Psyllid ID: psy17316

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------23
Protein Sequence
MMITPELLGLLPSSNYSDGETDKAGSLTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRSTPRPPPGNLKTSR
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHcccHHHHHHHHccccHHHHHHHHHHHcHHcccccccccccccHHHHHHHHHHHHcccccHHHHHHHHccccccHHHHHHHcccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccHHHHHcccccccccccccccccccccccccHHHHHHHHHHHHcccccHHHHHHHHccccHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHccccHcccHHHccccccccHHHHHHHHHHHHcccccHHHHHHHHccccHHHHHHHHHccccEccccccccccccHHHHHHHHHHHHcccccHHHHHHHHccccccEccccEccccccccccccccccc
Coil and Loop (DISEMBL)
mmitpellgllpssnysdgetdkagsltvtktwtHEDMDAALEALRAGQMSLTKasvsygipsttLWQRAHrlgihtpkkegptkswNEEILNVALDALRagsisankaskaygptkswNEEILNVALDALRagsisankaskaygipsstLYKIARKEGirlaqpfnasptawkpedLEIALEGIRSGQTTVQRAsaeygipsgtlygrcklsrstprpppgnlktsr
Flexible Loop (DISEMBL)
mmitpellgllpssnysdgetdKAGSLTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGihtpkkegptksWNEEILNVALDALRAGSISANKaskaygptkswNEEILNVALDALRAGSisankaskaygipsSTLYKIARKEGIRLAqpfnasptawKPEDLEIALEGIrsgqttvqrasaeygipsgtlygrcklsrstprpppgnlktsr
Low Complexity Region (SEG)
MMITPELLGLLPSSNYSDGETDKAGSLTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRSTPRPPPGNLKTSR
Disordered region (IsUnstruct)
****************************VTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHT********SWNEEILNVALDALRAGSIS******AYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRS*********AEYGIPSGTLYGRC******************
Disordered Region (DISOPRED)
***T********************************DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR************************************************************************YGIPSSTLY****************************************QRASAEYGIPSGTLYG********************
Disordered Region (DISEMBL)
MMITPELLGLLPSSNYSDGETDKAGSLTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR**************
Disordered Region (DISPRO)
******************************KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSI**NKA*****PTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRST************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMITPELLGLLPSSNYSDGETDKAGSLTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRSTPRPPPGNLKTSR
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	229
345491641	657	PREDICTED: hypothetical protein LOC10012	0.820	0.286	0.625	2e-68
383864280	675	PREDICTED: uncharacterized protein LOC10	0.820	0.278	0.612	2e-67
350400311	648	PREDICTED: hypothetical protein LOC10074	0.820	0.290	0.612	1e-66
340717913	645	PREDICTED: hypothetical protein LOC10064	0.820	0.291	0.612	1e-66
58585152	652	pipsqueak [Apis mellifera] gi|3746878|gb	0.820	0.288	0.612	2e-66
380012351	648	PREDICTED: uncharacterized protein LOC10	0.820	0.290	0.612	2e-66
193683716	701	PREDICTED: hypothetical protein LOC10015	0.820	0.268	0.583	2e-66
322794753	540	hypothetical protein SINV_02021 [Solenop	0.820	0.348	0.595	3e-65
242004638	698	pipsqueak, putative [Pediculus humanus c	0.803	0.263	0.595	3e-65
332026413	517	hypothetical protein G5I_05017 [Acromyrm	0.820	0.363	0.595	3e-65

>gi|345491641|ref|XP_001607008.2| PREDICTED: hypothetical protein LOC100123373 [Nasonia vitripennis]

 Score =  264 bits (675), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 147/235 (62%), Positives = 165/235 (70%), Gaps = 47/235 (20%)

Query: 1   MMITPELLGLLPS--SNYSD-GETD------KAGSLTV-TKTWTHEDMDAALEALRAGQM 50
           MMITPELLGL+PS  S +SD GE +      ++GS    +K+WT EDMDAALEALR   M
Sbjct: 373 MMITPELLGLMPSGSSVHSDSGENNSRTHSGQSGSHHHGSKSWTQEDMDAALEALRNHDM 432

Query: 51  SLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKAS 110
           SLTKAS ++GIPSTTLWQRAHRLGI TPKK+GPTKSW++E LN ALDALR G+ISANKAS
Sbjct: 433 SLTKASATFGIPSTTLWQRAHRLGIETPKKDGPTKSWSDESLNNALDALRTGTISANKAS 492

Query: 111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNAS 170
           KA                                +GIPSSTLYKIAR+EGIRLA PFNAS
Sbjct: 493 KA--------------------------------FGIPSSTLYKIARREGIRLAAPFNAS 520

Query: 171 PTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-----LSRSTPRP 220
           PT W P DL+ ALE IRSGQT+VQRA+ EYGIPSGTLYGRCK     LSRS P P
Sbjct: 521 PTTWSPADLDRALEAIRSGQTSVQRAATEYGIPSGTLYGRCKREGIELSRSNPTP 575

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383864280|ref|XP_003707607.1| PREDICTED: uncharacterized protein LOC100880546 [Megachile rotundata]

 Score =  261 bits (666), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 144/235 (61%), Positives = 162/235 (68%), Gaps = 47/235 (20%)

Query: 1   MMITPELLGLLPS--SNYSD-GETDKAGS-------LTVTKTWTHEDMDAALEALRAGQM 50
           MMITPELLGL+PS  S +SD GE +  G           +K+WT EDMDAALEALR   M
Sbjct: 392 MMITPELLGLMPSGSSVHSDSGENNSRGHSGQSTSHHHGSKSWTQEDMDAALEALRNHDM 451

Query: 51  SLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKAS 110
           SLTKAS ++GIPSTTLWQRAHRLGI TPKK+GPTKSW++E LN AL+ALR G+ISANKAS
Sbjct: 452 SLTKASATFGIPSTTLWQRAHRLGIDTPKKDGPTKSWSDESLNNALEALRTGTISANKAS 511

Query: 111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNAS 170
           KA+                                GIPSSTLYKIAR+EGIRLA PFNAS
Sbjct: 512 KAF--------------------------------GIPSSTLYKIARREGIRLAAPFNAS 539

Query: 171 PTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-----LSRSTPRP 220
           PT W P DL+ ALE IRSGQT+VQRAS E+GIP+GTLYGRCK     LSRS P P
Sbjct: 540 PTTWSPADLDRALEAIRSGQTSVQRASTEFGIPTGTLYGRCKREGIELSRSNPTP 594

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350400311|ref|XP_003485795.1| PREDICTED: hypothetical protein LOC100749194 [Bombus impatiens]

 Score =  258 bits (659), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 144/235 (61%), Positives = 162/235 (68%), Gaps = 47/235 (20%)

Query: 1   MMITPELLGLLPS--SNYSD-GETDKAGS-------LTVTKTWTHEDMDAALEALRAGQM 50
           MMITPELLGL+PS  S +SD GE +  G           +K+WT EDMDAALEALR   M
Sbjct: 365 MMITPELLGLMPSGSSVHSDSGENNSRGHPGQSSSHHHGSKSWTQEDMDAALEALRNHDM 424

Query: 51  SLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKAS 110
           SLTKAS ++GIPSTTLWQRAHRLGI TPKK+GPTKSW++E LN AL+ALR G+ISANKAS
Sbjct: 425 SLTKASATFGIPSTTLWQRAHRLGIDTPKKDGPTKSWSDESLNSALEALRTGTISANKAS 484

Query: 111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNAS 170
           KA+                                GIPSSTLYKIAR+EGIRLA PFNAS
Sbjct: 485 KAF--------------------------------GIPSSTLYKIARREGIRLAAPFNAS 512

Query: 171 PTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-----LSRSTPRP 220
           PT W P DL+ ALE IRSGQT+VQRAS E+GIP+GTLYGRCK     LSRS P P
Sbjct: 513 PTTWSPADLDRALEAIRSGQTSVQRASTEFGIPTGTLYGRCKREGIELSRSNPTP 567

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340717913|ref|XP_003397418.1| PREDICTED: hypothetical protein LOC100649846 [Bombus terrestris]

 Score =  258 bits (659), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 144/235 (61%), Positives = 162/235 (68%), Gaps = 47/235 (20%)

Query: 1   MMITPELLGLLPS--SNYSD-GETDKAGS-------LTVTKTWTHEDMDAALEALRAGQM 50
           MMITPELLGL+PS  S +SD GE +  G           +K+WT EDMDAALEALR   M
Sbjct: 362 MMITPELLGLMPSGSSVHSDSGENNSRGHPGQSSSHHHGSKSWTQEDMDAALEALRNHDM 421

Query: 51  SLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKAS 110
           SLTKAS ++GIPSTTLWQRAHRLGI TPKK+GPTKSW++E LN AL+ALR G+ISANKAS
Sbjct: 422 SLTKASATFGIPSTTLWQRAHRLGIDTPKKDGPTKSWSDESLNSALEALRTGTISANKAS 481

Query: 111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNAS 170
           KA+                                GIPSSTLYKIAR+EGIRLA PFNAS
Sbjct: 482 KAF--------------------------------GIPSSTLYKIARREGIRLAAPFNAS 509

Query: 171 PTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-----LSRSTPRP 220
           PT W P DL+ ALE IRSGQT+VQRAS E+GIP+GTLYGRCK     LSRS P P
Sbjct: 510 PTTWSPADLDRALEAIRSGQTSVQRASTEFGIPTGTLYGRCKREGIELSRSNPTP 564

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|58585152|ref|NP_001011602.1| pipsqueak [Apis mellifera] gi|3746878|gb|AAC71015.1| pipsqueak [Apis mellifera]

 Score =  258 bits (658), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 144/235 (61%), Positives = 162/235 (68%), Gaps = 47/235 (20%)

Query: 1   MMITPELLGLLPS--SNYSD-GETDK-------AGSLTVTKTWTHEDMDAALEALRAGQM 50
           MMITPELLGL+PS  S +SD GE +        +     +K+WT EDMDAALEALR   M
Sbjct: 369 MMITPELLGLMPSGSSVHSDSGENNSRGHSGQSSSHHHGSKSWTQEDMDAALEALRNHDM 428

Query: 51  SLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKAS 110
           SLTKAS ++GIPSTTLWQRAHRLGI TPKK+GPTKSW++E LN ALDALR G+ISANKAS
Sbjct: 429 SLTKASATFGIPSTTLWQRAHRLGIDTPKKDGPTKSWSDESLNNALDALRTGTISANKAS 488

Query: 111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNAS 170
           KA+                                GIPSSTLYKIAR+EGIRLA PFNAS
Sbjct: 489 KAF--------------------------------GIPSSTLYKIARREGIRLAAPFNAS 516

Query: 171 PTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-----LSRSTPRP 220
           PT W P DL+ ALE IRSGQT+VQRAS E+GIP+GTLYGRCK     LSRS P P
Sbjct: 517 PTTWSPADLDRALEAIRSGQTSVQRASTEFGIPTGTLYGRCKREGIELSRSNPTP 571

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380012351|ref|XP_003690248.1| PREDICTED: uncharacterized protein LOC100864657 [Apis florea]

 Score =  258 bits (658), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 144/235 (61%), Positives = 162/235 (68%), Gaps = 47/235 (20%)

Query: 1   MMITPELLGLLPS--SNYSD-GETD-------KAGSLTVTKTWTHEDMDAALEALRAGQM 50
           MMITPELLGL+PS  S +SD GE +        +     +K+WT EDMDAALEALR   M
Sbjct: 365 MMITPELLGLMPSGSSVHSDSGENNSRGHSGQSSSHHHGSKSWTQEDMDAALEALRNHDM 424

Query: 51  SLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKAS 110
           SLTKAS ++GIPSTTLWQRAHRLGI TPKK+GPTKSW++E LN ALDALR G+ISANKAS
Sbjct: 425 SLTKASATFGIPSTTLWQRAHRLGIDTPKKDGPTKSWSDESLNNALDALRTGTISANKAS 484

Query: 111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNAS 170
           KA+                                GIPSSTLYKIAR+EGIRLA PFNAS
Sbjct: 485 KAF--------------------------------GIPSSTLYKIARREGIRLAAPFNAS 512

Query: 171 PTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-----LSRSTPRP 220
           PT W P DL+ ALE IRSGQT+VQRAS E+GIP+GTLYGRCK     LSRS P P
Sbjct: 513 PTTWSPADLDRALEAIRSGQTSVQRASTEFGIPTGTLYGRCKREGIELSRSNPTP 567

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193683716|ref|XP_001947249.1| PREDICTED: hypothetical protein LOC100159948 isoform 1 [Acyrthosiphon pisum] gi|328700169|ref|XP_003241167.1| PREDICTED: hypothetical protein LOC100159948 isoform 2 [Acyrthosiphon pisum]

 Score =  257 bits (657), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 136/233 (58%), Positives = 160/233 (68%), Gaps = 45/233 (19%)

Query: 1   MMITPELLGLLPSSNYSDGETDKAGSLTVTKT--------WTHEDMDAALEALRAGQMSL 52
           MMITPELLGLLP+S+ +   ++ + S  + K         WT +DM+ ALEALR+  MSL
Sbjct: 389 MMITPELLGLLPNSSNTGDVSEDSSSNNINKQYGTNGGKGWTADDMENALEALRSHNMSL 448

Query: 53  TKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKA 112
           TKAS+++GIPSTTLWQRAHR GI TPKK+                               
Sbjct: 449 TKASITFGIPSTTLWQRAHRAGIDTPKKD------------------------------- 477

Query: 113 YGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPT 172
            GP KSWN+E LN+ALDALR G+ISANKASKAYGIPSSTLYKIAR+EGIRLA PFNA+PT
Sbjct: 478 -GPAKSWNDEALNIALDALRTGTISANKASKAYGIPSSTLYKIARREGIRLAAPFNAAPT 536

Query: 173 AWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-----LSRSTPRP 220
           +W  E L+ AL  IR+GQTTVQRA+A+YGIPSGTLYGRCK     LSRS P P
Sbjct: 537 SWGQEQLDQALHAIRTGQTTVQRAAADYGIPSGTLYGRCKREKIELSRSNPTP 589

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322794753|gb|EFZ17700.1| hypothetical protein SINV_02021 [Solenopsis invicta]

 Score =  253 bits (647), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 140/235 (59%), Positives = 156/235 (66%), Gaps = 47/235 (20%)

Query: 1   MMITPELLGLLP----------SSNYSDGETDKAGSLTVTKTWTHEDMDAALEALRAGQM 50
           MMITPELLGL+P           +N        +     +K+WT EDMDAALEALR   M
Sbjct: 257 MMITPELLGLMPSGSSGQSDSGENNSRGHSGQSSSHHHGSKSWTQEDMDAALEALRNHNM 316

Query: 51  SLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKAS 110
           SLTKAS ++GIPSTTLWQRAHRLGI TPKK+GPTKSW++E LN AL+ALR GSISANKAS
Sbjct: 317 SLTKASATFGIPSTTLWQRAHRLGIDTPKKDGPTKSWSDESLNNALEALRTGSISANKAS 376

Query: 111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNAS 170
           KAY                                GIPSSTLYKIAR+EGIRLA PFNAS
Sbjct: 377 KAY--------------------------------GIPSSTLYKIARREGIRLAAPFNAS 404

Query: 171 PTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-----LSRSTPRP 220
           PT W P DL+ ALE IRSGQT+VQRAS E+GIP+GTLYGRCK     LSRS P P
Sbjct: 405 PTTWTPADLDRALEAIRSGQTSVQRASTEFGIPTGTLYGRCKREGIELSRSNPTP 459

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242004638|ref|XP_002423187.1| pipsqueak, putative [Pediculus humanus corporis] gi|212506152|gb|EEB10449.1| pipsqueak, putative [Pediculus humanus corporis]

 Score =  253 bits (647), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 140/235 (59%), Positives = 157/235 (66%), Gaps = 51/235 (21%)

Query: 1   MMITPELLGLLPSSN-------YSD---GETDKAGSLTVTKTWTHEDMDAALEALRAGQM 50
           MMITPELLGL P+S+       Y D   GE+D  G    TK WT +DM+ AL+ALR   M
Sbjct: 424 MMITPELLGLFPTSSGNSVYRKYYDLDGGESDIKG----TKNWTQDDMELALDALRNHNM 479

Query: 51  SLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKAS 110
           SLTKAS +YGIPSTTLWQRAHRLGI TPKKEG TK+W E+ LN AL+ALR G+ISANKAS
Sbjct: 480 SLTKASSTYGIPSTTLWQRAHRLGIDTPKKEGNTKNWTEDNLNSALEALRTGTISANKAS 539

Query: 111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNAS 170
           KAY                                GIPSSTLYKIAR+EGIRLA PFNA+
Sbjct: 540 KAY--------------------------------GIPSSTLYKIARREGIRLAAPFNAA 567

Query: 171 PTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-----LSRSTPRP 220
           PT W  +DLE ALE IRSGQ +VQRAS E+GIP+GTLYGRCK     LSRS P P
Sbjct: 568 PTTWTQDDLERALESIRSGQASVQRASTEFGIPTGTLYGRCKREGIELSRSNPTP 622

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332026413|gb|EGI66542.1| hypothetical protein G5I_05017 [Acromyrmex echinatior]

 Score =  253 bits (647), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 140/235 (59%), Positives = 156/235 (66%), Gaps = 47/235 (20%)

Query: 1   MMITPELLGLLP----------SSNYSDGETDKAGSLTVTKTWTHEDMDAALEALRAGQM 50
           MMITPELLGL+P           +N        +     +K+WT EDMDAALEALR   M
Sbjct: 234 MMITPELLGLMPSGSSGQSDSGENNSRGHSGQSSSHHHGSKSWTQEDMDAALEALRNHNM 293

Query: 51  SLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKAS 110
           SLTKAS ++GIPSTTLWQRAHRLGI TPKK+GPTKSW++E LN AL+ALR GSISANKAS
Sbjct: 294 SLTKASATFGIPSTTLWQRAHRLGIDTPKKDGPTKSWSDESLNNALEALRTGSISANKAS 353

Query: 111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNAS 170
           KAY                                GIPSSTLYKIAR+EGIRLA PFNAS
Sbjct: 354 KAY--------------------------------GIPSSTLYKIARREGIRLAAPFNAS 381

Query: 171 PTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-----LSRSTPRP 220
           PT W P DL+ ALE IRSGQT+VQRAS E+GIP+GTLYGRCK     LSRS P P
Sbjct: 382 PTTWTPSDLDRALEAIRSGQTSVQRASTEFGIPTGTLYGRCKREGIELSRSNPTP 436

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	229
FB|FBgn0263102	1085	psq "pipsqueak" [Drosophila me	0.480	0.101	0.730	1.7e-39
WB|WBGene00011315	433	mbr-1 [Caenorhabditis elegans	0.187	0.099	0.395	6.8e-05
UNIPROTKB|G3N278	601	LCORL "Uncharacterized protein	0.262	0.099	0.327	0.0001
UNIPROTKB|Q95YM8	1598	Mblk-1 "Mushroom body large-ty	0.196	0.028	0.333	0.00026
UNIPROTKB|F1P637	558	LCORL "Uncharacterized protein	0.244	0.100	0.333	0.00042
UNIPROTKB|D3K5M5	603	LCORL "Ligand dependent nuclea	0.244	0.092	0.333	0.0005
UNIPROTKB|F1NH98	551	LCORL "Ligand-dependent nuclea	0.244	0.101	0.333	0.00051
UNIPROTKB|Q5ZJK5	600	LCORL "Ligand-dependent nuclea	0.244	0.093	0.333	0.00063

FB|FBgn0263102 psq "pipsqueak" [Drosophila melanogaster (taxid:7227)]

 Score = 419 (152.6 bits), Expect = 1.7e-39, Sum P(2) = 1.7e-39
 Identities = 84/115 (73%), Positives = 95/115 (82%)

Query:   111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNAS 170
             K  G TKSWNE+ L  AL+ALR+G ISANKASKA+GIPSSTLYKIAR+EGIRLA PFNA+
Sbjct:   773 KKEGGTKSWNEDALQNALEALRSGQISANKASKAFGIPSSTLYKIARREGIRLAAPFNAA 832

Query:   171 PTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-----LSRSTPRP 220
             PT W PEDLE ALE IR+G T+VQ+ASAE+GIP+GTLYGRCK     LSRS P P
Sbjct:   833 PTTWTPEDLERALEAIRAGNTSVQKASAEFGIPTGTLYGRCKREGIELSRSNPTP 887

GO:0007315 "pole plasm assembly" evidence=NAS

GO:0005634 "nucleus" evidence=IDA;TAS

GO:0003677 "DNA binding" evidence=NAS;TAS

GO:0006342 "chromatin silencing" evidence=IMP

GO:0031519 "PcG protein complex" evidence=IDA

GO:0043565 "sequence-specific DNA binding" evidence=IDA

GO:0016458 "gene silencing" evidence=TAS

GO:0008595 "anterior/posterior axis specification, embryo" evidence=IMP

GO:0042048 "olfactory behavior" evidence=IMP

GO:0007476 "imaginal disc-derived wing morphogenesis" evidence=IMP

GO:0031935 "regulation of chromatin silencing" evidence=IMP

GO:0009880 "embryonic pattern specification" evidence=IMP

WB|WBGene00011315 mbr-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 89 (36.4 bits), Expect = 6.8e-05, Sum P(2) = 6.8e-05
 Identities = 17/43 (39%), Positives = 29/43 (67%)

Query:    31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL 73
             + +T ED+  A+E +R G++   +ASV YGIP +TL  + ++L
Sbjct:   152 RNYTVEDLTQAVEDIRQGKLGTRRASVVYGIPRSTLRNKIYKL 194

GO:0003677 "DNA binding" evidence=IEA

GO:0019915 "lipid storage" evidence=IMP

UNIPROTKB|G3N278 LCORL "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 95 (38.5 bits), Expect = 0.00010, Sum P(2) = 0.00010
 Identities = 20/61 (32%), Positives = 33/61 (54%)

Query:   107 NKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTL-YKIARKEGIRLAQ 165
             NK  +  G  + ++ EI+  A+  + +G +S +KA   YG+P STL YK+  + G     
Sbjct:   512 NKQPRKRGRYRQYDHEIMEEAIAMVMSGKMSVSKAQGIYGVPHSTLEYKVKERSGTLKTP 571

Query:   166 P 166
             P
Sbjct:   572 P 572

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q95YM8 Mblk-1 "Mushroom body large-type Kenyon cell-specific protein 1" [Apis mellifera (taxid:7460)]

 Score = 89 (36.4 bits), Expect = 0.00026, Sum P(2) = 0.00026
 Identities = 15/45 (33%), Positives = 31/45 (68%)

Query:    31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI 75
             + +T E++ AAL  +++G++   +A+V YGIP +TL  + ++L +
Sbjct:   589 RAYTEEELQAALRDIQSGKLGTRRAAVIYGIPRSTLRNKVYKLAM 633

GO:0005634 "nucleus" evidence=IC

GO:0007613 "memory" evidence=NAS

GO:0042803 "protein homodimerization activity" evidence=NAS

GO:0043565 "sequence-specific DNA binding" evidence=IDA

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

UNIPROTKB|F1P637 LCORL "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 89 (36.4 bits), Expect = 0.00042, Sum P(2) = 0.00042
 Identities = 19/57 (33%), Positives = 31/57 (54%)

Query:   111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTL-YKIARKEGIRLAQP 166
             K  G  + ++ EI+  A+  + +G +S +KA   YG+P STL YK+  + G     P
Sbjct:   474 KKRGRYRQYDHEIMEEAIAMVMSGKMSVSKAQGIYGVPHSTLEYKVKERSGTLKTPP 530

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|D3K5M5 LCORL "Ligand dependent nuclear receptor corepressor-like protein" [Sus scrofa (taxid:9823)]

 Score = 89 (36.4 bits), Expect = 0.00050, Sum P(2) = 0.00050
 Identities = 19/57 (33%), Positives = 31/57 (54%)

Query:   111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTL-YKIARKEGIRLAQP 166
             K  G  + ++ EI+  A+  + +G +S +KA   YG+P STL YK+  + G     P
Sbjct:   518 KKRGRYRQYDHEIMEEAIAMVMSGKMSVSKAQGIYGVPHSTLEYKVKERSGTLKTPP 574

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1NH98 LCORL "Ligand-dependent nuclear receptor corepressor-like protein" [Gallus gallus (taxid:9031)]

 Score = 89 (36.4 bits), Expect = 0.00051, Sum P(2) = 0.00051
 Identities = 19/57 (33%), Positives = 31/57 (54%)

Query:   111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTL-YKIARKEGIRLAQP 166
             K  G  + ++ EI+  A+  + +G +S +KA   YG+P STL YK+  + G     P
Sbjct:   466 KKRGRYRQYDHEIMEEAIAMVMSGKMSVSKAQGIYGVPHSTLEYKVKERSGTLKTPP 522

GO:0003677 "DNA binding" evidence=IEA

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0006366 "transcription from RNA polymerase II promoter" evidence=IEA

UNIPROTKB|Q5ZJK5 LCORL "Ligand-dependent nuclear receptor corepressor-like protein" [Gallus gallus (taxid:9031)]

 Score = 89 (36.4 bits), Expect = 0.00063, Sum P(2) = 0.00063
 Identities = 19/57 (33%), Positives = 31/57 (54%)

Query:   111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTL-YKIARKEGIRLAQP 166
             K  G  + ++ EI+  A+  + +G +S +KA   YG+P STL YK+  + G     P
Sbjct:   515 KKRGRYRQYDHEIMEEAIAMVMSGKMSVSKAQGIYGVPHSTLEYKVKERSGTLKTPP 571

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

---

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 EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	229
pfam05225	43	pfam05225, HTH_psq, helix-turn-helix, Psq domain	3e-10
pfam05225	43	pfam05225, HTH_psq, helix-turn-helix, Psq domain	2e-07
pfam05225	43	pfam05225, HTH_psq, helix-turn-helix, Psq domain	2e-07

>gnl|CDD|203213 pfam05225, HTH_psq, helix-turn-helix, Psq domain

 Score = 53.3 bits (129), Expect = 3e-10
 Identities = 22/44 (50%), Positives = 28/44 (63%), Gaps = 1/44 (2%)

Query: 36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPK 79
          ED+  ALEA+R G+MSL KA+  YGIP +TLW R  R      +
Sbjct: 1  EDLAEALEAVRNGKMSLRKAARKYGIPRSTLW-RRLRGKYSLKR 43

This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence. Length = 43

>gnl|CDD|203213 pfam05225, HTH_psq, helix-turn-helix, Psq domain

 Score = 46.0 bits (110), Expect = 2e-07
 Identities = 19/40 (47%), Positives = 26/40 (65%), Gaps = 2/40 (5%)

Query: 122 EILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGI 161
           E L  AL+A+R G +S  KA++ YGIP STL++  R  G 
Sbjct: 1   EDLAEALEAVRNGKMSLRKAARKYGIPRSTLWR--RLRGK 38

This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence. Length = 43

>gnl|CDD|203213 pfam05225, HTH_psq, helix-turn-helix, Psq domain

 Score = 46.0 bits (110), Expect = 2e-07
 Identities = 18/43 (41%), Positives = 29/43 (67%)

Query: 177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRSTPR 219
           EDL  ALE +R+G+ ++++A+ +YGIP  TL+ R +   S  R
Sbjct: 1   EDLAEALEAVRNGKMSLRKAARKYGIPRSTLWRRLRGKYSLKR 43

This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence. Length = 43

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	229
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	99.2
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	99.05
COG3415	138	Transposase and inactivated derivatives [DNA repli	99.03
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	98.93
COG3415	138	Transposase and inactivated derivatives [DNA repli	98.89
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	98.82
cd00131	128	PAX Paired Box domain	98.81
smart00351	125	PAX Paired Box domain.	98.7
COG2963	116	Transposase and inactivated derivatives [DNA repli	98.66
PF13551	112	HTH_29: Winged helix-turn helix	98.63
PF13551	112	HTH_29: Winged helix-turn helix	98.63
cd00131	128	PAX Paired Box domain	98.58
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	98.57
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	98.54
smart00351	125	PAX Paired Box domain.	98.49
PRK09413	121	IS2 repressor TnpA; Reviewed	98.47
COG2963	116	Transposase and inactivated derivatives [DNA repli	98.46
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	98.42
PRK09413	121	IS2 repressor TnpA; Reviewed	98.4
PF13518	52	HTH_28: Helix-turn-helix domain	98.4
PF13518	52	HTH_28: Helix-turn-helix domain	98.38
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	98.34
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	98.25
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	98.23
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	98.09
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	97.98
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	97.97
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	97.8
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	97.79
PF09607	58	BrkDBD: Brinker DNA-binding domain; InterPro: IPR0	97.74
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	97.73
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	97.68
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	97.65
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	97.63
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	97.63
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	97.62
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	97.56
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	97.43
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	97.41
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	97.34
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	97.32
PRK13413	200	mpi multiple promoter invertase; Provisional	97.27
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	97.24
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	97.18
PF13565	77	HTH_32: Homeodomain-like domain	97.17
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	97.14
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	97.11
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	97.1
PHA02535	581	P terminase ATPase subunit; Provisional	97.08
KOG4565|consensus	206		97.05
PF09607	58	BrkDBD: Brinker DNA-binding domain; InterPro: IPR0	97.04
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	96.97
PRK11511	127	DNA-binding transcriptional activator MarA; Provis	96.9
PRK10219	107	DNA-binding transcriptional regulator SoxS; Provis	96.89
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	96.86
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	96.81
PF12116	82	SpoIIID: Stage III sporulation protein D; InterPro	96.81
cd04788	96	HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain	96.78
PHA00675	78	hypothetical protein	96.78
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	96.77
PHA02535	581	P terminase ATPase subunit; Provisional	96.75
KOG4565|consensus	206		96.74
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	96.67
cd04788	96	HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain	96.66
cd01106	103	HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain	96.64
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	96.62
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	96.61
PF00292	125	PAX: 'Paired box' domain; InterPro: IPR001523 The	96.61
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	96.61
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	96.55
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	96.55
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	96.55
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	96.53
PRK13182	175	racA polar chromosome segregation protein; Reviewe	96.52
PF10668	60	Phage_terminase: Phage terminase small subunit; In	96.5
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	96.49
TIGR01764	49	excise DNA binding domain, excisionase family. An	96.48
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	96.46
COG2826	318	Tra8 Transposase and inactivated derivatives, IS30	96.46
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	96.43
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	96.42
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	96.38
PRK11511	127	DNA-binding transcriptional activator MarA; Provis	96.3
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	96.27
PF02042	52	RWP-RK: RWP-RK domain; InterPro: IPR003035 This do	96.25
PRK04217	110	hypothetical protein; Provisional	96.23
cd04782	97	HTH_BltR Helix-Turn-Helix DNA binding domain of th	96.22
PF13565	77	HTH_32: Homeodomain-like domain	96.22
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	96.21
cd04775	102	HTH_Cfa-like Helix-Turn-Helix DNA binding domain o	96.16
COG1342	99	Predicted DNA-binding proteins [General function p	96.16
cd01106	103	HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain	96.15
PRK13413	200	mpi multiple promoter invertase; Provisional	96.14
cd01109	113	HTH_YyaN Helix-Turn-Helix DNA binding domain of th	96.13
cd01282	112	HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding dom	96.11
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	96.1
PF12728	51	HTH_17: Helix-turn-helix domain	96.1
PF10668	60	Phage_terminase: Phage terminase small subunit; In	96.1
cd00592	100	HTH_MerR-like Helix-Turn-Helix DNA binding domain	96.07
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	96.06
cd01110	139	HTH_SoxR Helix-Turn-Helix DNA binding domain of th	96.06
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	96.05
PF13309	64	HTH_22: HTH domain	96.04
cd01109	113	HTH_YyaN Helix-Turn-Helix DNA binding domain of th	96.01
PRK11608	326	pspF phage shock protein operon transcriptional ac	95.99
cd01282	112	HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding dom	95.99
PRK15044	295	transcriptional regulator SirC; Provisional	95.98
PF07900	220	DUF1670: Protein of unknown function (DUF1670); In	95.98
PRK15186	291	AraC family transcriptional regulator; Provisional	95.97
cd00592	100	HTH_MerR-like Helix-Turn-Helix DNA binding domain	95.96
cd01110	139	HTH_SoxR Helix-Turn-Helix DNA binding domain of th	95.92
cd04775	102	HTH_Cfa-like Helix-Turn-Helix DNA binding domain o	95.91
cd01107	108	HTH_BmrR Helix-Turn-Helix DNA binding domain of th	95.91
cd04790	172	HTH_Cfa-like_unk Helix-Turn-Helix DNA binding doma	95.89
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	95.89
PRK01905	77	DNA-binding protein Fis; Provisional	95.89
PRK04217	110	hypothetical protein; Provisional	95.87
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	95.86
cd01107	108	HTH_BmrR Helix-Turn-Helix DNA binding domain of th	95.85
TIGR01764	49	excise DNA binding domain, excisionase family. An	95.85
PRK10219	107	DNA-binding transcriptional regulator SoxS; Provis	95.84
cd04785	126	HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding do	95.83
cd04780	95	HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding dom	95.82
PRK13503	278	transcriptional activator RhaS; Provisional	95.75
cd04774	96	HTH_YfmP Helix-Turn-Helix DNA binding domain of th	95.75
cd04782	97	HTH_BltR Helix-Turn-Helix DNA binding domain of th	95.74
cd04780	95	HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding dom	95.73
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	95.72
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	95.72
cd04789	102	HTH_Cfa Helix-Turn-Helix DNA binding domain of the	95.71
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	95.7
cd04773	108	HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding	95.69
cd04789	102	HTH_Cfa Helix-Turn-Helix DNA binding domain of the	95.68
cd04781	120	HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding dom	95.68
cd04781	120	HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding dom	95.66
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	95.61
PRK09978	274	DNA-binding transcriptional regulator GadX; Provis	95.61
PRK01381	99	Trp operon repressor; Provisional	95.57
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	95.56
cd01108	127	HTH_CueR Helix-Turn-Helix DNA binding domain of Cu	95.55
PRK15185	309	transcriptional regulator HilD; Provisional	95.53
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	95.52
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	95.52
cd01111	107	HTH_MerD Helix-Turn-Helix DNA binding domain of th	95.5
cd04770	123	HTH_HMRTR Helix-Turn-Helix DNA binding domain of H	95.46
cd04773	108	HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding	95.45
cd04774	96	HTH_YfmP Helix-Turn-Helix DNA binding domain of th	95.44
PRK15115	444	response regulator GlrR; Provisional	95.43
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	95.41
TIGR02043	131	ZntR Zn(II)-responsive transcriptional regulator.	95.39
cd01108	127	HTH_CueR Helix-Turn-Helix DNA binding domain of Cu	95.36
PF12116	82	SpoIIID: Stage III sporulation protein D; InterPro	95.35
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	95.34
cd04783	126	HTH_MerR1 Helix-Turn-Helix DNA binding domain of t	95.32
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	95.31
PF12728	51	HTH_17: Helix-turn-helix domain	95.31
PRK13501	290	transcriptional activator RhaR; Provisional	95.3
cd04769	116	HTH_MerR2 Helix-Turn-Helix DNA binding domain of M	95.28
PRK13182	175	racA polar chromosome segregation protein; Reviewe	95.28
PRK15043	243	transcriptional regulator MirA; Provisional	95.26
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	95.23
TIGR02043	131	ZntR Zn(II)-responsive transcriptional regulator.	95.23
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	95.21
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	95.21
cd04785	126	HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding do	95.2
TIGR02044	127	CueR Cu(I)-responsive transcriptional regulator. T	95.2
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	95.2
cd04770	123	HTH_HMRTR Helix-Turn-Helix DNA binding domain of H	95.2
cd04790	172	HTH_Cfa-like_unk Helix-Turn-Helix DNA binding doma	95.18
TIGR02044	127	CueR Cu(I)-responsive transcriptional regulator. T	95.18
PRK00430	95	fis global DNA-binding transcriptional dual regula	95.17
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	95.16
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	95.14
cd04783	126	HTH_MerR1 Helix-Turn-Helix DNA binding domain of t	95.13
PF07750	162	GcrA: GcrA cell cycle regulator; InterPro: IPR0116	95.11
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	95.1
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	95.08
PHA00675	78	hypothetical protein	95.07
cd04786	131	HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding dom	95.06
cd04769	116	HTH_MerR2 Helix-Turn-Helix DNA binding domain of M	95.05
PRK09514	140	zntR zinc-responsive transcriptional regulator; Pr	95.05
cd01111	107	HTH_MerD Helix-Turn-Helix DNA binding domain of th	95.03
PRK09393	322	ftrA transcriptional activator FtrA; Provisional	95.03
TIGR02297	287	HpaA 4-hydroxyphenylacetate catabolism regulatory	95.01
PRK09514	140	zntR zinc-responsive transcriptional regulator; Pr	95.0
PRK13502	282	transcriptional activator RhaR; Provisional	94.99
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	94.99
PRK00118	104	putative DNA-binding protein; Validated	94.98
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	94.92
PF00292	125	PAX: 'Paired box' domain; InterPro: IPR001523 The	94.91
PHA00542	82	putative Cro-like protein	94.91
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	94.89
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	94.88
PRK10572	290	DNA-binding transcriptional regulator AraC; Provis	94.87
cd04784	127	HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain	94.86
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	94.85
PRK05022	509	anaerobic nitric oxide reductase transcription reg	94.84
TIGR02047	127	CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional	94.84
PF12833	81	HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_	94.83
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	94.83
COG1342	99	Predicted DNA-binding proteins [General function p	94.83
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	94.82
TIGR02047	127	CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional	94.77
PHA02591	83	hypothetical protein; Provisional	94.77
PRK15043	243	transcriptional regulator MirA; Provisional	94.75
COG0789	124	SoxR Predicted transcriptional regulators [Transcr	94.72
PRK15121	289	right oriC-binding transcriptional activator; Prov	94.69
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	94.69
TIGR02051	124	MerR Hg(II)-responsive transcriptional regulator.	94.68
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	94.66
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	94.64
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	94.64
cd04786	131	HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding dom	94.63
TIGR02844	80	spore_III_D sporulation transcriptional regulator	94.59
TIGR01950	142	SoxR redox-sensitive transcriptional activator Sox	94.59
COG2826	318	Tra8 Transposase and inactivated derivatives, IS30	94.56
cd04776	118	HTH_GnyR Helix-Turn-Helix DNA binding domain of th	94.56
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	94.51
COG2973	103	TrpR Trp operon repressor [Transcription]	94.51
cd04787	133	HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain	94.51
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	94.47
PRK13500	312	transcriptional activator RhaR; Provisional	94.47
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	94.46
PRK09940	253	transcriptional regulator YdeO; Provisional	94.46
PRK00118	104	putative DNA-binding protein; Validated	94.42
PF07750	162	GcrA: GcrA cell cycle regulator; InterPro: IPR0116	94.41
cd04784	127	HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain	94.41
cd04776	118	HTH_GnyR Helix-Turn-Helix DNA binding domain of th	94.37
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	94.34
cd04779	134	HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding dom	94.32
PRK15002	154	redox-sensitivie transcriptional activator SoxR; P	94.3
COG5484	279	Uncharacterized conserved protein [Function unknow	94.26
TIGR02054	120	MerD mercuric resistence transcriptional repressor	94.25
cd04779	134	HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding dom	94.23
PF03683	76	UPF0175: Uncharacterised protein family (UPF0175);	94.23
PRK10227	135	DNA-binding transcriptional regulator CueR; Provis	94.22
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	94.18
PF09824	160	ArsR: ArsR transcriptional regulator; InterPro: IP	94.17
TIGR01950	142	SoxR redox-sensitive transcriptional activator Sox	94.14
TIGR02054	120	MerD mercuric resistence transcriptional repressor	94.14
PF06627	90	DUF1153: Protein of unknown function (DUF1153); In	94.14
PHA02943	165	hypothetical protein; Provisional	94.13
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	94.13
PHA00542	82	putative Cro-like protein	94.11
cd04778	219	HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding dom	94.09
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	94.07
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	94.05
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	94.02
cd04787	133	HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain	93.99
PRK15424	538	propionate catabolism operon regulatory protein Pr	93.95
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	93.88
PF03683	76	UPF0175: Uncharacterised protein family (UPF0175);	93.87
PRK10371	302	DNA-binding transcriptional regulator MelR; Provis	93.87
TIGR03734	554	PRTRC_parB PRTRC system ParB family protein. A nov	93.83
PRK01381	99	Trp operon repressor; Provisional	93.75
PF08822	165	DUF1804: Protein of unknown function (DUF1804); In	93.74
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	93.73
COG0789	124	SoxR Predicted transcriptional regulators [Transcr	93.71
PRK10227	135	DNA-binding transcriptional regulator CueR; Provis	93.68
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	93.67
PRK15002	154	redox-sensitivie transcriptional activator SoxR; P	93.53
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	93.49
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	93.47
PF13309	64	HTH_22: HTH domain	93.45
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	93.45
cd04777	107	HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding dom	93.43
PF03333	91	PapB: Adhesin biosynthesis transcription regulator	93.39
TIGR02844	80	spore_III_D sporulation transcriptional regulator	93.39
TIGR02051	124	MerR Hg(II)-responsive transcriptional regulator.	93.38
PF13556	59	HTH_30: PucR C-terminal helix-turn-helix domain; P	93.3
PF14493	91	HTH_40: Helix-turn-helix domain	93.29
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	93.26
PRK15435	353	bifunctional DNA-binding transcriptional dual regu	93.23
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	93.2
COG2207	127	AraC AraC-type DNA-binding domain-containing prote	93.19
PRK15044	295	transcriptional regulator SirC; Provisional	93.19
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	93.16
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	93.04
PRK15186	291	AraC family transcriptional regulator; Provisional	93.04
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	92.98
PHA01976	67	helix-turn-helix protein	92.97
COG2204	464	AtoC Response regulator containing CheY-like recei	92.97
PRK13501	290	transcriptional activator RhaR; Provisional	92.93
PRK11169	164	leucine-responsive transcriptional regulator; Prov	92.9
COG3311	70	AlpA Predicted transcriptional regulator [Transcri	92.89
PRK13752	144	putative transcriptional regulator MerR; Provision	92.84
COG3677	129	Transposase and inactivated derivatives [DNA repli	92.79
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	92.78
PRK13749	121	transcriptional regulator MerD; Provisional	92.75
COG5484	279	Uncharacterized conserved protein [Function unknow	92.74
cd04777	107	HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding dom	92.58
PF14493	91	HTH_40: Helix-turn-helix domain	92.53
PF13556	59	HTH_30: PucR C-terminal helix-turn-helix domain; P	92.52
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	92.51
PF08822	165	DUF1804: Protein of unknown function (DUF1804); In	92.49
PRK13752	144	putative transcriptional regulator MerR; Provision	92.48
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	92.47
PF14549	60	P22_Cro: DNA-binding transcriptional regulator Cro	92.46
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	92.43
PRK15185	309	transcriptional regulator HilD; Provisional	92.42
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	92.39
PRK09726	88	antitoxin HipB; Provisional	92.39
cd04772	99	HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding d	92.34
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	92.29
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	92.29
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	92.29
PRK06759	154	RNA polymerase factor sigma-70; Validated	92.24
PRK09863	584	putative frv operon regulatory protein; Provisiona	92.16
PRK15435	353	bifunctional DNA-binding transcriptional dual regu	92.11
PF03374	111	ANT: Phage antirepressor protein KilAC domain; Int	92.11
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	92.1
PRK13502	282	transcriptional activator RhaR; Provisional	92.09
PF04936	186	DUF658: Protein of unknown function (DUF658); Inte	92.06
PRK09685	302	DNA-binding transcriptional activator FeaR; Provis	92.01
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	92.01
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	91.99
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	91.92
PF12844	64	HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_	91.87
PRK12537	182	RNA polymerase sigma factor; Provisional	91.84
PF05930	51	Phage_AlpA: Prophage CP4-57 regulatory protein (Al	91.82
PF07900	220	DUF1670: Protein of unknown function (DUF1670); In	91.8
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	91.79
PRK11608	326	pspF phage shock protein operon transcriptional ac	91.79
PRK09940	253	transcriptional regulator YdeO; Provisional	91.77
PRK10365	441	transcriptional regulatory protein ZraR; Provision	91.77
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	91.75
PRK09393	322	ftrA transcriptional activator FtrA; Provisional	91.74
PRK10371	302	DNA-binding transcriptional regulator MelR; Provis	91.74
TIGR02297	287	HpaA 4-hydroxyphenylacetate catabolism regulatory	91.74
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	91.7
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	91.56
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	91.52
PRK13503	278	transcriptional activator RhaS; Provisional	91.52
PF12833	81	HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_	91.51
PRK10572	290	DNA-binding transcriptional regulator AraC; Provis	91.51
PRK01905	77	DNA-binding protein Fis; Provisional	91.37
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	91.32
COG2207	127	AraC AraC-type DNA-binding domain-containing prote	91.32
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	91.28
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	91.26
COG2944	104	Predicted transcriptional regulator [Transcription	91.26
PRK13749	121	transcriptional regulator MerD; Provisional	91.19
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	91.18
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	91.16
PF00126	60	HTH_1: Bacterial regulatory helix-turn-helix prote	91.13
PRK10072	96	putative transcriptional regulator; Provisional	91.12
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	91.1
PRK09978	274	DNA-binding transcriptional regulator GadX; Provis	91.08
cd04772	99	HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding d	90.95
PF05344	65	DUF746: Domain of Unknown Function (DUF746); Inter	90.77
cd04778	219	HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding dom	90.74
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	90.67
PRK15340	216	transcriptional regulator InvF; Provisional	90.66
COG2901	98	Fis Factor for inversion stimulation Fis, transcri	90.65
PF12298	172	Bot1p: Eukaryotic mitochondrial regulator protein	90.63
PRK06759	154	RNA polymerase factor sigma-70; Validated	90.61
PRK15418	318	transcriptional regulator LsrR; Provisional	90.61
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	90.55
PRK12525	168	RNA polymerase sigma factor; Provisional	90.53
PRK10130	350	transcriptional regulator EutR; Provisional	90.5
COG2973	103	TrpR Trp operon repressor [Transcription]	90.49
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	90.44
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	90.43
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	90.4
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	90.37
PRK12547	164	RNA polymerase sigma factor; Provisional	90.37
PRK10072	96	putative transcriptional regulator; Provisional	90.36
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	90.25
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	90.22
PRK11924	179	RNA polymerase sigma factor; Provisional	90.21
PHA00738	108	putative HTH transcription regulator	90.1
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	90.1
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	90.1
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	90.07
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	90.07
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	90.05
TIGR02366	176	DHAK_reg probable dihydroxyacetone kinase regulato	90.04
PRK15115	444	response regulator GlrR; Provisional	89.97
PRK06474	178	hypothetical protein; Provisional	89.87
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	89.87
PF00376	38	MerR: MerR family regulatory protein; InterPro: IP	89.86
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	89.8
PF12759	46	HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR	89.8
PF05930	51	Phage_AlpA: Prophage CP4-57 regulatory protein (Al	89.79
PF06627	90	DUF1153: Protein of unknown function (DUF1153); In	89.79
PRK12520	191	RNA polymerase sigma factor; Provisional	89.77
PRK09047	161	RNA polymerase factor sigma-70; Validated	89.76
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	89.75
PHA02591	83	hypothetical protein; Provisional	89.75
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	89.73
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	89.72
TIGR02607	78	antidote_HigA addiction module antidote protein, H	89.69
PRK13919	186	putative RNA polymerase sigma E protein; Provision	89.68
PRK12528	161	RNA polymerase sigma factor; Provisional	89.68
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	89.62
PRK09415	179	RNA polymerase factor sigma C; Reviewed	89.61
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	89.57
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	89.48
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	89.46
PF07638	185	Sigma70_ECF: ECF sigma factor	89.46
PRK12543	179	RNA polymerase sigma factor; Provisional	89.41
PRK12540	182	RNA polymerase sigma factor; Provisional	89.39
PRK12532	195	RNA polymerase sigma factor; Provisional	89.37
TIGR00637	99	ModE_repress ModE molybdate transport repressor do	89.36
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	89.36
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	89.36
PRK15121	289	right oriC-binding transcriptional activator; Prov	89.36
PRK12539	184	RNA polymerase sigma factor; Provisional	89.27
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	89.27
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	89.25
PRK10365	441	transcriptional regulatory protein ZraR; Provision	89.24
PRK05602	186	RNA polymerase sigma factor; Reviewed	89.23
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	89.22
PRK12527	159	RNA polymerase sigma factor; Reviewed	89.21
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	89.21
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	89.21
PRK12514	179	RNA polymerase sigma factor; Provisional	89.19
PRK13500	312	transcriptional activator RhaR; Provisional	89.16
PRK12511	182	RNA polymerase sigma factor; Provisional	89.15
PRK12528	161	RNA polymerase sigma factor; Provisional	89.11
PF02042	52	RWP-RK: RWP-RK domain; InterPro: IPR003035 This do	89.08
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	89.08
COG1710	139	Uncharacterized protein conserved in archaea [Func	89.06
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	88.98
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	88.93
PRK12536	181	RNA polymerase sigma factor; Provisional	88.9
COG3877	122	Uncharacterized protein conserved in bacteria [Fun	88.86
PF14549	60	P22_Cro: DNA-binding transcriptional regulator Cro	88.84
PF00440	47	TetR_N: Bacterial regulatory proteins, tetR family	88.83
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	88.82
PRK12529	178	RNA polymerase sigma factor; Provisional	88.82
PRK15340	216	transcriptional regulator InvF; Provisional	88.77
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	88.77
PRK12530	189	RNA polymerase sigma factor; Provisional	88.74
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	88.74
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	88.71
PRK11169	164	leucine-responsive transcriptional regulator; Prov	88.69
PRK12519	194	RNA polymerase sigma factor; Provisional	88.65
PRK12529	178	RNA polymerase sigma factor; Provisional	88.62
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	88.61
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	88.59
PRK12516	187	RNA polymerase sigma factor; Provisional	88.56
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	88.56
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	88.54
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	88.53
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	88.51
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	88.51
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	88.47
PRK12514	179	RNA polymerase sigma factor; Provisional	88.47
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	88.41
PRK12541	161	RNA polymerase sigma factor; Provisional	88.4
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	88.36
PRK00430	95	fis global DNA-binding transcriptional dual regula	88.34
COG3413	215	Predicted DNA binding protein [General function pr	88.32
PRK12533	216	RNA polymerase sigma factor; Provisional	88.29
COG1961	222	PinR Site-specific recombinases, DNA invertase Pin	88.28
PRK09047	161	RNA polymerase factor sigma-70; Validated	88.26
PRK12547	164	RNA polymerase sigma factor; Provisional	88.22
PRK12519	194	RNA polymerase sigma factor; Provisional	88.19
PRK12523	172	RNA polymerase sigma factor; Reviewed	88.18
PRK11050	152	manganese transport regulator MntR; Provisional	88.16
PRK12542	185	RNA polymerase sigma factor; Provisional	88.13
PRK12524	196	RNA polymerase sigma factor; Provisional	88.05
COG1522	154	Lrp Transcriptional regulators [Transcription]	88.04
PRK12526	206	RNA polymerase sigma factor; Provisional	87.98
PF12298	172	Bot1p: Eukaryotic mitochondrial regulator protein	87.98
PRK12537	182	RNA polymerase sigma factor; Provisional	87.98
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	87.96
PRK12530	189	RNA polymerase sigma factor; Provisional	87.88
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	87.87
COG1710	139	Uncharacterized protein conserved in archaea [Func	87.85
PRK12527	159	RNA polymerase sigma factor; Reviewed	87.85
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	87.8
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	87.8
PRK08301	234	sporulation sigma factor SigE; Reviewed	87.67
PF00126	60	HTH_1: Bacterial regulatory helix-turn-helix prote	87.63
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	87.62
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	87.57
PF11198	180	DUF2857: Protein of unknown function (DUF2857); In	87.54
PRK12516	187	RNA polymerase sigma factor; Provisional	87.53
PRK10130	350	transcriptional regulator EutR; Provisional	87.51
PRK09685	302	DNA-binding transcriptional activator FeaR; Provis	87.44
PRK12522	173	RNA polymerase sigma factor; Provisional	87.43
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	87.38
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	87.34
PRK03975	141	tfx putative transcriptional regulator; Provisiona	87.34
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	87.33
PF07638	185	Sigma70_ECF: ECF sigma factor	87.33
PRK10783	456	mltD membrane-bound lytic murein transglycosylase	87.3
PRK05602	186	RNA polymerase sigma factor; Reviewed	87.29
PRK12542	185	RNA polymerase sigma factor; Provisional	87.29
PRK12512	184	RNA polymerase sigma factor; Provisional	87.27
PRK06811	189	RNA polymerase factor sigma-70; Validated	87.26
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	87.24
PRK12540	182	RNA polymerase sigma factor; Provisional	87.22
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	87.18
cd00093	58	HTH_XRE Helix-turn-helix XRE-family like proteins.	87.17
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	87.13
PRK12525	168	RNA polymerase sigma factor; Provisional	87.12
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	87.1

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

Probab=99.20  E-value=2.2e-10  Score=90.02  Aligned_cols=90  Identities=18%  Similarity=0.378  Sum_probs=69.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh--CCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHH
Q psy17316        118 SWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE--GIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQR  195 (229)
Q Consensus       118 kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~--g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~e  195 (229)
                      .||.|++..+|..+..|+ |..+||..|+|+.+|+++|+++.  |-....|.  ..++.+.++..+.|+.  +.+.++.|
T Consensus         2 aYS~DlR~rVl~~~~~g~-s~~eaa~~F~VS~~Tv~~W~k~~~~G~~~~k~r--~~~Kid~~~L~~~v~~--~pd~tl~E   76 (119)
T PF01710_consen    2 AYSLDLRQRVLAYIEKGK-SIREAAKRFGVSRNTVYRWLKRKETGDLEPKPR--GRKKIDRDELKALVEE--NPDATLRE   76 (119)
T ss_pred             CCCHHHHHHHHHHHHccc-hHHHHHHHhCcHHHHHHHHHHhccccccccccc--ccccccHHHHHHHHHH--CCCcCHHH
Confidence            699999999999888877 99999999999999999999843  32211121  1115554444444443  36688999


Q ss_pred             HHHHhCCChHHHHHHHH
Q psy17316        196 ASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       196 AA~~fgVp~~tv~~~vk  212 (229)
                      .|.+|||+.+||+..++
T Consensus        77 la~~l~Vs~~ti~~~Lk   93 (119)
T PF01710_consen   77 LAERLGVSPSTIWRALK   93 (119)
T ss_pred             HHHHcCCCHHHHHHHHH
Confidence            99999999999999998

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

>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=99.05  E-value=3e-10  Score=74.71  Aligned_cols=39  Identities=44%  Similarity=0.753  Sum_probs=33.3

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      |+|+|.+||++|.+|++|+++||+.||||++||+++++.
T Consensus         1 tee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g   39 (45)
T PF05225_consen    1 TEEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLRG   39 (45)
T ss_dssp             -HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            689999999999999999999999999999999998874

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.

