Citrus Sinensis ID: 046847

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------
Protein Sequence
MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNGVLELQHILLKSPKPMPEYCTD
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHccccHHHHHHHcccccHHHHHHHHHHHHHHHHccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHcccccccccEcHHHHHHHHHHHHHHHHHcHHHHHHcccccHHHHHHHHHHHHHHHHcHHHccccccccccccc
Coil and Loop (DISEMBL)
MDRKTFGLLFELLcsderlktdsvvFVDEQVCMFLHALAHHvknqtinnrfkhsgeTISRFNSILNGVLELQHILlkspkpmpeyctd
Flexible Loop (DISEMBL)
MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNGVLELQHillkspkpmpeyctd
Low Complexity Region (SEG)
MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNGVLELQHILLKSPKPMPEYCTD
Disordered region (IsUnstruct)
****TFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNGVLELQHILL************
Disordered Region (DISOPRED)
*DRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNGVLELQHILLK***********
Disordered Region (DISEMBL)
MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNGVLELQHILLKSPK********
Disordered Region (DISPRO)
*DRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNGVLELQHILLKSPK********
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNGVLELQHILLKSPKPMPEYCTD
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

No hits with e-value below 0.001 by BLAST

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	88
147841225	185	hypothetical protein VITISV_032219 [Viti	1.0	0.475	0.528	2e-16
147779878	579	hypothetical protein VITISV_027369 [Viti	1.0	0.151	0.528	3e-16
413941984	288	hypothetical protein ZEAMMB73_204913 [Ze	1.0	0.305	0.516	3e-14
307135889	623	retrotransposon protein [Cucumis melo su	1.0	0.141	0.483	8e-14
413950101	445	hypothetical protein ZEAMMB73_878123 [Ze	1.0	0.197	0.505	1e-13
147769233	568	hypothetical protein VITISV_010914 [Viti	1.0	0.154	0.505	4e-13
38346719	535	OSJNBa0086O06.17 [Oryza sativa Japonica	1.0	0.164	0.449	3e-12
222629452	504	hypothetical protein OsJ_15967 [Oryza sa	1.0	0.174	0.449	3e-12
125570642	598	hypothetical protein OsJ_02038 [Oryza sa	1.0	0.147	0.449	4e-12
307136287	657	retrotransposon protein [Cucumis melo su	0.795	0.106	0.535	6e-12

>gi|147841225|emb|CAN62415.1| hypothetical protein VITISV_032219 [Vitis vinifera]

 Score = 89.7 bits (221), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 47/89 (52%), Positives = 60/89 (67%), Gaps = 1/89 (1%)

Query: 1  MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60
          MDR TF +L  +L +  +LK    V V+E V +FLH LAHHVKN+ I  RF  SGETISR
Sbjct: 6  MDRHTFTMLCSMLRTIGKLKDSKYVDVEEMVALFLHILAHHVKNRVIKFRFLRSGETISR 65

Query: 61 -FNSILNGVLELQHILLKSPKPMPEYCTD 88
           FN++LN V+ LQ +LLK P+P+ E   D
Sbjct: 66 HFNAVLNAVIRLQGVLLKKPEPVSENSID 94

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147779878|emb|CAN65842.1| hypothetical protein VITISV_027369 [Vitis vinifera]

 Score = 89.4 bits (220), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 47/89 (52%), Positives = 60/89 (67%), Gaps = 1/89 (1%)

Query: 1   MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60
           MDR TF  L  +L +  +LK    + V+E V +FLH LAHHVKN+ I  RF  SGETISR
Sbjct: 74  MDRHTFTTLCSMLRTIGKLKDSKYIDVEEMVALFLHILAHHVKNRVIKFRFLRSGETISR 133

Query: 61  -FNSILNGVLELQHILLKSPKPMPEYCTD 88
            FN++LN V+ LQ +LLK P+P+ E  TD
Sbjct: 134 HFNAVLNAVIRLQGVLLKKPEPVSENSTD 162

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413941984|gb|AFW74633.1| hypothetical protein ZEAMMB73_204913 [Zea mays]

 Score = 82.8 bits (203), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 46/89 (51%), Positives = 60/89 (67%), Gaps = 1/89 (1%)

Query: 1   MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60
           MDR+TF +L E+L     LK    + ++E V  FL+ LAHH+KN+TI   F  SGET+SR
Sbjct: 21  MDRRTFFILCEMLRDVGGLKATRNMTLEEIVAHFLYTLAHHLKNRTIGRFFFRSGETVSR 80

Query: 61  -FNSILNGVLELQHILLKSPKPMPEYCTD 88
            FN  L  VL+LQH+LLK+P P+PE  TD
Sbjct: 81  QFNLCLLAVLKLQHLLLKTPDPIPENSTD 109

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307135889|gb|ADN33754.1| retrotransposon protein [Cucumis melo subsp. melo]

 Score = 80.9 bits (198), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 43/89 (48%), Positives = 54/89 (60%), Gaps = 1/89 (1%)

Query: 1   MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60
           MDR+TF +L  LL +   L +  +V V+E V MFLH LAH VKN+ I   F  SGET+SR
Sbjct: 15  MDRRTFAILCHLLRNVAGLSSTEIVDVEEMVAMFLHVLAHDVKNRVIQQEFVRSGETVSR 74

Query: 61  -FNSILNGVLELQHILLKSPKPMPEYCTD 88
            FN +L  VL L   L+K P P+   C D
Sbjct: 75  HFNIVLLAVLRLYEELIKRPVPVTSNCND 103

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|413950101|gb|AFW82750.1| hypothetical protein ZEAMMB73_878123 [Zea mays]

 Score = 80.5 bits (197), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 45/89 (50%), Positives = 59/89 (66%), Gaps = 1/89 (1%)

Query: 1   MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60
           MD +TF +L E+L     LK    + ++E V  FL+ LAHH+KN+TI   F  SGET+SR
Sbjct: 21  MDTRTFFILCEMLRDVGGLKATRNMTLEEVVAQFLYTLAHHLKNRTIGRFFFRSGETVSR 80

Query: 61  -FNSILNGVLELQHILLKSPKPMPEYCTD 88
            FN  L  VL+LQH+LLK+P P+PE  TD
Sbjct: 81  QFNLCLLAVLKLQHLLLKTPDPIPENSTD 109

Source: Zea mays

Species: Zea mays

Genus: Zea

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147769233|emb|CAN60760.1| hypothetical protein VITISV_010914 [Vitis vinifera]

 Score = 79.0 bits (193), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 45/89 (50%), Positives = 58/89 (65%), Gaps = 1/89 (1%)

Query: 1  MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60
          MDR TF  L  +L +  +LK    V V+E V +FLH LAHHVKNQ I  RF  SGET+SR
Sbjct: 6  MDRHTFTTLCFMLRTIGKLKDSKYVDVEEMVXLFLHILAHHVKNQXIKFRFLXSGETVSR 65

Query: 61 -FNSILNGVLELQHILLKSPKPMPEYCTD 88
           FN++LN V+ LQ +LLK  +P  +  T+
Sbjct: 66 HFNAVLNXVIRLQGVLLKKSEPFXKNSTN 94

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|38346719|emb|CAE04869.2| OSJNBa0086O06.17 [Oryza sativa Japonica Group]

 Score = 75.9 bits (185), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 40/89 (44%), Positives = 57/89 (64%), Gaps = 1/89 (1%)

Query: 1  MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60
          MDR+TF +L ++L     ++    + ++E V  FL+ L+HH+KN+TI   F  SGET+SR
Sbjct: 1  MDRRTFHILCDMLRDVGGIEDTRNMPLEESVASFLYILSHHLKNRTIGKFFYRSGETVSR 60

Query: 61 -FNSILNGVLELQHILLKSPKPMPEYCTD 88
           FN  L  VL L  +LLK P+P+PE  TD
Sbjct: 61 HFNLCLLAVLRLHQLLLKKPEPIPEDTTD 89

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|222629452|gb|EEE61584.1| hypothetical protein OsJ_15967 [Oryza sativa Japonica Group]

 Score = 75.9 bits (185), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 40/89 (44%), Positives = 57/89 (64%), Gaps = 1/89 (1%)

Query: 1  MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60
          MDR+TF +L ++L     ++    + ++E V  FL+ L+HH+KN+TI   F  SGET+SR
Sbjct: 1  MDRRTFHILCDMLRDVGGIEDTRNMPLEESVASFLYILSHHLKNRTIGKFFYRSGETVSR 60

Query: 61 -FNSILNGVLELQHILLKSPKPMPEYCTD 88
           FN  L  VL L  +LLK P+P+PE  TD
Sbjct: 61 HFNLCLLAVLRLHQLLLKKPEPIPEDTTD 89

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|125570642|gb|EAZ12157.1| hypothetical protein OsJ_02038 [Oryza sativa Japonica Group]

 Score = 75.1 bits (183), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 40/89 (44%), Positives = 57/89 (64%), Gaps = 1/89 (1%)

Query: 1  MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60
          MDR+TF +L ++L     ++    + ++E V  FL+ L+HH+KN+TI   F  SGET+SR
Sbjct: 1  MDRRTFHILCDMLRDVGGIEDTRNMPLEESVASFLYILSHHLKNRTIGKFFYRSGETVSR 60

Query: 61 -FNSILNGVLELQHILLKSPKPMPEYCTD 88
           FN  L  VL L  +LLK P+P+PE  TD
Sbjct: 61 HFNLCLLAVLRLHQLLLKKPEPIPEDTTD 89

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|307136287|gb|ADN34114.1| retrotransposon protein [Cucumis melo subsp. melo]

 Score = 74.7 bits (182), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 38/71 (53%), Positives = 46/71 (64%), Gaps = 1/71 (1%)

Query: 19  LKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLELQHILLK 77
           L +  VV V+E V MFLH LAH VK++ I   F  SGETISR FN +L  V+ L   LLK
Sbjct: 61  LTSTEVVDVEEMVAMFLHILAHDVKSRVIKREFMRSGETISRHFNMVLLAVIRLHEELLK 120

Query: 78  SPKPMPEYCTD 88
            P+P+P  CTD
Sbjct: 121 KPQPVPNECTD 131

Source: Cucumis melo subsp. melo

Species: Cucumis melo

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	88
TAIR|locus:2165775	374	AT5G41980 [Arabidopsis thalian	0.806	0.189	0.333	3.1e-06

TAIR|locus:2165775 AT5G41980 [Arabidopsis thaliana (taxid:3702)]

 Score = 115 (45.5 bits), Expect = 3.1e-06, P = 3.1e-06
 Identities = 24/72 (33%), Positives = 45/72 (62%)

Query:     1 MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60
             MD+  F  L +LL +   L+  + + ++ Q+ +FL  + H+++ + +   F +SGETISR
Sbjct:    48 MDKPVFYKLCDLLQTRGLLRHTNRIKIEAQLAIFLFIIGHNLRTRAVQELFCYSGETISR 107

Query:    61 -FNSILNGVLEL 71
              FN++LN V+ +
Sbjct:   108 HFNNVLNAVIAI 119


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.324   0.138   0.414    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0       88        88   0.00091  102 3  11 22  0.41    29
                                                     29  0.49    30


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  1
  No. of states in DFA:  526 (56 KB)
  Total size of DFA:  105 KB (2073 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  11.25u 0.10s 11.35t   Elapsed:  00:00:01
  Total cpu time:  11.25u 0.10s 11.35t   Elapsed:  00:00:01
  Start:  Fri May 10 02:31:11 2013   End:  Fri May 10 02:31:12 2013

GO:0005634 "nucleus" evidence=ISM

GO:0016788 "hydrolase activity, acting on ester bonds" evidence=IEA

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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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	88
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	98.74
PF12116	82	SpoIIID: Stage III sporulation protein D; InterPro	96.86
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	96.78
KOG4585	326	consensus Predicted transposase [Replication, reco	96.2
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	95.42
PF08299	70	Bac_DnaA_C: Bacterial dnaA protein helix-turn-heli	95.13
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	95.08
PRK06030	124	hypothetical protein; Provisional	95.05
COG3415	138	Transposase and inactivated derivatives [DNA repli	94.36
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	94.16
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	93.6
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	93.25
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	92.77
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	92.57
PRK10402	226	DNA-binding transcriptional activator YeiL; Provis	92.34
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	91.84
PRK00149	450	dnaA chromosomal replication initiation protein; R	91.51
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	91.28
smart00351	125	PAX Paired Box domain.	90.9
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	90.64
PRK14088	440	dnaA chromosomal replication initiation protein; P	90.46
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	90.42
cd00131	128	PAX Paired Box domain	89.97
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	89.93
PRK14087	450	dnaA chromosomal replication initiation protein; P	89.69
PRK04217	110	hypothetical protein; Provisional	89.66
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	89.54
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	89.5
PRK14086	617	dnaA chromosomal replication initiation protein; P	89.43
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	89.38
PRK09391	230	fixK transcriptional regulator FixK; Provisional	89.12
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	89.0
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	88.93
PF13730	55	HTH_36: Helix-turn-helix domain	88.87
PRK12422	445	chromosomal replication initiation protein; Provis	88.71
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	88.61
PRK09392	236	ftrB transcriptional activator FtrB; Provisional	88.31
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	87.43
PRK01381	99	Trp operon repressor; Provisional	86.8
PRK09492	315	treR trehalose repressor; Provisional	86.28
PF13340	75	DUF4096: Putative transposase of IS4/5 family (DUF	86.19
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	85.94
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	85.67
PF13518	52	HTH_28: Helix-turn-helix domain	85.54
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	84.85
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	84.25
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	82.85
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	82.58
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	82.35
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	82.0
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	81.74
COG0593	408	DnaA ATPase involved in DNA replication initiation	81.72
PRK09047	161	RNA polymerase factor sigma-70; Validated	81.62
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	81.56
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	81.45
smart00760	60	Bac_DnaA_C Bacterial dnaA protein helix-turn-helix	81.32
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	81.24
PRK09413	121	IS2 repressor TnpA; Reviewed	80.78
TIGR02844	80	spore_III_D sporulation transcriptional regulator	80.49

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=98.74  E-value=2e-08  Score=58.10  Aligned_cols=47  Identities=23%  Similarity=0.312  Sum_probs=44.6

Q ss_pred             ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847           24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE   70 (88)
Q Consensus        24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~   70 (88)
                      .++.|+|+.+.|..+.+|.++++++.+|+.|.+|||| |+++++.+..
T Consensus         2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~   49 (53)
T PF13613_consen    2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQ   49 (53)
T ss_pred             CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHH
Confidence            4689999999999999999999999999999999999 9999998865

>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D

Probab=96.86  E-value=0.001  Score=42.17  Aligned_cols=45  Identities=11%  Similarity=0.062  Sum_probs=33.6

Q ss_pred             HHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH-hhhh
Q 046847           30 QVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE-LQHI   74 (88)
Q Consensus        30 ~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~-L~~~   74 (88)
                      .+-+--||+.++++.|+++..||.|.+||++ ..+=|..|.. |+..
T Consensus         8 ~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~La~e   54 (82)
T PF12116_consen    8 VIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINPELARE   54 (82)
T ss_dssp             HHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHHHHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHHHHH
Confidence            4567789999999999999999999999999 9887777754 5543

It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.

