCcHHHHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLH---RW-P--HRK--------------IKSIQRRMSVASGRLRSNDAEERANAQ  141 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~---RW-P--yRk--------------ikSl~~~i~~L~~~~~~~~~eerar~~  141 (160)
                      +++.|+|+.+||++.||+-..++ |+-   +. +  ||.              ++.+.-.++.+++.+...+.+-..-..
T Consensus         1 ~ti~eva~~~gvs~~tLRyye~~-Gll~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~l~   79 (96)
T cd04768           1 LTIGEFAKLAGVSIRTLRHYDDI-GLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEMEELTAMLL   79 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCcHHHHHHHH
Confidence            47899999999999999988766 753   22 2  341              122222355666666654555566677


Q ss_pred             HHHHHHHHHHHHHh
Q 041600          142 IEIQRLQEEMAAAC  155 (160)
Q Consensus       142 ~eIerL~~Em~~~c  155 (160)
                      .+++.|++++.++-
T Consensus        80 ~~~~~l~~~i~~l~   93 (96)
T cd04768          80 EKKQAIQQKIDRLQ   93 (96)
T ss_pred             HHHHHHHHHHHHHH
Confidence            88888888888764

Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=95.08  E-value=0.11  Score=39.01  Aligned_cols=42  Identities=14%  Similarity=0.130  Sum_probs=31.7

Q ss_pred             hhccCCCCHHHHHhhc--CCcHHHHHHHcCCChhHHHHHHHHcC
Q 041600           65 RERTGKLTLRDLMIYF--HLPIEEAARRMKLCPTVVKKICRRDG  106 (160)
Q Consensus        65 r~r~~~lt~~~L~~yF--~lP~~eAA~~Lgv~~T~LKr~CR~~G  106 (160)
                      |..+..+-.+-+..++  +.+..++|+++||+.++|-+-.+++.
T Consensus        11 r~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~   54 (121)
T PRK09413         11 RRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQ   54 (121)
T ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence            3444444455555555  68999999999999999999988763

>PF12728 HTH_17: Helix-turn-helix domain

Probab=94.83  E-value=0.034  Score=35.32  Aligned_cols=28  Identities=21%  Similarity=0.326  Sum_probs=25.1

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLHR  109 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~R  109 (160)
                      |...|||+.||||.+++.+.+++-+|+.
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g~i~~   29 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQGKIPP   29 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCCe
Confidence            6789999999999999999999888843

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=94.76  E-value=0.039  Score=33.27  Aligned_cols=27  Identities=22%  Similarity=0.447  Sum_probs=23.1

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      +.+.|||+.||||.++|.+.+++-.++
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g~~~   27 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGKLK   27 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence            468999999999999999998875553

Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.

>PRK11302 DNA-binding transcriptional regulator HexR; Provisional

Probab=94.67  E-value=0.035  Score=45.92  Aligned_cols=38  Identities=18%  Similarity=0.329  Sum_probs=33.4

Q ss_pred             HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChh
Q 041600           75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPH  112 (160)
Q Consensus        75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPy  112 (160)
                      .......+++.+.|++.|||++|+=|.||++|..-++-
T Consensus        28 n~~~v~~~si~~lA~~~~vS~aTv~Rf~kklG~~gf~e   65 (284)
T PRK11302         28 SPQTAIHSSIATLAKMANVSEPTVNRFCRSLDTKGFPD   65 (284)
T ss_pred             CHHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHH
Confidence            33455689999999999999999999999999999873

>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]

Probab=94.63  E-value=0.065  Score=33.56  Aligned_cols=28  Identities=11%  Similarity=0.058  Sum_probs=21.8

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      ..++--+.+||+.|||+.++|.+..+++
T Consensus        15 ~~~~gn~~~aA~~Lgisr~tL~~klkk~   42 (42)
T PF02954_consen   15 ERCGGNVSKAARLLGISRRTLYRKLKKY   42 (42)
T ss_dssp             HHTTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred             HHhCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence            4567789999999999999999887654

It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....

>PRK15482 transcriptional regulator MurR; Provisional

Probab=94.63  E-value=0.035  Score=46.51  Aligned_cols=46  Identities=7%  Similarity=0.180  Sum_probs=37.4

Q ss_pred             CCCCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHH
Q 041600           69 GKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRK  114 (160)
Q Consensus        69 ~~lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRk  114 (160)
                      .+.=++.....-.+++.|.|++.|||++|+=|.|+++|..-|+-=|
T Consensus        22 a~yIl~n~~~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~Gf~efk   67 (285)
T PRK15482         22 ADFLRANVSELKSVSSRKMAKQLGISQSSIVKFAQKLGAQGFTELR   67 (285)
T ss_pred             HHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHH
Confidence            3333444456668999999999999999999999999999998433

>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator

Probab=94.54  E-value=0.14  Score=37.57  Aligned_cols=69  Identities=16%  Similarity=0.183  Sum_probs=41.6

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCCCCh------hH-----HHhhHH------H---HHHHHhhhccCCcHHHHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLHRWP------HR-----KIKSIQ------R---RMSVASGRLRSNDAEERANAQ  141 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWP------yR-----kikSl~------~---~i~~L~~~~~~~~~eerar~~  141 (160)
                      +++.|+|+.+|||++||+-..+. |+-. |      ||     .+.-+.      .   .++.+...++..  ...+...
T Consensus         2 ~~i~eva~~~gvs~~tlR~ye~~-Gll~-~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l~~~--~~~~~l~   77 (102)
T cd04789           2 YTISELAEKAGISRSTLLYYEKL-GLIT-GTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQGK--LTRSLLL   77 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCC-CCcCCCCCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHHcCC--cHHHHHH
Confidence            68999999999999999987765 6532 2      22     222222      1   223344444332  2234566


Q ss_pred             HHHHHHHHHHHHH
Q 041600          142 IEIQRLQEEMAAA  154 (160)
Q Consensus       142 ~eIerL~~Em~~~  154 (160)
                      .+++.|++++..+
T Consensus        78 ~~~~~l~~~i~~l   90 (102)
T cd04789          78 ERLSSLAEQIARK   90 (102)
T ss_pred             HHHHHHHHHHHHH
Confidence            6777777777665

Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=94.49  E-value=0.038  Score=35.09  Aligned_cols=25  Identities=24%  Similarity=0.409  Sum_probs=18.5

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      ++++.++|+.||++.+|+.+.++++
T Consensus        20 G~s~~~IA~~lg~s~sTV~relkR~   44 (44)
T PF13936_consen   20 GMSIREIAKRLGRSRSTVSRELKRN   44 (44)
T ss_dssp             ---HHHHHHHTT--HHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCcHHHHHHHhcC
Confidence            6999999999999999999998863

>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators

Probab=94.21  E-value=0.055  Score=36.32  Aligned_cols=27  Identities=30%  Similarity=0.281  Sum_probs=24.0

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      +++.|+|+.+||++++|+..+++.|+.
T Consensus         1 ~~i~e~A~~~gVs~~tlr~ye~~~gl~   27 (68)
T cd04763           1 YTIGEVALLTGIKPHVLRAWEREFGLL   27 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhcCCC
Confidence            478999999999999999999987764

Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen

>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators

Probab=94.10  E-value=0.33  Score=35.36  Aligned_cols=25  Identities=32%  Similarity=0.453  Sum_probs=21.9

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +++.++|+.+|||+++|+...+ .|+
T Consensus         2 ~~i~eva~~~gVs~~tLR~ye~-~Gl   26 (98)
T cd01279           2 YPISVAAELLGIHPQTLRVYDR-LGL   26 (98)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence            5899999999999999998865 664

Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily

Probab=94.06  E-value=0.061  Score=33.27  Aligned_cols=30  Identities=27%  Similarity=0.334  Sum_probs=23.4

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCCCChhH
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLHRWPHR  113 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyR  113 (160)
                      +++.|+|+.|||++.+|++..++-.|+  |.+
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~~~g~l~--~~~   30 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYERIGLLS--PAR   30 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHCCCCC--CCc
Confidence            578999999999999999876554443  544

Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=94.00  E-value=0.14  Score=38.84  Aligned_cols=45  Identities=27%  Similarity=0.321  Sum_probs=35.6

Q ss_pred             ccCCCCHHHHH-----hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           67 RTGKLTLRDLM-----IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        67 r~~~lt~~~L~-----~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      ..-.||+++|.     .|-+|.+.|||.++|||..||-+.             ++|-++++.+
T Consensus        30 ~~V~lt~eElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~-------------l~sAR~KvA~   79 (99)
T COG1342          30 EPVILTIEELEALRLVDYEGLTQEEAALRMGISRQTFWRL-------------LTSARKKVAD   79 (99)
T ss_pred             cceeecHHHHHHHHHHhHhhccHHHHHHHhcccHHHHHHH-------------HHHHHHHHHH
Confidence            34568888875     788999999999999999998665             5666665554

>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators

Probab=94.00  E-value=0.07  Score=35.63  Aligned_cols=27  Identities=15%  Similarity=0.191  Sum_probs=24.3

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      +++.|+|+.+||++++|+...++.|+.
T Consensus         1 ~~i~evA~~~gvs~~tlR~~~~~g~l~   27 (67)
T cd04764           1 YTIKEVSEIIGVKPHTLRYYEKEFNLY   27 (67)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhcCCC
Confidence            478999999999999999999987775

Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.

>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional

Probab=93.93  E-value=0.1  Score=38.49  Aligned_cols=31  Identities=19%  Similarity=0.210  Sum_probs=27.5

Q ss_pred             HhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      -..++-.+.+||+.|||+.++|.+..+++||
T Consensus        64 L~~~~gn~s~AAr~LGIsRsTL~rKLkr~gi   94 (95)
T PRK00430         64 MQYTRGNQTRAALMLGINRGTLRKKLKKYGM   94 (95)
T ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHHHHhCC
Confidence            3455678999999999999999999999997

>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator

Probab=93.91  E-value=0.25  Score=36.42  Aligned_cols=72  Identities=21%  Similarity=0.247  Sum_probs=45.6

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCC-C-C--h---hHH-----------HhhH---HHHHHHHhhhccCCcH-HHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLH-R-W--P---HRK-----------IKSI---QRRMSVASGRLRSNDA-EERAN  139 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~-R-W--P---yRk-----------ikSl---~~~i~~L~~~~~~~~~-eerar  139 (160)
                      +++.|+|+.+||+++||+-.+++ |+- . +  +   ||.           |+.+   .-.++.+...++..+. +-.+-
T Consensus         1 ~~i~eva~~~gis~~tlR~ye~~-GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~~~~~~~~~~~   79 (108)
T cd01107           1 FTIGEFAKLSNLSIKALRYYDKI-GLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADNDDELRKL   79 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc-CCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCCHHHHHHH
Confidence            57899999999999999998876 752 2 2  3   453           1111   2234455555554443 44445


Q ss_pred             HHHHHHHHHHHHHHH
Q 041600          140 AQIEIQRLQEEMAAA  154 (160)
Q Consensus       140 ~~~eIerL~~Em~~~  154 (160)
                      ...+++.|++++..+
T Consensus        80 l~~~~~~l~~~i~~l   94 (108)
T cd01107          80 LREKLAELEAEIEEL   94 (108)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            667777777777665

Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PRK11557 putative DNA-binding transcriptional regulator; Provisional

Probab=93.85  E-value=0.063  Score=44.56  Aligned_cols=39  Identities=21%  Similarity=0.234  Sum_probs=33.6

Q ss_pred             HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHH
Q 041600           76 LMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRK  114 (160)
Q Consensus        76 L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRk  114 (160)
                      ....-.+++.+.|++.|||++|+=|.||++|...|+-=|
T Consensus        25 ~~~v~~~si~elA~~~~vS~aTv~Rf~kklG~~Gf~efk   63 (278)
T PRK11557         25 PDTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPALK   63 (278)
T ss_pred             HHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHH
Confidence            345557999999999999999999999999999987433

>COG1737 RpiR Transcriptional regulators [Transcription]

Probab=93.77  E-value=0.055  Score=45.97  Aligned_cols=40  Identities=25%  Similarity=0.316  Sum_probs=34.3

Q ss_pred             HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHH
Q 041600           76 LMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKI  115 (160)
Q Consensus        76 L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRki  115 (160)
                      -...-+++++|.|+..|||++|+=|.||++|-.-||-=|+
T Consensus        31 ~~~~~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf~efk~   70 (281)
T COG1737          31 PDEVALLSIAELAERAGVSPATVVRFARKLGFEGFSEFKL   70 (281)
T ss_pred             HHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCHHHHHH
Confidence            3345579999999999999999999999999999994443

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=93.67  E-value=0.059  Score=33.92  Aligned_cols=24  Identities=25%  Similarity=0.390  Sum_probs=18.7

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      +++..++|+.||||.+|+.+..++
T Consensus        17 G~s~~~ia~~lgvs~~Tv~~w~kr   40 (50)
T PF13384_consen   17 GWSIREIAKRLGVSRSTVYRWIKR   40 (50)
T ss_dssp             T--HHHHHHHHTS-HHHHHHHHT-
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHH
Confidence            899999999999999999998655

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=93.57  E-value=0.33  Score=30.29  Aligned_cols=34  Identities=12%  Similarity=0.098  Sum_probs=28.6

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      +..++.-.++.+.++|+.+||+++++.++.  .|-.
T Consensus         7 l~~~r~~~gltq~~lA~~~gvs~~~vs~~e--~g~~   40 (58)
T TIGR03070         7 VRARRKALGLTQADLADLAGVGLRFIRDVE--NGKP   40 (58)
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH--CCCC
Confidence            556777889999999999999999999994  4543

Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.

>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)

Probab=93.55  E-value=0.34  Score=30.61  Aligned_cols=42  Identities=24%  Similarity=0.382  Sum_probs=29.3

Q ss_pred             HHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCh-hHHHhhH
Q 041600           74 RDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWP-HRKIKSI  118 (160)
Q Consensus        74 ~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWP-yRkikSl  118 (160)
                      ..++.-.++++.+.|+.+||+.+++.++.  .| .+.| ...+..+
T Consensus         2 k~~r~~~gls~~~la~~~gis~~~i~~~~--~g-~~~~~~~~~~~i   44 (55)
T PF01381_consen    2 KELRKEKGLSQKELAEKLGISRSTISRIE--NG-KRNPSLDTLKKI   44 (55)
T ss_dssp             HHHHHHTTS-HHHHHHHHTS-HHHHHHHH--TT-SSTSBHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHhCCCcchhHHHh--cC-CCCCCHHHHHHH
Confidence            45666778999999999999999999995  55 3444 4444443

; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=93.48  E-value=0.19  Score=32.91  Aligned_cols=46  Identities=11%  Similarity=0.263  Sum_probs=33.0

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcC-CCCChhHHHhhHHHHHHHHh
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDG-LHRWPHRKIKSIQRRMSVAS  126 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~G-I~RWPyRkikSl~~~i~~L~  126 (160)
                      .+++.++|+.+|+|.+.|.+++++.. ++-..|.+...+++.+..|.
T Consensus         1 ~~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~~r~~~a~~~l~   47 (84)
T smart00342        1 PLTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRDRRLERARRLLR   47 (84)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence            36889999999999999999998764 65455555444555444444

>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR

Probab=93.47  E-value=0.39  Score=34.77  Aligned_cols=74  Identities=20%  Similarity=0.236  Sum_probs=48.7

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCC-----------CChhHHHhhHH---------HHHHHHhhhccCCcHHHHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLH-----------RWPHRKIKSIQ---------RRMSVASGRLRSNDAEERANAQ  141 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~-----------RWPyRkikSl~---------~~i~~L~~~~~~~~~eerar~~  141 (160)
                      |.+.|+|+.+|||+.+|+-..+ .|+-           .+.-..+..+.         -.++.++..++..+.+-.+-..
T Consensus         1 m~i~eva~~~gvs~~tlR~ye~-~Gll~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~l~   79 (96)
T cd04788           1 WKIGELARRTGLSVRTLHHYDH-IGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGPDFDPLELLR   79 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhCCChhHHHHHH
Confidence            5789999999999999997764 4432           12222222222         2245555556544445567778


Q ss_pred             HHHHHHHHHHHHHhc
Q 041600          142 IEIQRLQEEMAAACA  156 (160)
Q Consensus       142 ~eIerL~~Em~~~c~  156 (160)
                      .+++.|++++.++..
T Consensus        80 ~~~~~l~~~i~~l~~   94 (96)
T cd04788          80 RQLARLEEQLELATR   94 (96)
T ss_pred             HHHHHHHHHHHHHHh
Confidence            899999999988753

Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional

Probab=93.44  E-value=0.082  Score=44.30  Aligned_cols=35  Identities=9%  Similarity=0.249  Sum_probs=31.7

Q ss_pred             HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCh
Q 041600           77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWP  111 (160)
Q Consensus        77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWP  111 (160)
                      .....+++.+.|+..|||++|+=|.||++|..-|+
T Consensus        42 ~~v~~~si~~lA~~~~vS~aTi~Rf~kkLGf~gf~   76 (292)
T PRK11337         42 DLSEATALKDIAEALAVSEAMIVKVAKKLGFSGFR   76 (292)
T ss_pred             HHHHhcCHHHHHHHhCCChHHHHHHHHHcCCCCHH
Confidence            34557899999999999999999999999999887

>PRK13182 racA polar chromosome segregation protein; Reviewed

Probab=93.39  E-value=0.24  Score=40.37  Aligned_cols=27  Identities=15%  Similarity=0.319  Sum_probs=24.7

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      |.+.++|+.+|||++||.+..++.||+
T Consensus         1 mti~evA~~lGVS~~TLRrw~k~g~L~   27 (175)
T PRK13182          1 MKTPFVAKKLGVSPKTVQRWVKQLNLP   27 (175)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence            478999999999999999999988885

>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA

Probab=93.36  E-value=0.11  Score=34.30  Aligned_cols=26  Identities=31%  Similarity=0.419  Sum_probs=23.2

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +++.|+|+.+||+.++|++..++.|+
T Consensus         1 ~s~~eva~~~gvs~~tlr~w~~~~g~   26 (68)
T cd01104           1 YTIGAVARLTGVSPDTLRAWERRYGL   26 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhCCC
Confidence            47899999999999999999887776

Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i

>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator

Probab=93.27  E-value=0.24  Score=36.08  Aligned_cols=27  Identities=26%  Similarity=0.356  Sum_probs=23.1

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLHR  109 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~R  109 (160)
                      +++.|+|+.+||++++|+...+. |+-.
T Consensus         1 ~~I~e~a~~~gvs~~tLR~ye~~-Gll~   27 (96)
T cd04774           1 YKVDEVAKRLGLTKRTLKYYEEI-GLVS   27 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence            57899999999999999999864 7644

Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>PRK00118 putative DNA-binding protein; Validated

Probab=93.15  E-value=0.52  Score=35.59  Aligned_cols=61  Identities=16%  Similarity=0.048  Sum_probs=38.9

Q ss_pred             HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhhhccCCcHHHHHHHHHHHHHHHH
Q 041600           77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRLRSNDAEERANAQIEIQRLQE  149 (160)
Q Consensus        77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~~~~~~~~eerar~~~eIerL~~  149 (160)
                      .-+-+++.+|+|+.+|||+.+++++-         +|-.+.+...++.|.-.-+   -.++...-+.++++.+
T Consensus        29 ~y~eg~S~~EIAe~lGIS~~TV~r~L---------~RArkkLr~~~~~~~~~~~---~~~~~~~~~~~~~~~~   89 (104)
T PRK00118         29 YYLDDYSLGEIAEEFNVSRQAVYDNI---------KRTEKLLEDYEEKLHLYEK---FIERNELFDKIAYLKE   89 (104)
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHHHChHHH---HHHHHHHHHHHHHHHH
Confidence            34557999999999999999999884         5555666665555543322   2333344445555443

>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator

Probab=93.06  E-value=0.52  Score=34.14  Aligned_cols=73  Identities=14%  Similarity=0.093  Sum_probs=47.4

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC--C-CCh---hHH--------------HhhHHHHHHHHhhhccCCcH-HHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL--H-RWP---HRK--------------IKSIQRRMSVASGRLRSNDA-EERANA  140 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI--~-RWP---yRk--------------ikSl~~~i~~L~~~~~~~~~-eerar~  140 (160)
                      +++.|+|+.+|||+.+|+-..+ .|+  + +-+   ||.              ++.+.-.++.+++.+...+. +-..-.
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~-~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~~l   79 (97)
T cd04782           1 FTTGEFAKLCGISKQTLFHYDK-IGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNRNPDELIELL   79 (97)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCCHHHHHHHH
Confidence            4789999999999999997764 576  2 222   332              22222335555665554333 345667


Q ss_pred             HHHHHHHHHHHHHHh
Q 041600          141 QIEIQRLQEEMAAAC  155 (160)
Q Consensus       141 ~~eIerL~~Em~~~c  155 (160)
                      +.+++.|++++..+-
T Consensus        80 ~~~~~~l~~~i~~l~   94 (97)
T cd04782          80 KKQEKEIKEEIEELQ   94 (97)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            788889999888763

Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=93.03  E-value=0.12  Score=34.80  Aligned_cols=28  Identities=32%  Similarity=0.605  Sum_probs=23.5

Q ss_pred             HhhcCCc----HHHHHHHcCCChhHHHHHHHH
Q 041600           77 MIYFHLP----IEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        77 ~~yF~lP----~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      ..||+.|    +.|.|+.||||.+++-..-|+
T Consensus        15 ~GYfd~PR~~tl~elA~~lgis~st~~~~LRr   46 (53)
T PF04967_consen   15 LGYFDVPRRITLEELAEELGISKSTVSEHLRR   46 (53)
T ss_pred             cCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence            3789877    899999999999998877554

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=92.93  E-value=0.14  Score=32.40  Aligned_cols=30  Identities=20%  Similarity=0.291  Sum_probs=24.6

Q ss_pred             HHHhhcCC-cHHHHHHHcCCChhHHHHHHHH
Q 041600           75 DLMIYFHL-PIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        75 ~L~~yF~l-P~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      -+....+. +++++|+.+|||.++++++-.+
T Consensus        20 i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~   50 (52)
T PF13542_consen   20 ILKLLRESRSFKDVARELGVSWSTVRRIFDR   50 (52)
T ss_pred             HHHHHhhcCCHHHHHHHHCCCHHHHHHHHHh
Confidence            34455556 9999999999999999999755

>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator

Probab=92.47  E-value=0.97  Score=35.03  Aligned_cols=27  Identities=22%  Similarity=0.350  Sum_probs=23.1

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      .|+|.|+|+.+||++.||+-..++ |+-
T Consensus         1 ~~~I~EvA~~~Gvs~~tLRyYE~~-GLl   27 (139)
T cd01110           1 ELSVGEVAKRSGVAVSALHFYEQK-GLI   27 (139)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence            378999999999999999988766 753

Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.

>PRK04217 hypothetical protein; Provisional

Probab=92.44  E-value=0.57  Score=35.73  Aligned_cols=41  Identities=22%  Similarity=0.196  Sum_probs=31.4

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhh
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASG  127 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~  127 (160)
                      .+-+++++|+|+.||||.+|++++.         +|-.+.|...+..-..
T Consensus        55 ~~eGlS~~EIAk~LGIS~sTV~r~L---------~RArkkLre~L~~~~~   95 (110)
T PRK04217         55 DYEGLTQEEAGKRMGVSRGTVWRAL---------TSARKKVAQMLVEGRE   95 (110)
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHhccc
Confidence            3346999999999999999999996         4556666666655444

>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=92.40  E-value=0.87  Score=33.81  Aligned_cols=26  Identities=23%  Similarity=0.264  Sum_probs=21.7

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      |++.|+|+.+|||+.||+-..+. |+-
T Consensus         1 m~i~eva~~~gvs~~tlR~Ye~~-GLl   26 (112)
T cd01282           1 MRIGELAARTGVSVRSLRYYEEQ-GLL   26 (112)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHC-CCC
Confidence            57899999999999999987764 643

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK01905 DNA-binding protein Fis; Provisional

Probab=92.39  E-value=0.25  Score=34.70  Aligned_cols=30  Identities=17%  Similarity=0.068  Sum_probs=26.1

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      ...+-...+||+.|||+.++|.+.-+++||
T Consensus        47 ~~~~gn~s~aAr~LGIsrstL~rklkk~gi   76 (77)
T PRK01905         47 EQAGGNQSLAAEYLGINRNTLRKKLQQHGL   76 (77)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHHHHhCC
Confidence            334567999999999999999999999987

>PRK09706 transcriptional repressor DicA; Reviewed

Probab=92.34  E-value=1.5  Score=33.21  Aligned_cols=82  Identities=10%  Similarity=0.059  Sum_probs=46.5

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHH---------------HHHHHcCCC-CChhHHH--------------hhHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVK---------------KICRRDGLH-RWPHRKI--------------KSIQRRM  122 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LK---------------r~CR~~GI~-RWPyRki--------------kSl~~~i  122 (160)
                      +..++.-.++.+.+.|+.+||+.+++-               ++|+-+||+ -|=.---              ..+...-
T Consensus        10 lk~~R~~~gltq~~lA~~~gvs~~~is~~E~g~~~p~~~~l~~la~~l~vs~~~l~~g~~~~~~~~~~~~~~~~~l~~~~   89 (135)
T PRK09706         10 IRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLFGDEDKQPTPPVPLNQPVELSEDQ   89 (135)
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHhcCCCcCCCCCcccccCCCCCCHHH
Confidence            456677778899999999999865554               455555552 1211000              0011112


Q ss_pred             HHHhhhccCCcHHHHHHHHHHHHHHHHHHHHH
Q 041600          123 SVASGRLRSNDAEERANAQIEIQRLQEEMAAA  154 (160)
Q Consensus       123 ~~L~~~~~~~~~eerar~~~eIerL~~Em~~~  154 (160)
                      ..|-..++.-+++++..+...++.+.++|+++
T Consensus        90 ~~ll~~~~~L~~~~~~~~l~~l~~~~~~~~~~  121 (135)
T PRK09706         90 KELLELFDALPESEQDAQLSEMRARVENFNKL  121 (135)
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
Confidence            23333444456777777777766666666654

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=92.24  E-value=0.28  Score=37.60  Aligned_cols=39  Identities=18%  Similarity=0.233  Sum_probs=30.7

Q ss_pred             HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      .-+.++|.+|+|..||||+.+++...         +|=.+.|.+.+..
T Consensus       148 ~~~~~~s~~eIA~~lgis~~~v~~~l---------~Rar~~Lr~~l~~  186 (187)
T PRK09641        148 KYIEDLSLKEISEILDLPVGTVKTRI---------HRGREALRKQLRH  186 (187)
T ss_pred             HHhhCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHhc
Confidence            35678999999999999999999885         5656666665543

>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators

Probab=92.08  E-value=0.59  Score=34.17  Aligned_cols=26  Identities=15%  Similarity=0.201  Sum_probs=22.0

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      +++.|+|+.+|||++||+-.-++ |+-
T Consensus         2 ~~i~eva~~~gvs~~tLR~ye~~-Gll   27 (102)
T cd04775           2 YTIGQMSRKFGVSRSTLLYYESI-GLI   27 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence            68999999999999999876654 754

Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil

>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A

Probab=92.07  E-value=0.18  Score=30.97  Aligned_cols=27  Identities=19%  Similarity=0.593  Sum_probs=21.7

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc-CC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD-GL  107 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI  107 (160)
                      .+++.++|..+|+|++.|.|+.++. |+
T Consensus         8 ~~~l~~iA~~~g~S~~~f~r~Fk~~~g~   35 (42)
T PF00165_consen    8 KLTLEDIAEQAGFSPSYFSRLFKKETGM   35 (42)
T ss_dssp             S--HHHHHHHHTS-HHHHHHHHHHHTSS
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHCc
Confidence            4889999999999999999999887 66

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=91.83  E-value=0.27  Score=36.90  Aligned_cols=39  Identities=21%  Similarity=0.330  Sum_probs=32.4

Q ss_pred             CCCHHHHH----hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           70 KLTLRDLM----IYFHLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        70 ~lt~~~L~----~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      .|..+.|.    .+=++++.|.|+.||||.+++-+...++|+.
T Consensus        56 Kid~~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t   98 (119)
T PF01710_consen   56 KIDRDELKALVEENPDATLRELAERLGVSPSTIWRALKRLGIT   98 (119)
T ss_pred             cccHHHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHcCch
Confidence            34455554    5568999999999999999999999999994

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=91.75  E-value=0.26  Score=30.19  Aligned_cols=23  Identities=26%  Similarity=0.215  Sum_probs=20.0

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHH
Q 041600           80 FHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+++..++|+.||||.+++++.-
T Consensus        17 ~g~s~~eia~~l~is~~tv~~~~   39 (58)
T smart00421       17 EGLTNKEIAERLGISEKTVKTHL   39 (58)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHH
Confidence            36899999999999999887763

lux regulon (activates the bioluminescence operon

>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB

Probab=91.73  E-value=0.64  Score=34.28  Aligned_cols=26  Identities=19%  Similarity=0.241  Sum_probs=21.4

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +++.|+|+.+|||+.||+...+.--|
T Consensus         1 ~~i~e~a~~~gvs~~tlr~ye~~gll   26 (113)
T cd01109           1 YTIKEVAEKTGLSADTLRYYEKEGLL   26 (113)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence            57899999999999999987654334

Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional

Probab=91.69  E-value=0.6  Score=33.51  Aligned_cols=33  Identities=12%  Similarity=0.108  Sum_probs=27.3

Q ss_pred             HHhhcC--CcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 041600           76 LMIYFH--LPIEEAARRMKLCPTVVKKICRRD-GLH  108 (160)
Q Consensus        76 L~~yF~--lP~~eAA~~Lgv~~T~LKr~CR~~-GI~  108 (160)
                      |...++  +++.++|+.+|+|+.+|.|++++. |++
T Consensus        14 i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s   49 (107)
T PRK10219         14 IDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQT   49 (107)
T ss_pred             HHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence            344444  899999999999999999999997 763

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=91.61  E-value=0.4  Score=36.58  Aligned_cols=37  Identities=14%  Similarity=0.195  Sum_probs=29.4

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS  123 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~  123 (160)
                      -+-+++.+|+|+.||++.+++|...         ||=++.|++.+.
T Consensus       131 ~~~g~s~~EIA~~lgis~~tV~~~l---------~ra~~~Lr~~l~  167 (173)
T PRK09645        131 YYRGWSTAQIAADLGIPEGTVKSRL---------HYALRALRLALQ  167 (173)
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHhh
Confidence            3448999999999999999999886         666666666544

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=91.40  E-value=0.49  Score=37.33  Aligned_cols=40  Identities=18%  Similarity=0.243  Sum_probs=33.8

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhhh
Q 041600           80 FHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGR  128 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~~  128 (160)
                      -+++.+|+|..|||+.+++|...         +|-.+.|.+.+..+...
T Consensus       149 ~g~s~~EIA~~lg~s~~tV~~rl---------~rar~~Lr~~l~~~~~~  188 (192)
T PRK09643        149 QGYSVADAARMLGVAEGTVKSRC---------ARGRARLAELLGYLRAG  188 (192)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHHhcCC
Confidence            46999999999999999999996         77778888888776644

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=91.40  E-value=0.27  Score=43.15  Aligned_cols=31  Identities=6%  Similarity=-0.080  Sum_probs=27.3

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      ..++--..+||+.||||.+||.|..+++||.
T Consensus       427 ~~~~gn~~~aA~~LGisr~tL~rkl~~~~i~  457 (457)
T PRK11361        427 EQQEGNRTRTALMLGISRRALMYKLQEYGID  457 (457)
T ss_pred             HHhCCCHHHHHHHHCCCHHHHHHHHHHhCCC
Confidence            3456789999999999999999999999983

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=91.36  E-value=0.38  Score=37.33  Aligned_cols=36  Identities=25%  Similarity=0.304  Sum_probs=29.0

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM  122 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i  122 (160)
                      -+.+++.+|+|+.||+|+.++|...         ||-++.|.+.+
T Consensus       142 ~~~g~s~~EIA~~l~is~~tV~~~l---------~rar~~Lr~~l  177 (181)
T PRK12536        142 KLEGLSVAETAQLTGLSESAVKVGI---------HRGLKALAAKI  177 (181)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHh
Confidence            3568999999999999999999985         66666665544

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=91.31  E-value=0.22  Score=39.88  Aligned_cols=27  Identities=22%  Similarity=0.372  Sum_probs=25.3