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

Probab=99.03  E-value=2.6e-09  Score=86.13  Aligned_cols=110  Identities=24%  Similarity=0.400  Sum_probs=86.3

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccC-CCCCCCCCCCHHHHHHHHHHHHhCCC
Q psy17316        116 TKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQ-PFNASPTAWKPEDLEIALEGIRSGQT  191 (229)
Q Consensus       116 ~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~-~~~~~~r~~t~e~r~eaV~~~~~~~~  191 (229)
                      ++.|+.+.+..++..+.-+++|.++||++|||+.+|+|+|++++   |..+.. +..+++++.+++++..+++.|..+..
T Consensus         2 ~k~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~w   81 (138)
T COG3415           2 AKPFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKDW   81 (138)
T ss_pred             CchhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhcccc
Confidence            35677888888888888888899999999999999999999876   544221 24577889999999999999999988


Q ss_pred             cHHHH----HHHhCCChH--HHHHHHH-----hhcCCCCCCCCCC
Q psy17316        192 TVQRA----SAEYGIPSG--TLYGRCK-----LSRSTPRPPPGNL  225 (229)
Q Consensus       192 s~~eA----A~~fgVp~~--tv~~~vk-----~~~~~~~~~~~~~  225 (229)
                      +..+.    ..+|||.|.  .|+.+++     ...+-..|...|.
T Consensus        82 Tl~~~~~~l~~e~gv~y~~~~v~~~l~~~GlsykK~~~~~~~~~~  126 (138)
T COG3415          82 TLKELVEELGLEFGVWYHASAVRRLLHELGLSYKKPRWTPAERDE  126 (138)
T ss_pred             hHHHHHHHHhhhcCeEEeHHHHHHHHHHcCCCcCCCCCCccccCh
Confidence            87666    668999999  8999998     3344444444443

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

Probab=98.93  E-value=1.3e-08  Score=79.88  Aligned_cols=100  Identities=12%  Similarity=0.247  Sum_probs=72.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhh
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASK  111 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~  111 (229)
                      .||.|-...+|..+.. |.|.++||+.|||+++||++|+++..........+.                           
T Consensus         2 aYS~DlR~rVl~~~~~-g~s~~eaa~~F~VS~~Tv~~W~k~~~~G~~~~k~r~---------------------------   53 (119)
T PF01710_consen    2 AYSLDLRQRVLAYIEK-GKSIREAAKRFGVSRNTVYRWLKRKETGDLEPKPRG---------------------------   53 (119)
T ss_pred             CCCHHHHHHHHHHHHc-cchHHHHHHHhCcHHHHHHHHHHhcccccccccccc---------------------------
Confidence            4888989999976656 559999999999999999999996443221111110                           


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccC
Q psy17316        112 AYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQ  165 (229)
Q Consensus       112 ~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~  165 (229)
                         .. +.+.+.+.+-|+.  +...++.++|..|||+.+||++.+++.|+..+.
T Consensus        54 ---~~-Kid~~~L~~~v~~--~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t~KK  101 (119)
T PF01710_consen   54 ---RK-KIDRDELKALVEE--NPDATLRELAERLGVSPSTIWRALKRLGITRKK  101 (119)
T ss_pred             ---cc-cccHHHHHHHHHH--CCCcCHHHHHHHcCCCHHHHHHHHHHcCchhcc
Confidence               01 2233333444444  456799999999999999999999999976653

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

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

Probab=98.89  E-value=2.9e-08  Score=80.09  Aligned_cols=110  Identities=16%  Similarity=0.319  Sum_probs=84.5

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhh
Q psy17316         30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKA  109 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~  109 (229)
                      +..++.+....++..+.-+|||.++||++|||+.+|+++|++++.-.|.. +..+                         
T Consensus         2 ~k~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~-l~~~-------------------------   55 (138)
T COG3415           2 AKPFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLD-LPPK-------------------------   55 (138)
T ss_pred             CchhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhcccccc-ccCc-------------------------
Confidence            45778888888888888899999999999999999999999998766544 2210                         


Q ss_pred             hhccCCCCCCCHHHHHHHHHHHHcCCCCHHHH----HHHhCCChH--HHHHHHHHhCCcccCC
Q psy17316        110 SKAYGPTKSWNEEILNVALDALRAGSISANKA----SKAYGIPSS--TLYKIARKEGIRLAQP  166 (229)
Q Consensus       110 ~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~----a~k~gIp~s--TL~~~ik~~g~k~~~~  166 (229)
                       ...|++.+-+++.+...++.+.....++.++    ..+|||..+  .|++++++.|+....|
T Consensus        56 -~~~GrP~kl~~~q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~~v~~~l~~~GlsykK~  117 (138)
T COG3415          56 -PRKGRPRKLSEEQLEILLERLREKDWTLKELVEELGLEFGVWYHASAVRRLLHELGLSYKKP  117 (138)
T ss_pred             -cCCCCCcccCHHHHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHHHHHHHHHHcCCCcCCC
Confidence             1235666777777666666666666666666    568999986  5999999999888754

>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=98.82  E-value=8e-09  Score=67.88  Aligned_cols=39  Identities=44%  Similarity=0.652  Sum_probs=32.7

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHH
Q psy17316        120 NEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARK  158 (229)
Q Consensus       120 s~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~  158 (229)
                      ++|.+++||++|.+|++|++++|++||||++||+++++.
T Consensus         1 tee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g   39 (45)
T PF05225_consen    1 TEEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLRG   39 (45)
T ss_dssp             -HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            578899999999999999999999999999999988764

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.

>cd00131 PAX Paired Box domain

Probab=98.81  E-value=1.5e-07  Score=74.89  Aligned_cols=104  Identities=10%  Similarity=0.085  Sum_probs=74.9

Q ss_pred             hhhccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccCCCCC-CCCCCCHHHHHHHHH
Q psy17316        109 ASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQPFNA-SPTAWKPEDLEIALE  184 (229)
Q Consensus       109 ~~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~~~~~-~~r~~t~e~r~eaV~  184 (229)
                      .+..+-..+-||.+.+.++|.++.+|. |..+||++|||+.+|+++|++++   |--...+..+ +++..+++....+++
T Consensus         8 ~~~~~~m~~~lS~d~R~rIv~~~~~G~-s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~   86 (128)
T cd00131           8 LGGVFVNGRPLPDSIRQRIVELAQSGI-RPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEI   86 (128)
T ss_pred             CCccccCCCcCCHHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHH
Confidence            333333468899999999999998665 99999999999999999999875   3211122222 255556655555665


Q ss_pred             HHHh-CCCcHHHHHHHh---CC-------ChHHHHHHHHh
Q psy17316        185 GIRS-GQTTVQRASAEY---GI-------PSGTLYGRCKL  213 (229)
Q Consensus       185 ~~~~-~~~s~~eAA~~f---gV-------p~~tv~~~vk~  213 (229)
                      ++.+ ...+..|.+..+   ||       |.+||.++++.
T Consensus        87 ~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~  126 (128)
T cd00131          87 YKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN  126 (128)
T ss_pred             HHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence            5555 457888888875   56       99999999874

>smart00351 PAX Paired Box domain

Probab=98.70  E-value=4.2e-07  Score=72.04  Aligned_cols=96  Identities=9%  Similarity=0.101  Sum_probs=70.0

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccCCCCC-CCCCCCHHHHHHHHHHHHh-CC
Q psy17316        116 TKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQPFNA-SPTAWKPEDLEIALEGIRS-GQ  190 (229)
Q Consensus       116 ~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~~~~~-~~r~~t~e~r~eaV~~~~~-~~  190 (229)
                      ...|+.+.+.++|.++.+|. |..+||++|||+.+|+++|++++   |.....|..+ +++..+++....|++.+.+ ..
T Consensus        15 ~~~~s~~~R~riv~~~~~G~-s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~   93 (125)
T smart00351       15 GRPLPDEERQRIVELAQNGV-RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPG   93 (125)
T ss_pred             CCCCCHHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCC
Confidence            45699999999999998665 99999999999999999999876   4322222222 4566666556666666555 45


Q ss_pred             CcHHHHHHHh---CC-------ChHHHHHHHH
Q psy17316        191 TTVQRASAEY---GI-------PSGTLYGRCK  212 (229)
Q Consensus       191 ~s~~eAA~~f---gV-------p~~tv~~~vk  212 (229)
                      .+..+++..+   ||       |.+|+.+|++
T Consensus        94 ~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l~  125 (125)
T smart00351       94 IFAWEIRDRLLSEGVCDKDNVPSVSSINRILR  125 (125)
T ss_pred             CCHHHHHHHHHHcCCCcCCCCCChhhHHHhhC
Confidence            8888887655   33       7888888763

>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=98.66  E-value=1.7e-07  Score=72.75  Aligned_cols=91  Identities=14%  Similarity=0.157  Sum_probs=65.9

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCC-ChHHHHHHHHHhCCc--ccCCCCCCCCCCCHHHHHHHHHHHHhCCCc
Q psy17316        116 TKSWNEEILNVALDALRAGSISANKASKAYGI-PSSTLYKIARKEGIR--LAQPFNASPTAWKPEDLEIALEGIRSGQTT  192 (229)
Q Consensus       116 ~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gI-p~sTL~~~ik~~g~k--~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s  192 (229)
                      +.+||+|||++||+++++++.|+.++|++||| +.++||+|++.+...  ...+.....+.+++++..++++.+...+.+
T Consensus         5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~e~   84 (116)
T COG2963           5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAFSGKGKTVSYDAEEILRLRKLAELREES   84 (116)
T ss_pred             cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcccccccCccccCCcCHHHHHHHHHHHHHHHHH
Confidence            67899999999999999988899999999996 999999999865221  111111234577888888887744444455


Q ss_pred             HHHHHHHhCCChHH
Q psy17316        193 VQRASAEYGIPSGT  206 (229)
Q Consensus       193 ~~eAA~~fgVp~~t  206 (229)
                      .......+.+....
T Consensus        85 ~il~~~~~~~~~~~   98 (116)
T COG2963          85 DILKKAAFYLANAG   98 (116)
T ss_pred             HHHHHHHHHHHhch
Confidence            55555555555543

>PF13551 HTH_29: Winged helix-turn helix

Probab=98.63  E-value=3.4e-07  Score=69.42  Aligned_cols=97  Identities=18%  Similarity=0.230  Sum_probs=63.2

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCC
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKS  118 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~k  118 (229)
                      ..+|.++.+|..++.+||+.+||++.|+++|+++|.-.|......                         .....|.+.+
T Consensus         2 ~~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~-------------------------~~~~~g~~~~   56 (112)
T PF13551_consen    2 AQILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLP-------------------------RKPRGGRPRK   56 (112)
T ss_pred             HHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHh-------------------------ccccCCCCCC
Confidence            356777777553599999999999999999999985544222110                         0011223333


Q ss_pred             -CCHHHHHHHHHHHHcC------CCCHHHHHHHh-------CCChHHHHHHHHHhC
Q psy17316        119 -WNEEILNVALDALRAG------SISANKASKAY-------GIPSSTLYKIARKEG  160 (229)
Q Consensus       119 -Ys~e~k~~AV~~~~~g------~~S~~~~a~k~-------gIp~sTL~~~ik~~g  160 (229)
                       .+++.....++.+.+.      ..+...++...       .++.+|+++|+++.|
T Consensus        57 ~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~~G  112 (112)
T PF13551_consen   57 RLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILKRAG  112 (112)
T ss_pred             CCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHHHCc
Confidence             5566666666666542      35677776643       678889999998765

>PF13551 HTH_29: Winged helix-turn helix

Probab=98.63  E-value=3.9e-07  Score=69.14  Aligned_cols=88  Identities=19%  Similarity=0.233  Sum_probs=69.3

Q ss_pred             HHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccCC---CCCCCCC-CCHHHHHHHHHHHHhCC------C
Q psy17316        125 NVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQP---FNASPTA-WKPEDLEIALEGIRSGQ------T  191 (229)
Q Consensus       125 ~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~~---~~~~~r~-~t~e~r~eaV~~~~~~~------~  191 (229)
                      .+++.++.+|..+..+||+.+||+..|+++|++++   |+....+   ..++++. .+++.+..+++++.++.      .
T Consensus         2 ~~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~   81 (112)
T PF13551_consen    2 AQILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRW   81 (112)
T ss_pred             HHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcc
Confidence            46778888887449999999999999999999875   4322222   2344555 79999999999999863      6


Q ss_pred             cHHHHHHHh-------CCChHHHHHHHH
Q psy17316        192 TVQRASAEY-------GIPSGTLYGRCK  212 (229)
Q Consensus       192 s~~eAA~~f-------gVp~~tv~~~vk  212 (229)
                      +..+++..+       .||.+||++|++
T Consensus        82 t~~~l~~~l~~~~~~~~~s~~ti~r~L~  109 (112)
T PF13551_consen   82 TLEELAEWLIEEEFGIDVSPSTIRRILK  109 (112)
T ss_pred             cHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence            788888755       899999999987

>cd00131 PAX Paired Box domain

Probab=98.58  E-value=1.5e-06  Score=69.17  Aligned_cols=103  Identities=11%  Similarity=0.068  Sum_probs=69.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhh
Q psy17316         27 LTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISA  106 (229)
Q Consensus        27 ~~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~  106 (229)
                      -..-+.||.+....+|.++. +|+|.++||+++||+++|+++|+++|.-.|.-..++                       
T Consensus        12 ~~m~~~lS~d~R~rIv~~~~-~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~-----------------------   67 (128)
T cd00131          12 FVNGRPLPDSIRQRIVELAQ-SGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGA-----------------------   67 (128)
T ss_pred             ccCCCcCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCC-----------------------
Confidence            34458899999999998886 578999999999999999999999985443211110                       


Q ss_pred             hhhhhccCC-CCCCCHHHHHHHHHHH-HcCCCCHHHHHHHh---CC-------ChHHHHHHHHH
Q psy17316        107 NKASKAYGP-TKSWNEEILNVALDAL-RAGSISANKASKAY---GI-------PSSTLYKIARK  158 (229)
Q Consensus       107 ~~~~~~~G~-~~kYs~e~k~~AV~~~-~~g~~S~~~~a~k~---gI-------p~sTL~~~ik~  158 (229)
                           ..|. +.+.+++.....+..+ .+...++.++++.+   ||       +.+|+.++.++
T Consensus        68 -----~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~  126 (128)
T cd00131          68 -----IGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN  126 (128)
T ss_pred             -----CCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence                 0011 2222332222222222 45667888888774   55       88999998764

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

Probab=98.57  E-value=4.7e-08  Score=69.91  Aligned_cols=47  Identities=17%  Similarity=0.251  Sum_probs=38.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         28 TVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        28 ~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      ..++.||.|+++.+|..+..+|.|+.++|++|||+.+||++|++++.
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~   48 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR   48 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence            35689999999999999988899999999999999999999999984

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

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

Probab=98.54  E-value=1e-07  Score=68.11  Aligned_cols=54  Identities=26%  Similarity=0.308  Sum_probs=40.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhcCCCCCCC
Q psy17316        169 ASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRSTPRPPP  222 (229)
Q Consensus       169 ~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~~~~~~~~  222 (229)
                      .+.+.||+||+..||+.+..++.++.++|..|||+.+|||+|++..+.|....+
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~~~~~~~~   55 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYREGQSAFP   55 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH--STT-S
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHhcCCCCCC
Confidence            456899999999999999888899999999999999999999996555554444

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

>smart00351 PAX Paired Box domain

Probab=98.49  E-value=2.2e-06  Score=67.84  Aligned_cols=48  Identities=8%  Similarity=-0.009  Sum_probs=41.8

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         28 TVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        28 ~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      ...+.|+.|....+|.++. +|+|..+||+++||+++|+++|+++|.-.
T Consensus        13 ~~~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~~   60 (125)
T smart00351       13 VNGRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYET   60 (125)
T ss_pred             cCCCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence            3346799999999999887 57799999999999999999999998443

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=98.47  E-value=3.9e-07  Score=71.65  Aligned_cols=49  Identities=10%  Similarity=0.104  Sum_probs=45.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         28 TVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        28 ~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      ..+++||.|.+..+|..+.++|.|+.++|++|||+.+||++|+++|...
T Consensus         8 ~~rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~~   56 (121)
T PRK09413          8 EKRRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQEG   56 (121)
T ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhhc
Confidence            4578999999999999999999999999999999999999999998543

>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=98.46  E-value=1.1e-06  Score=68.14  Aligned_cols=46  Identities=20%  Similarity=0.268  Sum_probs=43.3

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCC-ChhhHHHHHHHhCC
Q psy17316         30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGI-PSTTLWQRAHRLGI   75 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gI-p~sTL~~~i~~~gi   75 (229)
                      +++||.|+++++|+++.++|.|+.++|++||| +.++|++|++++.-
T Consensus         5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~   51 (116)
T COG2963           5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQK   51 (116)
T ss_pred             cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHH
Confidence            78999999999999999999999999999995 99999999998744

>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=98.42  E-value=3.4e-07  Score=59.89  Aligned_cols=43  Identities=21%  Similarity=0.414  Sum_probs=37.4

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHH
Q psy17316        114 GPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIAR  157 (229)
Q Consensus       114 G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik  157 (229)
                      |++++++++...++++++.+| +|+.+||+.|||+++|||++.+
T Consensus         1 GRp~~~~~~~~~~i~~l~~~G-~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen    1 GRPPKLSKEQIEEIKELYAEG-MSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             SSSSSSSHCCHHHHHHHHHTT---HHHHHHHTTS-HHHHHHHHC
T ss_pred             CcCCCCCHHHHHHHHHHHHCC-CCHHHHHHHHCcCHHHHHHHHh
Confidence            688999999999999999999 6999999999999999999764

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 ....

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=98.40  E-value=6.8e-07  Score=70.29  Aligned_cols=45  Identities=11%  Similarity=0.044  Sum_probs=41.8

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        170 SPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       170 ~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      +.+.||.||+.+||+.+..++.++.++|.+|||+++|||+|++..
T Consensus         9 ~rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y   53 (121)
T PRK09413          9 KRRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQY   53 (121)
T ss_pred             CCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            357899999999999999999999999999999999999999943

>PF13518 HTH_28: Helix-turn-helix domain

Probab=98.40  E-value=5.8e-07  Score=59.54  Aligned_cols=42  Identities=21%  Similarity=0.383  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccC
Q psy17316        123 ILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQ  165 (229)
Q Consensus       123 ~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~  165 (229)
                      ++.++|++|++|. |+.++|++|||+.+||++|++.+   |+..+.
T Consensus         1 ~r~~iv~~~~~g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~~~l~   45 (52)
T PF13518_consen    1 FRLQIVELYLEGE-SVREIAREFGISRSTVYRWIKRYREGGIEGLK   45 (52)
T ss_pred             CHHHHHHHHHcCC-CHHHHHHHHCCCHhHHHHHHHHHHhcCHHHhc
Confidence            3688999999988 99999999999999999999865   554444

>PF13518 HTH_28: Helix-turn-helix domain

Probab=98.38  E-value=3.9e-07  Score=60.37  Aligned_cols=43  Identities=16%  Similarity=0.202  Sum_probs=36.9

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCC
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKE   81 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~   81 (229)
                      ++++|+++.+|. |+.++|++|||+++||++|+++|...|+.++
T Consensus         2 r~~iv~~~~~g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~~~l   44 (52)
T PF13518_consen    2 RLQIVELYLEGE-SVREIAREFGISRSTVYRWIKRYREGGIEGL   44 (52)
T ss_pred             HHHHHHHHHcCC-CHHHHHHHHCCCHhHHHHHHHHHHhcCHHHh
Confidence            678999999866 9999999999999999999999866554443

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

Probab=98.34  E-value=3.7e-07  Score=60.37  Aligned_cols=46  Identities=15%  Similarity=0.240  Sum_probs=26.3

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCC
Q psy17316         34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKK   80 (229)
Q Consensus        34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~   80 (229)
                      +.+.+..+|.++.+ |.|..+||+.+|||++|+++|+++|.-.|+.+
T Consensus         3 ~~~~R~~ii~l~~~-G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~~g   48 (50)
T PF13384_consen    3 SEERRAQIIRLLRE-GWSIREIAKRLGVSRSTVYRWIKRYREEGLEG   48 (50)
T ss_dssp             -------HHHHHHH-T--HHHHHHHHTS-HHHHHHHHT---------
T ss_pred             chhHHHHHHHHHHC-CCCHHHHHHHHCcCHHHHHHHHHHcccccccc
Confidence            56778899999998 77999999999999999999999986555443

>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=98.25  E-value=2.2e-06  Score=58.09  Aligned_cols=44  Identities=18%  Similarity=0.247  Sum_probs=35.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         28 TVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        28 ~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..+..+|.++++++|+.+.+|. |..++|++|||+++||++|++.
T Consensus         2 rkR~~LTl~eK~~iI~~~e~g~-s~~~ia~~fgv~~sTv~~I~K~   45 (53)
T PF04218_consen    2 RKRKSLTLEEKLEIIKRLEEGE-SKRDIAREFGVSRSTVSTILKN   45 (53)
T ss_dssp             SSSSS--HHHHHHHHHHHHCTT--HHHHHHHHT--CCHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHHh
Confidence            4578899999999999997766 9999999999999999999984

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.

>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=98.23  E-value=1.5e-06  Score=56.89  Aligned_cols=43  Identities=19%  Similarity=0.359  Sum_probs=35.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        169 ASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       169 ~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +++++++++...+|++...+| +++.++|..||||.+|||++++
T Consensus         1 GRp~~~~~~~~~~i~~l~~~G-~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen    1 GRPPKLSKEQIEEIKELYAEG-MSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             SSSSSSSHCCHHHHHHHHHTT---HHHHHHHTTS-HHHHHHHHC
T ss_pred             CcCCCCCHHHHHHHHHHHHCC-CCHHHHHHHHCcCHHHHHHHHh
Confidence            357788888888999988888 9999999999999999999874

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 ....

>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=98.09  E-value=6.3e-06  Score=55.89  Aligned_cols=41  Identities=15%  Similarity=0.248  Sum_probs=33.8

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        171 PTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       171 ~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+.+|.+++.+||+.+.+|. ++.++|..||||.+||++|++
T Consensus         4 R~~LTl~eK~~iI~~~e~g~-s~~~ia~~fgv~~sTv~~I~K   44 (53)
T PF04218_consen    4 RKSLTLEEKLEIIKRLEEGE-SKRDIAREFGVSRSTVSTILK   44 (53)
T ss_dssp             SSS--HHHHHHHHHHHHCTT--HHHHHHHHT--CCHHHHHHH
T ss_pred             CccCCHHHHHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHH
Confidence            45779999999999999996 899999999999999999998

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.

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

Probab=97.98  E-value=9.5e-06  Score=52.86  Aligned_cols=42  Identities=19%  Similarity=0.168  Sum_probs=23.3

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ++.+|.+|...+-.. .+.|+|+++||+.+|++++||++++++
T Consensus         2 ~~~Lt~~eR~~I~~l-~~~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen    2 YKHLTPEERNQIEAL-LEQGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             ----------HHHHH-HCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred             ccchhhhHHHHHHHH-HHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            467788888876644 566799999999999999999999987

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

Probab=97.97  E-value=9.4e-06  Score=53.55  Aligned_cols=40  Identities=20%  Similarity=0.309  Sum_probs=26.2

Q ss_pred             CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      +.+.|.+||+.+.+| +|+.++|..||||.+|||+|++..+
T Consensus         3 ~~~~R~~ii~l~~~G-~s~~~ia~~lgvs~~Tv~~w~kr~~   42 (50)
T PF13384_consen    3 SEERRAQIIRLLREG-WSIREIAKRLGVSRSTVYRWIKRYR   42 (50)
T ss_dssp             -------HHHHHHHT---HHHHHHHHTS-HHHHHHHHT---
T ss_pred             chhHHHHHHHHHHCC-CCHHHHHHHHCcCHHHHHHHHHHcc
Confidence            356799999999995 9999999999999999999999544

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

Probab=97.80  E-value=0.00014  Score=50.73  Aligned_cols=64  Identities=14%  Similarity=0.229  Sum_probs=44.0

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +|+.++|+.+||+.+||++|.+++|+..+.....                               ....|++++  ....
T Consensus         1 ~s~~eva~~~gvs~~tlr~w~~~~g~~~~~r~~~-------------------------------~~r~yt~~~v~~l~~   49 (68)
T cd01104           1 YTIGAVARLTGVSPDTLRAWERRYGLPAPQRTDG-------------------------------GHRLYSEADVARLRL   49 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhCCCCCCCcCCC-------------------------------CCeecCHHHHHHHHH
Confidence            4789999999999999999999887755422111                               123444444  3444


Q ss_pred             HHHHHcCCCCHHHHHHH
Q psy17316        128 LDALRAGSISANKASKA  144 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k  144 (229)
                      |..+.+-++|+.+|.+.
T Consensus        50 i~~l~~~g~~l~~i~~~   66 (68)
T cd01104          50 IRRLTSEGVRISQAAAL   66 (68)
T ss_pred             HHHHHHCCCCHHHHHHH
Confidence            55666667799888764

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

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

Probab=97.79  E-value=5.1e-05  Score=52.44  Aligned_cols=43  Identities=21%  Similarity=0.230  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccC
Q psy17316        122 EILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQ  165 (229)
Q Consensus       122 e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~  165 (229)
                      |.+.+|..+|++|- ++.+||++.|||.+||+.|+.++++....
T Consensus         1 e~k~~A~~LY~~G~-~~~eIA~~Lg~~~~TV~~W~~r~~W~~~~   43 (58)
T PF06056_consen    1 EVKEQARSLYLQGW-SIKEIAEELGVPRSTVYSWKDRYKWDELL   43 (58)
T ss_pred             CHHHHHHHHHHcCC-CHHHHHHHHCCChHHHHHHHHhhCccccC
Confidence            35788999999976 99999999999999999999999887764

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

>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx

Probab=97.74  E-value=6.5e-05  Score=51.77  Aligned_cols=43  Identities=12%  Similarity=0.091  Sum_probs=32.0

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCC---cHHHHHHHhCCChHHHHHHHH
Q psy17316        170 SPTAWKPEDLEIALEGIRSGQT---TVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       170 ~~r~~t~e~r~eaV~~~~~~~~---s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+.|+.+|+++||++-..+..   |++.||.+|||+..+|..|.+
T Consensus         2 ~rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~k   47 (58)
T PF09607_consen    2 SRRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRK   47 (58)
T ss_dssp             ------HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHT
T ss_pred             CccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHH
Confidence            4578999999999999988755   689999999999999999987

100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.

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

Probab=97.73  E-value=0.00028  Score=49.15  Aligned_cols=64  Identities=16%  Similarity=0.208  Sum_probs=46.5

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPED--LEIALEGIRSGQTTVQRASAE  199 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~  199 (229)
                      +|+.++|+.+||+.+||++|.++.|........+..+.|++++  +...|..+.+-+++..++...
T Consensus         1 ~s~~eva~~~gvs~~tlr~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~   66 (68)
T cd01104           1 YTIGAVARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAAL   66 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHH
Confidence            4789999999999999999998766533221123457888776  455566667777999888764

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

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

Probab=97.68  E-value=4.1e-05  Score=49.81  Aligned_cols=40  Identities=15%  Similarity=0.218  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        172 TAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       172 r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +.+|+++|..|..+..+| +|+.++|..+|++.+||+++++
T Consensus         3 ~~Lt~~eR~~I~~l~~~G-~s~~~IA~~lg~s~sTV~relk   42 (44)
T PF13936_consen    3 KHLTPEERNQIEALLEQG-MSIREIAKRLGRSRSTVSRELK   42 (44)
T ss_dssp             ---------HHHHHHCS----HHHHHHHTT--HHHHHHHHH
T ss_pred             cchhhhHHHHHHHHHHcC-CCHHHHHHHHCcCcHHHHHHHh
Confidence            456788999988776555 9999999999999999999987

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

Probab=97.65  E-value=7.9e-05  Score=51.50  Aligned_cols=44  Identities=14%  Similarity=0.138  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKE   81 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~   81 (229)
                      -+..|..+|.. |.++.+||+.+|||.+||+.|+.+++=....+.
T Consensus         2 ~k~~A~~LY~~-G~~~~eIA~~Lg~~~~TV~~W~~r~~W~~~~~~   45 (58)
T PF06056_consen    2 VKEQARSLYLQ-GWSIKEIAEELGVPRSTVYSWKDRYKWDELLPI   45 (58)
T ss_pred             HHHHHHHHHHc-CCCHHHHHHHHCCChHHHHHHHHhhCccccCch
Confidence            46788999987 779999999999999999999999976654443

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

>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=97.63  E-value=0.00019  Score=42.22  Aligned_cols=41  Identities=27%  Similarity=0.438  Sum_probs=33.8

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHH
Q psy17316        170 SPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRC  211 (229)
Q Consensus       170 ~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~v  211 (229)
                      +++.++.+++..+++.+.++ .++.++|..|||+.+|||+|+
T Consensus         2 r~~~~~~~~~~~i~~~~~~~-~s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569           2 RPPKLTPEQIEEARRLLAAG-ESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CCCcCCHHHHHHHHHHHHcC-CCHHHHHHHHCCCHHHHHHhC
Confidence            34567778888888876655 799999999999999999984

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

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

Probab=97.63  E-value=0.00043  Score=48.36  Aligned_cols=66  Identities=15%  Similarity=0.261  Sum_probs=44.8

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHHHHHHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEILNVALD  129 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~k~~AV~  129 (229)
                      +|+.++|+.+||+.+||+.|.++.++..+......+-|++++..                              ....|.
T Consensus         1 ~~i~evA~~~gvs~~tlR~~~~~g~l~~~~~~~g~R~y~~~~l~------------------------------~l~~i~   50 (67)
T cd04764           1 YTIKEVSEIIGVKPHTLRYYEKEFNLYIPRTENGRRYYTDEDIE------------------------------LLKKIK   50 (67)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhcCCCCCCCCCCceeeCHHHHH------------------------------HHHHHH
Confidence            47899999999999999999998776644322222234444331                              344566


Q ss_pred             HHHcCCCCHHHHHHHh
Q psy17316        130 ALRAGSISANKASKAY  145 (229)
Q Consensus       130 ~~~~g~~S~~~~a~k~  145 (229)
                      .+.+.++|+.+|....
T Consensus        51 ~l~~~g~~l~~i~~~l   66 (67)
T cd04764          51 TLLEKGLSIKEIKEIL   66 (67)
T ss_pred             HHHHCCCCHHHHHHHh
Confidence            6666778999887643

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

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=97.62  E-value=0.00014  Score=53.99  Aligned_cols=49  Identities=10%  Similarity=0.131  Sum_probs=43.0

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316         30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~   78 (229)
                      ....|+.-.+..+..+.+++.++.++|.+|||++.|.++|+.+|-.+|.
T Consensus         6 nA~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~   54 (85)
T PF13011_consen    6 NARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAEGE   54 (85)
T ss_pred             CCCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCc
Confidence            3567888899999999999999999999999999999999999854443

>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=97.56  E-value=0.00024  Score=41.74  Aligned_cols=42  Identities=29%  Similarity=0.415  Sum_probs=35.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHH
Q psy17316        114 GPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIA  156 (229)
Q Consensus       114 G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~i  156 (229)
                      |++..++.+.+..++..+.+|. |+.++++.+||+.+|+++|+
T Consensus         1 Gr~~~~~~~~~~~i~~~~~~~~-s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569           1 GRPPKLTPEQIEEARRLLAAGE-SVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CCCCcCCHHHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHhC
Confidence            4567778888777788877665 99999999999999999984

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

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

Probab=97.43  E-value=0.00034  Score=48.83  Aligned_cols=64  Identities=17%  Similarity=0.217  Sum_probs=44.1

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +|+.++|+.+|||.+||+.|.+...+..+.....                                ...|++++  ++..
T Consensus         1 yti~eva~~~gvs~~tlr~y~~~gll~~~~~~~g--------------------------------~r~y~~~dv~~l~~   48 (69)
T PF13411_consen    1 YTIKEVAKLLGVSPSTLRYYEREGLLPPPRDENG--------------------------------YRYYSEEDVERLRE   48 (69)
T ss_dssp             EEHHHHHHHTTTTHHHHHHHHHTTSSTTBESTTS--------------------------------SEEE-HHHHHHHHH
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHhcCcccccccCc--------------------------------eeeccHHHHHHHHH
Confidence            4789999999999999999999866544332211                                23444444  3556


Q ss_pred             HHHHHcCCCCHHHHHHHh
Q psy17316        128 LDALRAGSISANKASKAY  145 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~  145 (229)
                      |..+.+.++|+.+|.+..
T Consensus        49 i~~l~~~G~sl~~I~~~l   66 (69)
T PF13411_consen   49 IKELRKQGMSLEEIKKLL   66 (69)
T ss_dssp             HHHHHHTTTHHHHHHHHH
T ss_pred             HHHHHHCcCCHHHHHHHH
Confidence            667777777988887653

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=97.41  E-value=0.0019  Score=50.49  Aligned_cols=77  Identities=16%  Similarity=0.158  Sum_probs=58.1

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHH----HhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCc
Q psy17316        117 KSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIAR----KEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTT  192 (229)
Q Consensus       117 ~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik----~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s  192 (229)
                      ..-++|++.-+...+++.+ |++++++.+|||.+|++.++.    +.|....      ...-...++.+|++.+.+|++|
T Consensus        32 ~~L~~E~~~Fi~~Fi~~rG-nlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~~------~~~~~~~~~~~IL~~L~~GeIs  104 (113)
T PF09862_consen   32 ARLSPEQLEFIKLFIKNRG-NLKEMEKELGISYPTVRNRLDKIIEKLGYEED------EEEEEEDERKEILDKLEKGEIS  104 (113)
T ss_pred             hcCCHHHHHHHHHHHHhcC-CHHHHHHHHCCCcHHHHHHHHHHHHHhCCCCC------cccccchhHHHHHHHHHcCCCC
Confidence            3456677766667777766 999999999999999888764    3454111      1223457799999999999999


Q ss_pred             HHHHHHHh
Q psy17316        193 VQRASAEY  200 (229)
Q Consensus       193 ~~eAA~~f  200 (229)
                      +.+|....
T Consensus       105 ~eeA~~~L  112 (113)
T PF09862_consen  105 VEEALEIL  112 (113)
T ss_pred             HHHHHHHh
Confidence            99998764

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=97.34  E-value=0.00073  Score=50.22  Aligned_cols=40  Identities=20%  Similarity=0.229  Sum_probs=37.8

Q ss_pred             CCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        173 AWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       173 ~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|+.-|...|+.|.+++.++.++|..||||..|++.|+.
T Consensus         8 ~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~   47 (85)
T PF13011_consen    8 RLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLA   47 (85)
T ss_pred             CCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHH
Confidence            4678889999999999999999999999999999999998

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

Probab=97.32  E-value=0.0019  Score=45.21  Aligned_cols=65  Identities=14%  Similarity=0.283  Sum_probs=45.1

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+||+.+||+.|.+..|+-.|....                               |....|+.++  +...
T Consensus         1 ~~i~e~A~~~gVs~~tlr~ye~~~gl~~~~r~~-------------------------------~g~R~yt~~di~~l~~   49 (68)
T cd04763           1 YTIGEVALLTGIKPHVLRAWEREFGLLKPQRSD-------------------------------GGHRLFNDADIDRILE   49 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhcCCCCCCcCC-------------------------------CCCcccCHHHHHHHHH
Confidence            478899999999999999998887765432211                               1134455555  3445


Q ss_pred             HHHHHcCCCCHHHHHHHh
Q psy17316        128 LDALRAGSISANKASKAY  145 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~  145 (229)
                      |..+.+.++|+.+|+...
T Consensus        50 i~~l~~~g~~l~~i~~~l   67 (68)
T cd04763          50 IKRWIDNGVQVSKVKKLL   67 (68)
T ss_pred             HHHHHHcCCCHHHHHHHh
Confidence            666677778999988653

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

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=97.27  E-value=0.0012  Score=55.76  Aligned_cols=70  Identities=13%  Similarity=0.197  Sum_probs=49.9

Q ss_pred             HHHHHHHHhhcchhhhhhhhccCCCCCCCHHH-----HHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCC
Q psy17316         92 LNVALDALRAGSISANKASKAYGPTKSWNEEI-----LNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGI  161 (229)
Q Consensus        92 ~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~-----k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~  161 (229)
                      ++...+-..+|...+++.|++.|++..+.+..     ..+.|..+..++.|+.+||+.+|||++|+|++++..|+
T Consensus       124 r~~i~~R~~~g~~~~~~~G~~~Grp~g~~~~~~~~~~~~~~i~~~~~~g~s~~~iak~lgis~~Tv~r~~k~~~~  198 (200)
T PRK13413        124 RNLISQRTKEALARKKAEGVTLGRPKGSTPKKYKLTGKEEKIKKLLDKGTSKSEIARKLGVSRTTLARFLKTRGL  198 (200)
T ss_pred             HHHHHHHHHHHHHHHHHcCCccCCCCCCcchhhhcchhHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHhccc
Confidence            33334445568888888888889876655432     22344444455569999999999999999999987664

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

Probab=97.24  E-value=0.00076  Score=47.04  Aligned_cols=64  Identities=13%  Similarity=0.153  Sum_probs=46.3

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHh
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEY  200 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~f  200 (229)
                      +++.++|+.+|||.+||+.|.+..-+..... .+..+.|+++  +++..|..+.+.+++..+|...+
T Consensus         1 yti~eva~~~gvs~~tlr~y~~~gll~~~~~-~~g~r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l   66 (69)
T PF13411_consen    1 YTIKEVAKLLGVSPSTLRYYEREGLLPPPRD-ENGYRYYSEEDVERLREIKELRKQGMSLEEIKKLL   66 (69)
T ss_dssp             EEHHHHHHHTTTTHHHHHHHHHTTSSTTBES-TTSSEEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHhcCcccccc-cCceeeccHHHHHHHHHHHHHHHCcCCHHHHHHHH
Confidence            3788999999999999999998543333321 1234777766  56677888888889999988754

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

Probab=97.18  E-value=0.0041  Score=43.51  Aligned_cols=65  Identities=12%  Similarity=0.121  Sum_probs=46.2

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHh
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEY  200 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~f  200 (229)
                      +++.++|+++||+.+||+.|.++.|........+..|.|+.+  ++...|..+.+.+++..+++..+
T Consensus         1 ~~i~e~A~~~gVs~~tlr~ye~~~gl~~~~r~~~g~R~yt~~di~~l~~i~~l~~~g~~l~~i~~~l   67 (68)
T cd04763           1 YTIGEVALLTGIKPHVLRAWEREFGLLKPQRSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL   67 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhcCCCCCCcCCCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHh
Confidence            378899999999999999998865643221112345678766  45556667777889998888754

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

>PF13565 HTH_32: Homeodomain-like domain

Probab=97.17  E-value=0.0017  Score=46.29  Aligned_cols=60  Identities=22%  Similarity=0.358  Sum_probs=43.1

Q ss_pred             HHHHHHHHh---CCcccC-----CCCCCCCCCCHHHHHHHHHHHHhC-CCcHHHHHHH----hC--C--ChHHHHHHH
Q psy17316        151 TLYKIARKE---GIRLAQ-----PFNASPTAWKPEDLEIALEGIRSG-QTTVQRASAE----YG--I--PSGTLYGRC  211 (229)
Q Consensus       151 TL~~~ik~~---g~k~~~-----~~~~~~r~~t~e~r~eaV~~~~~~-~~s~~eAA~~----fg--V--p~~tv~~~v  211 (229)
                      |+++|++++   |...+.     +..+++++ +++.+..|++.+.++ .++..+++..    ||  +  |++|||+++
T Consensus         1 Tv~rw~~ry~~~G~~gL~~~~~~~~~Grp~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L   77 (77)
T PF13565_consen    1 TVYRWLKRYREEGLEGLKDRKRRPRPGRPRK-DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRIL   77 (77)
T ss_pred             CHHHHHHHHHhhCchhhhcccccCCCCCCCC-cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence            688999765   644332     33455566 677779999998887 6888888775    34  3  999999874

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

Probab=97.14  E-value=0.0039  Score=43.44  Aligned_cols=64  Identities=11%  Similarity=0.161  Sum_probs=46.0

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHh
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPED--LEIALEGIRSGQTTVQRASAEY  200 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~f  200 (229)
                      +|+.++|+.+||+.+||+.|.++.++.... ..+..|.|+.++  +...+..+.+.+++..++....
T Consensus         1 ~~i~evA~~~gvs~~tlR~~~~~g~l~~~~-~~~g~R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l   66 (67)
T cd04764           1 YTIKEVSEIIGVKPHTLRYYEKEFNLYIPR-TENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL   66 (67)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhcCCCCCC-CCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence            478899999999999999999875554322 123457787664  4555666667778888887654

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

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

Probab=97.11  E-value=0.0012  Score=42.09  Aligned_cols=27  Identities=15%  Similarity=0.244  Sum_probs=23.7

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      +|+.++|+.+||+++||++|+++..+.
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g~~~   27 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGKLK   27 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence            588999999999999999999985443

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

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=97.10  E-value=0.0025  Score=44.72  Aligned_cols=77  Identities=21%  Similarity=0.257  Sum_probs=57.0

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHHHHHHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEILNVALD  129 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~k~~AV~  129 (229)
                      +|+.++|+++||+.++|.+.+++..-..+..              .+                       ....+..|++
T Consensus         2 ~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~--------------~~-----------------------~~~r~~~a~~   44 (84)
T smart00342        2 LTLEDLAEALGMSPRHLQRLFKKETGTTPKQ--------------YL-----------------------RDRRLERARR   44 (84)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHhCcCHHH--------------HH-----------------------HHHHHHHHHH
Confidence            6899999999999999999998752211100              00                       0123467788


Q ss_pred             HHHcCCCCHHHHHHHhCC-ChHHHHHHHHHh-CCcc
Q psy17316        130 ALRAGSISANKASKAYGI-PSSTLYKIARKE-GIRL  163 (229)
Q Consensus       130 ~~~~g~~S~~~~a~k~gI-p~sTL~~~ik~~-g~k~  163 (229)
                      .+.++.+++.++|..+|+ +.+.+.+..++. |...
T Consensus        45 ~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~g~sp   80 (84)
T smart00342       45 LLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTP   80 (84)
T ss_pred             HHHcCCCCHHHHHHHhCCCChHHHHHHHHHHHCcCh
Confidence            888887899999999999 778899988765 6543

>PHA02535 P terminase ATPase subunit; Provisional

Probab=97.08  E-value=0.00084  Score=65.62  Aligned_cols=48  Identities=19%  Similarity=0.374  Sum_probs=43.7

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCC
Q psy17316        118 SWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQP  166 (229)
Q Consensus       118 kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~  166 (229)
                      .|++|+|.+|+.+|.+| .|+.+||+.+||+.+|||+|++++++....|
T Consensus         2 ~yt~EfK~~Av~Ly~~G-~sv~eIA~~LGv~~~Tl~~W~kr~~w~~~~~   49 (581)
T PHA02535          2 AYDDDVRRAAKFLYWQG-WTVAEIAEELGLKSRTIYSWKERDGWRDLLP   49 (581)
T ss_pred             CCCHHHHHHHHHHHHcC-CCHHHHHHHhCCChhHHHHHhccccccccCC
Confidence            69999999999999995 5999999999999999999999998877654

>KOG4565|consensus

Probab=97.05  E-value=0.00024  Score=58.96  Aligned_cols=68  Identities=26%  Similarity=0.337  Sum_probs=53.0

Q ss_pred             HhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        144 AYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       144 k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -.|||..|--. ..+.+++..++..++.|.|+.|-+.|||..+..|+|++..|-..||||.+||-..||
T Consensus        93 ~tg~se~t~d~-~g~~~sKqpRkKRGrYRqYd~eileEAi~~VmsGkMsVskAqsiyGvPHSTLEYKVK  160 (206)
T KOG4565|consen   93 TTGISEKTQDM-HGNEESKQPRKKRGRYRQYDKEILEEAIRSVMSGKMSVSKAQSIYGVPHSTLEYKVK  160 (206)
T ss_pred             CCCCCCccccc-cCCccccCccccccchhhhhHHHHHHHHHHHhcCceeeecccceeccccchhhhhhH
Confidence            35666655211 111344444455678899999999999999999999999999999999999999998

>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx

Probab=97.04  E-value=0.0011  Score=45.70  Aligned_cols=45  Identities=11%  Similarity=0.237  Sum_probs=30.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCC---CCHHHHHHHhCCChHHHHHHHHH
Q psy17316        114 GPTKSWNEEILNVALDALRAGS---ISANKASKAYGIPSSTLYKIARK  158 (229)
Q Consensus       114 G~~~kYs~e~k~~AV~~~~~g~---~S~~~~a~k~gIp~sTL~~~ik~  158 (229)
                      |....|+.+||++||+.+....   .+++.++++|||++..+++|.+.
T Consensus         1 g~rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~kq   48 (58)
T PF09607_consen    1 GSRRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRKQ   48 (58)
T ss_dssp             -------HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHTT
T ss_pred             CCccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHHH
Confidence            3456799999999999996543   37799999999999999999863

100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.

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

Probab=96.97  E-value=0.0017  Score=41.65  Aligned_cols=33  Identities=24%  Similarity=0.332  Sum_probs=24.9

Q ss_pred             HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..+.+...+-++.++|+.+||+++||++++++|
T Consensus        10 i~~aL~~~~gn~~~aA~~Lgisr~tL~~klkk~   42 (42)
T PF02954_consen   10 IRQALERCGGNVSKAARLLGISRRTLYRKLKKY   42 (42)
T ss_dssp             HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred             HHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence            334454555589999999999999999999875

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

>PRK11511 DNA-binding transcriptional activator MarA; Provisional

Probab=96.90  E-value=0.008  Score=47.37  Aligned_cols=88  Identities=15%  Similarity=0.099  Sum_probs=63.9

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGP  115 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~  115 (229)
                      .+...|+.-....+++.++|+.+|+++++|.++.++. |...            .                         
T Consensus        13 ~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s~------------~-------------------------   55 (127)
T PRK11511         13 SILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSL------------G-------------------------   55 (127)
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH------------H-------------------------
Confidence            3444554445567999999999999999999999975 5431            1                         


Q ss_pred             CCCCCHHHH-HHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        116 TKSWNEEIL-NVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       116 ~~kYs~e~k-~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                        .|-...+ ..|.++++..+.++.+||...|-+... +.+..++. |..+
T Consensus        56 --~~l~~~Rl~~A~~~L~~t~~~i~eIA~~~Gf~s~s~F~r~Fkk~~G~tP  104 (127)
T PRK11511         56 --QYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPP  104 (127)
T ss_pred             --HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence              1112233 456777777778999999999999866 88877755 7544

>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional

Probab=96.89  E-value=0.029  Score=42.40  Aligned_cols=86  Identities=12%  Similarity=0.033  Sum_probs=62.6

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCC
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTK  117 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~  117 (229)
                      ...|+.-....+++.++|+.+|++.++|.+..++. |...            ..                          
T Consensus        11 ~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s~------------~~--------------------------   52 (107)
T PRK10219         11 IAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTL------------GD--------------------------   52 (107)
T ss_pred             HHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCH------------HH--------------------------
Confidence            34444434566899999999999999999999985 4431            11                          


Q ss_pred             CCCHH-HHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        118 SWNEE-ILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       118 kYs~e-~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                       |-.. -+..|.+.+.++..|+.+||...|-+..+ +.+..+++ |..+
T Consensus        53 -~i~~~Rl~~a~~~L~~~~~~i~~iA~~~Gf~~~s~f~~~Fk~~~G~tP  100 (107)
T PRK10219         53 -YIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRRQFDRTP  100 (107)
T ss_pred             -HHHHHHHHHHHHHHHccCCCHHHHHHHHCCCCHHHHHHHHHHHHCcCH
Confidence             1111 24667778888888999999999999977 88888765 6543

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=96.86  E-value=0.0075  Score=47.16  Aligned_cols=43  Identities=14%  Similarity=0.162  Sum_probs=36.5

Q ss_pred             CCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         29 VTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        29 ~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .-...+.||+..+..-+++.| |++++++.|||+-.|++.++.+
T Consensus        30 ~~~~L~~E~~~Fi~~Fi~~rG-nlKe~e~~lgiSYPTvR~rLd~   72 (113)
T PF09862_consen   30 WFARLSPEQLEFIKLFIKNRG-NLKEMEKELGISYPTVRNRLDK   72 (113)
T ss_pred             hhhcCCHHHHHHHHHHHHhcC-CHHHHHHHHCCCcHHHHHHHHH
Confidence            346678899887777777766 9999999999999999998886

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=96.81  E-value=0.0091  Score=41.47  Aligned_cols=23  Identities=13%  Similarity=0.117  Sum_probs=21.2

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +|+.++|+.+||+.+||+.|.+.
T Consensus         1 ~s~~eva~~~gvs~~tlr~~~~~   23 (70)
T smart00422        1 YTIGEVAKLAGVSVRTLRYYERI   23 (70)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57899999999999999999875

>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=96.81  E-value=0.002  Score=47.25  Aligned_cols=36  Identities=19%  Similarity=0.218  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHH
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRC  211 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~v  211 (229)
                      ++--+++.+++++++.++++||..||||.+||..-+
T Consensus         5 eeR~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDv   40 (82)
T PF12116_consen    5 EERVIEIANYIIETKATVRQAAKVFGVSKSTVHKDV   40 (82)
T ss_dssp             HHHHHHHHHHHHHH---HHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHH
Confidence            456689999999999999999999999999999865

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.

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

Probab=96.78  E-value=0.014  Score=43.94  Aligned_cols=74  Identities=9%  Similarity=0.039  Sum_probs=54.4

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGR  210 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~  210 (229)
                      +++.++|+.+|||..||+.|.+ .|.- ......+..|.|+++  +++..|..+.+-+++..++...++.+...+...
T Consensus         1 m~i~eva~~~gvs~~tlR~ye~-~Gll~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~~~~~~~~~~   77 (96)
T cd04788           1 WKIGELARRTGLSVRTLHHYDH-IGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGPDFDPLEL   77 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhCCChhHHHH
Confidence            4788999999999999999987 4532 221112346788766  566778888888899999999998765443333

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

>PHA00675 hypothetical protein

Probab=96.78  E-value=0.0037  Score=45.47  Aligned_cols=47  Identities=11%  Similarity=0.072  Sum_probs=40.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         25 GSLTVTKTWTHEDMDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        25 ~~~~~~~kyt~e~~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      |...++.+.|+.+..++..++ .+|. |...+|++||||++||+.....
T Consensus        15 Ge~h~~AKLt~~qV~~IR~l~~r~G~-s~~~IA~~fGVsrstV~~I~~g   62 (78)
T PHA00675         15 GEDHPNAKLTDAEVERIRELHEVEGM-SYAVLAEKFEQSKGAIAKICRY   62 (78)
T ss_pred             CCCCCCcccCHHHHHHHHHHHHhcCc-cHHHHHHHhCCCHHHHHHHHcc
Confidence            445668999999999999988 6755 9999999999999999987653

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=96.77  E-value=0.0077  Score=42.17  Aligned_cols=69  Identities=19%  Similarity=0.295  Sum_probs=55.3

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCC-CHHHHHHHHHHHHhCCCcHHHHHHHhCC-ChHHHHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAW-KPEDLEIALEGIRSGQTTVQRASAEYGI-PSGTLYGRCK  212 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~-t~e~r~eaV~~~~~~~~s~~eAA~~fgV-p~~tv~~~vk  212 (229)
                      .|+.++|+.+|++.++|++..+.. |....        .| .......|++++.++++++.++|..+|+ +.+.+.+..|
T Consensus         2 ~~~~~la~~~~~s~~~l~~~f~~~~~~s~~--------~~~~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk   73 (84)
T smart00342        2 LTLEDLAEALGMSPRHLQRLFKKETGTTPK--------QYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFK   73 (84)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHhCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHH
Confidence            589999999999999999988865 43332        12 2233556888888888999999999999 9999988886

>PHA02535 P terminase ATPase subunit; Provisional

Probab=96.75  E-value=0.0018  Score=63.40  Aligned_cols=43  Identities=16%  Similarity=0.193  Sum_probs=40.4

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      .||+|.+.+|+.+|.+ |.|+.+||+++||+.+||++|+++++=
T Consensus         2 ~yt~EfK~~Av~Ly~~-G~sv~eIA~~LGv~~~Tl~~W~kr~~w   44 (581)
T PHA02535          2 AYDDDVRRAAKFLYWQ-GWTVAEIAEELGLKSRTIYSWKERDGW   44 (581)
T ss_pred             CCCHHHHHHHHHHHHc-CCCHHHHHHHhCCChhHHHHHhccccc
Confidence            6999999999999999 889999999999999999999999863

>KOG4565|consensus

Probab=96.74  E-value=0.00097  Score=55.44  Aligned_cols=48  Identities=25%  Similarity=0.440  Sum_probs=43.3

Q ss_pred             CCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         27 LTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        27 ~~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      +..+++|..+.+.+||..+..|.||+..|.--||||++||--+++...
T Consensus       116 RGrYRqYd~eileEAi~~VmsGkMsVskAqsiyGvPHSTLEYKVKER~  163 (206)
T KOG4565|consen  116 RGRYRQYDKEILEEAIRSVMSGKMSVSKAQSIYGVPHSTLEYKVKERN  163 (206)
T ss_pred             ccchhhhhHHHHHHHHHHHhcCceeeecccceeccccchhhhhhHhhc
Confidence            334688999999999999999999999999999999999999998643

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

Probab=96.67  E-value=0.01  Score=43.96  Aligned_cols=65  Identities=15%  Similarity=0.168  Sum_probs=48.4

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCC-CCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHhC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFN-ASPTAWKPED--LEIALEGIRSGQTTVQRASAEYG  201 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~-~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~fg  201 (229)
                      +++.++|+.+||+.+||+.|.+. |.-...... +..|.|++++  ++..|..+.+.+++..++...+.
T Consensus         2 ~ti~evA~~~gvs~~tLR~ye~~-Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~   69 (88)
T cd01105           2 IGIGEVSKLTGVSPRQLRYWEEK-GLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLR   69 (88)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCCCceecCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            48899999999999999999774 532221111 2467887764  45778888888899999988765

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

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

Probab=96.66  E-value=0.018  Score=43.26  Aligned_cols=70  Identities=19%  Similarity=0.227  Sum_probs=48.9

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      |++.++|+.+|||..||+.|-+. |+-.|.....                              |....|++++  +...
T Consensus         1 m~i~eva~~~gvs~~tlR~ye~~-Gll~p~~r~~------------------------------~gyR~Y~~~~l~~l~~   49 (96)
T cd04788           1 WKIGELARRTGLSVRTLHHYDHI-GLLSPSQRTE------------------------------GGHRLYDRADIRRLHQ   49 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCC------------------------------CCceeeCHHHHHHHHH
Confidence            68899999999999999999874 4433321111                              1134455555  4566


Q ss_pred             HHHHHcCCCCHHHHHHHhCCChH
Q psy17316        128 LDALRAGSISANKASKAYGIPSS  150 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gIp~s  150 (229)
                      |..+.+-++|+.+|...++....
T Consensus        50 I~~lr~~G~~l~eI~~~l~~~~~   72 (96)
T cd04788          50 IIALRRLGFSLREIGRALDGPDF   72 (96)
T ss_pred             HHHHHHcCCCHHHHHHHHhCCCh
Confidence            77888888899999988876543

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

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

Probab=96.64  E-value=0.02  Score=43.39  Aligned_cols=69  Identities=14%  Similarity=0.136  Sum_probs=50.3

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCC-cccCCCCCCCCCCCHHHH--HHHHHHHHhCCCcHHHHHHHhCCChH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGI-RLAQPFNASPTAWKPEDL--EIALEGIRSGQTTVQRASAEYGIPSG  205 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~-k~~~~~~~~~r~~t~e~r--~eaV~~~~~~~~s~~eAA~~fgVp~~  205 (229)
                      +++.++|+.+||+.+||+.|.+. |. .......+..|.|++++.  +..|..+.+.+++..++...+.....
T Consensus         1 ~ti~eva~~~gvs~~tlR~ye~~-Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~~~~   72 (103)
T cd01106           1 YTVGEVAKLTGVSVRTLHYYDEI-GLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPSE   72 (103)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHcCcH
Confidence            47899999999999999999874 43 221111234577887654  45577888888999999998887653

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

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=96.62  E-value=0.017  Score=40.13  Aligned_cols=64  Identities=14%  Similarity=0.135  Sum_probs=42.1

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCC-cccCCCCCCCCCCCHHHH--HHHHHHHHhCCCcHHHHHHHh
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGI-RLAQPFNASPTAWKPEDL--EIALEGIRSGQTTVQRASAEY  200 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~-k~~~~~~~~~r~~t~e~r--~eaV~~~~~~~~s~~eAA~~f  200 (229)
                      +|+.++|+.+||+.+||+.|.+ .|+ ..........+.|+.++.  ...+..+.+.+++..++...+
T Consensus         1 ~s~~eva~~~gvs~~tlr~~~~-~gli~~~~~~~~g~r~y~~~dl~~l~~i~~lr~~g~~~~~i~~~l   67 (70)
T smart00422        1 YTIGEVAKLAGVSVRTLRYYER-IGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELL   67 (70)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCEecCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence            4789999999999999999987 443 222111233567776644  444555555667777766544

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

Probab=96.61  E-value=0.013  Score=43.45  Aligned_cols=66  Identities=11%  Similarity=0.159  Sum_probs=45.8

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+||+.+||+.|-+. |.-.|.....                              |....|+.++  +...
T Consensus         2 ~ti~evA~~~gvs~~tLR~ye~~-Gll~p~r~~~------------------------------~g~R~Ys~~dv~~l~~   50 (88)
T cd01105           2 IGIGEVSKLTGVSPRQLRYWEEK-GLIKSIRSDG------------------------------GGQRKYSLADVDRLLV   50 (88)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCC------------------------------CCceecCHHHHHHHHH
Confidence            68999999999999999999776 4332322111                              0134455555  3556


Q ss_pred             HHHHHcCCCCHHHHHHHhC
Q psy17316        128 LDALRAGSISANKASKAYG  146 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~g  146 (229)
                      |..+.+.++|+.+|.+...
T Consensus        51 I~~Lr~~G~sl~~i~~~l~   69 (88)
T cd01105          51 IKELLDEGFTLAAAVEKLR   69 (88)
T ss_pred             HHHHHHCCCCHHHHHHHHH
Confidence            7777777889999988765

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

>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]

Probab=96.61  E-value=0.014  Score=46.51  Aligned_cols=44  Identities=9%  Similarity=0.030  Sum_probs=34.9

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      -+.++.+....+|++..+ |++..+||+++.|+++.+.+++.+|.
T Consensus        15 GrPLp~~~R~rIvela~~-G~rp~~Isr~l~Vs~gcVsKIl~Ry~   58 (125)
T PF00292_consen   15 GRPLPNELRQRIVELAKE-GVRPCDISRQLRVSHGCVSKILSRYR   58 (125)
T ss_dssp             TSSS-HHHHHHHHHHHHT-T--HHHHHHHHT--HHHHHHHHHHHH
T ss_pred             CccCcHHHHHHHHHHhhh-cCCHHHHHHHHccchhHHHHHHHHHH
Confidence            366788999999999876 77999999999999999999999983

Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.