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

Probab=96.78  E-value=0.0012  Score=36.68  Aligned_cols=39  Identities=21%  Similarity=0.225  Sum_probs=21.8

Q ss_pred             CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HH
Q 046847           23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FN   62 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~   62 (88)
                      ++++.+|...|.-+ ...|.+.+.|+..+++|.+||++ .+
T Consensus         3 ~~Lt~~eR~~I~~l-~~~G~s~~~IA~~lg~s~sTV~relk   42 (44)
T PF13936_consen    3 KHLTPEERNQIEAL-LEQGMSIREIAKRLGRSRSTVSRELK   42 (44)
T ss_dssp             ---------HHHHH-HCS---HHHHHHHTT--HHHHHHHHH
T ss_pred             cchhhhHHHHHHHH-HHcCCCHHHHHHHHCcCcHHHHHHHh
Confidence            46778888888766 57889999999999999999998 65

>KOG4585 consensus Predicted transposase [Replication, recombination and repair]

Probab=96.20  E-value=0.005  Score=47.34  Aligned_cols=83  Identities=23%  Similarity=0.210  Sum_probs=63.0

Q ss_pred             CChHHHHHHHHHHhhCcCCcC-----CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHhHHHHHHHHHHhhhhh
Q 046847            1 MDRKTFGLLFELLCSDERLKT-----DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNGVLELQHIL   75 (88)
Q Consensus         1 M~~~~F~~L~~~L~~~~~L~~-----t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisrf~~Vl~ai~~L~~~~   75 (88)
                      +++.+|.++|........-+.     +..+++.+.+|+.+|.++++.+-+.++.+|++..+|+    ..+.+...+++.+
T Consensus        10 ~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~----~~~~~~~~~~~~~   85 (326)
T KOG4585|consen   10 KSYTTFDKICSLVQSLNVVKNSGFMLSSLLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC----KFLEEKEDLAPHF   85 (326)
T ss_pred             HHHHHHHHHhhhhhhhhhhcccchhhhccccHHhhhhhhhccccccchHHHHHHHcCCcchhh----hHHHhhhcccchh
Confidence            357788899888655322222     1222299999999999999999999999999999998    5666677789999


Q ss_pred             ccCCCCCCCCCC
Q 046847           76 LKSPKPMPEYCT   87 (88)
Q Consensus        76 ik~p~~~~~~~i   87 (88)
                      ++.|+...+.+|
T Consensus        86 ~~~p~~~~~~~i   97 (326)
T KOG4585|consen   86 LKWPSRRILYEI   97 (326)
T ss_pred             hcCchhhhhhhh
Confidence            999975444433

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=95.42  E-value=0.036  Score=34.72  Aligned_cols=47  Identities=15%  Similarity=0.167  Sum_probs=42.2

Q ss_pred             CccchhHHHHHHHHHhccccchhhhhhhcc-cccchhHh-HHHHHHHHH
Q 046847           23 SVVFVDEQVCMFLHALAHHVKNQTINNRFK-HSGETISR-FNSILNGVL   69 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~-~S~eTisr-f~~Vl~ai~   69 (88)
                      +.+..--++||+|-.--.+.++.+|+..|+ ++.+||+. .+.|=+.+-
T Consensus        26 ~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~   74 (90)
T cd06571          26 KEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLE   74 (90)
T ss_pred             cCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHH
Confidence            568889999999999999999999999999 99999999 888866553

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.

>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=95.13  E-value=0.026  Score=34.06  Aligned_cols=42  Identities=19%  Similarity=0.239  Sum_probs=34.5

Q ss_pred             CccchhHHHHHHHHHhccccchhhhhhhcc-cccchhHh-HHHH
Q 046847           23 SVVFVDEQVCMFLHALAHHVKNQTINNRFK-HSGETISR-FNSI   64 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~-~S~eTisr-f~~V   64 (88)
                      +.+.---++||+|-.--.+.+..+|+..|+ ++.+||.. .++|
T Consensus        27 ~~i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~ki   70 (70)
T PF08299_consen   27 RKIVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRKI   70 (70)
T ss_dssp             HHHHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred             hhhcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence            457778899999999999999999999999 99999988 7765

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.

>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=95.08  E-value=0.061  Score=29.85  Aligned_cols=43  Identities=19%  Similarity=0.194  Sum_probs=34.2

Q ss_pred             cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847           25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV   68 (88)
Q Consensus        25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai   68 (88)
                      .+.+|+-.+-++. ..+.++.+|+..++.|.+||++ -+..++-+
T Consensus         5 L~~~er~vi~~~y-~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL   48 (50)
T PF04545_consen    5 LPPREREVIRLRY-FEGLTLEEIAERLGISRSTVRRILKRALKKL   48 (50)
T ss_dssp             S-HHHHHHHHHHH-TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHh-cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence            5667777666666 8889999999999999999999 88877654

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 ....

>PRK06030 hypothetical protein; Provisional

Probab=95.05  E-value=0.035  Score=37.47  Aligned_cols=44  Identities=11%  Similarity=0.153  Sum_probs=40.1

Q ss_pred             CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847           23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      +.+..--|+||+|-.--.+.++..|+..||++-+||+. ++.|=+
T Consensus        51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~   95 (124)
T PRK06030         51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVED   95 (124)
T ss_pred             cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence            46888999999999999999999999999999999999 886644

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=94.36  E-value=0.054  Score=37.21  Aligned_cols=41  Identities=15%  Similarity=0.062  Sum_probs=36.3

Q ss_pred             CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHH
Q 046847           23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNS   63 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~   63 (88)
                      +.-+.+++-+.|-+.++.+.|.|+|+.+|++|.+||-+ .+.
T Consensus         3 k~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r   44 (138)
T COG3415           3 KPFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRR   44 (138)
T ss_pred             chhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHH
Confidence            34567899999999999999999999999999999987 654

>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=94.16  E-value=0.088  Score=30.22  Aligned_cols=37  Identities=16%  Similarity=0.224  Sum_probs=26.7

Q ss_pred             CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh
Q 046847           23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR   60 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr   60 (88)
                      +.+|++|++.|--.. -.|.+.++|+..|+.+.+||+.
T Consensus         5 ~~LTl~eK~~iI~~~-e~g~s~~~ia~~fgv~~sTv~~   41 (53)
T PF04218_consen    5 KSLTLEEKLEIIKRL-EEGESKRDIAREFGVSRSTVST   41 (53)
T ss_dssp             SS--HHHHHHHHHHH-HCTT-HHHHHHHHT--CCHHHH
T ss_pred             ccCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHH
Confidence            458999999996664 4455999999999999999997

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.

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=93.60  E-value=0.037  Score=38.05  Aligned_cols=62  Identities=16%  Similarity=0.174  Sum_probs=44.5

Q ss_pred             cCCCccchhHHHHHHHHHhcc-------------ccchhhhhhhcccccchhHh-HHHHHH-HHHHhhhhhccCCCC
Q 046847           20 KTDSVVFVDEQVCMFLHALAH-------------HVKNQTINNRFKHSGETISR-FNSILN-GVLELQHILLKSPKP   81 (88)
Q Consensus        20 ~~t~~v~veE~la~FL~i~~~-------------n~~~r~i~~~F~~S~eTisr-f~~Vl~-ai~~L~~~~ik~p~~   81 (88)
                      .+....++++++|-+|+.++.             ..+..++++..|-+.+|||| +++.-+ -++.....-|..|++
T Consensus       134 ~~~~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~~~i~i~~~  210 (211)
T PRK11753        134 GDLAFLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHGKTIVVYGT  210 (211)
T ss_pred             HHHHhcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCCEEEEecC
Confidence            344567899999999987653             34568999999999999999 887764 333444444555543

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=93.25  E-value=0.2  Score=27.10  Aligned_cols=42  Identities=21%  Similarity=0.322  Sum_probs=32.5

Q ss_pred             cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847           25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV   68 (88)
Q Consensus        25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai   68 (88)
                      ++.+|.- ++.+ ...+.++++|+..++.|..||.+ .+.++..+
T Consensus         4 l~~~e~~-i~~~-~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl   46 (58)
T smart00421        4 LTPRERE-VLRL-LAEGLTNKEIAERLGISEKTVKTHLSNIMRKL   46 (58)
T ss_pred             CCHHHHH-HHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            4445554 4444 46789999999999999999999 98887655

lux regulon (activates the bioluminescence operon

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=92.77  E-value=0.13  Score=34.74  Aligned_cols=58  Identities=14%  Similarity=0.240  Sum_probs=42.7

Q ss_pred             CccchhHHHHHHHHHhcc--------------ccchhhhhhhcccccchhHh-HHHHHHH-HHHhhhhhccCCC
Q 046847           23 SVVFVDEQVCMFLHALAH--------------HVKNQTINNRFKHSGETISR-FNSILNG-VLELQHILLKSPK   80 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~--------------n~~~r~i~~~F~~S~eTisr-f~~Vl~a-i~~L~~~~ik~p~   80 (88)
                      ..-+++++||-||..++.              +.+..++++.-|-|.+|||| +++.-+. ++.....-|..+|
T Consensus       111 ~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~d  184 (193)
T TIGR03697       111 AHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKKKLISIHKKKITVHD  184 (193)
T ss_pred             HhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEEEeC
Confidence            445899999999986532              35899999999999999999 9887652 4444444444443

Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.

>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression

Probab=92.57  E-value=0.22  Score=31.74  Aligned_cols=42  Identities=17%  Similarity=0.038  Sum_probs=33.2

Q ss_pred             hhHHHHHHHHHhccccchhhhhhhcccccchhHhHHHHHHHH
Q 046847           27 VDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNGV   68 (88)
Q Consensus        27 veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisrf~~Vl~ai   68 (88)
                      +..++.++=-++-.+.+||.|+...|.|..||+|....|+..
T Consensus        35 l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~Lk~~   76 (87)
T PF01371_consen   35 LAQRWQVAKELLDEGKSYREIAEETGVSIATITRVSRCLKYG   76 (87)
T ss_dssp             HHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHcC
Confidence            344555554567789999999999999999999987777643

The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....

>PRK10402 DNA-binding transcriptional activator YeiL; Provisional

Probab=92.34  E-value=0.24  Score=34.99  Aligned_cols=43  Identities=9%  Similarity=0.145  Sum_probs=35.8

Q ss_pred             ccchhHHHHHHHHHhcc----ccchhhhhhhcccccchhHh-HHHHHH
Q 046847           24 VVFVDEQVCMFLHALAH----HVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        24 ~v~veE~la~FL~i~~~----n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      ..+++|+||-||...+.    +.+..+++...|-|.+|||| +++.-+
T Consensus       148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~  195 (226)
T PRK10402        148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQ  195 (226)
T ss_pred             cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHH
Confidence            34899999999986543    24679999999999999999 998654

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

Probab=91.84  E-value=0.37  Score=26.14  Aligned_cols=36  Identities=19%  Similarity=0.237  Sum_probs=29.3

Q ss_pred             HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      ++.+ +..+.++++|+..++.|..||.+ .+++...+.
T Consensus         8 i~~~-~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~   44 (57)
T cd06170           8 VLRL-LAEGKTNKEIADILGISEKTVKTHLRNIMRKLG   44 (57)
T ss_pred             HHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence            4444 45889999999999999999999 998876543

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

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=91.51  E-value=0.26  Score=38.64  Aligned_cols=47  Identities=15%  Similarity=0.164  Sum_probs=42.0

Q ss_pred             CCccchhHHHHHHHHHhccccchhhhhhhc-ccccchhHh-HHHHHHHH
Q 046847           22 DSVVFVDEQVCMFLHALAHHVKNQTINNRF-KHSGETISR-FNSILNGV   68 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F-~~S~eTisr-f~~Vl~ai   68 (88)
                      ++.+..--|+||+|-.--.+.++.+|+..| +|+.+||+. .+.|=+-+
T Consensus       383 ~~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~  431 (450)
T PRK00149        383 TRNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLL  431 (450)
T ss_pred             CcccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHH
Confidence            377888999999999999999999999999 699999999 98886544

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=91.28  E-value=0.29  Score=33.43  Aligned_cols=57  Identities=9%  Similarity=0.099  Sum_probs=42.1

Q ss_pred             ccchhHHHHHHHHHhcc--------------ccchhhhhhhcccccchhHh-HHHHHH-HHHHhhhhhccCCC
Q 046847           24 VVFVDEQVCMFLHALAH--------------HVKNQTINNRFKHSGETISR-FNSILN-GVLELQHILLKSPK   80 (88)
Q Consensus        24 ~v~veE~la~FL~i~~~--------------n~~~r~i~~~F~~S~eTisr-f~~Vl~-ai~~L~~~~ik~p~   80 (88)
                      .-+++++||.||+.++.              +.+..+|++..|-+.+|||| +++.-+ -++......|..+|
T Consensus       118 ~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~d  190 (202)
T PRK13918        118 GQRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSREGYIRSGYGKIQLLD  190 (202)
T ss_pred             hCchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcCCCEEEEEC
Confidence            45689999999987653              24688999999999999999 988765 33344444454444

>smart00351 PAX Paired Box domain

Probab=90.90  E-value=0.37  Score=31.88  Aligned_cols=42  Identities=14%  Similarity=0.093  Sum_probs=35.6

Q ss_pred             CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHH
Q 046847           22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSI   64 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~V   64 (88)
                      .+..+.|++..|.+..- .+.+.++|+.+|+.|..||.+ .+..
T Consensus        15 ~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~   57 (125)
T smart00351       15 GRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRY   57 (125)
T ss_pred             CCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            35688889888887664 678999999999999999999 7765

>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=90.64  E-value=0.35  Score=27.50  Aligned_cols=26  Identities=23%  Similarity=0.351  Sum_probs=22.3

Q ss_pred             ccchhhhhhhcccccchhHh-HHHHHH
Q 046847           41 HVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        41 n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      ..+.+++++.++.|.+||+| ++...+
T Consensus        25 ~~s~~ela~~~g~s~~tv~r~l~~L~~   51 (67)
T cd00092          25 PLTRQEIADYLGLTRETVSRTLKELEE   51 (67)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            36889999999999999999 877653

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=90.46  E-value=0.36  Score=38.19  Aligned_cols=47  Identities=11%  Similarity=0.228  Sum_probs=41.9

Q ss_pred             CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847           22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV   68 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai   68 (88)
                      ++.+..--|+||+|-.=-.+.++..|+..||++..||++ .+.|=+.+
T Consensus       368 ~~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~  415 (440)
T PRK14088        368 NVKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL  415 (440)
T ss_pred             CccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence            467888899999999998999999999999999999999 88886644

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=90.42  E-value=0.17  Score=26.70  Aligned_cols=23  Identities=26%  Similarity=0.437  Sum_probs=17.9

Q ss_pred             cchhhhhhhcccccchhHh-HHHH
Q 046847           42 VKNQTINNRFKHSGETISR-FNSI   64 (88)
Q Consensus        42 ~~~r~i~~~F~~S~eTisr-f~~V   64 (88)
                      .+.++|++..+-+.||||| +.+.
T Consensus         3 mtr~diA~~lG~t~ETVSR~l~~l   26 (32)
T PF00325_consen    3 MTRQDIADYLGLTRETVSRILKKL   26 (32)
T ss_dssp             --HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             cCHHHHHHHhCCcHHHHHHHHHHH
Confidence            4678999999999999999 8764

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>cd00131 PAX Paired Box domain

Probab=89.97  E-value=0.48  Score=31.63  Aligned_cols=43  Identities=12%  Similarity=0.092  Sum_probs=36.5

Q ss_pred             CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847           22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      .+..|.+.+..|.+.. ..+.+.++|+.+|+.|..||.+ .+..-
T Consensus        15 ~~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~   58 (128)
T cd00131          15 GRPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYY   58 (128)
T ss_pred             CCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4778888988888765 5789999999999999999999 66544

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=89.93  E-value=0.36  Score=31.25  Aligned_cols=41  Identities=17%  Similarity=0.195  Sum_probs=31.4

Q ss_pred             chhHHHHHHHHHhccccchhhhhhhcccccchhHhHHHHHH
Q 046847           26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILN   66 (88)
Q Consensus        26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisrf~~Vl~   66 (88)
                      -+..+++++=-.+..+.++|.|+...|.|..||+|.-+.|.
T Consensus        40 ~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk   80 (94)
T TIGR01321        40 DLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNLK   80 (94)
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhcc
Confidence            34445555555566889999999999999999999555554

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.