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      ++++.++|+.||||.+|+.|++...|+
T Consensus       172 g~s~~~iak~lgis~~Tv~r~~k~~~~  198 (200)
T PRK13413        172 GTSKSEIARKLGVSRTTLARFLKTRGL  198 (200)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHhccc
Confidence            579999999999999999999998887

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

Probab=91.28  E-value=0.42  Score=37.19  Aligned_cols=40  Identities=25%  Similarity=0.250  Sum_probs=31.5

Q ss_pred             HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           76 LMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        76 L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      |..+.+++..|+|+.|||+.+|+|...         +|-++.|.+.+..
T Consensus       138 l~~~~gls~~EIA~~l~i~~~tVks~l---------~ra~~~l~~~l~~  177 (182)
T COG1595         138 LRYLEGLSYEEIAEILGISVGTVKSRL---------HRARKKLREQLEE  177 (182)
T ss_pred             hHhhcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHhh
Confidence            346668999999999999999999985         5666666665544

>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition

Probab=91.12  E-value=0.22  Score=33.47  Aligned_cols=33  Identities=18%  Similarity=0.273  Sum_probs=24.7

Q ss_pred             HHHHHhh--cCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           73 LRDLMIY--FHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        73 ~~~L~~y--F~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      ..-|..+  -+.++.++|+++||++++|.+-.+++
T Consensus        13 ~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~   47 (76)
T PF01527_consen   13 LQAVREYLESGESVSEVAREYGISPSTLYNWRKQY   47 (76)
T ss_dssp             HHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCceEeeecccccccccccHHHHHH
Confidence            3344444  36899999999999999999887666

This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=91.11  E-value=0.54  Score=35.40  Aligned_cols=38  Identities=18%  Similarity=0.043  Sum_probs=29.4

Q ss_pred             HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600           77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS  123 (160)
Q Consensus        77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~  123 (160)
                      .-+.+++.+|+|+.||+|..++|..-         ||=.+.|++.+.
T Consensus       118 ~~~~g~s~~EIA~~lgis~~tV~~~l---------~Rar~~Lr~~l~  155 (160)
T PRK09642        118 HYLEEKSYQEIALQEKIEVKTVEMKL---------YRARKWIKKHWK  155 (160)
T ss_pred             HHHhCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHh
Confidence            34558999999999999999999885         555555555543

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=91.07  E-value=0.32  Score=42.16  Aligned_cols=30  Identities=10%  Similarity=0.133  Sum_probs=27.0

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      ...+--..+||+.||||.+||-|..+++||
T Consensus       296 ~~~~gn~~~aA~~LGIsR~tLyrklk~~gi  325 (326)
T PRK11608        296 QQAKFNQKRAAELLGLTYHQLRALLKKHQI  325 (326)
T ss_pred             HHhCCCHHHHHHHhCCCHHHHHHHHHHcCC
Confidence            335778999999999999999999999998

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=91.02  E-value=0.52  Score=36.99  Aligned_cols=38  Identities=16%  Similarity=0.087  Sum_probs=31.1

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      -+.++|+.|+|..||||+.++|.+.         +|-+++|...+..
T Consensus       119 ~~~g~~~~EIA~~lgis~~tV~~~l---------~Rar~~Lr~~l~~  156 (181)
T PRK09637        119 ELEGLSQKEIAEKLGLSLSGAKSRV---------QRGRVKLKELLEG  156 (181)
T ss_pred             HhcCCCHHHHHHHhCCCHHHHHHHH---------HHHHHHHHHHHHH
Confidence            4568999999999999999999885         6666777766654

>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE

Probab=91.02  E-value=1.7  Score=32.03  Aligned_cols=25  Identities=24%  Similarity=0.438  Sum_probs=21.9

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      |++.|+|+.+|||+.||+...+. |+
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~~-Gl   25 (108)
T cd04773           1 MTIGELAHLLGVPPSTLRHWEKE-GL   25 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence            57899999999999999988764 64

Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=90.91  E-value=0.55  Score=36.77  Aligned_cols=39  Identities=15%  Similarity=0.227  Sum_probs=31.2

Q ss_pred             HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600           76 LMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS  123 (160)
Q Consensus        76 L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~  123 (160)
                      |.-+.+++.+|+|+.||+++.++|...         ||=++.|++.+.
T Consensus       147 L~~~~g~s~~EIA~~lgis~~tVk~~l---------~Rar~~Lr~~l~  185 (195)
T PRK12532        147 LKEILGFSSDEIQQMCGISTSNYHTIM---------HRARESLRQCLQ  185 (195)
T ss_pred             hHHHhCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHH
Confidence            345568999999999999999999885         666666666554

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=90.78  E-value=0.64  Score=34.75  Aligned_cols=36  Identities=19%  Similarity=0.365  Sum_probs=28.4

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS  123 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~  123 (160)
                      +-+++.+|+|..||||+.++|.+-         +|=++.|...+.
T Consensus       120 ~~g~s~~EIA~~lgis~~tV~~~l---------~ra~~~Lr~~l~  155 (161)
T PRK09047        120 WEDMDVAETAAAMGCSEGSVKTHC---------SRATHALAKALE  155 (161)
T ss_pred             HhcCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHH
Confidence            447999999999999999999884         555666655544

>PRK15115 response regulator GlrR; Provisional

Probab=90.78  E-value=0.34  Score=42.52  Aligned_cols=31  Identities=23%  Similarity=0.073  Sum_probs=27.6

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      ...+-...+||+.||||.+||-|..+++||.
T Consensus       408 ~~~~gn~~~aA~~Lgisr~tL~rkl~~~~~~  438 (444)
T PRK15115        408 QITKGNVTHAARMAGRNRTEFYKLLSRHELD  438 (444)
T ss_pred             HHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence            3446789999999999999999999999995

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=90.74  E-value=0.42  Score=30.43  Aligned_cols=27  Identities=19%  Similarity=0.241  Sum_probs=19.1

Q ss_pred             HHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           76 LMIYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        76 L~~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +.-+.++|..|+|+.||+|++++++.-
T Consensus        21 l~~~~g~s~~eIa~~l~~s~~~v~~~l   47 (54)
T PF08281_consen   21 LRYFQGMSYAEIAEILGISESTVKRRL   47 (54)
T ss_dssp             HHHTS---HHHHHHHCTS-HHHHHHHH
T ss_pred             HHHHHCcCHHHHHHHHCcCHHHHHHHH
Confidence            345568999999999999999999774

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators

Probab=90.73  E-value=2.1  Score=34.23  Aligned_cols=72  Identities=17%  Similarity=0.204  Sum_probs=42.1

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCCC----Ch--hH-----HHhhHH---------HHHHHHhhhccCCcHHHHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLHR----WP--HR-----KIKSIQ---------RRMSVASGRLRSNDAEERANAQ  141 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~R----WP--yR-----kikSl~---------~~i~~L~~~~~~~~~eerar~~  141 (160)
                      +++.|+|+.+|||++||.-.-+ .|+-.    =+  ||     .+..+.         -.++.++..++..+........
T Consensus         2 ~~I~evA~~~gvs~~tLRyYe~-~GLl~p~~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~~~~~~~~L~   80 (172)
T cd04790           2 LTISQLARQFGLSRSTLLYYER-IGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDATDVLR   80 (172)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCChhHHHHHH
Confidence            6899999999999999987654 46421    11  33     233331         1233444445443334444556


Q ss_pred             HHHHHHHHHHHHH
Q 041600          142 IEIQRLQEEMAAA  154 (160)
Q Consensus       142 ~eIerL~~Em~~~  154 (160)
                      .+++.|.+|+..+
T Consensus        81 ~~~~~l~~ei~~L   93 (172)
T cd04790          81 RRLAELNREIQRL   93 (172)
T ss_pred             HHHHHHHHHHHHH
Confidence            6677777776654

Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=90.72  E-value=0.61  Score=35.11  Aligned_cols=36  Identities=14%  Similarity=0.228  Sum_probs=27.6

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM  122 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i  122 (160)
                      -+.+++.+|+|+.||+|+.++|..-         +|-++.|++.+
T Consensus       122 ~~~~~s~~EIA~~lgis~~tV~~~l---------~ra~~~lr~~l  157 (163)
T PRK07037        122 RLHGETQKDIARELGVSPTLVNFMI---------RDALVHCRKCL  157 (163)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHH
Confidence            3458999999999999999999863         55555555544

>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A

Probab=90.72  E-value=0.32  Score=32.20  Aligned_cols=38  Identities=21%  Similarity=0.121  Sum_probs=26.3

Q ss_pred             HHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcC-CCCCh
Q 041600           74 RDLMIYFHLPIEEAARRMKLCPTVVKKICRRDG-LHRWP  111 (160)
Q Consensus        74 ~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~G-I~RWP  111 (160)
                      ..++.--++.+.++|+.+|||.+++.++.+--. .+.|+
T Consensus         7 r~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p~~~   45 (64)
T PF13560_consen    7 RRLRERAGLSQAQLADRLGVSQSTVSRIERGRRPRPSPD   45 (64)
T ss_dssp             HHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS-BHH
T ss_pred             HHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHH
Confidence            445566689999999999999999999965333 33344

>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators

Probab=90.68  E-value=1  Score=34.35  Aligned_cols=27  Identities=30%  Similarity=0.425  Sum_probs=21.4

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLHR  109 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~R  109 (160)
                      |.+.|+|+.+|||+.||+-. -+.|+-.
T Consensus         1 m~IgE~A~~~gvs~~TLRyY-E~~GLl~   27 (133)
T cd04787           1 MKVKELANAAGVTPDTVRFY-TRIGLLR   27 (133)
T ss_pred             CCHHHHHHHHCcCHHHHHHH-HHCCCCC
Confidence            57899999999999999544 5778643

Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=90.65  E-value=0.43  Score=37.24  Aligned_cols=36  Identities=17%  Similarity=0.138  Sum_probs=28.7

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS  123 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~  123 (160)
                      +.++|.+|+|+.||+|+.++|.+-         ||-++.|+..+.
T Consensus       153 ~~g~s~~EIA~~lgis~~tV~~~l---------~ra~~~Lr~~l~  188 (194)
T PRK12513        153 HGDLELEEIAELTGVPEETVKSRL---------RYALQKLRELLA  188 (194)
T ss_pred             ccCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHH
Confidence            458999999999999999999774         566666666554

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=90.64  E-value=0.24  Score=38.62  Aligned_cols=25  Identities=20%  Similarity=0.257  Sum_probs=21.7

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+.+++.+|+|+.||+|++++|.+-
T Consensus       144 ~~~~~s~~eIA~~lgis~~tV~~~l  168 (189)
T PRK12515        144 YYHEKSVEEVGEIVGIPESTVKTRM  168 (189)
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            4467999999999999999998773

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=90.61  E-value=0.32  Score=30.77  Aligned_cols=24  Identities=33%  Similarity=0.602  Sum_probs=20.6

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      ++++.|+|+.||+|..+++++.++
T Consensus        20 ~~t~~eIa~~lg~s~~~V~~~~~~   43 (50)
T PF04545_consen   20 GLTLEEIAERLGISRSTVRRILKR   43 (50)
T ss_dssp             T-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCcHHHHHHHHHH
Confidence            699999999999999999988643

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=90.60  E-value=0.69  Score=35.46  Aligned_cols=39  Identities=13%  Similarity=0.107  Sum_probs=30.5

Q ss_pred             HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      .-+-++|.+|+|..||+|+.++|..-         +|=.+.|.+.+..
T Consensus       131 ~~~~~~s~~EIA~~lgis~~tV~~~l---------~Ra~~~Lr~~l~~  169 (173)
T PRK12522        131 YYYEQYSYKEMSEILNIPIGTVKYRL---------NYAKKQMREHLEG  169 (173)
T ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHH---------HHHHHHHHHHHHH
Confidence            34568999999999999999999885         6666666665544

>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B

Probab=90.55  E-value=0.3  Score=32.32  Aligned_cols=26  Identities=23%  Similarity=0.361  Sum_probs=22.4

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +++.|+|+.+||++.+|+...++.-+
T Consensus         1 yti~eva~~~gvs~~tlr~y~~~gll   26 (69)
T PF13411_consen    1 YTIKEVAKLLGVSPSTLRYYEREGLL   26 (69)
T ss_dssp             EEHHHHHHHTTTTHHHHHHHHHTTSS
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHhcCc
Confidence            46899999999999999999876554

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=90.36  E-value=0.75  Score=35.60  Aligned_cols=43  Identities=19%  Similarity=0.212  Sum_probs=34.1

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhhhc
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRL  129 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~~~  129 (160)
                      -+-+++.+|+|+.||||..++|..-         +|-++.|++.+..+..-+
T Consensus       130 ~~e~~s~~EIA~~lgis~~tV~~~l---------~ra~~~Lr~~l~~~~~~~  172 (179)
T PRK12543        130 YLHDYSQEEIAQLLQIPIGTVKSRI---------HAALKKLRQKEQIEEIFL  172 (179)
T ss_pred             HHccCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHHHHHHH
Confidence            3457999999999999999999873         677777777777765544

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=90.35  E-value=0.63  Score=36.07  Aligned_cols=39  Identities=18%  Similarity=0.238  Sum_probs=31.2

Q ss_pred             HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      .-+.+++..|+|+.||+++.++|.+-         ||-++.|.+.+..
T Consensus       140 ~~~~g~s~~EIA~~lgis~~tV~~~l---------~Rar~~Lr~~l~~  178 (186)
T PRK05602        140 QYYQGLSNIEAAAVMDISVDALESLL---------ARGRRALRAQLAD  178 (186)
T ss_pred             HHhcCCCHHHHHHHhCcCHHHHHHHH---------HHHHHHHHHHHHh
Confidence            34558999999999999999999885         6666666666654

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=90.29  E-value=0.4  Score=44.24  Aligned_cols=26  Identities=23%  Similarity=0.356  Sum_probs=24.4

Q ss_pred             cHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           83 PIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        83 P~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      ...+||+.||||.|||-|.-|++||.
T Consensus       488 ~~~~aA~~LGisr~tL~rkl~~~gi~  513 (520)
T PRK10820        488 STRKLAKRLGVSHTAIANKLREYGLS  513 (520)
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence            77899999999999999999999994

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

Probab=90.28  E-value=0.59  Score=36.53  Aligned_cols=40  Identities=18%  Similarity=0.071  Sum_probs=32.4

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHh
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVAS  126 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~  126 (160)
                      -+.+++.+|+|+.||+|+.++|.+-         +|=++.|.+.+....
T Consensus       144 ~~~g~s~~EIA~~lgis~~tVk~~l---------~Rar~~Lr~~l~~~~  183 (193)
T TIGR02947       144 DVEGFAYKEIAEIMGTPIGTVMSRL---------HRGRKQLRKQLVDVA  183 (193)
T ss_pred             hhcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHHHH
Confidence            4458999999999999999999885         676777777776544

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.

>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators

Probab=90.28  E-value=2.6  Score=29.98  Aligned_cols=72  Identities=18%  Similarity=0.251  Sum_probs=43.2

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCCC----------Chh------HHHhhHHH---HHHHHhhhccCC-c----HHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLHR----------WPH------RKIKSIQR---RMSVASGRLRSN-D----AEER  137 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~R----------WPy------RkikSl~~---~i~~L~~~~~~~-~----~eer  137 (160)
                      +.+.|+|+.+||++++|+...+ .|+-.          +..      +.++.+.+   .++.+...+... .    ++.+
T Consensus         1 ~~~~eva~~~gi~~~tlr~~~~-~Gll~~~~~~~g~r~y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~~~~~~~~~~~~~   79 (100)
T cd00592           1 YTIGEVAKLLGVSVRTLRYYEE-KGLLPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDEELSLAALL   79 (100)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCcCCCcCCCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcccccchHHHHH
Confidence            4689999999999999998876 45422          111      22333332   234444444321 1    2345


Q ss_pred             HHHHHHHHHHHHHHHHH
Q 041600          138 ANAQIEIQRLQEEMAAA  154 (160)
Q Consensus       138 ar~~~eIerL~~Em~~~  154 (160)
                      .-....++.|++++..+
T Consensus        80 ~~~~~~~~~l~~~~~~l   96 (100)
T cd00592          80 ALLDEKLAELEEKIARL   96 (100)
T ss_pred             HHHHHHHHHHHHHHHHH
Confidence            55667777777777765

Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=90.22  E-value=0.7  Score=35.94  Aligned_cols=38  Identities=18%  Similarity=0.170  Sum_probs=31.8

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      -+-+++.+|+|..||++..+++...         +|-.+.|++.++.
T Consensus       151 ~~~g~s~~eIA~~lgis~~tv~~~l---------~Rar~~Lr~~l~~  188 (193)
T PRK11923        151 EFDGLSYEDIASVMQCPVGTVRSRI---------FRAREAIDKALQP  188 (193)
T ss_pred             HhcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHH
Confidence            3447999999999999999999986         7777777777765

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=90.20  E-value=0.69  Score=36.48  Aligned_cols=40  Identities=13%  Similarity=-0.025  Sum_probs=32.6

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHh
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVAS  126 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~  126 (160)
                      -+.+++.+|+|..||||++++|...         +|=++.|.+.+....
T Consensus       124 ~~eg~s~~EIA~~lgis~~tV~~~l---------~Rar~~Lr~~~~~~~  163 (182)
T PRK12511        124 AIEGLSYQEAAAVLGIPIGTLMSRI---------GRARAALRAFEEGTG  163 (182)
T ss_pred             HHcCCCHHHHHHHhCcCHHHHHHHH---------HHHHHHHHHHHHhcC
Confidence            4557999999999999999999986         666777777666554

>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE

Probab=90.20  E-value=3.5  Score=30.04  Aligned_cols=25  Identities=28%  Similarity=0.365  Sum_probs=21.1

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +++.|+|+.+|||+.||+...+ .|+
T Consensus         1 y~i~e~A~~~gvs~~tlR~Ye~-~Gl   25 (99)
T cd04772           1 YRTVDLARAIGLSPQTVRNYES-LGL   25 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-cCC
Confidence            4789999999999999998765 454

Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=90.15  E-value=0.53  Score=36.07  Aligned_cols=37  Identities=19%  Similarity=0.281  Sum_probs=28.7

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS  123 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~  123 (160)
                      -+.+++.+|+|+.||+++.+++...         +|-.+.|...+.
T Consensus       149 ~~~g~s~~eIA~~lgis~~~v~~~l---------~Rar~~Lr~~l~  185 (187)
T TIGR02948       149 YMEDLSLKEISEILDLPVGTVKTRI---------HRGREALRKQLR  185 (187)
T ss_pred             HhcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHhh
Confidence            3458999999999999999999885         555555555544

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

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=90.14  E-value=0.79  Score=34.56  Aligned_cols=38  Identities=18%  Similarity=0.190  Sum_probs=29.6

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      -+-++|.+|+|..||+|.+++|..-         +|=++.|...|..
T Consensus       118 ~~~~~s~~eIA~~lgis~~tv~~~l---------~ra~~~Lr~~l~~  155 (159)
T PRK12527        118 KLEGLSHQQIAEHLGISRSLVEKHI---------VNAMKHCRVRMRQ  155 (159)
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHH---------HHHHHHHHHHHHh
Confidence            3447999999999999999999884         5666666666553

>PF13518 HTH_28: Helix-turn-helix domain

Probab=90.12  E-value=0.37  Score=30.03  Aligned_cols=25  Identities=20%  Similarity=0.264  Sum_probs=21.5

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      +.++.++|+.+|||.++|.+..+++
T Consensus        12 g~s~~~~a~~~gis~~tv~~w~~~y   36 (52)
T PF13518_consen   12 GESVREIAREFGISRSTVYRWIKRY   36 (52)
T ss_pred             CCCHHHHHHHHCCCHhHHHHHHHHH
Confidence            4699999999999999999887554

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=89.97  E-value=0.45  Score=43.63  Aligned_cols=31  Identities=23%  Similarity=0.278  Sum_probs=27.7

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      ..++-.+.+||+.|||+.+||-|..+++||.
T Consensus       478 ~~~~gn~~~aA~~LGisr~tL~rklk~~gi~  508 (509)
T PRK05022        478 AQHQGNWAAAARALELDRANLHRLAKRLGLK  508 (509)
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence            4457788999999999999999999999994

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=89.95  E-value=0.58  Score=29.65  Aligned_cols=31  Identities=23%  Similarity=0.104  Sum_probs=22.0

Q ss_pred             HHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      .|+.-=-.|..+.|+.+|+|.+++.++-+++
T Consensus        11 ~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL   41 (42)
T PF13404_consen   11 LLQEDGRRSYAELAEELGLSESTVRRRIRRL   41 (42)
T ss_dssp             HHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             HHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence            3444446899999999999999998886553

...

>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A

Probab=89.92  E-value=0.64  Score=30.23  Aligned_cols=44  Identities=14%  Similarity=0.206  Sum_probs=25.5

Q ss_pred             HHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhH
Q 041600           74 RDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI  118 (160)
Q Consensus        74 ~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl  118 (160)
                      .++..--++.+.+.|+..||+.++|.+++..- +..|+.-.+..+
T Consensus         3 ~~~m~~~~it~~~La~~~gis~~tl~~~~~~~-~~~~~~~~l~~i   46 (63)
T PF13443_consen    3 KELMAERGITQKDLARKTGISRSTLSRILNGK-PSNPSLDTLEKI   46 (63)
T ss_dssp             HHHHHHTT--HHHHHHHHT--HHHHHHHHTTT------HHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcc-cccccHHHHHHH
Confidence            44555567899999999999999999998632 355655444433

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=89.78  E-value=0.84  Score=35.60  Aligned_cols=38  Identities=13%  Similarity=0.218  Sum_probs=30.2

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      -+.+++.+|+|..||+|..++|...         ||=++.|++.+..
T Consensus       144 ~~~g~s~~EIA~~lgis~~tV~~~l---------~Rar~~Lr~~l~~  181 (191)
T PRK12520        144 EWLELETEEICQELQITATNAWVLL---------YRARMRLRECLDL  181 (191)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHH
Confidence            4558999999999999999999886         6666666665554

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=89.68  E-value=0.8  Score=36.00  Aligned_cols=37  Identities=16%  Similarity=0.239  Sum_probs=29.1

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS  123 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~  123 (160)
                      -+.+++.+|+|..||+|+.++|.+.         ||=++.|+..+.
T Consensus       147 ~~~g~s~~EIA~~lgis~~tVk~~l---------~RAr~~Lr~~l~  183 (189)
T PRK12530        147 EYLELSSEQICQECDISTSNLHVLL---------YRARLQLQACLS  183 (189)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHH
Confidence            3458999999999999999999885         555566655543

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

Probab=89.62  E-value=0.69  Score=35.23  Aligned_cols=36  Identities=33%  Similarity=0.501  Sum_probs=27.8

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM  122 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i  122 (160)
                      -+.+++.+|+|+.|||++.++|..-         +|=++.|.+.+
T Consensus       132 ~~~g~s~~eiA~~lgis~~tv~~~l---------~Ra~~~Lr~~l  167 (169)
T TIGR02954       132 YYHDLTIKEIAEVMNKPEGTVKTYL---------HRALKKLKKRL  167 (169)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHh
Confidence            3457999999999999999999874         55555555543

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.

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=89.59  E-value=0.66  Score=36.01  Aligned_cols=36  Identities=22%  Similarity=0.404  Sum_probs=28.6

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM  122 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i  122 (160)
                      -+.+++.+|+|..||+|++++|...         +|=.+.|.+.+
T Consensus       135 ~~~g~s~~EIA~~lgis~~tVk~~l---------~Rar~~Lr~~l  170 (185)
T PRK12542        135 VFYNLTYQEISSVMGITEANVRKQF---------ERARKRVQNMI  170 (185)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHH
Confidence            4457999999999999999999884         56566665544

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=89.59  E-value=1.2  Score=28.78  Aligned_cols=21  Identities=19%  Similarity=0.379  Sum_probs=18.4

Q ss_pred             cHHHHHHHcCCChhHHHHHHH
Q 041600           83 PIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        83 P~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +++|+|+.+|||.+|+-|.-.
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln   21 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLN   21 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHT
T ss_pred             CHHHHHHHHCcCHHHHHHHHh
Confidence            478999999999999998843

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=89.59  E-value=0.83  Score=36.10  Aligned_cols=39  Identities=18%  Similarity=0.111  Sum_probs=31.6

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVA  125 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L  125 (160)
                      -+-+++.+|+|+.||+|+.++|..-         +|=++.|.+.+...
T Consensus       129 ~~~g~s~~EIA~~Lgis~~tVk~~l---------~Rar~~Lr~~l~~~  167 (187)
T PRK12516        129 GASGFAYEEAAEICGCAVGTIKSRV---------NRARQRLQEILQIE  167 (187)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHhh
Confidence            4558999999999999999999885         66677777766553

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=89.39  E-value=0.55  Score=35.34  Aligned_cols=33  Identities=30%  Similarity=0.288  Sum_probs=27.8

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      +..|+.-.-.|+.+.|+.||+|++++.++-+++
T Consensus        14 L~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L   46 (154)
T COG1522          14 LRLLQEDARISNAELAERVGLSPSTVLRRIKRL   46 (154)
T ss_pred             HHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            556677778999999999999999998887654

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=89.28  E-value=0.74  Score=38.08  Aligned_cols=41  Identities=12%  Similarity=0.079  Sum_probs=32.2

Q ss_pred             HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHh
Q 041600           77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVAS  126 (160)
Q Consensus        77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~  126 (160)
                      .-+-+++.+|+|+.||+|..++|.+-         +|-++.|++.+...+
T Consensus       183 ~~~eg~s~~EIA~~Lgis~~tVk~~l---------~RAr~kLr~~l~~~~  223 (233)
T PRK12538        183 SYHENMSNGEIAEVMDTTVAAVESLL---------KRGRQQLRDLLRRHE  223 (233)
T ss_pred             HHhcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHHhh
Confidence            34558999999999999999999885         666777776665443

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=89.25  E-value=0.53  Score=41.73  Aligned_cols=31  Identities=16%  Similarity=0.087  Sum_probs=27.3

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      ..++--..+||+.||||.+||-|..+++||.
T Consensus       439 ~~~~gn~~~aA~~Lgisr~tL~rkl~~~~i~  469 (469)
T PRK10923        439 RHTQGHKQEAARLLGWGRNTLTRKLKELGME  469 (469)
T ss_pred             HHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence            3457789999999999999999999999983

>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B

Probab=89.24  E-value=0.7  Score=30.14  Aligned_cols=33  Identities=21%  Similarity=0.352  Sum_probs=24.8

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +.+++.-.++.+.++|+.+|++.+++.++  +.|-
T Consensus         4 lk~~r~~~~lt~~~~a~~~~i~~~~i~~~--e~g~   36 (64)
T PF12844_consen    4 LKELREEKGLTQKDLAEKLGISRSTISKI--ENGK   36 (64)
T ss_dssp             HHHHHHHCT--HHHHHHHHTS-HHHHHHH--HTTS
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HCCC
Confidence            56778888999999999999998888888  5663

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=89.22  E-value=0.56  Score=41.17  Aligned_cols=30  Identities=13%  Similarity=0.229  Sum_probs=26.7

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      ..++--..+||+.||||.+||-|.-+++||
T Consensus       415 ~~~~gn~~~aA~~Lgisr~tl~rkl~~~~i  444 (445)
T TIGR02915       415 ARVDGNIARAAELLGITRPTLYDLMKKHGI  444 (445)
T ss_pred             HHhCCCHHHHHHHhCCCHHHHHHHHHHhCC
Confidence            445678899999999999999999999998

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>TIGR02044 CueR Cu(I)-responsive transcriptional regulator

Probab=89.13  E-value=1.6  Score=32.88  Aligned_cols=25  Identities=20%  Similarity=0.345  Sum_probs=20.4

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      |.+.|+|+.+|||+.||+-.- +.|+
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe-~~GL   25 (127)
T TIGR02044         1 MNIGQVAKLTGLSSKMIRYYE-EKGL   25 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH-HCCC
Confidence            578999999999999998554 4554

This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=89.12  E-value=0.96  Score=35.20  Aligned_cols=36  Identities=19%  Similarity=0.255  Sum_probs=28.6

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS  123 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~  123 (160)
                      +.+++.+|+|..||+|.+++|.+-         +|-++.|.+.+.
T Consensus       155 ~~g~s~~EIA~~lgis~~tV~~~l---------~Ra~~~Lr~~l~  190 (194)
T PRK12519        155 YEGLSQSEIAKRLGIPLGTVKARA---------RQGLLKLRELLQ  190 (194)
T ss_pred             hcCCCHHHHHHHhCCCHHHHHHHH---------HHHHHHHHHHHH
Confidence            457999999999999999999874         566666666554

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]

Probab=89.10  E-value=0.35  Score=46.44  Aligned_cols=31  Identities=23%  Similarity=0.327  Sum_probs=27.6

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHR  109 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R  109 (160)
                      --.--+.+||+.||||.|||-|.-|+|||.+
T Consensus       576 ~~~~~is~aa~~lgi~R~T~yrklk~~gi~~  606 (606)
T COG3284         576 ATNGNISEAARLLGISRSTLYRKLKRHGISK  606 (606)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhCCCC
Confidence            3367899999999999999999999999953

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=89.07  E-value=0.75  Score=36.16  Aligned_cols=36  Identities=19%  Similarity=0.195  Sum_probs=28.5

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM  122 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i  122 (160)
                      -+.+++.+|+|+.||||.+++|...         +|-++.|...+
T Consensus       155 ~~~~~s~~EIA~~Lgis~~tVk~~l---------~ra~~~Lr~~l  190 (194)
T PRK09646        155 YYGGLTYREVAERLAVPLGTVKTRM---------RDGLIRLRDCL  190 (194)
T ss_pred             HHcCCCHHHHHHHhCCChHhHHHHH---------HHHHHHHHHHh
Confidence            3458999999999999999999885         55555555544

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=89.03  E-value=0.84  Score=36.33  Aligned_cols=38  Identities=11%  Similarity=0.222  Sum_probs=30.1

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      -+.+++.+|+|..||+|++++|.+-         +|=++.|++.+..
T Consensus       152 ~~eg~s~~EIA~~lgis~~tVk~~l---------~RAr~~Lr~~l~~  189 (201)
T PRK12545        152 EFLDFEIDDICTELTLTANHCSVLL---------YRARTRLRTCLSE  189 (201)
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHH
Confidence            3457999999999999999999874         5666666666654

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

Probab=89.03  E-value=0.92  Score=34.80  Aligned_cols=24  Identities=21%  Similarity=0.275  Sum_probs=21.6

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +-+++.+|+|..||+|+.++|.+.
T Consensus       148 ~~g~s~~EIA~~lgis~~tVk~~l  171 (183)
T TIGR02999       148 FAGLTVEEIAELLGVSVRTVERDW  171 (183)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            346999999999999999999885

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.

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=88.92  E-value=0.76  Score=37.65  Aligned_cols=37  Identities=11%  Similarity=-0.023  Sum_probs=28.9

Q ss_pred             HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600           77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM  122 (160)
Q Consensus        77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i  122 (160)
                      .-+.++|.+|+|..||||+.++|.+.         ||=++.|.+.+
T Consensus       146 ~y~eg~s~~EIAe~LgiS~~tVk~~L---------~RAr~~Lr~~l  182 (216)
T PRK12533        146 RELEDMSYREIAAIADVPVGTVMSRL---------ARARRRLAALL  182 (216)
T ss_pred             HHhcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHH
Confidence            34568999999999999999999986         55555555544

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=88.89  E-value=0.74  Score=28.77  Aligned_cols=31  Identities=13%  Similarity=0.148  Sum_probs=22.8

Q ss_pred             HHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      .|...=.+++.|+|+.+|+|.+++.+..+++
T Consensus        11 ~l~~~~~~t~~ela~~~~is~~tv~~~l~~L   41 (48)
T PF13412_consen   11 YLRENPRITQKELAEKLGISRSTVNRYLKKL   41 (48)
T ss_dssp             HHHHCTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             HHHHcCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            3444446899999999999999999887654

...

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=88.85  E-value=0.84  Score=35.04  Aligned_cols=36  Identities=25%  Similarity=0.200  Sum_probs=29.6

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS  123 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~  123 (160)
                      +.+++.+|+|..||++..++|...         ||=.+.|.+.+.
T Consensus       152 ~~~~s~~EIA~~lgis~~tv~~~l---------~rar~~Lr~~l~  187 (190)
T TIGR02939       152 LEGLSYEDIARIMDCPVGTVRSRI---------FRAREAIAIRLR  187 (190)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHhh
Confidence            347999999999999999999886         666667766654

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.