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

Probab=96.61  E-value=0.013  Score=44.46  Aligned_cols=71  Identities=13%  Similarity=0.168  Sum_probs=49.0

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHH--HHHH-HhCCCcHHHHHHHhCCChHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIA--LEGI-RSGQTTVQRASAEYGIPSGT  206 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~ea--V~~~-~~~~~s~~eAA~~fgVp~~t  206 (229)
                      +++.++|+.+||+.+||+.|.+..|.-......+..|.|+.++...+  |+.| .+-+++..++....+-....
T Consensus         1 yti~EvA~~~gVs~~tLR~ye~~~gli~p~r~~~g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~~~~   74 (99)
T cd04765           1 FSIGEVAEILGLPPHVLRYWETEFPQLKPVKRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDGAA   74 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHcCCCCCcCCCCCCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhcccc
Confidence            37889999999999999999887553221111234678888765544  5554 55669998888877654443

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

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

Probab=96.55  E-value=0.0079  Score=38.20  Aligned_cols=47  Identities=21%  Similarity=0.359  Sum_probs=32.4

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIAL  183 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV  183 (229)
                      +|+.++|+.+||+.+||++|++.-.+.... ..+..+.|+.++..+.+
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g~~~~~~-~~~~~~~~~~~ei~~~~   47 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIR-TPGGHRRFPEEDLERLL   47 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCCcee-CCCCceecCHHHHHHHH
Confidence            478999999999999999999854333221 12245567776665543

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

>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=96.55  E-value=0.0046  Score=40.39  Aligned_cols=41  Identities=22%  Similarity=0.229  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      +.|.+|+..+.+|.+++.++|..+|+|+++|...++ +...|
T Consensus         2 ~~R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~g   43 (47)
T PF01022_consen    2 PTRLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLREAG   43 (47)
T ss_dssp             HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHHCc
Confidence            469999999999999999999999999999999988 44443

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 ....

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=96.55  E-value=0.0086  Score=39.11  Aligned_cols=37  Identities=19%  Similarity=0.227  Sum_probs=30.4

Q ss_pred             CCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        174 WKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       174 ~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+++++. ++.++.. ++++.++|..+|||.+||+.+++
T Consensus         4 l~~~e~~-i~~~~~~-g~s~~eia~~l~is~~tv~~~~~   40 (58)
T smart00421        4 LTPRERE-VLRLLAE-GLTNKEIAERLGISEKTVKTHLS   40 (58)
T ss_pred             CCHHHHH-HHHHHHc-CCCHHHHHHHHCCCHHHHHHHHH
Confidence            4555554 7777654 49999999999999999999987

lux regulon (activates the bioluminescence operon

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

Probab=96.53  E-value=0.014  Score=44.34  Aligned_cols=29  Identities=17%  Similarity=0.287  Sum_probs=24.7

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~   78 (229)
                      +++.++|+.+||+.+||+.|-+.+|+-.|
T Consensus         1 yti~EvA~~~gVs~~tLR~ye~~~gli~p   29 (99)
T cd04765           1 FSIGEVAEILGLPPHVLRYWETEFPQLKP   29 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHcCCCCC
Confidence            47889999999999999999888775444

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

>PRK13182 racA polar chromosome segregation protein; Reviewed

Probab=96.52  E-value=0.0091  Score=50.13  Aligned_cols=27  Identities=15%  Similarity=0.247  Sum_probs=25.0

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      |++.++|+.+||+..||++|.+++++.
T Consensus         1 mti~evA~~lGVS~~TLRrw~k~g~L~   27 (175)
T PRK13182          1 MKTPFVAKKLGVSPKTVQRWVKQLNLP   27 (175)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence            578999999999999999999998875

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

Probab=96.50  E-value=0.0041  Score=43.31  Aligned_cols=37  Identities=22%  Similarity=0.398  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHc--CCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         37 DMDAALEALRA--GQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        37 ~~~~AI~~~~~--g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +...|-+.|++  |++...+||.++||+.+||+.|-.+.
T Consensus         8 ~rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~d   46 (60)
T PF10668_consen    8 NRDKAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKSRD   46 (60)
T ss_pred             CHHHHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhhhc
Confidence            45677788874  88999999999999999999998874

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

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=96.49  E-value=0.0056  Score=45.81  Aligned_cols=36  Identities=17%  Similarity=0.132  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+|.+|++++.+| +++.++|..+|||.+|||++.+
T Consensus        37 Ls~R~~I~~ll~~G-~S~~eIA~~LgISrsTIyRi~R   72 (88)
T TIGR02531        37 LAQRLQVAKMLKQG-KTYSDIEAETGASTATISRVKR   72 (88)
T ss_pred             hhHHHHHHHHHHCC-CCHHHHHHHHCcCHHHHHHHHH
Confidence            34587777776666 8999999999999999999776

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.

>TIGR01764 excise DNA binding domain, excisionase family

Probab=96.48  E-value=0.0038  Score=39.96  Aligned_cols=29  Identities=14%  Similarity=0.282  Sum_probs=25.0

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~   78 (229)
                      +|+.++|+.+||+++||++|++...+...
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g~i~~~   30 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEGELPAY   30 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcCCCCeE
Confidence            68999999999999999999987655543

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

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=96.46  E-value=0.0093  Score=38.93  Aligned_cols=40  Identities=15%  Similarity=0.222  Sum_probs=32.6

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..++++.. ++..+. .|+|..+||+.+||+++|+++++++.
T Consensus         3 ~l~~~e~~-i~~~~~-~g~s~~eia~~l~is~~tv~~~~~~~   42 (58)
T smart00421        3 SLTPRERE-VLRLLA-EGLTNKEIAERLGISEKTVKTHLSNI   42 (58)
T ss_pred             CCCHHHHH-HHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            45677765 676664 57899999999999999999998863

lux regulon (activates the bioluminescence operon

>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]

Probab=96.46  E-value=0.033  Score=50.46  Aligned_cols=106  Identities=16%  Similarity=0.121  Sum_probs=68.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhh
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASK  111 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~  111 (229)
                      ..|.++..++ +.+..-++|.++||+++|..++||.+-+++.-...        .|+.+.=++..+.++..         
T Consensus         7 hLT~~eR~~I-~~l~~~~~S~reIA~~LgRh~sTIsRElkRn~~~~--------~Y~a~~A~~~~~~~rrr---------   68 (318)
T COG2826           7 HLTLFERYEI-ERLLKAKMSIREIAKQLNRHHSTISRELKRNRTRD--------IYSAVKAQERYRMLRRR---------   68 (318)
T ss_pred             hCCHHHHHHH-HHHHHcCCCHHHHHHHhCCCcchhhHHHhcCCccc--------eeeHHHHHHHHHHhhcc---------
Confidence            4566776654 45556689999999999999999999999864432        24433333333211111         


Q ss_pred             ccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHH--HhC-CChHHHHHHHH
Q psy17316        112 AYGPTKSWNEEILNVALDALRAGSISANKASK--AYG-IPSSTLYKIAR  157 (229)
Q Consensus       112 ~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~--k~g-Ip~sTL~~~ik  157 (229)
                       .-+..+.+.+....+++.+.+ ..|..+|+-  ..+ |+..|+|+|+-
T Consensus        69 -~~~k~~~~~eL~~~V~e~L~~-~wSPEQI~g~l~~~~i~~eTIYr~ly  115 (318)
T COG2826          69 -RIRKLKLNPELRELVLEKLKS-KWSPEQIIGRLKKSKISFETIYRWLY  115 (318)
T ss_pred             -cCCcccCCHHHHHHHHHHHHh-hCCHHHHHHHHHhcccCHHHHHHHHh
Confidence             112445666666666666544 458888854  333 88999999973

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

Probab=96.43  E-value=0.0066  Score=39.22  Aligned_cols=27  Identities=11%  Similarity=0.049  Sum_probs=23.9

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      +|+.++|+.+||+..||++|.++..+.
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~~~g~l~   27 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYERIGLLS   27 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence            588999999999999999999886554

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

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

Probab=96.42  E-value=0.0092  Score=38.20  Aligned_cols=35  Identities=23%  Similarity=0.359  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      |+.-|.+.+...+-|..+||...|||++|||+.++
T Consensus         6 E~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~klk   40 (42)
T PF02954_consen    6 EKQLIRQALERCGGNVSKAARLLGISRRTLYRKLK   40 (42)
T ss_dssp             HHHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence            57778888888888999999999999999999876

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

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

Probab=96.38  E-value=0.043  Score=41.24  Aligned_cols=70  Identities=13%  Similarity=0.089  Sum_probs=49.1

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+||+..||+.|-+. |+-.|.....+                              ....|+.++  +...
T Consensus         1 ~ti~eva~~~gvs~~tLRyye~~-Gll~p~~~~~~------------------------------gyR~Y~~~~l~~l~~   49 (96)
T cd04768           1 LTIGEFAKLAGVSIRTLRHYDDI-GLFKPAKIAEN------------------------------GYRYYSYAQLYQLQF   49 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCC------------------------------CeeeCCHHHHHHHHH
Confidence            47899999999999999999987 55433221111                              134455555  4566


Q ss_pred             HHHHHcCCCCHHHHHHHhCCChH
Q psy17316        128 LDALRAGSISANKASKAYGIPSS  150 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gIp~s  150 (229)
                      |..+.+-++|+.+|...+.-...
T Consensus        50 I~~lr~~G~~l~~I~~~l~~~~~   72 (96)
T cd04768          50 ILFLRELGFSLAEIKELLDTEME   72 (96)
T ss_pred             HHHHHHcCCCHHHHHHHHhcCcH
Confidence            77788878899999888876543

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

>PRK11511 DNA-binding transcriptional activator MarA; Provisional

Probab=96.30  E-value=0.037  Score=43.57  Aligned_cols=81  Identities=17%  Similarity=0.194  Sum_probs=62.1

Q ss_pred             HcCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHH-HHHHHHHhCCCcHHHHHHHhCCChHHHHH
Q psy17316        132 RAGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLE-IALEGIRSGQTTVQRASAEYGIPSGTLYG  209 (229)
Q Consensus       132 ~~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~-eaV~~~~~~~~s~~eAA~~fgVp~~tv~~  209 (229)
                      .....++.++|+..|++.++|.++.++. |....        .|-.+.|+ .|.+.+...++++.++|...|-+-+.-..
T Consensus        22 ~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s~~--------~~l~~~Rl~~A~~~L~~t~~~i~eIA~~~Gf~s~s~F~   93 (127)
T PRK11511         22 LESPLSLEKVSERSGYSKWHLQRMFKKETGHSLG--------QYIRSRKMTEIAQKLKESNEPILYLAERYGFESQQTLT   93 (127)
T ss_pred             cCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHH
Confidence            3455799999999999999999999976 75443        35445566 57888888889999999999988877776


Q ss_pred             HHHhhcCCCCC
Q psy17316        210 RCKLSRSTPRP  220 (229)
Q Consensus       210 ~vk~~~~~~~~  220 (229)
                      .+=....|-+|
T Consensus        94 r~Fkk~~G~tP  104 (127)
T PRK11511         94 RTFKNYFDVPP  104 (127)
T ss_pred             HHHHHHHCcCH
Confidence            65444444444

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

Probab=96.27  E-value=0.012  Score=38.76  Aligned_cols=44  Identities=18%  Similarity=0.117  Sum_probs=37.6

Q ss_pred             CCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         29 VTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        29 ~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .+..+|..-...+++++.+. .|+..+|+.+||+.+||++++.++
T Consensus         8 ~~~r~T~~~~~~i~~~~~~~-~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen    8 RYCRITKRLEQYILKLLRES-RSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             cCCcHHHHHHHHHHHHHhhc-CCHHHHHHHHCCCHHHHHHHHHhh
Confidence            45677777778888888776 799999999999999999998764

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

Probab=96.25  E-value=0.013  Score=39.66  Aligned_cols=39  Identities=33%  Similarity=0.541  Sum_probs=32.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      ..|.+++....      .+++.+||+++||+.++|.+..+++||.
T Consensus         4 ~lt~~~L~~~f------hlp~~eAA~~Lgv~~T~LKr~CR~~GI~   42 (52)
T PF02042_consen    4 SLTLEDLSQYF------HLPIKEAAKELGVSVTTLKRRCRRLGIP   42 (52)
T ss_pred             ccCHHHHHHHh------CCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence            44555555444      5899999999999999999999999985

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

>PRK04217 hypothetical protein; Provisional

Probab=96.23  E-value=0.014  Score=45.53  Aligned_cols=45  Identities=18%  Similarity=0.247  Sum_probs=38.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         27 LTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        27 ~~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ...-.+.+.+++ +++..+...++|+.+||+.+||+++||++.+++
T Consensus        37 ~~p~~~Lt~eer-eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~R   81 (110)
T PRK04217         37 PKPPIFMTYEEF-EALRLVDYEGLTQEEAGKRMGVSRGTVWRALTS   81 (110)
T ss_pred             CCCcccCCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            334567788885 788777767999999999999999999999885

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

Probab=96.22  E-value=0.059  Score=40.56  Aligned_cols=67  Identities=10%  Similarity=0.057  Sum_probs=51.6

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCccc-CCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLA-QPFNASPTAWKPED--LEIALEGIRSGQTTVQRASAEYGIP  203 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~-~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~fgVp  203 (229)
                      +++.++|+.+||+..||+.|.+ .|+-.. ....+..|.|+.++  ++..|..+.+-+++..++...+...
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~-~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~~   70 (97)
T cd04782           1 FTTGEFAKLCGISKQTLFHYDK-IGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNR   70 (97)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence            3788999999999999999987 564322 11123467888776  7888999999999999999877654

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

>PF13565 HTH_32: Homeodomain-like domain

Probab=96.22  E-value=0.02  Score=40.65  Aligned_cols=42  Identities=19%  Similarity=0.379  Sum_probs=26.6

Q ss_pred             cCCCCCCCHHHHHHHHHHHHcC-CCCHHHHHH----HhCC----ChHHHHHH
Q psy17316        113 YGPTKSWNEEILNVALDALRAG-SISANKASK----AYGI----PSSTLYKI  155 (229)
Q Consensus       113 ~G~~~kYs~e~k~~AV~~~~~g-~~S~~~~a~----k~gI----p~sTL~~~  155 (229)
                      .|++.+ +++.....++.+.+. ..|..+++.    +|||    +.+|++++
T Consensus        26 ~Grp~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~   76 (77)
T PF13565_consen   26 PGRPRK-DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI   76 (77)
T ss_pred             CCCCCC-cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence            345555 555556666666655 467777755    3453    88889986

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

Probab=96.21  E-value=0.058  Score=40.49  Aligned_cols=74  Identities=9%  Similarity=-0.030  Sum_probs=55.0

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCC-CCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQP-FNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGR  210 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~-~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~  210 (229)
                      +++.++|+.+||+..||+-|-+. |+-.... .....|.|+.+  .++..|..+.+-+++..++...+......+...
T Consensus         1 ~ti~eva~~~gvs~~tLRyye~~-Gll~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~   77 (96)
T cd04768           1 LTIGEFAKLAGVSIRTLRHYDDI-GLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEMEELTAM   77 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCcHHHHHH
Confidence            37899999999999999999985 6432211 12345778765  577888899998899999999888765444443

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

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

Probab=96.16  E-value=0.038  Score=41.99  Aligned_cols=67  Identities=13%  Similarity=0.178  Sum_probs=50.5

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP  203 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp  203 (229)
                      +++.++|+.+|||.+||+-|.+. |+-.........|.|+++  +++..|..+.+-+++..+++..+..+
T Consensus         2 ~~i~eva~~~gvs~~tLR~ye~~-Gll~~~r~~~g~R~Y~~~dl~~l~~I~~l~~~G~~l~ei~~~~~~~   70 (102)
T cd04775           2 YTIGQMSRKFGVSRSTLLYYESI-GLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQP   70 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCCCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHcCC
Confidence            58899999999999999999984 644222112345778765  56677778888889999999887665

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

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

Probab=96.16  E-value=0.0071  Score=45.80  Aligned_cols=37  Identities=22%  Similarity=0.114  Sum_probs=33.6

Q ss_pred             CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +.| =.||+++|.-.+++..+||.+.|||++|+|+-++
T Consensus        35 t~e-ElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~   71 (99)
T COG1342          35 TIE-ELEALRLVDYEGLTQEEAALRMGISRQTFWRLLT   71 (99)
T ss_pred             cHH-HHHHHHHHhHhhccHHHHHHHhcccHHHHHHHHH
Confidence            444 4789999999999999999999999999999987

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

Probab=96.15  E-value=0.056  Score=40.93  Aligned_cols=69  Identities=17%  Similarity=0.178  Sum_probs=45.2

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHHH--HHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEIL--NVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~k--~~A  127 (229)
                      +++.++|+.+||+.+||+.|.+. |.-.|.....                              |....|++++.  ...
T Consensus         1 ~ti~eva~~~gvs~~tlR~ye~~-Gll~~~~~~~------------------------------~g~R~y~~~di~~l~~   49 (103)
T cd01106           1 YTVGEVAKLTGVSVRTLHYYDEI-GLLKPSRRTE------------------------------NGYRLYTEEDLERLQQ   49 (103)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCC------------------------------CCceeeCHHHHHHHHH
Confidence            57899999999999999999775 4432211111                              01234555553  344


Q ss_pred             HHHHHcCCCCHHHHHHHhCCCh
Q psy17316        128 LDALRAGSISANKASKAYGIPS  149 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gIp~  149 (229)
                      |..+...++|+.+|........
T Consensus        50 i~~lr~~g~~l~~i~~~~~~~~   71 (103)
T cd01106          50 ILFLKELGFSLKEIKELLKDPS   71 (103)
T ss_pred             HHHHHHcCCCHHHHHHHHHcCc
Confidence            5666667789998888776664

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

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=96.14  E-value=0.011  Score=49.91  Aligned_cols=37  Identities=19%  Similarity=0.216  Sum_probs=31.0

Q ss_pred             HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      ..|..+..+|+|+.+||+.+||+++||+++++..++.
T Consensus       163 ~~i~~~~~~g~s~~~iak~lgis~~Tv~r~~k~~~~~  199 (200)
T PRK13413        163 EKIKKLLDKGTSKSEIARKLGVSRTTLARFLKTRGLR  199 (200)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHhcccC
Confidence            4555666778999999999999999999999977653

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

Probab=96.13  E-value=0.038  Score=42.62  Aligned_cols=66  Identities=14%  Similarity=0.145  Sum_probs=43.6

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+|||..||+.|-+..-+..+....                               +....|++++  +...
T Consensus         1 ~~i~e~a~~~gvs~~tlr~ye~~gll~~~~r~~-------------------------------~gyR~Y~~~~l~~l~~   49 (113)
T cd01109           1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDE-------------------------------NGIRDFTEEDLEWLEF   49 (113)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCCccCCHHHHHHHHH
Confidence            578999999999999999998864332221111                               0133455444  3556


Q ss_pred             HHHHHcCCCCHHHHHHHhC
Q psy17316        128 LDALRAGSISANKASKAYG  146 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~g  146 (229)
                      |..+.+-++|+.+|..-+.
T Consensus        50 I~~lr~~G~sL~eI~~~l~   68 (113)
T cd01109          50 IKCLRNTGMSIKDIKEYAE   68 (113)
T ss_pred             HHHHHHcCCCHHHHHHHHH
Confidence            6777776788888877554

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

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

Probab=96.11  E-value=0.043  Score=42.42  Aligned_cols=66  Identities=8%  Similarity=0.096  Sum_probs=50.0

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      +++.++|+.+|||.+||+.|-+ .|+-......+..|.|+++  .++..|..+.+-+++..++...+..
T Consensus         1 m~i~eva~~~gvs~~tlR~Ye~-~GLl~p~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~~   68 (112)
T cd01282           1 MRIGELAARTGVSVRSLRYYEE-QGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPC   68 (112)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH-CCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            4788999999999999999988 4643222122346788765  6778888888888999999887654

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

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=96.10  E-value=0.01  Score=44.43  Aligned_cols=32  Identities=6%  Similarity=0.087  Sum_probs=26.3

Q ss_pred             HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|..++++|+|..+||+.+||+++||+++.+
T Consensus        41 ~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~R   72 (88)
T TIGR02531        41 LQVAKMLKQGKTYSDIEAETGASTATISRVKR   72 (88)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            44445556678999999999999999999665

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.

>PF12728 HTH_17: Helix-turn-helix domain

Probab=96.10  E-value=0.0074  Score=39.74  Aligned_cols=29  Identities=17%  Similarity=0.260  Sum_probs=25.7

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~   78 (229)
                      +|+.+||..+||+++||++|+++.++...
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g~i~~~   30 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQGKIPPF   30 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCCeE
Confidence            68999999999999999999998766544

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

Probab=96.10  E-value=0.013  Score=40.73  Aligned_cols=41  Identities=17%  Similarity=0.268  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHc--CCCCHHHHHHHhCCChHHHHHHHHHhCCcc
Q psy17316        123 ILNVALDALRA--GSISANKASKAYGIPSSTLYKIARKEGIRL  163 (229)
Q Consensus       123 ~k~~AV~~~~~--g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~  163 (229)
                      .+.+|-+.|++  |.+.+.+||.++||+.+|++.|-.+..+..
T Consensus         8 ~rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~dkW~~   50 (60)
T PF10668_consen    8 NRDKAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKSRDKWDE   50 (60)
T ss_pred             CHHHHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhhhcchhh
Confidence            45677788874  779999999999999999999988766544

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

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

Probab=96.07  E-value=0.051  Score=40.66  Aligned_cols=67  Identities=12%  Similarity=0.118  Sum_probs=45.3

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPED--LEIALEGIRSGQTTVQRASAEYGIP  203 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~fgVp  203 (229)
                      +++.++|+.+||+.+||+.|.+ .|+-......+..+.|+.++  +...|..+...+++..+++..+.-.
T Consensus         1 ~~~~eva~~~gi~~~tlr~~~~-~Gll~~~~~~~g~r~y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~~~   69 (100)
T cd00592           1 YTIGEVAKLLGVSVRTLRYYEE-KGLLPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDAR   69 (100)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCcCCCcCCCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence            4789999999999999999988 45422111123456787664  4455556666668888887765543

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

>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=96.06  E-value=0.015  Score=39.93  Aligned_cols=40  Identities=25%  Similarity=0.240  Sum_probs=34.7

Q ss_pred             HHHHHHHHHH-HhCCCcHHHHHHHhCCChHHHHHHHH-hhcC
Q psy17316        177 EDLEIALEGI-RSGQTTVQRASAEYGIPSGTLYGRCK-LSRS  216 (229)
Q Consensus       177 e~r~eaV~~~-~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~  216 (229)
                      ..|.+|++++ ..+.++..++|..+|+|.+|++..++ +.+.
T Consensus        10 p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a   51 (61)
T PF12840_consen   10 PTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEA   51 (61)
T ss_dssp             HHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            5699999999 88999999999999999999999998 4433

...

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

Probab=96.06  E-value=0.031  Score=45.01  Aligned_cols=66  Identities=11%  Similarity=0.240  Sum_probs=46.9

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV  126 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~  126 (229)
                      .|++.++|+.+||+.+||+.|-+. |+-.|....                               |....|++++  +..
T Consensus         1 ~~~I~EvA~~~Gvs~~tLRyYE~~-GLl~p~r~~-------------------------------~g~R~Y~~~dl~~l~   48 (139)
T cd01110           1 ELSVGEVAKRSGVAVSALHFYEQK-GLIASWRNA-------------------------------GNQRRYPRDVLRRIA   48 (139)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCC-------------------------------CCCeEECHHHHHHHH
Confidence            479999999999999999999887 543231111                               1234455555  466


Q ss_pred             HHHHHHcCCCCHHHHHHHhC
Q psy17316        127 ALDALRAGSISANKASKAYG  146 (229)
Q Consensus       127 AV~~~~~g~~S~~~~a~k~g  146 (229)
                      .|..+.+-++|+.+|...+.
T Consensus        49 ~I~~lr~~G~sl~eI~~~l~   68 (139)
T cd01110          49 FIKVAQRLGLSLAEIAEALA   68 (139)
T ss_pred             HHHHHHHcCCCHHHHHHHHH
Confidence            67777888889999887653

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

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

Probab=96.05  E-value=0.022  Score=37.43  Aligned_cols=42  Identities=12%  Similarity=0.072  Sum_probs=37.5

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        170 SPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       170 ~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+..+|......|++.|... .|+.++|..+|||.+||+++.+
T Consensus         8 ~~~r~T~~~~~~i~~~~~~~-~s~~~vA~~~~vs~~TV~ri~~   49 (52)
T PF13542_consen    8 RYCRITKRLEQYILKLLRES-RSFKDVARELGVSWSTVRRIFD   49 (52)
T ss_pred             cCCcHHHHHHHHHHHHHhhc-CCHHHHHHHHCCCHHHHHHHHH
Confidence            45567888899999999999 8999999999999999999875

>PF13309 HTH_22: HTH domain

Probab=96.04  E-value=0.028  Score=39.37  Aligned_cols=40  Identities=15%  Similarity=0.230  Sum_probs=34.3

Q ss_pred             CCCHHHHHHHHHHHHhCC-----CcHHHHHHHhCCChHHHHHHHH
Q psy17316        173 AWKPEDLEIALEGIRSGQ-----TTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       173 ~~t~e~r~eaV~~~~~~~-----~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+.++|.++|+.+.+.+     -++..+|..+|||..|||+.++
T Consensus        20 ~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr   64 (64)
T PF13309_consen   20 RLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR   64 (64)
T ss_pred             hCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence            356789999999999865     3689999999999999999764

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

Probab=96.01  E-value=0.052  Score=41.84  Aligned_cols=65  Identities=9%  Similarity=0.137  Sum_probs=47.5

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYG  201 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fg  201 (229)
                      +++.++|+.+|||.+||+.|.+. |.- .........|.|+++  +++..|..+.+-+++..++...+.
T Consensus         1 ~~i~e~a~~~gvs~~tlr~ye~~-gll~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~   68 (113)
T cd01109           1 YTIKEVAEKTGLSADTLRYYEKE-GLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAE   68 (113)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            47899999999999999999874 432 211112346788766  566667777877799999988765

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

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=95.99  E-value=0.01  Score=54.09  Aligned_cols=38  Identities=13%  Similarity=0.176  Sum_probs=31.6

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      +..+++++...+....++|+.+||+++|||+++++|||
T Consensus       288 r~~I~~aL~~~~gn~~~aA~~LGIsR~tLyrklk~~gi  325 (326)
T PRK11608        288 KELLQRSLQQAKFNQKRAAELLGLTYHQLRALLKKHQI  325 (326)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHcCC
Confidence            33455566666668999999999999999999999987

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

Probab=95.99  E-value=0.044  Score=42.33  Aligned_cols=65  Identities=12%  Similarity=0.241  Sum_probs=45.0

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      |++.++|+.+|||.+||+.|-+. |+-.|... .                              +....|++++  ++..
T Consensus         1 m~i~eva~~~gvs~~tlR~Ye~~-GLl~p~r~-~------------------------------~g~R~Y~~~~~~~l~~   48 (112)
T cd01282           1 MRIGELAARTGVSVRSLRYYEEQ-GLLVPERS-A------------------------------NGYRDYDEAAVDRVRQ   48 (112)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHC-CCCCCCcC-C------------------------------CCCeecCHHHHHHHHH
Confidence            68899999999999999999875 55433111 1                              1234455554  4666


Q ss_pred             HHHHHcCCCCHHHHHHHhC
Q psy17316        128 LDALRAGSISANKASKAYG  146 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~g  146 (229)
                      |..+.+-++|+.+|..-+.
T Consensus        49 I~~lr~~G~sl~eI~~~l~   67 (112)
T cd01282          49 IRRLLAAGLTLEEIREFLP   67 (112)
T ss_pred             HHHHHHcCCCHHHHHHHHH
Confidence            7777777788888876553

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

>PRK15044 transcriptional regulator SirC; Provisional

Probab=95.98  E-value=0.028  Score=50.86  Aligned_cols=87  Identities=13%  Similarity=0.142  Sum_probs=64.3

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCC
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKS  118 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~k  118 (229)
                      .+.|..-.....++.++|+++|+++++|.+..+..|.. +.          +.                           
T Consensus       198 ~~~I~~nl~~~~SLeeLA~~lgmS~~tL~R~Fk~eg~T-~~----------~y---------------------------  239 (295)
T PRK15044        198 YNIIISDLTRKWSQAEVAGKLFMSVSSLKRKLAAEEVS-FS----------KI---------------------------  239 (295)
T ss_pred             HHHHHhCcccCCCHHHHHHHhCCCHHHHHHHHHHcCCC-HH----------HH---------------------------
Confidence            44444444568999999999999999999999975321 10          11                           


Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        119 WNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       119 Ys~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                      |.+.-+..|.+++..+..++.+||.+.|-...+ ..+..|+. |..+
T Consensus       240 ~~~~RL~~A~~LL~~t~~sIseIA~~~GFss~S~FsRaFKk~fG~TP  286 (295)
T PRK15044        240 YLDARMNQAIKLLRMGAGNISQVATMCGYDTPSYFIAIFKRHFKITP  286 (295)
T ss_pred             HHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHHCcCH
Confidence            122345788899999999999999999999977 77777754 6443

>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function

Probab=95.98  E-value=0.36  Score=41.87  Aligned_cols=113  Identities=10%  Similarity=0.164  Sum_probs=83.0

Q ss_pred             HHHc-CCCCHHHHHHHcCCChhhHHHHHHHh----CCCCCCCCC-CCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCC
Q psy17316         44 ALRA-GQMSLTKASVSYGIPSTTLWQRAHRL----GIHTPKKEG-PTKSWNEEILNVALDALRAGSISANKASKAYGPTK  117 (229)
Q Consensus        44 ~~~~-g~~S~~~aA~~~gIp~sTL~~~i~~~----gi~~~~~~~-~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~  117 (229)
                      +|.+ |-++..++|.-+|++.+||++.++.|    |...|..+. +.                            .|+  
T Consensus        99 Ay~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~D----------------------------iGp--  148 (220)
T PF07900_consen   99 AYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHD----------------------------IGP--  148 (220)
T ss_pred             HHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccc----------------------------cCC--
Confidence            4444 45899999999999999999999976    444443331 11                            011  


Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHH
Q psy17316        118 SWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRAS  197 (229)
Q Consensus       118 kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA  197 (229)
                        +---|..+|+.|++|. +..+|++.+.=+...+-+.++.               |      +-|..|.+.+++..++|
T Consensus       149 --~~tHK~~ii~~~l~g~-~~~eiar~t~HS~~av~rYi~~---------------F------~rV~~l~~~~~~~~eia  204 (220)
T PF07900_consen  149 --GVTHKKIIIRLYLKGK-PTPEIARRTNHSPEAVDRYIKD---------------F------KRVLMLYEKGMSPEEIA  204 (220)
T ss_pred             --cchHHHHHHHHHHcCC-CHHHHHHHhccCHHHHHHHHHh---------------h------HHhHHHHHcCCCHHHHH
Confidence              1122567789999986 9999999999999888887773               1      12667777889999999


Q ss_pred             HHhCCChHHHHHH
Q psy17316        198 AEYGIPSGTLYGR  210 (229)
Q Consensus       198 ~~fgVp~~tv~~~  210 (229)
                      .-.|+|..-|-..
T Consensus       205 ~~tg~S~~Lv~eY  217 (220)
T PF07900_consen  205 FITGMSERLVKEY  217 (220)
T ss_pred             HHHCCCHHHHHHH
Confidence            9999998766543

>PRK15186 AraC family transcriptional regulator; Provisional

Probab=95.97  E-value=0.031  Score=50.43  Aligned_cols=86  Identities=15%  Similarity=0.139  Sum_probs=63.9

Q ss_pred             HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCC
Q psy17316         40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSW  119 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kY  119 (229)
                      .+|..-.....++.++|+.+|++++||.+..++.|...           .+.                           |
T Consensus       188 ~~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~~g~s~-----------~~~---------------------------~  229 (291)
T PRK15186        188 NIIISDISRKWALKDISDSLYMSCSTLKRKLKQENTSF-----------SEV---------------------------Y  229 (291)
T ss_pred             HHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCH-----------HHH---------------------------H
Confidence            44444345689999999999999999999999753221           111                           1


Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        120 NEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       120 s~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                      ..--+..|..++.++..++.+||.+.|-...+ +.+..|++ |...
T Consensus       230 ~~~Rl~~A~~lL~~~~~sI~~IA~~~GY~s~S~Fsr~FK~~~G~TP  275 (291)
T PRK15186        230 LNARMNKATKLLRNSEYNITRVAYMCGYDSASYFTCVFKKHFKTTP  275 (291)
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence            12235778888888888999999999999877 88888765 7544

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

Probab=95.96  E-value=0.051  Score=40.64  Aligned_cols=23  Identities=13%  Similarity=0.219  Sum_probs=21.3

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +++.++|+.+||+.+||+.|.+.
T Consensus         1 ~~~~eva~~~gi~~~tlr~~~~~   23 (100)
T cd00592           1 YTIGEVAKLLGVSVRTLRYYEEK   23 (100)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57899999999999999999885

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

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

Probab=95.92  E-value=0.041  Score=44.29  Aligned_cols=66  Identities=11%  Similarity=0.099  Sum_probs=50.1

Q ss_pred             CCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhC
Q psy17316        135 SISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYG  201 (229)
Q Consensus       135 ~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fg  201 (229)
                      ++++.++|+.+||+.+||+-|-+. |+-......+..|.|+++  +++..|..+.+-+++..++...+.
T Consensus         1 ~~~I~EvA~~~Gvs~~tLRyYE~~-GLl~p~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~   68 (139)
T cd01110           1 ELSVGEVAKRSGVAVSALHFYEQK-GLIASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALA   68 (139)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCCCCCeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            368999999999999999999985 642221112345778765  677788888888899999998764

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

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

Probab=95.91  E-value=0.054  Score=41.15  Aligned_cols=68  Identities=15%  Similarity=0.237  Sum_probs=47.2

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+||+.+||+.|-+. |+-.|... .+                              ....|++++  +...
T Consensus         2 ~~i~eva~~~gvs~~tLR~ye~~-Gll~~~r~-~~------------------------------g~R~Y~~~dl~~l~~   49 (102)
T cd04775           2 YTIGQMSRKFGVSRSTLLYYESI-GLIPSARS-EA------------------------------NYRLYSEADLSRLEK   49 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCC-CC------------------------------CCeeeCHHHHHHHHH
Confidence            58899999999999999999987 55422111 11                              123455555  3555


Q ss_pred             HHHHHcCCCCHHHHHHHhCCCh
Q psy17316        128 LDALRAGSISANKASKAYGIPS  149 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gIp~  149 (229)
                      |..+.+-++|+.+|......+.
T Consensus        50 I~~l~~~G~~l~ei~~~~~~~~   71 (102)
T cd04775          50 IVFLQAGGLPLEEIAGCLAQPH   71 (102)
T ss_pred             HHHHHHCCCCHHHHHHHHcCCc
Confidence            6677777889999998776554

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

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

Probab=95.91  E-value=0.054  Score=41.52  Aligned_cols=70  Identities=11%  Similarity=0.111  Sum_probs=49.4

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCC-CCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGP-TKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV  126 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~-~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~  126 (229)
                      +++.++|+.+|||.+||+.|-+. |+-.|..... +                              ....|+++.  ...
T Consensus         1 ~~i~eva~~~gis~~tlR~ye~~-GLi~p~~~~~~n------------------------------gyR~Y~~~~i~~l~   49 (108)
T cd01107           1 FTIGEFAKLSNLSIKALRYYDKI-GLLKPAYVDPDT------------------------------GYRYYSAEQLERLN   49 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc-CCCCCCcCCCCC------------------------------CccccCHHHHHHHH
Confidence            57899999999999999999997 6544422111 1                              123444444  456


Q ss_pred             HHHHHHcCCCCHHHHHHHhCCChH
Q psy17316        127 ALDALRAGSISANKASKAYGIPSS  150 (229)
Q Consensus       127 AV~~~~~g~~S~~~~a~k~gIp~s  150 (229)
                      .|..+.+-++|+.+|..-+.-...
T Consensus        50 ~I~~lr~~G~sl~~i~~l~~~~~~   73 (108)
T cd01107          50 RIKYLRDLGFPLEEIKEILDADND   73 (108)
T ss_pred             HHHHHHHcCCCHHHHHHHHhcCCH
Confidence            677888877899999887776654

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

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

Probab=95.89  E-value=0.075  Score=44.27  Aligned_cols=71  Identities=13%  Similarity=0.195  Sum_probs=55.2

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCChHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIPSGTL  207 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv  207 (229)
                      +++.++|+.+|||.+||+.|-+ .|+- .........|.|+++  .++..|..+.+-+++..++...++.+...+
T Consensus         2 ~~I~evA~~~gvs~~tLRyYe~-~GLl~p~~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~~~~~   75 (172)
T cd04790           2 LTISQLARQFGLSRSTLLYYER-IGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGDDA   75 (172)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCChhH
Confidence            5889999999999999999887 4532 221112356888877  788899999998899999999888665543

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

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=95.89  E-value=0.016  Score=43.95  Aligned_cols=34  Identities=21%  Similarity=0.327  Sum_probs=28.4

Q ss_pred             HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..+..+.++++|+++||+.+||+++||.|+-+-.
T Consensus        46 ~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~l   79 (94)
T TIGR01321        46 RIVNELLNGNMSQREIASKLGVSIATITRGSNNL   79 (94)
T ss_pred             HHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhc
Confidence            3444556789999999999999999999998754

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.

>PRK01905 DNA-binding protein Fis; Provisional

Probab=95.89  E-value=0.019  Score=41.60  Aligned_cols=37  Identities=16%  Similarity=0.162  Sum_probs=30.5

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      ..+++.+...+.++.++|+.+||+++||+++++++|+
T Consensus        40 ~~i~~aL~~~~gn~s~aAr~LGIsrstL~rklkk~gi   76 (77)
T PRK01905         40 PLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQHGL   76 (77)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhCC
Confidence            3344555556668999999999999999999999886

>PRK04217 hypothetical protein; Provisional

Probab=95.87  E-value=0.019  Score=44.67  Aligned_cols=40  Identities=20%  Similarity=0.223  Sum_probs=35.1

Q ss_pred             CCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        172 TAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       172 r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...+++++ +|+..+..+++++.++|..+|||.+|||+.++
T Consensus        41 ~~Lt~eer-eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~   80 (110)
T PRK04217         41 IFMTYEEF-EALRLVDYEGLTQEEAGKRMGVSRGTVWRALT   80 (110)
T ss_pred             ccCCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45577776 88888887889999999999999999999987

>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=95.86  E-value=0.021  Score=37.91  Aligned_cols=34  Identities=21%  Similarity=0.172  Sum_probs=24.7

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..++..+.-.|+|..+||+.+||+.+|++.|+.+
T Consensus        16 r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l~r   49 (54)
T PF08281_consen   16 REIFLLRYFQGMSYAEIAEILGISESTVKRRLRR   49 (54)
T ss_dssp             HHHHHHHHTS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred             HHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHHHH
Confidence            4455565566899999999999999999999886

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.

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

Probab=95.85  E-value=0.064  Score=41.12  Aligned_cols=69  Identities=7%  Similarity=0.038  Sum_probs=52.5

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCC--CCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCChH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPF--NASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIPSG  205 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~--~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp~~  205 (229)
                      +++.++|+.+|||.+||+-|.+. |+-.....  ....|.|+++  +++..|..+.+-+++..++...+.-...
T Consensus         1 ~~i~eva~~~gis~~tlR~ye~~-GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~~~~~   73 (108)
T cd01107           1 FTIGEFAKLSNLSIKALRYYDKI-GLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADND   73 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc-CCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCCH
Confidence            47889999999999999999985 64332211  1346788765  5677788888888999999998877654

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

>TIGR01764 excise DNA binding domain, excisionase family

Probab=95.85  E-value=0.012  Score=37.62  Aligned_cols=46  Identities=15%  Similarity=0.290  Sum_probs=31.7

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIAL  183 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV  183 (229)
                      +|+.++|+.+||+.+||++|++.-.++...  .+....|+.++..+-+
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g~i~~~~--~g~~~~~~~~~l~~~~   47 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEGELPAYR--VGRHYRIPREDVDEYL   47 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcCCCCeEE--eCCeEEEeHHHHHHHH
Confidence            589999999999999999999854333322  1334556665555443

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

>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional

Probab=95.84  E-value=0.074  Score=40.14  Aligned_cols=80  Identities=14%  Similarity=0.165  Sum_probs=58.0

Q ss_pred             cCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHH-HHHHHHHHhCCCcHHHHHHHhCCChHHHHHH
Q psy17316        133 AGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDL-EIALEGIRSGQTTVQRASAEYGIPSGTLYGR  210 (229)
Q Consensus       133 ~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r-~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~  210 (229)
                      ....++.++|+.+|++.++|.+..+++ |....        .|=...| ..|.+.+..+++++.++|...|-+-++-...
T Consensus        19 ~~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s~~--------~~i~~~Rl~~a~~~L~~~~~~i~~iA~~~Gf~~~s~f~~   90 (107)
T PRK10219         19 DQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLG--------DYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSR   90 (107)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHccCCCHHHHHHHHCCCCHHHHHH
Confidence            344799999999999999999999886 65443        3433444 4566677777899999999999987776655


Q ss_pred             HHhhcCCCCC
Q psy17316        211 CKLSRSTPRP  220 (229)
Q Consensus       211 vk~~~~~~~~  220 (229)
                      +=...-|-+|
T Consensus        91 ~Fk~~~G~tP  100 (107)
T PRK10219         91 VFRRQFDRTP  100 (107)
T ss_pred             HHHHHHCcCH
Confidence            4333334444

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

Probab=95.83  E-value=0.058  Score=42.51  Aligned_cols=68  Identities=7%  Similarity=0.014  Sum_probs=50.9

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP  203 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp  203 (229)
                      +++.++|+.+||+.+||+-|-+.--+.......+..|.|+++  +++..|..+.+-+++..++...+...
T Consensus         1 ~~I~e~a~~~gvs~~tlR~Ye~~Gll~~~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~   70 (126)
T cd04785           1 LSIGELARRTGVNVETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALS   70 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHhhh
Confidence            478999999999999999988842232221112346788766  67788888888889999999988753

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

>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=95.82  E-value=0.051  Score=40.94  Aligned_cols=67  Identities=13%  Similarity=0.185  Sum_probs=44.9

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      |++.++|+.+||+..||+.|.+..-+..+.....+                               ...|+++.  +...
T Consensus         1 m~I~eva~~~gvs~~tlR~Ye~~GLl~p~~r~~~g-------------------------------~r~Y~~~dv~~l~~   49 (95)
T cd04780           1 MRMSELSKRSGVSVATIKYYLREGLLPEGRRLAPN-------------------------------QAEYSEAHVERLRL   49 (95)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCC-------------------------------CeecCHHHHHHHHH
Confidence            68899999999999999999997444332222111                               23455544  3555


Q ss_pred             HHHHHc-CCCCHHHHHHHhCC
Q psy17316        128 LDALRA-GSISANKASKAYGI  147 (229)
Q Consensus       128 V~~~~~-g~~S~~~~a~k~gI  147 (229)
                      |..+.. -++|+.+|...+..
T Consensus        50 I~~L~~~~G~~l~~I~~~l~~   70 (95)
T cd04780          50 IRALQQEGGLPISQIKEVLDA   70 (95)
T ss_pred             HHHHHHHcCCCHHHHHHHHHh
Confidence            666664 56799998887665

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK13503 transcriptional activator RhaS; Provisional

Probab=95.75  E-value=0.16  Score=44.19  Aligned_cols=80  Identities=16%  Similarity=0.187  Sum_probs=61.2

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHH-H
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEE-I  123 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e-~  123 (229)
                      -...+|+.++|+.+|+++++|.+-.++. |..            +-.                           |=.+ -
T Consensus       184 ~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S------------~~~---------------------------yi~~~R  224 (278)
T PRK13503        184 FAEEVNWEALADQFSLSLRTLHRQLKQQTGLT------------PQR---------------------------YLNRLR  224 (278)
T ss_pred             hcCCCCHHHHHHHHCCCHHHHHHHHHHHhCcC------------HHH---------------------------HHHHHH
Confidence            3468999999999999999999999874 443            111                           1112 2


Q ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCccc
Q psy17316        124 LNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRLA  164 (229)
Q Consensus       124 k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~~  164 (229)
                      +.+|.+++..+..|+.+||.+.|=+..+ ..+.-|++ |+.+.
T Consensus       225 l~~A~~LL~~~~~sI~eIA~~~GF~~~s~F~r~FKk~~G~TP~  267 (278)
T PRK13503        225 LLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRREFSWSPR  267 (278)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHH
Confidence            5788888888888999999999999987 88877765 76553

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

Probab=95.75  E-value=0.058  Score=40.66  Aligned_cols=70  Identities=13%  Similarity=0.096  Sum_probs=49.9

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHh-CCCcHHHHHHHhCCChHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRS-GQTTVQRASAEYGIPSGT  206 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~-~~~s~~eAA~~fgVp~~t  206 (229)
                      +++.++|+.+||+.+||+.|.+. |+-......+..|.|+++  +++..|..+.+ -+++..++....+...+.
T Consensus         1 ~~I~e~a~~~gvs~~tLR~ye~~-Gll~p~r~~~g~R~Y~~~dv~~l~~I~~L~~~~G~~l~ei~~~l~~~~~~   73 (96)
T cd04774           1 YKVDEVAKRLGLTKRTLKYYEEI-GLVSPERSEGRYRLYSEEDLKRLERILRLREVLGFSLQEVTHFLERPLEP   73 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCCCCCEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHhccccc
Confidence            47889999999999999999873 643322122346678755  46666777777 678888888877765543

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

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

Probab=95.74  E-value=0.15  Score=38.24  Aligned_cols=68  Identities=15%  Similarity=0.109  Sum_probs=47.3

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+||+..||+.|-+. |+-.|.....+                              ....|++++  ....
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~~-Gll~p~~~~~~------------------------------gyR~Y~~~~~~~l~~   49 (97)
T cd04782           1 FTTGEFAKLCGISKQTLFHYDKI-GLFKPEIVKEN------------------------------GYRYYTLEQFEQLDI   49 (97)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCC------------------------------CCccCCHHHHHHHHH
Confidence            47899999999999999999774 55433221111                              134555555  4666


Q ss_pred             HHHHHcCCCCHHHHHHHhCCC
Q psy17316        128 LDALRAGSISANKASKAYGIP  148 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gIp  148 (229)
                      |..+..-++|+.+|..-+.-.
T Consensus        50 I~~lr~~G~~l~eI~~~l~~~   70 (97)
T cd04782          50 ILLLKELGISLKEIKDYLDNR   70 (97)
T ss_pred             HHHHHHcCCCHHHHHHHHhcC
Confidence            778888888999998866544

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

>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=95.73  E-value=0.068  Score=40.25  Aligned_cols=66  Identities=12%  Similarity=0.230  Sum_probs=48.3

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCC-cccCCCCCCCCCCCHH--HHHHHHHHHHh-CCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGI-RLAQPFNASPTAWKPE--DLEIALEGIRS-GQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~-k~~~~~~~~~r~~t~e--~r~eaV~~~~~-~~~s~~eAA~~fgV  202 (229)
                      +++.++|+++||+.+||+.|.+ .|+ ..........+.|+++  .++..|+.+.+ -+++..++...+..
T Consensus         1 m~I~eva~~~gvs~~tlR~Ye~-~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~   70 (95)
T cd04780           1 MRMSELSKRSGVSVATIKYYLR-EGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA   70 (95)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            4789999999999999999998 443 2211111234667665  56777778876 57999999998876

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>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=95.72  E-value=0.029  Score=35.75  Aligned_cols=40  Identities=23%  Similarity=0.285  Sum_probs=30.4

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..++++..... ++--.++|..+||+.+|++.+|+++|+++
T Consensus        10 ~l~~~~~~~~~-~~~~~~~~~~~ia~~~~~s~~~i~~~~~~   49 (55)
T cd06171          10 KLPEREREVIL-LRFGEGLSYEEIAEILGISRSTVRQRLHR   49 (55)
T ss_pred             hCCHHHHHHHH-HHHhcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            34555544444 44345789999999999999999999886

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

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=95.72  E-value=0.022  Score=43.17  Aligned_cols=42  Identities=10%  Similarity=0.155  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhcCCC
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRSTP  218 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~~~~  218 (229)
                      ..|..++..+.++++|++++|.++|||.+||-++-+....++
T Consensus        42 ~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk~~~   83 (94)
T TIGR01321        42 GDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNLKTMD   83 (94)
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhcccCC
Confidence            357888888889999999999999999999999988554443

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.