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=89.69  E-value=0.48  Score=37.68  Aligned_cols=47  Identities=13%  Similarity=0.166  Sum_probs=42.1

Q ss_pred             CCccchhHHHHHHHHHhccccchhhhhhhcc-cccchhHh-HHHHHHHH
Q 046847           22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFK-HSGETISR-FNSILNGV   68 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~-~S~eTisr-f~~Vl~ai   68 (88)
                      ++.+..--|+||+|-.--.+.++..|+..|| |+-+||.. .+.|=+.+
T Consensus       382 ~~~i~~~RqiamyL~r~~t~~sl~~IG~~FggrdHsTV~~a~~ki~~~~  430 (450)
T PRK14087        382 SKSIVTARHIAMYLTKEILNHTLAQIGEEFGGRDHTTVINAERKIEKML  430 (450)
T ss_pred             CccccHHHHHHHHHHHHHcCCCHHHHHHHhCCCChHHHHHHHHHHHHHH
Confidence            5678899999999999999999999999997 99999998 88876554

>PRK04217 hypothetical protein; Provisional

Probab=89.66  E-value=0.81  Score=30.25  Aligned_cols=48  Identities=15%  Similarity=0.060  Sum_probs=37.8

Q ss_pred             CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847           22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE   70 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~   70 (88)
                      ...++.+|+- ++...--++.++.+|+..++.|..||.+ ++...+.+-.
T Consensus        40 ~~~Lt~eere-ai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre   88 (110)
T PRK04217         40 PIFMTYEEFE-ALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQ   88 (110)
T ss_pred             cccCCHHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            3667788874 4444455889999999999999999999 9987776643

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=89.54  E-value=0.42  Score=33.53  Aligned_cols=58  Identities=22%  Similarity=0.319  Sum_probs=41.8

Q ss_pred             CccchhHHHHHHHHHhcc--------------ccchhhhhhhcccccchhHh-HHHHHH-HHHHhhhhhccCCC
Q 046847           23 SVVFVDEQVCMFLHALAH--------------HVKNQTINNRFKHSGETISR-FNSILN-GVLELQHILLKSPK   80 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~--------------n~~~r~i~~~F~~S~eTisr-f~~Vl~-ai~~L~~~~ik~p~   80 (88)
                      ..-+++|++|-||..++.              +.+..+|++..|-|.+|||| +++.=+ -++++....|..+|
T Consensus       152 ~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~~~~i~i~d  225 (235)
T PRK11161        152 SKKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVKGKYITIEN  225 (235)
T ss_pred             hCCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEEEcC
Confidence            446889999999998753              35778999999999999999 876533 23334444444443

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

Probab=89.50  E-value=0.23  Score=27.22  Aligned_cols=27  Identities=22%  Similarity=0.209  Sum_probs=19.5

Q ss_pred             HhccccchhhhhhhcccccchhHh-HHH
Q 046847           37 ALAHHVKNQTINNRFKHSGETISR-FNS   63 (88)
Q Consensus        37 i~~~n~~~r~i~~~F~~S~eTisr-f~~   63 (88)
                      .+..+.+.++|+..|+.|..||++ .+.
T Consensus        13 l~~~G~s~~~ia~~lgvs~~Tv~~w~kr   40 (50)
T PF13384_consen   13 LLREGWSIREIAKRLGVSRSTVYRWIKR   40 (50)
T ss_dssp             HHHHT--HHHHHHHHTS-HHHHHHHHT-
T ss_pred             HHHCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            334499999999999999999999 654

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=89.43  E-value=0.63  Score=38.90  Aligned_cols=48  Identities=17%  Similarity=0.201  Sum_probs=42.8

Q ss_pred             CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      ++.+..--|+||||-.--.+.++..|+..|+|+-.||.. +++|=+.+-
T Consensus       550 ~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~  598 (617)
T PRK14086        550 SRVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMA  598 (617)
T ss_pred             CcccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHH
Confidence            467888899999999999999999999999999999999 998866443

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

Probab=89.38  E-value=0.34  Score=26.73  Aligned_cols=29  Identities=17%  Similarity=0.217  Sum_probs=24.0

Q ss_pred             HHhccccchhhhhhhcccccchhHh-HHHH
Q 046847           36 HALAHHVKNQTINNRFKHSGETISR-FNSI   64 (88)
Q Consensus        36 ~i~~~n~~~r~i~~~F~~S~eTisr-f~~V   64 (88)
                      ..+..+.++..|+..++.|-+||.| |++.
T Consensus        22 ~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   22 KLLRESRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             HHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            3445556999999999999999999 8763

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=89.12  E-value=0.47  Score=33.68  Aligned_cols=58  Identities=19%  Similarity=0.277  Sum_probs=41.6

Q ss_pred             CccchhHHHHHHHHHhcc----------ccchhhhhhhcccccchhHh-HHHHHH-HHHHhhh-hhccCCC
Q 046847           23 SVVFVDEQVCMFLHALAH----------HVKNQTINNRFKHSGETISR-FNSILN-GVLELQH-ILLKSPK   80 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~----------n~~~r~i~~~F~~S~eTisr-f~~Vl~-ai~~L~~-~~ik~p~   80 (88)
                      ...+++++||-||...+.          ..+..+|++..+-+.+|+|| +++.-+ -++.... ..|...|
T Consensus       151 ~~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~~~~~i~I~D  221 (230)
T PRK09391        151 GRKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQDRGLIGLSGARQIELRN  221 (230)
T ss_pred             cCCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCceEEEcC
Confidence            446899999999988643          35678999999999999999 876654 2333332 3444444

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=89.00  E-value=0.56  Score=29.79  Aligned_cols=37  Identities=19%  Similarity=0.127  Sum_probs=28.9

Q ss_pred             chhHHHHHHHHHhccccchhhhhhhcccccchhHhHHH
Q 046847           26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNS   63 (88)
Q Consensus        26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisrf~~   63 (88)
                      +..++-.|+.| ++.+.+++.|+..++.|..||+|..+
T Consensus        36 ~Ls~R~~I~~l-l~~G~S~~eIA~~LgISrsTIyRi~R   72 (88)
T TIGR02531        36 SLAQRLQVAKM-LKQGKTYSDIEAETGASTATISRVKR   72 (88)
T ss_pred             hhhHHHHHHHH-HHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            35666555555 66778999999999999999999333

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.

>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=88.93  E-value=0.17  Score=27.84  Aligned_cols=27  Identities=26%  Similarity=0.306  Sum_probs=19.7

Q ss_pred             HHhccccchhhhhhhcccccchhHh-HH
Q 046847           36 HALAHHVKNQTINNRFKHSGETISR-FN   62 (88)
Q Consensus        36 ~i~~~n~~~r~i~~~F~~S~eTisr-f~   62 (88)
                      -+...+.+..+|+..|+.|..||-| ++
T Consensus        16 ~l~~~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen   16 ELYAEGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             HHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             HHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence            3445669999999999999999988 54

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 ....

>PF13730 HTH_36: Helix-turn-helix domain

Probab=88.87  E-value=0.72  Score=25.65  Aligned_cols=23  Identities=17%  Similarity=0.306  Sum_probs=20.5

Q ss_pred             chhhhhhhcccccchhHh-HHHHH
Q 046847           43 KNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        43 ~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      |++.+++..+.|..||.| +++.-
T Consensus        27 S~~~la~~~g~s~~Tv~~~i~~L~   50 (55)
T PF13730_consen   27 SQETLAKDLGVSRRTVQRAIKELE   50 (55)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHH
Confidence            789999999999999999 87653

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=88.71  E-value=0.59  Score=37.20  Aligned_cols=47  Identities=17%  Similarity=0.235  Sum_probs=42.4

Q ss_pred             CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847           22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV   68 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai   68 (88)
                      ++.+..--|+||||-.-=.+.|+..|+..|||+-.||.. .++|=+.+
T Consensus       378 ~~~i~~~Rqiamyl~r~~t~~s~~~IG~~fgrdHsTV~~a~~ki~~~~  425 (445)
T PRK12422        378 SREYVLPRQVAMYLCRQKLSLSYVKIGDVFSRDHSTVISSIRAISQKL  425 (445)
T ss_pred             CcccccHHHHHHHHHHHhcCCCHHHHHHHhCCChHHHHHHHHHHHHHH
Confidence            477888899999999999999999999999999999998 88876555

>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A

Probab=88.61  E-value=0.56  Score=27.48  Aligned_cols=38  Identities=26%  Similarity=0.428  Sum_probs=28.5

Q ss_pred             HHHHHHHHHhcc---------------ccchhhhhhhcccccchhHh-HHHHHH
Q 046847           29 EQVCMFLHALAH---------------HVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        29 E~la~FL~i~~~---------------n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      |+||-||..++.               +.+..++++..+-|.+||+| +++.-+
T Consensus         1 ~Rla~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~   54 (76)
T PF13545_consen    1 QRLARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRETVSRILKRLKD   54 (76)
T ss_dssp             HHHHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            456666666553               34678999999999999999 887654

...

>PRK09392 ftrB transcriptional activator FtrB; Provisional

Probab=88.31  E-value=0.67  Score=32.57  Aligned_cols=44  Identities=14%  Similarity=0.243  Sum_probs=35.4

Q ss_pred             CCccchhHHHHHHHHHhcc----------ccchhhhhhhcccccchhHh-HHHHH
Q 046847           22 DSVVFVDEQVCMFLHALAH----------HVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~----------n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      ...-++++++|-||+..+.          +.+..+|+...|-+.+|||| +++.-
T Consensus       144 ~~~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~  198 (236)
T PRK09392        144 QKLRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALA  198 (236)
T ss_pred             hhcCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHH
Confidence            3456899999999997653          23457899999999999999 98853

>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=87.43  E-value=0.81  Score=25.37  Aligned_cols=35  Identities=11%  Similarity=0.252  Sum_probs=23.0

Q ss_pred             hHHHHHHHHHhccc-cchhhhhhhcccccchhHh-HH
Q 046847           28 DEQVCMFLHALAHH-VKNQTINNRFKHSGETISR-FN   62 (88)
Q Consensus        28 eE~la~FL~i~~~n-~~~r~i~~~F~~S~eTisr-f~   62 (88)
                      ||++.--+--+-.+ .|.|.++..|+.+.+|+++ .+
T Consensus         2 ee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~   38 (45)
T PF05225_consen    2 EEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLR   38 (45)
T ss_dssp             HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHc
Confidence            44444444444444 9999999999999999987 54

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.

>PRK01381 Trp operon repressor; Provisional

Probab=86.80  E-value=0.62  Score=30.48  Aligned_cols=42  Identities=17%  Similarity=0.176  Sum_probs=30.2

Q ss_pred             hhHHHHHHHHHhccccchhhhhhhcccccchhHhHHHHHHHH
Q 046847           27 VDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNGV   68 (88)
Q Consensus        27 veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisrf~~Vl~ai   68 (88)
                      +..++.|+=.-+....++|.|+...|.|..||+|--..|+..
T Consensus        41 l~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~~   82 (99)
T PRK01381         41 LGTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLKTA   82 (99)
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhccC
Confidence            334444444444556999999999999999999966665543

>PRK09492 treR trehalose repressor; Provisional

Probab=86.28  E-value=0.44  Score=34.34  Aligned_cols=32  Identities=16%  Similarity=0.121  Sum_probs=26.9

Q ss_pred             ccchhhhhhhcccccchhHh-HHH-----------HHHHHHHhh
Q 046847           41 HVKNQTINNRFKHSGETISR-FNS-----------ILNGVLELQ   72 (88)
Q Consensus        41 n~~~r~i~~~F~~S~eTisr-f~~-----------Vl~ai~~L~   72 (88)
                      ..+.++|+...|.|..|||| ++.           |++++-+|.
T Consensus         4 ~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elg   47 (315)
T PRK09492          4 KLTIKDIARLSGVGKSTVSRVLNNESGVSEETRERVEAVINQHG   47 (315)
T ss_pred             CCcHHHHHHHhCCCHHHHhHHhCCCCCCCHHHHHHHHHHHHHHC
Confidence            35789999999999999999 985           777776664

>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)

Probab=86.19  E-value=1.5  Score=26.36  Aligned_cols=63  Identities=16%  Similarity=0.144  Sum_probs=49.8

Q ss_pred             ChHHHHHHHHHHhhCcCCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847            2 DRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus         2 ~~~~F~~L~~~L~~~~~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      +-+.+..+...|.....-.....++..+-+--.||++.++..-|.+-..|+ +..||.+ |+.-.
T Consensus         2 sD~~W~~i~p~lp~~~~~~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~   65 (75)
T PF13340_consen    2 SDEEWALIEPLLPPRKPRGGRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWS   65 (75)
T ss_pred             CHHHHHHHHhhCCCCCCCCCCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHH
Confidence            445566666677665543344668888989888999999999999999999 8889999 98743

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=85.94  E-value=1.5  Score=28.95  Aligned_cols=44  Identities=5%  Similarity=0.080  Sum_probs=37.4

Q ss_pred             cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847           25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE   70 (88)
Q Consensus        25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~   70 (88)
                      ++.+++-++.|+.  .+.++..|+..++.|..||.. .+.....+-.
T Consensus       113 L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~  157 (166)
T PRK09639        113 MTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRK  157 (166)
T ss_pred             CCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            5666777777777  999999999999999999999 8888777654

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=85.67  E-value=1.3  Score=24.21  Aligned_cols=38  Identities=8%  Similarity=0.112  Sum_probs=30.4

Q ss_pred             HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847           29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      -++.|-........+..++++.++-|.+|||+ .+...+
T Consensus         3 ~R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~   41 (47)
T PF01022_consen    3 TRLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE   41 (47)
T ss_dssp             HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence            35666667777889999999999999999999 877653

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>PF13518 HTH_28: Helix-turn-helix domain

Probab=85.54  E-value=1.5  Score=23.72  Aligned_cols=35  Identities=17%  Similarity=0.126  Sum_probs=26.4

Q ss_pred             HHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847           31 VCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        31 la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      +.+-..+. .+.+.+.++..|+.|..||.+ .+....
T Consensus         3 ~~iv~~~~-~g~s~~~~a~~~gis~~tv~~w~~~y~~   38 (52)
T PF13518_consen    3 LQIVELYL-EGESVREIAREFGISRSTVYRWIKRYRE   38 (52)
T ss_pred             HHHHHHHH-cCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence            44444455 455999999999999999998 766554

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=84.85  E-value=1.8  Score=25.31  Aligned_cols=39  Identities=18%  Similarity=0.268  Sum_probs=30.2

Q ss_pred             hhHHHHHHHHHhc---cccchhhhhhhcccccchhHh-HHHHH
Q 046847           27 VDEQVCMFLHALA---HHVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        27 veE~la~FL~i~~---~n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      .+|.---.+|.+.   ...+..+|+.+++.|..||+. +++.-
T Consensus         5 ~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~   47 (60)
T PF01325_consen    5 SEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA   47 (60)
T ss_dssp             HHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH
Confidence            4455556667666   789999999999999999998 77654

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>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=84.25  E-value=2.3  Score=22.14  Aligned_cols=28  Identities=14%  Similarity=0.214  Sum_probs=24.4

Q ss_pred             ccccchhhhhhhcccccchhHh-HHHHHH
Q 046847           39 AHHVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        39 ~~n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      ..+.++.+|+..++.|..||.+ .+....
T Consensus        24 ~~~~~~~~ia~~~~~s~~~i~~~~~~~~~   52 (55)
T cd06171          24 GEGLSYEEIAEILGISRSTVRQRLHRALK   52 (55)
T ss_pred             hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3778999999999999999999 877654

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

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=82.85  E-value=1.9  Score=24.63  Aligned_cols=39  Identities=8%  Similarity=0.070  Sum_probs=32.3

Q ss_pred             hHHHHHHHHH-hccccchhhhhhhcccccchhHh-HHHHHH
Q 046847           28 DEQVCMFLHA-LAHHVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        28 eE~la~FL~i-~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      .-++.|.-+. .+.+.+..+++..++.+..|+++ .+..-+
T Consensus        10 p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~   50 (61)
T PF12840_consen   10 PTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEE   50 (61)
T ss_dssp             HHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4567777777 88899999999999999999999 887654

...

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

Probab=82.58  E-value=2.6  Score=26.37  Aligned_cols=44  Identities=14%  Similarity=0.095  Sum_probs=34.0

Q ss_pred             cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      ++-.|+-.+.++. ..+.+..+|+..++.|.+||++ .+.+++.+-
T Consensus       111 L~~~~~~ii~~~~-~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~  155 (158)
T TIGR02937       111 LPEREREVLVLRY-LEGLSYKEIAEILGISVGTVKRRLKRARKKLR  155 (158)
T ss_pred             CCHHHHHHHhhHH-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            4555555555543 3689999999999999999999 988877653

Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.