>TIGR02051 MerR Hg(II)-responsive transcriptional regulator

Probab=88.84  E-value=1.7  Score=32.85  Aligned_cols=24  Identities=25%  Similarity=0.311  Sum_probs=18.6

Q ss_pred             cHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           83 PIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        83 P~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      ++.|+|+.+|||+.||+-.. +.|+
T Consensus         1 ~I~e~a~~~gvs~~tlR~Ye-~~GL   24 (124)
T TIGR02051         1 TIGELAKAAGVNVETIRYYE-RKGL   24 (124)
T ss_pred             CHHHHHHHHCcCHHHHHHHH-HCCC
Confidence            47899999999999996554 4554

This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

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

Probab=88.81  E-value=0.76  Score=34.56  Aligned_cols=24  Identities=33%  Similarity=0.295  Sum_probs=21.5

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +.+++.+|+|+.||||.++++..-
T Consensus       136 ~~g~s~~eIA~~l~is~~tv~~~l  159 (170)
T TIGR02952       136 GQNLPIAEVARILGKTEGAVKILQ  159 (170)
T ss_pred             hcCCCHHHHHHHHCCCHHHHHHHH
Confidence            348999999999999999999885

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.

>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family

Probab=88.80  E-value=1.1  Score=35.34  Aligned_cols=38  Identities=11%  Similarity=0.180  Sum_probs=30.0

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      -+-+++.+|+|..||++++++|.+.         +|=++.|++.+..
T Consensus       144 ~~~g~s~~EIA~~lgis~~tvk~rl---------~Rar~~Lr~~l~~  181 (188)
T TIGR02943       144 EVLGFESDEICQELEISTSNCHVLL---------YRARLSLRACLSI  181 (188)
T ss_pred             HHhCCCHHHHHHHhCCCHHHHHHHH---------HHHHHHHHHHHHH
Confidence            4457999999999999999999885         6666666665543

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.

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=88.79  E-value=0.93  Score=35.35  Aligned_cols=39  Identities=15%  Similarity=0.212  Sum_probs=31.2

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHh
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVAS  126 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~  126 (160)
                      +-+++.+|+|..||||..++|..-         +|=++.|+..+..+.
T Consensus       148 ~~g~s~~EIA~~lgis~~tV~~~l---------~Ra~~~Lr~~l~~~~  186 (188)
T PRK09640        148 VAELEFQEIADIMHMGLSATKMRY---------KRALDKLREKFAGLA  186 (188)
T ss_pred             hcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHHHh
Confidence            347999999999999999999873         666777777666554

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=88.73  E-value=0.69  Score=36.89  Aligned_cols=41  Identities=12%  Similarity=0.090  Sum_probs=32.9

Q ss_pred             HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHh
Q 041600           77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVAS  126 (160)
Q Consensus        77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~  126 (160)
                      .-+.+++.+|+|..||||+.++|...         +|=++.|++.+...+
T Consensus       145 ~~~~g~s~~EIAe~lgis~~tV~~~l---------~Rar~~Lr~~l~~~~  185 (196)
T PRK12535        145 TQVLGYTYEEAAKIADVRVGTIRSRV---------ARARADLIAATATGQ  185 (196)
T ss_pred             HHHhCCCHHHHHHHhCCCHHHHHHHH---------HHHHHHHHHHhcccc
Confidence            34568999999999999999999885         676777777666544

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

Probab=88.66  E-value=0.88  Score=34.23  Aligned_cols=36  Identities=17%  Similarity=0.237  Sum_probs=27.8

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM  122 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i  122 (160)
                      -+.+++.+|+|..||+|.+++|..-         +|-++.|++.+
T Consensus       123 ~~~g~s~~eIA~~lgis~~tV~~~l---------~ra~~~Lr~~l  158 (162)
T TIGR02983       123 YYEDLSEAQVAEALGISVGTVKSRL---------SRALARLRELL  158 (162)
T ss_pred             HHhcCCHHHHHHHhCCCHHHHHHHH---------HHHHHHHHHHh
Confidence            4457999999999999999999884         55555555443

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.

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=88.64  E-value=1.3  Score=33.36  Aligned_cols=36  Identities=19%  Similarity=0.146  Sum_probs=26.9

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS  123 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~  123 (160)
                      +-++|.+|+|+.|||++++++..-         +|-++.|.+.+.
T Consensus       142 ~~~~s~~eIA~~lgis~~tV~~~l---------~ra~~~Lr~~l~  177 (182)
T PRK09652        142 IEGLSYEEIAEIMGCPIGTVRSRI---------FRAREALRAKLQ  177 (182)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHH
Confidence            348999999999999999998763         454555555444

>COG1476 Predicted transcriptional regulators [Transcription]

Probab=88.51  E-value=0.57  Score=33.22  Aligned_cols=29  Identities=24%  Similarity=0.300  Sum_probs=26.1

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKI  101 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~  101 (160)
                      +.+++..+++.+.+.|+.+|||..|+-.+
T Consensus         6 ~k~~R~~~~ltQ~elA~~vgVsRQTi~~i   34 (68)
T COG1476           6 LKELRAELGLTQEELAKLVGVSRQTIIAI   34 (68)
T ss_pred             HHHHHHHhCcCHHHHHHHcCcCHHHHHHH
Confidence            67889999999999999999998887665

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=88.47  E-value=1.3  Score=34.22  Aligned_cols=40  Identities=18%  Similarity=0.154  Sum_probs=31.1

Q ss_pred             HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHH
Q 041600           77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVA  125 (160)
Q Consensus        77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L  125 (160)
                      .-+.+++.+|+|+.||+|+.++|..-         +|-.+.|...+...
T Consensus       112 ~~~~g~s~~eIA~~lgis~~tV~~~l---------~Rar~~Lr~~l~~~  151 (170)
T TIGR02959       112 TELEGLSQQEIAEKLGLSLSGAKSRV---------QRGRKKLKELLETC  151 (170)
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHHh
Confidence            34568999999999999999999874         66666666666543

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=88.33  E-value=0.49  Score=34.67  Aligned_cols=23  Identities=4%  Similarity=0.098  Sum_probs=21.4

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +++.+++|+.||||.+|++|++|
T Consensus        50 G~S~~eIA~~LgISrsTIyRi~R   72 (88)
T TIGR02531        50 GKTYSDIEAETGASTATISRVKR   72 (88)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHH
Confidence            57999999999999999999886

This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=88.32  E-value=1.1  Score=35.17  Aligned_cols=33  Identities=18%  Similarity=0.274  Sum_probs=26.2

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM  122 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i  122 (160)
                      +++.+|+|..||||++++|.+.         ||=++.|++.+
T Consensus       157 g~s~~EIA~~lgis~~tVk~rl---------~ra~~~Lr~~l  189 (194)
T PRK12531        157 ELPHQQVAEMFDIPLGTVKSRL---------RLAVEKLRHSM  189 (194)
T ss_pred             CCCHHHHHHHhCcCHHHHHHHH---------HHHHHHHHHHh
Confidence            7999999999999999999874         55555555544

>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=88.32  E-value=2.3  Score=31.81  Aligned_cols=25  Identities=32%  Similarity=0.430  Sum_probs=20.2

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      |.+.|+|+..|||+.||+-..++ |+
T Consensus         1 m~IgevA~~~gvs~~tlRyYe~~-GL   25 (120)
T cd04781           1 LDIAEVARQSGLPASTLRYYEEK-GL   25 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence            57899999999999999866543 54

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=88.29  E-value=1  Score=35.07  Aligned_cols=36  Identities=28%  Similarity=0.363  Sum_probs=29.1

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS  123 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~  123 (160)
                      +-+++.+|+|+.||||..++|.+-         ||-++.|.+.+.
T Consensus       145 ~~g~s~~eIA~~lgis~~tV~~~l---------~ra~~~Lr~~l~  180 (184)
T PRK12539        145 LEGLSVAEAATRSGMSESAVKVSV---------HRGLKALAALIG  180 (184)
T ss_pred             HcCCcHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHh
Confidence            347999999999999999999885         666666666553

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=88.23  E-value=0.74  Score=35.09  Aligned_cols=36  Identities=25%  Similarity=0.407  Sum_probs=28.0

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM  122 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i  122 (160)
                      -+.++|.+|+|..||+++.+++...         ||=++.|.+.+
T Consensus       139 ~~~g~s~~eIA~~l~is~~~V~~~l---------~ra~~~l~~~l  174 (176)
T PRK09638        139 HYYGYTYEEIAKMLNIPEGTVKSRV---------HHGIKQLRKEW  174 (176)
T ss_pred             hhcCCCHHHHHHHHCCChhHHHHHH---------HHHHHHHHHHh
Confidence            3457999999999999999999886         55555555543

>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional

Probab=88.18  E-value=0.26  Score=46.29  Aligned_cols=35  Identities=23%  Similarity=0.393  Sum_probs=31.6

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChh
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPH  112 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPy  112 (160)
                      ..-.+++.|.|++.|||.+|+=|.||++|..-++-
T Consensus       371 ~v~~~si~eLA~~~~vS~aTV~Rf~kkLGf~Gf~e  405 (638)
T PRK14101        371 SIINDPIVDIARKADVSQPTVIRFCRSLGCQGLSD  405 (638)
T ss_pred             HHHhccHHHHHHHhCCCHHHHHHHHHHhCCCCHHH
Confidence            44578999999999999999999999999988873

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=88.08  E-value=1.2  Score=35.77  Aligned_cols=38  Identities=18%  Similarity=0.159  Sum_probs=31.2

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      -+-++|.+|+|+.|||+..++|...         +|-.+.|++.+..
T Consensus       151 ~~~g~s~~EIA~~Lgis~~tV~~~l---------~RArk~Lr~~l~~  188 (203)
T PRK09647        151 DIEGLSYEEIAATLGVKLGTVRSRI---------HRGRQQLRAALAA  188 (203)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHH
Confidence            4558999999999999999999886         6667777766665

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=88.05  E-value=1.2  Score=33.95  Aligned_cols=25  Identities=16%  Similarity=-0.037  Sum_probs=22.3

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+-+++.+|+|+.||+|+.++|...
T Consensus       125 ~~~g~s~~eIA~~lgis~~tV~~~l  149 (164)
T PRK12547        125 GASGFSYEDAAAICGCAVGTIKSRV  149 (164)
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence            3457999999999999999999885

>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family

Probab=87.99  E-value=1.9  Score=36.35  Aligned_cols=40  Identities=13%  Similarity=0.042  Sum_probs=30.8

Q ss_pred             HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           76 LMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        76 L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      |.-+++++.+|+|+.||+|+.++|.+-         ||=++.|++.+..
T Consensus       153 L~~~~g~s~~EIA~~lgis~~tV~~~l---------~Rar~~Lr~~l~~  192 (324)
T TIGR02960       153 LRDVLGWRAAETAELLGTSTASVNSAL---------QRARATLDEVGPS  192 (324)
T ss_pred             hHHHhCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHhccc
Confidence            345678999999999999999999884         5555566555443

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.

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=87.76  E-value=1.2  Score=34.97  Aligned_cols=42  Identities=17%  Similarity=0.158  Sum_probs=34.1

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhhhc
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASGRL  129 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~~~  129 (160)
                      +-+++.+|+|+.|||++.++|.+-         +|=++.|.+.+..+...+
T Consensus       150 ~~g~s~~eIA~~lgis~~tV~~~l---------~Ra~~~Lr~~l~~~~~~~  191 (196)
T PRK12524        150 IEGLSNPEIAEVMEIGVEAVESLT---------ARGKRALAALLAGQRAEL  191 (196)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHhccccc
Confidence            346999999999999999999884         777778888777765544

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=87.74  E-value=1.4  Score=34.30  Aligned_cols=46  Identities=15%  Similarity=0.321  Sum_probs=40.7

Q ss_pred             hccCCCCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCC-Ch
Q 041600           66 ERTGKLTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHR-WP  111 (160)
Q Consensus        66 ~r~~~lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R-WP  111 (160)
                      ..-..+++++|...+++|...+...|.-+...|++.....|+.| ||
T Consensus       143 ~~~~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~  189 (189)
T PRK12515        143 VYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLKAAGVERGWP  189 (189)
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHhccccCCC
Confidence            34577999999999999999999999999999999999988866 88

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

Probab=87.63  E-value=0.8  Score=34.14  Aligned_cols=25  Identities=12%  Similarity=0.016  Sum_probs=22.3

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+.+++.+|+|+.||||+++++...
T Consensus       124 ~~~g~~~~eIA~~l~is~~tv~~~l  148 (159)
T TIGR02989       124 YQRGVSLTALAEQLGRTVNAVYKAL  148 (159)
T ss_pred             HhcCCCHHHHHHHhCCCHHHHHHHH
Confidence            4558999999999999999999875

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).

>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator

Probab=87.61  E-value=2  Score=32.56  Aligned_cols=25  Identities=20%  Similarity=0.344  Sum_probs=20.4

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      |++.|+|+.+|||+.||+-..+ .|+
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~-~GL   25 (127)
T TIGR02047         1 MKIGELAQKTGVSVETIRFYEK-QGL   25 (127)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHH-CCC
Confidence            5789999999999999987664 443

This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=87.61  E-value=1.2  Score=34.64  Aligned_cols=26  Identities=27%  Similarity=0.252  Sum_probs=22.8

Q ss_pred             HhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           77 MIYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        77 ~~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      .-+.+++.+|+|+.||+|..++|..-
T Consensus       139 ~~~~g~s~~EIA~~l~is~~tv~~~l  164 (179)
T PRK09415        139 FYYEELSIKEIAEVTGVNENTVKTRL  164 (179)
T ss_pred             HHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence            34568999999999999999999885

>PHA01976 helix-turn-helix protein

Probab=87.60  E-value=2.7  Score=27.52  Aligned_cols=33  Identities=12%  Similarity=0.024  Sum_probs=27.7

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +..++.--++.+.++|+.+||+.+++.++  +.|.
T Consensus         7 l~~~R~~~glt~~~lA~~~gvs~~~v~~~--e~g~   39 (67)
T PHA01976          7 LIKARNARAWSAPELSRRAGVRHSLIYDF--EADK   39 (67)
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHH--HcCC
Confidence            55677888999999999999999999998  4443

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=87.44  E-value=1.1  Score=34.97  Aligned_cols=38  Identities=8%  Similarity=0.084  Sum_probs=29.1

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      -+.+++.+|+|..||||++++|..-         +|-.+.|.+.+..
T Consensus       167 ~~e~~s~~EIA~~lgis~~tV~~~l---------~rar~~Lr~~l~~  204 (208)
T PRK08295        167 YLDGKSYQEIAEELNRHVKSIDNAL---------QRVKRKLEKYLEN  204 (208)
T ss_pred             HHccCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHh
Confidence            3447999999999999999999763         5556666665544

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=87.28  E-value=1.4  Score=34.60  Aligned_cols=38  Identities=16%  Similarity=0.044  Sum_probs=31.1

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      -+.+++.+|+|..||+|..++|...         ||=.+.|++.+..
T Consensus       124 ~~~g~s~~EIA~~Lgis~~tV~~~l---------~RAr~~Lr~~l~~  161 (182)
T PRK12540        124 GASGFSYEDAAAICGCAVGTIKSRV---------NRARSKLSALLYV  161 (182)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHh
Confidence            4568999999999999999999986         6667777666654

>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators

Probab=87.19  E-value=2.3  Score=31.57  Aligned_cols=25  Identities=28%  Similarity=0.488  Sum_probs=20.4

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      |++.|+|+.+||++.||+ .--+.|+
T Consensus         1 ~~I~eva~~~gvs~~tLR-yYe~~GL   25 (123)
T cd04770           1 MKIGELAKAAGVSPDTIR-YYERIGL   25 (123)
T ss_pred             CCHHHHHHHHCcCHHHHH-HHHHCCC
Confidence            578999999999999995 5556664

Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases []

Probab=87.10  E-value=0.53  Score=28.39  Aligned_cols=21  Identities=29%  Similarity=0.339  Sum_probs=18.3

Q ss_pred             CcHHHHHHHcCCChhHHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -.+.|||+.||++.+++.+.|
T Consensus        17 ~Si~eAa~~l~i~~~~I~~~l   37 (37)
T PF07453_consen   17 DSIREAARYLGISHSTISKYL   37 (37)
T ss_pred             cCHHHHHHHhCCCHHHHHHhC
Confidence            578999999999999998764

>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR

Probab=87.08  E-value=4.4  Score=31.61  Aligned_cols=25  Identities=24%  Similarity=0.357  Sum_probs=21.5

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      |+|.|+|+.+|||+.||+-..+. |+
T Consensus         2 ~~IgevA~~~Gvs~~tLRyYE~~-GL   26 (142)
T TIGR01950         2 LTVGELAKRSGVAVSALHFYESK-GL   26 (142)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence            68999999999999999877654 54

SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.

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

Probab=87.01  E-value=1.2  Score=34.12  Aligned_cols=25  Identities=24%  Similarity=0.191  Sum_probs=22.1

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+.++|.+|+|..||||+.++++.-
T Consensus       153 ~~~g~s~~eIA~~lgis~~~v~~~l  177 (189)
T TIGR02984       153 HLEGLSFAEVAERMDRSEGAVSMLW  177 (189)
T ss_pred             HhcCCCHHHHHHHHCcCHHHHHHHH
Confidence            3457999999999999999999885

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).

>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators

Probab=86.96  E-value=2.2  Score=32.26  Aligned_cols=23  Identities=22%  Similarity=0.239  Sum_probs=20.0

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      |++.|+|+.+|||+.||+-..+.
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe~~   23 (127)
T cd01108           1 MNIGEAAKLTGLSAKMIRYYEEI   23 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57899999999999999977654

Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=86.93  E-value=1.5  Score=35.46  Aligned_cols=35  Identities=14%  Similarity=0.302  Sum_probs=27.8

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      +++.+|+|..||||+.++|++-         +|=++.|++.+..
T Consensus       198 g~s~~EIA~~lgis~~tVk~~~---------~rA~~~Lr~~l~~  232 (234)
T PRK08301        198 EKTQKEVADMLGISQSYISRLE---------KRIIKRLKKEINK  232 (234)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHh
Confidence            7999999999999999999884         5555666655543

>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR

Probab=86.78  E-value=1.9  Score=32.44  Aligned_cols=25  Identities=28%  Similarity=0.474  Sum_probs=20.2

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      ++|.|+|+.+|||+.||+-.-+. |+
T Consensus         1 ~~Igeva~~~gvs~~tlRyYe~~-GL   25 (118)
T cd04776           1 YTISELAREFDVTPRTLRFYEDK-GL   25 (118)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence            46889999999999999866543 65

Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>PRK09726 antitoxin HipB; Provisional

Probab=86.63  E-value=0.98  Score=32.00  Aligned_cols=31  Identities=6%  Similarity=0.062  Sum_probs=27.3

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +..++.-.++.+.++|+.+||+.+++.++.+
T Consensus        17 lk~~R~~~gltq~elA~~~gvs~~tis~~e~   47 (88)
T PRK09726         17 MKLVRQQNGWTQSELAKKIGIKQATISNFEN   47 (88)
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            5566777899999999999999999999976

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=86.51  E-value=1.4  Score=33.90  Aligned_cols=33  Identities=15%  Similarity=0.157  Sum_probs=26.2

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHH
Q 041600           80 FHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRR  121 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~  121 (160)
                      -+++.+|+|+.||+++.++|..-         +|=++.|.+.
T Consensus       144 ~g~s~~eIA~~lgis~~tV~~~l---------~Rar~~Lr~~  176 (179)
T PRK12514        144 EGLSYKELAERHDVPLNTMRTWL---------RRSLLKLREC  176 (179)
T ss_pred             cCCCHHHHHHHHCCChHHHHHHH---------HHHHHHHHHH
Confidence            38999999999999999999874         5555555544

>smart00497 IENR1 Intron encoded nuclease repeat motif

Probab=86.46  E-value=0.77  Score=28.90  Aligned_cols=23  Identities=22%  Similarity=0.296  Sum_probs=20.9

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      -.+.|||+.||++.+++.+.|+.
T Consensus        18 ~S~~eAa~~lg~~~~~I~~~~~~   40 (53)
T smart00497       18 SSIREAAKYLGISHSSISKYLNT   40 (53)
T ss_pred             cCHHHHHHHhCCCHHHHHHHHhC
Confidence            47899999999999999999875

Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=86.40  E-value=1.4  Score=33.28  Aligned_cols=25  Identities=24%  Similarity=0.186  Sum_probs=22.4

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+.++|.+|+|..||+|..++|...
T Consensus       125 ~~~~~s~~eIA~~lgis~~tv~~~l  149 (161)
T PRK12541        125 DYYGFSYKEIAEMTGLSLAKVKIEL  149 (161)
T ss_pred             HhcCCCHHHHHHHHCCCHHHHHHHH
Confidence            4578999999999999999999874

>PRK10072 putative transcriptional regulator; Provisional

Probab=86.33  E-value=1.3  Score=32.85  Aligned_cols=31  Identities=23%  Similarity=0.199  Sum_probs=27.6

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +..|+.-.++.+.++|+.||||.+++.+..+
T Consensus        38 ik~LR~~~glTQ~elA~~lGvS~~TVs~WE~   68 (96)
T PRK10072         38 FEQLRKGTGLKIDDFARVLGVSVAMVKEWES   68 (96)
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            6667788899999999999999999998854

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=86.26  E-value=1.4  Score=34.56  Aligned_cols=27  Identities=15%  Similarity=0.060  Sum_probs=23.5

Q ss_pred             HHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           76 LMIYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        76 L~~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      |.-+.+++.+|+|..||+|+.++|...
T Consensus       141 L~~~~g~s~~EIA~~lgis~~tVk~~l  167 (185)
T PRK09649        141 LTQLLGLSYADAAAVCGCPVGTIRSRV  167 (185)
T ss_pred             hHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            345568999999999999999999885

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=86.18  E-value=1.7  Score=32.73  Aligned_cols=39  Identities=13%  Similarity=0.102  Sum_probs=30.0

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVA  125 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L  125 (160)
                      .|.+++.+|+|..|||+..++|+.-         +|=++.|...+...
T Consensus       124 ~~~g~s~~eIA~~lgis~~tV~~~i---------~ra~~~Lr~~l~~~  162 (166)
T PRK09639        124 RFSGYSYKEIAEALGIKESSVGTTL---------ARAKKKFRKIYEQM  162 (166)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHHh
Confidence            4478999999999999999999873         55566666655543

>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain

Probab=86.00  E-value=0.86  Score=33.14  Aligned_cols=28  Identities=21%  Similarity=0.219  Sum_probs=25.9

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      .+.+.++|+.|||+...|-+..|+.||-
T Consensus        24 ~~ti~~~AK~L~i~~~~l~~~Lr~~g~l   51 (111)
T PF03374_consen   24 LYTIREAAKLLGIGRNKLFQWLREKGWL   51 (111)
T ss_pred             CccHHHHHHHhCCCHHHHHHHHHhCCce
Confidence            4889999999999999999999999973

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding

>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator

Probab=85.97  E-value=8.2  Score=28.94  Aligned_cols=25  Identities=28%  Similarity=0.349  Sum_probs=19.5

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      |++.|+|+.+|||+.||+-.. +.|+
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye-~~GL   25 (126)
T cd04783           1 LTIGELAKAAGVNVETIRYYQ-RRGL   25 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH-HCCC
Confidence            578999999999999996554 4453

Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=85.84  E-value=1.9  Score=32.79  Aligned_cols=38  Identities=24%  Similarity=0.146  Sum_probs=29.0

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      -+.+++.+|+|..||+|..+++..-         +|=.+.|++.+..
T Consensus       121 ~~~g~s~~eIA~~lgis~~tv~~~l---------~Rar~~Lr~~l~~  158 (165)
T PRK09644        121 DVHELTYEEAASVLDLKLNTYKSHL---------FRGRKRLKALLKE  158 (165)
T ss_pred             HHhcCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHh
Confidence            4568999999999999999998773         5555556555543

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=85.76  E-value=1  Score=29.66  Aligned_cols=25  Identities=24%  Similarity=0.244  Sum_probs=21.1

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +++.|+|+.+||++.+|++..+ .|+
T Consensus         1 ~s~~eva~~~gvs~~tlr~~~~-~gl   25 (70)
T smart00422        1 YTIGEVAKLAGVSVRTLRYYER-IGL   25 (70)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence            4689999999999999998876 443

>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional

Probab=85.69  E-value=6.6  Score=31.23  Aligned_cols=24  Identities=21%  Similarity=0.225  Sum_probs=20.6

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDG  106 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~G  106 (160)
                      |.+.|+|+.+||++.||+-.. +.|
T Consensus        12 ~~IgevAk~~gvs~~TlRyYE-~~G   35 (154)
T PRK15002         12 LTPGEVAKRSGVAVSALHFYE-SKG   35 (154)
T ss_pred             ccHHHHHHHHCcCHHHHHHHH-HCC
Confidence            799999999999999998765 444

>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family

Probab=85.65  E-value=1.8  Score=31.67  Aligned_cols=41  Identities=24%  Similarity=0.199  Sum_probs=31.1

Q ss_pred             hhccCCCCH---HHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           65 RERTGKLTL---RDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        65 r~r~~~lt~---~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      ++....++-   ..++...++.+.++|+.||++.+++.+.  +.|-
T Consensus        59 ~~~~~~~~~~~i~~~r~~~gltq~~lA~~lg~~~~tis~~--e~g~  102 (127)
T TIGR03830        59 RKVDGLLTPPEIRRIRKKLGLSQREAAELLGGGVNAFSRY--ERGE  102 (127)
T ss_pred             HHccCCcCHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH--HCCC
Confidence            344444444   4456888999999999999999999998  4554

This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.

>PRK11303 DNA-binding transcriptional regulator FruR; Provisional

Probab=85.60  E-value=1.7  Score=35.76  Aligned_cols=24  Identities=17%  Similarity=0.238  Sum_probs=20.7

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHc
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      |.++|+|+..|||.+|+-|.-...
T Consensus         1 ~ti~dIA~~aGVS~~TVSrvLn~~   24 (328)
T PRK11303          1 MKLDEIARLAGVSRTTASYVINGK   24 (328)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Confidence            478999999999999999996544

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=85.52  E-value=1.7  Score=33.68  Aligned_cols=25  Identities=20%  Similarity=-0.028  Sum_probs=21.8

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+-++|.+|+|+.||||+.++|..-
T Consensus       146 ~~~~~s~~eIA~~lgis~~tV~~~l  170 (182)
T PRK12537        146 YVDGCSHAEIAQRLGAPLGTVKAWI  170 (182)
T ss_pred             HHcCCCHHHHHHHHCCChhhHHHHH
Confidence            3457999999999999999999873

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=85.50  E-value=1.8  Score=33.62  Aligned_cols=24  Identities=25%  Similarity=0.236  Sum_probs=21.3

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +.+++.+|+|..|||++.++|..-
T Consensus       153 ~~g~s~~EIA~~lgis~~tV~~~l  176 (189)
T PRK09648        153 VVGLSAEETAEAVGSTPGAVRVAQ  176 (189)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHH
Confidence            458999999999999999999773

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=85.46  E-value=1.1  Score=34.82  Aligned_cols=25  Identities=16%  Similarity=0.170  Sum_probs=22.3

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+-+++.+|+|..||||+.++|...
T Consensus       140 ~~~g~s~~EIA~~lgis~~tVk~~l  164 (178)
T PRK12529        140 TLDGMKQKDIAQALDIALPTVKKYI  164 (178)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            4457999999999999999999885

>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators

Probab=85.43  E-value=3.2  Score=31.16  Aligned_cols=25  Identities=20%  Similarity=0.356  Sum_probs=19.1

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      |++.|+|+.+|||+.||.-.- +.|+
T Consensus         1 m~IgevA~~~gvs~~tLRyYe-~~GL   25 (127)
T cd04784           1 MKIGELAKKTGCSVETIRYYE-KEGL   25 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH-HCCC
Confidence            578899999999999987554 3443

Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []

Probab=85.43  E-value=1.4  Score=28.28  Aligned_cols=22  Identities=18%  Similarity=0.380  Sum_probs=16.8

Q ss_pred             CcHHHHHHHcCCChhHHHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +++.+||+..||+.|||-++-+
T Consensus        17 ~S~r~AA~~ygVp~sTL~~r~~   38 (45)
T PF05225_consen   17 MSIRKAAKKYGVPRSTLRRRLR   38 (45)
T ss_dssp             S-HHHHHHHHT--HHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHc
Confidence            9999999999999999997643

In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.

>PRK11511 DNA-binding transcriptional activator MarA; Provisional

Probab=85.38  E-value=2.8  Score=31.51  Aligned_cols=28  Identities=14%  Similarity=0.347  Sum_probs=25.3

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc-CCC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD-GLH  108 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~  108 (160)
                      .+++.++|+.+|+|+++|.|++++. |++
T Consensus        25 ~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s   53 (127)
T PRK11511         25 PLSLEKVSERSGYSKWHLQRMFKKETGHS   53 (127)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence            3899999999999999999999987 873

>TIGR01817 nifA Nif-specific regulatory protein

Probab=85.28  E-value=1.2  Score=40.88  Aligned_cols=31  Identities=19%  Similarity=0.118  Sum_probs=27.1

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      ..++--..+||+.||||.+||.+..|++||.
T Consensus       500 ~~~~gn~~~aA~~LGisr~tLy~klk~~gi~  530 (534)
T TIGR01817       500 EQAGWVQAKAARLLGMTPRQVGYALRKLNIE  530 (534)
T ss_pred             HHhCCCHHHHHHHHCCCHHHHHHHHHHcCCC
Confidence            4456678999999999999999999999983

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

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

Probab=85.20  E-value=1.5  Score=32.09  Aligned_cols=24  Identities=13%  Similarity=0.095  Sum_probs=21.3

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +.++|..|+|+.||||..+++.+-
T Consensus       127 ~~~~~~~eIA~~lgis~~tv~~~~  150 (161)
T TIGR02985       127 FEGKSYKEIAEELGISVKTVEYHI  150 (161)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHH
Confidence            348999999999999999999874

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=85.08  E-value=2  Score=32.17  Aligned_cols=33  Identities=9%  Similarity=-0.033  Sum_probs=22.5

Q ss_pred             HHHHHcCCChhHHHHHHHHcCCCCChhHHHhhH
Q 041600           86 EAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI  118 (160)
Q Consensus        86 eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl  118 (160)
                      +|...+--+-.++..+|+++||+..-..++...
T Consensus        20 ~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~   52 (121)
T PRK09413         20 AIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQ   52 (121)
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            344444334446788999999988777777554

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=85.08  E-value=1.7  Score=33.05  Aligned_cols=37  Identities=16%  Similarity=0.158  Sum_probs=29.3

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      +.+++..|+|..||+|+.++|..-         +|-.+.|...+.+
T Consensus       134 ~~g~s~~eIA~~lg~s~~tv~~~l---------~Rar~~L~~~l~~  170 (175)
T PRK12518        134 LEDLPQKEIAEILNIPVGTVKSRL---------FYARRQLRKFLQQ  170 (175)
T ss_pred             hcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHh
Confidence            457999999999999999999874         6666666665544

>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins

Probab=85.02  E-value=5.9  Score=28.24  Aligned_cols=26  Identities=23%  Similarity=0.141  Sum_probs=18.1

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           80 FHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      |++.+.|+|++||-|.+.+.+.-+=+
T Consensus         2 ~G~tq~eIA~~lGks~s~Vs~~l~Ll   27 (93)
T PF08535_consen    2 FGWTQEEIAKRLGKSRSWVSNHLALL   27 (93)
T ss_dssp             TT--HHHHHHHTT--HHHHHHHHGGG
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            78999999999999999988775433

The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=84.90  E-value=1.9  Score=34.16  Aligned_cols=38  Identities=18%  Similarity=0.106  Sum_probs=30.2

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      -+.+++..|+|..||||..++|..-         ||=.+.|++.+..
T Consensus       126 ~~~g~s~~EIA~~LgiS~~tVk~~l---------~Rar~~Lr~~l~~  163 (188)
T PRK12546        126 GASGFSYEEAAEMCGVAVGTVKSRA---------NRARARLAELLQL  163 (188)
T ss_pred             HhcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHhc
Confidence            4568999999999999999999885         6666666665543

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=84.84  E-value=1.2  Score=27.00  Aligned_cols=27  Identities=22%  Similarity=0.231  Sum_probs=22.6

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHHHHcC
Q 041600           80 FHLPIEEAARRMKLCPTVVKKICRRDG  106 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~CR~~G  106 (160)
                      |.+++.+.|+.+|++.+++.+..+++-
T Consensus         7 ~~~s~~~la~~l~~s~~tv~~~l~~L~   33 (48)
T smart00419        7 LPLTRQEIAELLGLTRETVSRTLKRLE   33 (48)
T ss_pred             eccCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            568899999999999999988866553

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=84.75  E-value=2  Score=33.11  Aligned_cols=24  Identities=25%  Similarity=0.171  Sum_probs=21.5

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +-+++.+|+|..||||+.++|..-
T Consensus       149 ~~~~s~~eIA~~lgis~~~V~~~l  172 (186)
T PRK13919        149 YQGYTHREAAQLLGLPLGTLKTRA  172 (186)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            457999999999999999999874

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=84.67  E-value=1.4  Score=35.99  Aligned_cols=36  Identities=11%  Similarity=0.274  Sum_probs=27.7

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVA  125 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L  125 (160)
                      +++.+|+|+.||||..++++.-         +|=++.|++.+..|
T Consensus       198 g~s~~EIA~~Lgis~~tV~~~l---------~ra~~~LR~~l~~~  233 (234)
T TIGR02835       198 EKTQKEVADMLGISQSYISRLE---------KRILKRLKKEINRM  233 (234)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHhhcc
Confidence            5999999999999999998773         45556666655543

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.