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

Probab=95.71  E-value=0.076  Score=40.37  Aligned_cols=66  Identities=12%  Similarity=0.136  Sum_probs=48.6

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      +++.++|+.+|||.+||+-|-+. |.-.........|.|+++  +++..|+.+.+-+++..++...+.-
T Consensus         2 ~~i~eva~~~gvs~~tlR~ye~~-Gll~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l~~   69 (102)
T cd04789           2 YTISELAEKAGISRSTLLYYEKL-GLITGTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQG   69 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCCCCCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHHcC
Confidence            58899999999999999999884 543222112346788766  5666777888877999998876643

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

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

Probab=95.70  E-value=0.028  Score=36.21  Aligned_cols=45  Identities=22%  Similarity=0.197  Sum_probs=31.5

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEI  181 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~e  181 (229)
                      +|+.++|+.+||+.+||+.|+++-.+.... ..+..+.|++++...
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~~~g~l~~~~-~~~~~~~y~~~~v~~   45 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYERIGLLSPAR-TEGGYRLYSDADLER   45 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHCCCCCCCc-CCCCCEEeCHHHHHH
Confidence            478999999999999999999854333211 123456788766544

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

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

Probab=95.69  E-value=0.051  Score=41.76  Aligned_cols=26  Identities=23%  Similarity=0.472  Sum_probs=22.8

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      |++.++|+.+|||..||+.|-+. |.-
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~~-Gll   26 (108)
T cd04773           1 MTIGELAHLLGVPPSTLRHWEKE-GLL   26 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence            68999999999999999999886 543

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

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

Probab=95.68  E-value=0.072  Score=40.47  Aligned_cols=65  Identities=15%  Similarity=0.232  Sum_probs=44.1

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+|||.+||+.|-+. |.-.|....                               +....|++++  +...
T Consensus         2 ~~i~eva~~~gvs~~tlR~ye~~-Gll~~~r~~-------------------------------~g~R~Y~~~~l~~l~~   49 (102)
T cd04789           2 YTISELAEKAGISRSTLLYYEKL-GLITGTRNA-------------------------------NGYRLYPDSDLQRLLL   49 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCC-------------------------------CCCeeCCHHHHHHHHH
Confidence            68899999999999999999886 543331111                               1234455554  3456


Q ss_pred             HHHHHcCCCCHHHHHHHhC
Q psy17316        128 LDALRAGSISANKASKAYG  146 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~g  146 (229)
                      |..+.+-++|+.+|...+.
T Consensus        50 I~~l~~~G~~l~ei~~~l~   68 (102)
T cd04789          50 IQQLQAGGLSLKECLACLQ   68 (102)
T ss_pred             HHHHHHCCCCHHHHHHHHc
Confidence            6777776788888866553

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

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

Probab=95.68  E-value=0.074  Score=41.50  Aligned_cols=67  Identities=16%  Similarity=0.196  Sum_probs=51.9

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP  203 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp  203 (229)
                      +++.++|+++|||..||+-|-+. |.-......+..|.|+++  +++..|..+.+-+++..++...++-.
T Consensus         1 m~IgevA~~~gvs~~tlRyYe~~-GLl~p~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~L~eI~~~l~~~   69 (120)
T cd04781           1 LDIAEVARQSGLPASTLRYYEEK-GLIASIGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHD   69 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence            47899999999999999999884 543222122356788765  67788889999889999999988765

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

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

Probab=95.66  E-value=0.064  Score=41.87  Aligned_cols=67  Identities=13%  Similarity=0.257  Sum_probs=47.4

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      |++.++|+.+|||..||+.|-+. |+-.|....                               |....|++++  ++..
T Consensus         1 m~IgevA~~~gvs~~tlRyYe~~-GLl~p~~~~-------------------------------~gyR~Y~~~~l~~l~~   48 (120)
T cd04781           1 LDIAEVARQSGLPASTLRYYEEK-GLIASIGRR-------------------------------GLRRQYDPQVLDRLAL   48 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCC-------------------------------CCceecCHHHHHHHHH
Confidence            68999999999999999999887 443231111                               1234455555  4566


Q ss_pred             HHHHHcCCCCHHHHHHHhCCC
Q psy17316        128 LDALRAGSISANKASKAYGIP  148 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gIp  148 (229)
                      |..+..-++|+.+|.+-++-.
T Consensus        49 I~~lr~~G~~L~eI~~~l~~~   69 (120)
T cd04781          49 IALGRAAGFSLDEIQAMLSHD   69 (120)
T ss_pred             HHHHHHcCCCHHHHHHHHhcc
Confidence            778888788999998877654

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

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=95.61  E-value=0.021  Score=53.55  Aligned_cols=39  Identities=21%  Similarity=0.319  Sum_probs=31.3

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      +..+.+++...+....++|+.+||+++|||+++++||+.
T Consensus       419 ~~~i~~al~~~~gn~~~aA~~LGisr~tL~rkl~~~~i~  457 (457)
T PRK11361        419 KRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEYGID  457 (457)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHhCCC
Confidence            333444555555689999999999999999999999874

>PRK09978 DNA-binding transcriptional regulator GadX; Provisional

Probab=95.61  E-value=0.061  Score=48.22  Aligned_cols=88  Identities=11%  Similarity=0.093  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPT  116 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~  116 (229)
                      .+...|+.-....+++.++|..+|+++++|.+..++.|..            +.                          
T Consensus       146 ~v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk~~G~S------------~~--------------------------  187 (274)
T PRK09978        146 RVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETS------------YS--------------------------  187 (274)
T ss_pred             HHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHhcCCC------------HH--------------------------
Confidence            3345555445568999999999999999999999865321            11                          


Q ss_pred             CCCCH-HHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        117 KSWNE-EILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       117 ~kYs~-e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                       .|-. .-+..|.+++..+..|+.+||...|-...+ +.+..|++ |+.+
T Consensus       188 -~yl~~~Rl~~A~~LL~~t~~sI~eIA~~~GF~s~S~Fsr~FKk~~G~TP  236 (274)
T PRK09978        188 -QLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTP  236 (274)
T ss_pred             -HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence             1111 224677888887888999999999999866 77777765 7544

>PRK01381 Trp operon repressor; Provisional

Probab=95.57  E-value=0.015  Score=44.48  Aligned_cols=35  Identities=20%  Similarity=0.271  Sum_probs=29.8

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..++..+..|++|+++||.++||+.+||.|=.+.+
T Consensus        45 ~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~L   79 (99)
T PRK01381         45 VRIVEELLRGELSQREIKQELGVGIATITRGSNSL   79 (99)
T ss_pred             HHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHh
Confidence            46677778999999999999999999999866643

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

Probab=95.56  E-value=0.022  Score=44.09  Aligned_cols=35  Identities=14%  Similarity=0.084  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +=.||++++.-.++++.+||.+.|||++|+++.+.
T Consensus        45 dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~   79 (106)
T PF02001_consen   45 DELEAIRLVDYEGLSQEEAAERMGVSRPTFQRILE   79 (106)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHH
Confidence            34789999999999999999999999999999886

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

Probab=95.55  E-value=0.065  Score=42.27  Aligned_cols=66  Identities=12%  Similarity=0.085  Sum_probs=44.3

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      |++.++|+.+||+..||+.|-+..-+..+....                               +....|++++  +...
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe~~GLl~~~~r~~-------------------------------~g~R~Y~~~~~~~l~~   49 (127)
T cd01108           1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSD-------------------------------NGYRVYNQRDIEELRF   49 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCceecCHHHHHHHHH
Confidence            689999999999999999998873333221111                               0133455444  4556


Q ss_pred             HHHHHcCCCCHHHHHHHhC
Q psy17316        128 LDALRAGSISANKASKAYG  146 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~g  146 (229)
                      |..+..-++|+.+|..-+.
T Consensus        50 I~~lr~~G~sL~eI~~~l~   68 (127)
T cd01108          50 IRRARDLGFSLEEIRELLA   68 (127)
T ss_pred             HHHHHHcCCCHHHHHHHHH
Confidence            6777777788888877654

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

>PRK15185 transcriptional regulator HilD; Provisional

Probab=95.53  E-value=0.061  Score=49.03  Aligned_cols=87  Identities=18%  Similarity=0.165  Sum_probs=63.2

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCC
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKS  118 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~k  118 (229)
                      ...|+.-.....|+.++|+.+|+++++|.++.+.+|...   .        +..                          
T Consensus       212 ~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK~~G~S~---~--------~yl--------------------------  254 (309)
T PRK15185        212 YNIISSSPSRQWKLTDVADHIFMSTSTLKRKLAEEGTSF---S--------DIY--------------------------  254 (309)
T ss_pred             HHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCH---H--------HHH--------------------------
Confidence            344443344678999999999999999999998654431   0        001                          


Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        119 WNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       119 Ys~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                       ....+..|.+++..+..|+.+||...|-...+ +.+..|++ |..+
T Consensus       255 -~~~Ri~~A~~LL~~t~~sIseIA~~~GFss~S~FsR~FKk~~G~TP  300 (309)
T PRK15185        255 -LSARMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCFKKYFKTTP  300 (309)
T ss_pred             -HHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence             11235778888888889999999999998866 88888765 6443

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

Probab=95.52  E-value=0.091  Score=39.66  Aligned_cols=66  Identities=15%  Similarity=0.140  Sum_probs=46.9

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHH--HHHHHHHHHh-CCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPED--LEIALEGIRS-GQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~--r~eaV~~~~~-~~~s~~eAA~~fgV  202 (229)
                      +++.++|+.+||+.+||+.|.+ .|+-......+..+.|+.++  ++..|..+.+ -+++..++...+..
T Consensus         2 ~~i~eva~~~gVs~~tLR~ye~-~Gli~p~r~~~g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~l~l   70 (98)
T cd01279           2 YPISVAAELLGIHPQTLRVYDR-LGLVSPARTNGGGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIEL   70 (98)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH-CCCCCCCcCCCCCeeECHHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            4789999999999999999987 56432211123457787664  4455556666 67999999887655

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

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

Probab=95.52  E-value=0.041  Score=35.94  Aligned_cols=38  Identities=16%  Similarity=0.174  Sum_probs=29.7

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ++.+.. ++..+. +++|..+||+.+||+.+|++.++++.
T Consensus         2 ~~~e~~-i~~~~~-~~~s~~eia~~l~~s~~tv~~~~~~~   39 (57)
T cd06170           2 TPRERE-VLRLLA-EGKTNKEIADILGISEKTVKTHLRNI   39 (57)
T ss_pred             CHHHHH-HHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            344444 555554 67899999999999999999998863

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

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

Probab=95.50  E-value=0.076  Score=40.84  Aligned_cols=66  Identities=12%  Similarity=0.156  Sum_probs=44.1

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+||+..||+.|-+. |.-.|.....                              |....|++++  ++..
T Consensus         1 y~Ige~A~~~gvs~~tlR~ye~~-GLl~p~~r~~------------------------------~g~R~Y~~~~l~~l~~   49 (107)
T cd01111           1 YSISQLALDAGVSVHIVRDYLLR-GLLHPVARTE------------------------------GGYGLFDDCALQRLRF   49 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCcCC------------------------------CCCeecCHHHHHHHHH
Confidence            47899999999999999999887 5433321111                              1234455555  4556


Q ss_pred             HHHHHcCCCCHHHHHHHhC
Q psy17316        128 LDALRAGSISANKASKAYG  146 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~g  146 (229)
                      |..+.+-++|+.+|.....
T Consensus        50 I~~lr~~G~~l~~I~~~l~   68 (107)
T cd01111          50 VRAAFEAGIGLDELARLCR   68 (107)
T ss_pred             HHHHHHcCCCHHHHHHHHH
Confidence            7777777778888876553

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

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

Probab=95.46  E-value=0.1  Score=40.63  Aligned_cols=67  Identities=10%  Similarity=0.062  Sum_probs=49.7

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcc-cCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRL-AQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP  203 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~-~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp  203 (229)
                      +++.++|+.+||+..||+-|-+ .|.-. .....+..|.|+++  .++..|..+.+-+++..++...++..
T Consensus         1 ~~I~eva~~~gvs~~tLRyYe~-~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~~   70 (123)
T cd04770           1 MKIGELAKAAGVSPDTIRYYER-IGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLR   70 (123)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCCCCCCCCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence            4789999999999999988777 35322 11112346788765  56778888888889999999888653

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

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

Probab=95.45  E-value=0.082  Score=40.59  Aligned_cols=66  Identities=14%  Similarity=0.228  Sum_probs=46.7

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCC-CCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPF-NASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~-~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      +++.++|+.+|||..||+.|.+. |.-..... .+..|.|+++  .++..|..+.+-+++..++...+..
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~~-Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~   69 (108)
T cd04773           1 MTIGELAHLLGVPPSTLRHWEKE-GLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQ   69 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence            47899999999999999999884 54222111 1345678766  4666777777777888888776653

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

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

Probab=95.44  E-value=0.083  Score=39.82  Aligned_cols=26  Identities=15%  Similarity=0.213  Sum_probs=22.6

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      +++.++|+.+||+.+||+.|.+. |+-
T Consensus         1 ~~I~e~a~~~gvs~~tLR~ye~~-Gll   26 (96)
T cd04774           1 YKVDEVAKRLGLTKRTLKYYEEI-GLV   26 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence            57899999999999999999875 544

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

>PRK15115 response regulator GlrR; Provisional

Probab=95.43  E-value=0.022  Score=53.24  Aligned_cols=41  Identities=15%  Similarity=0.186  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      ++..+.+++...+....++|+.+||+++|||+++++||+..
T Consensus       399 E~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~~~~~~~  439 (444)
T PRK15115        399 ELNYLRKLLQITKGNVTHAARMAGRNRTEFYKLLSRHELDA  439 (444)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhCCCc
Confidence            33444445555555899999999999999999999999963

>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators

Probab=95.41  E-value=0.071  Score=42.12  Aligned_cols=66  Identities=9%  Similarity=0.102  Sum_probs=44.8

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+||+.+||+.|-+. |+-.|....                                ....|++++  +++.
T Consensus         2 ysI~eVA~~~GVs~~TLR~wE~~-GLl~p~r~~--------------------------------G~R~Ys~~dv~rL~~   48 (120)
T cd04767           2 YPIGVVAELLNIHPETLRIWERH-GLIKPARRN--------------------------------GQRLYSNNDLKRLRF   48 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCcCCC--------------------------------CcEEECHHHHHHHHH
Confidence            68999999999999999999997 443332211                                234555555  3455


Q ss_pred             HHHHHc-CCCCHHHHHHHhCCC
Q psy17316        128 LDALRA-GSISANKASKAYGIP  148 (229)
Q Consensus       128 V~~~~~-g~~S~~~~a~k~gIp  148 (229)
                      |..+.. .++++.+|.....+-
T Consensus        49 I~~L~~e~G~~l~eI~~~L~l~   70 (120)
T cd04767          49 IKKLINEKGLNIAGVKQILSMY   70 (120)
T ss_pred             HHHHHHHcCCCHHHHHHHHHhC
Confidence            666655 667888887765544

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

>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator

Probab=95.39  E-value=0.091  Score=41.73  Aligned_cols=66  Identities=15%  Similarity=0.104  Sum_probs=50.3

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      +++.++|+.+||+..||+-|-+. |+- .........|.|+++  +++..|..+.+-+++..++...+..
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~~-GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~   70 (131)
T TIGR02043         2 FQIGELAKLCGVTSDTLRFYEKN-GLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLSI   70 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            58899999999999999999985 532 221112346788755  6778888888888999999988764

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

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

Probab=95.36  E-value=0.095  Score=41.31  Aligned_cols=65  Identities=8%  Similarity=0.074  Sum_probs=49.0

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcc-cCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRL-AQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYG  201 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~-~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fg  201 (229)
                      +++.++|+++||+..||+-|-+. |.-. ........|.|+++  +++..|..+.+=+++..++...+.
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe~~-GLl~~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~   68 (127)
T cd01108           1 MNIGEAAKLTGLSAKMIRYYEEI-GLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLA   68 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            47899999999999999999884 5322 21112346778765  567778888888899999998775

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

>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=95.35  E-value=0.017  Score=42.40  Aligned_cols=40  Identities=10%  Similarity=0.243  Sum_probs=28.4

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      |=++-.+++.+-+.+.+.+++++|+.||||+|||++=+..
T Consensus         3 yIeeR~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvte   42 (82)
T PF12116_consen    3 YIEERVIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTE   42 (82)
T ss_dssp             THHHHHHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHH
Confidence            3345556777777788999999999999999999987653

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.

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=95.34  E-value=0.025  Score=52.93  Aligned_cols=39  Identities=23%  Similarity=0.334  Sum_probs=31.5

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      +..+.+++...+..+.++|+.+||+++|||+++++||+.
T Consensus       407 ~~~i~~al~~~~gn~~~aA~~Lgisr~tl~rkl~~~~i~  445 (445)
T TIGR02915       407 REAVRKAIARVDGNIARAAELLGITRPTLYDLMKKHGIK  445 (445)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence            334445555556689999999999999999999999873

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

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

Probab=95.32  E-value=0.11  Score=40.81  Aligned_cols=67  Identities=12%  Similarity=0.091  Sum_probs=51.5

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcc-cCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRL-AQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP  203 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~-~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp  203 (229)
                      +++.++|+.+||+..||+-|-+ .|.-. .....+..|.|+++  .++..|..+.+-+++..++...++..
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~-~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~   70 (126)
T cd04783           1 LTIGELAKAAGVNVETIRYYQR-RGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELD   70 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence            4789999999999999988866 45322 22112356888877  66778888899889999999988765

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

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

Probab=95.31  E-value=0.053  Score=35.40  Aligned_cols=32  Identities=16%  Similarity=0.115  Sum_probs=27.2

Q ss_pred             HHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        180 EIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       180 ~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+++..+. +++++.++|..++||..||+.+++
T Consensus         6 ~~i~~~~~-~~~s~~eia~~l~~s~~tv~~~~~   37 (57)
T cd06170           6 REVLRLLA-EGKTNKEIADILGISEKTVKTHLR   37 (57)
T ss_pred             HHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHH
Confidence            33776655 559999999999999999999987

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

>PF12728 HTH_17: Helix-turn-helix domain

Probab=95.31  E-value=0.027  Score=36.96  Aligned_cols=46  Identities=24%  Similarity=0.283  Sum_probs=31.0

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIAL  183 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV  183 (229)
                      +|+.++|+.+||+.+|+++|++.-.++...  .++...|..++..+-+
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g~i~~~~--~g~~~~~~~~~l~~~~   47 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQGKIPPFK--IGRKWRIPKSDLDRWL   47 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCCeEE--eCCEEEEeHHHHHHHH
Confidence            589999999999999999999865543331  2233445554444433

>PRK13501 transcriptional activator RhaR; Provisional

Probab=95.30  E-value=0.27  Score=43.37  Aligned_cols=88  Identities=16%  Similarity=0.139  Sum_probs=66.4

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCC
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPT  116 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~  116 (229)
                      +..+|+.-....+++.++|+.+|+++++|.+..++. |..            +-..   +                    
T Consensus       181 i~~~I~~~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~~G~T------------~~qy---i--------------------  225 (290)
T PRK13501        181 IMSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMS------------ISHY---L--------------------  225 (290)
T ss_pred             HHHHHHHhhccCCCHHHHHHHHCcCHHHHHHHHHHHHCcC------------HHHH---H--------------------
Confidence            466666666678999999999999999999999974 332            1111   0                    


Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        117 KSWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       117 ~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                         .+--+.+|.+++..+..|+.+||.+.|=+..+ ..+..|++ |...
T Consensus       226 ---~~~Ri~~A~~LL~~t~~sI~eIA~~~GF~~~s~F~r~FKk~~G~TP  271 (290)
T PRK13501        226 ---RQIRLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTREAGMTP  271 (290)
T ss_pred             ---HHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence               01135788889999989999999999999877 77777765 6544

>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators

Probab=95.28  E-value=0.12  Score=40.12  Aligned_cols=67  Identities=9%  Similarity=0.079  Sum_probs=50.4

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP  203 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp  203 (229)
                      +++.++|+.+|||..||+-|.+. |.-.........|.|+++  .++..|..+.+-+++..++...+...
T Consensus         1 ~~ige~a~~~gvs~~tLryYe~~-GLi~p~~~~~~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~~   69 (116)
T cd04769           1 MYIGELAQQTGVTIKAIRLYEEK-GLLPSPKRSGNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGH   69 (116)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence            57899999999999999999884 542221112245778665  56778888999999999999887653

Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK13182 racA polar chromosome segregation protein; Reviewed

Probab=95.28  E-value=0.07  Score=44.79  Aligned_cols=62  Identities=11%  Similarity=0.139  Sum_probs=44.8

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPED--LEIALEGIRSGQTTVQRASA  198 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~  198 (229)
                      +++.++|+.+||+..||++|.+..++...+. .+..|.|++++  +++-|..+.+-+|+..++-.
T Consensus         1 mti~evA~~lGVS~~TLRrw~k~g~L~~~R~-~~G~R~y~~~dl~~L~~I~~l~~~Gm~i~~i~~   64 (175)
T PRK13182          1 MKTPFVAKKLGVSPKTVQRWVKQLNLPCEKN-EYGHYIFTEEDLQLLEYVKSQIEEGQNMQDTQK   64 (175)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCCCCcC-CCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence            4789999999999999999999888754321 23357787664  44455555566688888755

>PRK15043 transcriptional regulator MirA; Provisional

Probab=95.26  E-value=0.082  Score=46.61  Aligned_cols=68  Identities=12%  Similarity=0.071  Sum_probs=52.0

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP  203 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp  203 (229)
                      +++.++|+.+||+..||+.|.+++|.-......+..|-|+++  +++..|..+.+.+++..++...+.-.
T Consensus         4 ytIgeVA~~~GVs~~TLR~wErr~GLL~P~Rt~~G~R~Ys~~dv~rL~~I~~l~~~G~~i~eIk~ll~~~   73 (243)
T PRK15043          4 YTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSNE   73 (243)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhcCCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence            589999999999999999999888854322122446778766  56666777788889999998877543

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=95.23  E-value=0.025  Score=54.92  Aligned_cols=40  Identities=28%  Similarity=0.394  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      ++..+-+++...+-+...+|+.+||+++|||+|+++|++.
T Consensus       521 Ek~~I~~aL~~~~gn~~~aAk~LgIsrttL~rKlkk~~l~  560 (560)
T COG3829         521 EKHLIREALERHGGNKSKAAKELGISRTTLYRKLKKYGLR  560 (560)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhcCC
Confidence            3333334444445589999999999999999999999863

>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator

Probab=95.23  E-value=0.1  Score=41.45  Aligned_cols=66  Identities=11%  Similarity=0.109  Sum_probs=45.7

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+||+..||+.|-+. |+-.|.....                              +....|++++  ++..
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~~-GLl~p~~r~~------------------------------~gyR~Y~~~~l~~l~~   50 (131)
T TIGR02043         2 FQIGELAKLCGVTSDTLRFYEKN-GLIKPAGRTD------------------------------SGYRLYTDEDQKRLRF   50 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCcCC------------------------------CCceecCHHHHHHHHH
Confidence            68999999999999999999987 5433321111                              0134455544  4566


Q ss_pred             HHHHHcCCCCHHHHHHHhC
Q psy17316        128 LDALRAGSISANKASKAYG  146 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~g  146 (229)
                      |..+.+-++|+.+|..-+.
T Consensus        51 I~~lr~~G~sl~eI~~~l~   69 (131)
T TIGR02043        51 ILKAKELGFTLDEIKELLS   69 (131)
T ss_pred             HHHHHHcCCCHHHHHHHHH
Confidence            7777777789998887665

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

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

Probab=95.21  E-value=0.1  Score=39.42  Aligned_cols=28  Identities=29%  Similarity=0.413  Sum_probs=23.4

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~   78 (229)
                      +++.++|+.+||+.+||+.|.+ .|+-.|
T Consensus         2 ~~i~eva~~~gVs~~tLR~ye~-~Gli~p   29 (98)
T cd01279           2 YPISVAAELLGIHPQTLRVYDR-LGLVSP   29 (98)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH-CCCCCC
Confidence            5789999999999999999987 565433

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

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

Probab=95.21  E-value=0.05  Score=36.43  Aligned_cols=41  Identities=15%  Similarity=0.132  Sum_probs=34.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.|.+|.+-.+-.+...+.+...+|..|||+++|+.++++.
T Consensus         2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~   42 (53)
T PF13613_consen    2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHE   42 (53)
T ss_pred             CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHH
Confidence            45667776666677777889999999999999999999886

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

Probab=95.20  E-value=0.11  Score=40.80  Aligned_cols=67  Identities=10%  Similarity=0.074  Sum_probs=45.7

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      |++.++|+.+||+..||+.|-+..-+..+....                               |....|++++  +...
T Consensus         1 ~~I~e~a~~~gvs~~tlR~Ye~~Gll~~~~r~~-------------------------------~g~R~Y~~~~l~~l~~   49 (126)
T cd04785           1 LSIGELARRTGVNVETIRYYESIGLLPEPARTA-------------------------------GGYRLYGAAHVERLRF   49 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCccccCHHHHHHHHH
Confidence            688999999999999999998864443221111                               1133455554  4556


Q ss_pred             HHHHHcCCCCHHHHHHHhCC
Q psy17316        128 LDALRAGSISANKASKAYGI  147 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gI  147 (229)
                      |..+..-++|+.+|..-+..
T Consensus        50 I~~lr~~G~sL~eI~~~l~~   69 (126)
T cd04785          50 IRRARDLGFSLEEIRALLAL   69 (126)
T ss_pred             HHHHHHCCCCHHHHHHHHhh
Confidence            77777777899988876654

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

>TIGR02044 CueR Cu(I)-responsive transcriptional regulator

Probab=95.20  E-value=0.12  Score=40.63  Aligned_cols=65  Identities=9%  Similarity=0.106  Sum_probs=48.9

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYG  201 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fg  201 (229)
                      +++.++|+.+||+..||+-|-+ .|.- ......+..|.|+++  .++..|..+..=+++..++...+.
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe~-~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~   68 (127)
T TIGR02044         1 MNIGQVAKLTGLSSKMIRYYEE-KGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLN   68 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            5789999999999999999887 4432 221112346788766  567788888888899999998775

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

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

Probab=95.20  E-value=0.03  Score=52.83  Aligned_cols=36  Identities=28%  Similarity=0.262  Sum_probs=29.8

Q ss_pred             HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      +..++...+....++|+.+||+++|||+++++||++
T Consensus       434 i~~aL~~~~gn~~~aA~~Lgisr~tL~rkl~~~~i~  469 (469)
T PRK10923        434 LTTALRHTQGHKQEAARLLGWGRNTLTRKLKELGME  469 (469)
T ss_pred             HHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence            334555556689999999999999999999999874

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

Probab=95.20  E-value=0.13  Score=40.07  Aligned_cols=67  Identities=12%  Similarity=0.140  Sum_probs=44.7

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      |++.++|+.+||+..||+.|-+. |+-.|.....                              +....|+++.  .+..
T Consensus         1 ~~I~eva~~~gvs~~tLRyYe~~-GLl~p~~r~~------------------------------~gyR~Y~~~~i~~l~~   49 (123)
T cd04770           1 MKIGELAKAAGVSPDTIRYYERI-GLLPPPQRSE------------------------------NGYRLYGEADLARLRF   49 (123)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCCCC------------------------------CCCccCCHHHHHHHHH
Confidence            68899999999999999988775 4332211111                              1134455554  4566


Q ss_pred             HHHHHcCCCCHHHHHHHhCC
Q psy17316        128 LDALRAGSISANKASKAYGI  147 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gI  147 (229)
                      |..+.+-++|+.+|..-+..
T Consensus        50 I~~lr~~G~sl~eI~~~l~~   69 (123)
T cd04770          50 IRRAQALGFSLAEIRELLSL   69 (123)
T ss_pred             HHHHHHCCCCHHHHHHHHHh
Confidence            77777778898888776653

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

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

Probab=95.18  E-value=0.21  Score=41.54  Aligned_cols=70  Identities=14%  Similarity=0.263  Sum_probs=49.5

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+||+..||+.|-+. |+-.|.....                              +....|++++  ++..
T Consensus         2 ~~I~evA~~~gvs~~tLRyYe~~-GLl~p~~r~~------------------------------~gyR~Y~~~dl~rL~~   50 (172)
T cd04790           2 LTISQLARQFGLSRSTLLYYERI-GLLSPSARSE------------------------------SNYRLYGERDLERLEQ   50 (172)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCC------------------------------CCCccCCHHHHHHHHH
Confidence            58999999999999999999875 5443322111                              1234566654  5667


Q ss_pred             HHHHHcCCCCHHHHHHHhCCChH
Q psy17316        128 LDALRAGSISANKASKAYGIPSS  150 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gIp~s  150 (229)
                      |..+.+-++|+.+|..-...+..
T Consensus        51 I~~lr~~G~sL~eI~~ll~~~~~   73 (172)
T cd04790          51 ICAYRSAGVSLEDIRSLLQQPGD   73 (172)
T ss_pred             HHHHHHcCCCHHHHHHHHhcCCh
Confidence            88888888899999887765543

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

>TIGR02044 CueR Cu(I)-responsive transcriptional regulator

Probab=95.18  E-value=0.12  Score=40.74  Aligned_cols=66  Identities=12%  Similarity=0.155  Sum_probs=44.4

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      |++.++|+.+||+..||+.|-+..-+..+....                               +....|++++  +...
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe~~GLl~p~~r~~-------------------------------~gyR~Y~~~~l~~l~~   49 (127)
T TIGR02044         1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSE-------------------------------GGYRTYTQQHLDELRL   49 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCCeecCHHHHHHHHH
Confidence            689999999999999999998764333221111                               1134455554  3556


Q ss_pred             HHHHHcCCCCHHHHHHHhC
Q psy17316        128 LDALRAGSISANKASKAYG  146 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~g  146 (229)
                      |..+..-++|+.+|..-+.
T Consensus        50 I~~lr~~G~sL~eI~~~l~   68 (127)
T TIGR02044        50 ISRARQVGFSLEECKELLN   68 (127)
T ss_pred             HHHHHHCCCCHHHHHHHHH
Confidence            7777777788888877654

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

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

Probab=95.17  E-value=0.046  Score=41.35  Aligned_cols=33  Identities=21%  Similarity=0.347  Sum_probs=27.7

Q ss_pred             HHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         43 EALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        43 ~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      +.+...+..+.++|+.+||+++||+++++++|+
T Consensus        62 ~aL~~~~gn~s~AAr~LGIsRsTL~rKLkr~gi   94 (95)
T PRK00430         62 MVMQYTRGNQTRAALMLGINRGTLRKKLKKYGM   94 (95)
T ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhCC
Confidence            344444558999999999999999999999986

>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=95.16  E-value=0.059  Score=35.30  Aligned_cols=38  Identities=13%  Similarity=0.179  Sum_probs=28.4

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ++++. .+|..+--.++|+.+||+.+|||.+|++++.++
T Consensus         6 ~~~er-~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~   43 (50)
T PF04545_consen    6 PPRER-EVIRLRYFEGLTLEEIAERLGISRSTVRRILKR   43 (50)
T ss_dssp             -HHHH-HHHHHHHTST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CHHHH-HHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence            44444 444455567899999999999999999999875

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 ....

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=95.14  E-value=0.031  Score=54.19  Aligned_cols=34  Identities=18%  Similarity=0.256  Sum_probs=29.2

Q ss_pred             HHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         43 EALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        43 ~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      +++..++ +.+++|+++||+++|||+++++||+..
T Consensus       481 ~~l~~~~-~~~~aA~~LGisr~tL~rkl~~~gi~~  514 (520)
T PRK10820        481 RLYRNYP-STRKLAKRLGVSHTAIANKLREYGLSQ  514 (520)
T ss_pred             HHHHHCC-CHHHHHHHhCCCHHHHHHHHHHcCCCc
Confidence            3455555 899999999999999999999999963

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

Probab=95.13  E-value=0.12  Score=40.56  Aligned_cols=68  Identities=10%  Similarity=0.148  Sum_probs=45.5

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      |++.++|+.+||+..||+.|-+..-+..|....                               |....|++++  +...
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~~GLl~~~~r~~-------------------------------~gyR~Y~~~~l~~l~~   49 (126)
T cd04783           1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRPE-------------------------------GGYRRYPEETVTRLRF   49 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCCeecCHHHHHHHHH
Confidence            688999999999999999886653333221111                               1234455554  3556


Q ss_pred             HHHHHcCCCCHHHHHHHhCCC
Q psy17316        128 LDALRAGSISANKASKAYGIP  148 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gIp  148 (229)
                      |..+.+-++|+.+|..-+...
T Consensus        50 I~~lr~~G~sL~eI~~~l~~~   70 (126)
T cd04783          50 IKRAQELGFTLDEIAELLELD   70 (126)
T ss_pred             HHHHHHcCCCHHHHHHHHhcc
Confidence            777777788998888776654

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

>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator

Probab=95.11  E-value=0.034  Score=46.06  Aligned_cols=46  Identities=24%  Similarity=0.468  Sum_probs=37.6

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcC-CChhhHHHHHHHhCCCCC
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYG-IPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~g-Ip~sTL~~~i~~~gi~~~   78 (229)
                      .||+|.+...-++. ..|+|..+||+++| |++..|.-+++++|+.+.
T Consensus         2 ~Wtde~~~~L~~lw-~~G~SasqIA~~lg~vsRnAViGk~hRlgL~~~   48 (162)
T PF07750_consen    2 SWTDERVERLRKLW-AEGLSASQIARQLGGVSRNAVIGKAHRLGLSGR   48 (162)
T ss_pred             CCCHHHHHHHHHHH-HcCCCHHHHHHHhCCcchhhhhhhhhccccccc
Confidence            47877776555444 55889999999999 999999999999987654

These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].

>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=95.10  E-value=0.043  Score=35.60  Aligned_cols=35  Identities=20%  Similarity=0.288  Sum_probs=26.2

Q ss_pred             HHHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEALR-AGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .+++..+. ++++|+.++|+.+|++.+|+++.++++
T Consensus         6 ~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L   41 (48)
T PF13412_consen    6 RKILNYLRENPRITQKELAEKLGISRSTVNRYLKKL   41 (48)
T ss_dssp             HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            34444333 678999999999999999999999875

...

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

Probab=95.08  E-value=0.13  Score=38.10  Aligned_cols=65  Identities=9%  Similarity=0.066  Sum_probs=46.7

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHh-CCCcHHHHHHHhC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRS-GQTTVQRASAEYG  201 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~-~~~s~~eAA~~fg  201 (229)
                      +++.++|+.+||+.+||+.|.+ .|+-......+..+.|+++  ++...|..+.+ -+++..++...++
T Consensus         2 ~~i~e~A~~~gvs~~tLr~ye~-~Gli~p~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~   69 (91)
T cd04766           2 YVISVAAELSGMHPQTLRLYER-LGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRILE   69 (91)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH-CCCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            4789999999999999999987 4543221112335667665  45666676666 6799999988776

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

>PHA00675 hypothetical protein

Probab=95.07  E-value=0.06  Score=39.20  Aligned_cols=41  Identities=10%  Similarity=0.135  Sum_probs=31.7

Q ss_pred             CCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        172 TAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       172 r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -+.+..+-.+|-.....-++|+.++|.+||||++||+.+.+
T Consensus        21 AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~   61 (78)
T PHA00675         21 AKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR   61 (78)
T ss_pred             cccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHc
Confidence            35666666666666624447999999999999999999876

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

Probab=95.06  E-value=0.15  Score=40.67  Aligned_cols=66  Identities=11%  Similarity=0.117  Sum_probs=50.1

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCC-cccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGI-RLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~-k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      +++.++|+.+||+..||+-|-+ .|. ..........|.|+++  .++..|..+..-++|..++...+..
T Consensus         1 m~Ige~a~~~gvs~~tLRyYE~-~GLl~p~~r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~   69 (131)
T cd04786           1 MKIGELAKRSGMAASRIRFYEA-EGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPA   69 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            5789999999999999999987 443 2221112345778655  6788899999988999999998864

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

>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators

Probab=95.05  E-value=0.13  Score=39.88  Aligned_cols=66  Identities=8%  Similarity=0.108  Sum_probs=46.6

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      |++.++|+.+||+..||+.|-+. |+-.|.....                               ....|++++  +...
T Consensus         1 ~~ige~a~~~gvs~~tLryYe~~-GLi~p~~~~~-------------------------------~yR~Y~~~d~~~l~~   48 (116)
T cd04769           1 MYIGELAQQTGVTIKAIRLYEEK-GLLPSPKRSG-------------------------------NYRVYDAQHVECLRF   48 (116)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCCCC-------------------------------CceeeCHHHHHHHHH
Confidence            68999999999999999999887 4433321111                               123455555  4666


Q ss_pred             HHHHHcCCCCHHHHHHHhCC
Q psy17316        128 LDALRAGSISANKASKAYGI  147 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gI  147 (229)
                      |..+..-++|+.+|..-+..
T Consensus        49 I~~lr~~G~sl~eI~~~l~~   68 (116)
T cd04769          49 IKEARQLGFTLAELKAIFAG   68 (116)
T ss_pred             HHHHHHcCCCHHHHHHHHhc
Confidence            78888888899998776544

Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional

Probab=95.05  E-value=0.12  Score=41.56  Aligned_cols=66  Identities=9%  Similarity=0.034  Sum_probs=50.2

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      +++.++|+.+||+..||+.|.+. |+- .........|.|+++  +++..|..+.+-+++..++...++.
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~~-GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~   70 (140)
T PRK09514          2 YRIGELAKLAEVTPDTLRFYEKQ-GLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSI   70 (140)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHC-CCCCCcccCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            57899999999999999999884 542 211112346788766  5677788888888999999998864

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

Probab=95.03  E-value=0.14  Score=39.32  Aligned_cols=66  Identities=5%  Similarity=-0.047  Sum_probs=49.3

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCccc-CCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLA-QPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~-~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      +++.++|+.+||+..||+.|-+. |.-.. ....+..|.|+++  .++..|+.+.+-+++..++...+..
T Consensus         1 y~Ige~A~~~gvs~~tlR~ye~~-GLl~p~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~   69 (107)
T cd01111           1 YSISQLALDAGVSVHIVRDYLLR-GLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRA   69 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            37889999999999999999884 64322 1112346778766  5677888888888999999887643

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

>PRK09393 ftrA transcriptional activator FtrA; Provisional

Probab=95.03  E-value=0.098  Score=47.09  Aligned_cols=85  Identities=18%  Similarity=0.173  Sum_probs=62.0

Q ss_pred             HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCC
Q psy17316         41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSW  119 (229)
Q Consensus        41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kY  119 (229)
                      .|+.-.+..+|+.++|+.+|++.++|.+..++. |...            ...                          +
T Consensus       226 ~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~g~s~------------~~~--------------------------~  267 (322)
T PRK09393        226 WMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTP------------AEW--------------------------L  267 (322)
T ss_pred             HHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH------------HHH--------------------------H
Confidence            333333457999999999999999999999984 5531            111                          0


Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        120 NEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       120 s~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                      ..--+..|.+++.+...|+.+||...|-+..+ +.+..|++ |..+
T Consensus       268 ~~~Rl~~A~~lL~~~~~~i~~IA~~~Gf~~~s~F~r~Fk~~~G~tP  313 (322)
T PRK09393        268 LRERLARARDLLESSALSIDQIAERAGFGSEESLRHHFRRRAATSP  313 (322)
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence            11234678888888888999999999998855 88877765 6544

>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA

Probab=95.01  E-value=0.44  Score=41.65  Aligned_cols=87  Identities=18%  Similarity=0.234  Sum_probs=63.0

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCC
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTK  117 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~  117 (229)
                      ...|++--...+|+.++|+.+|+++++|.+..++. |...            -..   +                     
T Consensus       192 ~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t~------------~~y---i---------------------  235 (287)
T TIGR02297       192 NFLIEENYKQHLRLPEYADRLGISESRLNDICRRFSALSP------------KRL---I---------------------  235 (287)
T ss_pred             HHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhCCCH------------HHH---H---------------------
Confidence            34444333457899999999999999999999983 4431            111   0                     


Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        118 SWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       118 kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                        ..--+.+|..+++....|+.+||...|-+..+ ..+..|++ |..+
T Consensus       236 --~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~s~s~Fsr~FKk~~G~tP  281 (287)
T TIGR02297       236 --IERVMQEARRLLLFTQHSINQIAYDLGYKDPAYFARFFQKETGLSP  281 (287)
T ss_pred             --HHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence              01235777788887888999999999999966 88877765 7544

This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.

>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional

Probab=95.00  E-value=0.12  Score=41.66  Aligned_cols=67  Identities=9%  Similarity=0.074  Sum_probs=45.6

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+||+..||+.|-+. |+-.|.....+                              ....|++++  ++..
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~~-GLl~p~~r~~~------------------------------gyR~Y~~~~l~~l~~   50 (140)
T PRK09514          2 YRIGELAKLAEVTPDTLRFYEKQ-GLMDPEVRTEG------------------------------GYRLYTEQDLQRLRF   50 (140)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHC-CCCCCcccCCC------------------------------CCeeeCHHHHHHHHH
Confidence            68899999999999999999887 54333211111                              133455444  3555


Q ss_pred             HHHHHcCCCCHHHHHHHhCC
Q psy17316        128 LDALRAGSISANKASKAYGI  147 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gI  147 (229)
                      |..+..-++|+.+|..-++.
T Consensus        51 I~~lr~~G~sL~eI~~~l~~   70 (140)
T PRK09514         51 IRRAKQLGFTLEEIRELLSI   70 (140)
T ss_pred             HHHHHHcCCCHHHHHHHHHh
Confidence            66777777899998887653

>PRK13502 transcriptional activator RhaR; Provisional

Probab=94.99  E-value=0.27  Score=43.03  Aligned_cols=86  Identities=16%  Similarity=0.140  Sum_probs=63.6

Q ss_pred             HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCC
Q psy17316         40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKS  118 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~k  118 (229)
                      ..|+.-....+++.++|..+||+++.|.+.++++ |...            -..   +                      
T Consensus       183 ~~I~~~~~~~~~~~~lA~~~~iS~~~L~r~fk~~~G~t~------------~~y---i----------------------  225 (282)
T PRK13502        183 TALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTI------------NQY---L----------------------  225 (282)
T ss_pred             HHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH------------HHH---H----------------------
Confidence            3333334557899999999999999999999983 5542            000   0                      


Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        119 WNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       119 Ys~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                       ..--+.+|.+++.++..|+.+||.+.|-+..+ ..+..|++ |..+
T Consensus       226 -~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~d~s~F~r~FKk~~G~tP  271 (282)
T PRK13502        226 -RQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTP  271 (282)
T ss_pred             -HHHHHHHHHHHHHcCCCCHHHHHHHcCCCCHHHHHHHHHHHHCcCH
Confidence             01235788889988889999999999999977 88877765 7544

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=94.99  E-value=0.038  Score=54.56  Aligned_cols=40  Identities=25%  Similarity=0.455  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      ++..+++++...+..+.++|+.+||+++|||+++++||+.
T Consensus       592 E~~~i~~al~~~~gn~~~aA~~LGisR~TLyrklk~~~i~  631 (638)
T PRK11388        592 EKEAIINAAQVCGGRIQEMAALLGIGRTTLWRKMKQHGID  631 (638)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHcCCC
Confidence            4455555666556689999999999999999999999985

>PRK00118 putative DNA-binding protein; Validated

Probab=94.98  E-value=0.043  Score=42.29  Aligned_cols=40  Identities=13%  Similarity=0.253  Sum_probs=31.5

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..++.+... +.....+++|+.+||+.+|||++||++++++
T Consensus        17 ~L~ekqRev-l~L~y~eg~S~~EIAe~lGIS~~TV~r~L~R   56 (104)
T PRK00118         17 LLTEKQRNY-MELYYLDDYSLGEIAEEFNVSRQAVYDNIKR   56 (104)
T ss_pred             cCCHHHHHH-HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            345555544 4455566899999999999999999999986

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

Probab=94.92  E-value=0.061  Score=34.57  Aligned_cols=28  Identities=25%  Similarity=0.449  Sum_probs=23.0

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .++.+|+.++|+..|++.+|+++++++.
T Consensus        14 ~d~r~s~~~la~~lglS~~~v~~Ri~rL   41 (42)
T PF13404_consen   14 EDGRRSYAELAEELGLSESTVRRRIRRL   41 (42)
T ss_dssp             H-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             HcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence            3689999999999999999999999874

...

>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]

Probab=94.91  E-value=0.12  Score=41.08  Aligned_cols=79  Identities=16%  Similarity=0.169  Sum_probs=45.2

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---C-CcccCCCCCCCCCCCHHHHHHHHHHHHhCC-C
Q psy17316        117 KSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---G-IRLAQPFNASPTAWKPEDLEIALEGIRSGQ-T  191 (229)
Q Consensus       117 ~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g-~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~-~  191 (229)
                      .-++.+.+++.|++..+|. +..+||+++.|+.+.+.+|+.+|   | +....-...+++..+++.-..|.++..++- +
T Consensus        16 rPLp~~~R~rIvela~~G~-rp~~Isr~l~Vs~gcVsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v~~~I~~~k~enP~i   94 (125)
T PF00292_consen   16 RPLPNELRQRIVELAKEGV-RPCDISRQLRVSHGCVSKILSRYRETGSIRPGPIGGSKPRVATPEVVEKIEQYKRENPTI   94 (125)
T ss_dssp             SSS-HHHHHHHHHHHHTT---HHHHHHHHT--HHHHHHHHHHHHHHS-SS----S----SSS-HCHHHHHHHHHHH-TTS
T ss_pred             ccCcHHHHHHHHHHhhhcC-CHHHHHHHHccchhHHHHHHHHHHHhcccCcccccCCCCCCCChHHHHHHHHHHhcCCCc
Confidence            4577888899999998875 99999999999999999999866   3 221110123466666665555555555543 3


Q ss_pred             cHHHH
Q psy17316        192 TVQRA  196 (229)
Q Consensus       192 s~~eA  196 (229)
                      -.+|+
T Consensus        95 fawEi   99 (125)
T PF00292_consen   95 FAWEI   99 (125)
T ss_dssp             -HHHH
T ss_pred             chHHH
Confidence            34443

Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.

>PHA00542 putative Cro-like protein

Probab=94.91  E-value=0.061  Score=39.38  Aligned_cols=44  Identities=7%  Similarity=0.059  Sum_probs=34.9

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        171 PTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       171 ~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      +..++.+ ..+++..+...+++..++|..+||+.+||++|.++..
T Consensus        13 p~~~~~~-~~~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~~   56 (82)
T PHA00542         13 PAAYTQR-PDELVCALIRAGWSQEQIADATDVSQPTICRIYSGRH   56 (82)
T ss_pred             CcccCcC-HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCCC
Confidence            3444432 4466777888889999999999999999999998664

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

Probab=94.89  E-value=0.092  Score=33.99  Aligned_cols=40  Identities=23%  Similarity=0.247  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHhCC-CcHHHHHHHhCCChHHHHHHHH-hhcC
Q psy17316        177 EDLEIALEGIRSGQ-TTVQRASAEYGIPSGTLYGRCK-LSRS  216 (229)
Q Consensus       177 e~r~eaV~~~~~~~-~s~~eAA~~fgVp~~tv~~~vk-~~~~  216 (229)
                      +...+|+..+.++. ++..++|..+|+|.+||...++ +.+.
T Consensus         3 ~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~   44 (48)
T PF13412_consen    3 ETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEK   44 (48)
T ss_dssp             HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            45678888888844 9999999999999999999998 4433

...

>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators

Probab=94.88  E-value=0.12  Score=40.81  Aligned_cols=64  Identities=8%  Similarity=0.042  Sum_probs=45.5

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHh-CCCcHHHHHHHhC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRS-GQTTVQRASAEYG  201 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~-~~~s~~eAA~~fg  201 (229)
                      +++.++|+++||+.+||+.|.++ |+-.... .+..|.|+++  .+++.|..+.+ -+++..++...+.
T Consensus         2 ysI~eVA~~~GVs~~TLR~wE~~-GLl~p~r-~~G~R~Ys~~dv~rL~~I~~L~~e~G~~l~eI~~~L~   68 (120)
T cd04767           2 YPIGVVAELLNIHPETLRIWERH-GLIKPAR-RNGQRLYSNNDLKRLRFIKKLINEKGLNIAGVKQILS   68 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCcC-CCCcEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            58899999999999999999985 4322221 2446778766  45666777766 6687777776543

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

>PRK10572 DNA-binding transcriptional regulator AraC; Provisional

Probab=94.87  E-value=0.36  Score=42.43  Aligned_cols=87  Identities=13%  Similarity=0.184  Sum_probs=63.2

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCC
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTK  117 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~  117 (229)
                      ...|..-..+.+|+.++|+++|+++++|.+-.++. |...           .+                           
T Consensus       189 ~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~~~G~tp-----------~~---------------------------  230 (290)
T PRK10572        189 CQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISV-----------LR---------------------------  230 (290)
T ss_pred             HHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCH-----------HH---------------------------
Confidence            33443334578999999999999999999999985 5431           01                           


Q ss_pred             CCCHH-HHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCccc
Q psy17316        118 SWNEE-ILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRLA  164 (229)
Q Consensus       118 kYs~e-~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~~  164 (229)
                       |-.+ -+++|..++.....|+.+||...|-+... ..+.-|++ |..+.
T Consensus       231 -~l~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~d~s~Fsr~FKk~~G~SP~  279 (290)
T PRK10572        231 -WREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKCTGASPS  279 (290)
T ss_pred             -HHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHH
Confidence             1112 25777888887888999999999999766 77777765 75443

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

Probab=94.86  E-value=0.15  Score=40.11  Aligned_cols=66  Identities=14%  Similarity=0.153  Sum_probs=45.0

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHHH--HHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEIL--NVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~k--~~A  127 (229)
                      |++.++|+.+||+..||+.|-+..-+..+....                               +....|++++.  ...
T Consensus         1 m~IgevA~~~gvs~~tLRyYe~~GLl~p~~r~~-------------------------------~gyR~Y~~~~l~~l~~   49 (127)
T cd04784           1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSA-------------------------------NNYRLYDEEHLERLLF   49 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCCeecCHHHHHHHHH
Confidence            688999999999999999998864333221111                               12345555553  456


Q ss_pred             HHHHHcCCCCHHHHHHHhC
Q psy17316        128 LDALRAGSISANKASKAYG  146 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~g  146 (229)
                      |..+..-++|+.+|..-+.
T Consensus        50 I~~lr~~G~sL~eI~~~l~   68 (127)
T cd04784          50 IRRCRSLDMSLDEIRTLLQ   68 (127)
T ss_pred             HHHHHHcCCCHHHHHHHHH
Confidence            7777776788888877654

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

>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=94.85  E-value=0.071  Score=35.27  Aligned_cols=36  Identities=14%  Similarity=0.009  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +...+++...--.++++.++|..+|||.++|+.++.
T Consensus        13 ~~~r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l~   48 (54)
T PF08281_consen   13 ERQREIFLLRYFQGMSYAEIAEILGISESTVKRRLR   48 (54)
T ss_dssp             HHHHHHHHHHHTS---HHHHHHHCTS-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHHH
Confidence            334555666555669999999999999999999986

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.

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=94.84  E-value=0.048  Score=52.63  Aligned_cols=40  Identities=23%  Similarity=0.255  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      ++..+++++...+..+..+|+.+||+++|||+++++|||.
T Consensus       469 Er~~I~~aL~~~~gn~~~aA~~LGisr~tL~rklk~~gi~  508 (509)
T PRK05022        469 QRQLIRQALAQHQGNWAAAARALELDRANLHRLAKRLGLK  508 (509)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence            3445555666666688999999999999999999999985

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

Probab=94.84  E-value=0.16  Score=40.03  Aligned_cols=66  Identities=9%  Similarity=0.071  Sum_probs=44.5

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      |++.++|+.+||+..||+.|-+..-+..+....                               +....|++++  +...
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~~GLl~~~~r~~-------------------------------~gyR~Y~~~~l~~l~~   49 (127)
T TIGR02047         1 MKIGELAQKTGVSVETIRFYEKQGLLPPPARTD-------------------------------NNYRVYTVGHVERLAF   49 (127)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCCCcCCHHHHHHHHH
Confidence            678999999999999999998763333221111                               1134455555  3556


Q ss_pred             HHHHHcCCCCHHHHHHHhC
Q psy17316        128 LDALRAGSISANKASKAYG  146 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~g  146 (229)
                      |..+..-++|+.+|..-+.
T Consensus        50 I~~lr~lG~sL~eI~~~l~   68 (127)
T TIGR02047        50 IRNCRTLDMSLAEIRQLLR   68 (127)
T ss_pred             HHHHHHcCCCHHHHHHHHH
Confidence            7777777788888877654

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

>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B

Probab=94.83  E-value=0.36  Score=34.25  Aligned_cols=71  Identities=18%  Similarity=0.247  Sum_probs=46.9

Q ss_pred             HHHHcCCChhhHHHHHHH-hCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHHHHHHHHHHH-
Q psy17316         55 ASVSYGIPSTTLWQRAHR-LGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEILNVALDALR-  132 (229)
Q Consensus        55 aA~~~gIp~sTL~~~i~~-~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~k~~AV~~~~-  132 (229)
                      +|+.+||+..+|.+.+++ .|...            ...   +                       ...-+..|.+++. 
T Consensus         1 lA~~~~~s~~~l~~~f~~~~g~s~------------~~~---~-----------------------~~~R~~~a~~~L~~   42 (81)
T PF12833_consen    1 LADELGMSERYLSRIFKKETGMSF------------KQY---L-----------------------RELRLQRAKELLRQ   42 (81)
T ss_dssp             HHHHCTS-HHHHHHHHHHHHSS-H------------HHH---H-----------------------HHHHHHHHHHHHHH
T ss_pred             ChHHhCcCHHHHHHHHHHHHCcCH------------HHH---H-----------------------HHHHHHHHHHHHHH
Confidence            589999999999999998 45431            111   0                       0123466777775 


Q ss_pred             cCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        133 AGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       133 ~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                      +++.|+.+||.++|-+..+ +.+..++. |..+
T Consensus        43 ~~~~~i~~ia~~~Gf~~~~~f~~~fk~~~g~tP   75 (81)
T PF12833_consen   43 NTDLSIAEIAEECGFSSQSHFSRAFKRYFGMTP   75 (81)
T ss_dssp             HTT--HHHHHHHTT-SSHHHHHHHHHHHHSS-H
T ss_pred             hhcccHHHHHHHcCCCCHHHHHHHHHHHHCcCH
Confidence            4788999999999999877 88888765 6543

...

>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=94.83  E-value=0.093  Score=33.30  Aligned_cols=39  Identities=13%  Similarity=0.041  Sum_probs=29.1

Q ss_pred             CCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316        174 WKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       174 ~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      .+++.+. ++...--.++++.++|..+|+|..||++|++.
T Consensus        11 l~~~~~~-~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~   49 (55)
T cd06171          11 LPERERE-VILLRFGEGLSYEEIAEILGISRSTVRQRLHR   49 (55)
T ss_pred             CCHHHHH-HHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3444444 44444435599999999999999999999873

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

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

Probab=94.83  E-value=0.038  Score=41.87  Aligned_cols=38  Identities=24%  Similarity=0.365  Sum_probs=32.4

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      |.|+ ++||.++--.++++.+||.+.||++.|+|+-+..
T Consensus        35 t~eE-lEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~s   72 (99)
T COG1342          35 TIEE-LEALRLVDYEGLTQEEAALRMGISRQTFWRLLTS   72 (99)
T ss_pred             cHHH-HHHHHHHhHhhccHHHHHHHhcccHHHHHHHHHH
Confidence            4444 5788888778999999999999999999998874

>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=94.82  E-value=0.095  Score=34.27  Aligned_cols=37  Identities=16%  Similarity=0.120  Sum_probs=27.8

Q ss_pred             CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +++++ +||...--+++|+.++|..+|||.++|..+.+
T Consensus         6 ~~~er-~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~   42 (50)
T PF04545_consen    6 PPRER-EVIRLRYFEGLTLEEIAERLGISRSTVRRILK   42 (50)
T ss_dssp             -HHHH-HHHHHHHTST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred             CHHHH-HHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHH
Confidence            34444 45555556669999999999999999999876

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 ....

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

Probab=94.77  E-value=0.2  Score=39.52  Aligned_cols=66  Identities=6%  Similarity=0.082  Sum_probs=49.2

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      +++.++|+.+|||..||+-|-+ .|.- ......+..|.|+++  +++..|..+.+=+++..++...+..
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~-~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~~   69 (127)
T TIGR02047         1 MKIGELAQKTGVSVETIRFYEK-QGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRY   69 (127)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHH-CCCCCCCCcCCCCCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            4788999999999999999987 3432 211112346788766  4677788888878999999988764

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

>PHA02591 hypothetical protein; Provisional

Probab=94.77  E-value=0.053  Score=39.64  Aligned_cols=38  Identities=11%  Similarity=0.200  Sum_probs=34.2

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ++||.......+.+.|+|+.+||..+||+..++++.++
T Consensus        44 ~~dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         44 SEDDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             ccchHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            77888888888888899999999999999999998875

>PRK15043 transcriptional regulator MirA; Provisional

Probab=94.75  E-value=0.12  Score=45.64  Aligned_cols=30  Identities=20%  Similarity=0.335  Sum_probs=26.7

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~   78 (229)
                      -+++.++|+.+||+..||+.|-+++|+-.|
T Consensus         3 ~ytIgeVA~~~GVs~~TLR~wErr~GLL~P   32 (243)
T PRK15043          3 LYTIGEVALLCDINPVTLRAWQRRYGLLKP   32 (243)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHhcCCCCC
Confidence            378999999999999999999999887654

>COG0789 SoxR Predicted transcriptional regulators [Transcription]

Probab=94.72  E-value=0.19  Score=38.69  Aligned_cols=69  Identities=16%  Similarity=0.148  Sum_probs=49.1

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCCh
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIPS  204 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp~  204 (229)
                      +++.++|+.+||+..||+-|-+.--+.......+..|-|+++  .++.+|..+.+-+++..++-.......
T Consensus         1 ~~I~eva~~~gvs~~tLRyYE~~GLl~p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~~L~~I~~~l~~~~   71 (124)
T COG0789           1 YTIGEVAKLTGVSVRTLRFYERKGLLSPERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEIKELLDLLS   71 (124)
T ss_pred             CcHHHHHHHhCCCHHHHHHHHHcCCCCCcccCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccc
Confidence            478899999999999999998853333332222456788766  455667777766688888887766654

>PRK15121 right oriC-binding transcriptional activator; Provisional

Probab=94.69  E-value=0.5  Score=41.92  Aligned_cols=88  Identities=19%  Similarity=0.095  Sum_probs=61.9

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCC
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPT  116 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~  116 (229)
                      ++..|+.-....+|+.++|+..|+++.+|.|..+.. |...            ...-..                     
T Consensus        10 ~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~~~g~s~------------~~yi~~---------------------   56 (289)
T PRK15121         10 LLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAI------------GAYIRA---------------------   56 (289)
T ss_pred             HHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH------------HHHHHH---------------------
Confidence            344444444568999999999999999999999974 5532            111001                     


Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        117 KSWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       117 ~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                           --+..|..++..++.++.+||..+|-.... +.+..|+. |+..
T Consensus        57 -----~Rl~~A~~~L~~~~~~i~~iA~~~Gf~s~~~f~r~Fk~~~g~sP  100 (289)
T PRK15121         57 -----RRLSKAAVALRLTSRPILDIALQYRFDSQQTFTRAFKKQFAQTP  100 (289)
T ss_pred             -----HHHHHHHHHHHcCCCCHHHHHHHHCCCCHHHHHHHHHHHHCcCH
Confidence                 124667777877778999999999997755 77777654 6443

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

Probab=94.69  E-value=0.19  Score=37.23  Aligned_cols=65  Identities=14%  Similarity=0.163  Sum_probs=42.6

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+||+.+||+.|.+. |+-.|.....                               ....|++++  +...
T Consensus         2 ~~i~e~A~~~gvs~~tLr~ye~~-Gli~p~r~~~-------------------------------g~R~y~~~dv~~l~~   49 (91)
T cd04766           2 YVISVAAELSGMHPQTLRLYERL-GLLSPSRTDG-------------------------------GTRRYSERDIERLRR   49 (91)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHC-CCcCCCcCCC-------------------------------CCeeECHHHHHHHHH
Confidence            57899999999999999999884 5543421111                               123455444  3444


Q ss_pred             HHHHHc-CCCCHHHHHHHhC
Q psy17316        128 LDALRA-GSISANKASKAYG  146 (229)
Q Consensus       128 V~~~~~-g~~S~~~~a~k~g  146 (229)
                      |..+.. -++++.+|..-+.
T Consensus        50 i~~L~~d~g~~l~~i~~~l~   69 (91)
T cd04766          50 IQRLTQELGVNLAGVKRILE   69 (91)
T ss_pred             HHHHHHHcCCCHHHHHHHHH
Confidence            555554 6678888877765

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

>TIGR02051 MerR Hg(II)-responsive transcriptional regulator

Probab=94.68  E-value=0.17  Score=39.77  Aligned_cols=67  Identities=12%  Similarity=0.126  Sum_probs=48.9

Q ss_pred             CHHHHHHHhCCChHHHHHHHHHhCC-cccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCCh
Q psy17316        137 SANKASKAYGIPSSTLYKIARKEGI-RLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIPS  204 (229)
Q Consensus       137 S~~~~a~k~gIp~sTL~~~ik~~g~-k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp~  204 (229)
                      ++.++|+++||+..||+.|-+ .|+ .......+..|.|+++  +++..|..+..=+++..++...++...
T Consensus         1 ~I~e~a~~~gvs~~tlR~Ye~-~GLl~~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~~~~   70 (124)
T TIGR02051         1 TIGELAKAAGVNVETIRYYER-KGLLPEPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGLVD   70 (124)
T ss_pred             CHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHhccc
Confidence            468899999999999999876 343 2222112346777655  567778888888899999999887643

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

>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=94.66  E-value=0.054  Score=35.24  Aligned_cols=38  Identities=16%  Similarity=0.300  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +.+.+++..+.+|.+++.++|+.+|++++|+.+.++..
T Consensus         2 ~~R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L   39 (47)
T PF01022_consen    2 PTRLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKL   39 (47)
T ss_dssp             HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHH
Confidence            35678899999999999999999999999999988864

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 ....

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

Probab=94.64  E-value=0.059  Score=41.70  Aligned_cols=38  Identities=16%  Similarity=0.172  Sum_probs=32.0

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.|+ ++||.++--.++|+.++|.+.||+++|+++.+..
T Consensus        43 ~~dE-lEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~~   80 (106)
T PF02001_consen   43 TVDE-LEAIRLVDYEGLSQEEAAERMGVSRPTFQRILES   80 (106)
T ss_pred             eHHH-HHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHHH
Confidence            4444 5778877777899999999999999999998874

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

Probab=94.64  E-value=0.048  Score=53.63  Aligned_cols=40  Identities=33%  Similarity=0.485  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      ++...|.++...+--+.++|+.+|||++||||+++++||.
T Consensus       566 ~~~~l~~al~~~~~~is~aa~~lgi~R~T~yrklk~~gi~  605 (606)
T COG3284         566 EKAALLAALQATNGNISEAARLLGISRSTLYRKLKRHGIS  605 (606)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence            3344444454445578899999999999999999999984

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

Probab=94.63  E-value=0.19  Score=40.00  Aligned_cols=67  Identities=6%  Similarity=0.098  Sum_probs=45.5

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      |++.++|+.+||+..||+.|-+..-+..+....                               +....|++++  ++..
T Consensus         1 m~Ige~a~~~gvs~~tLRyYE~~GLl~p~~r~~-------------------------------~gyR~Y~~~~v~~l~~   49 (131)
T cd04786           1 MKIGELAKRSGMAASRIRFYEAEGLLSSVERSA-------------------------------NGYRDYPPETVWVLEI   49 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCC-------------------------------CCCeecCHHHHHHHHH
Confidence            689999999999999999998764443221111                               0133455544  3556


Q ss_pred             HHHHHcCCCCHHHHHHHhCC
Q psy17316        128 LDALRAGSISANKASKAYGI  147 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gI  147 (229)
                      |..+..-++|+.+|...+..
T Consensus        50 I~~lr~~GfsL~eI~~ll~~   69 (131)
T cd04786          50 ISSAQQAGFSLDEIRQLLPA   69 (131)
T ss_pred             HHHHHHcCCCHHHHHHHHhc
Confidence            77777777898888876643

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

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=94.59  E-value=0.09  Score=38.65  Aligned_cols=39  Identities=15%  Similarity=0.173  Sum_probs=35.0

Q ss_pred             CCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        174 WKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       174 ~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      |=++-+.+|++++..|..+..++|..||||.+||.+-++
T Consensus         3 ~~~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~   41 (80)
T TIGR02844         3 YIEERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVT   41 (80)
T ss_pred             cHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhc
Confidence            446778899999999999999999999999999999774

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.