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

Probab=82.35  E-value=3  Score=26.89  Aligned_cols=44  Identities=11%  Similarity=0.086  Sum_probs=34.7

Q ss_pred             ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847           24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV   68 (88)
Q Consensus        24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai   68 (88)
                      .++.+++-++-|+.+ .+.++..|+..+|.|.+||.. .+.....+
T Consensus       113 ~L~~~~r~il~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~L  157 (161)
T TIGR02985       113 KLPEQCRKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKEL  157 (161)
T ss_pred             HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            345666777777555 689999999999999999999 77776554

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.

>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=82.00  E-value=3.8  Score=22.54  Aligned_cols=42  Identities=12%  Similarity=0.099  Sum_probs=28.1

Q ss_pred             cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHH
Q 046847           25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNG   67 (88)
Q Consensus        25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~a   67 (88)
                      ++.+++-++.| .--.+.++.+|+..++.|.+||.. .+..++.
T Consensus        11 L~~~~r~i~~l-~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~   53 (54)
T PF08281_consen   11 LPERQREIFLL-RYFQGMSYAEIAEILGISESTVKRRLRRARKK   53 (54)
T ss_dssp             S-HHHHHHHHH-HHTS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHH-HHHHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence            55566665555 445679999999999999999998 8776543

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.

>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=81.74  E-value=3.2  Score=22.43  Aligned_cols=26  Identities=12%  Similarity=0.349  Sum_probs=21.4

Q ss_pred             ccchhhhhhhcccccchhHh-HHHHHH
Q 046847           41 HVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        41 n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      +.+.++++...+-|..||++ +++..+
T Consensus        17 ~~t~~ela~~~~is~~tv~~~l~~L~~   43 (48)
T PF13412_consen   17 RITQKELAEKLGISRSTVNRYLKKLEE   43 (48)
T ss_dssp             TS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            39999999999999999999 888763

...

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=81.72  E-value=2.8  Score=33.43  Aligned_cols=50  Identities=14%  Similarity=0.167  Sum_probs=43.9

Q ss_pred             cCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           20 KTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        20 ~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      +-++++..--|+||+|-.-=.+.|.-.|+..|+|.-.||.. .++|-+-+-
T Consensus       344 ~R~~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~~~  394 (408)
T COG0593         344 SRTRNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQLIE  394 (408)
T ss_pred             ccccccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHHHh
Confidence            34588889999999999999999999999999999999988 888765553

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=81.62  E-value=3.8  Score=26.79  Aligned_cols=43  Identities=9%  Similarity=0.055  Sum_probs=34.3

Q ss_pred             HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH-hhhhh
Q 046847           33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE-LQHIL   75 (88)
Q Consensus        33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~-L~~~~   75 (88)
                      +|+...-.+.+++.|+...+.|..||.. .+..+..+-. |....
T Consensus       114 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~  158 (161)
T PRK09047        114 AFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKG  158 (161)
T ss_pred             HHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence            4555556889999999999999999999 8888887754 44443

>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=81.56  E-value=2.2  Score=19.86  Aligned_cols=34  Identities=21%  Similarity=0.035  Sum_probs=23.5

Q ss_pred             chhHHHHHHHHHhccccchhhhhhhcccccchhHh
Q 046847           26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR   60 (88)
Q Consensus        26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr   60 (88)
                      +.++...+.. ..-.+.+.++++..|+.|..||++
T Consensus         7 ~~~~~~~i~~-~~~~~~s~~~ia~~~~is~~tv~~   40 (42)
T cd00569           7 TPEQIEEARR-LLAAGESVAEIARRLGVSRSTLYR   40 (42)
T ss_pred             CHHHHHHHHH-HHHcCCCHHHHHHHHCCCHHHHHH
Confidence            3344433333 344566999999999999999975

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

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=81.45  E-value=2.9  Score=23.10  Aligned_cols=35  Identities=14%  Similarity=0.224  Sum_probs=25.4

Q ss_pred             HHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847           31 VCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        31 la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      +-.+|..-..+.+-..+++.|+.|..||.+ .+++=
T Consensus         5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~   40 (55)
T PF08279_consen    5 ILKLLLESKEPITAKELAEELGVSRRTIRRDIKELR   40 (55)
T ss_dssp             HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            333444444458899999999999999999 88763

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain

Probab=81.32  E-value=1.9  Score=24.85  Aligned_cols=33  Identities=15%  Similarity=0.267  Sum_probs=29.5

Q ss_pred             CCccchhHHHHHHHHHhccccchhhhhhhcc-cc
Q 046847           22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFK-HS   54 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~-~S   54 (88)
                      ++.+..--++||+|-.--.+.++.+|+..|+ ++
T Consensus        26 ~~~~~~aR~iamyla~~~~~~sl~~Ig~~fg~rd   59 (60)
T smart00760       26 KREIVLARQIAMYLARELTDLSLPEIGKIFGGRD   59 (60)
T ss_pred             CcchhHHHHHHHHHHHHHHCCCHHHHHHHhCCCC
Confidence            5778889999999999999999999999998 54

Could be involved in DNA-binding.

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism

Probab=81.24  E-value=1.2  Score=25.63  Aligned_cols=26  Identities=27%  Similarity=0.333  Sum_probs=22.0

Q ss_pred             cccchhhhhhhcccccchhHh-HHHHH
Q 046847           40 HHVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        40 ~n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      ...+..++++.|+.|..||.| +++.-
T Consensus        13 ~~~s~~ela~~~~VS~~TiRRDl~~L~   39 (57)
T PF08220_consen   13 GKVSVKELAEEFGVSEMTIRRDLNKLE   39 (57)
T ss_pred             CCEEHHHHHHHHCcCHHHHHHHHHHHH
Confidence            347888899999999999999 88643

This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=80.78  E-value=3.4  Score=26.98  Aligned_cols=49  Identities=2%  Similarity=-0.001  Sum_probs=43.0

Q ss_pred             CCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847           18 RLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        18 ~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      +....+.-+.|+++.+-...+..+.+.++++..|+.|..|+.+ .++...
T Consensus         6 ~~~~rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~   55 (121)
T PRK09413          6 GPEKRRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE   55 (121)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence            4455678899999999999999999999999999999999999 888653

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=80.49  E-value=2  Score=26.87  Aligned_cols=24  Identities=13%  Similarity=0.165  Sum_probs=21.3

Q ss_pred             cccchhhhhhhcccccchhHh-HHH
Q 046847           40 HHVKNQTINNRFKHSGETISR-FNS   63 (88)
Q Consensus        40 ~n~~~r~i~~~F~~S~eTisr-f~~   63 (88)
                      +..+-.+++..||.|.+|||| ++.
T Consensus        18 ~~~ti~dvA~~~gvS~~TVsr~L~~   42 (80)
T TIGR02844        18 TKATVRETAKVFGVSKSTVHKDVTE   42 (80)
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHhcC
Confidence            567889999999999999999 864

Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.

---

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

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	88
1j1v_A	94	Chromosomal replication initiator protein DNAA, 5'	95.23
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	94.94
3pvv_A	101	Chromosomal replication initiator protein DNAA; he	94.22
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	93.94
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	92.34
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	92.2
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	92.15
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	91.89
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	91.84
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	91.83
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	91.18
3c57_A	95	Two component transcriptional regulatory protein;	90.95
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	90.67
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	90.55
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	90.49
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	90.48
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	90.21
3frw_A	107	Putative Trp repressor protein; structural genomic	90.1
1ft9_A	222	Carbon monoxide oxidation system transcription reg	90.1
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	90.04
1o5l_A	213	Transcriptional regulator, CRP family; TM1171, str	89.98
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	89.84
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	89.78
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	89.78
3b02_A	195	Transcriptional regulator, CRP family; structural	89.52
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	89.31
1u78_A	141	TC3 transposase, transposable element TC3 transpos	88.93
2bgc_A	238	PRFA; bacterial infection, human pathogen, transcr	88.74
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	88.65
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	88.64
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	88.6
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	88.48
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	88.43
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	88.22
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	88.01
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	87.98
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	87.91
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	87.87
2jrt_A	95	Uncharacterized protein; solution, structure, NESG	86.6
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	86.36
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	86.3
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	85.89
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	85.88
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	85.86
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	85.83
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	85.5
2oa4_A	101	SIR5; structure, structural genomics, PSI-2, prote	85.36
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	84.27
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	84.24
2k27_A	159	Paired box protein PAX-8; paired domain, solution	84.24
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	83.72
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	83.7
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	83.64
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	83.43
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	82.63
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	82.32
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	82.28
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	82.04

>1j1v_A Chromosomal replication initiator protein DNAA, 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3'; protein-DNA complex; 2.10A {Escherichia coli} SCOP: a.4.12.2

Probab=95.23  E-value=0.015  Score=36.22  Aligned_cols=47  Identities=17%  Similarity=0.074  Sum_probs=42.3

Q ss_pred             CCccchhHHHHHHHHHhccccchhhhhhhc-ccccchhHh-HHHHHHHH
Q 046847           22 DSVVFVDEQVCMFLHALAHHVKNQTINNRF-KHSGETISR-FNSILNGV   68 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F-~~S~eTisr-f~~Vl~ai   68 (88)
                      ++.+..--|+||+|-.--.+.|...|+..| +++-.||+. .+.+=+.+
T Consensus        27 ~~~i~~aRqiamyL~r~~t~~Sl~~IG~~fggrdHsTV~ha~~ki~~~~   75 (94)
T 1j1v_A           27 SRSVARPRQMAMALAKELTNHSLPEIGDAFGGRDHTTVLHACRKIEQLR   75 (94)
T ss_dssp             CHHHHHHHHHHHHHHHHHSCCCHHHHHHHTTSCCHHHHHHHHHHHHHHH
T ss_pred             CchhHHHHHHHHHHHHHHHCcCHHHHHHHhCCCCHHHHHHHHHHHHHHH
Confidence            478889999999999999999999999999 899999999 88876544

>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=94.94  E-value=0.019  Score=36.56  Aligned_cols=44  Identities=20%  Similarity=0.241  Sum_probs=32.8

Q ss_pred             cchhHH------HHHHHHHhccccchhhhhhhcccccchhHhHHHHHHHH
Q 046847           25 VFVDEQ------VCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNGV   68 (88)
Q Consensus        25 v~veE~------la~FL~i~~~n~~~r~i~~~F~~S~eTisrf~~Vl~ai   68 (88)
                      .+..|+      ++++=.-.+...++|.|+...|.|.+||||.+..|+-+
T Consensus        36 LT~~Er~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi~r~L~~l   85 (101)
T 1jhg_A           36 LTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRGSNSLKAA   85 (101)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHHHHHHHHS
T ss_pred             CCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHHHHHHHHc
Confidence            567777      55543333445999999999999999999986665543

>3pvv_A Chromosomal replication initiator protein DNAA; helix-turn-helix motif, interacting with DNAA-BOX, DNAA-box; HET: DNA; 2.00A {Mycobacterium tuberculosis} PDB: 3pvp_A*

Probab=94.22  E-value=0.051  Score=34.29  Aligned_cols=47  Identities=17%  Similarity=0.224  Sum_probs=41.8

Q ss_pred             CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847           22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV   68 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai   68 (88)
                      ++.+..--|+||+|-.--.+.|...|+..||+.-.||.. .+.|=+.+
T Consensus        31 ~~~i~~aRqiAmYL~r~~t~~Sl~~IG~~fgRDHsTV~ha~~ki~~~~   78 (101)
T 3pvv_A           31 TRALAQSRQIAMYLCRELTDLSLPKIGQAFGRDHTTVMYAQRKILSEM   78 (101)
T ss_dssp             CHHHHHHHHHHHHHHHHHCCCCHHHHHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             CchhhHHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence            467888999999999988999999999999999999999 88876544

>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=93.94  E-value=0.061  Score=27.38  Aligned_cols=38  Identities=11%  Similarity=0.083  Sum_probs=29.0

Q ss_pred             ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HH
Q 046847           24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FN   62 (88)
Q Consensus        24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~   62 (88)
                      .++.+++..+... ...+.+++.|+..++.|..||.+ .+
T Consensus         5 ~l~~~~~~~i~~~-~~~g~s~~~IA~~lgis~~Tv~~~~~   43 (51)
T 1tc3_C            5 ALSDTERAQLDVM-KLLNVSLHEMSRKISRSRHCIRVYLK   43 (51)
T ss_dssp             CCCHHHHHHHHHH-HHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence            3556666555544 35778999999999999999988 64

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=92.34  E-value=0.1  Score=34.30  Aligned_cols=44  Identities=23%  Similarity=0.290  Sum_probs=38.0

Q ss_pred             CccchhHHHHHHHHHhcc-------ccchhhhhhhcccccchhHh-HHHHHH
Q 046847           23 SVVFVDEQVCMFLHALAH-------HVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~-------n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      ..-++++++|-||...+.       +.+..++++..|-|.+|||| .++.-+
T Consensus       144 ~~~~~~~Rl~~~L~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~L~~  195 (220)
T 3dv8_A          144 MWKSLDKRVASFLLEETSIEGTNELKITHETIANHLGSHREVITRMLRYFQV  195 (220)
T ss_dssp             HHSCHHHHHHHHHHHHHHHHTSSEECCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHhhhhcCCceecCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            456899999999998876       67889999999999999999 877643

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=92.20  E-value=0.18  Score=27.45  Aligned_cols=32  Identities=13%  Similarity=0.189  Sum_probs=28.4

Q ss_pred             hccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           38 LAHHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        38 ~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      +..+.++++|+...+.|..||.. .+.+.+.+.
T Consensus        10 ~~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~   42 (61)
T 2jpc_A           10 IDEGYTNHGISEKLHISIKTVETHRMNMMRKLQ   42 (61)
T ss_dssp             HHTSCCSHHHHHHTCSCHHHHHHHHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHC
Confidence            57899999999999999999999 988876653

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=92.15  E-value=0.27  Score=27.44  Aligned_cols=45  Identities=11%  Similarity=0.124  Sum_probs=35.3

Q ss_pred             CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      ..++-.|+-.+.++  ..+.+++.|+..++.|..||++ .+.+.+.+.
T Consensus        10 ~~L~~~e~~il~~~--~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~   55 (74)
T 1fse_A           10 PLLTKREREVFELL--VQDKTTKEIASELFISEKTVRNHISNAMQKLG   55 (74)
T ss_dssp             CCCCHHHHHHHHHH--TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence            44566666555443  7889999999999999999999 998877664

>2fmy_A COOA, carbon monoxide oxidation system transcription RE COOA-1; DNA transcription regulator, DNA binding protein; HET: HEM; 2.20A {Carboxydothermus hydrogenoformans} PDB: 2hkx_A*

Probab=91.89  E-value=0.12  Score=34.23  Aligned_cols=43  Identities=16%  Similarity=0.130  Sum_probs=36.7

Q ss_pred             CccchhHHHHHHHHHhcc--------------ccchhhhhhhcccccchhHh-HHHHH
Q 046847           23 SVVFVDEQVCMFLHALAH--------------HVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~--------------n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      ..-+++++||-||..++.              +.+..++++..|-|.+|||| +++.-
T Consensus       135 ~~~~~~~Rl~~~L~~l~~~~g~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~  192 (220)
T 2fmy_A          135 VFKDARLRLAEFLVQAAMDTGLKVPQGIKLELGLNTEEIALMLGTTRQTVSVLLNDFK  192 (220)
T ss_dssp             HTHHHHHHHHHHHHHHHHHHCEEETTEEEEECSSCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHHHHHhCCCCCCcEEEeccCCHHHHHHHhCCcHHHHHHHHHHHH
Confidence            446899999999988753              46889999999999999999 88764

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=91.84  E-value=0.27  Score=27.15  Aligned_cols=45  Identities=11%  Similarity=0.081  Sum_probs=35.0

Q ss_pred             cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847           25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE   70 (88)
Q Consensus        25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~   70 (88)
                      ++..++-.+.| ....+.+++.|+..++.|..||.+ .+..+..+-.
T Consensus        16 L~~~~r~il~l-~~~~g~s~~eIA~~lgis~~tv~~~~~ra~~~l~~   61 (70)
T 2o8x_A           16 LTTDQREALLL-TQLLGLSYADAAAVCGCPVGTIRSRVARARDALLA   61 (70)
T ss_dssp             SCHHHHHHHHH-HHTSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHH-HHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            55555544444 446789999999999999999999 9888877653

>3ryp_A Catabolite gene activator; CAMP receptor protein (CRP), allostery, DNA binding cyclic A transcription regulator; HET: CMP; 1.60A {Escherichia coli} PDB: 2cgp_A* 3hif_A 1g6n_A* 3ryr_A* 1i5z_A* 1j59_A* 1lb2_A* 1run_A* 1zrc_A* 1zrd_A* 1zre_A* 1zrf_A* 2gzw_A* 2wc2_A 3iyd_G* 3n4m_A* 3qop_A* 3rdi_A* 3rou_A* 3rpq_A* ...