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=84.50  E-value=0.89  Score=43.11  Aligned_cols=24  Identities=29%  Similarity=0.357  Sum_probs=22.6

Q ss_pred             HHHHHHcCCChhHHHHHHHHcCCC
Q 041600           85 EEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        85 ~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      .+||+.|||+.|||-|..+++||.
T Consensus       661 ~~aA~~LGi~R~tL~rklk~~gi~  684 (686)
T PRK15429        661 KGAAQRLGLKRTTLLSRMKRLGID  684 (686)
T ss_pred             HHHHHHhCCCHHHHHHHHHHcCCC
Confidence            599999999999999999999994

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=84.33  E-value=1.5  Score=32.49  Aligned_cols=24  Identities=21%  Similarity=0.213  Sum_probs=21.3

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +-+++.+|+|..||+++.+++..-
T Consensus       119 ~~g~s~~eIA~~lgis~~tv~~~l  142 (154)
T TIGR02950       119 FKEFSYKEIAELLNLSLAKVKSNL  142 (154)
T ss_pred             hccCcHHHHHHHHCCCHHHHHHHH
Confidence            347999999999999999999874

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=84.32  E-value=2.8  Score=33.05  Aligned_cols=39  Identities=15%  Similarity=0.110  Sum_probs=31.0

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVA  125 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L  125 (160)
                      -+-+++.+|+|..||||..+++...         +|=++.|...+..-
T Consensus       141 ~~~g~s~~EIA~~lgis~~tV~~~l---------~Rar~~Lr~~l~~~  179 (188)
T PRK12517        141 VIGGFSGEEIAEILDLNKNTVMTRL---------FRARNQLKEALEKP  179 (188)
T ss_pred             HHhCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHHH
Confidence            3447999999999999999999885         66667776666543

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=84.29  E-value=2.4  Score=34.20  Aligned_cols=38  Identities=11%  Similarity=0.155  Sum_probs=31.0

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      -+-+++.+|+|..||++..++|...         ||=++.|.+.+..
T Consensus       161 ~~~g~s~~EIAe~lgis~~tV~~~l---------~RAr~~Lr~~l~~  198 (206)
T PRK12544        161 EFIELETNEICHAVDLSVSNLNVLL---------YRARLRLRECLEN  198 (206)
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHH
Confidence            4558999999999999999999885         6767777776653

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=84.29  E-value=2.2  Score=34.06  Aligned_cols=37  Identities=22%  Similarity=0.371  Sum_probs=28.5

Q ss_pred             hhc-CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600           78 IYF-HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS  123 (160)
Q Consensus        78 ~yF-~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~  123 (160)
                      .|| +++.+|+|..||||..++|..-         ||-++.|.+.+.
T Consensus       165 ~~~~g~s~~EIA~~lgis~~tV~~~l---------~Ra~~~Lr~~l~  202 (206)
T PRK12526        165 VYFQELSQEQLAQQLNVPLGTVKSRL---------RLALAKLKVQMG  202 (206)
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHh
Confidence            344 7999999999999999999773         555566655554

>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []

Probab=84.28  E-value=1.3  Score=29.99  Aligned_cols=27  Identities=19%  Similarity=0.090  Sum_probs=24.6

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +++++++|+.|||+.+|+..-..+.+=
T Consensus        13 G~~~~eIA~~Lg~~~~TV~~W~~r~~W   39 (58)
T PF06056_consen   13 GWSIKEIAEELGVPRSTVYSWKDRYKW   39 (58)
T ss_pred             CCCHHHHHHHHCCChHHHHHHHHhhCc
Confidence            699999999999999999999888764

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A

Probab=84.28  E-value=3.1  Score=29.01  Aligned_cols=30  Identities=23%  Similarity=0.258  Sum_probs=23.8

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +.++..--++++.++|+.|||+.+.+-++=
T Consensus        23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~   52 (80)
T PF13744_consen   23 IRELREERGLTQAELAERLGISQPRVSRLE   52 (80)
T ss_dssp             HHHHHHCCT--HHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCCChhHHHHHH
Confidence            667777789999999999999999999985

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=84.25  E-value=1  Score=33.78  Aligned_cols=26  Identities=8%  Similarity=0.120  Sum_probs=22.5

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDG  106 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~G  106 (160)
                      .+|++|+|+.||||.+++-|.-+-+.
T Consensus        55 ~~tQrEIa~~lGiS~atIsR~sn~lk   80 (94)
T TIGR01321        55 NMSQREIASKLGVSIATITRGSNNLK   80 (94)
T ss_pred             CCCHHHHHHHhCCChhhhhHHHhhcc
Confidence            59999999999999999998865544

This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=84.20  E-value=2.3  Score=33.73  Aligned_cols=25  Identities=20%  Similarity=0.061  Sum_probs=22.3

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +-+++++|+|+.||+|.++++++.+
T Consensus        19 ~~GlTq~EIAe~LGiS~~tVs~ie~   43 (141)
T PRK03975         19 ERGLTQQEIADILGTSRANVSSIEK   43 (141)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3579999999999999999999864

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=84.18  E-value=1.1  Score=32.90  Aligned_cols=24  Identities=21%  Similarity=0.236  Sum_probs=21.3

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      +.|+.+||+++|||.+|.+|.-.+
T Consensus        25 g~~~a~aA~~~gVS~~Ta~kW~~R   48 (85)
T PF13011_consen   25 GWPVAHAAAEFGVSRRTAYKWLAR   48 (85)
T ss_pred             CCcHHHHHHHhCCCHHHHHHHHHH
Confidence            589999999999999999987544

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=84.09  E-value=0.78  Score=34.03  Aligned_cols=22  Identities=14%  Similarity=0.259  Sum_probs=19.6

Q ss_pred             hcCCcHHHHHHHcCCChhHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKK  100 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr  100 (160)
                      +-+++.+|+|..||+|+.|+||
T Consensus       121 ~~~~s~~EIA~~l~is~~tV~~  142 (142)
T TIGR03209       121 FEDMKEIDIAKKLHISRQSVYK  142 (142)
T ss_pred             HcCCCHHHHHHHHCcCHHhhcC
Confidence            4479999999999999999985

Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=83.99  E-value=2.3  Score=32.77  Aligned_cols=23  Identities=17%  Similarity=0.208  Sum_probs=21.2

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHH
Q 041600           80 FHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+++..|+|..||+|..+++...
T Consensus       146 ~g~s~~eIA~~l~is~~tV~~~l  168 (184)
T PRK12512        146 EGASIKETAAKLSMSEGAVRVAL  168 (184)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Confidence            47999999999999999999885

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=83.89  E-value=1  Score=31.20  Aligned_cols=22  Identities=9%  Similarity=0.353  Sum_probs=19.7

Q ss_pred             CCcHHHHHHHcCCChhHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      .++.+++|+.|||+.+++++-=
T Consensus        22 ~i~lkdIA~~Lgvs~~tIr~WK   43 (60)
T PF10668_consen   22 KIKLKDIAEKLGVSESTIRKWK   43 (60)
T ss_pred             CccHHHHHHHHCCCHHHHHHHh
Confidence            5899999999999999998764

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=83.88  E-value=2.1  Score=35.77  Aligned_cols=37  Identities=16%  Similarity=0.173  Sum_probs=29.7

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS  123 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~  123 (160)
                      -+.+++.+|+|+.||+|..++|..-         +|-++.|...+.
T Consensus       129 ~~eg~S~~EIAe~LgiS~~tVksrL---------~Rark~Lr~~l~  165 (228)
T PRK06704        129 DVFQYSIADIAKVCSVSEGAVKASL---------FRSRNRLKTVSE  165 (228)
T ss_pred             HhhCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHH
Confidence            4568999999999999999999885         666666666554

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=83.80  E-value=3  Score=31.21  Aligned_cols=24  Identities=21%  Similarity=0.019  Sum_probs=21.3

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +.+++..|+|+.||+|+.++++.-
T Consensus       139 ~~~~~~~eIA~~lgis~~tv~~~~  162 (179)
T PRK11924        139 VEGLSYREIAEILGVPVGTVKSRL  162 (179)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHH
Confidence            458999999999999999999873

>smart00354 HTH_LACI helix_turn _helix lactose operon repressor

Probab=83.80  E-value=1  Score=30.68  Aligned_cols=24  Identities=17%  Similarity=0.296  Sum_probs=21.0

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHc
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      +++.|.|+.+|||.+++-++|+..
T Consensus         1 ~t~~~iA~~~gvS~~TVSr~ln~~   24 (70)
T smart00354        1 ATIKDVARLAGVSKATVSRVLNGN   24 (70)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCC
Confidence            368899999999999999999653

>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators

Probab=83.61  E-value=1.2  Score=31.73  Aligned_cols=25  Identities=20%  Similarity=0.363  Sum_probs=21.8

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +++.|+|+.+||++.+|+...++ |+
T Consensus         2 ~ti~evA~~~gvs~~tLR~ye~~-Gl   26 (88)
T cd01105           2 IGIGEVSKLTGVSPRQLRYWEEK-GL   26 (88)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence            68999999999999999988765 54

Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional

Probab=83.50  E-value=4.4  Score=31.34  Aligned_cols=25  Identities=24%  Similarity=0.392  Sum_probs=21.2

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +++.|+|+.+|||+.||+-.-++ |+
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~~-GL   26 (140)
T PRK09514          2 YRIGELAKLAEVTPDTLRFYEKQ-GL   26 (140)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHC-CC
Confidence            68999999999999999877654 54

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=83.41  E-value=2.6  Score=32.32  Aligned_cols=25  Identities=16%  Similarity=0.105  Sum_probs=22.1

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+-+++.+|+|..||||.+++|..-
T Consensus       132 ~~~g~s~~EIA~~lgis~~tV~~~l  156 (172)
T PRK12523        132 RLDGMGHAEIAERLGVSVSRVRQYL  156 (172)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            4457999999999999999999874

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=83.25  E-value=4.2  Score=28.99  Aligned_cols=34  Identities=15%  Similarity=0.093  Sum_probs=27.4

Q ss_pred             CCHHHHHhhcCCcHHHHHHHcC-CChhHHHHHHHH
Q 041600           71 LTLRDLMIYFHLPIEEAARRMK-LCPTVVKKICRR  104 (160)
Q Consensus        71 lt~~~L~~yF~lP~~eAA~~Lg-v~~T~LKr~CR~  104 (160)
                      +-.--+..++++|..++|+.|| .+.|++-.-|++
T Consensus        34 ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~r   68 (90)
T cd06571          34 IAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRK   68 (90)
T ss_pred             HHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHH
Confidence            3444556888999999999999 999999888654

The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=83.25  E-value=1.6  Score=34.57  Aligned_cols=28  Identities=29%  Similarity=0.478  Sum_probs=23.6

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      -+=+++..|+|+.||||+.|++|..+..
T Consensus       148 ~~~Gls~~EIA~~lgiS~~tV~r~l~~a  175 (185)
T PF07638_consen  148 FFEGLSVEEIAERLGISERTVRRRLRRA  175 (185)
T ss_pred             HHCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3447999999999999999999886543

>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function

Probab=83.11  E-value=1.8  Score=30.39  Aligned_cols=31  Identities=10%  Similarity=0.126  Sum_probs=28.4

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCCCCChh
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPH  112 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPy  112 (160)
                      .++...||+.+|+|.-.+-..++++||+ +.|
T Consensus        34 ~iS~gkAAelag~s~~eF~~~L~~~gI~-~~~   64 (76)
T PF03683_consen   34 KISLGKAAELAGMSRWEFLELLKERGIP-INY   64 (76)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHCCCC-CCC
Confidence            6999999999999999999999999998 544

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=82.96  E-value=1.8  Score=40.56  Aligned_cols=34  Identities=15%  Similarity=0.094  Sum_probs=28.9

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCh
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWP  111 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWP  111 (160)
                      ..++--+.+||+.||||.+||-|.-+++||..=|
T Consensus       601 ~~~~gn~~~aA~~LGisR~TLyrklk~~~i~~~~  634 (638)
T PRK11388        601 QVCGGRIQEMAALLGIGRTTLWRKMKQHGIDAGQ  634 (638)
T ss_pred             HHhCCCHHHHHHHHCCCHHHHHHHHHHcCCCccc
Confidence            4456789999999999999999999999995433

>PRK09393 ftrA transcriptional activator FtrA; Provisional

Probab=82.81  E-value=3.1  Score=35.33  Aligned_cols=45  Identities=11%  Similarity=0.118  Sum_probs=32.1

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc-CCCCChhHHHhhHHHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD-GLHRWPHRKIKSIQRRMSVA  125 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~RWPyRkikSl~~~i~~L  125 (160)
                      .+++.++|+.+|+|+.+|.|++++. |++-=-|.+...+++....|
T Consensus       234 ~~sl~~lA~~~~~S~~~l~r~fk~~~g~s~~~~~~~~Rl~~A~~lL  279 (322)
T PRK09393        234 PHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARARDLL  279 (322)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            3889999999999999999999986 87533343334444433433

>TIGR02607 antidote_HigA addiction module antidote protein, HigA family

Probab=82.74  E-value=4.9  Score=26.93  Aligned_cols=37  Identities=14%  Similarity=0.260  Sum_probs=28.0

Q ss_pred             HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhH
Q 041600           75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHR  113 (160)
Q Consensus        75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyR  113 (160)
                      .+..--++++.++|+.+||+.+++-++..  |-...+..
T Consensus        12 ~~~~~~~~t~~~lA~~~gis~~tis~~~~--g~~~~~~~   48 (78)
T TIGR02607        12 EFLEPLGLSIRALAKALGVSRSTLSRIVN--GRRGITAD   48 (78)
T ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHc--CCCCCCHH
Confidence            45666789999999999999999999864  54333333

Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.

>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins

Probab=82.70  E-value=7.1  Score=22.51  Aligned_cols=42  Identities=17%  Similarity=0.215  Sum_probs=28.7

Q ss_pred             HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhH
Q 041600           75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI  118 (160)
Q Consensus        75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl  118 (160)
                      .+..-.++...++|+.+|++..++.+...  |-...|.-.+..+
T Consensus         6 ~~~~~~~~s~~~~a~~~~~~~~~v~~~~~--g~~~~~~~~~~~i   47 (58)
T cd00093           6 ELRKEKGLTQEELAEKLGVSRSTISRIEN--GKRNPSLETLEKL   47 (58)
T ss_pred             HHHHHcCCCHHHHHHHHCCCHHHHHHHHc--CCCCCCHHHHHHH
Confidence            34445578899999999999999988743  4444555444444

Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=82.67  E-value=1.7  Score=33.69  Aligned_cols=25  Identities=12%  Similarity=0.110  Sum_probs=21.1

Q ss_pred             hhc-CCcHHHHHHHcCCChhHHHHHH
Q 041600           78 IYF-HLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        78 ~yF-~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      .|| +++.+|+|+.||+|.+++|..-
T Consensus       161 ~~~~~~s~~eIA~~l~~s~~tV~~~l  186 (198)
T TIGR02859       161 SYLDGKSYQEIACDLNRHVKSIDNAL  186 (198)
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            344 6999999999999999998653

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.

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=82.54  E-value=1.9  Score=36.77  Aligned_cols=27  Identities=15%  Similarity=0.054  Sum_probs=23.6

Q ss_pred             HHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           76 LMIYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        76 L~~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      |.-+.+++.+|+|..||+|+.++|.+-
T Consensus       164 L~~~~g~s~~EIA~~lgis~~tVk~~l  190 (339)
T PRK08241        164 LRDVLGWSAAEVAELLDTSVAAVNSAL  190 (339)
T ss_pred             hHHhhCCCHHHHHHHhCCCHHHHHHHH
Confidence            345678999999999999999999874

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=82.50  E-value=1.7  Score=26.66  Aligned_cols=23  Identities=22%  Similarity=0.138  Sum_probs=20.0

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +++..++|+.||+|+.++++.-+
T Consensus        15 ~~s~~eia~~l~~s~~tv~~~~~   37 (57)
T cd06170          15 GKTNKEIADILGISEKTVKTHLR   37 (57)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHH
Confidence            58999999999999999887743

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=82.42  E-value=1.5  Score=34.28  Aligned_cols=31  Identities=26%  Similarity=0.223  Sum_probs=25.5

Q ss_pred             HHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      .|+.-.-++..+.|+++|+|.+++.++-++|
T Consensus        22 ~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL   52 (164)
T PRK11169         22 ELQKDGRISNVELSKRVGLSPTPCLERVRRL   52 (164)
T ss_pred             HhccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4456667999999999999999998886654

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=82.41  E-value=2  Score=36.16  Aligned_cols=27  Identities=22%  Similarity=0.454  Sum_probs=24.1

Q ss_pred             HHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           76 LMIYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        76 L~~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      |.-+++++.+|+|+.||+|..++|.+.
T Consensus       126 L~~~~g~s~~EIA~~lg~s~~tVk~~l  152 (293)
T PRK09636        126 LHDVFGVPFDEIASTLGRSPAACRQLA  152 (293)
T ss_pred             HHHHhCCCHHHHHHHHCCCHHHHHHHH
Confidence            346789999999999999999999885

>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator

Probab=82.39  E-value=5.8  Score=30.22  Aligned_cols=25  Identities=20%  Similarity=0.283  Sum_probs=20.9

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +.+.|+|+.+|||+.||.-.-++ |+
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~~-GL   26 (131)
T TIGR02043         2 FQIGELAKLCGVTSDTLRFYEKN-GL   26 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence            68999999999999999866654 54

This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR

Probab=81.97  E-value=2.1  Score=37.52  Aligned_cols=30  Identities=23%  Similarity=0.079  Sum_probs=26.5

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      ..++-.+..||+.|||+.++|.+..+++||
T Consensus       413 ~~~~~n~~~aa~~lgi~r~~l~~~l~~~~~  442 (442)
T TIGR02040       413 ELTRDNRASAAEILGLSRQSLYVKLRRYGL  442 (442)
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHHhCc
Confidence            445677999999999999999999999886

This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=81.91  E-value=2  Score=28.22  Aligned_cols=36  Identities=19%  Similarity=0.251  Sum_probs=21.5

Q ss_pred             cCCCCHHHHH---hhc--CCcHHHHHHHcCCChhHHHHHHH
Q 041600           68 TGKLTLRDLM---IYF--HLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        68 ~~~lt~~~L~---~yF--~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      -..||+++=.   ..+  +....++|+.+||+.||+..+..
T Consensus         4 R~~LTl~eK~~iI~~~e~g~s~~~ia~~fgv~~sTv~~I~K   44 (53)
T PF04218_consen    4 RKSLTLEEKLEIIKRLEEGESKRDIAREFGVSRSTVSTILK   44 (53)
T ss_dssp             SSS--HHHHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHHH
T ss_pred             CccCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3456665432   222  46889999999999999988853

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators

Probab=81.90  E-value=4.9  Score=30.29  Aligned_cols=22  Identities=27%  Similarity=0.274  Sum_probs=18.6

Q ss_pred             CcHHHHHHHcCCChhHHHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      |++.|+|+.+|||+.||.-.-+
T Consensus         1 ~~I~e~a~~~gvs~~tlR~Ye~   22 (126)
T cd04785           1 LSIGELARRTGVNVETIRYYES   22 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5789999999999999985543

Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PRK15043 transcriptional regulator MirA; Provisional

Probab=81.89  E-value=1.5  Score=37.70  Aligned_cols=29  Identities=28%  Similarity=0.337  Sum_probs=25.8

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGLHR  109 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R  109 (160)
                      .++|.|+|+.+||++.||....|+.|+-.
T Consensus         3 ~ytIgeVA~~~GVs~~TLR~wErr~GLL~   31 (243)
T PRK15043          3 LYTIGEVALLCDINPVTLRAWQRRYGLLK   31 (243)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHhcCCCC
Confidence            47999999999999999999998888654

>PRK09685 DNA-binding transcriptional activator FeaR; Provisional

Probab=81.86  E-value=4.1  Score=33.68  Aligned_cols=51  Identities=12%  Similarity=0.030  Sum_probs=34.9

Q ss_pred             HHHhhcC---CcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHH
Q 041600           75 DLMIYFH---LPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVA  125 (160)
Q Consensus        75 ~L~~yF~---lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L  125 (160)
                      -|..+++   +.+.++|+.+|||+..|.+++++.|.+--=|-.-..|++....|
T Consensus       205 ~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~G~T~~~yi~~~RL~~A~~lL  258 (302)
T PRK09685        205 LIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGLVVAQYIRNRRLDRCADDL  258 (302)
T ss_pred             HHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHh
Confidence            3445553   78899999999999999999999887522233333344434444

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=81.83  E-value=1.8  Score=22.90  Aligned_cols=21  Identities=19%  Similarity=0.316  Sum_probs=18.2

Q ss_pred             CCcHHHHHHHcCCChhHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKI  101 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~  101 (160)
                      +.+..++|+.+|++.+++.++
T Consensus        21 ~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569          21 GESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             CCCHHHHHHHHCCCHHHHHHh
Confidence            569999999999999988764

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=81.74  E-value=3  Score=32.21  Aligned_cols=24  Identities=25%  Similarity=0.142  Sum_probs=21.6

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +-+++.+|+|..||||+.+++.+-
T Consensus       151 ~~g~s~~eIA~~lgis~~~v~~~l  174 (187)
T PRK12534        151 FEGITYEELAARTDTPIGTVKSWI  174 (187)
T ss_pred             HcCCCHHHHHHHhCCChhHHHHHH
Confidence            348999999999999999999885

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

Probab=81.66  E-value=2.1  Score=25.38  Aligned_cols=23  Identities=22%  Similarity=0.206  Sum_probs=20.4

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHH
Q 041600           80 FHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+++..++|+.||++..++++.-
T Consensus        25 ~~~~~~~ia~~~~~s~~~i~~~~   47 (55)
T cd06171          25 EGLSYEEIAEILGISRSTVRQRL   47 (55)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHH
Confidence            47999999999999999998764

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

>PHA00542 putative Cro-like protein

Probab=81.58  E-value=8.7  Score=27.11  Aligned_cols=27  Identities=15%  Similarity=0.117  Sum_probs=23.2

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      .--++.+.++|+.+||+.+++-++.+-
T Consensus        28 ~~~glTq~elA~~lgIs~~tIsr~e~g   54 (82)
T PHA00542         28 IRAGWSQEQIADATDVSQPTICRIYSG   54 (82)
T ss_pred             HHCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            344899999999999999999999643

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=81.23  E-value=1.8  Score=26.95  Aligned_cols=24  Identities=25%  Similarity=0.259  Sum_probs=20.4

Q ss_pred             C-cHHHHHHHcCCChhHHHHHHHHc
Q 041600           82 L-PIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        82 l-P~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      + ++.+.|+.+|||.+++.+..+++
T Consensus        20 l~s~~~la~~~~vs~~tv~~~l~~L   44 (60)
T smart00345       20 LPSERELAAQLGVSRTTVREALSRL   44 (60)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            5 59999999999999999886654

>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional

Probab=81.20  E-value=2.7  Score=34.80  Aligned_cols=24  Identities=13%  Similarity=0.225  Sum_probs=20.6

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHc
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      .+++|+|+..|||.+|+.|.-...
T Consensus         2 ~ti~dIA~~agVS~~TVSrvln~~   25 (327)
T PRK10339          2 ATLKDIAIEAGVSLATVSRVLNDD   25 (327)
T ss_pred             CCHHHHHHHhCCCHHhhhhhhcCC
Confidence            368999999999999999997543

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=80.97  E-value=2.8  Score=27.14  Aligned_cols=25  Identities=16%  Similarity=0.282  Sum_probs=22.2

Q ss_pred             CCcHHHHHHHcCC-ChhHHHHHHHHc
Q 041600           81 HLPIEEAARRMKL-CPTVVKKICRRD  105 (160)
Q Consensus        81 ~lP~~eAA~~Lgv-~~T~LKr~CR~~  105 (160)
                      ++++.++|..+|+ +++.|-+.+++.
T Consensus        50 ~~~~~~ia~~~g~~s~~~f~r~Fk~~   75 (84)
T smart00342       50 DLSVTEIALRVGFSSQSYFSRAFKKL   75 (84)
T ss_pred             CCCHHHHHHHhCCCChHHHHHHHHHH
Confidence            5899999999999 999999998654

>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family

Probab=80.90  E-value=2.1  Score=27.64  Aligned_cols=26  Identities=19%  Similarity=0.221  Sum_probs=21.6

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      .+.+++.++|+.+|++.+++.+..++
T Consensus        23 ~~~~s~~ela~~~g~s~~tv~r~l~~   48 (67)
T cd00092          23 QLPLTRQEIADYLGLTRETVSRTLKE   48 (67)
T ss_pred             cCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence            34689999999999999998887643

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=80.84  E-value=2.6  Score=34.30  Aligned_cols=22  Identities=18%  Similarity=0.212  Sum_probs=20.4

Q ss_pred             CCcHHHHHHHcCCChhHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +++.+|+|+.||+++++++++.
T Consensus       194 ~~S~~EIAe~lgis~~tV~~~~  215 (227)
T TIGR02846       194 RKTQREIAKILGISRSYVSRIE  215 (227)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHH
Confidence            5899999999999999999885

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.

>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD

Probab=80.74  E-value=7.3  Score=29.80  Aligned_cols=28  Identities=25%  Similarity=0.273  Sum_probs=23.3

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGLHR  109 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R  109 (160)
                      .++|.|+|+..|||+.||+-..+. |+-.
T Consensus         3 ~~tI~elA~~~gvs~~tlR~Ye~~-GLL~   30 (120)
T TIGR02054         3 AYTISRLAEDAGVSVHVVRDYLLR-GLLH   30 (120)
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHHC-CCCC
Confidence            478999999999999999987755 7543

This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=80.69  E-value=2.8  Score=29.91  Aligned_cols=31  Identities=23%  Similarity=0.375  Sum_probs=25.3

Q ss_pred             HHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      .|...-.+|..++|+.+|++.+++.++.+++
T Consensus        11 ~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L   41 (108)
T smart00344       11 ELQKDARISLAELAKKVGLSPSTVHNRVKRL   41 (108)
T ss_pred             HHHHhCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3445557999999999999999998887655

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=80.67  E-value=7.3  Score=29.94  Aligned_cols=24  Identities=21%  Similarity=0.358  Sum_probs=18.8

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDG  106 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~G  106 (160)
                      |+|.|+|+.+||++.||.-.= +.|
T Consensus         1 m~Ige~a~~~gvs~~tLRyYE-~~G   24 (131)
T cd04786           1 MKIGELAKRSGMAASRIRFYE-AEG   24 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH-HCC
Confidence            578999999999999997443 444

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=80.64  E-value=2.7  Score=30.03  Aligned_cols=24  Identities=13%  Similarity=0.059  Sum_probs=21.9

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHHH
Q 041600           80 FHLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      -++++.|+|+.||||+.++|.+-+
T Consensus        31 eGlS~kEIAe~LGIS~~TVk~~l~   54 (73)
T TIGR03879        31 AGKTASEIAEELGRTEQTVRNHLK   54 (73)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHh
Confidence            579999999999999999998855

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator

Probab=80.50  E-value=15  Score=27.27  Aligned_cols=26  Identities=23%  Similarity=0.280  Sum_probs=21.4

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      +++.|+|+.+|||+.||+-..+. |+-
T Consensus         1 y~Ige~A~~~gvs~~tlR~ye~~-GLl   26 (107)
T cd01111           1 YSISQLALDAGVSVHIVRDYLLR-GLL   26 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence            47899999999999999977654 753

Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=80.41  E-value=2.8  Score=34.15  Aligned_cols=38  Identities=24%  Similarity=0.324  Sum_probs=30.1

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      -+.+++.+|+|..||||.+++|.+-         +|-++.|++.+..
T Consensus       162 ~~~g~s~~EIAe~lgis~~tVk~~l---------~Rar~kLr~~l~~  199 (231)
T PRK11922        162 VVEELSVEETAQALGLPEETVKTRL---------HRARRLLRESLAR  199 (231)
T ss_pred             hhcCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHH
Confidence            3457999999999999999999884         6666666666653

>KOG0251 consensus Clathrin assembly protein AP180 and related proteins, contain ENTH domain [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]

Probab=80.17  E-value=1.4  Score=41.35  Aligned_cols=56  Identities=20%  Similarity=0.363  Sum_probs=41.7

Q ss_pred             HHHhhcCCcHHHHHHHcCCChhHHH---------HHHHHcCCCCC-hhHHHhhH-HHHHHHHhhhcc
Q 041600           75 DLMIYFHLPIEEAARRMKLCPTVVK---------KICRRDGLHRW-PHRKIKSI-QRRMSVASGRLR  130 (160)
Q Consensus        75 ~L~~yF~lP~~eAA~~Lgv~~T~LK---------r~CR~~GI~RW-PyRkikSl-~~~i~~L~~~~~  130 (160)
                      -|..||+|...+|.+.|.+-.+.++         +.||.+|+.|| .|=.|+.. .+.++.|++.++
T Consensus       223 Llekffem~~~~a~~al~iykr~~~q~e~L~~f~~~ck~~g~~r~~~iP~l~~i~~s~l~~lEe~l~  289 (491)
T KOG0251|consen  223 LLEKFFEMSKHDAIKALDIYKRFLSQTEKLSEFLKVCKSVGVDRGFEIPVLKRIPISLLEALEEHLR  289 (491)
T ss_pred             HHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccCcchhhcCHHHHHHHHHHHh
Confidence            3457999999999999999866665         78999999999 55544433 455666666554

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=80.05  E-value=3.3  Score=33.70  Aligned_cols=23  Identities=17%  Similarity=0.213  Sum_probs=20.9

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHH
Q 041600           80 FHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+++.+|+|+.||||..++|++-
T Consensus       199 ~g~s~~EIA~~lgis~~tV~~~~  221 (236)
T PRK06986        199 EELNLKEIGAVLGVSESRVSQIH  221 (236)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHH
Confidence            46999999999999999999884

---

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	160
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-07

>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 = 46.4 bits (109), Expect = 9e-07
 Identities = 29/189 (15%), Positives = 53/189 (28%), Gaps = 62/189 (32%)

Query: 3   KKSIENVKEYLVQYCEERKQAGFMMLPDPLSDFYEAVCVGLVLDD--N------------ 48
           K  I +++  L +  + +         + L          LVL +  N            
Sbjct: 224 KLRIHSIQAELRRLLKSKP------YENCL----------LVLLNVQNAKAWNAFNLSCK 267

Query: 49  --LTTDDYSQPPMTNSVQRERTGKLTLRD-------------LMIYFHLPIEEAARRMKL 93
             LTT       +T+ +    T  ++L               L+ Y     ++  R +  
Sbjct: 268 ILLTTRFKQ---VTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLT 324