>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR

Probab=94.59  E-value=0.17  Score=40.85  Aligned_cols=65  Identities=11%  Similarity=0.141  Sum_probs=49.6

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYG  201 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fg  201 (229)
                      +++.++|+.+|||..||+-|-+. |+-......+..|.|+++  +++..|..+.+-+++..++...+.
T Consensus         2 ~~IgevA~~~Gvs~~tLRyYE~~-GLl~~~r~~~g~R~Y~~~di~~l~~I~~lr~~G~sL~eI~~~l~   68 (142)
T TIGR01950         2 LTVGELAKRSGVAVSALHFYESK-GLITSIRNSGNQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALA   68 (142)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            68999999999999999999885 643222112335788766  457788888888899999998775

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

>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]

Probab=94.56  E-value=0.18  Score=45.69  Aligned_cols=84  Identities=18%  Similarity=0.203  Sum_probs=58.0

Q ss_pred             HHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcc--c-----------CCCCCCCCCCCHHHHHHHHHHHHhCCCcHH
Q psy17316        128 LDALRAGSISANKASKAYGIPSSTLYKIARKEGIRL--A-----------QPFNASPTAWKPEDLEIALEGIRSGQTTVQ  194 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~--~-----------~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~  194 (229)
                      |+.+..-++|.++||++.|-..+|+++.+++.-...  .           +.....+-+.+++=+..|++.+.+ ..|..
T Consensus        16 I~~l~~~~~S~reIA~~LgRh~sTIsRElkRn~~~~~Y~a~~A~~~~~~~rrr~~~k~~~~~eL~~~V~e~L~~-~wSPE   94 (318)
T COG2826          16 IERLLKAKMSIREIAKQLNRHHSTISRELKRNRTRDIYSAVKAQERYRMLRRRRIRKLKLNPELRELVLEKLKS-KWSPE   94 (318)
T ss_pred             HHHHHHcCCCHHHHHHHhCCCcchhhHHHhcCCccceeeHHHHHHHHHHhhcccCCcccCCHHHHHHHHHHHHh-hCCHH
Confidence            444555557999999999999999999987532111  0           001123446677766666666554 59999


Q ss_pred             HHHHHh--C-CChHHHHHHHH
Q psy17316        195 RASAEY--G-IPSGTLYGRCK  212 (229)
Q Consensus       195 eAA~~f--g-Vp~~tv~~~vk  212 (229)
                      +++...  + |+.+|+|+|+-
T Consensus        95 QI~g~l~~~~i~~eTIYr~ly  115 (318)
T COG2826          95 QIIGRLKKSKISFETIYRWLY  115 (318)
T ss_pred             HHHHHHHhcccCHHHHHHHHh
Confidence            998743  4 89999999986

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

Probab=94.56  E-value=0.22  Score=38.89  Aligned_cols=65  Identities=11%  Similarity=0.209  Sum_probs=44.5

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+|||..||+-|=+. |+-.|....-                                ...|++++  +...
T Consensus         1 ~~Igeva~~~gvs~~tlRyYe~~-GLl~p~r~~g--------------------------------yR~Y~~~~l~~l~~   47 (118)
T cd04776           1 YTISELAREFDVTPRTLRFYEDK-GLLSPERRGQ--------------------------------TRVYSRRDRARLKL   47 (118)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCcCCCC--------------------------------ccccCHHHHHHHHH
Confidence            47899999999999999999886 5544422111                                34455555  3455


Q ss_pred             HHHHHcCCCCHHHHHHHhCC
Q psy17316        128 LDALRAGSISANKASKAYGI  147 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gI  147 (229)
                      |..+.+-++|+.+|..-+..
T Consensus        48 I~~lr~~G~~L~~I~~~l~~   67 (118)
T cd04776          48 ILRGKRLGFSLEEIRELLDL   67 (118)
T ss_pred             HHHHHHCCCCHHHHHHHHHh
Confidence            66777777888888765543

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

>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I

Probab=94.51  E-value=0.077  Score=42.97  Aligned_cols=42  Identities=19%  Similarity=0.209  Sum_probs=27.2

Q ss_pred             CCCCHHHHHHHHHH----HH---cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         31 KTWTHEDMDAALEA----LR---AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        31 ~kyt~e~~~~AI~~----~~---~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .+.|.+++.+|.-.    +.   .+..|..+||++.||+++|||+|.++
T Consensus         9 ~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~~   57 (142)
T PF13022_consen    9 AKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQQ   57 (142)
T ss_dssp             TTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             HHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHhc
Confidence            45666766544322    22   25688999999999999999999975

>COG2973 TrpR Trp operon repressor [Transcription]

Probab=94.51  E-value=0.042  Score=41.77  Aligned_cols=32  Identities=19%  Similarity=0.246  Sum_probs=28.9

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHH
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQR   69 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~   69 (229)
                      ...+|+++++|++|+++|+.++||+-+|+.|=
T Consensus        49 Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRG   80 (103)
T COG2973          49 RVRIVEELLRGELSQREIAQKLGVSIATITRG   80 (103)
T ss_pred             HHHHHHHHHhccccHHHHHHHhCcchhhhccc
Confidence            35889999999999999999999999999763

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

Probab=94.51  E-value=0.23  Score=39.38  Aligned_cols=67  Identities=9%  Similarity=0.023  Sum_probs=50.0

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCC-CCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFN-ASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP  203 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~-~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp  203 (229)
                      +++.++|+.+||+..||+-|-+ .|+-...... ...|.|+++  +++..|..+.+-+++..++...+...
T Consensus         1 m~IgE~A~~~gvs~~TLRyYE~-~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~   70 (133)
T cd04787           1 MKVKELANAAGVTPDTVRFYTR-IGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHA   70 (133)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhh
Confidence            4788999999999999988765 4642222111 345778665  67788888999889999999988753

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

>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=94.47  E-value=0.068  Score=39.93  Aligned_cols=35  Identities=11%  Similarity=0.011  Sum_probs=28.7

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..+++...+.+|+|+++||+.+||+.+||.|--+-
T Consensus        38 R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~   72 (87)
T PF01371_consen   38 RWQVAKELLDEGKSYREIAEETGVSIATITRVSRC   72 (87)
T ss_dssp             HHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            34566646678999999999999999999987664

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 ....

>PRK13500 transcriptional activator RhaR; Provisional

Probab=94.47  E-value=0.43  Score=42.90  Aligned_cols=88  Identities=17%  Similarity=0.152  Sum_probs=63.7

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCC
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTK  117 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~  117 (229)
                      ...|++-....+++.++|+.+||++++|.+..++. |...            -..   +                     
T Consensus       212 ~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~tG~T~------------~~y---i---------------------  255 (312)
T PRK13500        212 ITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTI------------NQY---L---------------------  255 (312)
T ss_pred             HHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH------------HHH---H---------------------
Confidence            34444333447999999999999999999999985 5531            000   0                     


Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCccc
Q psy17316        118 SWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRLA  164 (229)
Q Consensus       118 kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~~  164 (229)
                        .+--+.+|..++..+..|+.+||...|-+.++ ..+..|++ |+.++
T Consensus       256 --~~~RL~~A~~LL~~t~~sI~eIA~~~GF~d~s~Fsr~FKk~~G~TP~  302 (312)
T PRK13500        256 --RQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPS  302 (312)
T ss_pred             --HHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHH
Confidence              01125788888888889999999999999977 77777765 75543

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

Probab=94.46  E-value=0.12  Score=34.59  Aligned_cols=38  Identities=18%  Similarity=0.057  Sum_probs=28.3

Q ss_pred             CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +.+++.-++=.-.+.+.++.+.|..||||.+||.++++
T Consensus         4 s~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~   41 (53)
T PF13613_consen    4 SLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFH   41 (53)
T ss_pred             CHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHH
Confidence            34444444444444448899999999999999999887

>PRK09940 transcriptional regulator YdeO; Provisional

Probab=94.46  E-value=0.28  Score=43.52  Aligned_cols=88  Identities=16%  Similarity=0.103  Sum_probs=65.7

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCC
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGP  115 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~  115 (229)
                      +....+|..-..+..++.++|...|+++++|.|..++.|..            +.                         
T Consensus       137 ~kv~~~I~~~~~~~~tl~~LA~~~gmS~s~l~R~FK~~G~T------------~~-------------------------  179 (253)
T PRK09940        137 GKVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQEQTT------------FS-------------------------  179 (253)
T ss_pred             HHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHcCCC------------HH-------------------------
Confidence            45577777777788999999999999999999999975421            10                         


Q ss_pred             CCCCCHH-HHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        116 TKSWNEE-ILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       116 ~~kYs~e-~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                        .|-.+ -+..|.+++..+. |+.+||...|-...+ ..++.+++ |..+
T Consensus       180 --eyl~~~Rl~~A~~LL~~~~-sI~eIA~~~GF~s~S~Fsr~FKr~~G~TP  227 (253)
T PRK09940        180 --QILLDARMQHAKNLIRVEG-SVNKIAEQCGYASTSYFIYAFRKHFGNSP  227 (253)
T ss_pred             --HHHHHHHHHHHHHHHccCC-CHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence              11112 2467777776654 999999999999977 88888765 7544

>PRK00118 putative DNA-binding protein; Validated

Probab=94.42  E-value=0.086  Score=40.64  Aligned_cols=35  Identities=11%  Similarity=0.172  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .-.+++..+..+++|+.++|..+|||.+||++++.
T Consensus        21 kqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~   55 (104)
T PRK00118         21 KQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIK   55 (104)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            35566677777779999999999999999999986

>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator

Probab=94.41  E-value=0.094  Score=43.45  Aligned_cols=39  Identities=10%  Similarity=0.340  Sum_probs=35.3

Q ss_pred             CCCHHHHHHHHHHHHhCCCcHHHHHHHhC-CChHHHHHHHH
Q psy17316        173 AWKPEDLEIALEGIRSGQTTVQRASAEYG-IPSGTLYGRCK  212 (229)
Q Consensus       173 ~~t~e~r~eaV~~~~~~~~s~~eAA~~fg-Vp~~tv~~~vk  212 (229)
                      .||+ ++++.|..+...++|+.+||.++| ||++.|.+.+.
T Consensus         2 ~Wtd-e~~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~h   41 (162)
T PF07750_consen    2 SWTD-ERVERLRKLWAEGLSASQIARQLGGVSRNAVIGKAH   41 (162)
T ss_pred             CCCH-HHHHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhh
Confidence            4774 588888999998899999999999 99999999998

These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].

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

Probab=94.41  E-value=0.25  Score=38.76  Aligned_cols=66  Identities=12%  Similarity=0.124  Sum_probs=48.6

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcc-cCCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRL-AQPFNASPTAWKPED--LEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~-~~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      +++.++|+.+||+..||+-|-+ .|.-. ........|.|++++  ++..|..+.+=+++..++...+..
T Consensus         1 m~IgevA~~~gvs~~tLRyYe~-~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~   69 (127)
T cd04784           1 MKIGELAKKTGCSVETIRYYEK-EGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQL   69 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            4788999999999999999887 44322 111123468888764  457777888877999999988764

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

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

Probab=94.37  E-value=0.29  Score=38.23  Aligned_cols=65  Identities=8%  Similarity=0.095  Sum_probs=49.2

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPED--LEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      +++.++|+.+|||..||+-|-+. |+-.... ....|.|+++.  ++..|..+.+-+++..++...+..
T Consensus         1 ~~Igeva~~~gvs~~tlRyYe~~-GLl~p~r-~~gyR~Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~~   67 (118)
T cd04776           1 YTISELAREFDVTPRTLRFYEDK-GLLSPER-RGQTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDL   67 (118)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCcC-CCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            36889999999999999999884 6533221 22568888774  555578888888999999887765

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

>TIGR01817 nifA Nif-specific regulatory protein

Probab=94.34  E-value=0.068  Score=51.70  Aligned_cols=41  Identities=17%  Similarity=0.210  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      ++..+++++...+-.+.++|+.+||+++|||+++++|||..
T Consensus       491 Er~~i~~aL~~~~gn~~~aA~~LGisr~tLy~klk~~gi~~  531 (534)
T TIGR01817       491 ERERLIAALEQAGWVQAKAARLLGMTPRQVGYALRKLNIEM  531 (534)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHcCCCc
Confidence            34445555554455799999999999999999999999964

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

>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=94.32  E-value=0.24  Score=39.70  Aligned_cols=67  Identities=7%  Similarity=0.090  Sum_probs=49.2

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP  203 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp  203 (229)
                      +++.++|+.+||+..||+.|.+ .|.-.........|-|+++  +++..|..+.+-+++..++...+..-
T Consensus         1 y~I~e~a~~~gvs~~TLR~Ye~-~GLl~p~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~   69 (134)
T cd04779           1 YRIGQLAHLAGVSKRTIDYYTN-LGLLTPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEV   69 (134)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCccCCCCCeeECHHHHHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence            3678999999999999999986 4532221112235667665  57788888888889999998877543

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional

Probab=94.30  E-value=0.19  Score=41.24  Aligned_cols=67  Identities=10%  Similarity=0.171  Sum_probs=49.8

Q ss_pred             CCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        135 SISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       135 ~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      -+++.++|+.+||+..||+-|-+ .|.-.........|.|+++  +++..|..+.+=++|..++...+..
T Consensus        11 ~~~IgevAk~~gvs~~TlRyYE~-~GLi~~~r~~~g~R~Y~~~~i~~L~~I~~lr~lG~sL~eIk~ll~~   79 (154)
T PRK15002         11 LLTPGEVAKRSGVAVSALHFYES-KGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGV   79 (154)
T ss_pred             cccHHHHHHHHCcCHHHHHHHHH-CCCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            47999999999999999999987 3432211112235777665  5777788888888999999998763

>COG5484 Uncharacterized conserved protein [Function unknown]

Probab=94.26  E-value=0.067  Score=47.32  Aligned_cols=40  Identities=15%  Similarity=0.287  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCc
Q psy17316        122 EILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIR  162 (229)
Q Consensus       122 e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k  162 (229)
                      +.+..|-.+|+.| +-+.+||++|||+..|++.|.+++||.
T Consensus         7 ~~r~~Akk~yl~g-mk~~dIAeklGvspntiksWKrr~gWs   46 (279)
T COG5484           7 DKRIIAKKDYLKG-MKLKDIAEKLGVSPNTIKSWKRRDGWS   46 (279)
T ss_pred             chHHHHHHHHHhh-ccHHHHHHHhCCChHHHHHHHHhcCCC
Confidence            4567888999999 699999999999999999999999984

>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD

Probab=94.25  E-value=0.23  Score=39.08  Aligned_cols=68  Identities=9%  Similarity=0.129  Sum_probs=47.5

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV  126 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~  126 (229)
                      .+++.++|+.+||+..||+.|-+. |+-.|.....+                              ....|++++  +++
T Consensus         3 ~~tI~elA~~~gvs~~tlR~Ye~~-GLL~p~~r~~~------------------------------gyR~Y~~~~l~rL~   51 (120)
T TIGR02054         3 AYTISRLAEDAGVSVHVVRDYLLR-GLLHPVRRTTS------------------------------GYGIFDDASLQRLR   51 (120)
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCC------------------------------CCeeCCHHHHHHHH
Confidence            479999999999999999999887 54333222111                              234455554  466


Q ss_pred             HHHHHHcCCCCHHHHHHHhCC
Q psy17316        127 ALDALRAGSISANKASKAYGI  147 (229)
Q Consensus       127 AV~~~~~g~~S~~~~a~k~gI  147 (229)
                      .|..+...++|+.+|..-...
T Consensus        52 ~I~~lr~~G~~L~eI~~ll~~   72 (120)
T TIGR02054        52 FVRAAFEAGIGLGELARLCRA   72 (120)
T ss_pred             HHHHHHHcCCCHHHHHHHHHh
Confidence            777878888899998776543

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

>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=94.23  E-value=0.22  Score=39.93  Aligned_cols=66  Identities=12%  Similarity=0.181  Sum_probs=43.8

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+||+..||+.|-+. |.-.|.....                               ....|+++.  +...
T Consensus         1 y~I~e~a~~~gvs~~TLR~Ye~~-GLl~p~r~~~-------------------------------g~R~Y~~~~l~~l~~   48 (134)
T cd04779           1 YRIGQLAHLAGVSKRTIDYYTNL-GLLTPERSDS-------------------------------NYRYYDETALDRLQL   48 (134)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCccCCC-------------------------------CCeeECHHHHHHHHH
Confidence            47889999999999999999865 4432322110                               123345444  4556


Q ss_pred             HHHHHcCCCCHHHHHHHhCC
Q psy17316        128 LDALRAGSISANKASKAYGI  147 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gI  147 (229)
                      |..+.+-++|+.+|......
T Consensus        49 I~~lr~~G~sL~eI~~~l~~   68 (134)
T cd04779          49 IEHLKGQRLSLAEIKDQLEE   68 (134)
T ss_pred             HHHHHHCCCCHHHHHHHHHh
Confidence            77777777888888776543

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

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

Probab=94.23  E-value=0.12  Score=37.35  Aligned_cols=38  Identities=24%  Similarity=0.325  Sum_probs=36.3

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      ..||..|..|.+|..+||+-.|+++..+..-+.++|+.
T Consensus        24 ~~Ai~lY~~g~iS~gkAAelag~s~~eF~~~L~~~gI~   61 (76)
T PF03683_consen   24 ELAIKLYEEGKISLGKAAELAGMSRWEFLELLKERGIP   61 (76)
T ss_pred             HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHCCCC
Confidence            67899999999999999999999999999999999986

>PRK10227 DNA-binding transcriptional regulator CueR; Provisional

Probab=94.22  E-value=0.28  Score=39.30  Aligned_cols=66  Identities=11%  Similarity=0.125  Sum_probs=48.9

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      +++.++|+.+||+..||+-|-+. |.- .........|-|+++  .++..|..+.+=+++..++...++.
T Consensus         1 m~Ige~a~~~gvs~~tlRyYE~~-GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~   69 (135)
T PRK10227          1 MNISDVAKITGLTSKAIRFYEEK-GLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNL   69 (135)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCcccCCCCcccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            57899999999999999998873 432 211112346788765  5777888888877999999887764

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=94.18  E-value=0.097  Score=37.84  Aligned_cols=36  Identities=14%  Similarity=0.111  Sum_probs=28.3

Q ss_pred             HHHHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         38 MDAALEALR-AGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        38 ~~~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ...|..... ..++|+.+||+.+|||.+|++.|+++.
T Consensus        20 ~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~   56 (73)
T TIGR03879        20 AEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGE   56 (73)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence            334444433 468999999999999999999999963

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

>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family

Probab=94.17  E-value=0.95  Score=37.38  Aligned_cols=108  Identities=19%  Similarity=0.260  Sum_probs=70.6

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC-----CCCCCCC-CCCCC-------------cHHHHHH
Q psy17316         34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI-----HTPKKEG-PTKSW-------------NEEILNV   94 (229)
Q Consensus        34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi-----~~~~~~~-~~k~~-------------s~e~~~~   94 (229)
                      ..+......+++..|=++..++...+|-..+-=-..+++-|.     ..|.+.. +.|.|             |=++..+
T Consensus        15 ~s~~~kkV~~~Ls~~W~T~~El~e~~G~d~~~~L~~LkK~gLiE~qWrmP~pG~kPeKEYhtsYs~vqaNFqcs~~DLsd   94 (160)
T PF09824_consen   15 NSEVYKKVYDELSKGWMTEEELEEKYGKDVRESLLILKKGGLIESQWRMPEPGEKPEKEYHTSYSKVQANFQCSMEDLSD   94 (160)
T ss_pred             CCHHHHHHHHHHHhccCCHHHHHHHHCcCHHHHHHHHHHcCchhhccccCCCCCCchHHHHhhHhheeeeeEeeHHHHHH
Confidence            345556778888899999999999999887555556665442     1344442 32322             2222222


Q ss_pred             HHHHHhhcchhhhhhhhccCCCCCCCHH-H---HHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh
Q psy17316         95 ALDALRAGSISANKASKAYGPTKSWNEE-I---LNVALDALRAGSISANKASKAYGIPSSTLYKIARKE  159 (229)
Q Consensus        95 a~~ll~~G~ls~~~~~~~~G~~~kYs~e-~---k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~  159 (229)
                      .+.                  -..-+.| +   ..+.++.+.+|..|+..+++++|++..-++-.+|+.
T Consensus        95 ii~------------------i~f~~deel~~~~e~i~~~v~~Gn~Sl~~lsr~l~~sp~firglAKRs  145 (160)
T PF09824_consen   95 IIY------------------IAFMSDEELRDYVEKIEKEVEAGNTSLSDLSRKLGISPVFIRGLAKRS  145 (160)
T ss_pred             HHh------------------eeecCHHHHHHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHhc
Confidence            221                  0111112 2   355677888899999999999999999999988865

>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR

Probab=94.14  E-value=0.23  Score=40.11  Aligned_cols=66  Identities=12%  Similarity=0.268  Sum_probs=45.0

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV  126 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~  126 (229)
                      .|++.++|+.+||+..||+.|=+. |+-.|... .                              |....|++++  ++.
T Consensus         1 ~~~IgevA~~~Gvs~~tLRyYE~~-GLl~~~r~-~------------------------------~g~R~Y~~~di~~l~   48 (142)
T TIGR01950         1 ELTVGELAKRSGVAVSALHFYESK-GLITSIRN-S------------------------------GNQRRYKRDVLRRVA   48 (142)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHC-CCCCCccC-C------------------------------CCCEEECHHHHHHHH
Confidence            378999999999999999999887 54333111 1                              1134555555  355


Q ss_pred             HHHHHHcCCCCHHHHHHHhC
Q psy17316        127 ALDALRAGSISANKASKAYG  146 (229)
Q Consensus       127 AV~~~~~g~~S~~~~a~k~g  146 (229)
                      .|..+.+-++|+.+|..-+.
T Consensus        49 ~I~~lr~~G~sL~eI~~~l~   68 (142)
T TIGR01950        49 VIKAAQRVGIPLATIGEALA   68 (142)
T ss_pred             HHHHHHHcCCCHHHHHHHHH
Confidence            56677777788888877654

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

>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD

Probab=94.14  E-value=0.28  Score=38.63  Aligned_cols=66  Identities=3%  Similarity=-0.023  Sum_probs=51.1

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCC-CCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQP-FNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~-~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      +++.++|+++||+..||+-|-+. |.-.... ..+..|.|+++  +++..|..+..-+++..++...++.
T Consensus         4 ~tI~elA~~~gvs~~tlR~Ye~~-GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll~~   72 (120)
T TIGR02054         4 YTISRLAEDAGVSVHVVRDYLLR-GLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLCRA   72 (120)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            68999999999999999998874 5432211 12346778766  6788899999999999999987764

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

>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function

Probab=94.14  E-value=0.2  Score=37.45  Aligned_cols=57  Identities=21%  Similarity=0.341  Sum_probs=44.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCC
Q psy17316         28 TVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPT   84 (229)
Q Consensus        28 ~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~   84 (229)
                      .-.+.|+.--+.+.|.+|..|-+|+.+|+++|+++..=+-.|.+...-.|..+++.|
T Consensus        28 ~~t~RWva~RKAaVV~aV~~Glis~~EA~~rY~Ls~eEf~~W~~av~rhge~aLraT   84 (90)
T PF06627_consen   28 PDTRRWVARRKAAVVRAVRGGLISVEEACRRYGLSEEEFESWQRAVDRHGENALRAT   84 (90)
T ss_dssp             SS-S---HHHHHHHHHHHHCTTS-HHHHHHCTTSSHHHHHHHHHHCCT--TTSS-TC
T ss_pred             cccccchhhHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhHHHHHHH
Confidence            346899999999999999999999999999999999999999999877776666543

; PDB: 2OA4_A 2JRT_A.

>PHA02943 hypothetical protein; Provisional

Probab=94.13  E-value=0.12  Score=42.61  Aligned_cols=42  Identities=14%  Similarity=0.181  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      .+.+.+|++++..|..|..++|+.+|+|++++...++ +.+.|
T Consensus        10 ~~R~~eILE~Lk~G~~TtseIAkaLGlS~~qa~~~LyvLErEG   52 (165)
T PHA02943         10 HTRMIKTLRLLADGCKTTSRIANKLGVSHSMARNALYQLAKEG   52 (165)
T ss_pred             HHHHHHHHHHHhcCCccHHHHHHHHCCCHHHHHHHHHHHHHcC
Confidence            3678999999988889999999999999999999998 66665

>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=94.13  E-value=0.082  Score=36.13  Aligned_cols=38  Identities=21%  Similarity=0.288  Sum_probs=32.3

Q ss_pred             HHHHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         36 EDMDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        36 e~~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .....++..+ .++.++..++|..+|||.+|+++.++.+
T Consensus        10 p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L   48 (61)
T PF12840_consen   10 PTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKL   48 (61)
T ss_dssp             HHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            4456777777 7899999999999999999999999975

...

>PHA00542 putative Cro-like protein

Probab=94.11  E-value=0.075  Score=38.87  Aligned_cols=30  Identities=13%  Similarity=0.049  Sum_probs=26.6

Q ss_pred             HHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         42 LEALRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        42 I~~~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +..+...++|+.++|+.+||+++||++|..
T Consensus        24 ~~~l~~~glTq~elA~~lgIs~~tIsr~e~   53 (82)
T PHA00542         24 VCALIRAGWSQEQIADATDVSQPTICRIYS   53 (82)
T ss_pred             HHHHHHCCCCHHHHHHHHCcCHHHHHHHHc
Confidence            345567899999999999999999999987

>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=94.09  E-value=3.6  Score=35.66  Aligned_cols=153  Identities=11%  Similarity=0.112  Sum_probs=86.0

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCC-CCCCCCCCCcHHHHHHH--HHHHhhcchhhhhhhhccCCCCC-CCHHHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTP-KKEGPTKSWNEEILNVA--LDALRAGSISANKASKAYGPTKS-WNEEILN  125 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~-~~~~~~k~~s~e~~~~a--~~ll~~G~ls~~~~~~~~G~~~k-Ys~e~k~  125 (229)
                      +++.++|+..||+..||+.|-++ |+-.| .....+.-|+++.....  +..+.+-..+-++|...+.-... -.-...+
T Consensus         2 y~i~elA~~~Gvs~~tIR~Ye~~-GLL~p~r~~~~~r~Y~~~~v~rL~~I~~l~~~G~~L~~I~~~l~~~~~g~~l~~~l   80 (219)
T cd04778           2 YRIDDLARAAGTTVRNVRAYQDR-GLLPPPRRRGRVAIYNDSHLARLRLINQLLERGYTLAHIAELLAAWEQGRDLGDVL   80 (219)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCcccCCCCcccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhhcCCCHHHHH
Confidence            68999999999999999999988 54333 33233457887655332  22333333346666654322111 0111111


Q ss_pred             HHHHHH-------HcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHH
Q psy17316        126 VALDAL-------RAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASA  198 (229)
Q Consensus       126 ~AV~~~-------~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~  198 (229)
                      ......       ..+.+|..++++.+| +.++|.+|+. .|+-...+  ...+.++. ...+++..+...++....+..
T Consensus        81 ~~~~~~~~~~~~~~~~~~t~~eL~~~~G-~~~~l~~l~~-~Gll~pd~--~~~~~~~~-~~~~~~~~L~~~Gi~~~~i~~  155 (219)
T cd04778          81 GLQAAIDGPWSTEEPGTALLAELQSEFG-DERALARAVA-LGLLEPDG--DRVLVPSP-RLLEALAELVDAGIPLRAVLD  155 (219)
T ss_pred             hhhccccCCccCCCCCccCHHHHHHHHC-CHHHHHHHHH-CCCceeCC--CCCcccCH-HHHHHHHHHHHcCCCHHHHHH
Confidence            110110       123568999999999 8788999988 66433221  11233333 456666666666677776655


Q ss_pred             HhCCChHHHH
Q psy17316        199 EYGIPSGTLY  208 (229)
Q Consensus       199 ~fgVp~~tv~  208 (229)
                      +...=++.+-
T Consensus       156 ~lr~~r~~ad  165 (219)
T cd04778         156 LVAAVRRHAD  165 (219)
T ss_pred             HHHHHHHHHH
Confidence            5544443333

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>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=94.07  E-value=0.12  Score=35.06  Aligned_cols=38  Identities=21%  Similarity=0.402  Sum_probs=30.6

Q ss_pred             HHHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        180 EIALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       180 ~eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      ..|++++.. +..++.++|..||||..|+++-++ +...|
T Consensus         3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g   42 (57)
T PF08220_consen    3 QQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQG   42 (57)
T ss_pred             HHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            466777765 568999999999999999999887 44444

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

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=94.05  E-value=0.087  Score=42.70  Aligned_cols=46  Identities=15%  Similarity=0.372  Sum_probs=33.9

Q ss_pred             CCCCHHHH-HHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         31 KTWTHEDM-DAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        31 ~kyt~e~~-~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      .+++.|++ ...|+.+ .+|..|..++|+++|++++|+++++++..-.
T Consensus         3 ~~~~lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~   50 (153)
T PRK11179          3 ENYQIDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQA   50 (153)
T ss_pred             cccccCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            34444555 3334433 5789999999999999999999999986433

>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT)

Probab=94.02  E-value=0.082  Score=40.57  Aligned_cols=36  Identities=22%  Similarity=0.269  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +.-.+++++....++|+.|+|..+|||++.|+.+++
T Consensus        20 ~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ik   55 (101)
T PF04297_consen   20 EKQREILELYYEEDLSLSEIAEELGISRQAVYDSIK   55 (101)
T ss_dssp             HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHH
T ss_pred             HHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHH
Confidence            345678888889999999999999999999999998

Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.

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

Probab=93.99  E-value=0.3  Score=38.79  Aligned_cols=67  Identities=12%  Similarity=0.142  Sum_probs=45.9

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      |++.++|+.+||+..||+.|-+ .|+-.|.....+                              ....|++++  +...
T Consensus         1 m~IgE~A~~~gvs~~TLRyYE~-~GLl~p~r~~~~------------------------------gyR~Y~~~~~~~l~~   49 (133)
T cd04787           1 MKVKELANAAGVTPDTVRFYTR-IGLLRPTRDPVN------------------------------GYRLYSEKDLSRLRF   49 (133)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCcCCCC------------------------------CeeeCCHHHHHHHHH
Confidence            6889999999999999988854 455434221101                              134555555  4566


Q ss_pred             HHHHHcCCCCHHHHHHHhCC
Q psy17316        128 LDALRAGSISANKASKAYGI  147 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gI  147 (229)
                      |..+.+-++|+.+|..-+..
T Consensus        50 I~~lr~~G~sL~eI~~~l~~   69 (133)
T cd04787          50 ILSARQLGFSLKDIKEILSH   69 (133)
T ss_pred             HHHHHHcCCCHHHHHHHHhh
Confidence            77888888899998776654

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

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=93.95  E-value=0.086  Score=51.50  Aligned_cols=40  Identities=28%  Similarity=0.222  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      ++..+.+.+...+....++|+.+||+++|||+++++||..
T Consensus       498 Er~~I~~~L~~~~Gn~~~aA~~LGIsRtTL~RkLk~~g~~  537 (538)
T PRK15424        498 LAATLQQALERFNGDKTAAANYLGISRTTLWRRLKAEAKA  537 (538)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence            4444445555556689999999999999999999999753

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=93.88  E-value=0.075  Score=53.06  Aligned_cols=40  Identities=28%  Similarity=0.414  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHcCCCCH---HHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         37 DMDAALEALRAGQMSL---TKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~---~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      ++..+++++...+..+   ..+|+.+||+++|||+++++|||.
T Consensus       642 Er~~I~~aL~~~~gn~~~~~~aA~~LGi~R~tL~rklk~~gi~  684 (686)
T PRK15429        642 EYQLIVRVLKETNGVVAGPKGAAQRLGLKRTTLLSRMKRLGID  684 (686)
T ss_pred             HHHHHHHHHHHcCCCcccHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence            4445555555544344   599999999999999999999985

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

Probab=93.87  E-value=0.33  Score=35.04  Aligned_cols=49  Identities=24%  Similarity=0.411  Sum_probs=41.4

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHH
Q psy17316        124 LNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEI  181 (229)
Q Consensus       124 k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~e  181 (229)
                      ..-||.+|..|.+|+.++|+..|+++......++++|+. .        .|+.++..+
T Consensus        23 ~~~Ai~lY~~g~iS~gkAAelag~s~~eF~~~L~~~gI~-~--------~~~~eel~~   71 (76)
T PF03683_consen   23 EELAIKLYEEGKISLGKAAELAGMSRWEFLELLKERGIP-I--------NYDEEELEE   71 (76)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHCCCC-C--------CCCHHHHHH
Confidence            477899999999999999999999999999999988877 3        266665544

>PRK10371 DNA-binding transcriptional regulator MelR; Provisional

Probab=93.87  E-value=1.1  Score=40.15  Aligned_cols=78  Identities=13%  Similarity=0.147  Sum_probs=58.9

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH-H
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI-L  124 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~-k  124 (229)
                      ...+++.++|+.+||++++|.+..++. |...            .                           .|-... +
T Consensus       205 ~~~~tl~~lA~~~~~S~~~l~r~Fk~~~G~t~------------~---------------------------~~l~~~Rl  245 (302)
T PRK10371        205 DQALTINDVAEHVKLNANYAMGIFQRVMQLTM------------K---------------------------QYITAMRI  245 (302)
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHhCCCH------------H---------------------------HHHHHHHH
Confidence            357999999999999999999999984 4421            1                           111222 4


Q ss_pred             HHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        125 NVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       125 ~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                      ..|..++.++..|+.+||...|-+..+ ..+-.|+. |..+
T Consensus       246 ~~A~~lL~~~~~si~eIA~~~Gf~~~s~F~r~Fk~~~G~tP  286 (302)
T PRK10371        246 NHVRALLSDTDKSILDIALTAGFRSSSRFYSTFGKYVGMSP  286 (302)
T ss_pred             HHHHHHHhcCCCCHHHHHHHcCCCCHHHHHHHHHHHHCcCH
Confidence            678888888888999999999999977 66666654 6444

>TIGR03734 PRTRC_parB PRTRC system ParB family protein

Probab=93.83  E-value=0.67  Score=45.49  Aligned_cols=93  Identities=17%  Similarity=0.097  Sum_probs=62.4

Q ss_pred             CCCCCCHHHHHHHHHHHHc-CCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhh
Q psy17316         29 VTKTWTHEDMDAALEALRA-GQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISAN  107 (229)
Q Consensus        29 ~~~kyt~e~~~~AI~~~~~-g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~  107 (229)
                      -+...++-|...++..+.. |..+..+||+++|+++++|+++++-..      .      +|+    .+++|.+|.++-.
T Consensus        88 qRedLtP~EeA~A~~rLl~~g~~t~eeIA~~lG~S~~~V~rrLkL~~------L------~p~----ll~al~~g~Itl~  151 (554)
T TIGR03734        88 QRADMSPAEEAEAAARLLGRCKGDREEAARRLGWSPATLDRRLALMN------C------TDE----VRQALIDRKILLG  151 (554)
T ss_pred             ccCCCCHHHHHHHHHHHhhhcCCCHHHHHHHHCCCHHHHHHHHHHcC------C------CHH----HHHHHHcCCCChH
Confidence            3566777777777766655 444999999999999999999998421      2      333    5678888988777


Q ss_pred             hhhhccCCCCCCCHHHHHHHHHHHHcCCCCHHHH
Q psy17316        108 KASKAYGPTKSWNEEILNVALDALRAGSISANKA  141 (229)
Q Consensus       108 ~~~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~  141 (229)
                      ++-...+.+    .+.-.++++.+..+..++.+|
T Consensus       152 ~A~aLA~l~----~e~Q~~vl~~~~~~~~sv~~i  181 (554)
T TIGR03734       152 HAELLAGLP----KDKQDNVLTAILAEKPTVAEL  181 (554)
T ss_pred             HHHHHhcCC----HHHHHHHHHHHHHcCCCHHHH
Confidence            766543332    444455566665554444433

A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family the member related to ParB, and is designated PRTRC system ParB family protein.

>PRK01381 Trp operon repressor; Provisional

Probab=93.75  E-value=0.062  Score=41.04  Aligned_cols=36  Identities=14%  Similarity=0.165  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|..|++.+.+|++|++++|.++|||..||-+=.+
T Consensus        42 ~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn   77 (99)
T PRK01381         42 GTRVRIVEELLRGELSQREIKQELGVGIATITRGSN   77 (99)
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHH
Confidence            358889999999999999999999999999877655

>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24

Probab=93.74  E-value=0.15  Score=42.39  Aligned_cols=41  Identities=22%  Similarity=0.237  Sum_probs=34.8

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +.+|.+..+=.+|..+++|+-.||..+|||.+|.++|-++-
T Consensus         3 h~~e~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~~A   43 (165)
T PF08822_consen    3 HPQETRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKREA   43 (165)
T ss_pred             CcHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            34556666667899899999999999999999999999864

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=93.73  E-value=0.07  Score=37.15  Aligned_cols=39  Identities=18%  Similarity=0.345  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .+..-.+..+.+|.++..+||+..|||++++++.++.+.
T Consensus         9 ~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~   47 (68)
T PF01978_consen    9 NEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLE   47 (68)
T ss_dssp             HHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            333333334579999999999999999999999998763

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>COG0789 SoxR Predicted transcriptional regulators [Transcription]

Probab=93.71  E-value=0.46  Score=36.54  Aligned_cols=69  Identities=14%  Similarity=0.162  Sum_probs=45.5

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+||+..||+.|-+...+..+....                               |...-|++++  ++..
T Consensus         1 ~~I~eva~~~gvs~~tLRyYE~~GLl~p~~~~~-------------------------------~gyR~Ys~~dl~~l~~   49 (124)
T COG0789           1 YTIGEVAKLTGVSVRTLRFYERKGLLSPERRDE-------------------------------GGYRYYTPEDLELLQI   49 (124)
T ss_pred             CcHHHHHHHhCCCHHHHHHHHHcCCCCCcccCC-------------------------------CCceecCHHHHHHHHH
Confidence            578999999999999999998886555432221                               1133444444  3444


Q ss_pred             HHHHHcCCCCHHHHHHHhCCCh
Q psy17316        128 LDALRAGSISANKASKAYGIPS  149 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gIp~  149 (229)
                      |....+-++|+.+|-.-.....
T Consensus        50 I~~~r~~G~~L~~I~~~l~~~~   71 (124)
T COG0789          50 IKTLRELGFSLAEIKELLDLLS   71 (124)
T ss_pred             HHHHHHcCCCHHHHHHHHhccc
Confidence            5566655668888877665554

>PRK10227 DNA-binding transcriptional regulator CueR; Provisional

Probab=93.68  E-value=0.36  Score=38.62  Aligned_cols=66  Identities=9%  Similarity=0.145  Sum_probs=43.4

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      |++.++|+.+||+..||+.|=+..-+..+... .                              +....|++++  ++..
T Consensus         1 m~Ige~a~~~gvs~~tlRyYE~~GLl~p~~r~-~------------------------------~gyR~Y~~~~l~~l~~   49 (135)
T PRK10227          1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRS-E------------------------------NGYRTYTQQHLNELTL   49 (135)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCcccC-C------------------------------CCcccCCHHHHHHHHH
Confidence            68999999999999999999776433322111 1                              1133455444  3556


Q ss_pred             HHHHHcCCCCHHHHHHHhC
Q psy17316        128 LDALRAGSISANKASKAYG  146 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~g  146 (229)
                      |..+.+-++|+.+|..-++
T Consensus        50 I~~lr~~G~sl~eI~~~l~   68 (135)
T PRK10227         50 LRQARQVGFNLEESGELVN   68 (135)
T ss_pred             HHHHHHCCCCHHHHHHHHH
Confidence            6666666678888876654

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

Probab=93.67  E-value=0.12  Score=34.05  Aligned_cols=30  Identities=13%  Similarity=0.046  Sum_probs=25.0

Q ss_pred             HHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316        184 EGIRSGQTTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       184 ~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      +.+.+.++|+.+.|...|||+++|.+|.++
T Consensus         3 ~~r~~~gls~~~la~~~gis~~~i~~~~~g   32 (55)
T PF01381_consen    3 ELRKEKGLSQKELAEKLGISRSTISRIENG   32 (55)
T ss_dssp             HHHHHTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred             HHHHHcCCCHHHHHHHhCCCcchhHHHhcC
Confidence            455678899999999999999999999987

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

>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional

Probab=93.53  E-value=0.31  Score=40.02  Aligned_cols=66  Identities=11%  Similarity=0.205  Sum_probs=45.9

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV  126 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~  126 (229)
                      -+++.++|+.+||+..||+.|-+.--+...+..                                |....|+++.  ++.
T Consensus        11 ~~~IgevAk~~gvs~~TlRyYE~~GLi~~~r~~--------------------------------~g~R~Y~~~~i~~L~   58 (154)
T PRK15002         11 LLTPGEVAKRSGVAVSALHFYESKGLITSIRNS--------------------------------GNQRRYKRDVLRYVA   58 (154)
T ss_pred             cccHHHHHHHHCcCHHHHHHHHHCCCCCCccCC--------------------------------CCCEEECHHHHHHHH
Confidence            489999999999999999999886333221111                                1234555555  355


Q ss_pred             HHHHHHcCCCCHHHHHHHhC
Q psy17316        127 ALDALRAGSISANKASKAYG  146 (229)
Q Consensus       127 AV~~~~~g~~S~~~~a~k~g  146 (229)
                      .|..+.+-++|+.+|..-+.
T Consensus        59 ~I~~lr~lG~sL~eIk~ll~   78 (154)
T PRK15002         59 IIKIAQRIGIPLATIGEAFG   78 (154)
T ss_pred             HHHHHHHcCCCHHHHHHHHH
Confidence            67777777789999888664

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=93.49  E-value=0.13  Score=34.65  Aligned_cols=31  Identities=19%  Similarity=0.267  Sum_probs=26.8

Q ss_pred             HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +++.++..| ++..++|..++||..||+.+.+
T Consensus        10 ~vl~~l~~G-~~~~eIA~~l~is~~tV~~~~~   40 (58)
T PF00196_consen   10 EVLRLLAQG-MSNKEIAEELGISEKTVKSHRR   40 (58)
T ss_dssp             HHHHHHHTT-S-HHHHHHHHTSHHHHHHHHHH
T ss_pred             HHHHHHHhc-CCcchhHHhcCcchhhHHHHHH
Confidence            477777777 9999999999999999999886

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

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

Probab=93.47  E-value=0.28  Score=33.20  Aligned_cols=39  Identities=21%  Similarity=0.327  Sum_probs=30.3

Q ss_pred             CHHHHHHHHHHHHcC------CCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         34 THEDMDAALEALRAG------QMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        34 t~e~~~~AI~~~~~g------~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      |+.++.....+|..|      +.++.++|+++||+++|+...+++
T Consensus         2 T~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRr   46 (53)
T PF04967_consen    2 TDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRR   46 (53)
T ss_pred             CHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence            444554445566554      689999999999999999999986

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

>PF13309 HTH_22: HTH domain

Probab=93.45  E-value=0.11  Score=36.40  Aligned_cols=42  Identities=12%  Similarity=0.189  Sum_probs=35.3

Q ss_pred             CCCCCHHHHHHHHHHHHcCC-----CCHHHHHHHcCCChhhHHHHHH
Q psy17316         30 TKTWTHEDMDAALEALRAGQ-----MSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~-----~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ....+.+++.++|+.+.+.|     -++..+|+.+||++.|||+.++
T Consensus        18 ~~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr   64 (64)
T PF13309_consen   18 PSRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR   64 (64)
T ss_pred             hhhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence            35678899999999886644     5899999999999999998763

>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT)

Probab=93.45  E-value=0.1  Score=39.98  Aligned_cols=34  Identities=21%  Similarity=0.358  Sum_probs=27.6

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..+++.|-..++|+.+||..+||++..+++++++
T Consensus        23 ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr   56 (101)
T PF04297_consen   23 REILELYYEEDLSLSEIAEELGISRQAVYDSIKR   56 (101)
T ss_dssp             HHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred             HHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4678899999999999999999999999999997

Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.

>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=93.43  E-value=0.57  Score=35.60  Aligned_cols=65  Identities=18%  Similarity=0.180  Sum_probs=44.0

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      |++.++|+.+||+..||+.|-+. |+-.|....                                ....|++++  +...
T Consensus         1 m~Ige~a~~~gvs~~tlRyYe~~-GLl~p~~~~--------------------------------g~r~Y~~~~~~~l~~   47 (107)
T cd04777           1 MKIGKFAKKNNITIDTVRHYIDL-GLLIPEKKG--------------------------------GQYFFDEKCQDDLEF   47 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCcCCccCC--------------------------------CccccCHHHHHHHHH
Confidence            68899999999999999999775 433232211                                122355444  3556


Q ss_pred             HHHHHcCCCCHHHHHHHhCC
Q psy17316        128 LDALRAGSISANKASKAYGI  147 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gI  147 (229)
                      |..+.+=++|+.+|..-+..
T Consensus        48 I~~lr~~G~sL~eI~~~l~~   67 (107)
T cd04777          48 ILELKGLGFSLIEIQKIFSY   67 (107)
T ss_pred             HHHHHHCCCCHHHHHHHHHh
Confidence            67777767899888876654

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []

Probab=93.39  E-value=0.18  Score=37.94  Aligned_cols=43  Identities=21%  Similarity=0.213  Sum_probs=31.3

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ++...+++..|+++++-.|.|.++||.+|||+.+-+...+.+.
T Consensus        35 s~IrS~kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL   77 (91)
T PF03333_consen   35 SSIRSEKIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRL   77 (91)
T ss_dssp             S----HHHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHH
Confidence            4567789999999999999999999999999999999988864

At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=93.39  E-value=0.16  Score=37.28  Aligned_cols=57  Identities=11%  Similarity=0.176  Sum_probs=40.4

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHH
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDAL   99 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll   99 (229)
                      |-++-..++++.+..|.+++.++|+.+||+.+|+++-+...    +.      ..+++.+....++.
T Consensus         3 ~~~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~~~----~~------~Vs~~Tr~rV~~aa   59 (80)
T TIGR02844         3 YIEERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVTER----LP------EINPELAEEVKEVL   59 (80)
T ss_pred             cHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhcCC----CC------CCCHHHHHHHHHHH
Confidence            44555567777776799999999999999999999965310    01      13677776666544

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.

>TIGR02051 MerR Hg(II)-responsive transcriptional regulator

Probab=93.38  E-value=0.38  Score=37.78  Aligned_cols=68  Identities=12%  Similarity=0.148  Sum_probs=43.7

Q ss_pred             CHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHHH
Q psy17316         51 SLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVAL  128 (229)
Q Consensus        51 S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~AV  128 (229)
                      ++.++|+.+||+..||+.|-+..-+..+... .                              |....|++++  +...|
T Consensus         1 ~I~e~a~~~gvs~~tlR~Ye~~GLl~~~~r~-~------------------------------~g~R~Y~~~~l~~l~~I   49 (124)
T TIGR02051         1 TIGELAKAAGVNVETIRYYERKGLLPEPDRP-E------------------------------GGYRRYPEETVKRLRFI   49 (124)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHCCCCCCCccC-C------------------------------CCCEeECHHHHHHHHHH
Confidence            5789999999999999999665333322111 1                              1123444444  34556


Q ss_pred             HHHHcCCCCHHHHHHHhCCCh
Q psy17316        129 DALRAGSISANKASKAYGIPS  149 (229)
Q Consensus       129 ~~~~~g~~S~~~~a~k~gIp~  149 (229)
                      ..+..-++|+.+|..-+....
T Consensus        50 ~~l~~~G~sl~eI~~~l~~~~   70 (124)
T TIGR02051        50 KRAQELGFSLEEIGGLLGLVD   70 (124)
T ss_pred             HHHHHCCCCHHHHHHHHhccc
Confidence            666777789999988776543

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

>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B

Probab=93.30  E-value=0.14  Score=34.91  Aligned_cols=35  Identities=20%  Similarity=0.217  Sum_probs=28.3

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .+.+..|.+.+.++.++|+.++|.+.||+.++++.
T Consensus         2 ~~TL~~yl~~~~n~~~tA~~L~iHrNTl~yRl~ki   36 (59)
T PF13556_consen    2 LETLRAYLENNGNISKTARALHIHRNTLRYRLKKI   36 (59)
T ss_dssp             --HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             hhHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            45677888888899999999999999999999984

>PF14493 HTH_40: Helix-turn-helix domain

Probab=93.29  E-value=0.88  Score=33.60  Aligned_cols=78  Identities=14%  Similarity=0.165  Sum_probs=54.6

Q ss_pred             HHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccCCCCCCCCCCCHHHHHHHHHHHHhCC-CcHHHHHHHh
Q psy17316        125 NVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQPFNASPTAWKPEDLEIALEGIRSGQ-TTVQRASAEY  200 (229)
Q Consensus       125 ~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~-~s~~eAA~~f  200 (229)
                      +...+++.+|. |+.+||++-|+..+|++.++-+.   |.....     ..-.+.|+...|.+.+.+.+ .+++.+=..+
T Consensus         4 ~~T~~l~~~G~-si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~-----~~~l~~e~~~~I~~~~~~~~~~~lk~i~e~l   77 (91)
T PF14493_consen    4 QITYELFQKGL-SIEEIAKIRGLKESTIYGHLAELIESGEPLDI-----EELLSEEEIKQIEDAIEKLGSEKLKPIKEAL   77 (91)
T ss_pred             HHHHHHHHcCC-CHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCH-----HHhCCHHHHHHHHHHHHHcCcccHHHHHHHC
Confidence            55677888775 99999999999999988887543   322211     12246677777777776533 5677777777


Q ss_pred             C--CChHHHH
Q psy17316        201 G--IPSGTLY  208 (229)
Q Consensus       201 g--Vp~~tv~  208 (229)
                      +  ++|..+.
T Consensus        78 ~~~~sy~~iR   87 (91)
T PF14493_consen   78 PGDYSYFEIR   87 (91)
T ss_pred             CCCCCHHHHH
Confidence            7  8877764

>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=93.26  E-value=0.2  Score=37.37  Aligned_cols=36  Identities=8%  Similarity=0.072  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|.+|++.+..++++|++++..+|||-.|+-+--+
T Consensus        36 ~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr   71 (87)
T PF01371_consen   36 AQRWQVAKELLDEGKSYREIAEETGVSIATITRVSR   71 (87)
T ss_dssp             HHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            358899996677779999999999999999977655

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 ....