Probab=91.83  E-value=0.14  Score=33.36  Aligned_cols=44  Identities=23%  Similarity=0.289  Sum_probs=36.6

Q ss_pred             CccchhHHHHHHHHHhcc-------------ccchhhhhhhcccccchhHh-HHHHHH
Q 046847           23 SVVFVDEQVCMFLHALAH-------------HVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~-------------n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      ...+++++||-||..++.             +.+..++++..|-|.+|||| +++.-+
T Consensus       136 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~iA~~lg~sr~tvsR~l~~L~~  193 (210)
T 3ryp_A          136 AFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLED  193 (210)
T ss_dssp             HHSCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHHHHHHHHhcCcCCCCCceEeccCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            456899999999998764             34678999999999999999 877643

>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix, transcription factor, CAMP-B proteins, CAMP receptor protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP: a.4.5.4 b.82.3.2

Probab=91.18  E-value=0.18  Score=32.75  Aligned_cols=44  Identities=23%  Similarity=0.268  Sum_probs=36.2

Q ss_pred             CccchhHHHHHHHHHhcc-------------ccchhhhhhhcccccchhHh-HHHHHH
Q 046847           23 SVVFVDEQVCMFLHALAH-------------HVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~-------------n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      ...++++++|-||..++.             ..+..+++...|-|.+|||| +++.-+
T Consensus       133 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~~  190 (207)
T 2oz6_A          133 AFLDVTGRVARTLLDLCQQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKSLEE  190 (207)
T ss_dssp             HHCCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHhcCCCCCCCceecccCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            446899999999987654             35778999999999999999 887653

>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=90.95  E-value=0.31  Score=29.44  Aligned_cols=45  Identities=18%  Similarity=0.189  Sum_probs=37.3

Q ss_pred             CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      ..++-.|+-.+.|+  ..+.+++.|+...+.|..||.. .+.+++.+.
T Consensus        26 ~~Lt~~e~~vl~l~--~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~   71 (95)
T 3c57_A           26 SGLTDQERTLLGLL--SEGLTNKQIADRMFLAEKTVKNYVSRLLAKLG   71 (95)
T ss_dssp             -CCCHHHHHHHHHH--HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             hcCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHc
Confidence            34677777777775  8899999999999999999999 998877664

>3iwz_A CAP-like, catabolite activation-like protein; XCC, pathogenicity, CRP, CLP, C-DI-GMP receptor, quorum SENS binding, transcription; 2.30A {Xanthomonas campestris PV}

Probab=90.67  E-value=0.24  Score=32.72  Aligned_cols=44  Identities=20%  Similarity=0.290  Sum_probs=36.6

Q ss_pred             CccchhHHHHHHHHHhccc-------------cchhhhhhhcccccchhHh-HHHHHH
Q 046847           23 SVVFVDEQVCMFLHALAHH-------------VKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n-------------~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      ..-+++|+||-||..++..             .+..++++..|-|.+|||| +++.-+
T Consensus       156 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~lt~~~lA~~lg~sr~tvsR~l~~L~~  213 (230)
T 3iwz_A          156 AFLDVTDRIVRTLHDLSKEPEAMSHPQGTQLRVSRQELARLVGCSREMAGRVLKKLQA  213 (230)
T ss_dssp             HHCCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHhhCCCCCCCceecCCCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            4568999999999987652             4689999999999999999 877643

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=90.55  E-value=0.31  Score=27.70  Aligned_cols=43  Identities=12%  Similarity=0.092  Sum_probs=34.4

Q ss_pred             cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      .+..|+-.+.|+  ..+.++..|+..++.|..||.. .+.+++.+-
T Consensus        17 L~~~e~~vl~l~--~~g~s~~eIA~~l~is~~tV~~~~~r~~~kl~   60 (79)
T 1x3u_A           17 LSERERQVLSAV--VAGLPNKSIAYDLDISPRTVEVHRANVMAKMK   60 (79)
T ss_dssp             HCHHHHHHHHHH--TTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHc
Confidence            455566666664  7899999999999999999999 888876543

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=90.49  E-value=0.25  Score=32.58  Aligned_cols=60  Identities=20%  Similarity=0.225  Sum_probs=43.0

Q ss_pred             CccchhHHHHHHHHHhcc-----------ccchhhhhhhcccccchhHh-HHHHHHH-HHHhhhhhccCCCCC
Q 046847           23 SVVFVDEQVCMFLHALAH-----------HVKNQTINNRFKHSGETISR-FNSILNG-VLELQHILLKSPKPM   82 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~-----------n~~~r~i~~~F~~S~eTisr-f~~Vl~a-i~~L~~~~ik~p~~~   82 (88)
                      ..-+++++||-||...+.           ..+..++++..|-|.+|||| +++.-+. ++.....-|...|++
T Consensus       149 ~~~~~~~Rl~~~L~~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~~~~~i~i~d~~  221 (227)
T 3dkw_A          149 SLKNATHRVVRYLLTLAAHAPGENCRVEIPVAKQLVAGHLSIQPETFSRIMHRLGDEGIIHLDGREISILDRE  221 (227)
T ss_dssp             HHHHHHHHHHHHHHHHHCSSSSSCCCCCCCSCTHHHHHHTTSCHHHHHHHHHHHHHHTSEEESSSCEEESCST
T ss_pred             hcCCHHHHHHHHHHHhhhhcCCCCeEEEecCCHHHHHHHhCCCHHHHHHHHHHHHHCCcEEecCCEEEEeCHH
Confidence            345889999999977654           35778999999999999999 8876542 333444444444443

>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=90.48  E-value=0.3  Score=28.67  Aligned_cols=45  Identities=18%  Similarity=0.205  Sum_probs=36.2

Q ss_pred             CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      ..++-.|+-.+.|+  ..+.+++.|+...+.|..||.. .+.+++.+.
T Consensus        20 ~~Lt~~e~~vl~l~--~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~   65 (82)
T 1je8_A           20 NQLTPRERDILKLI--AQGLPNKMIARRLDITESTVKVHVKHMLKKMK   65 (82)
T ss_dssp             GGSCHHHHHHHHHH--TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTT
T ss_pred             ccCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHc
Confidence            34666777666664  7889999999999999999999 888876653

>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural genomics, joint center for structura genomics, JCSG; 2.15A {Bacteroides thetaiotaomicron} SCOP: a.4.5.4 b.82.3.2

Probab=90.21  E-value=0.31  Score=32.66  Aligned_cols=46  Identities=13%  Similarity=0.234  Sum_probs=38.3

Q ss_pred             cCCCccchhHHHHHHHHHhcc--------ccchhhhhhhcccccchhHh-HHHHH
Q 046847           20 KTDSVVFVDEQVCMFLHALAH--------HVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        20 ~~t~~v~veE~la~FL~i~~~--------n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      .....-+++++||-||..++.        ..+..++++..|-|.+|||| +++.-
T Consensus       157 ~~l~~~~~~~Rl~~~L~~l~~~~~~~~~~~~t~~~lA~~lG~sr~tvsR~l~~l~  211 (232)
T 1zyb_A          157 WDEPTLDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQ  211 (232)
T ss_dssp             TSCCCCSHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHHhhcCHHHHHHHHHHHHHhhcCCeEEecCCHHHHHHHhCCChhHHHHHHHHHH
Confidence            445567899999999998653        35889999999999999999 88764

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=90.10  E-value=0.31  Score=31.31  Aligned_cols=30  Identities=33%  Similarity=0.319  Sum_probs=26.0

Q ss_pred             HhccccchhhhhhhcccccchhHhHHHHHH
Q 046847           37 ALAHHVKNQTINNRFKHSGETISRFNSILN   66 (88)
Q Consensus        37 i~~~n~~~r~i~~~F~~S~eTisrf~~Vl~   66 (88)
                      ++..+.+||+|+..-|.|..||+|....|+
T Consensus        54 lL~~G~SyreIa~~tG~StaTIsRv~r~L~   83 (107)
T 3frw_A           54 MLTDKRTYLDISEKTGASTATISRVNRSLN   83 (107)
T ss_dssp             HHHTTCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHCccHHHHHHHHHHHH
Confidence            367789999999999999999999666654

>1ft9_A Carbon monoxide oxidation system transcription regulator; heme sensor, catabolite gene activator protein; HET: HEM; 2.60A {Rhodospirillum rubrum} SCOP: a.4.5.4 b.82.3.1

Probab=90.10  E-value=0.24  Score=32.87  Aligned_cols=43  Identities=21%  Similarity=0.255  Sum_probs=36.2

Q ss_pred             CccchhHHHHHHHHHhcc--------------ccchhhhhhhcccccchhHh-HHHHH
Q 046847           23 SVVFVDEQVCMFLHALAH--------------HVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~--------------n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      ..-+++++||-||..++.              ..+..++++..|-|.+|||| +++.-
T Consensus       131 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~~t~~~lA~~lG~sr~tvsR~l~~L~  188 (222)
T 1ft9_A          131 MFHDIKQRIAGFFIDHANTTGRQTQGGVIVSVDFTVEEIANLIGSSRQTTSTALNSLI  188 (222)
T ss_dssp             HTHHHHHHHHHHHHHTCBCCCSCC--CCCCEECCCHHHHHHHHCSCHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHhCCCCCCcEEEeccCCHHHHHHHhCCcHHHHHHHHHHHH
Confidence            456899999999988762              25789999999999999999 88754

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=90.04  E-value=0.3  Score=31.92  Aligned_cols=43  Identities=9%  Similarity=0.200  Sum_probs=36.1

Q ss_pred             CccchhHHHHHHHHHhcc-------------ccchhhhhhhcccccchhHh-HHHHH
Q 046847           23 SVVFVDEQVCMFLHALAH-------------HVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~-------------n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      ..-+++++||-||..++.             ..+..++++..+-|.+|||| +++.-
T Consensus       115 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~L~  171 (202)
T 2zcw_A          115 ATQRLKNRMAAALLELSETPLAHEEEGKVVLKATHDELAAAVGSVRETVTKVIGELA  171 (202)
T ss_dssp             HHCCHHHHHHHHHHHHTTSTTEEEETTEEEEECCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHhcCCCCCCcEEccCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            456789999999998753             25778999999999999999 88764

>1o5l_A Transcriptional regulator, CRP family; TM1171, structural GE JCSG, PSI, protein structure initiative, joint center for S genomics; 2.30A {Thermotoga maritima} SCOP: b.82.3.2

Probab=89.98  E-value=0.058  Score=35.90  Aligned_cols=60  Identities=20%  Similarity=0.241  Sum_probs=1.6

Q ss_pred             CccchhHHHHHHHHHhcc-------ccchhhhhhhcccccchhHh-HHHHHH-HHHHhhhhhccCCCCC
Q 046847           23 SVVFVDEQVCMFLHALAH-------HVKNQTINNRFKHSGETISR-FNSILN-GVLELQHILLKSPKPM   82 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~-------n~~~r~i~~~F~~S~eTisr-f~~Vl~-ai~~L~~~~ik~p~~~   82 (88)
                      ..-+++|+||-||...+.       ..+..++++..|-|.+|||| +++.-+ -++......|..+|++
T Consensus       139 ~~~~~~~Rl~~~L~~~~~~~g~~~~~~t~~~lA~~lg~sr~tvsR~l~~L~~~G~I~~~~~~i~I~d~~  207 (213)
T 1o5l_A          139 TTKTLREKLMNFLVRHMNEKRELTLPVTLEELSRLFGCARPALSRVFQELEREGYIEKHGRRIKVLKNP  207 (213)
T ss_dssp             HCC------------------------------------------------------------------
T ss_pred             hhCCHHHHHHHHHHHHhccCCcccCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEcCCEEEEechH
Confidence            446789999999987763       46789999999999999999 888754 4556666666666654

>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=89.84  E-value=0.37  Score=29.06  Aligned_cols=43  Identities=14%  Similarity=0.148  Sum_probs=34.2

Q ss_pred             CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847           22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      .+..+.|++..+.... ..+.+.+.|+..|+.|..||++ ++.--
T Consensus        15 ~~~~s~~~r~~i~~~~-~~g~s~~~ia~~lgis~~Tv~~w~~~~~   58 (128)
T 1pdn_C           15 GRPLPNNIRLKIVEMA-ADGIRPCVISRQLRVSHGCVSKILNRYQ   58 (128)
T ss_dssp             TSCCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3567888887776554 4788999999999999999999 77643

>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription, transcription regulation; HET: BOG; 1.90A {Anabaena} PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*

Probab=89.78  E-value=0.29  Score=33.11  Aligned_cols=59  Identities=15%  Similarity=0.289  Sum_probs=42.7

Q ss_pred             CccchhHHHHHHHHHhcc--------------ccchhhhhhhcccccchhHh-HHHHHH-HHHHhhhhhccCCCC
Q 046847           23 SVVFVDEQVCMFLHALAH--------------HVKNQTINNRFKHSGETISR-FNSILN-GVLELQHILLKSPKP   81 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~--------------n~~~r~i~~~F~~S~eTisr-f~~Vl~-ai~~L~~~~ik~p~~   81 (88)
                      ..-+++++||-||..++.              ..+..++++..|-|.+|||| +++.-+ -++.....-|...|+
T Consensus       161 ~~~~~~~Rla~~L~~l~~~~g~~~~~~~~i~~~lt~~~lA~~lG~sr~tvsR~l~~L~~~GlI~~~~~~i~I~d~  235 (243)
T 3la7_A          161 AHRDMGSRLVSFLLILCRDFGVPCADGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLREKKMISIHKKKITVHKP  235 (243)
T ss_dssp             HCSSHHHHHHHHHHHHHHHHEEECSSSEEECSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTEEEECC-
T ss_pred             hcCCHHHHHHHHHHHHHHHhCCCCCCCeEEeccCCHHHHHHHHCCcHHHHHHHHHHHHHCCCEEEcCCEEEECCH
Confidence            345899999999998753              45789999999999999999 887654 233344444444443

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=89.78  E-value=0.25  Score=32.33  Aligned_cols=44  Identities=20%  Similarity=0.261  Sum_probs=36.3

Q ss_pred             CccchhHHHHHHHHHhc-------cccchhhhhhhcccccchhHh-HHHHHH
Q 046847           23 SVVFVDEQVCMFLHALA-------HHVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~-------~n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      ..-+++++||-||..++       -+.+..+++...|-|.+|||| +++.-+
T Consensus       138 ~~~~~~~Rl~~~L~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~~  189 (216)
T 4ev0_A          138 SFEEARNRVAYALLKLLRQGLGPLFQIRHHELAALAGTSRETVSRVLHALAE  189 (216)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCCSEEECCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHhhcCCccCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            34678999999998664       345899999999999999999 887643

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=89.52  E-value=0.26  Score=32.10  Aligned_cols=43  Identities=16%  Similarity=0.244  Sum_probs=36.0

Q ss_pred             CccchhHHHHHHHHHhcc-------------ccchhhhhhhcccccchhHh-HHHHH
Q 046847           23 SVVFVDEQVCMFLHALAH-------------HVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~-------------n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      ..-+++++||-||..++.             ..+..++++..+-|.+|||| +++.-
T Consensus       108 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~L~  164 (195)
T 3b02_A          108 QTGELRARIARYLLFLADTPLSARDRQGIYVTVSHEEIADATASIRESVSKVLADLR  164 (195)
T ss_dssp             TSSCHHHHHHHHHHHHTTSTTEEEETTEEEEECCHHHHHHTTTSCHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHcCCCCCCCeeeccCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            457889999999988653             25778999999999999999 88754