Query: 94  C-PTVVKKICR--RDGLHRW---PHRKIKSIQRRMSVASGRLRSNDAEE--------RAN 139
             P  +  I    RDGL  W    H     +   +  +   L   +  +          +
Sbjct: 325 TNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPS 384

Query: 140 AQIEIQRLQ 148
           A I    L 
Sbjct: 385 AHIPTILLS 393

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	160
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	96.6
3iwf_A	107	Transcription regulator RPIR family; transcription	96.1
3e7l_A	63	Transcriptional regulator (NTRC family); sigma43 a	95.99
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	95.57
1g2h_A	61	Transcriptional regulatory protein TYRR homolog; p	95.43
2vz4_A	108	Tipal, HTH-type transcriptional activator TIPA; tr	95.22
1r8d_A	109	Transcription activator MTAN; protein-DNA complex,	95.11
1umq_A	81	Photosynthetic apparatus regulatory protein; DNA-b	95.0
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	94.59
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	94.56
1eto_A	98	FIS, factor for inversion stimulation; transcripti	94.56
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	94.44
1ntc_A	91	Protein (nitrogen regulation protein (NTRC)); heli	94.28
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	94.27
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	93.92
3lsg_A	103	Two-component response regulator YESN; structural	93.74
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	93.69
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	93.55
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	93.38
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	93.34
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	93.3
3mlf_A	111	Transcriptional regulator; structural genomics, he	93.25
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	93.23
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	93.18
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	93.18
3mkl_A	120	HTH-type transcriptional regulator GADX; PSI2, MCS	93.17
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	93.13
3mn2_A	108	Probable ARAC family transcriptional regulator; st	93.13
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	93.08
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	92.89
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	92.82
1j9i_A	68	GPNU1 DBD;, terminase small subunit; DNA binding d	92.73
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	92.65
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	92.54
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	92.46
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	92.29
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	92.27
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	92.26
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	92.21
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	92.15
1bl0_A	129	Protein (multiple antibiotic resistance protein),	91.93
1b0n_A	111	Protein (SINR protein); transcription regulator, a	91.7
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	91.53
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	91.53
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	91.46
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	91.39
1r8e_A	278	Multidrug-efflux transporter regulator; protein-DN	91.25
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	91.23
3ivp_A	126	Putative transposon-related DNA-binding protein; A	91.14
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	91.1
3t76_A	88	VANU, transcriptional regulator vanug; structural	91.1
3c57_A	95	Two component transcriptional regulatory protein;	90.98
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	90.89
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	90.89
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	90.86
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	90.83
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	90.57
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	90.55
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	90.22
2zhg_A	154	Redox-sensitive transcriptional activator SOXR; ox	90.19
3vk0_A	114	NHTF, transcriptional regulator; HTH motif, XRE tr	90.05
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	90.03
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	89.99
3qao_A	249	LMO0526 protein, MERR-like transcriptional regulat	89.96
3g5g_A	99	Regulatory protein; transcriptional regulator, hel	89.75
1rzs_A	61	Antirepressor, regulatory protein CRO; helix-turn-	89.64
3f52_A	117	CLP gene regulator (CLGR); helix-turn-helix motif,	89.4
3hh0_A	146	Transcriptional regulator, MERR family; protein st	89.31
3gp4_A	142	Transcriptional regulator, MERR family; structural	89.28
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	89.18
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	89.11
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	88.67
2hin_A	71	GP39, repressor protein; transcription factor, dim	88.65
2ppx_A	99	AGR_C_3184P, uncharacterized protein ATU1735; HTH-	88.53
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	88.14
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	87.89
2jml_A	81	DNA binding domain/transcriptional regulator; anti	87.84
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	87.64
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	87.55
2ict_A	94	Antitoxin HIGA; helix-turn-helix, structural genom	87.43
1q06_A	135	Transcriptional regulator CUER; MERR family transc	87.38
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	87.37
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	87.29
3gbg_A	276	TCP pilus virulence regulatory protein; cupin, hel	87.28
1y6u_A	70	XIS, excisionase from transposon TN916; structure,	87.28
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	87.24
3cec_A	104	Putative antidote protein of plasmid maintenance;	86.57
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	86.55
1y9q_A	192	Transcriptional regulator, HTH_3 family; transcrip	86.08
2auw_A	170	Hypothetical protein NE0471; alpha-beta structure,	85.99
3gpv_A	148	Transcriptional regulator, MERR family; protein st	85.83
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	85.81
2pij_A	67	Prophage PFL 6 CRO; transcription factor, helix-tu	85.63
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	85.63
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	85.62
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	85.59
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	85.14
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	85.13
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	85.0
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	84.98
2bnm_A	198	Epoxidase; oxidoreductase, cupin, HTH, cation-depe	84.57
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	84.56
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	84.35
2eby_A	113	Putative HTH-type transcriptional regulator YBAQ;	84.26
1u78_A	141	TC3 transposase, transposable element TC3 transpos	84.0
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	83.99
1z4h_A	66	TORI, TOR inhibition protein; winged helix, revers	83.9
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	83.89
2o38_A	120	Hypothetical protein; alpha-beta, helix-turn-helix	83.79
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	83.41
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	83.24
3trb_A	104	Virulence-associated protein I; mobIle and extrach	83.2
4ghj_A	101	Probable transcriptional regulator; structural gen	83.1
1d5y_A	292	ROB transcription factor; protein-DNA complex, DNA	82.74
2wus_R	112	RODZ, putative uncharacterized protein; structural	82.48
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	82.12
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	82.06
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	81.89
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	81.79
3r8n_M	114	30S ribosomal protein S13; protein biosynthesis, R	81.69
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	81.69
3uj3_X	193	DNA-invertase; helix-turn-helix, site-specific rec	81.53
4fe7_A	412	Xylose operon regulatory protein; HTH_ARAC, helix-	81.5
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	81.22
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	80.77
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	80.46
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	80.05

>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20

Probab=96.60  E-value=0.0017  Score=47.22  Aligned_cols=40  Identities=13%  Similarity=0.193  Sum_probs=34.4

Q ss_pred             HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHH
Q 041600           76 LMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKI  115 (160)
Q Consensus        76 L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRki  115 (160)
                      ....-++++.|.|+..|||++|+-|.||++|..-|+-=|.
T Consensus        34 ~~~~~~~si~elA~~~~vS~aTv~Rf~kklG~~gf~efk~   73 (111)
T 2o3f_A           34 PHXAIESTVNEISALANSSDAAVIRLCXSLGLKGFQDLXM   73 (111)
T ss_dssp             HHHHHTCCHHHHHHHTTCCHHHHHHHHHHTTCSSHHHHHH
T ss_pred             hHHHHhcCHHHHHHHHCCCHHHHHHHHHHcCCCCHHHHHH
Confidence            3345589999999999999999999999999999885443

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=96.10  E-value=0.0034  Score=45.67  Aligned_cols=40  Identities=10%  Similarity=0.143  Sum_probs=33.7

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChh
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPH  112 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPy  112 (160)
                      ++.....-++++.+.|+..|||++++=|.||++|...|+-
T Consensus        27 l~~~~~~~~~si~elA~~~~vS~aTv~Rf~kkLGf~gf~e   66 (107)
T 3iwf_A           27 LNYPHKVVNMTSQEIANQLETSSTSIIRLSKKVTPGGFNE   66 (107)
T ss_dssp             HHCHHHHTTCCHHHHHHHHTSCHHHHHHHHHHHSTTHHHH
T ss_pred             HhCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHhCCCCHHH
Confidence            3334455689999999999999999999999999877663

>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} PDB: 4fth_A

Probab=95.99  E-value=0.0096  Score=38.87  Aligned_cols=31  Identities=3%  Similarity=0.082  Sum_probs=27.3

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      ..++-.+.+||+.||||.++|-+..+++||.
T Consensus        29 ~~~~gn~~~aA~~LGisr~tL~rklkk~gi~   59 (63)
T 3e7l_A           29 REYDYDLKRTAEEIGIDLSNLYRKIKSLNIR   59 (63)
T ss_dssp             HHTTTCHHHHHHHHTCCHHHHHHHHHHTTCC
T ss_pred             HHhCCCHHHHHHHHCcCHHHHHHHHHHhCCC
Confidence            3446778999999999999999999999994

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=95.57  E-value=0.019  Score=33.35  Aligned_cols=25  Identities=8%  Similarity=0.280  Sum_probs=22.5

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      +++..++|+.||||.+|+++..+++
T Consensus        21 g~s~~~IA~~lgis~~Tv~~~~~~~   45 (51)
T 1tc3_C           21 NVSLHEMSRKISRSRHCIRVYLKDP   45 (51)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHCS
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHhhH
Confidence            6899999999999999999987654

>1g2h_A Transcriptional regulatory protein TYRR homolog; protein structure, , DNA-binding domain, helix- turn-helix motif; NMR {Haemophilus influenzae} SCOP: a.4.1.12

Probab=95.43  E-value=0.018  Score=37.54  Aligned_cols=27  Identities=15%  Similarity=0.260  Sum_probs=24.9

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      --..+||+.||||.++|.+..+++||.
T Consensus        34 gn~~~aA~~LGIsr~tL~rklkk~gi~   60 (61)
T 1g2h_A           34 PSTRKLAQRLGVSHTAIANKLKQYGIG   60 (61)
T ss_dssp             CSHHHHHHHTTSCTHHHHHHHHTTTCC
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence            478899999999999999999999984

>2vz4_A Tipal, HTH-type transcriptional activator TIPA; transcription, resistance, antibiotic; 2.90A {Streptomyces lividans}

Probab=95.22  E-value=0.023  Score=40.61  Aligned_cols=26  Identities=12%  Similarity=0.092  Sum_probs=22.4

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      .+++.|+|+.+|||+.||+..-+. |+
T Consensus         1 ~~~i~e~A~~~gvs~~tLR~ye~~-Gl   26 (108)
T 2vz4_A            1 SYSVGQVAGFAGVTVRTLHHYDDI-GL   26 (108)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHH-TS
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHC-CC
Confidence            368999999999999999988765 75

>1r8d_A Transcription activator MTAN; protein-DNA complex, transcription/DNA complex; 2.70A {Bacillus subtilis} SCOP: a.6.1.3 PDB: 1jbg_A

Probab=95.11  E-value=0.028  Score=40.08  Aligned_cols=73  Identities=11%  Similarity=0.142  Sum_probs=43.9

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCCCC-----------ChhHHHhhHHH---------HHHHHhhhccCCcHHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGLHR-----------WPHRKIKSIQR---------RMSVASGRLRSNDAEERANA  140 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R-----------WPyRkikSl~~---------~i~~L~~~~~~~~~eerar~  140 (160)
                      .+++.|+|+.+|||+.||+..-+ .|+-.           +....+..+..         .++.+...+...+.+.+...
T Consensus         2 ~~~i~e~A~~~gvs~~tLR~ye~-~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~l~~~G~~l~~I~~~l~~~~~~~~~~l   80 (109)
T 1r8d_A            2 KYQVKQVAEISGVSIRTLHHYDN-IELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRLDEIKEMLDHPNFDRKAAL   80 (109)
T ss_dssp             CBCHHHHHHHHSCCHHHHHHHHH-TTSSCCSEECTTCCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHHCTTSCHHHHH
T ss_pred             CccHHHHHHHHCcCHHHHHHHHH-CCCCCCCeECCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHhCCCHHHHHHH
Confidence            37899999999999999998765 56532           22222222221         24555555543322344556


Q ss_pred             HHHHHHHHHHHHHH
Q 041600          141 QIEIQRLQEEMAAA  154 (160)
Q Consensus       141 ~~eIerL~~Em~~~  154 (160)
                      ..+++.|++++..+
T Consensus        81 ~~~~~~l~~~i~~l   94 (109)
T 1r8d_A           81 QSQKEILMKKKQRM   94 (109)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            66667777666655

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=94.59  E-value=0.017  Score=34.18  Aligned_cols=27  Identities=7%  Similarity=0.074  Sum_probs=24.0

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      ++++.++|+.||||.+|+.+..+++++
T Consensus        21 g~s~~~ia~~lgvs~~Tv~r~l~~~~~   47 (52)
T 1jko_C           21 GHPRQQLAIIFGIGVSTLYRYFPASSI   47 (52)
T ss_dssp             TCCHHHHHHTTSCCHHHHHHHSCTTC-
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHccc
Confidence            589999999999999999999887775

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=94.56  E-value=0.059  Score=36.92  Aligned_cols=34  Identities=12%  Similarity=0.193  Sum_probs=27.5

Q ss_pred             HHHHhhc---CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           74 RDLMIYF---HLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        74 ~~L~~yF---~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      .-+..|.   +.++.++|+.+|||.++|.+..+++..
T Consensus        13 ~~v~~~~~~~g~s~~~ia~~~gIs~~tl~rW~~~~~~   49 (97)
T 2jn6_A           13 DAVALYENSDGASLQQIANDLGINRVTLKNWIIKYGS   49 (97)
T ss_dssp             HHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHHCC
T ss_pred             HHHHHHHHcCCChHHHHHHHHCcCHHHHHHHHHHHhh
Confidence            3344554   689999999999999999999887755

>1eto_A FIS, factor for inversion stimulation; transcriptional activation region, DNA-binding protein, transcription activator; 1.90A {Escherichia coli} SCOP: a.4.1.12 PDB: 1etq_A 1ety_A 1fia_A 3fis_A 3iv5_A* 3jr9_A* 3jra_A* 3jrb_A* 3jrc_A* 3jrd_A* 3jre_A* 3jrf_A* 3jrg_A* 3jrh_A* 3jri_A* 1f36_A 1etv_A 1etk_A 1etx_A 1fip_A ...

Probab=94.56  E-value=0.042  Score=39.48  Aligned_cols=30  Identities=20%  Similarity=0.159  Sum_probs=26.8

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      ...+--+.+||+.|||+.++|.+..+++||
T Consensus        68 ~~~~gn~~~AA~~LGIsR~TL~rkLkk~gi   97 (98)
T 1eto_A           68 QYTLGNQTRAALMMGINRGTLRKKLKKYGM   97 (98)
T ss_dssp             HHTTTCHHHHHHHHTSCHHHHHHHHHHTTC
T ss_pred             HHhCCCHHHHHHHhCCCHHHHHHHHHHhCC
Confidence            445678899999999999999999999998

>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}

Probab=94.44  E-value=0.099  Score=36.20  Aligned_cols=51  Identities=18%  Similarity=0.290  Sum_probs=38.2

Q ss_pred             HHhhc---CCcHHHHHHHcCCChhHHHHHHHHc-CCCCChhHHHhhHHHHHHHHh
Q 041600           76 LMIYF---HLPIEEAARRMKLCPTVVKKICRRD-GLHRWPHRKIKSIQRRMSVAS  126 (160)
Q Consensus        76 L~~yF---~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~RWPyRkikSl~~~i~~L~  126 (160)
                      |..++   .+++.+.|+.+|+|+++|.|++++. |++---|.....+++...-|.
T Consensus        12 i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~~~~~~~~Rl~~A~~lL~   66 (107)
T 2k9s_A           12 ISDHLADSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLS   66 (107)
T ss_dssp             HHHTSSCSSCCHHHHHHHTTSCHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            44444   3889999999999999999999986 987655665555555555444

>1ntc_A Protein (nitrogen regulation protein (NTRC)); helix-turn-helix, FIS, four-helix bundle, transcription regulation; NMR {Salmonella typhimurium} SCOP: a.4.1.12

Probab=94.28  E-value=0.019  Score=40.02  Aligned_cols=28  Identities=18%  Similarity=0.125  Sum_probs=24.5

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           80 FHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      ++-.+.+||+.||||.++|.+..+++||
T Consensus        63 ~~gn~~~aA~~LGIsr~tL~rklkk~~i   90 (91)
T 1ntc_A           63 TQGHKQEAARLLGWGAATLTAKLKELGM   90 (91)
T ss_dssp             TTTCTTHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             hCCCHHHHHHHHCcCHHHHHHHHHHhCc
Confidence            4567789999999999999999988876

>2xi8_A Putative transcription regulator; HTH DNA-binding motif; HET: GOL; 1.21A {Enterococcus faecalis} PDB: 2gzu_A 1utx_A* 2xj3_A 2xiu_A

Probab=94.27  E-value=0.1  Score=32.07  Aligned_cols=39  Identities=10%  Similarity=0.007  Sum_probs=30.8

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHR  113 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyR  113 (160)
                      +..++...++++.+.|+.+|||.+++.++.  .|-...+..
T Consensus         6 l~~~r~~~g~s~~~lA~~~gis~~~i~~~e--~g~~~~~~~   44 (66)
T 2xi8_A            6 LKLIREKKKISQSELAALLEVSRQTINGIE--KNKYNPSLQ   44 (66)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSCHHHHHHHH--TTSCCCCHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHH--cCCCCCCHH
Confidence            567778889999999999999999999985  454333333

>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix, DNA-binding, transcription, transcription regulation; 1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB: 3jxb_C 3jxc_L 3jxd_L

Probab=93.92  E-value=0.12  Score=31.98  Aligned_cols=39  Identities=3%  Similarity=-0.020  Sum_probs=30.3

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHR  113 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyR  113 (160)
                      +..++...++++.++|+.+||+.+++.++  +.|-...+..
T Consensus        10 l~~~r~~~g~s~~~lA~~~gis~~~i~~~--e~g~~~~~~~   48 (68)
T 2r1j_L           10 IRARRKKLKIRQAALGKMVGVSNVAISQW--ERSETEPNGE   48 (68)
T ss_dssp             HHHHHHHHTCCHHHHHHHHTSCHHHHHHH--HTTSSCCBHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHH--HcCCCCCCHH
Confidence            55677778999999999999999999998  4554333333

>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}

Probab=93.74  E-value=0.11  Score=35.72  Aligned_cols=46  Identities=7%  Similarity=0.145  Sum_probs=36.5

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc-CCCCChhHHHhhHHHHHHHHh
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD-GLHRWPHRKIKSIQRRMSVAS  126 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~RWPyRkikSl~~~i~~L~  126 (160)
                      .+++.+.|+.+|+|+++|.+++++. |++---|.+...+++...-|.
T Consensus        19 ~~~~~~lA~~~~~S~~~l~r~fk~~~g~s~~~~~~~~Rl~~A~~lL~   65 (103)
T 3lsg_A           19 QFTLSVLSEKLDLSSGYLSIMFKKNFGIPFQDYLLQKRMEKAKLLLL   65 (103)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            5799999999999999999999998 986555666656665555554

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=93.69  E-value=0.14  Score=32.54  Aligned_cols=40  Identities=18%  Similarity=0.128  Sum_probs=31.1

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRK  114 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRk  114 (160)
                      +..++.-.++.+.++|+.+||+.+++.++  +.|-...+...
T Consensus        15 l~~~r~~~glsq~~lA~~~gis~~~i~~~--e~g~~~~~~~~   54 (77)
T 2b5a_A           15 LKKIRTQKGVSQEELADLAGLHRTYISEV--ERGDRNISLIN   54 (77)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHH--HTTCSCCBHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHH--HCCCCCCCHHH
Confidence            55667778999999999999999999998  45654444433

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=93.55  E-value=0.16  Score=31.97  Aligned_cols=41  Identities=24%  Similarity=0.122  Sum_probs=31.3

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKI  115 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRki  115 (160)
                      +..++...++.+.+.|+.+||+.+++.++  +.|-...+...+
T Consensus        18 l~~~r~~~g~s~~~lA~~~gis~~~i~~~--e~g~~~~~~~~l   58 (74)
T 1y7y_A           18 LRELRTAKGLSQETLAFLSGLDRSYVGGV--ERGQRNVSLVNI   58 (74)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHH--HTTCSCCBHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HCCCCCCCHHHH
Confidence            55667778999999999999999999998  456544334443

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=93.38  E-value=0.24  Score=31.54  Aligned_cols=44  Identities=23%  Similarity=0.295  Sum_probs=33.1

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCC-CChhHHHhhH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLH-RWPHRKIKSI  118 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~-RWPyRkikSl  118 (160)
                      +..++.-.++.+.+.|+.+|||.+++.++.  .|-. ..+...+..+
T Consensus        12 l~~~r~~~g~sq~~lA~~~gis~~~i~~~e--~g~~~~~~~~~l~~i   56 (78)
T 3b7h_A           12 LMELITQQNLTINRVATLAGLNQSTVNAMF--EGRSKRPTITTIRKV   56 (78)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHHH--CTTCCCCCHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHH--cCCCCCCCHHHHHHH
Confidence            556777789999999999999999999994  5654 4444444443

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=93.34  E-value=0.24  Score=31.39  Aligned_cols=43  Identities=7%  Similarity=0.035  Sum_probs=33.3

Q ss_pred             CCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHH
Q 041600           71 LTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKI  115 (160)
Q Consensus        71 lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRki  115 (160)
                      -.+..++...++.+.+.|+.+||+.+++.++.  .|-...+...+
T Consensus        13 ~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e--~g~~~~~~~~l   55 (76)
T 3bs3_A           13 NRIKVVLAEKQRTNRWLAEQMGKSENTISRWC--SNKSQPSLDML   55 (76)
T ss_dssp             BCHHHHHHHTTCCHHHHHHHHTCCHHHHHHHH--TTSSCCCHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH--cCCCCCCHHHH
Confidence            35778888889999999999999999999984  46443333333

>3s8q_A R-M controller protein; protein-DNA complex, helix-turn-helix; HET: DNA; 2.10A {Enterobacter SP} SCOP: a.35.1.0 PDB: 3clc_A* 3ufd_A*

Probab=93.30  E-value=0.18  Score=32.86  Aligned_cols=39  Identities=13%  Similarity=0.155  Sum_probs=31.3

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHR  113 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyR  113 (160)
                      +..++.--++++.+.|+.+||+.+++.++  +.|-...+..
T Consensus        16 lk~~R~~~glsq~~lA~~~gis~~~i~~~--e~g~~~~~~~   54 (82)
T 3s8q_A           16 IKKIRLEKGMTQEDLAYKSNLDRTYISGI--ERNSRNLTIK   54 (82)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHH--HTTCCCCBHH
T ss_pred             HHHHHHHcCCCHHHHHHHhCcCHHHHHHH--HCCCCCCCHH
Confidence            56677778999999999999999999999  5676443333

>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp}

Probab=93.25  E-value=0.56  Score=33.15  Aligned_cols=34  Identities=18%  Similarity=0.315  Sum_probs=30.3

Q ss_pred             CHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           72 TLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        72 t~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      .+..++.-.++.+.++|+.+|||.+++.++  +.|-
T Consensus        27 ~Lk~~R~~~gltq~elA~~~gis~~~is~~--E~G~   60 (111)
T 3mlf_A           27 TLKELRTDYGLTQKELGDLFKVSSRTIQNM--EKDS   60 (111)
T ss_dssp             EHHHHHHHTTCCHHHHHHHHTSCHHHHHHH--HHCC
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HCCC
Confidence            478889999999999999999999999999  4565

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=93.23  E-value=0.17  Score=32.01  Aligned_cols=40  Identities=3%  Similarity=-0.012  Sum_probs=30.7

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRK  114 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRk  114 (160)
                      +..++..-++.+.+.|+.+|||.+++.++  +.|-...+...
T Consensus        10 l~~~r~~~gls~~~lA~~~gis~~~i~~~--e~g~~~~~~~~   49 (76)
T 1adr_A           10 IRARRKKLKIRQAALGKMVGVSNVAISQW--ERSETEPNGEN   49 (76)
T ss_dssp             HHHHHHHHTCCHHHHHHHHTSCHHHHHHH--HTTSSCCCHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HcCCCCCCHHH
Confidence            55667777999999999999999999998  45644433333

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=93.18  E-value=0.18  Score=34.23  Aligned_cols=35  Identities=11%  Similarity=0.184  Sum_probs=27.2

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHH
Q 041600           80 FHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMS  123 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~  123 (160)
                      -+++.+|+|+.||||..++|.+-         +|=++.|++.+.
T Consensus        52 ~g~s~~eIA~~lgis~~tV~~~l---------~ra~~~Lr~~l~   86 (92)
T 3hug_A           52 RGWSTAQIATDLGIAEGTVKSRL---------HYAVRALRLTLQ   86 (92)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHH---------HHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHH
Confidence            37999999999999999999885         444555555444

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=93.18  E-value=0.27  Score=31.37  Aligned_cols=45  Identities=13%  Similarity=0.023  Sum_probs=34.3

Q ss_pred             CHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhH
Q 041600           72 TLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI  118 (160)
Q Consensus        72 t~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl  118 (160)
                      .+..++.--++++.+.|+.+||+.+++.++.  .|-...+...+..+
T Consensus        12 ~l~~~r~~~glsq~~lA~~~gis~~~is~~e--~g~~~~~~~~l~~i   56 (73)
T 3omt_A           12 RLKSVLAEKGKTNLWLTETLDKNKTTVSKWC--TNDVQPSLETLFDI   56 (73)
T ss_dssp             CHHHHHHHHTCCHHHHHHHTTCCHHHHHHHH--TTSSCCCHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH--cCCCCCCHHHHHHH
Confidence            4778888889999999999999999999995  45444444444433

>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}

Probab=93.17  E-value=0.15  Score=36.08  Aligned_cols=45  Identities=16%  Similarity=0.207  Sum_probs=34.2

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVA  125 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L  125 (160)
                      .+++.+.|+.+|||+++|.|.+++.|++---|.....++....-|
T Consensus        23 ~~~~~~lA~~~~~S~~~l~r~fk~~G~s~~~~~~~~Rl~~A~~lL   67 (120)
T 3mkl_A           23 EWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRMQRALQLI   67 (120)
T ss_dssp             CCCHHHHHHHTTCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence            478999999999999999999999988644455555555544444

>3oou_A LIN2118 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; HET: BTB; 1.57A {Listeria innocua}

Probab=93.13  E-value=0.13  Score=35.57  Aligned_cols=46  Identities=4%  Similarity=0.057  Sum_probs=35.3

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc-CCCCChhHHHhhHHHHHHHHh
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD-GLHRWPHRKIKSIQRRMSVAS  126 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~RWPyRkikSl~~~i~~L~  126 (160)
                      .+++.+.|+.+|||+++|.|.+++. |++---|.....+++...-|.
T Consensus        21 ~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~~~~~~~~Rl~~A~~lL~   67 (108)
T 3oou_A           21 GMSLKTLGNDFHINAVYLGQLFQKEMGEHFTDYLNRYRVNYAKEELL   67 (108)
T ss_dssp             CCCHHHHHHHHTSCHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            4889999999999999999999988 986555555555555444443

>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=93.13  E-value=0.13  Score=35.62  Aligned_cols=46  Identities=17%  Similarity=0.178  Sum_probs=35.7

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc-CCCCChhHHHhhHHHHHHHHh
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD-GLHRWPHRKIKSIQRRMSVAS  126 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~RWPyRkikSl~~~i~~L~  126 (160)
                      .+++.+.|+.+|+|+++|.|++++. |++---|.....+++...-|.
T Consensus        18 ~~~~~~lA~~~~~s~~~l~r~fk~~~G~s~~~~~~~~Rl~~A~~lL~   64 (108)
T 3mn2_A           18 PITIEKLTALTGISSRGIFKAFQRSRGYSPMAFAKRVRLQHAHNLLS   64 (108)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence            4789999999999999999999997 986555655555555554444

>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, transcription regulat; HET: MSE; 1.90A {Listeria innocua}

Probab=93.08  E-value=0.7  Score=31.96  Aligned_cols=44  Identities=16%  Similarity=0.079  Sum_probs=32.0

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI  118 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl  118 (160)
                      +..++.-.++.+.+.|+.+|||.+++.++.  .|...-+...+..+
T Consensus        14 l~~~r~~~glsq~~lA~~~gis~~~i~~~e--~g~~~p~~~~l~~l   57 (114)
T 3op9_A           14 LSRLKKEHGLKNHQIAELLNVQTRTVAYYM--SGETKPDIEKLIRL   57 (114)
T ss_dssp             HHHHHHHHTCCHHHHHHHHTSCHHHHHHHH--HTSSCCCHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHH--cCCCCCCHHHHHHH
Confidence            567778889999999999999999999884  45433333344333

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=92.89  E-value=0.34  Score=30.36  Aligned_cols=42  Identities=14%  Similarity=0.161  Sum_probs=31.6

Q ss_pred             HHHHHhhcCCcHHHHHHHcC--CChhHHHHHHHHcCCCCChhHHHh
Q 041600           73 LRDLMIYFHLPIEEAARRMK--LCPTVVKKICRRDGLHRWPHRKIK  116 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lg--v~~T~LKr~CR~~GI~RWPyRkik  116 (160)
                      +..++.-.++++.+.|+.+|  |+.+++.++  +.|-...+...+.
T Consensus        13 l~~~r~~~glsq~~lA~~~g~~is~~~i~~~--e~g~~~~~~~~l~   56 (71)
T 2ewt_A           13 LRAIRTQQGLSLHGVEEKSQGRWKAVVVGSY--ERGDRAVTVQRLA   56 (71)
T ss_dssp             HHHHHHHTTCCHHHHHHHTTTSSCHHHHHHH--HHTCSCCCHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCCcCCHHHHHHH--HCCCCCCCHHHHH
Confidence            55677778999999999999  999999998  4565443343333

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=92.82  E-value=0.31  Score=31.78  Aligned_cols=41  Identities=15%  Similarity=0.163  Sum_probs=30.7

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKI  115 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRki  115 (160)
                      +..++.-.++++.+.|+.+|||.+++.++  +.|-...+...+
T Consensus        17 l~~~r~~~gltq~~lA~~~gvs~~~is~~--e~g~~~~~~~~~   57 (80)
T 3kz3_A           17 WEKKKNELGLSYESVADKMGMGQSAVAAL--FNGINALNAYNA   57 (80)
T ss_dssp             HHHHHHHHTCCHHHHHHHTTSCHHHHHHH--HTTSSCCCHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHhCcCHHHHHHH--HcCCCCCCHHHH
Confidence            44556667899999999999999999998  456544444333

>1j9i_A GPNU1 DBD;, terminase small subunit; DNA binding domain, homodimer, viral assembly, winged helix-turn-helix, viral protein; NMR {Enterobacteria phage lambda} SCOP: a.6.1.5

Probab=92.73  E-value=0.035  Score=36.38  Aligned_cols=30  Identities=10%  Similarity=0.117  Sum_probs=24.0

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKI  115 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRki  115 (160)
                      |...|||+.||||.+||.+..+ .|+   |+.++
T Consensus         3 lt~~e~a~~LgvS~~Tl~rw~~-~G~---P~~~~   32 (68)
T 1j9i_A            3 VNKKQLADIFGASIRTIQNWQE-QGM---PVLRG   32 (68)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHTT-TTC---CCSSC
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH-CCC---CeEee
Confidence            6789999999999999988764 476   65443

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=92.65  E-value=0.068  Score=32.90  Aligned_cols=23  Identities=9%  Similarity=0.215  Sum_probs=21.1

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +++..++|+.||||.+|+++..+
T Consensus        31 g~s~~eIA~~lgis~~TV~~~l~   53 (55)
T 2x48_A           31 GYTVQQIANALGVSERKVRRYLE   53 (55)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHH
Confidence            68999999999999999998864

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2}

Probab=92.54  E-value=0.45  Score=30.67  Aligned_cols=35  Identities=26%  Similarity=0.135  Sum_probs=29.5

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHR  109 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R  109 (160)
                      +..++...++.+.++|+.+||+.+++.++  +.|-..
T Consensus        15 l~~~r~~~glsq~~lA~~~gis~~~i~~~--e~g~~~   49 (84)
T 2ef8_A           15 LTKLRKEASLSQSELAIFLGLSQSDISKI--ESFERR   49 (84)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHH--HTTSSC
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHH--HcCCCC
Confidence            56777888999999999999999999998  556533

>1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L*

Probab=92.46  E-value=0.19  Score=31.33  Aligned_cols=35  Identities=17%  Similarity=0.281  Sum_probs=29.3

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHR  109 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R  109 (160)
                      +..++...++.+.+.|+.+|||.+++.++  +.|-..
T Consensus         8 l~~~r~~~glsq~~lA~~~gis~~~i~~~--e~g~~~   42 (71)
T 1zug_A            8 LKKRRIALKMTQTELATKAGVKQQSIQLI--EAGVTK   42 (71)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSCHHHHHHH--HTTCCS
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHH--HcCCCC
Confidence            55677788999999999999999999998  456544