>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional

Probab=93.23  E-value=0.64  Score=43.06  Aligned_cols=87  Identities=18%  Similarity=0.218  Sum_probs=59.9

Q ss_pred             HHHHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCC
Q psy17316         38 MDAALEALR-AGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGP  115 (229)
Q Consensus        38 ~~~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~  115 (229)
                      +..+++.+. +..+++.++|..+|++.++|.++.++. |..            +......+                   
T Consensus        87 i~~a~~~I~~~~~lsl~eLA~~lG~S~~~L~R~Fkk~~G~T------------P~~yl~~~-------------------  135 (353)
T PRK15435         87 ITHACRLLEQETPVTLEALADQVAMSPFHLHRLFKATTGMT------------PKAWQQAW-------------------  135 (353)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcC------------HHHHHHHH-------------------
Confidence            455655553 467999999999999999999999984 543            11111111                   


Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        116 TKSWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       116 ~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                             -+..|.+++..+ .|+.+||...|-+..+ +++..++. |...
T Consensus       136 -------Rl~~A~~lL~~~-~sI~eIA~~~Gf~s~s~F~~~Fkk~~G~TP  177 (353)
T PRK15435        136 -------RARRLREALAKG-ESVTTSILNAGFPDSSSYYRKADETLGMTA  177 (353)
T ss_pred             -------HHHHHHHHHhCC-CCHHHHHHHhCCCChHHHHHHHHHHHCcCc
Confidence                   134555666554 6999999999998866 77777654 5433

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=93.20  E-value=0.24  Score=35.84  Aligned_cols=37  Identities=22%  Similarity=0.123  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++....|...+. ..++|+.|+|..+|||.+||..++.
T Consensus        17 ~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~   54 (73)
T TIGR03879        17 DSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLK   54 (73)
T ss_pred             CHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence            344555555554 4779999999999999999999988

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

>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]

Probab=93.19  E-value=2.5  Score=31.47  Aligned_cols=89  Identities=18%  Similarity=0.209  Sum_probs=63.7

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH-hCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR-LGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGP  115 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~-~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~  115 (229)
                      .+...|.....+++++.++|...|+++++|.+..++ .|....           +..                       
T Consensus        24 ~~~~~i~~~~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~~-----------~~~-----------------------   69 (127)
T COG2207          24 RALDYIEENLAEPLTLEDLARRLGMSRRTLSRLFKKETGTSPS-----------QYL-----------------------   69 (127)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH-----------HHH-----------------------
Confidence            555555555566789999999999999999999995 344310           000                       


Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        116 TKSWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       116 ~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                          ..-.+..|...+..+..++.+||...|-+... ..+..++. |..+
T Consensus        70 ----~~~Rl~~A~~lL~~~~~~i~~iA~~~Gf~~~s~F~~~Fk~~~g~tP  115 (127)
T COG2207          70 ----RQLRLEEARRLLRSTDLSITEIALRLGYSSPSHFSRAFKRLFGVTP  115 (127)
T ss_pred             ----HHHHHHHHHHHHHcCCCCHHHHHHHhCcCCHHHHHHHHHHHhCCCh
Confidence                01235778888888888999999999999977 66655543 5433

>PRK15044 transcriptional regulator SirC; Provisional

Probab=93.19  E-value=0.4  Score=43.48  Aligned_cols=82  Identities=11%  Similarity=0.126  Sum_probs=60.1

Q ss_pred             HcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHH
Q psy17316        132 RAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRC  211 (229)
Q Consensus       132 ~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~v  211 (229)
                      .....++.++|++.|++.++|.+..+..|....       .-+....+..|.+.+..+++++.++|.+.|-+..+-...+
T Consensus       205 l~~~~SLeeLA~~lgmS~~tL~R~Fk~eg~T~~-------~y~~~~RL~~A~~LL~~t~~sIseIA~~~GFss~S~FsRa  277 (295)
T PRK15044        205 LTRKWSQAEVAGKLFMSVSSLKRKLAAEEVSFS-------KIYLDARMNQAIKLLRMGAGNISQVATMCGYDTPSYFIAI  277 (295)
T ss_pred             cccCCCHHHHHHHhCCCHHHHHHHHHHcCCCHH-------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHH
Confidence            344579999999999999999999987652221       1233444567788888899999999999998888777665


Q ss_pred             HhhcCCCCC
Q psy17316        212 KLSRSTPRP  220 (229)
Q Consensus       212 k~~~~~~~~  220 (229)
                      =...-|-+|
T Consensus       278 FKk~fG~TP  286 (295)
T PRK15044        278 FKRHFKITP  286 (295)
T ss_pred             HHHHHCcCH
Confidence            433334444

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

Probab=93.16  E-value=0.099  Score=34.46  Aligned_cols=27  Identities=15%  Similarity=0.212  Sum_probs=22.6

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ...++|+.++|+..||+++||.+|...
T Consensus         6 ~~~gls~~~la~~~gis~~~i~~~~~g   32 (55)
T PF01381_consen    6 KEKGLSQKELAEKLGISRSTISRIENG   32 (55)
T ss_dssp             HHTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred             HHcCCCHHHHHHHhCCCcchhHHHhcC
Confidence            467999999999999999999999883

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

>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=93.04  E-value=0.34  Score=38.58  Aligned_cols=42  Identities=21%  Similarity=0.295  Sum_probs=36.2

Q ss_pred             CCCCCHHHHHHHHHHHHh-----CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        171 PTAWKPEDLEIALEGIRS-----GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       171 ~r~~t~e~r~eaV~~~~~-----~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+.+|+|+|.++...|++     |.++..+++..+|+++.|+...++
T Consensus         2 a~~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lr   48 (127)
T PF06163_consen    2 ARVFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLR   48 (127)
T ss_pred             CCcCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHH
Confidence            367889998887666665     789999999999999999999988

>PRK15186 AraC family transcriptional regulator; Provisional

Probab=93.04  E-value=0.45  Score=42.91  Aligned_cols=87  Identities=13%  Similarity=0.140  Sum_probs=59.7

Q ss_pred             HHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHH
Q psy17316        127 ALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGT  206 (229)
Q Consensus       127 AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~t  206 (229)
                      +|..-.....++.++|+.+|++.+||.+..++.|....       ..+..-.+..|.+++..+++++.++|...|-+-++
T Consensus       189 ~I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~~g~s~~-------~~~~~~Rl~~A~~lL~~~~~sI~~IA~~~GY~s~S  261 (291)
T PRK15186        189 IIISDISRKWALKDISDSLYMSCSTLKRKLKQENTSFS-------EVYLNARMNKATKLLRNSEYNITRVAYMCGYDSAS  261 (291)
T ss_pred             HHHhCccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHH-------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHH
Confidence            33333445679999999999999999999987653222       11223345566777777789999999999987766


Q ss_pred             HHHHHHhhcCCCCC
Q psy17316        207 LYGRCKLSRSTPRP  220 (229)
Q Consensus       207 v~~~vk~~~~~~~~  220 (229)
                      -...+=...-|-+|
T Consensus       262 ~Fsr~FK~~~G~TP  275 (291)
T PRK15186        262 YFTCVFKKHFKTTP  275 (291)
T ss_pred             HHHHHHHHHHCcCH
Confidence            66554333334444

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=92.98  E-value=0.28  Score=31.36  Aligned_cols=36  Identities=17%  Similarity=0.323  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .++..+.  .++.+++.++|+.+||+++|+++.+..+.
T Consensus         4 ~il~~l~--~~~~~s~~~l~~~l~~s~~tv~~~l~~L~   39 (53)
T smart00420        4 QILELLA--QQGKVSVEELAELLGVSEMTIRRDLNKLE   39 (53)
T ss_pred             HHHHHHH--HcCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3445543  36789999999999999999999998763

>PHA01976 helix-turn-helix protein

Probab=92.97  E-value=0.37  Score=33.08  Aligned_cols=25  Identities=16%  Similarity=0.158  Sum_probs=23.0

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-++|+.++|+..||++++|.+|..
T Consensus        13 ~~glt~~~lA~~~gvs~~~v~~~e~   37 (67)
T PHA01976         13 ARAWSAPELSRRAGVRHSLIYDFEA   37 (67)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            4689999999999999999999976

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=92.97  E-value=0.15  Score=48.93  Aligned_cols=34  Identities=26%  Similarity=0.391  Sum_probs=28.9

Q ss_pred             HHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         44 ALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      ++...+-.+.++|+.+||+++|||+++++||+..
T Consensus       425 aL~~~~g~~~~aA~~LGi~R~tLy~Klk~~g~~~  458 (464)
T COG2204         425 ALERTGGNKSEAAERLGISRKTLYRKLKEYGIDR  458 (464)
T ss_pred             HHHHhCCCHHHHHHHHCCCHHHHHHHHHHhCCCc
Confidence            4444455899999999999999999999999875

>PRK13501 transcriptional activator RhaR; Provisional

Probab=92.93  E-value=0.69  Score=40.78  Aligned_cols=79  Identities=13%  Similarity=0.174  Sum_probs=60.1

Q ss_pred             HHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHH-HHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        125 NVALDALRAGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPED-LEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       125 ~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~-r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      ...|+.-....+++.++|+++|++.++|.+..+++ |....        .|=.+- ..+|-+++...++++.++|...|=
T Consensus       182 ~~~I~~~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~~G~T~~--------qyi~~~Ri~~A~~LL~~t~~sI~eIA~~~GF  253 (290)
T PRK13501        182 MSALQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSIS--------HYLRQIRLCHAKCLLRGSEHRISDIAARCGF  253 (290)
T ss_pred             HHHHHHhhccCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCC
Confidence            44555555667899999999999999999999976 64443        232333 446777778888999999999999


Q ss_pred             ChHHHHHHH
Q psy17316        203 PSGTLYGRC  211 (229)
Q Consensus       203 p~~tv~~~v  211 (229)
                      +..+-..++
T Consensus       254 ~~~s~F~r~  262 (290)
T PRK13501        254 EDSNYFSAV  262 (290)
T ss_pred             CCHHHHHHH
Confidence            877766654

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=92.90  E-value=0.19  Score=41.23  Aligned_cols=42  Identities=24%  Similarity=0.369  Sum_probs=32.7

Q ss_pred             HHHH-HHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         35 HEDM-DAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        35 ~e~~-~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      -|++ .++|+.+ .+|.+|..++|++.|++.+|++++++++.-.
T Consensus        12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~   55 (164)
T PRK11169         12 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQ   55 (164)
T ss_pred             HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            3444 3444444 5789999999999999999999999986433

>COG3311 AlpA Predicted transcriptional regulator [Transcription]

Probab=92.89  E-value=0.37  Score=34.58  Aligned_cols=54  Identities=11%  Similarity=0.336  Sum_probs=38.6

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSG  189 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~  189 (229)
                      +.+.+++.++|++++|+|++++.-.......-.++---|.+.|-.+-++.++..
T Consensus        14 lrl~ev~~~~GlSrstiYr~i~~~~FPkpvklG~r~v~W~~SEI~~Wi~~~~~~   67 (70)
T COG3311          14 LRLPEVAQLTGLSRSTIYRLIKDGTFPKPVKLGGRSVAWPESEIDEWIASRKAA   67 (70)
T ss_pred             hhHHHHHHHHCccHHHHHHHHccCCCCCCeecCcccccccHHHHHHHHHHHHhc
Confidence            588999999999999999999854222211112234568888888888887765

>PRK13752 putative transcriptional regulator MerR; Provisional

Probab=92.84  E-value=0.62  Score=37.72  Aligned_cols=67  Identities=10%  Similarity=0.062  Sum_probs=50.5

Q ss_pred             CCCHHHHHHHhCCChHHHHHHHHHhCCcc-cCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        135 SISANKASKAYGIPSSTLYKIARKEGIRL-AQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       135 ~~S~~~~a~k~gIp~sTL~~~ik~~g~k~-~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      .+++.++|+.+||+..||+-|-+ .|.-. .....+..|-|+++  .++..|..+.+-+++..++...++.
T Consensus         7 ~~~IgevAk~~Gvs~~TLRyYE~-~GLl~p~~r~~~gyR~Y~~~~l~rl~~I~~lr~~G~sL~eI~~ll~~   76 (144)
T PRK13752          7 NLTIGVFAKAAGVNVETIRFYQR-KGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRL   76 (144)
T ss_pred             cccHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            36999999999999999999876 45322 11112335788765  6778888888888999999998854

>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=92.79  E-value=0.15  Score=40.63  Aligned_cols=40  Identities=18%  Similarity=0.229  Sum_probs=32.5

Q ss_pred             HHH-HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         36 EDM-DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        36 e~~-~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      .++ +.++ .+..++++++++|+..||+..++.+|+++++-.
T Consensus        76 ~~~~~~~~-~~~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~  116 (129)
T COG3677          76 YKIKLQAV-TLYMLGLGIRDIARTLGISINTVNRWSKRFGSR  116 (129)
T ss_pred             hHHHHHHH-HHHHcCCCcccHHHHhcccHHHHHHHHHhhcch
Confidence            444 5555 556778999999999999999999999997543

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=92.78  E-value=0.17  Score=35.12  Aligned_cols=32  Identities=25%  Similarity=0.429  Sum_probs=27.5

Q ss_pred             HHHHHH-HhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        181 IALEGI-RSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       181 eaV~~~-~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +|..++ ..|.++..++|...|||+++||+.++
T Consensus        12 ~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~   44 (68)
T PF01978_consen   12 KVYLALLKNGPATAEEIAEELGISRSTVYRALK   44 (68)
T ss_dssp             HHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344444 58899999999999999999999998

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>PRK13749 transcriptional regulator MerD; Provisional

Probab=92.75  E-value=0.84  Score=36.05  Aligned_cols=66  Identities=3%  Similarity=-0.045  Sum_probs=49.4

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccC-CCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQ-PFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~-~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      +++.++|+++||+..||+-+-+. |.-... ...+..|.|+++  .++..|..|.+=++++.++...+++
T Consensus         4 ~tIgelA~~~gvS~~tiR~YE~~-GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l   72 (121)
T PRK13749          4 YTVSRLALDAGVSVHIVRDYLLR-GLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRA   72 (121)
T ss_pred             CcHHHHHHHHCCCHHHHHHHHHC-CCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhh
Confidence            68999999999999999997763 532221 112456788766  5677788888888999999887766

>COG5484 Uncharacterized conserved protein [Function unknown]

Probab=92.74  E-value=0.15  Score=45.23  Aligned_cols=39  Identities=21%  Similarity=0.230  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      +....|-.+|..| |-+.+||.+|||++.||+.|.++.|-
T Consensus         7 ~~r~~Akk~yl~g-mk~~dIAeklGvspntiksWKrr~gW   45 (279)
T COG5484           7 DKRIIAKKDYLKG-MKLKDIAEKLGVSPNTIKSWKRRDGW   45 (279)
T ss_pred             chHHHHHHHHHhh-ccHHHHHHHhCCChHHHHHHHHhcCC
Confidence            4567788899995 99999999999999999999999876

>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=92.58  E-value=0.92  Score=34.45  Aligned_cols=65  Identities=9%  Similarity=0.075  Sum_probs=47.4

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      +++.++|+++||+..||+-+-+ .|.-.... ....+.|+++  +++..|..+.+=++|..++...+..
T Consensus         1 m~Ige~a~~~gvs~~tlRyYe~-~GLl~p~~-~~g~r~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~   67 (107)
T cd04777           1 MKIGKFAKKNNITIDTVRHYID-LGLLIPEK-KGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFSY   67 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCcCCcc-CCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            4789999999999999998776 35322121 1234567655  5677788888877999999998865

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PF14493 HTH_40: Helix-turn-helix domain

Probab=92.53  E-value=0.59  Score=34.56  Aligned_cols=59  Identities=15%  Similarity=0.153  Sum_probs=39.7

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCC-CCCCCCCCCcHHHHHHHHHHH
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTP-KKEGPTKSWNEEILNVALDAL   99 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~-~~~~~~k~~s~e~~~~a~~ll   99 (229)
                      ....++.+.+ |+|+.+||+.-|+..+||...+-.+-..|+ .....  -.+++..+...+.+
T Consensus         3 ~~~T~~l~~~-G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~~~--~l~~e~~~~I~~~~   62 (91)
T PF14493_consen    3 AQITYELFQK-GLSIEEIAKIRGLKESTIYGHLAELIESGEPLDIEE--LLSEEEIKQIEDAI   62 (91)
T ss_pred             HHHHHHHHHc-CCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCHHH--hCCHHHHHHHHHHH
Confidence            3456677776 789999999999999999999998755443 22211  13555554444433

>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B

Probab=92.52  E-value=0.15  Score=34.82  Aligned_cols=43  Identities=14%  Similarity=-0.002  Sum_probs=30.2

Q ss_pred             HHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH--hhcCCCCCCC
Q psy17316        180 EIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK--LSRSTPRPPP  222 (229)
Q Consensus       180 ~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk--~~~~~~~~~~  222 (229)
                      .+.++...+++.|+.+||...+|.++||+.+++  ..-.|..+.+
T Consensus         2 ~~TL~~yl~~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~dl~~   46 (59)
T PF13556_consen    2 LETLRAYLENNGNISKTARALHIHRNTLRYRLKKIEELLGLDLDD   46 (59)
T ss_dssp             --HHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--TTS
T ss_pred             hhHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcCCCC
Confidence            356778888889999999999999999999998  3334444443

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

Probab=92.51  E-value=0.4  Score=31.43  Aligned_cols=38  Identities=16%  Similarity=0.160  Sum_probs=28.7

Q ss_pred             CHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHH
Q psy17316         51 SLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDAL   99 (229)
Q Consensus        51 S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll   99 (229)
                      ++++||+..||+.+|+.+-+..-     .      ..+++.++..++..
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~~-----~------~vs~~tr~rI~~~a   38 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNGP-----P------RVSEETRERILEAA   38 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTTC-----S------SSTHHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHhCC-----C------CCCHHHHHHHHHHH
Confidence            57899999999999999998732     1      24677777666543

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

>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24

Probab=92.49  E-value=0.33  Score=40.43  Aligned_cols=40  Identities=18%  Similarity=0.188  Sum_probs=34.7

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHH
Q psy17316        119 WNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARK  158 (229)
Q Consensus       119 Ys~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~  158 (229)
                      +++|.+..+=.+|..+.+|+..+|.++|||..|.++|-++
T Consensus         3 h~~e~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~~   42 (165)
T PF08822_consen    3 HPQETRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKRE   42 (165)
T ss_pred             CcHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            4567777777899988889999999999999999999753

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK13752 putative transcriptional regulator MerR; Provisional

Probab=92.48  E-value=0.64  Score=37.66  Aligned_cols=68  Identities=10%  Similarity=0.113  Sum_probs=46.5

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV  126 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~  126 (229)
                      .+++.++|+.+||+..||+-|=+..-+..+... .                              |...-|++++  +..
T Consensus         7 ~~~IgevAk~~Gvs~~TLRyYE~~GLl~p~~r~-~------------------------------~gyR~Y~~~~l~rl~   55 (144)
T PRK13752          7 NLTIGVFAKAAGVNVETIRFYQRKGLLPEPDKP-Y------------------------------GSIRRYGEADVTRVR   55 (144)
T ss_pred             cccHHHHHHHHCcCHHHHHHHHHCCCCCCCccC-C------------------------------CCCeecCHHHHHHHH
Confidence            489999999999999999999875323211111 0                              1134455555  456


Q ss_pred             HHHHHHcCCCCHHHHHHHhCC
Q psy17316        127 ALDALRAGSISANKASKAYGI  147 (229)
Q Consensus       127 AV~~~~~g~~S~~~~a~k~gI  147 (229)
                      .|..+..-++|+.+|..-...
T Consensus        56 ~I~~lr~~G~sL~eI~~ll~~   76 (144)
T PRK13752         56 FVKSAQRLGFSLDEIAELLRL   76 (144)
T ss_pred             HHHHHHHcCCCHHHHHHHHhc
Confidence            677777778899999887653

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=92.47  E-value=0.85  Score=33.70  Aligned_cols=61  Identities=13%  Similarity=0.159  Sum_probs=45.4

Q ss_pred             HHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhC-CCcHHHHHHHhC-CChHHHHHHHH
Q psy17316        138 ANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSG-QTTVQRASAEYG-IPSGTLYGRCK  212 (229)
Q Consensus       138 ~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~-~~s~~eAA~~fg-Vp~~tv~~~vk  212 (229)
                      +..+|+.|||+...|..             ..+.+... ..|.-++-.|... ++|+.+++..|| ..++||..-++
T Consensus         5 i~~Va~~~~v~~~~i~~-------------~~R~~~~~-~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~   67 (90)
T cd06571           5 IEAVAEYFGISVEDLRS-------------KSRKKEIA-LARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVR   67 (90)
T ss_pred             HHHHHHHhCCCHHHHhc-------------CCCCcCcc-hHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHH
Confidence            34578899999877644             11222332 3577777777774 899999999999 99999998876

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.

>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B

Probab=92.46  E-value=0.53  Score=32.65  Aligned_cols=50  Identities=12%  Similarity=0.161  Sum_probs=32.3

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhh
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISAN  107 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~  107 (229)
                      .+||+-+   | |+..+|+.+||++++|++|  ...             -|+.+--.+|.+.+|.+.+.
T Consensus         3 ~~aI~~~---G-~~~~lAkalGVs~~aVs~W--~~~-------------IP~~ra~~Ie~~T~G~l~~~   52 (60)
T PF14549_consen    3 KDAIKYF---G-GQSKLAKALGVSPQAVSQW--GER-------------IPAERAYQIEKLTNGKLKCE   52 (60)
T ss_dssp             HHHHHHH---S-SHHHHHHHHTS-HHHHHHH--HTS---------------HHHHHHHHHHTTTSS--H
T ss_pred             HHHHHHH---C-CHHHHHHHHCCCHHHHHHh--cCc-------------cCHHHHHHHHHHhCCceeeC
Confidence            3455443   4 7899999999999999999  211             13445556777777876654

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

Probab=92.43  E-value=0.13  Score=34.99  Aligned_cols=29  Identities=14%  Similarity=0.137  Sum_probs=21.8

Q ss_pred             HHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         44 ALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .+.+.++|+.++|+..||+++||++|+..
T Consensus         5 ~m~~~~it~~~La~~~gis~~tl~~~~~~   33 (63)
T PF13443_consen    5 LMAERGITQKDLARKTGISRSTLSRILNG   33 (63)
T ss_dssp             HHHHTT--HHHHHHHHT--HHHHHHHHTT
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            44567899999999999999999999983

>PRK15185 transcriptional regulator HilD; Provisional

Probab=92.42  E-value=0.6  Score=42.62  Aligned_cols=79  Identities=16%  Similarity=0.204  Sum_probs=57.3

Q ss_pred             CCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCC-CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        134 GSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAW-KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       134 g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~-t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...|+.++|+..|++.++|.++.+.+|....        .| ..-....|.+++..++++..++|...|-+.++-...+=
T Consensus       221 ~~~SledLA~~lgmS~~tL~R~FK~~G~S~~--------~yl~~~Ri~~A~~LL~~t~~sIseIA~~~GFss~S~FsR~F  292 (309)
T PRK15185        221 RQWKLTDVADHIFMSTSTLKRKLAEEGTSFS--------DIYLSARMNQAAKLLRIGNHNVNAVALKCGYDSTSYFIQCF  292 (309)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHcCCCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHH
Confidence            4469999999999999999999986664432        22 23345566777778889999999999997766665553


Q ss_pred             hhcCCCCC
Q psy17316        213 LSRSTPRP  220 (229)
Q Consensus       213 ~~~~~~~~  220 (229)
                      ...-|-+|
T Consensus       293 Kk~~G~TP  300 (309)
T PRK15185        293 KKYFKTTP  300 (309)
T ss_pred             HHHHCcCH
Confidence            33334433

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=92.39  E-value=0.19  Score=47.26  Aligned_cols=34  Identities=21%  Similarity=0.136  Sum_probs=27.2

Q ss_pred             HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .+.+++...+..+.++|+.+||+++|||++++++
T Consensus       430 ~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~~~  463 (463)
T TIGR01818       430 LLEAALQHTRGHKQEAAALLGWGRNTLTRKLKEL  463 (463)
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence            3444555556689999999999999999999864

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>PRK09726 antitoxin HipB; Provisional

Probab=92.39  E-value=0.28  Score=36.04  Aligned_cols=41  Identities=12%  Similarity=0.233  Sum_probs=34.4

Q ss_pred             CCCCHHHHHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         31 KTWTHEDMDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-|+...+...|+.+ ...++|+.++|+..||+++||.+|.+
T Consensus         6 ~~~~~~~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~   47 (88)
T PRK09726          6 KIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFEN   47 (88)
T ss_pred             cccCHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            457788887666655 46789999999999999999999987

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

Probab=92.34  E-value=0.99  Score=34.03  Aligned_cols=59  Identities=10%  Similarity=0.072  Sum_probs=38.1

Q ss_pred             CHHHHHHHhCCChHHHHHHHHHhCCccc-CCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHH
Q psy17316        137 SANKASKAYGIPSSTLYKIARKEGIRLA-QPFNASPTAWKPED--LEIALEGIRSGQTTVQRAS  197 (229)
Q Consensus       137 S~~~~a~k~gIp~sTL~~~ik~~g~k~~-~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA  197 (229)
                      ++.++|+.+||+..||+.|-+ .|.-.. .......|.|++++  ++..|+.+.. ++++.++.
T Consensus         2 ~i~e~A~~~gvs~~tlR~Ye~-~Gll~~~~r~~~g~R~Y~~~~v~~l~~I~~l~~-g~~l~~i~   63 (99)
T cd04772           2 RTVDLARAIGLSPQTVRNYES-LGLIPPAERTANGYRIYTDKHIAALRAYRALLP-GYGYRVAQ   63 (99)
T ss_pred             CHHHHHHHHCcCHHHHHHHHH-cCCCCCCCcCCCCCeecCHHHHHHHHHHHHHhh-CCCHHHHH
Confidence            678999999999999999977 453221 11123467787764  4445555543 46666653

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

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

Probab=92.29  E-value=0.39  Score=30.78  Aligned_cols=31  Identities=19%  Similarity=0.369  Sum_probs=23.3

Q ss_pred             HHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        182 ALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       182 aV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      |++.+. ++..++.++|...|||.++|+.+++
T Consensus         8 Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~   39 (42)
T PF13404_consen    8 ILRLLQEDGRRSYAELAEELGLSESTVRRRIR   39 (42)
T ss_dssp             HHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHcCCccHHHHHHHHCcCHHHHHHHHH
Confidence            444433 4779999999999999999999987

...

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=92.29  E-value=0.2  Score=45.73  Aligned_cols=30  Identities=23%  Similarity=0.214  Sum_probs=25.2

Q ss_pred             HHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         44 ALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .+...+..+.++|+.+||+++|||+++++|
T Consensus       300 aL~~~~gn~~~aA~~LGisr~tL~rklkk~  329 (329)
T TIGR02974       300 ALAEAQFNQRKAAELLGLTYHQLRGLLRKH  329 (329)
T ss_pred             HHHHhCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence            444445589999999999999999999875

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

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

Probab=92.29  E-value=0.17  Score=36.38  Aligned_cols=30  Identities=20%  Similarity=0.367  Sum_probs=25.6

Q ss_pred             CCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         48 GQMSLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        48 g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      ..+|+.++|+..||+.+||.|-+++.|..|
T Consensus        33 ~~~si~elA~~~~vS~sti~Rf~kkLG~~g   62 (77)
T PF01418_consen   33 AFMSISELAEKAGVSPSTIVRFCKKLGFSG   62 (77)
T ss_dssp             CT--HHHHHHHCTS-HHHHHHHHHHCTTTC
T ss_pred             HHccHHHHHHHcCCCHHHHHHHHHHhCCCC
Confidence            579999999999999999999999999887

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

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=92.24  E-value=0.32  Score=38.41  Aligned_cols=40  Identities=3%  Similarity=-0.022  Sum_probs=29.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.++.+..-.+..+.+ |+|+.+||..+|||.+||+.++.+
T Consensus       106 ~L~~~~r~ii~l~~~~-~~s~~EIA~~l~is~~tV~~~~~r  145 (154)
T PRK06759        106 VLDEKEKYIIFERFFV-GKTMGEIALETEMTYYQVRWIYRQ  145 (154)
T ss_pred             hCCHHHHHHHHHHHhc-CCCHHHHHHHHCCCHHHHHHHHHH
Confidence            3444444444434445 789999999999999999999886

>PRK09863 putative frv operon regulatory protein; Provisional

Probab=92.16  E-value=2  Score=42.07  Aligned_cols=96  Identities=13%  Similarity=0.066  Sum_probs=59.2

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-------CCCCCCCCCCCCCC-----cHHHHHHHHHHHhhcchhh
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-------GIHTPKKEGPTKSW-----NEEILNVALDALRAGSISA  106 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-------gi~~~~~~~~~k~~-----s~e~~~~a~~ll~~G~ls~  106 (229)
                      ...++.+.++.+|..++|+.+||+..|+++-++..       |+.....   .+.|     +++.....+          
T Consensus         7 ~~iL~~L~~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~~---~~Gy~l~~~~~~~~~~~~----------   73 (584)
T PRK09863          7 LKIVDLLEQQDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISG---SAKYHLEILNRRSLFQLL----------   73 (584)
T ss_pred             HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhheec---CCceEEEeCCHHHHHHHH----------
Confidence            34455556788999999999999999999987753       3321111   1123     222111111          


Q ss_pred             hhhhhccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHH
Q psy17316        107 NKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIAR  157 (229)
Q Consensus       107 ~~~~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik  157 (229)
                                ...+++.+.-....+.+...++.++|.++.|+++||.+-++
T Consensus        74 ----------~~~~~e~~~il~~Ll~~~~~~~~~La~~l~vS~sTi~~dl~  114 (584)
T PRK09863         74 ----------QKSDNEDRLLLLRLLLNTFTPMAQLASALNLSRTWVAERLP  114 (584)
T ss_pred             ----------hcCCHHHHHHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHH
Confidence                      01123333333334456668999999999999999777654

>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional

Probab=92.11  E-value=1  Score=41.75  Aligned_cols=91  Identities=13%  Similarity=0.143  Sum_probs=62.2

Q ss_pred             HHHHHHHHHHc-CCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHh
Q psy17316        123 ILNVALDALRA-GSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEY  200 (229)
Q Consensus       123 ~k~~AV~~~~~-g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~f  200 (229)
                      .+.+|++.+.+ ..+++.++|..+|++.++|.++.+++ |....        .|-..-|.+.+...+..++++.++|...
T Consensus        86 ~i~~a~~~I~~~~~lsl~eLA~~lG~S~~~L~R~Fkk~~G~TP~--------~yl~~~Rl~~A~~lL~~~~sI~eIA~~~  157 (353)
T PRK15435         86 KITHACRLLEQETPVTLEALADQVAMSPFHLHRLFKATTGMTPK--------AWQQAWRARRLREALAKGESVTTSILNA  157 (353)
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHhCCCCHHHHHHHh
Confidence            35666666643 55799999999999999999999876 75443        2333345554444455669999999999


Q ss_pred             CCChHHHHHHHHhhcCCCCCC
Q psy17316        201 GIPSGTLYGRCKLSRSTPRPP  221 (229)
Q Consensus       201 gVp~~tv~~~vk~~~~~~~~~  221 (229)
                      |-+-++=....=...-|-+|.
T Consensus       158 Gf~s~s~F~~~Fkk~~G~TPs  178 (353)
T PRK15435        158 GFPDSSSYYRKADETLGMTAK  178 (353)
T ss_pred             CCCChHHHHHHHHHHHCcCch
Confidence            987666555443344444444

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

Probab=92.11  E-value=0.27  Score=37.43  Aligned_cols=41  Identities=20%  Similarity=0.217  Sum_probs=34.1

Q ss_pred             HHHHHHHHH--cCCCCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316         38 MDAALEALR--AGQMSLTKASVSYGIPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        38 ~~~AI~~~~--~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~   78 (229)
                      +.++.+.+.  +|.++++++|+.+||++..|.+|++..|+-..
T Consensus        11 Ka~~~d~~~~~~~~~ti~~~AK~L~i~~~~l~~~Lr~~g~l~~   53 (111)
T PF03374_consen   11 KAEFYDAFVDSDGLYTIREAAKLLGIGRNKLFQWLREKGWLYR   53 (111)
T ss_pred             hhHHHHHHHcCCCCccHHHHHHHhCCCHHHHHHHHHhCCceEE
Confidence            356666665  47799999999999999999999999887643

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

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

Probab=92.10  E-value=0.28  Score=33.24  Aligned_cols=32  Identities=19%  Similarity=0.052  Sum_probs=24.5

Q ss_pred             HHHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        183 LEGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       183 V~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      =+.+.+.+++..+.|...|||++||++|+++.
T Consensus         3 ~~~m~~~~it~~~La~~~gis~~tl~~~~~~~   34 (63)
T PF13443_consen    3 KELMAERGITQKDLARKTGISRSTLSRILNGK   34 (63)
T ss_dssp             HHHHHHTT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred             HHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence            35677888999999999999999999999854

>PRK13502 transcriptional activator RhaR; Provisional

Probab=92.09  E-value=0.79  Score=40.04  Aligned_cols=81  Identities=10%  Similarity=0.125  Sum_probs=59.5

Q ss_pred             HcCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCC-CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHH
Q psy17316        132 RAGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAW-KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYG  209 (229)
Q Consensus       132 ~~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~-t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~  209 (229)
                      ....+++.++|..+||+.+.|.+..+++ |.....        | ..--..+|.+++...++++.++|...|-+-.+-..
T Consensus       189 ~~~~~~~~~lA~~~~iS~~~L~r~fk~~~G~t~~~--------yi~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~d~s~F~  260 (282)
T PRK13502        189 LECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQ--------YLRQVRICHAQYLLQHSPLMISEISMQCGFEDSNYFS  260 (282)
T ss_pred             ccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHH--------HHHHHHHHHHHHHHHcCCCCHHHHHHHcCCCCHHHHH
Confidence            3445799999999999999999999975 755432        3 22335566777777889999999999999877766


Q ss_pred             HHHhhcCCCCC
Q psy17316        210 RCKLSRSTPRP  220 (229)
Q Consensus       210 ~vk~~~~~~~~  220 (229)
                      .+=.+.-|-+|
T Consensus       261 r~FKk~~G~tP  271 (282)
T PRK13502        261 VVFTRETGMTP  271 (282)
T ss_pred             HHHHHHHCcCH
Confidence            65433334333

>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18

Probab=92.06  E-value=0.071  Score=44.20  Aligned_cols=96  Identities=14%  Similarity=0.198  Sum_probs=58.5

Q ss_pred             HHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHH-HHHhhcchhhhhhhhccCCCCCCCHHH
Q psy17316         45 LRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVAL-DALRAGSISANKASKAYGPTKSWNEEI  123 (229)
Q Consensus        45 ~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~-~ll~~G~ls~~~~~~~~G~~~kYs~e~  123 (229)
                      .+.+.-++.++|+.|+|++++++-|++. |+..   ...+.+|..+.++.-. +.+.++             .++-..+.
T Consensus        10 ~k~~tgt~~e~~~~~~VS~~sv~~WiKN-G~~~---~~a~~~yKhAvlN~E~t~e~~e~-------------~kke~kkl   72 (186)
T PF04936_consen   10 EKKATGTIDELADYFDVSRTSVSVWIKN-GKDP---KRAKPKYKHAVLNYEKTDELNEQ-------------KKKEEKKL   72 (186)
T ss_pred             cccccccHHHHHHHHccCHHHHHHHHHc-CCCc---ccccchhhHHHhcccchhhhhhh-------------hcchhhhc
Confidence            3445568999999999999999999996 4432   2222233222211100 000000             12222233


Q ss_pred             HHHHHHHHHcCC----CCHHHHHHHhCCChHHHHHHHH
Q psy17316        124 LNVALDALRAGS----ISANKASKAYGIPSSTLYKIAR  157 (229)
Q Consensus       124 k~~AV~~~~~g~----~S~~~~a~k~gIp~sTL~~~ik  157 (229)
                      ...++..|..|.    ++-.++|+.|+|-+-++|-|+.
T Consensus        73 p~sVy~~y~kG~~~~TGta~eisq~~~i~k~~Vy~yis  110 (186)
T PF04936_consen   73 PASVYDYYDKGIFIMTGTAREISQFFSIKKQNVYYYIS  110 (186)
T ss_pred             cHHHHHHHhccccccCccHHHHHhhhccccccEEEEEe
Confidence            456677776665    4889999999999999888864

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.

>PRK09685 DNA-binding transcriptional activator FeaR; Provisional

Probab=92.01  E-value=1  Score=39.74  Aligned_cols=86  Identities=14%  Similarity=0.194  Sum_probs=57.3

Q ss_pred             HHHHHHHHcC-CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCC
Q psy17316         39 DAALEALRAG-QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTK  117 (229)
Q Consensus        39 ~~AI~~~~~g-~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~  117 (229)
                      ...|++-... .+|+.++|..+||++.+|++-.++.|...                                       .
T Consensus       203 ~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~G~T~---------------------------------------~  243 (302)
T PRK09685        203 VALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGLVV---------------------------------------A  243 (302)
T ss_pred             HHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHcCCCH---------------------------------------H
Confidence            3444444333 48999999999999999999998754321                                       1


Q ss_pred             CCCHHH-HHHHHHHHHc--CCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        118 SWNEEI-LNVALDALRA--GSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       118 kYs~e~-k~~AV~~~~~--g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                      .|=.+. +..|.+++..  ...|+.+||...|-+... ..+..|++ |..+
T Consensus       244 ~yi~~~RL~~A~~lL~~~~~~~sI~eIA~~~GF~d~s~Fsr~Fkk~~G~sP  294 (302)
T PRK09685        244 QYIRNRRLDRCADDLRPAADDEKITSIAYKWGFSDSSHFSTAFKQRFGVSP  294 (302)
T ss_pred             HHHHHHHHHHHHHHhhhhccCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence            111223 3445555522  246999999999999977 77766654 7544

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=92.01  E-value=0.18  Score=33.40  Aligned_cols=35  Identities=29%  Similarity=0.482  Sum_probs=26.7

Q ss_pred             HHHHHHHH--cCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEALR--AGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~~--~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +.+++.+.  .+++++.+||++.|+|++|+++-+..+
T Consensus         6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL   42 (52)
T PF09339_consen    6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTL   42 (52)
T ss_dssp             HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            44555444  345789999999999999999999875

One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.

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

Probab=91.99  E-value=0.34  Score=38.41  Aligned_cols=41  Identities=12%  Similarity=0.149  Sum_probs=30.2

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .+.++++..-++--+. +|+|+.+||..+|||.+|++.++++
T Consensus       110 ~~L~~~~r~v~~l~~~-~g~~~~eIA~~l~is~~tv~~~l~R  150 (159)
T TIGR02989       110 EKLPERQRELLQLRYQ-RGVSLTALAEQLGRTVNAVYKALSR  150 (159)
T ss_pred             HHCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            3444444444443344 5889999999999999999999886

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

>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=91.92  E-value=0.39  Score=31.74  Aligned_cols=33  Identities=21%  Similarity=0.237  Sum_probs=26.9

Q ss_pred             HHHHHHHH-hCC-CcHHHHHHHhCCChHHHHHHHH
Q psy17316        180 EIALEGIR-SGQ-TTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       180 ~eaV~~~~-~~~-~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+++.+. +++ ++..+.|..|+||..||++.++
T Consensus         3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~   37 (55)
T PF08279_consen    3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIK   37 (55)
T ss_dssp             HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHH
T ss_pred             HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHH
Confidence            46777773 333 8999999999999999999998

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 ....

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

Probab=91.87  E-value=0.28  Score=33.38  Aligned_cols=26  Identities=12%  Similarity=0.185  Sum_probs=20.9

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+.++|+.++|+..||++++|++|..
T Consensus         9 ~~~~lt~~~~a~~~~i~~~~i~~~e~   34 (64)
T PF12844_consen    9 EEKGLTQKDLAEKLGISRSTISKIEN   34 (64)
T ss_dssp             HHCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            35689999999999999999999987

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=91.84  E-value=0.37  Score=39.57  Aligned_cols=26  Identities=19%  Similarity=0.165  Sum_probs=23.9

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.|+|+.+||..+|||.+||+.++.+
T Consensus       147 ~~~~s~~eIA~~lgis~~tV~~~l~r  172 (182)
T PRK12537        147 VDGCSHAEIAQRLGAPLGTVKAWIKR  172 (182)
T ss_pred             HcCCCHHHHHHHHCCChhhHHHHHHH
Confidence            45889999999999999999999886

>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88

Probab=91.82  E-value=0.11  Score=34.57  Aligned_cols=29  Identities=10%  Similarity=0.296  Sum_probs=21.2

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~   78 (229)
                      ++..++++.+||+++||++|++.-...-|
T Consensus         4 l~~~ev~~~~g~s~~ti~~~~k~g~FP~p   32 (51)
T PF05930_consen    4 LRIKEVAELLGVSRSTIYRLIKDGKFPKP   32 (51)
T ss_dssp             E-HHHHHHHHSS-HHHHHHHHHHHH---S
T ss_pred             ccHHHHHHHHCCCHHHHHHHHhcccCCCC
Confidence            57889999999999999999997554433

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.

>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function

Probab=91.80  E-value=1.8  Score=37.62  Aligned_cols=82  Identities=12%  Similarity=0.099  Sum_probs=62.6

Q ss_pred             HHHHHcCC-CCHHHHHHHhCCChHHHHHHHHHhC--CcccCCCCC----CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHh
Q psy17316        128 LDALRAGS-ISANKASKAYGIPSSTLYKIARKEG--IRLAQPFNA----SPTAWKPEDLEIALEGIRSGQTTVQRASAEY  200 (229)
Q Consensus       128 V~~~~~g~-~S~~~~a~k~gIp~sTL~~~ik~~g--~k~~~~~~~----~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~f  200 (229)
                      =++|.+|. ++..+++..+|||.+|+++.++.+-  .....|..+    .++..|  -+..||+.+..| .++.++|...
T Consensus        97 ~EAy~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~t--HK~~ii~~~l~g-~~~~eiar~t  173 (220)
T PF07900_consen   97 NEAYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHDIGPGVT--HKKIIIRLYLKG-KPTPEIARRT  173 (220)
T ss_pred             HHHHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccccCCcch--HHHHHHHHHHcC-CCHHHHHHHh
Confidence            35666666 7999999999999999999987541  122234322    123333  388899999998 8899999999


Q ss_pred             CCChHHHHHHHH
Q psy17316        201 GIPSGTLYGRCK  212 (229)
Q Consensus       201 gVp~~tv~~~vk  212 (229)
                      .-|-..|-+.++
T Consensus       174 ~HS~~av~rYi~  185 (220)
T PF07900_consen  174 NHSPEAVDRYIK  185 (220)
T ss_pred             ccCHHHHHHHHH
Confidence            999999998887

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=91.79  E-value=0.33  Score=34.16  Aligned_cols=31  Identities=13%  Similarity=0.202  Sum_probs=26.3

Q ss_pred             cCC--CCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         47 AGQ--MSLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        47 ~g~--~S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      .|+  ++..++|+.+||+++++++-+..+.-.|
T Consensus        18 ~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G   50 (68)
T smart00550       18 SGDETSTALQLAKNLGLPKKEVNRVLYSLEKKG   50 (68)
T ss_pred             CCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence            356  9999999999999999999998764443

Helix-turn-helix-containing domain. Also known as Zab.

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=91.79  E-value=0.28  Score=44.71  Aligned_cols=36  Identities=17%  Similarity=0.236  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -||..|++.+..++.|..+||+..|||++|+|+++|
T Consensus       286 ~Er~~I~~aL~~~~gn~~~aA~~LGIsR~tLyrklk  321 (326)
T PRK11608        286 QEKELLQRSLQQAKFNQKRAAELLGLTYHQLRALLK  321 (326)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            367778888888889999999999999999999988

>PRK09940 transcriptional regulator YdeO; Provisional

Probab=91.77  E-value=1.3  Score=39.38  Aligned_cols=81  Identities=11%  Similarity=0.059  Sum_probs=58.1

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        123 ILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       123 ~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      .....|..-..+..++.++|+..|++.++|.+..++.|...        ..|-.+.|.+....+...+.++.++|...|-
T Consensus       138 kv~~~I~~~~~~~~tl~~LA~~~gmS~s~l~R~FK~~G~T~--------~eyl~~~Rl~~A~~LL~~~~sI~eIA~~~GF  209 (253)
T PRK09940        138 KVRNIVNMKLAHPWKLKDICDCLYISESLLKKKLKQEQTTF--------SQILLDARMQHAKNLIRVEGSVNKIAEQCGY  209 (253)
T ss_pred             HHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHcCCCH--------HHHHHHHHHHHHHHHHccCCCHHHHHHHhCC
Confidence            34555666666778999999999999999999998765322        2454445554444444445799999999988


Q ss_pred             ChHHHHHHH
Q psy17316        203 PSGTLYGRC  211 (229)
Q Consensus       203 p~~tv~~~v  211 (229)
                      +..+=.+.+
T Consensus       210 ~s~S~Fsr~  218 (253)
T PRK09940        210 ASTSYFIYA  218 (253)
T ss_pred             CCHHHHHHH
Confidence            777766654

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=91.77  E-value=0.21  Score=46.45  Aligned_cols=35  Identities=29%  Similarity=0.304  Sum_probs=27.6

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +..+.+++...+..+.++|+.+||+++|||+++++
T Consensus       407 ~~~i~~~l~~~~gn~~~aa~~Lgisr~tl~rk~~~  441 (441)
T PRK10365        407 KEVILAALEKTGGNKTEAARQLGITRKTLLAKLSR  441 (441)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHhhC
Confidence            33444556555668999999999999999999874

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=91.75  E-value=0.34  Score=33.76  Aligned_cols=34  Identities=21%  Similarity=0.219  Sum_probs=29.4

Q ss_pred             HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..++.+.++.++..++|.++||+++|+++.++..
T Consensus         4 ~il~~L~~~~~~~~eLa~~l~vS~~tv~~~l~~L   37 (69)
T TIGR00122         4 RLLALLADNPFSGEKLGEALGMSRTAVNKHIQTL   37 (69)
T ss_pred             HHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3455567889999999999999999999999876

This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.

>PRK09393 ftrA transcriptional activator FtrA; Provisional

Probab=91.74  E-value=0.83  Score=41.06  Aligned_cols=91  Identities=15%  Similarity=0.191  Sum_probs=61.9

Q ss_pred             HHHHHHHHHHHc---CCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHH-HHHHHHHhCCCcHHHH
Q psy17316        122 EILNVALDALRA---GSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLE-IALEGIRSGQTTVQRA  196 (229)
Q Consensus       122 e~k~~AV~~~~~---g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~-eaV~~~~~~~~s~~eA  196 (229)
                      ....++++.+.+   ..+|+.++|+.+|++.++|.+..++. |....        .|=.+.|+ .|.+.+...++++.++
T Consensus       218 ~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~g~s~~--------~~~~~~Rl~~A~~lL~~~~~~i~~I  289 (322)
T PRK09393        218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPA--------EWLLRERLARARDLLESSALSIDQI  289 (322)
T ss_pred             HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHH
Confidence            345555555544   34799999999999999999999976 75443        24333444 5566666778999999


Q ss_pred             HHHhCCChHHHHHHHHhhcCCCCC
Q psy17316        197 SAEYGIPSGTLYGRCKLSRSTPRP  220 (229)
Q Consensus       197 A~~fgVp~~tv~~~vk~~~~~~~~  220 (229)
                      |...|-+.++-....=...-|-+|
T Consensus       290 A~~~Gf~~~s~F~r~Fk~~~G~tP  313 (322)
T PRK09393        290 AERAGFGSEESLRHHFRRRAATSP  313 (322)
T ss_pred             HHHhCCCCHHHHHHHHHHHHCcCH
Confidence            999998775555444333333333

>PRK10371 DNA-binding transcriptional regulator MelR; Provisional

Probab=91.74  E-value=1.1  Score=40.06  Aligned_cols=89  Identities=7%  Similarity=0.038  Sum_probs=63.3

Q ss_pred             HHHHHHHHHc---CCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHH-HHHHHHHhCCCcHHHHHH
Q psy17316        124 LNVALDALRA---GSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLE-IALEGIRSGQTTVQRASA  198 (229)
Q Consensus       124 k~~AV~~~~~---g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~-eaV~~~~~~~~s~~eAA~  198 (229)
                      ..+++..+.+   ..+++.++|...|++.++|.+..++. |....        .|-.+-|+ .|.+.+..+++++.++|.
T Consensus       193 i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~~~G~t~~--------~~l~~~Rl~~A~~lL~~~~~si~eIA~  264 (302)
T PRK10371        193 VSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMK--------QYITAMRINHVRALLSDTDKSILDIAL  264 (302)
T ss_pred             HHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHHhCCCHH--------HHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            3444444433   35799999999999999999999875 64443        34445555 566777777899999999


Q ss_pred             HhCCChHHHHHHHHhhcCCCCC
Q psy17316        199 EYGIPSGTLYGRCKLSRSTPRP  220 (229)
Q Consensus       199 ~fgVp~~tv~~~vk~~~~~~~~  220 (229)
                      ..|-+.++-...+=...-|-+|
T Consensus       265 ~~Gf~~~s~F~r~Fk~~~G~tP  286 (302)
T PRK10371        265 TAGFRSSSRFYSTFGKYVGMSP  286 (302)
T ss_pred             HcCCCCHHHHHHHHHHHHCcCH
Confidence            9998888777765444444444

>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA

Probab=91.74  E-value=1.3  Score=38.66  Aligned_cols=81  Identities=14%  Similarity=0.157  Sum_probs=59.7

Q ss_pred             cCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCC-CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHH
Q psy17316        133 AGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAW-KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGR  210 (229)
Q Consensus       133 ~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~-t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~  210 (229)
                      ....|+.++|+++|++.++|.+..++. |....        .| ..--+.+|.+++...++++.++|...|-+.++-...
T Consensus       200 ~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t~~--------~yi~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~s~s~Fsr  271 (287)
T TIGR02297       200 KQHLRLPEYADRLGISESRLNDICRRFSALSPK--------RLIIERVMQEARRLLLFTQHSINQIAYDLGYKDPAYFAR  271 (287)
T ss_pred             ccCCCHHHHHHHHCCCHHHHHHHHHHHhCCCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHH
Confidence            346799999999999999999999874 64432        23 222355566667778899999999999998887777


Q ss_pred             HHhhcCCCCCC
Q psy17316        211 CKLSRSTPRPP  221 (229)
Q Consensus       211 vk~~~~~~~~~  221 (229)
                      +=.+.-|-+|.
T Consensus       272 ~FKk~~G~tP~  282 (287)
T TIGR02297       272 FFQKETGLSPS  282 (287)
T ss_pred             HHHHHHCcCHH
Confidence            65444444443

This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=91.70  E-value=0.38  Score=38.68  Aligned_cols=26  Identities=23%  Similarity=0.277  Sum_probs=23.7

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.++|+.+||..+|||.+||+.++++
T Consensus       142 ~~~~s~~eIA~~lgis~~tV~~~l~r  167 (182)
T PRK09652        142 IEGLSYEEIAEIMGCPIGTVRSRIFR  167 (182)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            35889999999999999999999885

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

Probab=91.56  E-value=0.4  Score=36.70  Aligned_cols=40  Identities=15%  Similarity=0.133  Sum_probs=29.7

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..++.+..-. ..+.-+|+|..+||+.+|||++||++++++
T Consensus       110 ~L~~~~~~ii-~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~  149 (158)
T TIGR02937       110 KLPEREREVL-VLRYLEGLSYKEIAEILGISVGTVKRRLKR  149 (158)
T ss_pred             hCCHHHHHHH-hhHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4455555433 333235789999999999999999999886

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.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=91.52  E-value=0.48  Score=34.27  Aligned_cols=37  Identities=24%  Similarity=0.296  Sum_probs=29.9

Q ss_pred             HHHHHHHHHc--CCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         38 MDAALEALRA--GQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        38 ~~~AI~~~~~--g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .+.+++.+..  +.+++.++|+.+|||++|+++-+..+.
T Consensus         7 ~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~   45 (91)
T smart00346        7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQ   45 (91)
T ss_pred             HHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            3455555543  579999999999999999999999763

>PRK13503 transcriptional activator RhaS; Provisional

Probab=91.52  E-value=1.3  Score=38.40  Aligned_cols=82  Identities=15%  Similarity=0.165  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHH---cCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHH-HHHHHHHhCCCcHHHH
Q psy17316        122 EILNVALDALR---AGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLE-IALEGIRSGQTTVQRA  196 (229)
Q Consensus       122 e~k~~AV~~~~---~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~-eaV~~~~~~~~s~~eA  196 (229)
                      +...++++.+.   ....|+.++|+.+|++.++|.+-.|+. |....        .|=.+-|+ +|.+.+..+++++.++
T Consensus       171 ~~i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S~~--------~yi~~~Rl~~A~~LL~~~~~sI~eI  242 (278)
T PRK13503        171 ARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQ--------RYLNRLRLLKARHLLRHSDASVTDI  242 (278)
T ss_pred             HHHHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHHHhCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHH
Confidence            33444444443   346799999999999999999999876 64432        34334444 6666677778999999


Q ss_pred             HHHhCCChHHHHHHH
Q psy17316        197 SAEYGIPSGTLYGRC  211 (229)
Q Consensus       197 A~~fgVp~~tv~~~v  211 (229)
                      |...|=+.++=...+
T Consensus       243 A~~~GF~~~s~F~r~  257 (278)
T PRK13503        243 AYRCGFGDSNHFSTL  257 (278)
T ss_pred             HHHhCCCCHHHHHHH
Confidence            999998887665554

>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B

Probab=91.51  E-value=0.41  Score=33.95  Aligned_cols=62  Identities=23%  Similarity=0.327  Sum_probs=40.5

Q ss_pred             HHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHH-HHHHHHHh-CCCcHHHHHHHhCCChHHHHHH
Q psy17316        141 ASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLE-IALEGIRS-GQTTVQRASAEYGIPSGTLYGR  210 (229)
Q Consensus       141 ~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~-eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~  210 (229)
                      +|+.+|++..+|.+..++. |....        .|-.+.|+ .|.+.+.+ ++++..++|..+|-+.++-...
T Consensus         1 lA~~~~~s~~~l~~~f~~~~g~s~~--------~~~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~   65 (81)
T PF12833_consen    1 LADELGMSERYLSRIFKKETGMSFK--------QYLRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHFSR   65 (81)
T ss_dssp             HHHHCTS-HHHHHHHHHHHHSS-HH--------HHHHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHHHH
T ss_pred             ChHHhCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHHHH
Confidence            5899999999999999874 75443        23334444 45555544 8899999999999986654443

...

>PRK10572 DNA-binding transcriptional regulator AraC; Provisional

Probab=91.51  E-value=1.1  Score=39.36  Aligned_cols=81  Identities=14%  Similarity=0.229  Sum_probs=59.0

Q ss_pred             HcCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHH-HHHHHHHhCCCcHHHHHHHhCCChHHHHH
Q psy17316        132 RAGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLE-IALEGIRSGQTTVQRASAEYGIPSGTLYG  209 (229)
Q Consensus       132 ~~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~-eaV~~~~~~~~s~~eAA~~fgVp~~tv~~  209 (229)
                      ..+.+++.++|+++|++.++|.+..|+. |....        .|-.+.|+ +|.+.+...++++.++|...|-+.+.-.+
T Consensus       196 ~~~~isl~~lA~~~~lS~~~l~r~Fk~~~G~tp~--------~~l~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~d~s~Fs  267 (290)
T PRK10572        196 LASEFDIESVAQHVCLSPSRLAHLFRQQLGISVL--------RWREDQRISRAKLLLQTTRMPIATIGRNVGYDDQLYFS  267 (290)
T ss_pred             ccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHH
Confidence            3466899999999999999999999876 75443        34334444 45555666789999999999998777666


Q ss_pred             HHHhhcCCCCC
Q psy17316        210 RCKLSRSTPRP  220 (229)
Q Consensus       210 ~vk~~~~~~~~  220 (229)
                      ++=.+.-|-+|
T Consensus       268 r~FKk~~G~SP  278 (290)
T PRK10572        268 RVFKKCTGASP  278 (290)
T ss_pred             HHHHHHHCcCH
Confidence            65444444444

>PRK01905 DNA-binding protein Fis; Provisional

Probab=91.37  E-value=0.52  Score=34.02  Aligned_cols=36  Identities=14%  Similarity=0.073  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      ++.-+++.+...+-+..+||...||+++|+|++++.
T Consensus        38 E~~~i~~aL~~~~gn~s~aAr~LGIsrstL~rklkk   73 (77)
T PRK01905         38 EKPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQ   73 (77)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            466677888888888999999999999999999873

>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=91.32  E-value=0.38  Score=31.81  Aligned_cols=35  Identities=14%  Similarity=0.265  Sum_probs=26.0

Q ss_pred             HHHHHH-Hc-CCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         40 AALEAL-RA-GQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        40 ~AI~~~-~~-g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      ..+..+ .+ +.+|..++|+++||++.|+++-+....
T Consensus         4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~   40 (55)
T PF08279_consen    4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKELR   40 (55)
T ss_dssp             HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            344444 23 349999999999999999999988753

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 ....

>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]

Probab=91.32  E-value=2.4  Score=31.59  Aligned_cols=81  Identities=20%  Similarity=0.271  Sum_probs=58.1

Q ss_pred             HcCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCC-CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHH
Q psy17316        132 RAGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAW-KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYG  209 (229)
Q Consensus       132 ~~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~-t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~  209 (229)
                      ..+..++.++|..+|++.++|.+..++. |....        .| ..-.+..|.+++..++.++.++|...|-+-+.-..
T Consensus        33 ~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~~--------~~~~~~Rl~~A~~lL~~~~~~i~~iA~~~Gf~~~s~F~  104 (127)
T COG2207          33 LAEPLTLEDLARRLGMSRRTLSRLFKKETGTSPS--------QYLRQLRLEEARRLLRSTDLSITEIALRLGYSSPSHFS  104 (127)
T ss_pred             hcCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCcCCHHHHH
Confidence            3444799999999999999999998854 64432        12 23456777888888888999999999988877554


Q ss_pred             HHHhhcCCCCC
Q psy17316        210 RCKLSRSTPRP  220 (229)
Q Consensus       210 ~vk~~~~~~~~  220 (229)
                      ..=...-|-+|
T Consensus       105 ~~Fk~~~g~tP  115 (127)
T COG2207         105 RAFKRLFGVTP  115 (127)
T ss_pred             HHHHHHhCCCh
Confidence            44333333333

>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors

Probab=91.28  E-value=0.5  Score=31.85  Aligned_cols=36  Identities=17%  Similarity=0.294  Sum_probs=29.1

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ....+..+..++++..++|+.+||+.+|+++.+...
T Consensus         9 ~~~il~~l~~~~~~~~ei~~~~~i~~~~i~~~l~~L   44 (78)
T cd00090           9 RLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKL   44 (78)
T ss_pred             HHHHHHHHHHCCcCHHHHHHHHCcCHhHHHHHHHHH
Confidence            344455555556999999999999999999999875

ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=91.26  E-value=0.37  Score=31.65  Aligned_cols=31  Identities=19%  Similarity=0.230  Sum_probs=27.5

Q ss_pred             HHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        182 ALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       182 aV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      |++.+..+..+..+++.+++||.++++..++
T Consensus         2 il~~l~~~~~~~~~i~~~l~is~~~v~~~l~   32 (66)
T smart00418        2 ILKLLAEGELCVCELAEILGLSQSTVSHHLK   32 (66)
T ss_pred             HHHHhhcCCccHHHHHHHHCCCHHHHHHHHH
Confidence            4566667789999999999999999999998

>COG2944 Predicted transcriptional regulator [Transcription]

Probab=91.26  E-value=0.71  Score=35.61  Aligned_cols=36  Identities=14%  Similarity=0.128  Sum_probs=27.7

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+.+++.++=+.   -++|+..+|+.+||+.+||++|=+
T Consensus        44 ls~~eIk~iRe~---~~lSQ~vFA~~L~vs~~Tv~~WEq   79 (104)
T COG2944          44 LSPTEIKAIREK---LGLSQPVFARYLGVSVSTVRKWEQ   79 (104)
T ss_pred             CCHHHHHHHHHH---hCCCHHHHHHHHCCCHHHHHHHHc
Confidence            455554443333   489999999999999999999965

>PRK13749 transcriptional regulator MerD; Provisional

Probab=91.19  E-value=1.5  Score=34.66  Aligned_cols=68  Identities=10%  Similarity=0.147  Sum_probs=45.6

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV  126 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~  126 (229)
                      .+++.++|+++||+..||+.+-+. |+-.|.....                              |....|+++.  ++.
T Consensus         3 ~~tIgelA~~~gvS~~tiR~YE~~-GLl~p~~r~~------------------------------~gyR~Y~~~~l~rL~   51 (121)
T PRK13749          3 AYTVSRLALDAGVSVHIVRDYLLR-GLLRPVACTT------------------------------GGYGLFDDAALQRLC   51 (121)
T ss_pred             CCcHHHHHHHHCCCHHHHHHHHHC-CCCCCCCcCC------------------------------CCCccCCHHHHHHHH
Confidence            478999999999999999999776 4432221111                              1234555555  456


Q ss_pred             HHHHHHcCCCCHHHHHHHhCC
Q psy17316        127 ALDALRAGSISANKASKAYGI  147 (229)
Q Consensus       127 AV~~~~~g~~S~~~~a~k~gI  147 (229)
                      .|.....-++|+.+|..-..+
T Consensus        52 ~I~~~r~~G~sL~eI~~ll~l   72 (121)
T PRK13749         52 FVRAAFEAGIGLDALARLCRA   72 (121)
T ss_pred             HHHHHHHcCCCHHHHHHHHhh
Confidence            677767777788888766555

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=91.18  E-value=0.55  Score=32.68  Aligned_cols=38  Identities=8%  Similarity=0.051  Sum_probs=31.1

Q ss_pred             HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH-hhcCCC
Q psy17316        181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-LSRSTP  218 (229)
Q Consensus       181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~~  218 (229)
                      .+++.+.++.++..+.|..||||.+||+..++ +...|-
T Consensus         4 ~il~~L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~   42 (69)
T TIGR00122         4 RLLALLADNPFSGEKLGEALGMSRTAVNKHIQTLREWGV   42 (69)
T ss_pred             HHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence            46667778889999999999999999999998 434443

This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=91.16  E-value=0.41  Score=31.59  Aligned_cols=39  Identities=18%  Similarity=0.221  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHhCC--CcHHHHHHHhCCChHHHHHHHH-hhcC
Q psy17316        178 DLEIALEGIRSGQ--TTVQRASAEYGIPSGTLYGRCK-LSRS  216 (229)
Q Consensus       178 ~r~eaV~~~~~~~--~s~~eAA~~fgVp~~tv~~~vk-~~~~  216 (229)
                      .-..|++.+..++  ++..++|.+.|+|++|+++.++ +...
T Consensus         4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~   45 (52)
T PF09339_consen    4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEE   45 (52)
T ss_dssp             HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            3456777777644  6899999999999999999988 4433

One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.