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=89.31  E-value=0.27  Score=26.35  Aligned_cols=35  Identities=17%  Similarity=0.044  Sum_probs=26.6

Q ss_pred             hhHHHHHHHHHhccccchhhhhhhcccccchhHh-HH
Q 046847           27 VDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FN   62 (88)
Q Consensus        27 veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~   62 (88)
                      .++.-.++.+ ...+.+++.|+..++.|..||++ .+
T Consensus        18 ~~~~~~i~~l-~~~g~s~~eIA~~lgis~~TV~~~l~   53 (55)
T 2x48_A           18 DDLVSVAHEL-AKMGYTVQQIANALGVSERKVRRYLE   53 (55)
T ss_dssp             HHHHHHHHHH-HHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3444444444 46788999999999999999998 54

>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=88.93  E-value=0.36  Score=29.92  Aligned_cols=40  Identities=13%  Similarity=0.115  Sum_probs=30.8

Q ss_pred             CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHH
Q 046847           23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNS   63 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~   63 (88)
                      ...+.+++..|.... ..+.+.+.|+..|+.|..||.+ ++.
T Consensus         5 ~~~s~~~r~~i~~~~-~~G~s~~~ia~~lgis~~Tv~r~~~~   45 (141)
T 1u78_A            5 SALSDTERAQLDVMK-LLNVSLHEMSRKISRSRHCIRVYLKD   45 (141)
T ss_dssp             CCCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             ccCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHc
Confidence            345667766555443 5678999999999999999999 764

>2bgc_A PRFA; bacterial infection, human pathogen, transcriptional regulat transcription; HET: PR3; 2.3A {Listeria monocytogenes} SCOP: a.4.5.4 b.82.3.3 PDB: 2beo_A* 1omi_A

Probab=88.74  E-value=0.39  Score=32.30  Aligned_cols=43  Identities=16%  Similarity=0.145  Sum_probs=35.4

Q ss_pred             CccchhHHHHHHHHHhc--------------c-ccchhhhhhhccccc-chhHh-HHHHH
Q 046847           23 SVVFVDEQVCMFLHALA--------------H-HVKNQTINNRFKHSG-ETISR-FNSIL   65 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~--------------~-n~~~r~i~~~F~~S~-eTisr-f~~Vl   65 (88)
                      ..-+++++||-||..++              - ..+..++++..|-|. +|||| +++.-
T Consensus       136 ~~~~~~~Rla~~L~~l~~~~g~~~~~~~~i~~~~~t~~~lA~~lG~sr~etvsR~l~~l~  195 (238)
T 2bgc_A          136 SINGKLGSICSQLLILTYVYGKETPDGIKITLDNLTMQELGYSSGIAHSSAVSRIISKLK  195 (238)
T ss_dssp             HTTHHHHHHHHHHHHHHHHHEEEETTEEEECCSCCCHHHHHHHTTCCCHHHHHHHHHHHH
T ss_pred             HccCHHHHHHHHHHHHHHHhCCCCCCceEEEeccCCHHHHHHHhCCChHHHHHHHHHHHH
Confidence            34578999999998653              2 567889999999999 89999 88764

>3fx3_A Cyclic nucleotide-binding protein; helix_TURN_helix, CAMP regulatory protein, structural genomi 2, protein structure initiative; 2.20A {Ruegeria pomeroyi} PDB: 3h3z_A*

Probab=88.65  E-value=0.44  Score=31.69  Aligned_cols=45  Identities=22%  Similarity=0.260  Sum_probs=36.9

Q ss_pred             CCCccchhHHHHHHHHHhcc----------ccchhhhhhhcccccchhHh-HHHHH
Q 046847           21 TDSVVFVDEQVCMFLHALAH----------HVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        21 ~t~~v~veE~la~FL~i~~~----------n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      ....-+++++||-||..++.          +.+..+++...|-|.+|||| .++.-
T Consensus       148 ~l~~~~~~~Rl~~~L~~~~~~~~~~~~~~l~~t~~~iA~~lg~sr~tvsR~l~~L~  203 (237)
T 3fx3_A          148 QLKAQTGAQRVAEFLLELCDCDTGACEVTLPYDKMLIAGRLGMKPESLSRAFSRLK  203 (237)
T ss_dssp             HCCCCCHHHHHHHHHHHHCCC-----EEECCSCTHHHHHHTTCCHHHHHHHHHHHG
T ss_pred             HHhcCCHHHHHHHHHHHHhhhcCCCeEEEecCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            34567899999999999864          24578999999999999999 87753

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=88.64  E-value=0.37  Score=28.60  Aligned_cols=44  Identities=20%  Similarity=0.208  Sum_probs=35.7

Q ss_pred             CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847           23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV   68 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai   68 (88)
                      ..++-.|+-.+.|+  ..+.+++.|+..++.|..||.. .+.+++.+
T Consensus        28 ~~Lt~~e~~vl~l~--~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL   72 (91)
T 2rnj_A           28 EMLTEREMEILLLI--AKGYSNQEIASASHITIKTVKTHVSNILSKL   72 (91)
T ss_dssp             GGCCSHHHHHHHHH--HTTCCTTHHHHHHTCCHHHHHHHHHHHHHHT
T ss_pred             hcCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            34666677666664  7899999999999999999999 88877654

>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=88.60  E-value=0.47  Score=26.54  Aligned_cols=46  Identities=11%  Similarity=0.153  Sum_probs=36.3

Q ss_pred             cchhHHHHHHHHH-h--ccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847           25 VFVDEQVCMFLHA-L--AHHVKNQTINNRFKHSGETISR-FNSILNGVLE   70 (88)
Q Consensus        25 v~veE~la~FL~i-~--~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~   70 (88)
                      .+..|+-.+-|+. +  ..+.+++.|+...+.|.+||.. .+..++.+-.
T Consensus         6 L~~~er~il~l~~~l~~~~g~s~~eIA~~lgis~~tV~~~~~ra~~kLr~   55 (68)
T 2p7v_B            6 LTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRH   55 (68)
T ss_dssp             CCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGS
T ss_pred             CCHHHHHHHHHHHccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            5566666666655 2  5899999999999999999999 8888776643

>3kcc_A Catabolite gene activator; helix-turn-helix, CAMP, CAMP-binding, DNA-binding nucleotide-binding, transcription, transcription regulation; HET: CMP; 1.66A {Escherichia coli}

Probab=88.48  E-value=0.36  Score=33.11  Aligned_cols=44  Identities=23%  Similarity=0.339  Sum_probs=36.2

Q ss_pred             CccchhHHHHHHHHHhcc-------------ccchhhhhhhcccccchhHh-HHHHHH
Q 046847           23 SVVFVDEQVCMFLHALAH-------------HVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~-------------n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      ...+++++||-||..++.             +.+..++++..|-|.+|||| +++.-+
T Consensus       186 ~~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~l~lt~~~lA~~lG~sr~tvsR~l~~L~~  243 (260)
T 3kcc_A          186 AFLLVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLED  243 (260)
T ss_dssp             HHCCHHHHHHHHHHHHHTSTTCEEETTEEEEECCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHhcCCCCCCCceeecCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            446899999999988764             34678999999999999999 887653

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=88.43  E-value=0.46  Score=30.19  Aligned_cols=43  Identities=12%  Similarity=0.054  Sum_probs=35.0

Q ss_pred             CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847           22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      .+..+.|++..|.... ..+.+.+.|+..|+.|..||++ ++..-
T Consensus        30 ~~~~s~e~r~~iv~~~-~~G~s~~~iA~~lgis~~TV~rw~~~~~   73 (149)
T 1k78_A           30 GRPLPDVVRQRIVELA-HQGVRPCDISRQLRVSHGCVSKILGRYY   73 (149)
T ss_dssp             TSCCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4567888887776655 4679999999999999999999 77654

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=88.22  E-value=0.82  Score=26.91  Aligned_cols=45  Identities=13%  Similarity=0.116  Sum_probs=36.5

Q ss_pred             cchhHHHHHHHHH-hc--cccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           25 VFVDEQVCMFLHA-LA--HHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        25 v~veE~la~FL~i-~~--~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      .+..|+-.+-|+. ++  .+.+++.|+...+.|.+||.. .+..+..+-
T Consensus        19 L~~~er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~kLr   67 (87)
T 1tty_A           19 LSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLR   67 (87)
T ss_dssp             SCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHB
T ss_pred             CCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            5667777776755 34  889999999999999999999 888777664

>3e97_A Transcriptional regulator, CRP/FNR family; YP_604437.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.86A {Deinococcus geothermalis dsm 11300}

Probab=88.01  E-value=0.38  Score=31.91  Aligned_cols=42  Identities=21%  Similarity=0.172  Sum_probs=35.1

Q ss_pred             cchh-HHHHHHHHHhcc-------------ccchhhhhhhcccccchhHh-HHHHHH
Q 046847           25 VFVD-EQVCMFLHALAH-------------HVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        25 v~ve-E~la~FL~i~~~-------------n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      -+++ ++||-||...+.             ..+..+++...|-|.+|||| +++.-+
T Consensus       145 ~~~~~~Rl~~~L~~~~~~~~~~~~~~~~~~~~t~~~iA~~lg~sr~tvsR~l~~L~~  201 (231)
T 3e97_A          145 GQNTEAALTHVFANLYRQRLAAGVPQPEVLPLGTQDIMARTSSSRETVSRVLKRLEA  201 (231)
T ss_dssp             HHCHHHHHHHHHHHHHHHHHHHTCSSTTEECCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             ccChHHHHHHHHHHHHHhcCCCCCCceEecCCCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            4566 999999998764             45789999999999999999 887643

>3d0s_A Transcriptional regulatory protein; CAMP receptor protein (CRP), dimer, inactive(APO, unliganded allostery, DNA binding, cyclic AMP; 2.00A {Mycobacterium tuberculosis} PDB: 3i54_A* 3i59_A* 3mzh_A* 3h3u_A* 3r6s_A*

Probab=87.98  E-value=0.42  Score=31.58  Aligned_cols=43  Identities=23%  Similarity=0.253  Sum_probs=35.8

Q ss_pred             CccchhHHHHHHHHHhc--------------cccchhhhhhhcccccchhHh-HHHHH
Q 046847           23 SVVFVDEQVCMFLHALA--------------HHVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~--------------~n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      ...+++++||-||..++              ...+..++++..|-|.+|||| +++.-
T Consensus       145 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~i~~~~t~~~lA~~lg~sr~tvsR~l~~l~  202 (227)
T 3d0s_A          145 IFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFA  202 (227)
T ss_dssp             HHSCHHHHHHHHHHHHHHHHEEEETTEEEEECCCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHhCCcCCCceEEcCCCCHHHHHHHhCCcHHHHHHHHHHHH
Confidence            44689999999998764              235788999999999999999 88754

>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration; HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} SCOP: a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A 3e5x_A* 3e5q_A 2h6b_A* 2h6c_A

Probab=87.91  E-value=0.41  Score=32.38  Aligned_cols=42  Identities=14%  Similarity=0.141  Sum_probs=35.6

Q ss_pred             CccchhHHHHHHHHHhcc--------------ccchhhhhhhcccccchhHh-HHHH
Q 046847           23 SVVFVDEQVCMFLHALAH--------------HVKNQTINNRFKHSGETISR-FNSI   64 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~--------------n~~~r~i~~~F~~S~eTisr-f~~V   64 (88)
                      ..-+++++||-||..++.              ..+..+++...|-|.+|||| +++.
T Consensus       145 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~i~~~~t~~~iA~~lG~sr~tvsR~l~~L  201 (250)
T 3e6c_C          145 NTYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLASL  201 (250)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHCEEETTEEEEECCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHhCCCCCCCcEecCCCCHHHHHHHhCCcHHHHHHHHHHH
Confidence            456899999999987542              45889999999999999999 8874

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=87.87  E-value=0.79  Score=27.09  Aligned_cols=45  Identities=4%  Similarity=0.029  Sum_probs=35.7

Q ss_pred             cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847           25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE   70 (88)
Q Consensus        25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~   70 (88)
                      ++-.++-.+.|+ ...+.+++.|+...+.|..||.. .+..+..+-.
T Consensus        38 L~~~~r~vl~l~-~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~   83 (92)
T 3hug_A           38 LSAEHRAVIQRS-YYRGWSTAQIATDLGIAEGTVKSRLHYAVRALRL   83 (92)
T ss_dssp             SCHHHHHHHHHH-HTSCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            555666655553 35779999999999999999999 8888877765

>2jrt_A Uncharacterized protein; solution, structure, NESG, PSI, target RHR5, structural genomics, protein structure initiative; NMR {Rhodobacter sphaeroides}

Probab=86.60  E-value=1.1  Score=27.79  Aligned_cols=44  Identities=7%  Similarity=0.113  Sum_probs=39.5

Q ss_pred             CCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHH
Q 046847           21 TDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSI   64 (88)
Q Consensus        21 ~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~V   64 (88)
                      ..+.=+.++++++.+..+..+.+..+++.+|+-|.++|.+ -++.
T Consensus        29 ~~rrWs~~~Kl~VV~~~~~g~~s~~e~arry~Is~s~i~~W~r~~   73 (95)
T 2jrt_A           29 DTRRWVASRKAAVVKAVIHGLITEREALDRYSLSEEEFALWRSAV   73 (95)
T ss_dssp             SCCCCCHHHHHHHHHHHHTTSSCHHHHHHHTTCCHHHHHHHHHHT
T ss_pred             hhhccCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            3367889999999999999999999999999999999988 6665

>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=86.36  E-value=1.2  Score=25.17  Aligned_cols=46  Identities=13%  Similarity=0.087  Sum_probs=36.8

Q ss_pred             ccchhHHHHHHHHHh-c--cccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           24 VVFVDEQVCMFLHAL-A--HHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        24 ~v~veE~la~FL~i~-~--~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      ..+..|+-.+-|+.. +  .+.++..|+...+.|.+||.. .+..++.+-
T Consensus        10 ~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr   59 (73)
T 1ku3_A           10 KLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK   59 (73)
T ss_dssp             TSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            356667766666552 2  789999999999999999999 888887776

>1iuf_A Centromere ABP1 protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; NMR {Schizosaccharomyces pombe} SCOP: a.4.1.7 a.4.1.7

Probab=86.30  E-value=0.56  Score=30.40  Aligned_cols=42  Identities=17%  Similarity=0.206  Sum_probs=34.6

Q ss_pred             CCccchhHHHHHHHHH--hccccchhhhhh----hc--ccccchhHh-HHH
Q 046847           22 DSVVFVDEQVCMFLHA--LAHHVKNQTINN----RF--KHSGETISR-FNS   63 (88)
Q Consensus        22 t~~v~veE~la~FL~i--~~~n~~~r~i~~----~F--~~S~eTisr-f~~   63 (88)
                      -..+|++++++|-.|.  -..+.+..+++.    .|  +.|.+|||+ .+.
T Consensus         9 R~~lT~~qK~~i~~~~~~~~~~~~q~~la~wa~~~f~~~is~stis~ilk~   59 (144)
T 1iuf_A            9 RRAITEHEKRALRHYFFQLQNRSGQQDLIEWFREKFGKDISQPSVSQILSS   59 (144)
T ss_dssp             SSCCCSHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHSSCCSSSSTTHHHHH
T ss_pred             CccCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCCCCcHHHHHHHHhh
Confidence            3678999999999999  345567888999    99  889999998 654

>2gau_A Transcriptional regulator, CRP/FNR family; structural genomics, porphyromona gingivalis, PSI, protein structure initiative; 1.90A {Porphyromonas gingivalis} SCOP: a.4.5.4 b.82.3.2

Probab=85.89  E-value=0.72  Score=30.52  Aligned_cols=43  Identities=9%  Similarity=0.081  Sum_probs=34.9