>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3

Probab=92.29  E-value=0.59  Score=33.76  Aligned_cols=24  Identities=13%  Similarity=0.094  Sum_probs=20.9

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHHH
Q 041600           80 FHLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      -+++..|+|+.||||++++++..+
T Consensus        37 ~g~s~~EIA~~lgiS~~tV~~~l~   60 (113)
T 1s7o_A           37 DDYSLAEIADEFGVSRQAVYDNIK   60 (113)
T ss_dssp             TCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHH
Confidence            379999999999999999887654

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=92.27  E-value=0.36  Score=32.52  Aligned_cols=44  Identities=16%  Similarity=0.265  Sum_probs=32.1

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI  118 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl  118 (160)
                      +..++...++.+.++|+.+||+.+++.++.  .|-...+...+..+
T Consensus        14 lk~~r~~~glsq~~lA~~~gis~~~is~~e--~G~~~p~~~~l~~i   57 (94)
T 2kpj_A           14 LNSYIAKSEKTQLEIAKSIGVSPQTFNTWC--KGIAIPRMGKVQAL   57 (94)
T ss_dssp             HHHHHTTSSSCHHHHHHHHTCCHHHHHHHH--TTSCCCCHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHH--hCCCCCCHHHHHHH
Confidence            556677789999999999999999999984  45433334333333

>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response E family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV}

Probab=92.26  E-value=0.36  Score=31.33  Aligned_cols=35  Identities=20%  Similarity=0.140  Sum_probs=29.2

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHR  109 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R  109 (160)
                      +..++.--++++.+.|+.+||+.+++.++  +.|-..
T Consensus        19 l~~~R~~~gltq~elA~~~gis~~~is~~--e~g~~~   53 (83)
T 3f6w_A           19 LLEARSAAGITQKELAARLGRPQSFVSKT--ENAERR   53 (83)
T ss_dssp             HHHHHHHHTCCHHHHHHHHTSCHHHHHHH--HTTSSC
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HCCCCC
Confidence            56677778999999999999999999999  456533

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=92.21  E-value=0.3  Score=31.56  Aligned_cols=33  Identities=18%  Similarity=0.147  Sum_probs=28.4

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +..++..-++.+.+.|+.+||+.+++.++.  .|-
T Consensus         7 lk~~r~~~glsq~~lA~~~gis~~~i~~~e--~g~   39 (77)
T 2k9q_A            7 LKVERIRLSLTAKSVAEEMGISRQQLCNIE--QSE   39 (77)
T ss_dssp             HHHHHHHHTCCHHHHHHHHTSCHHHHHHHH--TCC
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH--cCC
Confidence            566778889999999999999999999984  564

>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}

Probab=92.15  E-value=0.21  Score=34.79  Aligned_cols=51  Identities=8%  Similarity=0.060  Sum_probs=36.0

Q ss_pred             HHhhc--CCcHHHHHHHcCCChhHHHHHHHHc-CCCCChhHHHhhHHHHHHHHh
Q 041600           76 LMIYF--HLPIEEAARRMKLCPTVVKKICRRD-GLHRWPHRKIKSIQRRMSVAS  126 (160)
Q Consensus        76 L~~yF--~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~RWPyRkikSl~~~i~~L~  126 (160)
                      |..++  .+++.+.|+.+|||+++|.+++++. |++---|.....+++...-|.
T Consensus        16 i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~~~~~~~~Rl~~A~~lL~   69 (113)
T 3oio_A           16 MEANIEEPLSTDDIAYYVGVSRRQLERLFKQYLGTVPSKYYLELRLNRARQLLQ   69 (113)
T ss_dssp             HHTCSSSCCCHHHHHHHHTSCHHHHHHHHHHHTSSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHhhhcCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            34444  4789999999999999999999998 886444444444444444443

>1bl0_A Protein (multiple antibiotic resistance protein), DNA (5'- D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP *AP*AP*TP* CP*C)-3')...; transcriptional activator; HET: DNA; 2.30A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 PDB: 1xs9_A

Probab=91.93  E-value=0.26  Score=35.30  Aligned_cols=45  Identities=9%  Similarity=0.141  Sum_probs=33.5

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc-CCCCChhHHHhhHHHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD-GLHRWPHRKIKSIQRRMSVA  125 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~RWPyRkikSl~~~i~~L  125 (160)
                      .+++.++|+.+|+|+++|.|++++. |++--=|.+...+++...-|
T Consensus        27 ~~sl~~lA~~~~~S~~~l~r~fk~~~G~s~~~~l~~~Rl~~A~~lL   72 (129)
T 1bl0_A           27 PLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMTEIAQKL   72 (129)
T ss_dssp             CCCCHHHHHHSSSCHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            3889999999999999999999987 88544444444444444444

>1b0n_A Protein (SINR protein); transcription regulator, antagonist, sporulation; 1.90A {Bacillus subtilis} SCOP: a.34.1.1 a.35.1.3 PDB: 2yal_A

Probab=91.70  E-value=0.46  Score=32.33  Aligned_cols=46  Identities=7%  Similarity=0.074  Sum_probs=32.7

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcC-CCCChhHHHhhHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDG-LHRWPHRKIKSIQR  120 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~G-I~RWPyRkikSl~~  120 (160)
                      +..++...++++.+.|+.+|||.+++.++  +.| ....+...+..+-.
T Consensus         6 l~~~r~~~gltq~~lA~~~gis~~~i~~~--e~g~~~~p~~~~l~~ia~   52 (111)
T 1b0n_A            6 IKQYRKEKGYSLSELAEKAGVAKSYLSSI--ERNLQTNPSIQFLEKVSA   52 (111)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHH--HTTCCSCCCHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HcCCCCCCCHHHHHHHHH
Confidence            45677778899999999999999999888  456 44434444444433

>3fmy_A HTH-type transcriptional regulator MQSA (YGIT/B3021); helix-turn-helix, DNA-binding, transcription regulation, DNA binding protein; HET: MEQ; 1.40A {Escherichia coli k-12}

Probab=91.53  E-value=0.17  Score=33.06  Aligned_cols=40  Identities=15%  Similarity=0.140  Sum_probs=31.8

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKI  115 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRki  115 (160)
                      +..++.-.++++.+.|+.+|||.+++.++  +.|- +-|-..+
T Consensus        16 lr~~R~~~gltq~elA~~~gvs~~tis~~--E~G~-~~p~~~~   55 (73)
T 3fmy_A           16 IVKVRKKLSLTQKEASEIFGGGVNAFSRY--EKGN-AXPHPST   55 (73)
T ss_dssp             HHHHHHHTTCCHHHHHHHHCSCTTHHHHH--HTTS-SCCCHHH
T ss_pred             HHHHHHHcCCCHHHHHHHhCcCHHHHHHH--HcCC-CCCCHHH
Confidence            56677888999999999999999999999  5564 2454433

>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription complex, serine kinase, DNA-bindin mercury derivative, repressor; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B*

Probab=91.53  E-value=0.25  Score=32.25  Aligned_cols=31  Identities=6%  Similarity=0.062  Sum_probs=27.1

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +..++...++.+.++|+.+||+.+++.++.+
T Consensus        17 l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   47 (88)
T 2wiu_B           17 MKLVRQQNGWTQSELAKKIGIKQATISNFEN   47 (88)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            5566777899999999999999999999954

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}

Probab=91.46  E-value=0.3  Score=34.52  Aligned_cols=36  Identities=11%  Similarity=0.009  Sum_probs=28.1

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHH
Q 041600           80 FHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSV  124 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~  124 (160)
                      -+++.+|+|+.||||..+++++-         +|=++.|++.+..
T Consensus       123 ~g~s~~EIA~~lgis~~tV~~~~---------~ra~~~Lr~~l~~  158 (164)
T 3mzy_A          123 RGYSYREIATILSKNLKSIDNTI---------QRIRKKSEEWIKE  158 (164)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHH---------HHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHHHH
Confidence            47999999999999999999885         5555555555544

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=91.39  E-value=0.59  Score=30.69  Aligned_cols=32  Identities=9%  Similarity=0.141  Sum_probs=28.1

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDG  106 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~G  106 (160)
                      +.+++.--++.+.++|+.+||+.+++.++  +.|
T Consensus        15 ik~~R~~~gltq~elA~~~gis~~~is~~--E~G   46 (78)
T 3qq6_A           15 IKQYRKEKGYSLSELAEKAGVAKSYLSSI--ERN   46 (78)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHH--HTT
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HcC
Confidence            66777888999999999999999999999  456

>1r8e_A Multidrug-efflux transporter regulator; protein-DNA complex, MERR-family transcription activator, MU binding protein; HET: P4P; 2.40A {Bacillus subtilis} SCOP: a.6.1.3 d.60.1.1 PDB: 1exi_A* 1exj_A* 3iao_A 3q5p_A* 3d71_A* 3q3d_A* 3q1m_A* 3q2y_A* 3q5r_A* 3q5s_A* 3d70_A 3d6z_A* 3d6y_A* 1bow_A 2bow_A*

Probab=91.25  E-value=0.27  Score=39.12  Aligned_cols=25  Identities=12%  Similarity=0.154  Sum_probs=21.1

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +++.|+|+.+|||+.||+..-+. |+
T Consensus         6 ~~i~e~a~~~gvs~~tlr~y~~~-gl   30 (278)
T 1r8e_A            6 YSIGEVSKLANVSIKALRYYDKI-DL   30 (278)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHT-TS
T ss_pred             EeHHHHHHHHCcCHHHHHHHHHC-CC
Confidence            78999999999999999976543 65

>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A

Probab=91.23  E-value=0.31  Score=34.93  Aligned_cols=40  Identities=15%  Similarity=0.135  Sum_probs=31.8

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKI  115 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRki  115 (160)
                      +..++.-.+|.+.++|+.||||.+++.++  +.|. +-|-..+
T Consensus        76 l~~~R~~~glsq~~la~~~g~s~~~i~~~--E~g~-~~p~~~~  115 (133)
T 3o9x_A           76 IVKVRKKLSLTQKEASEIFGGGVNAFSRY--EKGN-AQPHPST  115 (133)
T ss_dssp             HHHHHHHTTCCHHHHHHHHCSCTTHHHHH--HHTS-SCCCHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHH--HCCC-CCCCHHH
Confidence            55667889999999999999999999999  4564 3365444

>3ivp_A Putative transposon-related DNA-binding protein; APC62618, clostridium diffic structural genomics, PSI-2, protein structure initiative; HET: PG4; 2.02A {Clostridium difficile}

Probab=91.14  E-value=2.5  Score=29.67  Aligned_cols=29  Identities=14%  Similarity=0.217  Sum_probs=22.1

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKI  101 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~  101 (160)
                      +..++.--++++.+.|+.+|||.+++.++
T Consensus        17 lk~~R~~~glsq~~lA~~~gis~~~is~~   45 (126)
T 3ivp_A           17 IKEARKKQGLTREQVGAMIEIDPRYLTNI   45 (126)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHhCcCHHHHHHH
Confidence            55667777888888888888887766555

>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434} SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A 2r63_A 1sq8_A

Probab=91.10  E-value=0.23  Score=30.76  Aligned_cols=35  Identities=14%  Similarity=0.286  Sum_probs=28.9

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHR  109 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R  109 (160)
                      +..++...++++.+.|+.+||+.+++.++  +.|-..
T Consensus         6 l~~~r~~~glsq~~lA~~~gis~~~i~~~--e~g~~~   40 (69)
T 1r69_A            6 VKSKRIQLGLNQAELAQKVGTTQQSIEQL--ENGKTK   40 (69)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSCHHHHHHH--HTTSCS
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HcCCCC
Confidence            45677778999999999999999999998  455433

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=90.98  E-value=0.31  Score=33.68  Aligned_cols=25  Identities=28%  Similarity=0.196  Sum_probs=21.5

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +-+++.+|+|+.||||..+++...+
T Consensus        40 ~~g~s~~eIA~~l~is~~tV~~~l~   64 (95)
T 3c57_A           40 SEGLTNKQIADRMFLAEKTVKNYVS   64 (95)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4579999999999999999887643

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=90.89  E-value=0.28  Score=31.50  Aligned_cols=22  Identities=14%  Similarity=0.365  Sum_probs=20.5

Q ss_pred             CCcHHHHHHHcCCChhHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +++.+|+|+.||||..+++.+-
T Consensus        25 g~s~~eIA~~lgis~~tV~~~~   46 (68)
T 2p7v_B           25 DYTLEEVGKQFDVTRERIRQIE   46 (68)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHH
Confidence            7999999999999999999874

>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix, transcription/DNA complex; HET: DNA; 1.80A {Enterobacteria phage lambda} SCOP: a.35.1.2 PDB: 1lrp_A 1rio_A 1lli_A*

Probab=90.89  E-value=0.59  Score=30.85  Aligned_cols=39  Identities=15%  Similarity=0.121  Sum_probs=28.9

Q ss_pred             HHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHh
Q 041600           76 LMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIK  116 (160)
Q Consensus        76 L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkik  116 (160)
                      ++.-.++.+.+.|+.+||+.+++.++  +.|-...+...+.
T Consensus        25 ~R~~~glsq~~lA~~~gis~~~is~~--e~g~~~~~~~~l~   63 (92)
T 1lmb_3           25 KKNELGLSQESVADKMGMGQSGVGAL--FNGINALNAYNAA   63 (92)
T ss_dssp             HHHHHTCCHHHHHHHHTSCHHHHHHH--HTTSSCCCHHHHH
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHH--HcCCCCCCHHHHH
Confidence            34556999999999999999999998  4565443334333

>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A

Probab=90.86  E-value=0.42  Score=32.03  Aligned_cols=35  Identities=9%  Similarity=-0.105  Sum_probs=29.3

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHR  109 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R  109 (160)
                      +..++...++.+.+.|+.+||+.+++.++  +.|-..
T Consensus         9 l~~~r~~~gltq~~lA~~~gis~~~is~~--e~g~~~   43 (99)
T 2l49_A            9 IVLMRKSEYLSRQQLADLTGVPYGTLSYY--ESGRST   43 (99)
T ss_dssp             HHHHHHHTTCCHHHHHHHHCCCHHHHHHH--TTTSSC
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HcCCCC
Confidence            56778888999999999999999999998  456433

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12

Probab=90.83  E-value=0.61  Score=30.99  Aligned_cols=31  Identities=13%  Similarity=0.093  Sum_probs=27.3

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +..++...++.+.+.|+.+||+.+++.++-+
T Consensus        18 l~~~r~~~glsq~~lA~~~gis~~~is~~e~   48 (91)
T 1x57_A           18 IQQGRQSKGLTQKDLATKINEKPQVIADYES   48 (91)
T ss_dssp             HHHHHHTTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            5667788899999999999999999999844

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=90.57  E-value=0.32  Score=30.56  Aligned_cols=23  Identities=13%  Similarity=0.049  Sum_probs=21.0

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHH
Q 041600           80 FHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      .+++..|+|+.||+|.+++++..
T Consensus        30 ~g~s~~eIA~~lgis~~tv~~~~   52 (70)
T 2o8x_A           30 LGLSYADAAAVCGCPVGTIRSRV   52 (70)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHH
Confidence            47999999999999999999875

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi}

Probab=90.55  E-value=0.64  Score=30.97  Aligned_cols=33  Identities=21%  Similarity=0.200  Sum_probs=28.9

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +..++.-.++++.+.|+.+|||.+++.++  +.|-
T Consensus        19 l~~~R~~~gltq~elA~~~gis~~~is~~--E~G~   51 (86)
T 3eus_A           19 LRQARLDAGLTQADLAERLDKPQSFVAKV--ETRE   51 (86)
T ss_dssp             HHHHHHHTTCCHHHHHHHTTCCHHHHHHH--HTTS
T ss_pred             HHHHHHHcCCCHHHHHHHhCcCHHHHHHH--HCCC
Confidence            56677888999999999999999999999  6675

>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=90.22  E-value=0.31  Score=35.89  Aligned_cols=24  Identities=25%  Similarity=0.052  Sum_probs=21.5

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +-+++.+|+|+.||||+.++|++-
T Consensus       154 ~~g~s~~EIA~~lgis~~tV~~~l  177 (194)
T 1or7_A          154 LDGLSYEEIAAIMDCPVGTVRSRI  177 (194)
T ss_dssp             TTCCCHHHHHHHTTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHH
Confidence            347999999999999999999884

>2zhg_A Redox-sensitive transcriptional activator SOXR; oxidative stress, MERR family, activator; HET: DNA; 2.80A {Escherichia coli} PDB: 2zhh_A

Probab=90.19  E-value=0.56  Score=35.63  Aligned_cols=26  Identities=23%  Similarity=0.259  Sum_probs=21.9

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      +++.|+|+.+|||+.||+..-+. |+-
T Consensus        12 ~~i~e~A~~~gvs~~TLR~ye~~-Gll   37 (154)
T 2zhg_A           12 LTPGEVAKRSGVAVSALHFYESK-GLI   37 (154)
T ss_dssp             BCHHHHHHHHTSCHHHHHHHHHT-TSS
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc-CCC
Confidence            79999999999999999977544 653

>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}

Probab=90.05  E-value=0.71  Score=32.29  Aligned_cols=45  Identities=20%  Similarity=0.154  Sum_probs=33.5

Q ss_pred             CHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhH
Q 041600           72 TLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI  118 (160)
Q Consensus        72 t~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl  118 (160)
                      .+..++.--++.+.++|+.+||+.+++.++  +.|-...+...+..+
T Consensus        25 ~lr~~R~~~gltq~elA~~~gis~~~is~~--E~G~~~p~~~~l~~i   69 (114)
T 3vk0_A           25 NMRLFRVNKGWSQEELARQCGLDRTYVSAV--ERKRWNIALSNIEKM   69 (114)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHH--TTTCCCCCHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HcCCCCCCHHHHHHH
Confidence            366777888999999999999999999998  556544333333333

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=90.03  E-value=0.41  Score=32.01  Aligned_cols=33  Identities=24%  Similarity=0.356  Sum_probs=27.9

Q ss_pred             CCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           71 LTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        71 lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      +++..+....  .+.+||+.|||+.+++-+.||..
T Consensus         5 ~~Lk~l~~~~--sq~~~A~~Lgvsq~aVS~~~~~~   37 (65)
T 2cw1_A            5 LDLKKFVEDK--NQEYAARALGLSQKLIEEVLKRG   37 (65)
T ss_dssp             CCHHHHHTTS--CHHHHHHHSSSCHHHHHHHHHTT
T ss_pred             HHHHHHHHHc--CHHHHHHHhCCCHHHHHHHHHhc
Confidence            4677776664  99999999999999999999764

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B

Probab=89.99  E-value=0.61  Score=33.24  Aligned_cols=47  Identities=13%  Similarity=0.295  Sum_probs=32.4

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHH--HHHHhhhccC-CcHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRR--MSVASGRLRS-NDAEE  136 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~--i~~L~~~~~~-~~~ee  136 (160)
                      +++.+|+|..||||..++|.+-         +|=++.|+..  ...|..++.. +.+|+
T Consensus        39 ~~s~~EIA~~lgiS~~tVr~~~---------~rAlkkLR~~~~~~~l~~~~~~~~~~~~   88 (99)
T 3t72_q           39 DYTLEEVGKQFDVTRERIRQIE---------AKALRKLRHPSRSEVLRSGSSGSGTPEE   88 (99)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHhcCCCHH
Confidence            5999999999999999999986         3334444433  3456666653 34443

>3qao_A LMO0526 protein, MERR-like transcriptional regulator; structural genomics, the center for structural genomics of I diseases, csgid; 1.87A {Listeria monocytogenes}

Probab=89.96  E-value=0.3  Score=39.98  Aligned_cols=27  Identities=19%  Similarity=0.186  Sum_probs=22.5

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      .+++.|+|+.+|||+.||+-.-+ .|+-
T Consensus         3 ~~tI~evA~~~gvs~~TLRyYe~-~GLL   29 (249)
T 3qao_A            3 AMQIKELAELTGVSVRTLHHYDK-IGLL   29 (249)
T ss_dssp             CBCHHHHHHHHCCCHHHHHHHHH-TTSS
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHH-CCCC
Confidence            47899999999999999997654 6753

>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A

Probab=89.75  E-value=0.69  Score=32.09  Aligned_cols=35  Identities=14%  Similarity=0.171  Sum_probs=29.8

Q ss_pred             CHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           72 TLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        72 t~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      .+..++.--++.+.+.|+.+||+.+++.++  +.|-.
T Consensus        32 ~lr~~R~~~gltq~elA~~~gis~~~is~i--E~G~~   66 (99)
T 3g5g_A           32 VIKKIRLEKGMTQEDLAYKSNLDRTYISGI--ERNSR   66 (99)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHH--HTTCS
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HCCCC
Confidence            366777888999999999999999999999  56653

>1rzs_A Antirepressor, regulatory protein CRO; helix-turn-helix, DNA-binding protein, structural evolution, transcription; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=89.64  E-value=0.37  Score=30.90  Aligned_cols=30  Identities=13%  Similarity=0.141  Sum_probs=25.8

Q ss_pred             CHHHHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           72 TLRDLMIYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        72 t~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +++++...+ +.+.+.|+.||||.+++-+..
T Consensus         2 ~~~~~i~~~-~tq~~lA~~lGvs~~~Vs~we   31 (61)
T 1rzs_A            2 YKKDVIDHF-GTQRAVAKALGISDAAVSQWK   31 (61)
T ss_dssp             BHHHHHHHH-SSHHHHHHHHTCCHHHHHHCC
T ss_pred             CHHHHHHHc-CCHHHHHHHhCCCHHHHHHHH
Confidence            567777776 599999999999999999876

>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional ACTI human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A

Probab=89.40  E-value=0.94  Score=31.43  Aligned_cols=43  Identities=14%  Similarity=0.233  Sum_probs=32.4

Q ss_pred             CHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHh
Q 041600           72 TLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIK  116 (160)
Q Consensus        72 t~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkik  116 (160)
                      .+..++.--++++.+.|+.+|||.+++.++  +.|-..-+...+.
T Consensus        32 ~l~~~R~~~glsq~~lA~~~gis~~~is~~--E~g~~~~~~~~l~   74 (117)
T 3f52_A           32 ALRSFRADKGVTLRELAEASRVSPGYLSEL--ERGRKEVSSELLA   74 (117)
T ss_dssp             HHHHHHHHHTCCHHHHHHHTTSCHHHHHHH--HTTSSCCCHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HCCCCCCCHHHHH
Confidence            466777888999999999999999999998  5665433333333

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=89.31  E-value=0.93  Score=34.10  Aligned_cols=26  Identities=15%  Similarity=0.022  Sum_probs=22.4

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      .+++.|+|+.+|||+.||+..-+. |+
T Consensus         4 ~~tI~evA~~~Gvs~~tLR~ye~~-GL   29 (146)
T 3hh0_A            4 AWLISEFASVGDVTVRALRYYDKI-NL   29 (146)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHT-TS
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHHC-CC
Confidence            378999999999999999987665 64

>3gp4_A Transcriptional regulator, MERR family; structural genomics, DNA-BI transcription regulator, PSI-2; 1.85A {Listeria monocytogenes str}

Probab=89.28  E-value=0.6  Score=35.00  Aligned_cols=26  Identities=27%  Similarity=0.397  Sum_probs=22.2

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      .+++.|+|+.+|||+.||+-.-+. |+
T Consensus         2 ~~~I~e~A~~~gvs~~tLR~Ye~~-GL   27 (142)
T 3gp4_A            2 SLNIKEASEKSGVSADTIRYYERI-GL   27 (142)
T ss_dssp             CBCHHHHHHHHTSCHHHHHHHHHH-TS
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHHC-CC
Confidence            478999999999999999977655 54

>2a6c_A Helix-turn-helix motif; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: CIT; 1.90A {Nitrosomonas europaea} SCOP: a.35.1.13

Probab=89.18  E-value=0.38  Score=31.82  Aligned_cols=30  Identities=17%  Similarity=0.118  Sum_probs=26.7

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +..++...++.+.++|+.+||+.+++.++-
T Consensus        23 l~~~r~~~glsq~elA~~~gis~~~is~~e   52 (83)
T 2a6c_A           23 LQEHLRNSGLTQFKAAELLGVTQPRVSDLM   52 (83)
T ss_dssp             HHHHHHTTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            667777889999999999999999999984

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=89.11  E-value=0.54  Score=30.63  Aligned_cols=34  Identities=6%  Similarity=0.076  Sum_probs=29.0

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +.+++...+ .+.+.|+.+||+.+++-++.+-..+
T Consensus         4 l~~~r~~~g-sq~~lA~~lgvs~~~is~~e~g~~~   37 (79)
T 3bd1_A            4 IDIAINKLG-SVSALAASLGVRQSAISNWRARGRV   37 (79)
T ss_dssp             HHHHHHHHS-SHHHHHHHHTCCHHHHHHHHHHTCC
T ss_pred             HHHHHHHhC-CHHHHHHHHCCCHHHHHHHHHCCCC
Confidence            567788889 9999999999999999999765444

>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3

Probab=88.67  E-value=0.94  Score=32.48  Aligned_cols=48  Identities=15%  Similarity=0.082  Sum_probs=31.0

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHHHHcC-------CCCChhHHHhhHHHHHHHHh
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKICRRDG-------LHRWPHRKIKSIQRRMSVAS  126 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~CR~~G-------I~RWPyRkikSl~~~i~~L~  126 (160)
                      +-+++.+|+|+.||||.+++++.-++.-       -..+-+.+...++..+..|.
T Consensus        39 ~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l~~~~~~~~~~~~~~~~~~~~   93 (113)
T 1xsv_A           39 LEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYEKKLELYQKFEQRREIYDEMK   93 (113)
T ss_dssp             TSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhHHhHHHHHHHHHHHHH
Confidence            3479999999999999998886543210       01133555555556666654

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=88.65  E-value=0.67  Score=31.50  Aligned_cols=37  Identities=19%  Similarity=0.264  Sum_probs=30.5

Q ss_pred             CCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           71 LTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        71 lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      ++++++..+|. .+.++|+.||||..++-+--+..+|+
T Consensus         1 M~~~~ai~~~G-~~~~lA~~lGVs~~aVs~W~~g~~iP   37 (71)
T 2hin_A            1 MKPEELVRHFG-DVEKAAVGVGVTPGAVYQWLQAGEIP   37 (71)
T ss_dssp             CCHHHHHHHHS-SHHHHHHHHTSCHHHHHHHHHHTSCC
T ss_pred             CcHHHHHHHHC-CHHHHHHHHCCCHHHHHHHHhCCCCC
Confidence            36788888885 59999999999999999886666674

>2ppx_A AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif, XRE-family, structural genomics, PSI-2, protein structure initiative; 2.00A {Agrobacterium tumefaciens str} SCOP: a.35.1.3

Probab=88.53  E-value=1.2  Score=30.30  Aligned_cols=35  Identities=14%  Similarity=0.156  Sum_probs=30.8

Q ss_pred             CCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           71 LTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        71 lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      -.+..++...++.+.+.|+.+||+.+++.++  +.|-
T Consensus        33 ~~lk~~R~~~glsq~elA~~lgvs~~~is~~--E~G~   67 (99)
T 2ppx_A           33 PRIKIIRRALKLTQEEFSARYHIPLGTLRDW--EQGR   67 (99)
T ss_dssp             CHHHHHHHHTTCCHHHHHHHHTCCHHHHHHH--HTTS
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCcCHHHHHHH--HcCC
Confidence            3578888999999999999999999999999  5664

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=88.14  E-value=0.35  Score=29.91  Aligned_cols=23  Identities=4%  Similarity=-0.011  Sum_probs=19.9

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHH
Q 041600           80 FHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+++.+|+|+.||+|..+++..-
T Consensus        12 ~g~s~~eIA~~l~is~~tV~~~~   34 (61)
T 2jpc_A           12 EGYTNHGISEKLHISIKTVETHR   34 (61)
T ss_dssp             TSCCSHHHHHHTCSCHHHHHHHH
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Confidence            37999999999999999888664

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=87.89  E-value=0.37  Score=31.87  Aligned_cols=24  Identities=17%  Similarity=0.238  Sum_probs=21.0

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHc
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      ++++|+|+.+|||.+|+-+++.--
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLng~   24 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVINGK   24 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHTC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCC
Confidence            478999999999999999998643

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=87.84  E-value=0.36  Score=32.45  Aligned_cols=27  Identities=26%  Similarity=0.313  Sum_probs=24.2

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      .+++.|+|+.+||++.||+..-++.|+
T Consensus         5 ~~~i~e~A~~~gvs~~tlR~ye~~~gl   31 (81)
T 2jml_A            5 TLRIRTIARMTGIREATLRAWERRYGF   31 (81)
T ss_dssp             CEEHHHHHHTTSTTHHHHHHHHHHTCC
T ss_pred             cccHHHHHHHHCcCHHHHHHHHHhCCC
Confidence            478999999999999999999887675

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=87.64  E-value=0.49  Score=34.49  Aligned_cols=22  Identities=5%  Similarity=0.043  Sum_probs=20.2

Q ss_pred             CcHHHHHHHcCCChhHHHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +++.|+|+.||||.+++-|+-|
T Consensus        59 ~TQREIA~~lGiS~stISRi~r   80 (101)
T 1jhg_A           59 MSQRELKNELGAGIATITRGSN   80 (101)
T ss_dssp             SCHHHHHHHHCCCHHHHHHHHH
T ss_pred             cCHHHHHHHHCCChhhhhHHHH
Confidence            9999999999999999998843

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=87.55  E-value=0.39  Score=30.32  Aligned_cols=24  Identities=13%  Similarity=0.126  Sum_probs=20.3

Q ss_pred             CCc----HHHHHHHcCCChhHHHHHHHH
Q 041600           81 HLP----IEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        81 ~lP----~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      +.+    +.++|+.+||++++|.+..++
T Consensus        21 g~s~~~~~~~vA~~~gIs~~tl~~W~~~   48 (59)
T 2glo_A           21 DNDCKGNQRATARKYNIHRRQIQKWLQC   48 (59)
T ss_dssp             CTTTTTCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             CCCcchHHHHHHHHHCcCHHHHHHHHHH
Confidence            467    999999999999999987543

>2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2, protein struct initiative, northeast structural genomics consortium, NESG; 1.63A {Escherichia coli} SCOP: a.35.1.3 PDB: 2icp_A

Probab=87.43  E-value=0.6  Score=31.23  Aligned_cols=31  Identities=16%  Similarity=0.426  Sum_probs=27.1

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +..++...++++.+.|+.+||+.+++.++.+
T Consensus        13 l~~~r~~~gltq~~lA~~~gis~~~is~~e~   43 (94)
T 2ict_A           13 IQESLDELNVSLREFARAMEIAPSTASRLLT   43 (94)
T ss_dssp             HHHHHHHHTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            5667777899999999999999999999854

>1q06_A Transcriptional regulator CUER; MERR family transcriptional regulator, copper efflux regulator; 2.07A {Escherichia coli} SCOP: a.6.1.3 PDB: 1q05_A 1q07_A

Probab=87.38  E-value=1.1  Score=33.03  Aligned_cols=25  Identities=20%  Similarity=0.325  Sum_probs=21.0

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      |++.|+|+.+|||+.||+..-+ .|+
T Consensus         1 ~~I~e~A~~~gvs~~tLR~ye~-~Gl   25 (135)
T 1q06_A            1 MNISDVAKITGLTSKAIRFYEE-KGL   25 (135)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH-TTC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCC
Confidence            5789999999999999997755 454

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=87.37  E-value=0.49  Score=30.70  Aligned_cols=22  Identities=14%  Similarity=0.212  Sum_probs=20.5

Q ss_pred             CCcHHHHHHHcCCChhHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +++..|+|+.||||..+++++-
T Consensus        30 ~~s~~eIA~~l~is~~tV~~~~   51 (73)
T 1ku3_A           30 EHTLEEVGAYFGVTRERIRQIE   51 (73)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHH
Confidence            6999999999999999999875

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=87.29  E-value=0.42  Score=32.45  Aligned_cols=24  Identities=13%  Similarity=0.257  Sum_probs=20.6

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      +.++.++|+.|||+.++|.+..++
T Consensus        38 g~s~~~iA~~~gIs~sTl~rW~k~   61 (87)
T 2elh_A           38 GESKASVARDIGVPESTLRGWCKN   61 (87)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHH
Confidence            589999999999999999887543

>3gbg_A TCP pilus virulence regulatory protein; cupin, helix-turn-helix, ARAC family, activator, DNA-binding transcription, transcription regulation; HET: PAM; 1.90A {Vibrio cholerae}