>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=91.13  E-value=0.43  Score=32.45  Aligned_cols=33  Identities=18%  Similarity=0.263  Sum_probs=26.8

Q ss_pred             HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +++..+.+.+ |+..||+.+||+.++|++.+++.
T Consensus         5 ~~f~~v~~~g-s~~~AA~~l~is~~~vs~~i~~L   37 (60)
T PF00126_consen    5 RYFLAVAETG-SISAAAEELGISQSAVSRQIKQL   37 (60)
T ss_dssp             HHHHHHHHHS-SHHHHHHHCTSSHHHHHHHHHHH
T ss_pred             HHHHHHHHhC-CHHHHHHHhhccchHHHHHHHHH
Confidence            3444555545 99999999999999999999974

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....

>PRK10072 putative transcriptional regulator; Provisional

Probab=91.12  E-value=0.44  Score=36.13  Aligned_cols=37  Identities=5%  Similarity=0.129  Sum_probs=29.4

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..+..++...-   ..-++|+.++|+.+||+.+||.+|..
T Consensus        32 ~~~~~eik~LR---~~~glTQ~elA~~lGvS~~TVs~WE~   68 (96)
T PRK10072         32 TTSFTEFEQLR---KGTGLKIDDFARVLGVSVAMVKEWES   68 (96)
T ss_pred             cCChHHHHHHH---HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            44666654443   34589999999999999999999977

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=91.10  E-value=0.26  Score=47.99  Aligned_cols=34  Identities=32%  Similarity=0.321  Sum_probs=27.3

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..+.+.+...+....++|+.+||+++|||+++++
T Consensus       493 ~~I~~aL~~~~Gn~~~aA~~LGIsRtTL~Rklk~  526 (526)
T TIGR02329       493 LAVRAALERFGGDRDAAAKALGISRTTLWRRLKA  526 (526)
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhC
Confidence            3444455666668999999999999999999873

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

>PRK09978 DNA-binding transcriptional regulator GadX; Provisional

Probab=91.08  E-value=1.3  Score=39.85  Aligned_cols=83  Identities=16%  Similarity=0.063  Sum_probs=59.2

Q ss_pred             HHHHHHHHHH---HcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHH-HHHHHHHhCCCcHHHHH
Q psy17316        122 EILNVALDAL---RAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLE-IALEGIRSGQTTVQRAS  197 (229)
Q Consensus       122 e~k~~AV~~~---~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~-eaV~~~~~~~~s~~eAA  197 (229)
                      ....++++.+   .....++.++|..+|++.++|.+..++.|...        ..|=.+.|+ .|.+.+...++++.++|
T Consensus       142 ~~~~~v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk~~G~S~--------~~yl~~~Rl~~A~~LL~~t~~sI~eIA  213 (274)
T PRK09978        142 NMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSY--------SQLLTECRMQRALQLIVIHGFSIKRVA  213 (274)
T ss_pred             HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHhcCCCH--------HHHHHHHHHHHHHHHHHcCCCCHHHHH
Confidence            3344444444   33557999999999999999999998755322        234334455 45666666889999999


Q ss_pred             HHhCCChHHHHHHHH
Q psy17316        198 AEYGIPSGTLYGRCK  212 (229)
Q Consensus       198 ~~fgVp~~tv~~~vk  212 (229)
                      ...|-+.++-.+.+=
T Consensus       214 ~~~GF~s~S~Fsr~F  228 (274)
T PRK09978        214 VSCGYHSVSYFIYVF  228 (274)
T ss_pred             HHhCCCCHHHHHHHH
Confidence            999998877776653

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

Probab=90.95  E-value=1.4  Score=33.15  Aligned_cols=23  Identities=9%  Similarity=0.036  Sum_probs=20.6

Q ss_pred             CHHHHHHHcCCChhhHHHHHHHh
Q psy17316         51 SLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        51 S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ++.++|+.+||+..||+.|-+.-
T Consensus         2 ~i~e~A~~~gvs~~tlR~Ye~~G   24 (99)
T cd04772           2 RTVDLARAIGLSPQTVRNYESLG   24 (99)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHcC
Confidence            67899999999999999997753

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

>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons

Probab=90.77  E-value=0.39  Score=33.93  Aligned_cols=34  Identities=21%  Similarity=0.235  Sum_probs=28.7

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ...| .++...+|..+||+++|+...++.+|+..+
T Consensus         4 ~~fI-rlLs~~~s~~~Aa~~lG~~~~~v~~wv~~f   37 (65)
T PF05344_consen    4 RAFI-RLLSQQISVAQAADRLGTDPGTVRRWVRMF   37 (65)
T ss_pred             HHHH-HHhcccccHHHHHHHHCcCHHHHHHHHHHH
Confidence            3445 455778999999999999999999999975

>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=90.74  E-value=1.4  Score=38.22  Aligned_cols=66  Identities=6%  Similarity=0.037  Sum_probs=49.4

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      +++.++|+.+||+..||+.|-++ |.-......+..+.|+++  +++..|..+..-+++..+|...+..
T Consensus         2 y~i~elA~~~Gvs~~tIR~Ye~~-GLL~p~r~~~~~r~Y~~~~v~rL~~I~~l~~~G~~L~~I~~~l~~   69 (219)
T cd04778           2 YRIDDLARAAGTTVRNVRAYQDR-GLLPPPRRRGRVAIYNDSHLARLRLINQLLERGYTLAHIAELLAA   69 (219)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCcccCCCCcccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            58899999999999999998875 543221112234678765  6788888888777999999887765

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=90.67  E-value=0.42  Score=38.13  Aligned_cols=29  Identities=17%  Similarity=0.054  Sum_probs=24.9

Q ss_pred             HHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         44 ALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +..-.|+|+.+||+.+|||.+||+.++.+
T Consensus       117 l~~~~g~s~~EIA~~lgis~~tV~~~l~R  145 (160)
T PRK09642        117 AHYLEEKSYQEIALQEKIEVKTVEMKLYR  145 (160)
T ss_pred             HHHHhCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            33345889999999999999999999886

>PRK15340 transcriptional regulator InvF; Provisional

Probab=90.66  E-value=1  Score=39.04  Aligned_cols=78  Identities=15%  Similarity=0.181  Sum_probs=56.6

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH-H
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI-L  124 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~-k  124 (229)
                      ....++.++|+.+|++.++|.|..+++ |... ..           .   +                        ... +
T Consensus       123 ~~~~sleeLA~~~gvS~r~f~RlFk~~~G~tp-k~-----------y---l------------------------~~~Rl  163 (216)
T PRK15340        123 TSGNTMRMLGEDYGVSYTHFRRLCSRALGGKA-KS-----------E---L------------------------RNWRM  163 (216)
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH-HH-----------H---H------------------------HHHHH
Confidence            367899999999999999999999985 4431 00           0   0                        111 2


Q ss_pred             HHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        125 NVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       125 ~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                      .+|+..+.++..|+.+||..+|-.... +.+..+++ |..+
T Consensus       164 ~~all~L~~s~~sItdIA~~~GY~d~ShFsr~FKk~~G~TP  204 (216)
T PRK15340        164 AQSLLNSVEGHENITQLAVNHGYSSPSHFSSEIKELIGVSP  204 (216)
T ss_pred             HHHHHhhhcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence            455666667788999999999998866 77777765 6544

>COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]

Probab=90.65  E-value=0.5  Score=35.43  Aligned_cols=30  Identities=27%  Similarity=0.479  Sum_probs=25.2

Q ss_pred             HHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         44 ALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      .+..|  .+..||..+||.|+||++++++||.
T Consensus        68 ~~~~g--NQtrAa~mLGinR~TLRKKLkqygl   97 (98)
T COG2901          68 QYTRG--NQTRAALMLGINRGTLRKKLKKYGL   97 (98)
T ss_pred             HHhcc--cHHHHHHHHcccHHHHHHHHHHhCC
Confidence            44444  4788999999999999999999985

>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes

Probab=90.63  E-value=1.1  Score=37.62  Aligned_cols=44  Identities=20%  Similarity=0.209  Sum_probs=40.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        169 ASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       169 ~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ......+.+.|.+|.+.+..++++++++|.+|||..+.|.-.++
T Consensus        12 ~~~~~lse~~r~~Iy~~~~~~~~sv~~vS~~ygi~~~RV~AIvr   55 (172)
T PF12298_consen   12 RSNPVLSEELREQIYEDVMQDGKSVREVSQKYGIKIQRVEAIVR   55 (172)
T ss_pred             CCCCcCCHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            44556799999999999999999999999999999999999887

This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=90.61  E-value=0.61  Score=36.79  Aligned_cols=36  Identities=14%  Similarity=0.057  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +.+|.-++.....| +|+.|+|..+|||.+||+.++.
T Consensus       109 ~~~r~ii~l~~~~~-~s~~EIA~~l~is~~tV~~~~~  144 (154)
T PRK06759        109 EKEKYIIFERFFVG-KTMGEIALETEMTYYQVRWIYR  144 (154)
T ss_pred             HHHHHHHHHHHhcC-CCHHHHHHHHCCCHHHHHHHHH
Confidence            34444444444555 9999999999999999999976

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=90.61  E-value=0.46  Score=43.31  Aligned_cols=36  Identities=3%  Similarity=-0.041  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .+..+-.+|-..+|++.+||+++||+|+++.|-+.+
T Consensus        17 l~~~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~   52 (318)
T PRK15418         17 LVARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEK   52 (318)
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            367788899999999999999999999999997775

>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors

Probab=90.55  E-value=0.8  Score=30.82  Aligned_cols=36  Identities=19%  Similarity=0.170  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +....++..+..+..+..+++..+++|..+++..++
T Consensus         7 ~~~~~il~~l~~~~~~~~ei~~~~~i~~~~i~~~l~   42 (78)
T cd00090           7 PTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLK   42 (78)
T ss_pred             hHHHHHHHHHHHCCcCHHHHHHHHCcCHhHHHHHHH
Confidence            457788888888879999999999999999999998

ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=90.53  E-value=0.63  Score=37.65  Aligned_cols=41  Identities=10%  Similarity=0.087  Sum_probs=30.5

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .+.++.+..-.+ +..-.|+|+.+||..+|||.+|++.++++
T Consensus       117 ~~L~~~~r~v~~-L~~~eg~s~~EIA~~l~is~~tV~~~l~r  157 (168)
T PRK12525        117 DGLSGKARAAFL-MSQLEGLTYVEIGERLGVSLSRIHQYMVE  157 (168)
T ss_pred             HhCCHHHHHHHH-HHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            445555544333 43345889999999999999999999876

>PRK10130 transcriptional regulator EutR; Provisional

Probab=90.50  E-value=1.7  Score=40.10  Aligned_cols=86  Identities=14%  Similarity=0.134  Sum_probs=56.8

Q ss_pred             HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCC
Q psy17316         40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKS  118 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~k  118 (229)
                      +.|++-.+..+++.++|+.+||++.+|.+-.++. |...                                       ..
T Consensus       247 ~~i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk~~~G~sp---------------------------------------~~  287 (350)
T PRK10130        247 EYVLENMSEPVTVLDLCNQLHVSRRTLQNAFHAILGIGP---------------------------------------NA  287 (350)
T ss_pred             HHHHhhhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCH---------------------------------------HH
Confidence            3333334556999999999999999999999874 4431                                       11


Q ss_pred             CCHHHHHHHH-HHHHc---CCCCHHHHHHHhCCChHH-HHHHHHHh-CCccc
Q psy17316        119 WNEEILNVAL-DALRA---GSISANKASKAYGIPSST-LYKIARKE-GIRLA  164 (229)
Q Consensus       119 Ys~e~k~~AV-~~~~~---g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~~  164 (229)
                      |=...+++.+ .++.+   ...|+.+||.++|..... ..+..|+. |...+
T Consensus       288 ylr~~RL~~ar~lL~~~~~~~~sI~eIA~~~GF~~~s~Fs~~fk~~fG~tPs  339 (350)
T PRK10130        288 WLKRIRLNAVRRELISPWSQSTTVKDAAMQWGFWHLGQFATDYQQLFAEKPS  339 (350)
T ss_pred             HHHHHHHHHHHHHHhccCCCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCcH
Confidence            1123334443 44443   356999999999998866 66665544 65443

>COG2973 TrpR Trp operon repressor [Transcription]

Probab=90.49  E-value=0.38  Score=36.66  Aligned_cols=36  Identities=11%  Similarity=0.171  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|+.||+.+.+|++|.+|++.++|||-.|+-+=.+
T Consensus        47 ~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN   82 (103)
T COG2973          47 GTRVRIVEELLRGELSQREIAQKLGVSIATITRGSN   82 (103)
T ss_pred             HHHHHHHHHHHhccccHHHHHHHhCcchhhhccchh
Confidence            358899999999999999999999999988765433

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.44  E-value=0.61  Score=35.79  Aligned_cols=34  Identities=15%  Similarity=0.219  Sum_probs=30.0

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -.+.++.....++|..|+|..|+||+|.||..+|
T Consensus        22 Q~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIK   55 (105)
T COG2739          22 QKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIK   55 (105)
T ss_pred             HHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHH
Confidence            3456777778889999999999999999999988

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

Probab=90.43  E-value=0.46  Score=38.72  Aligned_cols=31  Identities=10%  Similarity=0.039  Sum_probs=26.0

Q ss_pred             HHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         42 LEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        42 I~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.+..-.|+|+.+||..+|||.+||+.++++
T Consensus       143 ~~l~~~~g~s~~EIA~~lgis~~tVk~~l~R  173 (183)
T TIGR02999       143 VELRFFAGLTVEEIAELLGVSVRTVERDWRF  173 (183)
T ss_pred             HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            3344446899999999999999999999886

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.

>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I

Probab=90.40  E-value=0.81  Score=37.13  Aligned_cols=25  Identities=24%  Similarity=0.399  Sum_probs=19.5

Q ss_pred             CCCCHHHHHHHhCCChHHHHHHHHH
Q psy17316        134 GSISANKASKAYGIPSSTLYKIARK  158 (229)
Q Consensus       134 g~~S~~~~a~k~gIp~sTL~~~ik~  158 (229)
                      +..|..+||+..||+++|||+|-++
T Consensus        33 ~r~T~~eiAee~Gis~~tLYrWr~~   57 (142)
T PF13022_consen   33 ERRTQAEIAEEVGISRSTLYRWRQQ   57 (142)
T ss_dssp             --S-HHHHHHHHTS-HHHHHHHHHH
T ss_pred             ccchHHHHHHHhCCCHHHHHHHHhc
Confidence            4579999999999999999999863

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=90.37  E-value=7.5  Score=34.11  Aligned_cols=33  Identities=12%  Similarity=0.185  Sum_probs=24.5

Q ss_pred             HHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHH
Q psy17316        125 NVALDALRAGSISANKASKAYGIPSSTLYKIAR  157 (229)
Q Consensus       125 ~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik  157 (229)
                      ..++.+..-.++|+.+||..+|||..|+++++.
T Consensus       218 r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~~~  250 (268)
T PRK06288        218 KKVLILYYYEDLTLKEIGKVLGVTESRISQLHT  250 (268)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344444333345999999999999999887664

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=90.37  E-value=0.63  Score=37.51  Aligned_cols=26  Identities=27%  Similarity=0.288  Sum_probs=23.9

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -+|+|+.+||..+|||.+|++.++.+
T Consensus       126 ~~g~s~~eIA~~lgis~~tV~~~l~R  151 (164)
T PRK12547        126 ASGFSYEDAAAICGCAVGTIKSRVSR  151 (164)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            36889999999999999999999886

>PRK10072 putative transcriptional regulator; Provisional

Probab=90.36  E-value=0.54  Score=35.64  Aligned_cols=35  Identities=3%  Similarity=-0.131  Sum_probs=28.9

Q ss_pred             HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      ++-+.....+++..+.|..+|||.+||.+|-++.+
T Consensus        37 eik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~r   71 (96)
T PRK10072         37 EFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRV   71 (96)
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC
Confidence            34445567789999999999999999999988553

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

Probab=90.25  E-value=0.56  Score=37.14  Aligned_cols=34  Identities=9%  Similarity=0.054  Sum_probs=27.7

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+|+....-+++++.++|..+|||.+||+.++.
T Consensus       116 ~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~  149 (159)
T TIGR02989       116 QRELLQLRYQRGVSLTALAEQLGRTVNAVYKALS  149 (159)
T ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4455555455669999999999999999999976

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

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=90.22  E-value=0.56  Score=37.39  Aligned_cols=34  Identities=9%  Similarity=-0.093  Sum_probs=28.1

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+|+....-.++|+.|+|..+|||.+||+.++.
T Consensus       111 ~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~  144 (160)
T PRK09642        111 YRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLY  144 (160)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4456666665669999999999999999999876

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=90.21  E-value=0.61  Score=37.35  Aligned_cols=39  Identities=18%  Similarity=0.196  Sum_probs=28.8

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .++.+..-.+--+. .++|+.+||..+|||.+||++++++
T Consensus       126 L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~r  164 (179)
T PRK11924        126 LPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRR  164 (179)
T ss_pred             CCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            44444433332333 5889999999999999999999886

>PHA00738 putative HTH transcription regulator

Probab=90.10  E-value=0.68  Score=35.93  Aligned_cols=41  Identities=17%  Similarity=-0.010  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        177 EDLEIALEGIRSG-QTTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       177 e~r~eaV~~~~~~-~~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      .-|..||+++..| .+++.+++..|++|.++|-..++ +...|
T Consensus        12 ptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAG   54 (108)
T PHA00738         12 ILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQG   54 (108)
T ss_pred             HHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCC
Confidence            4699999999997 59999999999999999999998 44444

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=90.10  E-value=0.52  Score=37.69  Aligned_cols=39  Identities=18%  Similarity=0.142  Sum_probs=30.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.++++. .++.+.. .|+|+.+||..+|||.+|++.++.+
T Consensus       112 ~L~~~~r-~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~r  150 (166)
T PRK09639        112 KMTERDR-TVLLLRF-SGYSYKEIAEALGIKESSVGTTLAR  150 (166)
T ss_pred             cCCHHHH-HHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            3444444 3444555 7899999999999999999999886

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=90.10  E-value=9.2  Score=32.77  Aligned_cols=102  Identities=13%  Similarity=0.080  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCC--------------CCCcHHH----------
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPT--------------KSWNEEI----------   91 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~--------------k~~s~e~----------   91 (229)
                      ......+....+...+..++|..+||+...+......-....+......              ...+++.          
T Consensus        98 ~~~~~~~~~~~~~~~~~~ela~~l~i~~~~v~~~~~~~~~~~~~sl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  177 (236)
T PRK06986         98 AQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDELRGEHGDSILVTEDHQDEDPLQQLEDEELREA  177 (236)
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHcCCCHHHHHHHHHHHhccCCccccccccCCCcccccccCCCCCCHHHHHHHHHHHHH


Q ss_pred             HHHHHHHHhhcchhhhhhhhccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHH
Q psy17316         92 LNVALDALRAGSISANKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARK  158 (229)
Q Consensus        92 ~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~  158 (229)
                      ...+++.|                     ++.-..++.+..-.++|+.+||..+|||..|++.++++
T Consensus       178 l~~~l~~L---------------------~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~r  223 (236)
T PRK06986        178 LVEAIESL---------------------PEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQ  223 (236)
T ss_pred             HHHHHHhC---------------------CHHHHHHHHhHhccCCCHHHHHHHHCCCHHHHHHHHHH

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

Probab=90.07  E-value=0.7  Score=36.94  Aligned_cols=25  Identities=8%  Similarity=0.106  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         48 GQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        48 g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .|+|+.+||+.+|||.+|++.++++
T Consensus       137 ~g~s~~eIA~~l~is~~tv~~~l~r  161 (170)
T TIGR02952       137 QNLPIAEVARILGKTEGAVKILQFR  161 (170)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            5889999999999999999999886

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

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.07  E-value=0.47  Score=36.38  Aligned_cols=33  Identities=15%  Similarity=0.347  Sum_probs=30.3

Q ss_pred             HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..+++|-...+|+.+||..++|+++.|++-+++
T Consensus        24 ~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr   56 (105)
T COG2739          24 NYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKR   56 (105)
T ss_pred             HHHHHHHHhhccHHHHHHHhCccHHHHHHHHHH
Confidence            567788888999999999999999999999997

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=90.05  E-value=0.67  Score=38.47  Aligned_cols=40  Identities=15%  Similarity=0.214  Sum_probs=29.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.++.++.-.+.-+. +|+|+.+||+.+|||.+||+.++++
T Consensus       142 ~L~~~~r~vl~l~~~-~~~s~~EIA~~Lgis~~tVk~~l~r  181 (194)
T PRK09646        142 ALTDTQRESVTLAYY-GGLTYREVAERLAVPLGTVKTRMRD  181 (194)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChHhHHHHHHH
Confidence            344444433332333 5789999999999999999999886

>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator

Probab=90.04  E-value=0.46  Score=38.47  Aligned_cols=40  Identities=13%  Similarity=0.223  Sum_probs=30.2

Q ss_pred             CCCHHHHHHH-HHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         32 TWTHEDMDAA-LEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        32 kyt~e~~~~A-I~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|.+.+.+| ++++.+   ..+|+.+||++.||+|+|+|+...
T Consensus         2 ~~Tk~~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~   45 (176)
T TIGR02366         2 IITKKKIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYNHFQ   45 (176)
T ss_pred             hHHHHHHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHCC
Confidence            3566667666 444443   569999999999999999998644

The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.

>PRK15115 response regulator GlrR; Provisional

Probab=89.97  E-value=0.49  Score=44.21  Aligned_cols=35  Identities=14%  Similarity=0.119  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ||..|.+.+...+.|..+||+..|||++|+|+.+|
T Consensus       399 E~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~  433 (444)
T PRK15115        399 ELNYLRKLLQITKGNVTHAARMAGRNRTEFYKLLS  433 (444)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            67788888888888999999999999999999998

>PRK06474 hypothetical protein; Provisional

Probab=89.87  E-value=0.64  Score=38.87  Aligned_cols=37  Identities=14%  Similarity=0.060  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHHhCC--CcHHHHHHHh-CCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRSGQ--TTVQRASAEY-GIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~--~s~~eAA~~f-gVp~~tv~~~vk  212 (229)
                      ...|..|++.+..++  ++..+++..+ +||.+|||+.++
T Consensus        10 ~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~   49 (178)
T PRK06474         10 HPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQ   49 (178)
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHH
Confidence            456999999998854  8999999999 899999999998

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

Probab=89.87  E-value=0.68  Score=36.32  Aligned_cols=32  Identities=16%  Similarity=0.077  Sum_probs=25.9

Q ss_pred             HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ++.++.-.|+|+.+||+.+|||.+|++.++++
T Consensus       121 il~l~~~~~~~~~eIA~~lgis~~tv~~~~~r  152 (161)
T TIGR02985       121 IFILSRFEGKSYKEIAEELGISVKTVEYHISK  152 (161)
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            34442335889999999999999999999886

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.

>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=89.86  E-value=0.23  Score=31.19  Aligned_cols=22  Identities=14%  Similarity=0.222  Sum_probs=19.2

Q ss_pred             CHHHHHHHcCCChhhHHHHHHH
Q psy17316         51 SLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        51 S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      |+.++|+.+||+..||+.|-+.
T Consensus         1 ti~e~A~~~gvs~~tlR~ye~~   22 (38)
T PF00376_consen    1 TIGEVAKLLGVSPRTLRYYERE   22 (38)
T ss_dssp             EHHHHHHHHTS-HHHHHHHHHT
T ss_pred             CHHHHHHHHCCCHHHHHHHHHC
Confidence            4789999999999999999887

One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=89.80  E-value=0.58  Score=30.54  Aligned_cols=25  Identities=8%  Similarity=-0.019  Sum_probs=23.2

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-++|+.++|+..||++++|.+|..
T Consensus        13 ~~gltq~~lA~~~gvs~~~vs~~e~   37 (58)
T TIGR03070        13 ALGLTQADLADLAGVGLRFIRDVEN   37 (58)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence            5689999999999999999999976

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

>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA

Probab=89.80  E-value=0.57  Score=30.86  Aligned_cols=41  Identities=24%  Similarity=0.191  Sum_probs=35.1

Q ss_pred             CCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        174 WKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       174 ~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      +.++-+..||+...+| .-.+++|+..+|+..||.+.+|.+|
T Consensus         6 ~kpgikeqIvema~nG-~GiRdtaRvL~I~~nTVlrtLK~sr   46 (46)
T PF12759_consen    6 RKPGIKEQIVEMAFNG-SGIRDTARVLKISINTVLRTLKNSR   46 (46)
T ss_pred             cCccHHHHHHHHHhcC-CcchhhHhHhcchHHHHHHHHhcCC
Confidence            3466788999999988 7799999999999999999888543

>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88

Probab=89.79  E-value=0.22  Score=32.96  Aligned_cols=23  Identities=17%  Similarity=0.553  Sum_probs=19.4

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARK  158 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~  158 (229)
                      ++..++++.+||+++|+|++++.
T Consensus         4 l~~~ev~~~~g~s~~ti~~~~k~   26 (51)
T PF05930_consen    4 LRIKEVAELLGVSRSTIYRLIKD   26 (51)
T ss_dssp             E-HHHHHHHHSS-HHHHHHHHHH
T ss_pred             ccHHHHHHHHCCCHHHHHHHHhc
Confidence            47899999999999999999984

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.

>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function

Probab=89.79  E-value=0.79  Score=34.31  Aligned_cols=43  Identities=16%  Similarity=0.387  Sum_probs=36.4

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        170 SPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       170 ~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+.|...-+.++|..|+.|-++..||+..|++|-+=+-.|.+
T Consensus        29 ~t~RWva~RKAaVV~aV~~Glis~~EA~~rY~Ls~eEf~~W~~   71 (90)
T PF06627_consen   29 DTRRWVARRKAAVVRAVRGGLISVEEACRRYGLSEEEFESWQR   71 (90)
T ss_dssp             S-S---HHHHHHHHHHHHCTTS-HHHHHHCTTSSHHHHHHHHH
T ss_pred             ccccchhhHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3568999999999999999999999999999999999999998

; PDB: 2OA4_A 2JRT_A.

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=89.77  E-value=0.74  Score=38.01  Aligned_cols=39  Identities=10%  Similarity=0.040  Sum_probs=28.3

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .++++..-.+-.+. .|+|+.+||..+|||.+||+.++.+
T Consensus       132 Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~R  170 (191)
T PRK12520        132 LPPRTGRVFMMREW-LELETEEICQELQITATNAWVLLYR  170 (191)
T ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            33444333332333 4789999999999999999999885

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=89.76  E-value=0.55  Score=37.28  Aligned_cols=26  Identities=12%  Similarity=0.233  Sum_probs=23.7

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.|+|+.+||..+|||.+|++.++.+
T Consensus       120 ~~g~s~~EIA~~lgis~~tV~~~l~r  145 (161)
T PRK09047        120 WEDMDVAETAAAMGCSEGSVKTHCSR  145 (161)
T ss_pred             HhcCCHHHHHHHHCCCHHHHHHHHHH
Confidence            35889999999999999999999886

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=89.75  E-value=0.52  Score=44.04  Aligned_cols=36  Identities=28%  Similarity=0.324  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -+|..|.+.+...+.|..+||+..|||++|+|++++
T Consensus       405 ~E~~~i~~al~~~~gn~~~aA~~Lgisr~tl~rkl~  440 (445)
T TIGR02915       405 AEREAVRKAIARVDGNIARAAELLGITRPTLYDLMK  440 (445)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            367778888888889999999999999999999987

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

>PHA02591 hypothetical protein; Provisional

Probab=89.75  E-value=0.79  Score=33.58  Aligned_cols=38  Identities=13%  Similarity=0.148  Sum_probs=34.3

Q ss_pred             CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++++...+.+.+.+-++|..++|...||+..+|...++
T Consensus        44 ~~dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         44 SEDDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             ccchHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            67788889999999889999999999999999998765

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=89.73  E-value=0.53  Score=30.88  Aligned_cols=30  Identities=17%  Similarity=0.365  Sum_probs=26.4

Q ss_pred             HHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         45 LRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        45 ~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      +..+.++..++++.+||+++|+++.++++.
T Consensus         6 l~~~~~~~~~i~~~l~is~~~v~~~l~~L~   35 (66)
T smart00418        6 LAEGELCVCELAEILGLSQSTVSHHLKKLR   35 (66)
T ss_pred             hhcCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence            337789999999999999999999999863

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=89.72  E-value=0.68  Score=37.22  Aligned_cols=41  Identities=15%  Similarity=0.081  Sum_probs=30.8

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ...+++++.-.+-.+.+ |+|+.+||..+|||.+|++.++++
T Consensus       107 ~~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tv~~~l~R  147 (165)
T PRK09644        107 HTLPVIEAQAILLCDVH-ELTYEEAASVLDLKLNTYKSHLFR  147 (165)
T ss_pred             HhCCHHHHHHHHhHHHh-cCCHHHHHHHHCCCHHHHHHHHHH
Confidence            44455555444434444 779999999999999999999886

>TIGR02607 antidote_HigA addiction module antidote protein, HigA family

Probab=89.69  E-value=1.4  Score=31.02  Aligned_cols=26  Identities=15%  Similarity=0.217  Sum_probs=23.8

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ...++++.++|+..||+++||.+|..
T Consensus        15 ~~~~~t~~~lA~~~gis~~tis~~~~   40 (78)
T TIGR02607        15 EPLGLSIRALAKALGVSRSTLSRIVN   40 (78)
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            45689999999999999999999976

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

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=89.68  E-value=0.77  Score=37.54  Aligned_cols=26  Identities=31%  Similarity=0.326  Sum_probs=23.7

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.++|+.+||..+||+.+||+.++++
T Consensus       149 ~~~~s~~eIA~~lgis~~~V~~~l~r  174 (186)
T PRK13919        149 YQGYTHREAAQLLGLPLGTLKTRARR  174 (186)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            35889999999999999999999886

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=89.68  E-value=0.6  Score=37.32  Aligned_cols=32  Identities=13%  Similarity=0.173  Sum_probs=26.6

Q ss_pred             HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ++.+..-+|+|..+||..+|||.+|++.++++
T Consensus       121 v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~r  152 (161)
T PRK12528        121 AFLLAQVDGLGYGEIATELGISLATVKRYLNK  152 (161)
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            34344446899999999999999999999886

>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A

Probab=89.62  E-value=0.52  Score=32.94  Aligned_cols=39  Identities=18%  Similarity=0.148  Sum_probs=29.7

Q ss_pred             HHHHHHHHHh--CCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        179 LEIALEGIRS--GQTTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       179 r~eaV~~~~~--~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      +.+|++++..  +.++..++|..+||+..|++.++. +..+|
T Consensus         2 ke~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG   43 (62)
T PF04703_consen    2 KEKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEG   43 (62)
T ss_dssp             HHCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCT
T ss_pred             cHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            3456666666  779999999999999999999998 55444

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=89.61  E-value=0.65  Score=38.04  Aligned_cols=26  Identities=15%  Similarity=0.263  Sum_probs=23.8

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -+|+|+.+||..+|||.+|++.++.+
T Consensus       141 ~~g~s~~EIA~~l~is~~tv~~~l~R  166 (179)
T PRK09415        141 YEELSIKEIAEVTGVNENTVKTRLKK  166 (179)
T ss_pred             hcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            35889999999999999999999886

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=89.57  E-value=1  Score=32.45  Aligned_cols=36  Identities=17%  Similarity=0.162  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHh--CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRS--GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~--~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +.-..|++++..  +.++..++|..+|||.+||++.++
T Consensus         5 ~r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~   42 (91)
T smart00346        5 ERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLN   42 (91)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHH
Confidence            345678888766  469999999999999999999998

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=89.48  E-value=0.67  Score=31.13  Aligned_cols=38  Identities=24%  Similarity=0.329  Sum_probs=27.5

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +|+.++. ++..+.. |+|..+||..+||+..||+.+++.
T Consensus         4 LT~~E~~-vl~~l~~-G~~~~eIA~~l~is~~tV~~~~~~   41 (58)
T PF00196_consen    4 LTERELE-VLRLLAQ-GMSNKEIAEELGISEKTVKSHRRR   41 (58)
T ss_dssp             S-HHHHH-HHHHHHT-TS-HHHHHHHHTSHHHHHHHHHHH
T ss_pred             cCHHHHH-HHHHHHh-cCCcchhHHhcCcchhhHHHHHHH
Confidence            3444443 5555555 779999999999999999988775

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

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

Probab=89.46  E-value=0.55  Score=37.45  Aligned_cols=26  Identities=23%  Similarity=0.265  Sum_probs=24.0

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.|+|..+||..+|||.+||+.++.+
T Consensus       124 ~~g~s~~eIA~~lgis~~tV~~~l~r  149 (162)
T TIGR02983       124 YEDLSEAQVAEALGISVGTVKSRLSR  149 (162)
T ss_pred             HhcCCHHHHHHHhCCCHHHHHHHHHH
Confidence            45889999999999999999999886

This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=89.46  E-value=0.69  Score=38.45  Aligned_cols=33  Identities=21%  Similarity=0.247  Sum_probs=27.0

Q ss_pred             HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.|+...-+|+|..+||..+||+..|++++++.
T Consensus       142 ~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~~  174 (185)
T PF07638_consen  142 RVVELRFFEGLSVEEIAERLGISERTVRRRLRR  174 (185)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            444444457999999999999999999998774

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=89.41  E-value=0.81  Score=37.40  Aligned_cols=25  Identities=24%  Similarity=0.211  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         48 GQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        48 g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .++|+.+||..+|||.+|++.++++
T Consensus       132 e~~s~~EIA~~lgis~~tV~~~l~r  156 (179)
T PRK12543        132 HDYSQEEIAQLLQIPIGTVKSRIHA  156 (179)
T ss_pred             ccCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4789999999999999999999886

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=89.39  E-value=0.96  Score=37.39  Aligned_cols=34  Identities=24%  Similarity=0.206  Sum_probs=26.9

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -.+|+....-.++|+.|+|..+|||..||+..+.
T Consensus       116 ~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~  149 (182)
T PRK12540        116 QREALILVGASGFSYEDAAAICGCAVGTIKSRVN  149 (182)
T ss_pred             HHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4445555444559999999999999999999875

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=89.37  E-value=0.75  Score=38.10  Aligned_cols=40  Identities=13%  Similarity=0.028  Sum_probs=29.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.++.+..-.+-.+. .|+|+.+||..+|||.+|++.++.+
T Consensus       136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~R  175 (195)
T PRK12532        136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHR  175 (195)
T ss_pred             hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            334444433332344 4889999999999999999999886

>TIGR00637 ModE_repress ModE molybdate transport repressor domain

Probab=89.36  E-value=0.73  Score=34.91  Aligned_cols=34  Identities=24%  Similarity=0.353  Sum_probs=28.4

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +.++.++.+.+ |+..||+.+||+.+|+++.+++.
T Consensus         7 l~~~~av~~~g-Sis~AA~~L~iS~stvs~~I~~L   40 (99)
T TIGR00637         7 VALLKAIARMG-SISQAAKDAGISYKSAWDYIRAM   40 (99)
T ss_pred             HHHHHHHHHhC-CHHHHHHHHCCCHHHHHHHHHHH
Confidence            44555666656 99999999999999999999985

ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=89.36  E-value=0.91  Score=35.62  Aligned_cols=43  Identities=14%  Similarity=0.025  Sum_probs=36.2

Q ss_pred             CHHHHHHHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        175 KPEDLEIALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       175 t~e~r~eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      ....|..|+..+.+ +++++.+++..+++|.+||-.+++ +.+.|
T Consensus        14 adptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AG   58 (117)
T PRK10141         14 SDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESG   58 (117)
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            34679999999976 689999999999999999999998 44333

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=89.36  E-value=0.6  Score=43.82  Aligned_cols=35  Identities=20%  Similarity=0.176  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ||..|.+.+...+.|..+||+..|||++|+|+++|
T Consensus       427 E~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~  461 (463)
T TIGR01818       427 ERPLLEAALQHTRGHKQEAAALLGWGRNTLTRKLK  461 (463)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            56677788888888999999999999999999987

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>PRK15121 right oriC-binding transcriptional activator; Provisional

Probab=89.36  E-value=2  Score=38.02  Aligned_cols=70  Identities=14%  Similarity=0.217  Sum_probs=52.0

Q ss_pred             cCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHH-HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHH
Q psy17316        133 AGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPED-LEIALEGIRSGQTTVQRASAEYGIPSGTLYGR  210 (229)
Q Consensus       133 ~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~-r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~  210 (229)
                      ...+++.++|+..|+|..+|.+..++. |.....        |-..- +..|.+.+...+++..++|..+|-+-++-...
T Consensus        19 ~~~~~l~~lA~~~~~S~~~l~r~F~~~~g~s~~~--------yi~~~Rl~~A~~~L~~~~~~i~~iA~~~Gf~s~~~f~r   90 (289)
T PRK15121         19 DQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGA--------YIRARRLSKAAVALRLTSRPILDIALQYRFDSQQTFTR   90 (289)
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHH--------HHHHHHHHHHHHHHHcCCCCHHHHHHHHCCCCHHHHHH
Confidence            445799999999999999999999876 755532        32222 45566777777899999999999855544443

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=89.27  E-value=0.59  Score=38.43  Aligned_cols=40  Identities=15%  Similarity=0.130  Sum_probs=29.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..++.+..-.+..+. +|+|+.+||+.+|||.+||+.++.+
T Consensus       131 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~r  170 (184)
T PRK12539        131 RLPEKMRLAIQAVKL-EGLSVAEAATRSGMSESAVKVSVHR  170 (184)
T ss_pred             hCCHHHHHHHHHHHH-cCCcHHHHHHHHCcCHHHHHHHHHH
Confidence            334444333332333 5889999999999999999999886

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

Probab=89.27  E-value=0.87  Score=39.84  Aligned_cols=35  Identities=14%  Similarity=0.025  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...+|+..+.-+++||.|||..+|||.+||+.++.
T Consensus       165 ~~R~v~~L~~~eg~S~~EIA~~Lgis~~TVk~rl~  199 (244)
T TIGR03001       165 RERHLLRLHFVDGLSMDRIGAMYQVHRSTVSRWVA  199 (244)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34556666666779999999999999999999885

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=89.25  E-value=1.2  Score=28.34  Aligned_cols=32  Identities=19%  Similarity=0.245  Sum_probs=26.2

Q ss_pred             HHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        181 IALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       181 eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+++.+.. +.++..+++..|+||.+|+++.++
T Consensus         4 ~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~   36 (53)
T smart00420        4 QILELLAQQGKVSVEELAELLGVSEMTIRRDLN   36 (53)
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            34444444 569999999999999999999998

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=89.24  E-value=0.6  Score=43.39  Aligned_cols=37  Identities=19%  Similarity=0.274  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .-|+..|.+.+..++.+..+||+..|||++|+|+.+|
T Consensus       404 ~~e~~~i~~~l~~~~gn~~~aa~~Lgisr~tl~rk~~  440 (441)
T PRK10365        404 EVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKLS  440 (441)
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHhh
Confidence            3467778888888889999999999999999999876

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=89.23  E-value=0.75  Score=37.73  Aligned_cols=39  Identities=15%  Similarity=0.072  Sum_probs=28.4

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .++++..-.+..+. .|+|+.+||+.+|||..||+.++++
T Consensus       129 L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~R  167 (186)
T PRK05602        129 LPERQREAIVLQYY-QGLSNIEAAAVMDISVDALESLLAR  167 (186)
T ss_pred             CCHHHHHHhhHHHh-cCCCHHHHHHHhCcCHHHHHHHHHH
Confidence            34443333333343 5889999999999999999999886

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=89.22  E-value=0.62  Score=43.57  Aligned_cols=36  Identities=17%  Similarity=0.215  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -++..|.+.+...+.|..+||+..|||++|+|++++
T Consensus       417 ~E~~~i~~al~~~~gn~~~aA~~LGisr~tL~rkl~  452 (457)
T PRK11361        417 VEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQ  452 (457)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence            367777777888788999999999999999999987

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=89.21  E-value=0.68  Score=36.94  Aligned_cols=26  Identities=12%  Similarity=0.104  Sum_probs=23.8

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.++|+.+||..+|||.+|++.++.+
T Consensus       119 ~~~~s~~eIA~~lgis~~tv~~~l~r  144 (159)
T PRK12527        119 LEGLSHQQIAEHLGISRSLVEKHIVN  144 (159)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            35889999999999999999999885

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=89.21  E-value=1.4  Score=35.68  Aligned_cols=37  Identities=19%  Similarity=0.399  Sum_probs=29.5

Q ss_pred             HHHHHH-HhCCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        181 IALEGI-RSGQTTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       181 eaV~~~-~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      .|++.+ .+++.++.++|+..|+|.+||.++++ +..+|
T Consensus        13 ~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~G   51 (153)
T PRK11179         13 GILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAG   51 (153)
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            444544 55789999999999999999999998 44444

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=89.21  E-value=0.84  Score=30.40  Aligned_cols=31  Identities=19%  Similarity=0.298  Sum_probs=26.5

Q ss_pred             HHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         44 ALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      ...+|++++.++|+.++++++++.+.+++..
T Consensus        12 l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~   42 (59)
T PF01047_consen   12 LYENGGITQSELAEKLGISRSTVTRIIKRLE   42 (59)
T ss_dssp             HHHHSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             HHHcCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence            3457889999999999999999999999863

This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=89.19  E-value=0.87  Score=37.05  Aligned_cols=39  Identities=15%  Similarity=0.153  Sum_probs=28.6

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .++++..-.+..+. .|+|+.+||..+|||.+||+.++.+
T Consensus       130 L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~R  168 (179)
T PRK12514        130 LEKDRAAAVRRAYL-EGLSYKELAERHDVPLNTMRTWLRR  168 (179)
T ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHHCCChHHHHHHHHH
Confidence            34444333333344 4789999999999999999999886

>PRK13500 transcriptional activator RhaR; Provisional

Probab=89.16  E-value=2.1  Score=38.46  Aligned_cols=79  Identities=11%  Similarity=0.155  Sum_probs=57.6

Q ss_pred             CCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHH-HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHH
Q psy17316        134 GSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPED-LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRC  211 (229)
Q Consensus       134 g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~-r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~v  211 (229)
                      ..+++.++|+++||+.++|.+..|+. |....        .|=.+. ..+|.+.+...++++.++|...|=+-++=.+.+
T Consensus       221 e~isl~~lA~~~~iS~~~L~r~FK~~tG~T~~--------~yi~~~RL~~A~~LL~~t~~sI~eIA~~~GF~d~s~Fsr~  292 (312)
T PRK13500        221 SPFALDKFCDEASCSERVLRQQFRQQTGMTIN--------QYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVV  292 (312)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHH
Confidence            35799999999999999999999976 75443        232233 445566666678999999999999887776665


Q ss_pred             HhhcCCCCC
Q psy17316        212 KLSRSTPRP  220 (229)
Q Consensus       212 k~~~~~~~~  220 (229)
                      =.+.-|-+|
T Consensus       293 FKk~~G~TP  301 (312)
T PRK13500        293 FTRETGMTP  301 (312)
T ss_pred             HHHHHCcCH
Confidence            444444433

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=89.15  E-value=0.83  Score=37.82  Aligned_cols=40  Identities=28%  Similarity=0.263  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.++.+..-.+-.+.+ |+|+.+||..+|||.+|++.++.+
T Consensus       111 ~Lp~~~R~v~~L~~~e-g~s~~EIA~~lgis~~tV~~~l~R  150 (182)
T PRK12511        111 DLPEEQRAALHLVAIE-GLSYQEAAAVLGIPIGTLMSRIGR  150 (182)
T ss_pred             hCCHHHHHHHHHHHHc-CCCHHHHHHHhCcCHHHHHHHHHH

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=89.11  E-value=0.82  Score=36.54  Aligned_cols=34  Identities=15%  Similarity=0.052  Sum_probs=27.7

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+|+....-+++++.++|..+|||.+||+.++.
T Consensus       118 ~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~  151 (161)
T PRK12528        118 VKRAFLLAQVDGLGYGEIATELGISLATVKRYLN  151 (161)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4445555555559999999999999999999987

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

Probab=89.08  E-value=0.69  Score=31.24  Aligned_cols=28  Identities=29%  Similarity=0.489  Sum_probs=25.7

Q ss_pred             CCCHHHHHHHhCCChHHHHHHHHHhCCc
Q psy17316        135 SISANKASKAYGIPSSTLYKIARKEGIR  162 (229)
Q Consensus       135 ~~S~~~~a~k~gIp~sTL~~~ik~~g~k  162 (229)
                      ++++.++|+..||+.++|.+.+++.||.
T Consensus        15 hlp~~eAA~~Lgv~~T~LKr~CR~~GI~   42 (52)
T PF02042_consen   15 HLPIKEAAKELGVSVTTLKRRCRRLGIP   42 (52)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence            5799999999999999999999998874

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

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

Probab=89.08  E-value=0.75  Score=37.77  Aligned_cols=35  Identities=20%  Similarity=0.163  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +.|..++-... +++||.|||..+|||.+||.+++.
T Consensus       131 ~~R~~~~l~~~-~gls~~EIA~~l~i~~~tVks~l~  165 (182)
T COG1595         131 RQREAFLLRYL-EGLSYEEIAEILGISVGTVKSRLH  165 (182)
T ss_pred             HHhHHhhhHhh-cCCCHHHHHHHHCCCHHHHHHHHH
Confidence            33433333333 559999999999999999999987

>COG1710 Uncharacterized protein conserved in archaea [Function unknown]

Probab=89.06  E-value=1  Score=35.62  Aligned_cols=44  Identities=30%  Similarity=0.399  Sum_probs=36.0

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        168 NASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       168 ~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+++++|+...+.-|=+++.+| +..+++|+..|||--|||..++
T Consensus        88 rGrprkyd~~t~~~i~emlr~g-k~preIsk~lGIpirTvyY~l~  131 (139)
T COG1710          88 RGRPRKYDRNTLLRIREMLRNG-KTPREISKDLGIPIRTVYYLLK  131 (139)
T ss_pred             CCCCcccchhHHHHHHHHHHcC-CCHHHHHHhhCCchhhhHHHHH
Confidence            4678899876666665655555 8899999999999999999887

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=88.98  E-value=0.73  Score=36.79  Aligned_cols=26  Identities=8%  Similarity=-0.016  Sum_probs=23.6

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.++|+.+||..+|||.+||+.++.+
T Consensus       123 ~~~~s~~EIA~~lgis~~tV~~~l~r  148 (163)
T PRK07037        123 LHGETQKDIARELGVSPTLVNFMIRD  148 (163)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            35889999999999999999999875

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

Probab=88.93  E-value=0.68  Score=45.76  Aligned_cols=39  Identities=33%  Similarity=0.479  Sum_probs=31.1

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCc
Q psy17316        124 LNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIR  162 (229)
Q Consensus       124 k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k  162 (229)
                      +..-+.++..-...+.++|+..|||++|||+.+|++|+.
T Consensus       567 ~~~l~~al~~~~~~is~aa~~lgi~R~T~yrklk~~gi~  605 (606)
T COG3284         567 KAALLAALQATNGNISEAARLLGISRSTLYRKLKRHGIS  605 (606)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence            344455555545689999999999999999999999873

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=88.90  E-value=0.68  Score=37.93  Aligned_cols=27  Identities=15%  Similarity=0.277  Sum_probs=24.3

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .-.|+|+.+||+.+|||.+||+.++.+
T Consensus       142 ~~~g~s~~EIA~~l~is~~tV~~~l~r  168 (181)
T PRK12536        142 KLEGLSVAETAQLTGLSESAVKVGIHR  168 (181)
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            346889999999999999999999886

>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=88.86  E-value=3.9  Score=31.76  Aligned_cols=38  Identities=16%  Similarity=0.219  Sum_probs=29.0

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      |.|++ +.++.+..-.-+++++-+.+|++-.||+-++..
T Consensus        43 t~d~L-eFv~lf~r~RGnlKEvEr~lg~sYptvR~kld~   80 (122)
T COG3877          43 TSDQL-EFVELFLRCRGNLKEVERELGISYPTVRTKLDE   80 (122)
T ss_pred             CHhHh-HHHHHHHHHccCHHHHHHHHCCccHHHHHHHHH
Confidence            55554 555566554559999999999999999987765

>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B

Probab=88.84  E-value=2.1  Score=29.67  Aligned_cols=51  Identities=18%  Similarity=0.307  Sum_probs=34.6

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHH
Q psy17316        124 LNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQ  194 (229)
Q Consensus       124 k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~  194 (229)
                      +.+||..+   + |...+|+.+||+.+++++| . ..    .          |..|.--|+.+-+|.+.+.
T Consensus         2 k~~aI~~~---G-~~~~lAkalGVs~~aVs~W-~-~~----I----------P~~ra~~Ie~~T~G~l~~~   52 (60)
T PF14549_consen    2 KKDAIKYF---G-GQSKLAKALGVSPQAVSQW-G-ER----I----------PAERAYQIEKLTNGKLKCE   52 (60)
T ss_dssp             HHHHHHHH---S-SHHHHHHHHTS-HHHHHHH-H-TS----------------HHHHHHHHHHTTTSS--H
T ss_pred             HHHHHHHH---C-CHHHHHHHHCCCHHHHHHh-c-Cc----c----------CHHHHHHHHHHhCCceeeC
Confidence            35667776   3 8999999999999999999 2 11    1          3457777777777776554

>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor

Probab=88.83  E-value=0.93  Score=29.19  Aligned_cols=24  Identities=8%  Similarity=0.207  Sum_probs=21.4

Q ss_pred             CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         48 GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        48 g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .++|+++||++.||++++|++...
T Consensus        15 ~~~s~~~Ia~~~gvs~~~~y~~f~   38 (47)
T PF00440_consen   15 EAVSIRDIARRAGVSKGSFYRYFP   38 (47)
T ss_dssp             TTSSHHHHHHHHTSCHHHHHHHCS
T ss_pred             HhCCHHHHHHHHccchhhHHHHcC
Confidence            578999999999999999998743

Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=88.82  E-value=0.62  Score=46.04  Aligned_cols=38  Identities=21%  Similarity=0.239  Sum_probs=34.5

Q ss_pred             CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+-||..|.+.+...+-|..+||+..|||++|||+++|
T Consensus       589 ~~~E~~~i~~al~~~~gn~~~aA~~LGisR~TLyrklk  626 (638)
T PRK11388        589 AELEKEAIINAAQVCGGRIQEMAALLGIGRTTLWRKMK  626 (638)
T ss_pred             HHHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34578889999999889999999999999999999998

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=88.82  E-value=0.72  Score=37.80  Aligned_cols=31  Identities=13%  Similarity=0.087  Sum_probs=25.7

Q ss_pred             HHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         42 LEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        42 I~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.+..-.|+|+.+||..+|||.+|++.++++
T Consensus       136 ~~L~~~~g~s~~EIA~~lgis~~tVk~~l~r  166 (178)
T PRK12529        136 FLMATLDGMKQKDIAQALDIALPTVKKYIHQ  166 (178)
T ss_pred             HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            3343346889999999999999999999885

>PRK15340 transcriptional regulator InvF; Provisional

Probab=88.77  E-value=2.9  Score=36.32  Aligned_cols=70  Identities=10%  Similarity=0.149  Sum_probs=51.5

Q ss_pred             CCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHH-HHHHHHHHhCCCcHHHHHHHhCCChHHHHHHH
Q psy17316        134 GSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDL-EIALEGIRSGQTTVQRASAEYGIPSGTLYGRC  211 (229)
Q Consensus       134 g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r-~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~v  211 (229)
                      ...++.++|+.+|++.+++.+..+++ |.....        |=...| .+++..+.+++.+..++|..+|-+.+.-....
T Consensus       124 ~~~sleeLA~~~gvS~r~f~RlFk~~~G~tpk~--------yl~~~Rl~~all~L~~s~~sItdIA~~~GY~d~ShFsr~  195 (216)
T PRK15340        124 SGNTMRMLGEDYGVSYTHFRRLCSRALGGKAKS--------ELRNWRMAQSLLNSVEGHENITQLAVNHGYSSPSHFSSE  195 (216)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHH--------HHHHHHHHHHHHhhhcCCCCHHHHHHHhCCCCHHHHHHH
Confidence            45699999999999999999999876 754431        212223 35566666788999999999888666655544

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=88.77  E-value=0.66  Score=45.26  Aligned_cols=35  Identities=20%  Similarity=0.184  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++..|.+.+..++.|..+||+..|||++|||+++|
T Consensus       491 Er~~I~~aL~~~~Gn~~~aA~~LGIsRtTL~Rklk  525 (526)
T TIGR02329       491 EALAVRAALERFGGDRDAAAKALGISRTTLWRRLK  525 (526)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            57778888888889999999999999999999986

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=88.74  E-value=0.69  Score=38.34  Aligned_cols=26  Identities=15%  Similarity=0.075  Sum_probs=23.8

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.|+|+.+||..+|||.+||+.++++
T Consensus       148 ~~g~s~~EIA~~lgis~~tVk~~l~R  173 (189)
T PRK12530        148 YLELSSEQICQECDISTSNLHVLLYR  173 (189)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            35899999999999999999999886

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

Probab=88.74  E-value=0.95  Score=37.53  Aligned_cols=26  Identities=8%  Similarity=-0.049  Sum_probs=23.5

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.|+|+.+||..+|||.+||+.++.+
T Consensus       145 ~~g~s~~EIA~~lgis~~tvk~rl~R  170 (188)
T TIGR02943       145 VLGFESDEICQELEISTSNCHVLLYR  170 (188)
T ss_pred             HhCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            35889999999999999999999875

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.

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

Probab=88.71  E-value=0.99  Score=34.41  Aligned_cols=37  Identities=19%  Similarity=0.089  Sum_probs=27.7

Q ss_pred             CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++.++ .++...--+++++.++|..+|||.++|+.+.+
T Consensus       112 ~~~~~-~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~  148 (158)
T TIGR02937       112 PERER-EVLVLRYLEGLSYKEIAEILGISVGTVKRRLK  148 (158)
T ss_pred             CHHHH-HHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34444 44444433459999999999999999999987

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.