Q ss_pred             CccchhHHHHHHHHHhc-------------cccchhhhhhhcccccchhHh-HHHHH
Q 046847           23 SVVFVDEQVCMFLHALA-------------HHVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~-------------~n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      ..-++++++|-||..++             -..+..++++..+-|.+|||| +++.-
T Consensus       149 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~  205 (232)
T 2gau_A          149 TQKHVRGRLAETLLILKENFGFENDGATLSIYLSREELATLSNMTVSNAIRTLSTFV  205 (232)
T ss_dssp             HHSCHHHHHHHHHHHHHHHHCBCTTSSBBSCCCCHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHcCCCCCCcEEEcccCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            34678999999996533             245788999999999999999 88764

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=85.88  E-value=0.47  Score=30.97  Aligned_cols=31  Identities=26%  Similarity=0.232  Sum_probs=26.1

Q ss_pred             HHhccccchhhhhhhcccccchhHhHHHHHH
Q 046847           36 HALAHHVKNQTINNRFKHSGETISRFNSILN   66 (88)
Q Consensus        36 ~i~~~n~~~r~i~~~F~~S~eTisrf~~Vl~   66 (88)
                      -.+..+.+||+|+...+.|..||+|..+.|+
T Consensus        70 klL~~G~syreIA~~~g~S~aTIsRv~r~L~  100 (119)
T 3kor_A           70 KMIKQGYTYATIEQESGASTATISRVKRSLQ  100 (119)
T ss_dssp             HHHHHTCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHh
Confidence            3467789999999999999999999666553

>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=85.86  E-value=1  Score=28.26  Aligned_cols=45  Identities=9%  Similarity=-0.023  Sum_probs=34.3

Q ss_pred             cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847           25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE   70 (88)
Q Consensus        25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~   70 (88)
                      .+..++- +|......+.+++.|+..++.|..||.+ .+.....+-.
T Consensus        23 L~~~~r~-vl~l~y~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~   68 (113)
T 1s7o_A           23 LTDKQMN-YIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEKILET   68 (113)
T ss_dssp             SCHHHHH-HHHHHHHTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            4555554 4444456789999999999999999999 8888776643

>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=85.83  E-value=0.58  Score=23.91  Aligned_cols=25  Identities=24%  Similarity=0.216  Sum_probs=21.3

Q ss_pred             hccccchhhhhhhcccccchhHh-HH
Q 046847           38 LAHHVKNQTINNRFKHSGETISR-FN   62 (88)
Q Consensus        38 ~~~n~~~r~i~~~F~~S~eTisr-f~   62 (88)
                      ...+.+.+.|+..++.|..||.+ ++
T Consensus        18 ~~~g~s~~~ia~~lgvs~~Tv~r~l~   43 (52)
T 1jko_C           18 LEKGHPRQQLAIIFGIGVSTLYRYFP   43 (52)
T ss_dssp             HHTTCCHHHHHHTTSCCHHHHHHHSC
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34568999999999999999988 54

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=85.50  E-value=0.86  Score=27.06  Aligned_cols=41  Identities=10%  Similarity=-0.113  Sum_probs=33.0

Q ss_pred             ccchhHHHHHHHHHhcc-ccchhhhhhhcccccchhHh-HHHH
Q 046847           24 VVFVDEQVCMFLHALAH-HVKNQTINNRFKHSGETISR-FNSI   64 (88)
Q Consensus        24 ~v~veE~la~FL~i~~~-n~~~r~i~~~F~~S~eTisr-f~~V   64 (88)
                      ..|.|.+..+.-..... +.+.+.|+..||.|..||.+ ....
T Consensus         5 ~ys~e~k~~~v~~~~~~~g~s~~~ia~~~gIs~~tl~rW~~~~   47 (97)
T 2jn6_A            5 TYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKY   47 (97)
T ss_dssp             CCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCChHHHHHHHHCcCHHHHHHHHHHH
Confidence            46777787777666655 88999999999999999998 7653

>2oa4_A SIR5; structure, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; NMR {Silicibacter pomeroyi} SCOP: a.4.12.3

Probab=85.36  E-value=1.5  Score=27.75  Aligned_cols=50  Identities=6%  Similarity=0.090  Sum_probs=40.4

Q ss_pred             CcCCcCC--CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847           16 DERLKTD--SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        16 ~~~L~~t--~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      +++|.++  +.=....++++-.++.+++.|.+.+..+|+-|.+||.+ -..+-
T Consensus        23 ~~dlp~~~~rRWva~rK~~VV~~v~~g~lS~~EAa~ry~Is~~ei~~W~r~y~   75 (101)
T 2oa4_A           23 RADLPPANTRRWVASRKIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVSALA   75 (101)
T ss_dssp             TTSSCCSCCSCCCHHHHHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHHHHH
T ss_pred             hcCCChHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            3455444  44455579999999999999999999999999999998 76653

>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=84.27  E-value=1.5  Score=27.28  Aligned_cols=45  Identities=9%  Similarity=0.024  Sum_probs=34.2

Q ss_pred             cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847           25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE   70 (88)
Q Consensus        25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~   70 (88)
                      .+..++ .+|......+.+++.|+..++.|..||.+ .+..+..+-.
T Consensus        26 L~~~~r-~vl~l~~~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~   71 (113)
T 1xsv_A           26 LTNKQR-NYLELFYLEDYSLSEIADTFNVSRQAVYDNIRRTGDLVED   71 (113)
T ss_dssp             SCHHHH-HHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            444444 44555556789999999999999999998 8887766643

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=84.24  E-value=1.4  Score=31.15  Aligned_cols=46  Identities=15%  Similarity=0.204  Sum_probs=37.6

Q ss_pred             cCCCccchhHHHHHHHHHhccccchhhhhhhc-ccccchhHh-HHHHH
Q 046847           20 KTDSVVFVDEQVCMFLHALAHHVKNQTINNRF-KHSGETISR-FNSIL   65 (88)
Q Consensus        20 ~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F-~~S~eTisr-f~~Vl   65 (88)
                      +.++.+....++||||-.=-.+.++.+|+..| +++..||.. ++.+=
T Consensus       252 ~~~~~~~~~r~i~~~l~r~~~~~s~~~ig~~~g~~~~~tv~~~~~~~~  299 (324)
T 1l8q_A          252 KRNKRTSEARKIAMYLCRKVCSASLIEIARAFKRKDHTTVIHAIRSVE  299 (324)
T ss_dssp             CCCSSSHHHHHHHHHHHHHHHCCCHHHHHHHSSCCCSTHHHHHHHHHH
T ss_pred             CCCCccchHHHHHHHHHHHHhCCCHHHHHHHhCCCCchHHHHHHHHHH
Confidence            34567889999999986544468999999999 899999988 87763

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=84.24  E-value=0.79  Score=29.49  Aligned_cols=40  Identities=13%  Similarity=0.061  Sum_probs=32.4

Q ss_pred             CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHH
Q 046847           23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNS   63 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~   63 (88)
                      +..+.|++..|..+. ..+.+.+.|+..|+.|..||++ ++.
T Consensus        24 ~~~s~e~r~~ii~l~-~~G~s~~~IA~~lgis~~TV~rwl~r   64 (159)
T 2k27_A           24 RPLPEVVRQRIVDLA-HQGVRPCDISRQLRVSHGCVSKILGR   64 (159)
T ss_dssp             CSSCHHHHHHHHHHH-HHTCCHHHHHHHHTCCSHHHHHHHCC
T ss_pred             CCCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            467788887775554 4679999999999999999998 754

>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=83.72  E-value=1.3  Score=26.54  Aligned_cols=45  Identities=22%  Similarity=0.189  Sum_probs=34.4

Q ss_pred             CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      ..++-.|+-.+.|+ . .+.++.+|+...+.|..||.. ...+++.+.
T Consensus        28 ~~Lt~rE~~Vl~l~-~-~G~s~~eIA~~L~iS~~TV~~~~~~i~~Klg   73 (90)
T 3ulq_B           28 DVLTPRECLILQEV-E-KGFTNQEIADALHLSKRSIEYSLTSIFNKLN   73 (90)
T ss_dssp             -CCCHHHHHHHHHH-H-TTCCHHHHHHHHTCCHHHHHHHHHHHHHHTT
T ss_pred             cCCCHHHHHHHHHH-H-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence            44566666554443 3 899999999999999999999 888876553

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=83.70  E-value=2.8  Score=25.43  Aligned_cols=39  Identities=5%  Similarity=0.106  Sum_probs=31.1

Q ss_pred             hHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847           28 DEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        28 eE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      ..++.++.++.....+..+++..++.|..|||+ .+..-+
T Consensus        32 ~~~~~il~~L~~~~~s~~ela~~l~is~stvsr~l~~Le~   71 (119)
T 2lkp_A           32 PSRLMILTQLRNGPLPVTDLAEAIGMEQSAVSHQLRVLRN   71 (119)
T ss_dssp             HHHHHHHHHHHHCCCCHHHHHHHHSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            456677666655579999999999999999999 776543

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=83.64  E-value=1.9  Score=26.47  Aligned_cols=46  Identities=22%  Similarity=0.139  Sum_probs=36.7

Q ss_pred             CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      ...++-.|+-.+.|  +..+.++++|+...+.|..||.. ...+++.+.
T Consensus        32 ~~~Lt~re~~Vl~l--~~~G~s~~EIA~~L~iS~~TV~~~l~ri~~KLg   78 (99)
T 1p4w_A           32 DKRLSPKESEVLRL--FAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLG   78 (99)
T ss_dssp             SSSCCHHHHHHHHH--HHHTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             cCCCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence            45577777765555  35899999999999999999999 888876553

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=83.43  E-value=0.72  Score=28.47  Aligned_cols=29  Identities=14%  Similarity=0.181  Sum_probs=23.7

Q ss_pred             HHHhccccchhhhhhhcccccchhHh-HHH
Q 046847           35 LHALAHHVKNQTINNRFKHSGETISR-FNS   63 (88)
Q Consensus        35 L~i~~~n~~~r~i~~~F~~S~eTisr-f~~   63 (88)
                      -++..++.+..+++..+|.|..|||| ++.
T Consensus        14 ~~l~~~~~ti~dlA~~~gVS~~TVsR~L~~   43 (93)
T 2l0k_A           14 KYIVETKKTVRVIAKEFGVSKSTVHKDLTE   43 (93)
T ss_dssp             HHHHHHCCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             HHHHHcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence            34444558999999999999999999 865

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=82.63  E-value=1  Score=24.67  Aligned_cols=39  Identities=5%  Similarity=0.177  Sum_probs=31.1

Q ss_pred             ccchhHHHHHHHHHhccccc----hhhhhhhcccccchhHh-HHH
Q 046847           24 VVFVDEQVCMFLHALAHHVK----NQTINNRFKHSGETISR-FNS   63 (88)
Q Consensus        24 ~v~veE~la~FL~i~~~n~~----~r~i~~~F~~S~eTisr-f~~   63 (88)
                      .-+.|.++.+ +-.+..+.+    .+.++..|+.|.+||.+ .++
T Consensus         5 ~ys~efK~~~-~~~~~~g~s~~~~~~~vA~~~gIs~~tl~~W~~~   48 (59)
T 2glo_A            5 IFTPHFKLQV-LESYRNDNDCKGNQRATARKYNIHRRQIQKWLQC   48 (59)
T ss_dssp             CCCHHHHHHH-HHHHHHCTTTTTCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             cCCHHHHHHH-HHHHHcCCCcchHHHHHHHHHCcCHHHHHHHHHH
Confidence            4677888877 555666678    99999999999999988 543

>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi}

Probab=82.32  E-value=0.6  Score=32.96  Aligned_cols=31  Identities=23%  Similarity=0.279  Sum_probs=26.8

Q ss_pred             cchhhhhhhcccccchhHh-HHH-----------HHHHHHHhh
Q 046847           42 VKNQTINNRFKHSGETISR-FNS-----------ILNGVLELQ   72 (88)
Q Consensus        42 ~~~r~i~~~F~~S~eTisr-f~~-----------Vl~ai~~L~   72 (88)
                      .+-++|+...|.|..|||| +|.           |++++-+|.
T Consensus        11 ~ti~diA~~agVS~~TVSr~Ln~~~~vs~~tr~rV~~~~~~lg   53 (344)
T 3kjx_A           11 LTLRDVSEASGVSEMTVSRVLRNRGDVSDATRARVLAAAKELG   53 (344)
T ss_dssp             CCHHHHHHHHCCCSHHHHHHHTTCSCCCHHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhC
Confidence            5778999999999999999 975           888877765

>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=82.28  E-value=2  Score=26.47  Aligned_cols=47  Identities=11%  Similarity=0.075  Sum_probs=38.3

Q ss_pred             ccchhHHHHHHHHHh---ccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847           24 VVFVDEQVCMFLHAL---AHHVKNQTINNRFKHSGETISR-FNSILNGVLE   70 (88)
Q Consensus        24 ~v~veE~la~FL~i~---~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~   70 (88)
                      ..+-.|+-.+-|+..   +.+.++..|+..++.|.+||.. .+..++.+-.
T Consensus        19 ~Lp~reR~Vi~Lry~l~~~e~~s~~EIA~~lgiS~~tVr~~~~rAlkkLR~   69 (99)
T 3t72_q           19 GLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRH   69 (99)
T ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            367778887777664   3789999999999999999999 8887776653

>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A

Probab=82.04  E-value=1.2  Score=27.51  Aligned_cols=41  Identities=15%  Similarity=0.147  Sum_probs=32.1

Q ss_pred             CccchhHHHHHHHHHhccccch-hhhhhhcccccchhHh-HHH
Q 046847           23 SVVFVDEQVCMFLHALAHHVKN-QTINNRFKHSGETISR-FNS   63 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n~~~-r~i~~~F~~S~eTisr-f~~   63 (88)
                      +..|.|++..+--+...++.+. ++++..|+.|..||++ .+.
T Consensus         6 ~~~t~e~K~~iv~~~~~~g~~~~~~~A~~~gvs~stl~~~~~~   48 (131)
T 1hlv_A            6 RQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKN   48 (131)
T ss_dssp             CCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHT
T ss_pred             eeCCHHHHHHHHHHHHHCCCCcHHHHHHHhCCCHHHHHHHHhc
Confidence            5688899888876664455554 4999999999999999 765

---

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	88
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	95.41
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	95.23
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	94.82
d1zyba1	73	Probable transcription regulator BT4300, C-termina	94.68
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	94.46
d1hlva1	66	DNA-binding domain of centromere binding protein B	93.27
d1l8qa1	110	Chromosomal replication initiation factor DnaA C-t	92.35
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	91.57
d1j1va_	94	Chromosomal replication initiation factor DnaA C-t	90.93
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	89.59
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	88.32
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	87.12
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	86.83
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	84.69
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	84.63
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	83.95
d1jhga_	101	Trp repressor, TrpR {Escherichia coli [TaxId: 562]	83.35
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	82.72
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	82.54
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	81.92
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	81.49

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=95.41  E-value=0.0038  Score=33.36  Aligned_cols=35  Identities=17%  Similarity=0.099  Sum_probs=31.4

Q ss_pred             hhHHHHHHHHHhccccchhhhhhhcccccchhHh-H
Q 046847           27 VDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-F   61 (88)
Q Consensus        27 veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f   61 (88)
                      .+||++-..-+++.+.+..+|+..|+.|..||.| |
T Consensus         7 t~~q~~~a~~l~~~G~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           7 NKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             CHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             CHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHhhC
Confidence            3678888888889999999999999999999988 5

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.23  E-value=0.0099  Score=33.07  Aligned_cols=39  Identities=26%  Similarity=0.320  Sum_probs=31.5

Q ss_pred             hhHHHHHHHHHhcc-------------ccchhhhhhhcccccchhHh-HHHHH
Q 046847           27 VDEQVCMFLHALAH-------------HVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        27 veE~la~FL~i~~~-------------n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      ++++||-||+.++.             +.+..++++.-+-|.+|||| +++.-
T Consensus         2 v~~Rla~~Ll~l~~~~g~~~~~~~i~l~lt~~~lA~~~G~sRetvsr~L~~l~   54 (69)
T d1i5za1           2 VTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLE   54 (69)
T ss_dssp             HHHHHHHHHHHGGGSTTCCCCSSSCEEECCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCCCCCeeecCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            56777888777653             37889999999999999999 88754