Probab=87.28  E-value=0.76  Score=36.04  Aligned_cols=41  Identities=10%  Similarity=0.050  Sum_probs=30.1

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRR  121 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~  121 (160)
                      .+++.+.|+.+|||++.|.|.+++.|++--=|-.-..+++.
T Consensus       185 ~~sl~~lA~~~~~S~~~l~r~fk~~G~t~~~~l~~~Rl~~A  225 (276)
T 3gbg_A          185 NWRWADICGELRTNRMILKKELESRGVKFRELINSIRISYS  225 (276)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHTTTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            47899999999999999999999877753223333333333

>1y6u_A XIS, excisionase from transposon TN916; structure, DNA architectural protein, tyrosine recombinase, winged-helix protein; NMR {Enterococcus faecalis}

Probab=87.28  E-value=0.52  Score=31.90  Aligned_cols=27  Identities=19%  Similarity=0.439  Sum_probs=24.5

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc-CC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD-GL  107 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI  107 (160)
                      -|+++|||.-||||.++|.++.++. +.
T Consensus        16 ~LTi~EaAeylgIg~~~l~~L~~~~~~~   43 (70)
T 1y6u_A           16 TLTIEEASKYFRIGENKLRRLAEENKNA   43 (70)
T ss_dssp             EEEHHHHHHHTCSCHHHHHHHHHHCTTC
T ss_pred             eeCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence            4899999999999999999999986 44

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=87.24  E-value=0.76  Score=30.79  Aligned_cols=24  Identities=29%  Similarity=0.309  Sum_probs=20.9

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +-+++.+|+|+.||||..++++..
T Consensus        34 ~~g~s~~eIA~~l~is~~tV~~~l   57 (82)
T 1je8_A           34 AQGLPNKMIARRLDITESTVKVHV   57 (82)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            457999999999999999988764

>3cec_A Putative antidote protein of plasmid maintenance; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.60A {Nostoc punctiforme}

Probab=86.57  E-value=1.7  Score=29.58  Aligned_cols=30  Identities=7%  Similarity=0.214  Sum_probs=26.2

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +..++.-.++++.+.|+.+|||.+++-++-
T Consensus        23 l~~~r~~~gltq~~lA~~~gis~~~is~~e   52 (104)
T 3cec_A           23 IADILDDLDINTANFAEILGVSNQTIQEVI   52 (104)
T ss_dssp             HHHHHHHHTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            566777789999999999999999999984

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae}

Probab=86.55  E-value=1.6  Score=32.26  Aligned_cols=35  Identities=17%  Similarity=0.065  Sum_probs=30.3

Q ss_pred             CCHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           71 LTLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        71 lt~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      -.+..++.-.++++.++|+.+|||.+++.++-  .|-
T Consensus        71 ~~L~~~R~~~glTq~elA~~lGis~s~is~~E--~G~  105 (141)
T 3kxa_A           71 ETFVSLRMKKGFTQSELATAAGLPQPYLSRIE--NSK  105 (141)
T ss_dssp             CCHHHHHHHTTCCHHHHHHHTTCCHHHHHHHH--HTC
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH--cCC
Confidence            45777888999999999999999999999994  454

>1y9q_A Transcriptional regulator, HTH_3 family; transcriptional regulaator, strucutral genomics, protein structure initiative, PSI; 1.90A {Vibrio cholerae} SCOP: a.35.1.8 b.82.1.15

Probab=86.08  E-value=1.6  Score=32.63  Aligned_cols=34  Identities=18%  Similarity=0.261  Sum_probs=28.7

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      +..++.--++.+++.|+.+|||.+++.++  +.|-.
T Consensus        16 l~~~r~~~gltq~~lA~~~gis~~~is~~--e~g~~   49 (192)
T 1y9q_A           16 LKNLRKSRGLSLDATAQLTGVSKAMLGQI--ERGES   49 (192)
T ss_dssp             HHHHHHHTTCCHHHHHHHHSSCHHHHHHH--HTTCS
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HcCCC
Confidence            56677778999999999999999999999  45643

>2auw_A Hypothetical protein NE0471; alpha-beta structure, structural genomics, PSI, protein STRU initiative; 1.85A {Nitrosomonas europaea} SCOP: a.35.1.10 d.331.1.1

Probab=85.99  E-value=0.84  Score=36.00  Aligned_cols=96  Identities=13%  Similarity=0.062  Sum_probs=59.5

Q ss_pred             CCceeecCchhHHHHHhhcc-----cccCCCCCCCC--CCCCCCCchhhhhccCCCCHHHHHhhcCCcHHHHHHHcCCCh
Q 041600           23 AGFMMLPDPLSDFYEAVCVG-----LVLDDNLTTDD--YSQPPMTNSVQRERTGKLTLRDLMIYFHLPIEEAARRMKLCP   95 (160)
Q Consensus        23 ~g~~~~qd~~s~f~~alc~~-----~~~~~~~~~d~--~~~ps~s~s~~r~r~~~lt~~~L~~yF~lP~~eAA~~Lgv~~   95 (160)
                      .-|.-++|  -+||...-++     +.|++++ .+.  ....   ...+..-...-.+.+|+.-.+++++++|+.||||.
T Consensus        44 ~~F~~LkD--~~~F~~v~V~~~g~tV~W~~g~-iaPd~LY~~---~~~~~~~~s~~~lk~lR~~~glTQ~elA~~LGvsr  117 (170)
T 2auw_A           44 PDLAPILD--PEAFARVHIAEWEGSVEWFDTE-FGRDNVYAW---AKEQAGEVSHEMFGDWMHRNNLSLTTAAEALGISR  117 (170)
T ss_dssp             GGGGGGGS--HHHHTTCEECTTTCCEESSSCC-BCHHHHHHH---HHHHTTCCCHHHHHHHHHHTTCCHHHHHHHHTSCH
T ss_pred             chhhhhcC--HHHhCcEEEcCCCCEEEcCCCC-CCHHHHHHh---hhhhccCCCcHHHHHHHHHcCCCHHHHHHHhCCCH
Confidence            45666777  3466666554     6887776 431  1000   00111111122377888999999999999999999


Q ss_pred             hHHHHHHHHcCCCCChhHHHhhHHHHHHHHhh
Q 041600           96 TVVKKICRRDGLHRWPHRKIKSIQRRMSVASG  127 (160)
Q Consensus        96 T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~  127 (160)
                      +++-++  +.|...-|.--+-...- ++.++.
T Consensus       118 ~tis~y--E~G~r~iP~~~~lac~~-~~~~~~  146 (170)
T 2auw_A          118 RMVSYY--RTAHKIIPRTIWLACLG-WEATRP  146 (170)
T ss_dssp             HHHHHH--HTTSSCCCHHHHHHHHH-HHHTCS
T ss_pred             HHHHHH--HcCCCCCCHHHHHHHHH-HHhhcc
Confidence            999998  77875577554333332 566554

>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian}

Probab=85.83  E-value=1.3  Score=33.31  Aligned_cols=27  Identities=19%  Similarity=0.257  Sum_probs=22.2

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      .+++.|+|+.+|||+.||+..-+ .|+-
T Consensus        16 ~~~I~evA~~~gvs~~tLR~Ye~-~Gll   42 (148)
T 3gpv_A           16 YYTIGQVAKMQHLTISQIRYYDK-QGLF   42 (148)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHHH-TTCC
T ss_pred             ceeHHHHHHHHCcCHHHHHHHHH-CCCC
Confidence            38999999999999999997654 4543

>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=85.81  E-value=1.5  Score=32.96  Aligned_cols=23  Identities=22%  Similarity=0.297  Sum_probs=21.1

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHH
Q 041600           80 FHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+++.+|+|+.||||..+++++-
T Consensus       202 ~g~s~~EIA~~lgis~~~V~~~~  224 (239)
T 1rp3_A          202 EELPAKEVAKILETSVSRVSQLK  224 (239)
T ss_dssp             SCCCHHHHHHHTTSCHHHHHHHH
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Confidence            37999999999999999999885

>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens}

Probab=85.63  E-value=0.98  Score=28.24  Aligned_cols=31  Identities=10%  Similarity=0.149  Sum_probs=26.0

Q ss_pred             CHHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600           72 TLRDLMIYFHLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        72 t~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      .+..+..-.+ .+.++|+.|||+.+++-++.|
T Consensus         5 ~l~~~~~~~g-s~~~~A~~lgis~~~vs~~~~   35 (67)
T 2pij_A            5 PLSKYLEEHG-TQSALAAALGVNQSAISQMVR   35 (67)
T ss_dssp             EHHHHHHHTC-CHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHcC-CHHHHHHHHCcCHHHHHHHHc
Confidence            3555666677 999999999999999999875

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=85.63  E-value=0.64  Score=34.75  Aligned_cols=33  Identities=21%  Similarity=0.187  Sum_probs=27.9

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      +..|+.-.-+|..+.|+.||+|.+++.++-+++
T Consensus         9 l~~L~~~~~~s~~~la~~lg~s~~tv~~rl~~L   41 (162)
T 3i4p_A            9 LRILQEDSTLAVADLAKKVGLSTTPCWRRIQKM   41 (162)
T ss_dssp             HHHHTTCSCSCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            345666677999999999999999999888776

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=85.62  E-value=0.89  Score=30.47  Aligned_cols=35  Identities=14%  Similarity=0.263  Sum_probs=27.9

Q ss_pred             CCCCHHHHHhhc---CCcHHHHHHHcCCChhHHHHHHH
Q 041600           69 GKLTLRDLMIYF---HLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        69 ~~lt~~~L~~yF---~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      .+...++|....   ++++.+.|+.+|||.++|.+...
T Consensus         7 ~~~~~~ri~~~l~~~glT~~~LA~~~Gvs~stls~~~~   44 (74)
T 1neq_A            7 RDWHRADVIAGLKKRKLSLSALSRQFGYAPTTLANALE   44 (74)
T ss_dssp             SSCCHHHHHHHHHTTSCCHHHHHHHHSSCHHHHHHTTT
T ss_pred             CCCCHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            356666666443   79999999999999999998854

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=85.59  E-value=0.79  Score=29.54  Aligned_cols=24  Identities=21%  Similarity=0.238  Sum_probs=20.8

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +.+++.+|+|+.||||..+++...
T Consensus        29 ~~g~s~~eIA~~l~is~~tV~~~~   52 (79)
T 1x3u_A           29 VAGLPNKSIAYDLDISPRTVEVHR   52 (79)
T ss_dssp             TTTCCHHHHHHHTTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            447999999999999999888664

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei}

Probab=85.14  E-value=1.4  Score=30.74  Aligned_cols=33  Identities=9%  Similarity=0.034  Sum_probs=27.9

Q ss_pred             HHHHHh--hcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           73 LRDLMI--YFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        73 ~~~L~~--yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +..++.  ..++.+.+.|+.+||+.+++.++  +.|-
T Consensus        39 lk~~R~~~~~glsq~elA~~~gis~~~is~~--E~G~   73 (107)
T 2jvl_A           39 IEQGRQKFEPTMTQAELGKEIGETAATVASY--ERGT   73 (107)
T ss_dssp             HHHHHTTSSSCCCHHHHHHHHTCCHHHHHHH--TTTC
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HcCC
Confidence            566777  78899999999999999999998  4554

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A

Probab=85.13  E-value=2.3  Score=28.66  Aligned_cols=33  Identities=12%  Similarity=0.128  Sum_probs=26.4

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhH----HHHHHHHcCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTV----VKKICRRDGL  107 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~----LKr~CR~~GI  107 (160)
                      +..++.--++++.+.|+.+||+.++    +.++  +.|-
T Consensus         6 lk~~R~~~glsq~~lA~~~gis~~~~~~~is~~--E~g~   42 (98)
T 3lfp_A            6 LKDARLRAGISQEKLGVLAGIDEASASARMNQY--EKGK   42 (98)
T ss_dssp             HHHHHHHHTCCHHHHHHHTTCCHHHHHHHHHHH--HHTS
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCcchhhhHHHHH--HCCC
Confidence            4566777889999999999999998    7777  4454

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=85.00  E-value=0.73  Score=31.08  Aligned_cols=22  Identities=14%  Similarity=0.247  Sum_probs=20.2

Q ss_pred             CCcHHHHHHHcCCChhHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +++.+|+|+.||||..+++.+-
T Consensus        38 ~~s~~EIA~~lgis~~tV~~~~   59 (87)
T 1tty_A           38 PKTLEEVGQYFNVTRERIRQIE   59 (87)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHH
Confidence            5999999999999999999873

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=84.98  E-value=0.7  Score=29.24  Aligned_cols=23  Identities=13%  Similarity=0.109  Sum_probs=19.8

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHH
Q 041600           80 FHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+++.+|+|+.||+|.+++++.-
T Consensus        25 ~g~s~~eIA~~l~is~~tV~~~~   47 (74)
T 1fse_A           25 QDKTTKEIASELFISEKTVRNHI   47 (74)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHH
Confidence            36899999999999998887664

>2bnm_A Epoxidase; oxidoreductase, cupin, HTH, cation-dependant, zinc, fosfomycin; 1.7A {Streptomyces wedmorensis} SCOP: a.35.1.3 b.82.1.10 PDB: 1zz7_A 1zz8_A 1zz9_A 1zzb_A 1zz6_A 1zzc_A 2bnn_A 2bno_A 3scf_A 3scg_A 3sch_A

Probab=84.57  E-value=1.8  Score=32.42  Aligned_cols=34  Identities=18%  Similarity=0.141  Sum_probs=28.6

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      +..++.-.++.+++.|+.+|||.++|.++  +.|..
T Consensus        15 l~~~r~~~g~s~~~la~~~gis~~~ls~~--e~g~~   48 (198)
T 2bnm_A           15 LKDRREQVKMDHAALASLLGETPETVAAW--ENGEG   48 (198)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHH--HTTTC
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HcCCC
Confidence            56677888999999999999999999999  45543

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=84.56  E-value=0.49  Score=34.70  Aligned_cols=24  Identities=17%  Similarity=0.153  Sum_probs=21.4

Q ss_pred             hcCCcHHHHHHHcCCChhHHHHHH
Q 041600           79 YFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        79 yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +-+++.+|+|+.||||+.++|..-
T Consensus       107 ~~g~s~~EIA~~lgis~~tV~~~l  130 (157)
T 2lfw_A          107 MEGFSPEDAAYLIEVDTSEVETLV  130 (157)
T ss_dssp             SSCCCHHHHHHTTTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            347999999999999999999874

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=84.35  E-value=0.71  Score=31.47  Aligned_cols=25  Identities=20%  Similarity=0.216  Sum_probs=22.6

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      ++++.++|+.||||.+|+.+..+++
T Consensus        33 g~s~~~ia~~lgis~~Tv~~w~~~~   57 (128)
T 1pdn_C           33 GIRPCVISRQLRVSHGCVSKILNRY   57 (128)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            6899999999999999999887764

>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli}

Probab=84.26  E-value=1.9  Score=29.64  Aligned_cols=27  Identities=19%  Similarity=0.224  Sum_probs=22.0

Q ss_pred             HHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           76 LMIYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        76 L~~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      ++...++++.+.|+.+|||.+++.++.
T Consensus        19 ~r~~~glsq~~lA~~~gis~~~is~~e   45 (113)
T 2eby_A           19 YLEPLDLKINELAELLHVHRNSVSALI   45 (113)
T ss_dssp             TTTTTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            556668899999999999988888774

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=84.00  E-value=0.68  Score=32.49  Aligned_cols=25  Identities=8%  Similarity=0.280  Sum_probs=22.8

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      +++..++|+.||||.+|+.+..+++
T Consensus        22 G~s~~~ia~~lgis~~Tv~r~~~~~   46 (141)
T 1u78_A           22 NVSLHEMSRKISRSRHCIRVYLKDP   46 (141)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHSG
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHcc
Confidence            6899999999999999999988764

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=83.99  E-value=2.8  Score=33.55  Aligned_cols=25  Identities=12%  Similarity=0.102  Sum_probs=21.5

Q ss_pred             cCCcHHHHHHHcCCChhHHHHHHHH
Q 041600           80 FHLPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        80 F~lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      -++++.|+|+.||||.+++-|.-+.
T Consensus        23 ~g~tQ~eIA~~lGiSr~~VSR~L~~   47 (192)
T 1zx4_A           23 DGMSQKDIAAKEGLSQAKVTRALQA   47 (192)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             cCCCHHHHHHHhCcCHHHHHHHHHH
Confidence            4799999999999999999887543

>1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli}

Probab=83.90  E-value=0.6  Score=30.33  Aligned_cols=26  Identities=8%  Similarity=0.051  Sum_probs=22.8

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +.+.|+|+.||||.+|+-+..++-.+
T Consensus        11 l~~~eva~~lgvsrstiy~~~~~g~f   36 (66)
T 1z4h_A           11 VDLKFIMADTGFGKTFIYDRIKSGDL   36 (66)
T ss_dssp             ECHHHHHHHHSSCHHHHHHHHHHHHC
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence            78999999999999999999876444

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=83.89  E-value=0.99  Score=30.52  Aligned_cols=24  Identities=0%  Similarity=0.044  Sum_probs=20.2

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      .++..|.|+.|||+.+++.+.-.+
T Consensus        31 ~~t~~eLA~~Lgvs~~tV~~~L~~   54 (77)
T 1qgp_A           31 ATTAHDLSGKLGTPKKEINRVLYS   54 (77)
T ss_dssp             CEEHHHHHHHHCCCHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHH
Confidence            589999999999999998877443

>2o38_A Hypothetical protein; alpha-beta, helix-turn-helix, structural genomics, PSI-2, PR structure initiative; 1.83A {Rhodopseudomonas palustris} SCOP: a.35.1.13

Probab=83.79  E-value=2  Score=31.01  Aligned_cols=34  Identities=21%  Similarity=0.204  Sum_probs=29.1

Q ss_pred             CHHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           72 TLRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        72 t~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      .+..++...++++.++|+.+||+.+++-++  +.|-
T Consensus        44 ~L~~~R~~~glTQ~eLA~~lGis~~~Is~i--E~G~   77 (120)
T 2o38_A           44 ALNAVIDRARLSQAAAAARLGINQPKVSAL--RNYK   77 (120)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHH--HTTC
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HcCC
Confidence            466777888999999999999999999999  4564

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=83.41  E-value=1.1  Score=33.12  Aligned_cols=33  Identities=21%  Similarity=0.147  Sum_probs=26.0

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      +..|+....+|..|.|+.||+|.+++.++.+++
T Consensus        16 l~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L   48 (162)
T 2p5v_A           16 LQVLQENGRLTNVELSERVALSPSPCLRRLKQL   48 (162)
T ss_dssp             HHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            344556667999999999999999988876643

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=83.24  E-value=1.3  Score=30.58  Aligned_cols=30  Identities=3%  Similarity=-0.047  Sum_probs=22.9

Q ss_pred             HHHHhhc---CCcHHHHHHHcCCChhHHHHHHH
Q 041600           74 RDLMIYF---HLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        74 ~~L~~yF---~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +.|...=   .++..+.|+.|||+.+++.+.-.
T Consensus        17 ~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~   49 (81)
T 1qbj_A           17 KFLEELGEGKATTAHDLSGKLGTPKKEINRVLY   49 (81)
T ss_dssp             HHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            3444444   58999999999999999887743

>3trb_A Virulence-associated protein I; mobIle and extrachromosomal element functions, DNA binding P; 2.00A {Coxiella burnetii}

Probab=83.20  E-value=3  Score=29.30  Aligned_cols=31  Identities=16%  Similarity=0.256  Sum_probs=25.7

Q ss_pred             HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +++.-.++++.+.|+.+|||.+++-++-  .|-
T Consensus        21 ~lr~~~gltq~eLA~~lGis~~~is~ie--~G~   51 (104)
T 3trb_A           21 ELGFLDKMSANQLAKHLAIPTNRVTAIL--NGA   51 (104)
T ss_dssp             HHHHTTSCCHHHHHHHHTSCHHHHHHHH--TTS
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHH--cCC
Confidence            3667778999999999999999999884  554

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus}

Probab=83.10  E-value=1.1  Score=31.73  Aligned_cols=33  Identities=18%  Similarity=0.176  Sum_probs=28.8

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +..++.--+|.+++.|+.+|||.+++.++  +.|-
T Consensus        41 ir~~R~~~glTQ~eLA~~~gvs~~~is~~--E~G~   73 (101)
T 4ghj_A           41 LKQARLNRDLTQSEVAEIAGIARKTVLNA--EKGK   73 (101)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSCHHHHHHH--HTTC
T ss_pred             HHHHHHHcCCCHHHHHHHcCCCHHHHHHH--HCCC
Confidence            55667778999999999999999999999  7784

>1d5y_A ROB transcription factor; protein-DNA complex, DNA, transcription/DNA complex; HET: DNA; 2.70A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 d.60.1.2

Probab=82.74  E-value=1.1  Score=35.37  Aligned_cols=51  Identities=8%  Similarity=0.075  Sum_probs=37.5

Q ss_pred             HHhhc--CCcHHHHHHHcCCChhHHHHHHHHc-CCCCChhHHHhhHHHHHHHHh
Q 041600           76 LMIYF--HLPIEEAARRMKLCPTVVKKICRRD-GLHRWPHRKIKSIQRRMSVAS  126 (160)
Q Consensus        76 L~~yF--~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~RWPyRkikSl~~~i~~L~  126 (160)
                      |..++  .+++.+.|+.+|+|+.+|.|++++. |++--=|.+...+++....|.
T Consensus        12 i~~~~~~~~~~~~la~~~~~s~~~l~r~f~~~~g~s~~~~~~~~Rl~~a~~~L~   65 (292)
T 1d5y_A           12 LEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSKSAVALR   65 (292)
T ss_dssp             HHTTSSSSCCCHHHHTTTSSCHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHhCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence            34444  4889999999999999999999987 886444555555555555554

>2wus_R RODZ, putative uncharacterized protein; structural protein, cell WALL morphogenesis, bacterial cytos bacterial actin; 2.90A {Thermotoga maritima}

Probab=82.48  E-value=1.3  Score=31.73  Aligned_cols=33  Identities=18%  Similarity=0.255  Sum_probs=28.6

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +..++.--++++.++|+.+||+.++|.++  +.|-
T Consensus        12 Lr~~R~~~glSq~eLA~~~gis~~~is~i--E~G~   44 (112)
T 2wus_R           12 FRKKREERRITLLDASLFTNINPSKLKRI--EEGD   44 (112)
T ss_dssp             HHHHHHTTTCCHHHHHHHSSCCHHHHHHH--HHTC
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHH--HCCC
Confidence            55677788999999999999999999999  5664

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=82.12  E-value=1.3  Score=33.66  Aligned_cols=33  Identities=21%  Similarity=0.148  Sum_probs=26.7

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      +..|+..-.+|..|.|+.||+|.+++.++.+++
T Consensus        23 L~~L~~~~~~s~~eLA~~lglS~~tv~~~l~~L   55 (171)
T 2ia0_A           23 LRLLKKDARLTISELSEQLKKPESTIHFRIKKL   55 (171)
T ss_dssp             HHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            445556667999999999999999998887654

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=81.89  E-value=1.4  Score=32.16  Aligned_cols=32  Identities=16%  Similarity=0.149  Sum_probs=25.3

Q ss_pred             HHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           74 RDLMIYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        74 ~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      ..|+..-.+|..+.|+.||+|.+++.++.+++
T Consensus        14 ~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L   45 (151)
T 2cyy_A           14 KILQNDGKAPLREISKITGLAESTIHERIRKL   45 (151)
T ss_dssp             HHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             HHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            34555557999999999999999988876644

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=81.79  E-value=1.3  Score=30.50  Aligned_cols=42  Identities=17%  Similarity=0.210  Sum_probs=26.8

Q ss_pred             hccCCCCHHHHH----hhcCCcHHHHHHHcCCChhHHHH----HHHHcCC
Q 041600           66 ERTGKLTLRDLM----IYFHLPIEEAARRMKLCPTVVKK----ICRRDGL  107 (160)
Q Consensus        66 ~r~~~lt~~~L~----~yF~lP~~eAA~~Lgv~~T~LKr----~CR~~GI  107 (160)
                      .....||-.+..    -+-+++.+|+|+.||||..|++.    +.+++|+
T Consensus        25 ~~~~~Lt~rE~~Vl~l~~~G~s~~eIA~~L~iS~~TV~~~~~~i~~Klgv   74 (90)
T 3ulq_B           25 KEQDVLTPRECLILQEVEKGFTNQEIADALHLSKRSIEYSLTSIFNKLNV   74 (90)
T ss_dssp             ----CCCHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             ccccCCCHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence            344556666554    22379999999999999877665    4445554

>2l8n_A Transcriptional repressor CYTR; bacterial gene repressor, helix turn helix binding domain, L family, transcription regulation, binding protein; NMR {Escherichia coli} PDB: 2lcv_A

Probab=81.69  E-value=3.1  Score=27.46  Aligned_cols=22  Identities=14%  Similarity=0.238  Sum_probs=19.6

Q ss_pred             CcHHHHHHHcCCChhHHHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +++.|+|+.+|||.+|+-++..
T Consensus        10 ~t~~diA~~aGVS~sTVSr~ln   31 (67)
T 2l8n_A           10 ATMKDVALKAKVSTATVSRALM   31 (67)
T ss_dssp             CCHHHHHHHTTCCHHHHHHTTT
T ss_pred             CCHHHHHHHHCCCHHHHHHHHc
Confidence            6899999999999999998864

>3uj3_X DNA-invertase; helix-turn-helix, site-specific recombinase, recombination; 3.51A {Enterobacteria phage MU} PDB: 3plo_X

Probab=81.53  E-value=0.29  Score=37.42  Aligned_cols=34  Identities=12%  Similarity=0.068  Sum_probs=0.0

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRK  114 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRk  114 (160)
                      +++..++|+.||||.+|+.|..+..+-.++|-++
T Consensus       158 G~s~~~Ia~~l~vs~~Tvyr~l~~~~~~~~~~~~  191 (193)
T 3uj3_X          158 GIPRKQVALIYDVALSTLYKKHPAKRAHIENDDR  191 (193)
T ss_dssp             ----------------------------------
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHhhhcCCCCCC
Confidence            5799999999999999999998887766666443

>4fe7_A Xylose operon regulatory protein; HTH_ARAC, helix-turn-helix, PBP, periplasmic binding protein binding transcription regulator, DNA xylose; HET: XYS; 2.90A {Escherichia coli} PDB: 4fe4_A

Probab=81.50  E-value=1.9  Score=35.80  Aligned_cols=46  Identities=7%  Similarity=0.153  Sum_probs=36.7

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc-CCCCChhHHHhhHHHHHHHHh
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD-GLHRWPHRKIKSIQRRMSVAS  126 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~-GI~RWPyRkikSl~~~i~~L~  126 (160)
                      .+++.+.|+.+|+|.++|.|++++. |++--=|.+...+++...-|.
T Consensus       321 ~~~~~~~a~~~~~s~~~l~r~f~~~~g~s~~~~~~~~r~~~a~~~L~  367 (412)
T 4fe7_A          321 GIKVDQVLDAVGISRSNLEKRFKEEVGETIHAMIHAEKLEKARSLLI  367 (412)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence            5899999999999999999999998 986544666666666555553

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=81.22  E-value=1.3  Score=32.07  Aligned_cols=32  Identities=13%  Similarity=0.178  Sum_probs=24.9

Q ss_pred             HHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           74 RDLMIYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        74 ~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      ..|+..-.+|..+.|+.||+|.+++.++-+++
T Consensus        10 ~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L   41 (150)
T 2pn6_A           10 KILQYNAKYSLDEIAREIRIPKATLSYRIKKL   41 (150)
T ss_dssp             HHHTTCTTSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            34445556999999999999999988776644

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=80.77  E-value=1.8  Score=31.39  Aligned_cols=31  Identities=13%  Similarity=0.049  Sum_probs=24.7

Q ss_pred             HHHHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 041600           74 RDLMIYFHLPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        74 ~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      ..|+..=.+|..|.|+.||+|.+++.++.++
T Consensus        16 ~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~   46 (151)
T 2dbb_A           16 KILSENSRLTYRELADILNTTRQRIARRIDK   46 (151)
T ss_dssp             HHHHHCTTCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3344444699999999999999998887765

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=80.05  E-value=1.8  Score=30.78  Aligned_cols=31  Identities=23%  Similarity=0.229  Sum_probs=24.0

Q ss_pred             HHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      .|+..=.+|..+.|+.||+|.+++.+..+++
T Consensus        12 ~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L   42 (141)
T 1i1g_A           12 ILEKDARTPFTEIAKKLGISETAVRKRVKAL   42 (141)
T ss_dssp             HHHHCTTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3443335899999999999999998877643

---

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	160
d1g2ha_	61	Transcriptional regulator TyrR, C-terminal domain	96.56
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	96.2
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	95.78
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	95.27
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	94.67
d1etxa_	89	FIS protein {Escherichia coli [TaxId: 562]}	94.57
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	94.47
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	94.42
d1ntca_	91	DNA-binding domain of NTRC {Salmonella typhimurium	94.36
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	93.65
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	92.55
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	92.4
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	92.4
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	92.35
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	91.34
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	90.57
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	90.24
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	90.18
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	90.17
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	89.66
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	89.53
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	88.71
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	88.13
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	88.12
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	88.0
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	87.95
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	87.88
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	87.45
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	87.13
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	86.97
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	86.96
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	86.95
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	86.85
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	86.68
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	86.57
d1y7ya1	69	Restriction-modification controller protein C.AhdI	85.74
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	84.54
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	83.75
d1hlva1	66	DNA-binding domain of centromere binding protein B	82.98
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	82.93
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	82.62
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	82.54
d1io1a_	395	Phase 1 flagellin {Salmonella typhimurium [TaxId:	82.13
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	81.97
d2g7sa1	74	Putative transcriptional regulator Atu0279 {Agroba	81.71
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	81.61
d1r8ea1	118	Transcription activator BmrR {Bacillus subtilis [T	81.31
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	81.15
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	80.93

>d1g2ha_ a.4.1.12 (A:) Transcriptional regulator TyrR, C-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Transcriptional regulator TyrR, C-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=96.56  E-value=0.0012  Score=42.34  Aligned_cols=33  Identities=15%  Similarity=0.251  Sum_probs=28.2

Q ss_pred             HHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600           75 DLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHR  109 (160)
Q Consensus        75 ~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R  109 (160)
                      -|..+ + -..+||+.|||+.++|-+..+++||.|
T Consensus        29 aL~~~-g-n~~~aA~~Lgisr~tL~rKlkk~gi~k   61 (61)
T d1g2ha_          29 FYAEY-P-STRKLAQRLGVSHTAIANKLKQYGIGK   61 (61)
T ss_dssp             HHHHS-C-SHHHHHHHTTSCTHHHHHHHHTTTCCC
T ss_pred             HHHHC-C-CHHHHHHHHCCCHHHHHHHHHHhCCCC
Confidence            34454 5 678999999999999999999999975

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=96.20  E-value=0.002  Score=43.47  Aligned_cols=39  Identities=13%  Similarity=0.218  Sum_probs=33.6

Q ss_pred             HHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChh
Q 041600           74 RDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPH  112 (160)
Q Consensus        74 ~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPy  112 (160)
                      +.....-.+++++.|+..|||++++=|.|+++|..-|+-
T Consensus        29 ~~~~~~~~~si~~lA~~~~vS~sTi~Rf~kklG~~gf~e   67 (83)
T d2o3fa1          29 AHPHKAIESTVNEISALANSSDAAVIRLCKSLGLKGFQD   67 (83)
T ss_dssp             HCHHHHHTCCHHHHHHHTTCCHHHHHHHHHHTTCSSHHH
T ss_pred             cCHHHHHHccHHHHHHHHCCCHHHHHHHHHHhCCCCHHH
Confidence            333455689999999999999999999999999988774

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=95.78  E-value=0.0035  Score=42.04  Aligned_cols=38  Identities=11%  Similarity=0.183  Sum_probs=30.4

Q ss_pred             CCHHHHHhhc---CCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           71 LTLRDLMIYF---HLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        71 lt~~~L~~yF---~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      |-.+-+..|.   ++++.++|+.|||+.++|.+-.++++..
T Consensus        10 fK~~aV~l~~~~~g~s~~~vA~~lGIs~~tl~~W~k~~~~~   50 (89)
T d2jn6a1          10 FKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKYGSN   50 (89)
T ss_dssp             HHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHHCCC
T ss_pred             HHHHHHHHHHHcCCCcHHHHHHHHCCCHHHHHHHHHHHhhc
Confidence            3344455564   4899999999999999999999988764

>d1umqa_ a.4.1.12 (A:) Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain {Rhodobacter sphaeroides [TaxId: 1063]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=95.27  E-value=0.011  Score=37.46  Aligned_cols=30  Identities=17%  Similarity=0.283  Sum_probs=27.0

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      ...+--+.+||+.||||.+||.+.-++++|
T Consensus        30 ~~~~gn~~~aA~~LGIsR~TL~rkmkky~~   59 (60)
T d1umqa_          30 EMCDRNVSETARRLNMHRRTLQRILAKRSP   59 (60)
T ss_dssp             HHTTSCHHHHHHHHTSCHHHHHHHHHTSSC
T ss_pred             HHhcCcHHHHHHHHCCCHHHHHHHHHHcCC
Confidence            455778999999999999999999999987

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=94.67  E-value=0.027  Score=35.23  Aligned_cols=37  Identities=16%  Similarity=0.387  Sum_probs=28.6

Q ss_pred             HhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHH
Q 041600           77 MIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRM  122 (160)
Q Consensus        77 ~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i  122 (160)
                      .-+.+++..|+|..||+|..+++.+-         +|=++.|++.+
T Consensus        33 ~~~~~~s~~eIA~~lgis~~tv~~~~---------~ra~~~Lr~~L   69 (71)
T d1rp3a2          33 IFYEELPAKEVAKILETSVSRVSQLK---------AKALERLREML   69 (71)
T ss_dssp             HHTSCCCHHHHHHHTTSCHHHHHHHH---------HHHHHHHHHHH
T ss_pred             HHhHhCCHHHHHHHHCCCHHHHHHHH---------HHHHHHHHHHc
Confidence            34457999999999999999999885         55555555544

>d1etxa_ a.4.1.12 (A:) FIS protein {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: FIS protein
species: Escherichia coli [TaxId: 562]

Probab=94.57  E-value=0.02  Score=38.85  Aligned_cols=31  Identities=19%  Similarity=0.205  Sum_probs=27.9

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      ...+--+.+||+.|||+.+||.+.-+++||.
T Consensus        59 ~~~~gn~~~aA~~LGisR~tL~~klk~~gi~   89 (89)
T d1etxa_          59 QYTRGNATRAALMMGINRGTLRKKLKKYGMN   89 (89)
T ss_dssp             HHTTTCHHHHHHHHTSCHHHHHHHHHHTTCC
T ss_pred             HHcCCcHHHHHHHHCCCHHHHHHHHHHhCcC
Confidence            5557789999999999999999999999983

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=94.47  E-value=0.038  Score=34.67  Aligned_cols=26  Identities=23%  Similarity=-0.008  Sum_probs=22.9

Q ss_pred             HhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           77 MIYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        77 ~~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      .-+.+++.+|+|+.||||..++|...
T Consensus        30 ~~~~~~s~~eIA~~lgis~~tv~~~l   55 (68)
T d1or7a1          30 RELDGLSYEEIAAIMDCPVGTVRSRI   55 (68)
T ss_dssp             HHTTCCCHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHCcCHHHHHHHH
Confidence            34557999999999999999999886

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=94.42  E-value=0.052  Score=33.92  Aligned_cols=38  Identities=16%  Similarity=0.210  Sum_probs=32.6

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHR  113 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyR  113 (160)
                      +..++.-.+|++++.|+.|||+.+++.+.  +.|- +.|-.
T Consensus         4 ik~~R~~~gltQ~elA~~lGvs~~tvs~~--E~G~-~~P~~   41 (62)
T d2ppxa1           4 IKIIRRALKLTQEEFSARYHIPLGTLRDW--EQGR-SEPDQ   41 (62)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHH--HTTS-SCCCH
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHH--HCCC-CCCCH
Confidence            56788889999999999999999999999  7883 56654

>d1ntca_ a.4.1.12 (A:) DNA-binding domain of NTRC {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: DNA-binding domain of NTRC
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.36  E-value=0.0084  Score=40.23  Aligned_cols=30  Identities=17%  Similarity=0.066  Sum_probs=27.2

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      ...+--+.+||+.|||+.+||.+.-+++||
T Consensus        61 ~~~~Gn~~~AA~~LGI~R~TL~~Klk~~gi   90 (91)
T d1ntca_          61 RHTQGHKQEAARLLGWGAATLTAKLKELGM   90 (91)
T ss_dssp             HHTTTCTTHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHhCCcHHHHHHHHCCCHHHHHHHHHHHCc
Confidence            566788899999999999999999999987

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=93.65  E-value=0.18  Score=35.11  Aligned_cols=27  Identities=15%  Similarity=0.137  Sum_probs=22.8

Q ss_pred             HHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           76 LMIYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        76 L~~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      |.-+.+++..|+|..||||.++++...
T Consensus        29 L~~~e~ls~~EIA~~lgiS~~aV~~~l   55 (106)
T d1xsva_          29 LFYLEDYSLSEIADTFNVSRQAVYDNI   55 (106)
T ss_dssp             HHHTSCCCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHhCCcHHHHHHHHCcCHHHHHHHH
Confidence            445558999999999999999988775

>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: SinR repressor, DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=92.55  E-value=0.17  Score=31.35  Aligned_cols=37  Identities=14%  Similarity=0.203  Sum_probs=31.1

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCh
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWP  111 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWP  111 (160)
                      +..++.-.++.+.+.|+.+||+.+++-++  +.|....|
T Consensus         6 ik~~R~~~gltq~~la~~~gis~~~i~~~--E~g~~~~p   42 (68)
T d1b0na2           6 IKQYRKEKGYSLSELAEKAGVAKSYLSSI--ERNLQTNP   42 (68)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHH--HTTCCSCC
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHH--HcCCCCCC
Confidence            56778888999999999999999999999  45655556

>d1y9qa1 a.35.1.8 (A:4-82) Probable transcriptional regulator VC1968, N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Probable transcriptional regulator VC1968, N-terminal domain
domain: Probable transcriptional regulator VC1968, N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=92.40  E-value=0.081  Score=33.75  Aligned_cols=36  Identities=19%  Similarity=0.287  Sum_probs=29.9

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCh
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWP  111 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWP  111 (160)
                      +..++...++++.+.|+.+||+.+++.++  +.|- +.|
T Consensus        13 lr~~R~~~g~sq~~lA~~~gis~~~i~~~--E~g~-~~p   48 (79)
T d1y9qa1          13 LKNLRKSRGLSLDATAQLTGVSKAMLGQI--ERGE-SSP   48 (79)
T ss_dssp             HHHHHHHTTCCHHHHHHHHSSCHHHHHHH--HTTC-SCC
T ss_pred             HHHHHHHcCCCHHHHHHHHCcchhHHHHH--HcCC-CCC
Confidence            56778888999999999999999999998  5664 345

>d2hsga1 a.35.1.5 (A:2-58) Glucose-resistance amylase regulator CcpA, N-terminal domain {Bacillus megaterium [TaxId: 1404]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Glucose-resistance amylase regulator CcpA, N-terminal domain
species: Bacillus megaterium [TaxId: 1404]

Probab=92.40  E-value=0.17  Score=31.82  Aligned_cols=24  Identities=17%  Similarity=0.318  Sum_probs=21.1

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      ++.++|+|+..|||.+|+-|..+.
T Consensus         1 NvTi~dvA~~agvS~~TVSr~Ln~   24 (57)
T d2hsga1           1 NVTIYDVAREASVSMATVSRVVNG   24 (57)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             CcCHHHHHHHHCcCHHHHHHHhCC
Confidence            468999999999999999999754

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=92.35  E-value=0.063  Score=32.75  Aligned_cols=35  Identities=6%  Similarity=-0.021  Sum_probs=25.5

Q ss_pred             cCCCCHHHHH---hh--cCCcHHHHHHHcCCChhHHHHHH
Q 041600           68 TGKLTLRDLM---IY--FHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        68 ~~~lt~~~L~---~y--F~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      ...+|-+++.   ..  -+.|..++|+.||||.+||-|..
T Consensus         3 ~~~lt~~q~~~a~~l~~~G~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           3 PRAINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             CCSSCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             CCcCCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHhhC
Confidence            3445555544   22  27899999999999999998764

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=91.34  E-value=0.1  Score=32.76  Aligned_cols=32  Identities=28%  Similarity=0.459  Sum_probs=26.4

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      +..|+.-..+|..+.|+.||+|++++.++-++
T Consensus        11 L~~L~~n~r~s~~~iA~~lgis~~tv~~Ri~~   42 (63)
T d2cfxa1          11 IEELKKDSRLSMRELGRKIKLSPPSVTERVRQ   42 (63)
T ss_dssp             HHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45567777899999999999999999877543

>d1x57a1 a.35.1.12 (A:8-85) Endothelial differentiation-related factor 1, EDF1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: EDF1-like
domain: Endothelial differentiation-related factor 1, EDF1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.57  E-value=0.15  Score=32.99  Aligned_cols=33  Identities=15%  Similarity=0.173  Sum_probs=26.1

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +..++.-.++++.+.|+.+|||.+++-++  +.|.
T Consensus        11 I~~~R~~~gltq~~lA~~~gis~~~is~~--E~G~   43 (78)
T d1x57a1          11 IQQGRQSKGLTQKDLATKINEKPQVIADY--ESGR   43 (78)
T ss_dssp             HHHHHHTTTCCHHHHHHHHTSCHHHHHHH--HHTC
T ss_pred             HHHHHHHcCCChhHHHHcCCCCHHHHHHH--HccC
Confidence            45667778899999999999998888777  5554

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=90.24  E-value=0.15  Score=31.80  Aligned_cols=32  Identities=19%  Similarity=0.259  Sum_probs=25.7

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      +..|+.---+|..+.|+.+|+|.+++.++-++
T Consensus        11 L~~L~~~~r~s~~eiA~~l~ls~~~v~~Ri~r   42 (63)
T d2cg4a1          11 LEALMGNARTAYAELAKQFGVSPETIHVRVEK   42 (63)
T ss_dssp             HHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            34566666799999999999999999887443

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=90.18  E-value=0.16  Score=31.36  Aligned_cols=32  Identities=16%  Similarity=0.219  Sum_probs=26.1

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      +..|+.-.-+|..+.|+.||+|.+++.++-++
T Consensus         9 l~~L~~n~r~s~~eiA~~l~ls~~~v~~Ri~~   40 (60)
T d2cyya1           9 IKILQNDGKAPLREISKITGLAESTIHERIRK   40 (60)
T ss_dssp             HHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45667777899999999999999998877443

>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]}

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

Probab=90.17  E-value=0.1  Score=31.32  Aligned_cols=30  Identities=10%  Similarity=0.141  Sum_probs=24.2

Q ss_pred             HHhhcC--CcHHHHHHHcCCChhHHHHHHHHc
Q 041600           76 LMIYFH--LPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        76 L~~yF~--lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      |.++++  +++.+.|+.+|+|++.|.|+.++.
T Consensus        12 i~~~~~~~itl~~lA~~~~~S~~~l~r~Fk~~   43 (54)
T d1d5ya1          12 LEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDV   43 (54)
T ss_dssp             HHTTSSSSCCCHHHHTTTSSCHHHHHHHHHHH
T ss_pred             HHHccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            344443  788999999999999999998764

>d2icta1 a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Antitoxin HigA
species: Escherichia coli [TaxId: 562]

Probab=89.66  E-value=0.14  Score=33.85  Aligned_cols=30  Identities=17%  Similarity=0.442  Sum_probs=26.5

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +.+++...++++.+.|+.+||+.++|-++-
T Consensus         6 lke~r~~~glsq~~LA~~lGvs~~~is~ie   35 (87)
T d2icta1           6 IQESLDELNVSLREFARAMEIAPSTASRLL   35 (87)
T ss_dssp             HHHHHHHHTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHhhcHHHHHHHH
Confidence            567888889999999999999999988884

>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=89.53  E-value=0.15  Score=30.36  Aligned_cols=25  Identities=12%  Similarity=0.328  Sum_probs=22.3

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      .+++.+.|+.+|+|++.|.|..++.
T Consensus        19 ~~tl~~lA~~~~~s~~~l~r~Fk~~   43 (54)
T d1bl0a1          19 PLSLEKVSERSGYSKWHLQRMFKKE   43 (54)
T ss_dssp             CCCCHHHHHHSSSCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3788999999999999999998865

>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Regulatory protein C.BclI
species: Bacillus caldolyticus [TaxId: 1394]

Probab=88.71  E-value=0.2  Score=31.61  Aligned_cols=31  Identities=23%  Similarity=0.196  Sum_probs=26.9

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +..++..-++++.++|+.+|||.+++.++.+
T Consensus        15 ik~~R~~~gltq~~lA~~~gis~~~i~~~e~   45 (77)
T d2b5aa1          15 LKKIRTQKGVSQEELADLAGLHRTYISEVER   45 (77)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            5667777899999999999999999999843

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=88.13  E-value=0.32  Score=31.38  Aligned_cols=37  Identities=22%  Similarity=0.255  Sum_probs=31.2

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCCh
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWP  111 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWP  111 (160)
                      +.+++.-.+++++++|+.||||..++.+.  +.|-..=|
T Consensus         6 ~k~~R~~~gltQ~elA~~LGvs~~ti~~y--E~G~r~iP   42 (67)
T d2auwa1           6 FGDWMHRNNLSLTTAAEALGISRRMVSYY--RTAHKIIP   42 (67)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSCHHHHHHH--HTTSSCCC
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHH--HcCCCCCC
Confidence            56778889999999999999999999987  77764445

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

Probab=88.12  E-value=0.25  Score=30.06  Aligned_cols=33  Identities=15%  Similarity=0.226  Sum_probs=28.7

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +..++.--++++.|.|+.+||+.+++-++.+  |-
T Consensus         6 ik~~R~~~g~sq~elA~~~gvs~~~is~~E~--g~   38 (63)
T d1r69a_           6 VKSKRIQLGLNQAELAQKVGTTQQSIEQLEN--GK   38 (63)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSCHHHHHHHHT--TS
T ss_pred             HHHHHHHcCCcHHHHHHHhCcCHHHHHHHHC--CC
Confidence            5667788899999999999999999999964  64

>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Purine repressor (PurR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=88.00  E-value=0.63  Score=29.01  Aligned_cols=22  Identities=23%  Similarity=0.480  Sum_probs=19.6

Q ss_pred             cHHHHHHHcCCChhHHHHHHHH
Q 041600           83 PIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        83 P~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      +++|+|+..|||++|+-|....
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~   23 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINK   23 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHT
T ss_pred             CHHHHHHHHCcCHHHHHHHHCC
Confidence            5789999999999999999764

>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: HTH-motif protein NE1354
species: Nitrosomonas europaea [TaxId: 915]

Probab=87.95  E-value=0.25  Score=30.96  Aligned_cols=31  Identities=19%  Similarity=0.164  Sum_probs=26.7

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +.+++.--++.++++|+.+||+++++-++.+
T Consensus        11 i~~~r~~~gltq~elA~~~gv~~~~is~ie~   41 (69)
T d2a6ca1          11 LQEHLRNSGLTQFKAAELLGVTQPRVSDLMR   41 (69)
T ss_dssp             HHHHHHTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHcCCCHHHHHHHHHcCHhHHHHHHc
Confidence            5567777899999999999999999999864

>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro 434
species: Bacteriophage 434 [TaxId: 10712]

Probab=87.88  E-value=0.4  Score=29.37  Aligned_cols=34  Identities=18%  Similarity=0.229  Sum_probs=28.7

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLH  108 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~  108 (160)
                      +..++.--++.+.+.|+.+||+.+++-++.  .|-.
T Consensus         8 lr~~R~~~gltq~~lA~~~gvs~~ti~~~E--~g~~   41 (65)
T d2croa_           8 LKKRRIALKMTQTELATKAGVKQQSIQLIE--AGVT   41 (65)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSCHHHHHHHH--TTCC
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHhHHHHHH--CCCC
Confidence            556778889999999999999999999984  5643

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=87.45  E-value=0.26  Score=30.77  Aligned_cols=27  Identities=15%  Similarity=0.251  Sum_probs=21.5

Q ss_pred             CCcHHHHHHHcCCChhHHHH----HHHHcCC
Q 041600           81 HLPIEEAARRMKLCPTVVKK----ICRRDGL  107 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr----~CR~~GI  107 (160)
                      +++.+|+|..||+|..|++.    +.+++|+
T Consensus        19 G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v   49 (67)
T d1fsea_          19 DKTTKEIASELFISEKTVRNHISNAMQKLGV   49 (67)
T ss_dssp             TCCHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            68999999999999877665    4555555

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=87.13  E-value=0.42  Score=28.80  Aligned_cols=35  Identities=14%  Similarity=0.255  Sum_probs=27.4

Q ss_pred             cCCCCHHHHHhhc--CCcHHHHHHHcCCChhHHHHHH
Q 041600           68 TGKLTLRDLMIYF--HLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        68 ~~~lt~~~L~~yF--~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      ...|..+.+...+  ++...++|++|||+.+++-|+-
T Consensus         3 k~~Id~~~V~~L~~~G~gat~IAk~lgI~R~SVYR~L   39 (43)
T d1gdta1           3 KRKIDRDAVLNMWQQGLGASHISKTMNIARSTVYKVI   39 (43)
T ss_dssp             CCCSCHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCccCHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            3456667776555  6899999999999999988764

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=86.97  E-value=0.35  Score=29.83  Aligned_cols=33  Identities=12%  Similarity=0.111  Sum_probs=28.5

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +..++.--++++.+.|+.+||+.+++-++  +.|.
T Consensus         6 i~~lR~~~g~tq~elA~~~gis~~~is~~--e~g~   38 (66)
T d1utxa_           6 LKLIREKKKISQSELAALLEVSRQTINGI--EKNK   38 (66)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSCHHHHHHH--HTTS
T ss_pred             HHHHHHHcCCCHHHHHHhcccCHHHHHHH--HcCC
Confidence            56778888999999999999999999988  5665

>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: P22 C2 repressor, DNA-binding domain
species: Salmonella bacteriophage P22 [TaxId: 10754]

Probab=86.96  E-value=0.29  Score=30.01  Aligned_cols=35  Identities=3%  Similarity=0.043  Sum_probs=29.4

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHR  109 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~R  109 (160)
                      +..++.--++++.+.|+.+||+.+++.++  +.|...
T Consensus         8 ik~~R~~~g~tq~~lA~~~gvs~~~i~~~--e~g~~~   42 (66)
T d2r1jl1           8 IRARRKKLKIRQAALGKMVGVSNVAISQW--ERSETE   42 (66)
T ss_dssp             HHHHHHHHTCCHHHHHHHHTSCHHHHHHH--HTTSSC
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHH--HcCCCC
Confidence            55677778999999999999999999998  667643

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=86.95  E-value=0.28  Score=30.71  Aligned_cols=27  Identities=30%  Similarity=0.438  Sum_probs=22.0

Q ss_pred             CCcHHHHHHHcCCChhHHHH----HHHHcCC
Q 041600           81 HLPIEEAARRMKLCPTVVKK----ICRRDGL  107 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr----~CR~~GI  107 (160)
                      +++.+++|+.||||+.|+|.    +++++|+
T Consensus        21 G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   51 (67)
T d1a04a1          21 GLPNKMIARRLDITESTVKVHVKHMLKKMKL   51 (67)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            79999999999999887764    5556665

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=86.85  E-value=0.35  Score=29.84  Aligned_cols=30  Identities=23%  Similarity=0.292  Sum_probs=24.3

Q ss_pred             HHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600           74 RDLMIYFHLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        74 ~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      ..|+.--.+|..+.|+.+|+|.+++.++-+
T Consensus        10 ~~L~~n~r~s~~~lA~~~gls~~~v~~Ri~   39 (60)
T d1i1ga1          10 EILEKDARTPFTEIAKKLGISETAVRKRVK   39 (60)
T ss_dssp             HHHHHCTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            345566679999999999999999987743

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=86.68  E-value=0.62  Score=32.20  Aligned_cols=25  Identities=12%  Similarity=0.016  Sum_probs=22.1

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHH
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      -+-+++..|+|..||||.++++...
T Consensus        29 y~~~ls~~EIA~~lgiS~~aV~~~l   53 (106)
T d1s7oa_          29 YADDYSLAEIADEFGVSRQAVYDNI   53 (106)
T ss_dssp             HHTCCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            3447999999999999999999886

>d1lmb3_ a.35.1.2 (3:) lambda C1 repressor, DNA-binding domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: lambda C1 repressor, DNA-binding domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=86.57  E-value=0.58  Score=30.54  Aligned_cols=43  Identities=14%  Similarity=0.122  Sum_probs=33.0

Q ss_pred             HHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhH
Q 041600           74 RDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSI  118 (160)
Q Consensus        74 ~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl  118 (160)
                      ..++.-.++.+.+.|+.|||+.+++-++  +.|......-.+..+
T Consensus        18 ~~~R~~~gltq~~lA~~lgis~~~is~~--E~g~~~~s~~~l~~i   60 (87)
T d1lmb3_          18 EKKKNELGLSQESVADKMGMGQSGVGAL--FNGINALNAYNAALL   60 (87)
T ss_dssp             HHHHHHHTCCHHHHHHHHTSCHHHHHHH--HTTSSCCCHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHhCccHHHHHHH--HhccCCCcHHHHHHH
Confidence            3446777999999999999999999999  677766655544443

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

Probab=85.74  E-value=0.84  Score=28.10  Aligned_cols=33  Identities=27%  Similarity=0.156  Sum_probs=28.1

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      +..++.--++.+.+.|+.+||+.+++-++  +.|-
T Consensus        14 ik~~R~~~gltq~~lA~~~gis~~~i~~~--E~g~   46 (69)
T d1y7ya1          14 LRELRTAKGLSQETLAFLSGLDRSYVGGV--ERGQ   46 (69)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHH--HTTC
T ss_pred             HHHHHHHcCCCHHHHHhHhCCCHHHHHHH--HCCC
Confidence            55677788999999999999999999999  4554

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=84.54  E-value=0.47  Score=29.98  Aligned_cols=27  Identities=19%  Similarity=0.233  Sum_probs=22.4

Q ss_pred             CCcHHHHHHHcCCChhHHH----HHHHHcCC
Q 041600           81 HLPIEEAARRMKLCPTVVK----KICRRDGL  107 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LK----r~CR~~GI  107 (160)
                      +++.+++|..||||+.|++    ++.+++|+
T Consensus        27 G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv   57 (70)
T d1yioa1          27 GLMNKQIAGELGIAEVTVKVHRHNIMQKLNV   57 (70)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHHHHHHHTTC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence            7999999999999987765    56667776

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=83.75  E-value=0.6  Score=29.13  Aligned_cols=33  Identities=15%  Similarity=0.148  Sum_probs=26.4

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      +.-|..+=.++..|.|+.+|+|.+++.++.++|
T Consensus        12 l~~l~~~g~~sr~eLa~~~glS~~Tv~~~l~~L   44 (71)
T d1z05a1          12 YKLIDQKGPISRIDLSKESELAPASITKITREL   44 (71)
T ss_dssp             HHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            344556557899999999999999999986654

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=82.98  E-value=0.4  Score=31.02  Aligned_cols=35  Identities=29%  Similarity=0.497  Sum_probs=26.4

Q ss_pred             CCCHHH---HHhhcC----CcHHHHHHHcCCChhHHHHHHHH
Q 041600           70 KLTLRD---LMIYFH----LPIEEAARRMKLCPTVVKKICRR  104 (160)
Q Consensus        70 ~lt~~~---L~~yF~----lP~~eAA~~Lgv~~T~LKr~CR~  104 (160)
                      .||+++   +.++++    +.+.|+|+.+||+.+||-++++.
T Consensus         7 ~LT~~eK~~ii~~~e~g~k~sq~eIA~~fGv~~STvs~IlKn   48 (66)
T d1hlva1           7 QLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKN   48 (66)
T ss_dssp             CCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHT
T ss_pred             cCCHHHHHHHHHHHHcCCcchHHHHHHHhCCChhHHHHHHHH
Confidence            467664   334443    46899999999999999999753

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=82.93  E-value=1.1  Score=29.14  Aligned_cols=51  Identities=14%  Similarity=0.146  Sum_probs=33.1

Q ss_pred             CCCCCCCCCchhhhhccCCCCHHHH---HhhcC-------Cc----HHHHHHHcCCChhHHHHHH
Q 041600           52 DDYSQPPMTNSVQRERTGKLTLRDL---MIYFH-------LP----IEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        52 d~~~~ps~s~s~~r~r~~~lt~~~L---~~yF~-------lP----~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +....|+.+....|+.--.+|-+.+   ..||.       .|    +.+.|++||++..++|--.
T Consensus         5 ~s~~~~~~~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWF   69 (80)
T d1wh7a_           5 SSGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWM   69 (80)
T ss_dssp             CCCCCCCCCCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHH
T ss_pred             CCCCCCCCCccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeec
Confidence            3444555555544444455665555   45564       45    8889999999999998654

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=82.62  E-value=0.58  Score=30.64  Aligned_cols=31  Identities=19%  Similarity=0.188  Sum_probs=26.8

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHH
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +..++.--++.+.++|+.+||+.+++.++.+
T Consensus        16 i~~~r~~~gltq~~lA~~~gis~~~is~ie~   46 (89)
T d2o38a1          16 LNAVIDRARLSQAAAAARLGINQPKVSALRN   46 (89)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHcCCCHHHHHHHHHhhHhHHHHHHc
Confidence            5566677799999999999999999999954

>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Fructose repressor (FruR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=82.54  E-value=0.35  Score=30.32  Aligned_cols=22  Identities=18%  Similarity=0.267  Sum_probs=19.0

Q ss_pred             CcHHHHHHHcCCChhHHHHHHH
Q 041600           82 LPIEEAARRMKLCPTVVKKICR  103 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR  103 (160)
                      +.++|+|+.+|||.+|+-+.-.
T Consensus         1 vTl~diA~~agvS~sTVSrvLn   22 (59)
T d1uxda_           1 MKLDEIARLAGVSRTTASYVIN   22 (59)
T ss_dssp             CCHHHHHHHHTSCTTHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHc
Confidence            4689999999999999998853

>d1io1a_ e.32.1.1 (A:) Phase 1 flagellin {Salmonella typhimurium [TaxId: 90371]}

class: Multi-domain proteins (alpha and beta)
fold: Phase 1 flagellin
superfamily: Phase 1 flagellin
family: Phase 1 flagellin
domain: Phase 1 flagellin
species: Salmonella typhimurium [TaxId: 90371]

Probab=82.13  E-value=1.3  Score=32.75  Aligned_cols=24  Identities=21%  Similarity=0.253  Sum_probs=22.3

Q ss_pred             CcHHHHHHHHHHHHHHHHHHHHHh
Q 041600          132 NDAEERANAQIEIQRLQEEMAAAC  155 (160)
Q Consensus       132 ~~~eerar~~~eIerL~~Em~~~c  155 (160)
                      .++.+|+.++.||+.|.+||..+.
T Consensus        48 ~~~~dr~ai~~E~~~l~~ei~~ia   71 (395)
T d1io1a_          48 NSQSDLDSIQAEITQRLNEIDRVS   71 (395)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHH
Confidence            589999999999999999999886

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=81.97  E-value=0.78  Score=28.81  Aligned_cols=33  Identities=18%  Similarity=0.157  Sum_probs=27.2

Q ss_pred             HHHHHhhcCCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           73 LRDLMIYFHLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        73 ~~~L~~yF~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      +..|..+=.++-.|.|+.+|+|.+++.+++.++
T Consensus        11 l~~i~~~g~~sr~eLa~~~gLS~~Tvs~iv~~L   43 (70)
T d1z6ra1          11 YRLIDQLGPVSRIDLSRLAQLAPASITKIVHEM   43 (70)
T ss_dssp             HHHHHSSCSCCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            345566667899999999999999999997654

>d2g7sa1 a.4.1.9 (A:3-76) Putative transcriptional regulator Atu0279 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator Atu0279
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=81.71  E-value=0.98  Score=28.02  Aligned_cols=37  Identities=8%  Similarity=0.099  Sum_probs=24.4

Q ss_pred             hhcCCcHHHHHHHcCCChhHHHHHHHHcCCCCChhHHHhhHHHHHHHHhh
Q 041600           78 IYFHLPIEEAARRMKLCPTVVKKICRRDGLHRWPHRKIKSIQRRMSVASG  127 (160)
Q Consensus        78 ~yF~lP~~eAA~~Lgv~~T~LKr~CR~~GI~RWPyRkikSl~~~i~~L~~  127 (160)
                      .|-.+.+.++|++.||+.+++             |+-+.+.+.++..+-.
T Consensus        21 G~~~~s~~~Ia~~agvs~~~i-------------Y~~F~sK~~L~~~~~~   57 (74)
T d2g7sa1          21 GYNSFSYADISQVVGIRNASI-------------HHHFPSKSDLVCKLVS   57 (74)
T ss_dssp             CGGGCCHHHHHHHHCCCHHHH-------------HHHCSSHHHHHHHHHH
T ss_pred             CccccCHHHHHHHHCcCcchH-------------HHHCcCHHHHHHHHHH
Confidence            344567777777777776665             6667777777766543

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=81.61  E-value=0.67  Score=28.66  Aligned_cols=22  Identities=18%  Similarity=-0.017  Sum_probs=18.7

Q ss_pred             CCcHHHHHHHcCCChhHHHHHH
Q 041600           81 HLPIEEAARRMKLCPTVVKKIC  102 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~C  102 (160)
                      +++.+|+|+.||+|..|+|..-
T Consensus        19 G~s~~eIA~~l~iS~~TV~~~~   40 (65)
T d1l3la1          19 GKTMEEIADVEGVKYNSVRVKL   40 (65)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHH
T ss_pred             cCCHHHHHHHHCCCHHHHHHHH
Confidence            7999999999999988776543

>d1r8ea1 a.6.1.3 (A:3-120) Transcription activator BmrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Transcription activator BmrR
species: Bacillus subtilis [TaxId: 1423]

Probab=81.31  E-value=2.1  Score=28.62  Aligned_cols=25  Identities=12%  Similarity=0.135  Sum_probs=21.6

Q ss_pred             CcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           82 LPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        82 lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      ++|.|+|+.+|||+.||+-.- +.|+
T Consensus         4 ytI~evA~~~gvs~~tlR~Ye-~~GL   28 (118)
T d1r8ea1           4 YSIGEVSKLANVSIKALRYYD-KIDL   28 (118)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHH-HTTS
T ss_pred             ccHHHHHHHHCcCHHHHHHHH-HcCC
Confidence            579999999999999998877 4674

>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Putative transcriptional regulator RHA1 ro03477
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=81.15  E-value=0.44  Score=29.95  Aligned_cols=25  Identities=8%  Similarity=0.117  Sum_probs=21.5

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHc
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRD  105 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~  105 (160)
                      -+|..+.|+.+|||.+++.+..++|
T Consensus        25 ~l~~~~La~~~~vSr~tvr~Al~~L   49 (69)
T d2hs5a1          25 RLSEPDICAALDVSRNTVREAFQIL   49 (69)
T ss_dssp             EECHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3799999999999999999886654

>d1r8da_ a.6.1.3 (A:) Multidrug transporter activator MtaN {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Multidrug transporter activator MtaN
species: Bacillus subtilis [TaxId: 1423]

Probab=80.93  E-value=2.7  Score=27.75  Aligned_cols=26  Identities=8%  Similarity=0.050  Sum_probs=21.4

Q ss_pred             CCcHHHHHHHcCCChhHHHHHHHHcCC
Q 041600           81 HLPIEEAARRMKLCPTVVKKICRRDGL  107 (160)
Q Consensus        81 ~lP~~eAA~~Lgv~~T~LKr~CR~~GI  107 (160)
                      .++|.|+|+.+|||+.+|+-.-+. |+
T Consensus         2 ~ytI~e~A~~~gvs~~tlR~Ye~~-GL   27 (109)
T d1r8da_           2 KYQVKQVAEISGVSIRTLHHYDNI-EL   27 (109)
T ss_dssp             CBCHHHHHHHHSCCHHHHHHHHHT-TS
T ss_pred             cccHHHHHHHHCcCHHHHHHHHHc-CC
Confidence            368999999999999999977644 53