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=94.82  E-value=0.013  Score=33.30  Aligned_cols=40  Identities=23%  Similarity=0.346  Sum_probs=32.9

Q ss_pred             hhHHHHHHHHHhcc--------------ccchhhhhhhcccccchhHh-HHHHHH
Q 046847           27 VDEQVCMFLHALAH--------------HVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        27 veE~la~FL~i~~~--------------n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      ++++||=||+.++.              +.+..++++.-|-|.+||+| +++.-+
T Consensus         2 v~~Rla~~Ll~l~~~~g~~~~~~~~i~~~~t~~eiA~~lG~sretvsr~l~~l~~   56 (80)
T d1ft9a1           2 IKQRIAGFFIDHANTTGRQTQGGVIVSVDFTVEEIANLIGSSRQTTSTALNSLIK   56 (80)
T ss_dssp             HHHHHHHHHHHTCBCCCSCC--CCCCEECCCHHHHHHHHCSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCCeEEecCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            67888888877644              46788999999999999999 887654

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=94.68  E-value=0.014  Score=33.15  Aligned_cols=56  Identities=18%  Similarity=0.343  Sum_probs=40.5

Q ss_pred             cchhHHHHHHHHHhccc--------cchhhhhhhcccccchhHh-HHHHHH-HHHHhhhhhccCCC
Q 046847           25 VFVDEQVCMFLHALAHH--------VKNQTINNRFKHSGETISR-FNSILN-GVLELQHILLKSPK   80 (88)
Q Consensus        25 v~veE~la~FL~i~~~n--------~~~r~i~~~F~~S~eTisr-f~~Vl~-ai~~L~~~~ik~p~   80 (88)
                      .+++++||-||...+..        .+.+++++..|-|.+|||| +++.-+ -+++....-|..+|
T Consensus         3 ~dv~~Rla~~Ll~~~~~~~~~~~i~lt~~elA~~lg~sr~tvsr~l~~l~~~g~I~~~~~~i~I~d   68 (73)
T d1zyba1           3 LDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQDNGLIELHRKEILIPD   68 (73)
T ss_dssp             CSHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSCEEETTEEEESC
T ss_pred             CCHHHHHHHHHHHhhhhhCCCeEeecCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCEEEEcc
Confidence            46888999888766542        4788999999999999999 888754 23344444444444

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=94.46  E-value=0.017  Score=32.65  Aligned_cols=40  Identities=10%  Similarity=0.130  Sum_probs=32.4

Q ss_pred             hhHHHHHHHHHhcc-------------ccchhhhhhhcccccchhHh-HHHHHH
Q 046847           27 VDEQVCMFLHALAH-------------HVKNQTINNRFKHSGETISR-FNSILN   66 (88)
Q Consensus        27 veE~la~FL~i~~~-------------n~~~r~i~~~F~~S~eTisr-f~~Vl~   66 (88)
                      |+++||-+|+.++.             +.+..++++.-+-|.+|||| +++.-+
T Consensus         2 v~~Rla~~Ll~l~~~~g~~~~~~~i~~~lt~~eLA~~~G~sretvsr~L~~l~~   55 (81)
T d2gaua1           2 VRGRLAETLLILKENFGFENDGATLSIYLSREELATLSNMTVSNAIRTLSTFVS   55 (81)
T ss_dssp             HHHHHHHHHHHHHHHHCBCTTSSBBSCCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCCEEeecCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            67788888776553             46788999999999999999 888654

>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=93.27  E-value=0.033  Score=31.54  Aligned_cols=40  Identities=15%  Similarity=0.226  Sum_probs=33.8

Q ss_pred             CccchhHHHHHHHHHhccc-cchhhhhhhcccccchhHh-HH
Q 046847           23 SVVFVDEQVCMFLHALAHH-VKNQTINNRFKHSGETISR-FN   62 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n-~~~r~i~~~F~~S~eTisr-f~   62 (88)
                      +.++++|++.|--+.=.+. .+..+|+..||.+.+|||. .+
T Consensus         6 k~LT~~eK~~ii~~~e~g~k~sq~eIA~~fGv~~STvs~IlK   47 (66)
T d1hlva1           6 RQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILK   47 (66)
T ss_dssp             CCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHcCCcchHHHHHHHhCCChhHHHHHHH
Confidence            4589999999887776654 6999999999999999998 54

>d1l8qa1 a.4.12.2 (A:290-399) Chromosomal replication initiation factor DnaA C-terminal domain IV {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: Chromosomal replication initiation factor DnaA C-terminal domain IV
domain: Chromosomal replication initiation factor DnaA C-terminal domain IV
species: Aquifex aeolicus [TaxId: 63363]

Probab=92.35  E-value=0.11  Score=31.63  Aligned_cols=43  Identities=16%  Similarity=0.182  Sum_probs=37.4

Q ss_pred             CccchhHHHHHHHHHhccccchhhhhhhcc-cccchhHh-HHHHH
Q 046847           23 SVVFVDEQVCMFLHALAHHVKNQTINNRFK-HSGETISR-FNSIL   65 (88)
Q Consensus        23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~-~S~eTisr-f~~Vl   65 (88)
                      +.+.---++||+|-.--.+.++.+|+..|+ ++-.||.. .+.|=
T Consensus        41 ~~vv~aR~ia~yL~r~~t~~sl~~IG~~fg~rdHsTV~~a~kki~   85 (110)
T d1l8qa1          41 KRTSEARKIAMYLCRKVCSASLIEIARAFKRKDHTTVIHAIRSVE   85 (110)
T ss_dssp             SSSHHHHHHHHHHHHHHHCCCHHHHHHHSSCCCSTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCCccHHHHHHHHHH
Confidence            567777889999988888999999999996 99999998 87763

>d1j1va_ a.4.12.2 (A:) Chromosomal replication initiation factor DnaA C-terminal domain IV {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: Chromosomal replication initiation factor DnaA C-terminal domain IV
domain: Chromosomal replication initiation factor DnaA C-terminal domain IV
species: Escherichia coli [TaxId: 562]

Probab=90.93  E-value=0.14  Score=30.06  Aligned_cols=47  Identities=17%  Similarity=0.074  Sum_probs=40.5

Q ss_pred             CCccchhHHHHHHHHHhccccchhhhhhhcc-cccchhHh-HHHHHHHH
Q 046847           22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFK-HSGETISR-FNSILNGV   68 (88)
Q Consensus        22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~-~S~eTisr-f~~Vl~ai   68 (88)
                      ++.+..--++||||-.--.+.++.+|+..|| ++-.||.. .+.|=+.+
T Consensus        27 ~~~iv~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHsTV~~a~kki~~~~   75 (94)
T d1j1va_          27 SRSVARPRQMAMALAKELTNHSLPEIGDAFGGRDHTTVLHACRKIEQLR   75 (94)
T ss_dssp             CHHHHHHHHHHHHHHHHHSCCCHHHHHHHTTSCCHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHhCCCHHHHHHHhCCCCchHHHHHHHHHHHHH
Confidence            3566777899999999999999999999995 89999999 88876544

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=89.59  E-value=0.15  Score=28.52  Aligned_cols=53  Identities=13%  Similarity=0.126  Sum_probs=33.9

Q ss_pred             hhHHHHHHHHHhcc--------------ccchhhhhhhcccccchhHh-HHHHHHH-HHHhhhhhccCC
Q 046847           27 VDEQVCMFLHALAH--------------HVKNQTINNRFKHSGETISR-FNSILNG-VLELQHILLKSP   79 (88)
Q Consensus        27 veE~la~FL~i~~~--------------n~~~r~i~~~F~~S~eTisr-f~~Vl~a-i~~L~~~~ik~p   79 (88)
                      ..++||-+|+.++.              +.+..++++.-+-|.+||+| +++.-+. +++.....|..+
T Consensus         2 ~~~Rla~~L~~L~~~~g~~~~~~~~i~~~lt~~elA~~~g~sretvsr~l~~l~~~glI~~~~~~i~I~   70 (80)
T d3e5ua1           2 PTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLASLKRENILDKKKNKIIVY   70 (80)
T ss_dssp             HHHHHHHHHHHHHHHHCEEETTEEECCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC----CEES
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCCeEEeeCCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCEEEEc
Confidence            45666666665432              25678899999999999999 9987653 344444444433

>d2bgca1 a.4.5.4 (A:138-237) Listeriolysin regulatory protein PrfA, C-terminal domain {Bacteria (Listeria monocytogenes) [TaxId: 1639]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Listeriolysin regulatory protein PrfA, C-terminal domain
species: Bacteria (Listeria monocytogenes) [TaxId: 1639]

Probab=88.32  E-value=0.17  Score=30.11  Aligned_cols=25  Identities=12%  Similarity=0.189  Sum_probs=21.4

Q ss_pred             ccchhhhhhhcccc-cchhHh-HHHHH
Q 046847           41 HVKNQTINNRFKHS-GETISR-FNSIL   65 (88)
Q Consensus        41 n~~~r~i~~~F~~S-~eTisr-f~~Vl   65 (88)
                      +.+..++++..+-| .+||+| +++.=
T Consensus        31 ~lTqeeLA~~lG~s~ReTVsR~L~~L~   57 (100)
T d2bgca1          31 NLTMQELGYSSGIAHSSAVSRIISKLK   57 (100)
T ss_dssp             CCCHHHHHHHTTCCCHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHhCCchHHHHHHHHHHHH
Confidence            36889999999997 799999 88864

>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=87.12  E-value=0.091  Score=28.64  Aligned_cols=23  Identities=26%  Similarity=0.219  Sum_probs=20.6

Q ss_pred             ccchhhhhhhcccccchhHh-HHH
Q 046847           41 HVKNQTINNRFKHSGETISR-FNS   63 (88)
Q Consensus        41 n~~~r~i~~~F~~S~eTisr-f~~   63 (88)
                      |.+-++|+..-|.|..|||| ++.
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            56788999999999999999 875

>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=86.83  E-value=0.55  Score=25.11  Aligned_cols=46  Identities=13%  Similarity=0.103  Sum_probs=36.2

Q ss_pred             ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847           24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE   70 (88)
Q Consensus        24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~   70 (88)
                      .++..++-++-|+. -.+.++.+|+..+|.|..||.. .+..++.+-.
T Consensus        21 ~L~~~~r~v~~l~~-~~~~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~   67 (71)
T d1rp3a2          21 KLPEREKLVIQLIF-YEELPAKEVAKILETSVSRVSQLKAKALERLRE   67 (71)
T ss_dssp             TSCHHHHHHHHHHH-TSCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH-hHhCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            35666666665654 5779999999999999999999 8888776644

>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=84.69  E-value=0.42  Score=25.79  Aligned_cols=35  Identities=9%  Similarity=-0.023  Sum_probs=30.5

Q ss_pred             HHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           35 LHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        35 L~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      |..++.+.++..|+...+-|..||.. ...+.+-+.
T Consensus        13 l~l~~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klg   48 (65)
T d1l3la1          13 LRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFD   48 (65)
T ss_dssp             HHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             HHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            45678899999999999999999999 998877653

>d1vz0a1 a.4.14.1 (A:116-208) Putative partitioning protein ParB/Spo0J {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Putative partitioning protein ParB/Spo0J
species: Thermus thermophilus [TaxId: 274]

Probab=84.63  E-value=0.36  Score=28.30  Aligned_cols=36  Identities=11%  Similarity=0.123  Sum_probs=30.3

Q ss_pred             chhHHHHHHHHHhccccchhhhhhhcccccchhHh-HH
Q 046847           26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FN   62 (88)
Q Consensus        26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~   62 (88)
                      ++||..|.=-.+ ..+.+..+|+.++|.|..||+. ..
T Consensus         5 piEeA~a~~~L~-e~g~t~~~iA~~~Gks~~~V~~~Lr   41 (93)
T d1vz0a1           5 PVEEARGYQALL-EMGLTQEEVARRVGKARSTVANALR   41 (93)
T ss_dssp             HHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHH-HcCCCHHHHHHHHccchHHHHHHHH
Confidence            678888876554 6889999999999999999998 53

>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=83.95  E-value=0.19  Score=27.35  Aligned_cols=21  Identities=24%  Similarity=0.286  Sum_probs=18.9

Q ss_pred             chhhhhhhcccccchhHh-HHH
Q 046847           43 KNQTINNRFKHSGETISR-FNS   63 (88)
Q Consensus        43 ~~r~i~~~F~~S~eTisr-f~~   63 (88)
                      +.++|+..-|.|..|||| ++.
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            568899999999999999 985

>d1jhga_ a.4.12.1 (A:) Trp repressor, TrpR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: Trp repressor, TrpR
domain: Trp repressor, TrpR
species: Escherichia coli [TaxId: 562]

Probab=83.35  E-value=0.68  Score=27.87  Aligned_cols=42  Identities=17%  Similarity=0.199  Sum_probs=30.1

Q ss_pred             chhHHHHHHHHHhccccchhhhhhhcccccchhHhHHHHHHH
Q 046847           26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNG   67 (88)
Q Consensus        26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisrf~~Vl~a   67 (88)
                      .+..++.|+=..+....+||.|+...|.|..||+|....|+.
T Consensus        43 ~la~R~~ia~~L~~G~~s~reI~~~~gvs~aTItR~s~~Lk~   84 (101)
T d1jhga_          43 ALGTRVRIIEELLRGEMSQRELKNELGAGIATITRGSNSLKA   84 (101)
T ss_dssp             HHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCcCHHHHHHHhCCChHHHHHHHHHHHh
Confidence            344444444334445589999999999999999996666653

>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=82.72  E-value=0.56  Score=25.29  Aligned_cols=34  Identities=12%  Similarity=0.167  Sum_probs=29.3

Q ss_pred             HHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           36 HALAHHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        36 ~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      ..++.+.++.+|+...+.|..||.. ...+.+-+.
T Consensus        14 ~l~~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~   48 (67)
T d1fsea_          14 ELLVQDKTTKEIASELFISEKTVRNHISNAMQKLG   48 (67)
T ss_dssp             HHHTTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHT
T ss_pred             HHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence            4477899999999999999999999 888876553

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=82.54  E-value=0.33  Score=28.29  Aligned_cols=51  Identities=12%  Similarity=0.237  Sum_probs=35.9

Q ss_pred             HHHHhhCcCCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847           10 FELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL   65 (88)
Q Consensus        10 ~~~L~~~~~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl   65 (88)
                      .+.|+..++|.++     +-++-.+|+.-..+.+..+|+.+++.|..||++ .+...
T Consensus        10 ~~~l~~~~gLs~~-----~~~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~l~~L~   61 (109)
T d2d1ha1          10 KDEIRCCYKITDT-----DVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLI   61 (109)
T ss_dssp             HHHHHHHHTCCHH-----HHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHhcCcCHH-----HHHHHHHHHHcCCCCCHHHHHHHHCccHhHHHHHHHHHH
Confidence            3455556666544     234444555545568999999999999999999 77765

>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=81.92  E-value=0.59  Score=25.28  Aligned_cols=34  Identities=18%  Similarity=0.299  Sum_probs=29.3

Q ss_pred             HHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847           36 HALAHHVKNQTINNRFKHSGETISR-FNSILNGVL   69 (88)
Q Consensus        36 ~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~   69 (88)
                      -.++.+.++.+|+...+.|..||.. ...+++.+.
T Consensus        16 ~ll~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klg   50 (67)
T d1a04a1          16 KLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMK   50 (67)
T ss_dssp             HHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHT
T ss_pred             HHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence            3456789999999999999999999 998887654

>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=81.49  E-value=0.5  Score=25.92  Aligned_cols=32  Identities=13%  Similarity=0.148  Sum_probs=28.0

Q ss_pred             HhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847           37 ALAHHVKNQTINNRFKHSGETISR-FNSILNGV   68 (88)
Q Consensus        37 i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai   68 (88)
                      .++.+.+++.|+...+.|..||.. ...+.+.+
T Consensus        23 ~l~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl   55 (70)
T d1yioa1          23 LTIRGLMNKQIAGELGIAEVTVKVHRHNIMQKL   55 (70)
T ss_dssp             HHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHT
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence            367889999999999999999999 88887654