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=88.69  E-value=0.74  Score=37.69  Aligned_cols=38  Identities=18%  Similarity=0.307  Sum_probs=30.5

Q ss_pred             HHHHHHH-HhCCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        180 EIALEGI-RSGQTTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       180 ~eaV~~~-~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      .+|+..+ .++.+++.++|+..|+|.+||+++++ +.++|
T Consensus        17 ~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~G   56 (164)
T PRK11169         17 RNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQG   56 (164)
T ss_pred             HHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            4555555 55789999999999999999999998 54444

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=88.65  E-value=0.59  Score=38.56  Aligned_cols=26  Identities=27%  Similarity=0.326  Sum_probs=23.8

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.|+|+.+||..+|||.+||+.++++
T Consensus       155 ~~g~s~~EIA~~lgis~~tV~~~l~R  180 (194)
T PRK12519        155 YEGLSQSEIAKRLGIPLGTVKARARQ  180 (194)
T ss_pred             hcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            35889999999999999999999886

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=88.62  E-value=0.89  Score=37.26  Aligned_cols=35  Identities=9%  Similarity=-0.057  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...+|+....-.++|+.|||..+|||.+||..++.
T Consensus       131 ~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~  165 (178)
T PRK12529        131 RVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIH  165 (178)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34556666555669999999999999999999876

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=88.61  E-value=1.3  Score=33.26  Aligned_cols=29  Identities=24%  Similarity=0.414  Sum_probs=26.1

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      ++.+|..++|+.+|++++|++++++++.-
T Consensus        15 ~~~~~~~~la~~l~~s~~tv~~~l~~L~~   43 (108)
T smart00344       15 DARISLAELAKKVGLSPSTVHNRVKRLEE   43 (108)
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            57899999999999999999999998633

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

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=88.59  E-value=1  Score=36.23  Aligned_cols=37  Identities=11%  Similarity=-0.078  Sum_probs=28.8

Q ss_pred             CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +++.|.-++-....| +++.++|..+|||..||+.++.
T Consensus       110 ~~~~r~v~~l~~~~g-~s~~eIA~~lgis~~tv~~~l~  146 (165)
T PRK09644        110 PVIEAQAILLCDVHE-LTYEEAASVLDLKLNTYKSHLF  146 (165)
T ss_pred             CHHHHHHHHhHHHhc-CCHHHHHHHHCCCHHHHHHHHH
Confidence            445555444455555 9999999999999999999976

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=88.56  E-value=1.1  Score=37.31  Aligned_cols=35  Identities=20%  Similarity=0.209  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...+|+.+..-+++++.|+|..+|||..||..++.
T Consensus       120 ~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~  154 (187)
T PRK12516        120 DQREAIILVGASGFAYEEAAEICGCAVGTIKSRVN  154 (187)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34556666555669999999999999999999875

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=88.56  E-value=0.93  Score=37.38  Aligned_cols=40  Identities=13%  Similarity=0.072  Sum_probs=29.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.+++++.-.+..+. .|+|+.+||..+|||.+|++.++.+
T Consensus       106 ~L~~~~r~i~~l~~~-~g~~~~EIA~~lgis~~tV~~~l~R  145 (181)
T PRK09637        106 ALPEKYAEALRLTEL-EGLSQKEIAEKLGLSLSGAKSRVQR  145 (181)
T ss_pred             hCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            344444443333333 5889999999999999999998875

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

Probab=88.54  E-value=1.3  Score=28.99  Aligned_cols=42  Identities=17%  Similarity=0.174  Sum_probs=33.1

Q ss_pred             CHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCC
Q psy17316        137 SANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQ  190 (229)
Q Consensus       137 S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~  190 (229)
                      ++++||+..||+.+|+.+.+...            ...+++-|..|.+.+.+-+
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~~------------~~vs~~tr~rI~~~a~~lg   42 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNGP------------PRVSEETRERILEAAEELG   42 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTTC------------SSSTHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHCcCHHHHHHHHhCC------------CCCCHHHHHHHHHHHHHHC
Confidence            57899999999999999977632            2466788888888877644

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

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

Probab=88.53  E-value=0.73  Score=37.14  Aligned_cols=26  Identities=15%  Similarity=0.212  Sum_probs=23.8

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -+|+|..+||..+|||.+|++.++.+
T Consensus       133 ~~g~s~~eiA~~lgis~~tv~~~l~R  158 (169)
T TIGR02954       133 YHDLTIKEIAEVMNKPEGTVKTYLHR  158 (169)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            35889999999999999999999886

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=88.51  E-value=0.89  Score=44.12  Aligned_cols=34  Identities=21%  Similarity=0.285  Sum_probs=28.4

Q ss_pred             HHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCccc
Q psy17316        130 ALRAGSISANKASKAYGIPSSTLYKIARKEGIRLA  164 (229)
Q Consensus       130 ~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~  164 (229)
                      ++..+. +.+++|+..||+++|||+.+++||+...
T Consensus       482 ~l~~~~-~~~~aA~~LGisr~tL~rkl~~~gi~~~  515 (520)
T PRK10820        482 LYRNYP-STRKLAKRLGVSHTAIANKLREYGLSQK  515 (520)
T ss_pred             HHHHCC-CHHHHHHHhCCCHHHHHHHHHHcCCCcc
Confidence            344444 8999999999999999999999998643

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

Probab=88.51  E-value=0.9  Score=36.96  Aligned_cols=34  Identities=15%  Similarity=0.024  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -.+|+....-.++|+.|+|..+|||.+||+.++.
T Consensus       139 ~r~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l~  172 (183)
T TIGR02999       139 QAEVVELRFFAGLTVEEIAELLGVSVRTVERDWR  172 (183)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3445555544559999999999999999999886

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=88.47  E-value=0.78  Score=37.75  Aligned_cols=41  Identities=15%  Similarity=0.102  Sum_probs=29.7

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .+.++.+. ++|....-+|+|+.+||..+|||.+||+.++++
T Consensus       138 ~~L~~~~r-~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~R  178 (189)
T PRK09648        138 DTLPEKQR-EILILRVVVGLSAEETAEAVGSTPGAVRVAQHR  178 (189)
T ss_pred             HhCCHHHH-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            34444443 344443345889999999999999999999886

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=88.47  E-value=1.1  Score=36.51  Aligned_cols=36  Identities=8%  Similarity=0.120  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++.+.-++.....| +|+.++|..+|||..||+.++.
T Consensus       132 ~~~r~i~~l~~~~g-~s~~eIA~~lgis~~tV~~~l~  167 (179)
T PRK12514        132 KDRAAAVRRAYLEG-LSYKELAERHDVPLNTMRTWLR  167 (179)
T ss_pred             HHHHHHHHHHHHcC-CCHHHHHHHHCCChHHHHHHHH
Confidence            44444444444545 9999999999999999999876

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=88.41  E-value=0.8  Score=41.85  Aligned_cols=35  Identities=17%  Similarity=0.312  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      |+.-|.+.+..++.|..+||+..|||++|+|+++|
T Consensus       293 E~~~I~~aL~~~~gn~~~aA~~LGisr~tL~rklk  327 (329)
T TIGR02974       293 EIELLQQALAEAQFNQRKAAELLGLTYHQLRGLLR  327 (329)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            56667777777888999999999999999999987

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=88.40  E-value=0.93  Score=36.22  Aligned_cols=39  Identities=15%  Similarity=0.044  Sum_probs=28.4

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .++.+..-.+-.+. .|+|..+||..+|||.+|++.++.+
T Consensus       113 L~~~~r~v~~l~~~-~~~s~~eIA~~lgis~~tv~~~l~R  151 (161)
T PRK12541        113 LPLERRNVLLLRDY-YGFSYKEIAEMTGLSLAKVKIELHR  151 (161)
T ss_pred             CCHHHHHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            34444333332333 5889999999999999999999886

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=88.36  E-value=0.83  Score=37.13  Aligned_cols=40  Identities=15%  Similarity=0.141  Sum_probs=29.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.++++. .++.+..-.|+|+.+||..+|||.+|++.++.+
T Consensus       100 ~L~~~~r-~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~R  139 (170)
T TIGR02959       100 ELPDEYR-EAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQR  139 (170)
T ss_pred             hCCHHHH-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4444433 333343345889999999999999999998875

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

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

Probab=88.34  E-value=1.2  Score=33.64  Aligned_cols=36  Identities=22%  Similarity=0.194  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      ++.-+.+.+...+.+..+||...||+++|+|++++.
T Consensus        56 Er~~i~~aL~~~~gn~s~AAr~LGIsRsTL~rKLkr   91 (95)
T PRK00430         56 EAPLLDMVMQYTRGNQTRAALMLGINRGTLRKKLKK   91 (95)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            355566666667778999999999999999999873

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=88.32  E-value=1.5  Score=37.40  Aligned_cols=43  Identities=23%  Similarity=0.353  Sum_probs=38.3

Q ss_pred             CCCCCHHHHHHHHHHHHcC------CCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         30 TKTWTHEDMDAALEALRAG------QMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g------~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +...|+.|+.-...+|..|      ..+..++|+++||+++|+.+.+++
T Consensus       153 ~~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRr  201 (215)
T COG3413         153 KNDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRR  201 (215)
T ss_pred             cccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHH
Confidence            3469999998888899876      589999999999999999999986

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=88.29  E-value=0.92  Score=38.87  Aligned_cols=25  Identities=24%  Similarity=0.316  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         48 GQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        48 g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .++|+.+||..+|||.+||+.++++
T Consensus       149 eg~s~~EIAe~LgiS~~tVk~~L~R  173 (216)
T PRK12533        149 EDMSYREIAAIADVPVGTVMSRLAR  173 (216)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            5889999999999999999999886

>COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]

Probab=88.28  E-value=1.4  Score=37.49  Aligned_cols=73  Identities=30%  Similarity=0.256  Sum_probs=51.5

Q ss_pred             cHHHHHHHHHHHhhcchhhhhhhhccCCCC-------CC-CHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh
Q psy17316         88 NEEILNVALDALRAGSISANKASKAYGPTK-------SW-NEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE  159 (229)
Q Consensus        88 s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~-------kY-s~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~  159 (229)
                      .+.+++...+=..+|...+++.++..|.+.       .. .++....++..+..|..+...++..++|+.+|++++.++.
T Consensus       122 Ae~Er~~i~er~~~g~~~a~~~G~~~g~~~~~~~~~~~~~~~~~~~~v~~l~~~~~~~~~~~a~~~~i~~~t~~r~~~~~  201 (222)
T COG1961         122 AEFERELISERTRAGIEAARKAGKEGGRPPGYKIKKGRKKAEEQAAAVRRLLADGLGSYSEIARALGISRSTVYRILNKL  201 (222)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCcCCCCCccccccccccccchhHHHHHHHHHhccchHHHHHHHcCccHHHHHHhhhhh
Confidence            556666666666778888888888887652       22 3333444444444442699999999999999999998765


Q ss_pred             C
Q psy17316        160 G  160 (229)
Q Consensus       160 g  160 (229)
                      .
T Consensus       202 ~  202 (222)
T COG1961         202 K  202 (222)
T ss_pred             h
Confidence            3

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=88.26  E-value=0.95  Score=35.89  Aligned_cols=35  Identities=17%  Similarity=0.169  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...+|+.+..-.++++.|+|..+|||..||+.++.
T Consensus       110 ~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~  144 (161)
T PRK09047        110 RQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCS  144 (161)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence            34556666555559999999999999999999876

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=88.22  E-value=0.98  Score=36.37  Aligned_cols=34  Identities=24%  Similarity=0.196  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -.+|+....-+++|+.|+|..+|||.+||+.++.
T Consensus       117 ~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~  150 (164)
T PRK12547        117 QREAIILIGASGFSYEDAAAICGCAVGTIKSRVS  150 (164)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3445555444669999999999999999999986

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=88.19  E-value=0.74  Score=37.97  Aligned_cols=35  Identities=23%  Similarity=0.262  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...+|+....-+++++.++|..+|||.+||+.++.
T Consensus       145 ~~~~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~  179 (194)
T PRK12519        145 SQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARAR  179 (194)
T ss_pred             HHhhhhhhhhhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            34555555544559999999999999999999986

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=88.18  E-value=0.86  Score=36.95  Aligned_cols=32  Identities=16%  Similarity=0.135  Sum_probs=26.0

Q ss_pred             HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ++.+..-.|+|+.+||..+|||.+||+.++.+
T Consensus       127 v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~r  158 (172)
T PRK12523        127 AFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQ  158 (172)
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            33333335889999999999999999999886

>PRK11050 manganese transport regulator MntR; Provisional

Probab=88.16  E-value=1.1  Score=36.27  Aligned_cols=47  Identities=17%  Similarity=0.185  Sum_probs=36.3

Q ss_pred             CCCCHHHHHHHHHHHH--cCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         31 KTWTHEDMDAALEALR--AGQMSLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~--~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      .....++.+..|..+.  .|++++.++|+.+||+++|+.++++++.-.+
T Consensus        31 ~~~~~e~~l~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~G   79 (152)
T PRK11050         31 RRELIEDYVELIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDG   79 (152)
T ss_pred             hHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence            4555666666666443  3789999999999999999999999875444

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=88.13  E-value=1.1  Score=36.81  Aligned_cols=26  Identities=15%  Similarity=0.221  Sum_probs=23.6

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.|+|+.+||..+|||.+||+.++.+
T Consensus       136 ~~g~s~~EIA~~lgis~~tVk~~l~R  161 (185)
T PRK12542        136 FYNLTYQEISSVMGITEANVRKQFER  161 (185)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            35889999999999999999999886

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=88.05  E-value=0.84  Score=37.95  Aligned_cols=26  Identities=12%  Similarity=-0.010  Sum_probs=24.0

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.++|+.+||+.+|||.+||+.++++
T Consensus       150 ~~g~s~~eIA~~lgis~~tV~~~l~R  175 (196)
T PRK12524        150 IEGLSNPEIAEVMEIGVEAVESLTAR  175 (196)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            36889999999999999999999986

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=88.04  E-value=1.3  Score=35.18  Aligned_cols=30  Identities=20%  Similarity=0.322  Sum_probs=26.8

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      .++.+|+.++|++.|+|.+|++++++++.-
T Consensus        19 ~d~r~~~~eia~~lglS~~~v~~Ri~~L~~   48 (154)
T COG1522          19 EDARISNAELAERVGLSPSTVLRRIKRLEE   48 (154)
T ss_pred             HhCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            368899999999999999999999998633

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=87.98  E-value=1.1  Score=37.69  Aligned_cols=26  Identities=15%  Similarity=0.164  Sum_probs=23.6

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.|+|+.+||..+|||.+||+.++++
T Consensus       167 ~~g~s~~EIA~~lgis~~tV~~~l~R  192 (206)
T PRK12526        167 FQELSQEQLAQQLNVPLGTVKSRLRL  192 (206)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            35889999999999999999999875

>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes

Probab=87.98  E-value=1.8  Score=36.29  Aligned_cols=46  Identities=17%  Similarity=0.130  Sum_probs=39.6

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      ...|++.+..+++++.++++|++++|.+|||...+|.-.++-..++
T Consensus        15 ~~lse~~r~~Iy~~~~~~~~sv~~vS~~ygi~~~RV~AIvrLkeiE   60 (172)
T PF12298_consen   15 PVLSEELREQIYEDVMQDGKSVREVSQKYGIKIQRVEAIVRLKEIE   60 (172)
T ss_pred             CcCCHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            3458999999999999999999999999999999998777755444

This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=87.98  E-value=0.98  Score=37.01  Aligned_cols=32  Identities=16%  Similarity=0.133  Sum_probs=26.2

Q ss_pred             HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +|+....-+++++.++|..+|||.+||+.++.
T Consensus       140 ~i~~l~~~~~~s~~eIA~~lgis~~tV~~~l~  171 (182)
T PRK12537        140 NCILHAYVDGCSHAEIAQRLGAPLGTVKAWIK  171 (182)
T ss_pred             HHHHHHHHcCCCHHHHHHHHCCChhhHHHHHH
Confidence            44555444559999999999999999999886

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=87.96  E-value=1  Score=37.04  Aligned_cols=38  Identities=18%  Similarity=0.121  Sum_probs=29.9

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      |++++...+..+.+|  ....+..-|..-..-|++++..+
T Consensus         7 ~~~~~~~l~~~~~~g--d~~a~~~l~~~~~~~l~~~~~~~   44 (189)
T PRK09648          7 TGEELDALVAEAVAG--DRRALREVLEIIRPLVVRYCRAR   44 (189)
T ss_pred             CchHHHHHHHHHHcC--CHHHHHHHHHHHHHHHHHHHHHH
Confidence            778888888888876  46777777777788888888875

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=87.88  E-value=0.98  Score=37.42  Aligned_cols=34  Identities=9%  Similarity=-0.093  Sum_probs=27.7

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+|+....-++++|.|+|..+|||.+||+.++.
T Consensus       139 ~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~  172 (189)
T PRK12530        139 QARVFMMREYLELSSEQICQECDISTSNLHVLLY  172 (189)
T ss_pred             HHHHHhHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4455555555569999999999999999999876

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=87.87  E-value=0.93  Score=36.60  Aligned_cols=31  Identities=26%  Similarity=0.242  Sum_probs=25.5

Q ss_pred             HHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         42 LEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        42 I~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.+..-.|+|+.+||+.+|||.+|++.++++
T Consensus       127 l~L~~~~g~s~~EIA~~lgis~~tV~~~l~r  157 (173)
T PRK09645        127 LVRSYYRGWSTAQIAADLGIPEGTVKSRLHY  157 (173)
T ss_pred             HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3333345889999999999999999999886

>COG1710 Uncharacterized protein conserved in archaea [Function unknown]

Probab=87.85  E-value=1.5  Score=34.70  Aligned_cols=45  Identities=29%  Similarity=0.506  Sum_probs=38.6

Q ss_pred             cCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHH
Q psy17316        113 YGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARK  158 (229)
Q Consensus       113 ~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~  158 (229)
                      -|++.+|+...++..-+...+|. +-++|++..|||-.|||=.+++
T Consensus        88 rGrprkyd~~t~~~i~emlr~gk-~preIsk~lGIpirTvyY~l~k  132 (139)
T COG1710          88 RGRPRKYDRNTLLRIREMLRNGK-TPREISKDLGIPIRTVYYLLKK  132 (139)
T ss_pred             CCCCcccchhHHHHHHHHHHcCC-CHHHHHHhhCCchhhhHHHHHH
Confidence            37899999988888777777776 9999999999999998877664

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=87.85  E-value=1.1  Score=35.72  Aligned_cols=36  Identities=8%  Similarity=-0.040  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +...+|+..+--+++++.++|..+|||.+||+..+.
T Consensus       108 ~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~  143 (159)
T PRK12527        108 PACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIV  143 (159)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            345567777666679999999999999999999876

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

Probab=87.80  E-value=0.95  Score=36.45  Aligned_cols=34  Identities=15%  Similarity=0.082  Sum_probs=27.9

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -.+|+....-+++++.++|..+|||.+||+.++.
T Consensus       124 ~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~  157 (169)
T TIGR02954       124 YQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLH  157 (169)
T ss_pred             HhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3456655555669999999999999999999986

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.

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

Probab=87.80  E-value=0.99  Score=35.97  Aligned_cols=34  Identities=15%  Similarity=0.109  Sum_probs=27.4

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+|+....-+++++.++|..+|||..||+.++.
T Consensus       115 ~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~  148 (162)
T TIGR02983       115 QRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLS  148 (162)
T ss_pred             HHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHH
Confidence            4445555445569999999999999999999986

This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=87.67  E-value=0.91  Score=38.86  Aligned_cols=26  Identities=12%  Similarity=0.169  Sum_probs=23.7

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.++|+.+||..+|||.+||+.++++
T Consensus       196 ~eg~s~~EIA~~lgis~~tVk~~~~r  221 (234)
T PRK08301        196 GEEKTQKEVADMLGISQSYISRLEKR  221 (234)
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            46899999999999999999998775

>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=87.63  E-value=1.1  Score=30.29  Aligned_cols=33  Identities=15%  Similarity=0.177  Sum_probs=27.3

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+++..+.+.+ |+..||..++|++++|...++
T Consensus         3 ~l~~f~~v~~~g-s~~~AA~~l~is~~~vs~~i~   35 (60)
T PF00126_consen    3 QLRYFLAVAETG-SISAAAEELGISQSAVSRQIK   35 (60)
T ss_dssp             HHHHHHHHHHHS-SHHHHHHHCTSSHHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CHHHHHHHhhccchHHHHHHH
Confidence            345666666663 799999999999999999998

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....

>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=87.62  E-value=1  Score=30.46  Aligned_cols=30  Identities=17%  Similarity=0.418  Sum_probs=26.1

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      +|.+|+.++|..|||+..|+++=+..+.-.
T Consensus        12 ~~~~s~~ela~~~~VS~~TiRRDl~~L~~~   41 (57)
T PF08220_consen   12 KGKVSVKELAEEFGVSEMTIRRDLNKLEKQ   41 (57)
T ss_pred             cCCEEHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            688999999999999999999988865433

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

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

Probab=87.57  E-value=0.56  Score=38.79  Aligned_cols=25  Identities=24%  Similarity=0.361  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         48 GQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        48 g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .|+|+.+||..+|||.+||+.++.+
T Consensus       146 ~g~s~~EIA~~lgis~~tVk~~l~R  170 (193)
T TIGR02947       146 EGFAYKEIAEIMGTPIGTVMSRLHR  170 (193)
T ss_pred             cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            6899999999999999999999886

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

>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins

Probab=87.54  E-value=15  Score=30.79  Aligned_cols=153  Identities=18%  Similarity=0.213  Sum_probs=93.0

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh--CCC--CCCCCC-CCCCCcHHHHHHHHHHHhhcchhhhhhh
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL--GIH--TPKKEG-PTKSWNEEILNVALDALRAGSISANKAS  110 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~--gi~--~~~~~~-~~k~~s~e~~~~a~~ll~~G~ls~~~~~  110 (229)
                      .-+..++.++++|.   -.-++.+|.+.-.|..--+--  .+.  ...... -....+.+....+++-.+.         
T Consensus         5 avL~~~l~~l~~G~---~~~c~~lG~~~eel~~L~~ls~~~l~~L~~~~v~~~~i~in~~~l~~~L~~~~~---------   72 (180)
T PF11198_consen    5 AVLTQALHDLKEGN---IRRCEALGFSPEELDALQQLSLDDLHYLANSSVSFVSISINHDVLWRLLEQARR---------   72 (180)
T ss_pred             HHHHHHHHHHHccc---HHHHHHcCCCHHHHHHHhCCCHHHHHHHhcCCcceeeeeeCHHHHHHHHHHHHH---------
Confidence            44578888998877   456777888877665422210  000  001111 1123455656555532210         


Q ss_pred             hccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHH---
Q psy17316        111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIR---  187 (229)
Q Consensus       111 ~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~---  187 (229)
                               .++..+.+-.++..|. |..=+..-||++..-+..|=+-.|+...   .++++.-++|+..+|-+.-.   
T Consensus        73 ---------~~~~~~~idr~L~lGA-S~~mm~~~FGls~~ev~~rR~llgi~~~---~GR~~~~~ee~~~~iW~~W~~~~  139 (180)
T PF11198_consen   73 ---------EQQEQQLIDRALRLGA-SIEMMQRLFGLSSAEVAARRRLLGIPVR---KGRPPALSEEEEAAIWRRWQQLM  139 (180)
T ss_pred             ---------HHHHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHHHHHhCCCCC---CCCCCCcCHHHHHHHHHHHHHHH
Confidence                     1122344455666666 9999999999988776665555576553   35667777777777776654   


Q ss_pred             -hCCC------cHH----HHHHHhCCChHHHHHHHHh
Q psy17316        188 -SGQT------TVQ----RASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       188 -~~~~------s~~----eAA~~fgVp~~tv~~~vk~  213 (229)
                       +++.      .+-    .+|...+||-++||+.++.
T Consensus       140 ~~~~~~~~~~~~~Le~~m~~Ae~~~isL~~iW~~i~~  176 (180)
T PF11198_consen  140 KKRGVDNLDSPDALELMMLLAEETNISLTVIWSLIQE  176 (180)
T ss_pred             hhcCCCCccchHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence             2222      233    4999999999999998873

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=87.53  E-value=0.94  Score=37.61  Aligned_cols=32  Identities=22%  Similarity=0.246  Sum_probs=26.1

Q ss_pred             HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ++.+..-.|+|+.+||+.+|||.+||+.++.+
T Consensus       124 i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~R  155 (187)
T PRK12516        124 AIILVGASGFAYEEAAEICGCAVGTIKSRVNR  155 (187)
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            33333346899999999999999999999886

>PRK10130 transcriptional regulator EutR; Provisional

Probab=87.51  E-value=3.3  Score=38.25  Aligned_cols=83  Identities=17%  Similarity=0.132  Sum_probs=59.3

Q ss_pred             HHHHHHHHHHHH---cCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHHHHHHHHHHh----CCCc
Q psy17316        121 EEILNVALDALR---AGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDLEIALEGIRS----GQTT  192 (229)
Q Consensus       121 ~e~k~~AV~~~~---~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r~eaV~~~~~----~~~s  192 (229)
                      .....+|.+.+.   ...+++.++|+..||+..+|.+-.++. |....        .|=..-|++.++....    .+.+
T Consensus       239 ~~~v~~~~~~i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk~~~G~sp~--------~ylr~~RL~~ar~lL~~~~~~~~s  310 (350)
T PRK10130        239 RRLLSRAREYVLENMSEPVTVLDLCNQLHVSRRTLQNAFHAILGIGPN--------AWLKRIRLNAVRRELISPWSQSTT  310 (350)
T ss_pred             HHHHHHHHHHHHhhhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHhccCCCCCC
Confidence            444555555543   344799999999999999999999875 64443        3444567777775554    3588


Q ss_pred             HHHHHHHhCCChHHHHHHH
Q psy17316        193 VQRASAEYGIPSGTLYGRC  211 (229)
Q Consensus       193 ~~eAA~~fgVp~~tv~~~v  211 (229)
                      +.++|.++|.....-....
T Consensus       311 I~eIA~~~GF~~~s~Fs~~  329 (350)
T PRK10130        311 VKDAAMQWGFWHLGQFATD  329 (350)
T ss_pred             HHHHHHHhCCCCHHHHHHH
Confidence            9999999998776655543

>PRK09685 DNA-binding transcriptional activator FeaR; Provisional

Probab=87.44  E-value=3.5  Score=36.28  Aligned_cols=78  Identities=10%  Similarity=0.180  Sum_probs=57.3

Q ss_pred             CCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhC---CCcHHHHHHHhCCChHHHHHHH
Q psy17316        135 SISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSG---QTTVQRASAEYGIPSGTLYGRC  211 (229)
Q Consensus       135 ~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~---~~s~~eAA~~fgVp~~tv~~~v  211 (229)
                      .+|+.++|..+||+.++|++..++.|...        ..|=.+.|++.....+..   +.++.++|...|-+-.+-.+.+
T Consensus       214 ~ls~~~lA~~~giS~r~L~r~Fk~~G~T~--------~~yi~~~RL~~A~~lL~~~~~~~sI~eIA~~~GF~d~s~Fsr~  285 (302)
T PRK09685        214 ILRPEWIAGELGISVRSLYRLFAEQGLVV--------AQYIRNRRLDRCADDLRPAADDEKITSIAYKWGFSDSSHFSTA  285 (302)
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHcCCCH--------HHHHHHHHHHHHHHHhhhhccCCCHHHHHHHhCCCCHHHHHHH
Confidence            37999999999999999999998766433        235455677666555542   5799999999999887777665


Q ss_pred             HhhcCCCCC
Q psy17316        212 KLSRSTPRP  220 (229)
Q Consensus       212 k~~~~~~~~  220 (229)
                      =.+.-|-+|
T Consensus       286 Fkk~~G~sP  294 (302)
T PRK09685        286 FKQRFGVSP  294 (302)
T ss_pred             HHHHHCcCH
Confidence            444444444

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=87.43  E-value=0.94  Score=36.70  Aligned_cols=26  Identities=27%  Similarity=0.155  Sum_probs=23.8

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.|+|+.+||..+|||.+||+.++.+
T Consensus       133 ~~~~s~~EIA~~lgis~~tV~~~l~R  158 (173)
T PRK12522        133 YEQYSYKEMSEILNIPIGTVKYRLNY  158 (173)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            35889999999999999999999886

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

Probab=87.38  E-value=0.89  Score=37.34  Aligned_cols=26  Identities=27%  Similarity=0.307  Sum_probs=24.1

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.|+|+.+||..+|||.+||..++++
T Consensus       141 ~~gls~~EIA~~l~i~~~tVks~l~r  166 (182)
T COG1595         141 LEGLSYEEIAEILGISVGTVKSRLHR  166 (182)
T ss_pred             hcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            35899999999999999999999986

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

Probab=87.34  E-value=2.6  Score=28.51  Aligned_cols=24  Identities=25%  Similarity=0.393  Sum_probs=21.0

Q ss_pred             CCCHHHHHHHhCCChHHHHHHHHH
Q psy17316        135 SISANKASKAYGIPSSTLYKIARK  158 (229)
Q Consensus       135 ~~S~~~~a~k~gIp~sTL~~~ik~  158 (229)
                      +.++.++|+.+||+.+|+..++++
T Consensus        23 ~~tl~elA~~lgis~st~~~~LRr   46 (53)
T PF04967_consen   23 RITLEELAEELGISKSTVSEHLRR   46 (53)
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHH
Confidence            459999999999999998887764

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

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=87.34  E-value=1.2  Score=36.12  Aligned_cols=40  Identities=10%  Similarity=0.097  Sum_probs=30.4

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +..|+.++ +++.++ ..|+|+.+||+.+|||++|+..|.++
T Consensus         5 ~~Lt~rqr-eVL~lr-~~GlTq~EIAe~LGiS~~tVs~ie~r   44 (141)
T PRK03975          5 SFLTERQI-EVLRLR-ERGLTQQEIADILGTSRANVSSIEKR   44 (141)
T ss_pred             cCCCHHHH-HHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            33444444 445554 56899999999999999999999875

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

Probab=87.33  E-value=1.3  Score=37.68  Aligned_cols=40  Identities=10%  Similarity=0.098  Sum_probs=29.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..++.+..-.+..| -.++|+.+||+.+||+.+|+++++++
T Consensus       178 ~L~~~~r~vl~l~y-~~~~s~~eIA~~lgis~~~v~~~~~r  217 (227)
T TIGR02980       178 ALPERERRILLLRF-FEDKTQSEIAERLGISQMHVSRLLRR  217 (227)
T ss_pred             cCCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            34444443333333 35789999999999999999999875

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

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=87.33  E-value=1.2  Score=37.08  Aligned_cols=35  Identities=17%  Similarity=0.107  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...++|+...-+++|+.|||..+|||-.||++.++
T Consensus       139 ~~~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~  173 (185)
T PF07638_consen  139 RQRRVVELRFFEGLSVEEIAERLGISERTVRRRLR  173 (185)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34566666655679999999999999999999887

>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional

Probab=87.30  E-value=0.83  Score=43.79  Aligned_cols=81  Identities=9%  Similarity=0.055  Sum_probs=48.1

Q ss_pred             HHHcCCCCHHHHHHHhCCChHHHHHHHHHh------CCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316        130 ALRAGSISANKASKAYGIPSSTLYKIARKE------GIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIP  203 (229)
Q Consensus       130 ~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~------g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp  203 (229)
                      .|..|. |+..||++|||+...|.+|=...      |-.+..|....... ... ....+.+...-+=|+..+|.+|||+
T Consensus       347 ~Vk~GD-TL~sIA~r~gvs~~~L~~~N~l~~~~L~~Gq~L~Ip~~~~~~~-~~~-~~~~~~Y~Vr~GDTL~sIA~kygVt  423 (456)
T PRK10783        347 KVRSGD-TLSGIASRLNVSTKDLQQWNNLRGSKLKVGQTLTIGAGSSAQR-LAN-NSDSITYRVRKGDSLSSIAKRHGVN  423 (456)
T ss_pred             EECCCC-cHHHHHHHHCcCHHHHHHHcCCCcccCCCCCEEEecCCccccc-ccc-cccceeEEeCCCCCHHHHHHHhCCC
Confidence            345666 99999999999999999884211      21221121100000 000 0111223333335699999999999


Q ss_pred             hHHHHHHHHh
Q psy17316        204 SGTLYGRCKL  213 (229)
Q Consensus       204 ~~tv~~~vk~  213 (229)
                      -..|..|=.+
T Consensus       424 v~~L~~~N~l  433 (456)
T PRK10783        424 IKDVMRWNSD  433 (456)
T ss_pred             HHHHHHhcCC
Confidence            9999988553

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=87.29  E-value=1.3  Score=36.30  Aligned_cols=32  Identities=16%  Similarity=-0.094  Sum_probs=25.3

Q ss_pred             HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +|+....-+++++.++|..+|||..||+.++.
T Consensus       135 ~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~  166 (186)
T PRK05602        135 EAIVLQYYQGLSNIEAAAVMDISVDALESLLA  166 (186)
T ss_pred             HHhhHHHhcCCCHHHHHHHhCcCHHHHHHHHH
Confidence            34444334559999999999999999999875

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=87.29  E-value=1.1  Score=36.78  Aligned_cols=34  Identities=15%  Similarity=0.011  Sum_probs=27.9

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+|+....-.++|+.++|..+|||.+||+.++.
T Consensus       127 ~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~  160 (185)
T PRK12542        127 NRQVFKYKVFYNLTYQEISSVMGITEANVRKQFE  160 (185)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4456666555569999999999999999999875

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=87.27  E-value=1  Score=36.86  Aligned_cols=25  Identities=12%  Similarity=0.219  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         48 GQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        48 g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .|+|+.+||..+|||.+||+.++.+
T Consensus       146 ~g~s~~eIA~~l~is~~tV~~~l~r  170 (184)
T PRK12512        146 EGASIKETAAKLSMSEGAVRVALHR  170 (184)
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            5889999999999999999999886

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=87.26  E-value=1  Score=37.25  Aligned_cols=40  Identities=10%  Similarity=0.111  Sum_probs=29.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.++++..-.+--+. .|+|+.+||..+|||.+|++.++.+
T Consensus       131 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~R  170 (189)
T PRK06811        131 DLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSR  170 (189)
T ss_pred             hCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHH
Confidence            444444333332233 5789999999999999999999886

>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A

Probab=87.24  E-value=0.72  Score=32.22  Aligned_cols=40  Identities=10%  Similarity=0.112  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      |++++.|+.. ++.++-+++|+.+||++.++++++..+.-+
T Consensus         3 e~Il~~i~~~-~~p~~T~eiA~~~gls~~~aR~yL~~Le~e   42 (62)
T PF04703_consen    3 EKILEYIKEQ-NGPLKTREIADALGLSIYQARYYLEKLEKE   42 (62)
T ss_dssp             HCHHHHHHHH-TS-EEHHHHHHHHTS-HHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            5567777666 678999999999999999999999976433

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=87.22  E-value=1.3  Score=36.59  Aligned_cols=26  Identities=27%  Similarity=0.306  Sum_probs=23.6

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      -.|+|+.+||..+|||.+|++.++++
T Consensus       125 ~~g~s~~EIA~~Lgis~~tV~~~l~R  150 (182)
T PRK12540        125 ASGFSYEDAAAICGCAVGTIKSRVNR  150 (182)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            35889999999999999999998885

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=87.18  E-value=9.6  Score=32.58  Aligned_cols=104  Identities=13%  Similarity=0.046  Sum_probs=0.0

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhh
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKAS  110 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~  110 (229)
                      +.-+.+++.+||+.+.+|+         .=+|+....+.+...+........ ....++-++                  
T Consensus       110 K~~~~~~L~~aI~~v~~G~---------~~~~~~~~~~l~~~~~~~~~~~~~-~~~Lt~rE~------------------  161 (216)
T PRK10100        110 AMEDQERVVNGLQGVLRGE---------CYFTQKLASYLITHSGNYRYNSTE-SALLTHREK------------------  161 (216)
T ss_pred             CCCCHHHHHHHHHHHHcCC---------cccCHHHHHHHHHhhcccccCCCc-cCCCCHHHH------------------


Q ss_pred             hccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy17316        111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSG  189 (229)
Q Consensus       111 ~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~  189 (229)
                                     +++.++.+|. |.++||++.+||..|+..++.+.-.++..           ..|.+++.+..++
T Consensus       162 ---------------~Vl~l~~~G~-s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v-----------~nr~elv~~a~~~  213 (216)
T PRK10100        162 ---------------EILNKLRIGA-SNNEIARSLFISENTVKTHLYNLFKKIAV-----------KNRTQAVSWANDN  213 (216)
T ss_pred             ---------------HHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCC-----------CCHHHHHHHHHHh

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

Probab=87.17  E-value=1.1  Score=27.74  Aligned_cols=25  Identities=8%  Similarity=0.182  Sum_probs=23.0

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..++|..++|+.+|++..+|.+|..
T Consensus        10 ~~~~s~~~~a~~~~~~~~~v~~~~~   34 (58)
T cd00093          10 EKGLTQEELAEKLGVSRSTISRIEN   34 (58)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            4588999999999999999999977

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

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=87.13  E-value=0.71  Score=30.24  Aligned_cols=28  Identities=21%  Similarity=0.325  Sum_probs=24.0

Q ss_pred             CC-CHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         49 QM-SLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        49 ~~-S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      .+ |.+++|+.+||+++|+++.++.+.-.
T Consensus        19 ~l~s~~~la~~~~vs~~tv~~~l~~L~~~   47 (60)
T smart00345       19 KLPSERELAAQLGVSRTTVREALSRLEAE   47 (60)
T ss_pred             cCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            35 89999999999999999999876433

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=87.12  E-value=1.3  Score=35.88  Aligned_cols=36  Identities=8%  Similarity=-0.066  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +..| +|+.+..-+++++.|+|..+|||..||+.+++
T Consensus       121 ~~~r-~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~  156 (168)
T PRK12525        121 GKAR-AAFLMSQLEGLTYVEIGERLGVSLSRIHQYMV  156 (168)
T ss_pred             HHHH-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4444 45555445559999999999999999999987

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=87.10  E-value=1.2  Score=35.89  Aligned_cols=38  Identities=13%  Similarity=0.106  Sum_probs=29.8

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .|+.++ .++.++ ..|+|+.+||+.+|++++|+.++.++
T Consensus         7 Lte~qr-~VL~Lr-~~GlTq~EIAe~LgiS~stV~~~e~r   44 (137)
T TIGR00721         7 LTERQI-KVLELR-EKGLSQKEIAKELKTTRANVSAIEKR   44 (137)
T ss_pred             CCHHHH-HHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            344444 455554 57899999999999999999999886

Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	229
2cob_A	70	LCOR protein; MLR2, KIAA1795, helix-turn-helix, st	2e-10
2cob_A	70	LCOR protein; MLR2, KIAA1795, helix-turn-helix, st	7e-08
2cob_A	70	LCOR protein; MLR2, KIAA1795, helix-turn-helix, st	1e-05

>2cob_A LCOR protein; MLR2, KIAA1795, helix-turn-helix, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.15 Length = 70

 Score = 54.4 bits (130), Expect = 2e-10
 Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 1/62 (1%)

Query: 106 ANKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTL-YKIARKEGIRLA 164
            +  S   G  + +N EIL  A+  + +G +S +KA   YGIP STL YK+  + G    
Sbjct: 1   GSSGSSGRGRYRQYNSEILEEAISVVMSGKMSVSKAQSIYGIPHSTLEYKVKERLGTLKN 60

Query: 165 QP 166
            P
Sbjct: 61  PP 62

>2cob_A LCOR protein; MLR2, KIAA1795, helix-turn-helix, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.15 Length = 70

 Score = 47.5 bits (112), Expect = 7e-08
 Identities = 13/48 (27%), Positives = 25/48 (52%)

Query: 30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHT 77
           + +  E ++ A+  + +G+MS++KA   YGIP +TL  +        
Sbjct: 11 YRQYNSEILEEAISVVMSGKMSVSKAQSIYGIPHSTLEYKVKERLGTL 58

>2cob_A LCOR protein; MLR2, KIAA1795, helix-turn-helix, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.15 Length = 70

 Score = 41.3 bits (96), Expect = 1e-05
 Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 174 WKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-LSRSTPRPPPGNLKTSR 229
           +  E LE A+  + SG+ +V +A + YGIP  TL  + K    +   PP   +K  R
Sbjct: 14  YNSEILEEAISVVMSGKMSVSKAQSIYGIPHSTLEYKVKERLGTLKNPPKKKMKLMR 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	229
1u78_A	141	TC3 transposase, transposable element TC3 transpos	99.38
2k27_A	159	Paired box protein PAX-8; paired domain, solution	99.37
1u78_A	141	TC3 transposase, transposable element TC3 transpos	99.31
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	99.29
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	99.22
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	99.17
2cob_A	70	LCOR protein; MLR2, KIAA1795, helix-turn-helix, st	99.16
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	99.11
2k27_A	159	Paired box protein PAX-8; paired domain, solution	99.04
2cob_A	70	LCOR protein; MLR2, KIAA1795, helix-turn-helix, st	98.9
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	98.7
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	98.61
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	98.52
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	98.51
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	98.49
2jrt_A	95	Uncharacterized protein; solution, structure, NESG	98.48
2rn7_A	108	IS629 ORFA; helix, all alpha, unknown function, st	98.47
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	98.35
2rn7_A	108	IS629 ORFA; helix, all alpha, unknown function, st	98.3
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	98.28
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	98.26
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	98.24
2jrt_A	95	Uncharacterized protein; solution, structure, NESG	98.21
3hot_A	345	Transposable element mariner, complete CDS; protei	98.2
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	98.05
3hot_A	345	Transposable element mariner, complete CDS; protei	98.05
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	98.05
2oa4_A	101	SIR5; structure, structural genomics, PSI-2, prote	97.95
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	97.9
2oa4_A	101	SIR5; structure, structural genomics, PSI-2, prote	97.78
2ao9_A	155	Phage protein; structural genomics, nine-fold NCS.	97.66
4dyq_A	140	Gene 1 protein; GP1, octamer, DNA-binding, viral p	97.66
2ao9_A	155	Phage protein; structural genomics, nine-fold NCS.	97.47
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	97.36
3uj3_X	193	DNA-invertase; helix-turn-helix, site-specific rec	97.36
3lsg_A	103	Two-component response regulator YESN; structural	97.35
3e7l_A	63	Transcriptional regulator (NTRC family); sigma43 a	97.23
3mn2_A	108	Probable ARAC family transcriptional regulator; st	97.2
1g2h_A	61	Transcriptional regulatory protein TYRR homolog; p	97.18
3mkl_A	120	HTH-type transcriptional regulator GADX; PSI2, MCS	97.14
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	97.11
4dyq_A	140	Gene 1 protein; GP1, octamer, DNA-binding, viral p	97.09
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	97.07
1gdt_A	183	GD resolvase, protein (gamma delta resolvase); pro	97.06
2r0q_C	209	Putative transposon TN552 DNA-invertase BIN3; site	97.02
1umq_A	81	Photosynthetic apparatus regulatory protein; DNA-b	96.97
3plo_X	193	DNA-invertase; resolvase, helix-turn-helix, serine	96.91
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	96.89
1bl0_A	129	Protein (multiple antibiotic resistance protein),	96.83
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	96.71
1ntc_A	91	Protein (nitrogen regulation protein (NTRC)); heli	96.68
4ich_A	311	Transcriptional regulator; structural genomics, PS	96.65
2jml_A	81	DNA binding domain/transcriptional regulator; anti	96.56
1vz0_A	230	PARB, chromosome partitioning protein PARB; nuclea	96.53
3lsg_A	103	Two-component response regulator YESN; structural	96.44
1eto_A	98	FIS, factor for inversion stimulation; transcripti	96.42
2jml_A	81	DNA binding domain/transcriptional regulator; anti	96.38
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	96.34
3e7l_A	63	Transcriptional regulator (NTRC family); sigma43 a	96.31
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	96.22
3gbg_A	276	TCP pilus virulence regulatory protein; cupin, hel	96.18
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	96.18
3mn2_A	108	Probable ARAC family transcriptional regulator; st	96.16
4fcy_A	529	Transposase; rnaseh, DDE transposase, DNA binding	96.14
2vz4_A	108	Tipal, HTH-type transcriptional activator TIPA; tr	95.95
3uj3_X	193	DNA-invertase; helix-turn-helix, site-specific rec	95.91
1bl0_A	129	Protein (multiple antibiotic resistance protein),	95.84
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	95.79
4fcy_A	529	Transposase; rnaseh, DDE transposase, DNA binding	95.73
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	95.65
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	95.6
1r8d_A	109	Transcription activator MTAN; protein-DNA complex,	95.57
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	95.53
4fe7_A	412	Xylose operon regulatory protein; HTH_ARAC, helix-	95.48
2vz4_A	108	Tipal, HTH-type transcriptional activator TIPA; tr	95.34
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	95.32
3mkl_A	120	HTH-type transcriptional regulator GADX; PSI2, MCS	95.31
1q06_A	135	Transcriptional regulator CUER; MERR family transc	95.3
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	95.29
1umq_A	81	Photosynthetic apparatus regulatory protein; DNA-b	95.27
3gp4_A	142	Transcriptional regulator, MERR family; structural	95.04
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	95.01
1d5y_A	292	ROB transcription factor; protein-DNA complex, DNA	95.01
1r8d_A	109	Transcription activator MTAN; protein-DNA complex,	95.01
1ntc_A	91	Protein (nitrogen regulation protein (NTRC)); heli	94.99
1y0u_A	96	Arsenical resistance operon repressor, putative; s	94.97
1g2h_A	61	Transcriptional regulatory protein TYRR homolog; p	94.95
1j9i_A	68	GPNU1 DBD;, terminase small subunit; DNA binding d	94.95
2l1p_A	83	DNA-binding protein SATB1; PSI-biology, NESG, stru	94.95
1z4h_A	66	TORI, TOR inhibition protein; winged helix, revers	94.9
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	94.84
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	94.83
3hh0_A	146	Transcriptional regulator, MERR family; protein st	94.8
1q06_A	135	Transcriptional regulator CUER; MERR family transc	94.73
3gp4_A	142	Transcriptional regulator, MERR family; structural	94.65
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	94.53
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	94.5
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	94.44
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	94.43
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	94.43
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	94.42
3hh0_A	146	Transcriptional regulator, MERR family; protein st	94.41
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	94.35
2hin_A	71	GP39, repressor protein; transcription factor, dim	94.32
3plo_X	193	DNA-invertase; resolvase, helix-turn-helix, serine	94.24
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	94.21
3gpv_A	148	Transcriptional regulator, MERR family; protein st	94.16
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	94.16
3jth_A	98	Transcription activator HLYU; transcription factor	94.16
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	94.12
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	94.09
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	94.01
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	93.93
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	93.91
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	93.9
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	93.86
3gpv_A	148	Transcriptional regulator, MERR family; protein st	93.81
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	93.8
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	93.78
1y0u_A	96	Arsenical resistance operon repressor, putative; s	93.77
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	93.76
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	93.74
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	93.67
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	93.67
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	93.65
1z4h_A	66	TORI, TOR inhibition protein; winged helix, revers	93.51
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	93.48
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	93.46
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	93.4
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	93.39
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	93.37
3gbg_A	276	TCP pilus virulence regulatory protein; cupin, hel	93.31
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	93.28
2zhg_A	154	Redox-sensitive transcriptional activator SOXR; ox	93.27
1gdt_A	183	GD resolvase, protein (gamma delta resolvase); pro	93.26
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	93.26
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	93.21
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	93.19
1eto_A	98	FIS, factor for inversion stimulation; transcripti	93.19
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	93.19
2r0q_C	209	Putative transposon TN552 DNA-invertase BIN3; site	93.13
2hin_A	71	GP39, repressor protein; transcription factor, dim	93.12
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	93.04
2dg6_A	222	Putative transcriptional regulator; winged-helix m	93.04
2dg6_A	222	Putative transcriptional regulator; winged-helix m	93.01
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	93.0
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	92.99
3c57_A	95	Two component transcriptional regulatory protein;	92.94
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	92.9
1d5y_A	292	ROB transcription factor; protein-DNA complex, DNA	92.89
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	92.86
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	92.85
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	92.85
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	92.8
3m8j_A	111	FOCB protein; all-alpha, helix-turn-helix, transcr	92.78
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	92.77
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	92.69
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	92.64
2kko_A	108	Possible transcriptional regulatory protein (possi	92.64
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	92.61
3frw_A	107	Putative Trp repressor protein; structural genomic	92.61
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	92.59
2zhg_A	154	Redox-sensitive transcriptional activator SOXR; ox	92.53
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	92.51
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	92.51
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	92.49
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	92.42
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	92.39
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	92.38
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	92.22
1r71_A	178	Transcriptional repressor protein KORB; INCP, plas	92.21
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	92.2
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	92.18
3qao_A	249	LMO0526 protein, MERR-like transcriptional regulat	92.14
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	92.13
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	92.12
3jth_A	98	Transcription activator HLYU; transcription factor	92.05
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	92.05
2kko_A	108	Possible transcriptional regulatory protein (possi	91.99
3c57_A	95	Two component transcriptional regulatory protein;	91.97
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	91.97
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	91.95
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	91.92
1j9i_A	68	GPNU1 DBD;, terminase small subunit; DNA binding d	91.92
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	91.9
4fe7_A	412	Xylose operon regulatory protein; HTH_ARAC, helix-	91.87
3frw_A	107	Putative Trp repressor protein; structural genomic	91.8
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	91.79
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	91.74
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	91.71
1rzs_A	61	Antirepressor, regulatory protein CRO; helix-turn-	91.69
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	91.62
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	91.54
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	91.5
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	91.47
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	91.46
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	91.45
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	91.42
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	91.17
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	91.16
2pij_A	67	Prophage PFL 6 CRO; transcription factor, helix-tu	91.14
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	91.07
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	91.06
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	90.98
3qao_A	249	LMO0526 protein, MERR-like transcriptional regulat	90.96
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	90.8
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	90.8
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	90.73
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	90.71
3r0a_A	123	Putative transcriptional regulator; structural gen	90.7
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	90.64
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	90.63
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	90.61
3osg_A	126	MYB21; transcription-DNA complex, MYB2, R2R3 domai	90.6
1b0n_A	111	Protein (SINR protein); transcription regulator, a	90.57
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	90.51
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	90.48
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	90.4
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	90.37
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	90.36
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	90.36
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	90.34
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	90.3
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	90.28
3trb_A	104	Virulence-associated protein I; mobIle and extrach	90.22
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	90.16
2ovg_A	66	Phage lambda CRO; transcription factor, helix-turn	90.15
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	90.08
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	90.07
2pij_A	67	Prophage PFL 6 CRO; transcription factor, helix-tu	90.0
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	89.97
1sfx_A	109	Conserved hypothetical protein AF2008; structural	89.95
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	89.93
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	89.92
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	89.87
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	89.85
3ivp_A	126	Putative transposon-related DNA-binding protein; A	89.77
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	89.72
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	89.71
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	89.68
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	89.68
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	89.61
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	89.59
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	89.52
1sfx_A	109	Conserved hypothetical protein AF2008; structural	89.51
1h89_C	159	C-MYB, MYB proto-oncogene protein; transcription/D	89.47
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	89.43
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	89.41
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	89.41
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	89.34
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	89.31
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	89.26
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	89.25
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	89.21
4g6q_A	182	Putative uncharacterized protein; structural genom	89.19
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	89.18
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	89.0
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	88.99
3iwf_A	107	Transcription regulator RPIR family; transcription	88.95
2w25_A	150	Probable transcriptional regulatory protein; trans	88.94
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	88.87
3ppb_A	195	Putative TETR family transcription regulator; DNA-	88.8
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	88.75
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	88.7
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	88.64
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	88.56
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	88.54
3t76_A	88	VANU, transcriptional regulator vanug; structural	88.47
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	88.42
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	88.39
2qko_A	215	Possible transcriptional regulator, TETR family P;	88.37
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	88.3
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	88.29
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	88.24
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	88.21
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	88.21
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	88.21
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	88.12
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	88.06
2opt_A	234	Actii protein; helical protein, TETR family, APO-p	88.01
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	87.98
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	87.95
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	87.93
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	87.93
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	87.89
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	87.82
3dcf_A	218	Transcriptional regulator of the TETR/ACRR family;	87.76
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	87.74
2ict_A	94	Antitoxin HIGA; helix-turn-helix, structural genom	87.7
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	87.67
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	87.56
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	87.54
3qkx_A	188	Uncharacterized HTH-type transcriptional regulato;	87.54
3nxc_A	212	HTH-type protein SLMA; nucleoid occlusion, cell di	87.53
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	87.49
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	87.44
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	87.43
1ku9_A	152	Hypothetical protein MJ223; putative transcription	87.38
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	87.35
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	87.34
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	87.28
2w25_A	150	Probable transcriptional regulatory protein; trans	87.13
2l1p_A	83	DNA-binding protein SATB1; PSI-biology, NESG, stru	87.03
1r8e_A	278	Multidrug-efflux transporter regulator; protein-DN	86.98
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	86.94
2yve_A	185	Transcriptional regulator; helix-turn-helix, TETR-	86.9
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	86.86
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	86.86
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	86.84
2g7g_A	213	RHA04620, putative transcriptional regulator; heli	86.82
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	86.82
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	86.81
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	86.78
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	86.77
2hxi_A	241	Putative transcriptional regulator; structural gen	86.77
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	86.76
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	86.68
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	86.68
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	86.65
3r0a_A	123	Putative transcriptional regulator; structural gen	86.63
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	86.63
4hku_A	178	LMO2814 protein, TETR transcriptional regulator; s	86.62
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	86.6
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	86.6
2pz9_A	226	Putative regulatory protein; structural genomics,	86.59
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	86.58
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	86.56
1sgm_A	191	Putative HTH-type transcriptional regulator YXAF;	86.4
3dew_A	206	Transcriptional regulator, TETR family; S genomics	86.38
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	86.38
2xpw_A	207	Tetracycline repressor protein class D; transcript	86.37
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	86.35
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	86.35
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	86.33
2ev1_A	222	Hypothetical protein RV1264/MT1302; alpha-helical,	86.32
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	86.3
3fiw_A	211	Putative TETR-family transcriptional regulator; TE	86.25
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	86.25
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	86.16
3egq_A	170	TETR family transcriptional regulator; DNA-binding	85.99
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	85.96
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	85.91
1zk8_A	183	Transcriptional regulator, TETR family; TETR membe	85.91
2ppx_A	99	AGR_C_3184P, uncharacterized protein ATU1735; HTH-	85.83
2dg7_A	195	Putative transcriptional regulator; helix-turn-hel	85.79
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	85.74
1r8e_A	278	Multidrug-efflux transporter regulator; protein-DN	85.74
2qwt_A	196	Transcriptional regulator, TETR family; structural	85.73
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	85.68
3iuo_A	122	ATP-dependent DNA helicase RECQ; C-terminal, GI PS	85.41
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	85.4
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	85.36
3kz9_A	206	SMCR; transcriptional regulator, quorum S DNA-bind	85.28
3bqz_B	194	HTH-type transcriptional regulator QACR; multidrug	85.24
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	85.24
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	85.19
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	85.18
4ghj_A	101	Probable transcriptional regulator; structural gen	85.17
2fq4_A	192	Transcriptional regulator, TETR family; DNA-bindin	85.01
1b0n_A	111	Protein (SINR protein); transcription regulator, a	84.97
3gzi_A	218	Transcriptional regulator, TETR family; TETR famil	84.9
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	84.89
3by6_A	126	Predicted transcriptional regulator; structural ge	84.86
1rzs_A	61	Antirepressor, regulatory protein CRO; helix-turn-	84.84
2nnn_A	140	Probable transcriptional regulator; structural gen	84.83
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	84.8
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	84.78
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	84.72
3vp5_A	189	Transcriptional regulator; heme, sensor protein, T	84.68
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	84.65
2rae_A	207	Transcriptional regulator, ACRR family protein; TE	84.65
2h09_A	155	Transcriptional regulator MNTR; transcription regu	84.64
3f1b_A	203	TETR-like transcriptional regulator; APC5888, rhod	84.63
4ac0_A	202	Tetracycline repressor protein class B from trans	84.59
1z0x_A	220	Transcriptional regulator, TETR family; structural	84.56
1vz0_A	230	PARB, chromosome partitioning protein PARB; nuclea	84.54
3lwj_A	202	Putative TETR-family transcriptional regulator; st	84.46
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	84.4
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	84.4
3lhq_A	220	Acrab operon repressor (TETR/ACRR family); structu	84.4
3ljl_A	156	Transcriptional regulator LUXT; structural genomic	84.31
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	84.29
2zcm_A	192	Biofilm operon icaabcd HTH-type negative transcri	84.27
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	84.24
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	84.15
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	84.1
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	83.95
4aci_A	191	HTH-type transcriptional repressor ACNR; aconitase	83.82
2qtq_A	213	Transcriptional regulator, TETR family; transcript	83.77
3vpr_A	190	Transcriptional regulator, TETR family; all alpha,	83.73
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	83.65
3on4_A	191	Transcriptional regulator, TETR family; structural	83.59
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	83.56
1y6u_A	70	XIS, excisionase from transposon TN916; structure,	83.56
3o60_A	185	LIN0861 protein; PSI, MCSG, structural genomics, m	83.48
2hxo_A	237	Putative TETR-family transcriptional regulator; TE	83.45
3t76_A	88	VANU, transcriptional regulator vanug; structural	83.41
2g7s_A	194	Transcriptional regulator, TETR family; APC5906, P	83.4
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	83.37
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	83.34
2dg8_A	193	Putative TETR-family transcriptional regulatory P;	83.34
2d6y_A	202	Putative TETR family regulatory protein; helix-tur	83.29
3bjb_A	207	Probable transcriptional regulator, TETR family P;	83.27
2np5_A	203	Transcriptional regulator; TETR family, structural	83.26
2hku_A	215	A putative transcriptional regulator; structural g	83.25
2jj7_A	186	Hemolysin II regulatory protein; DNA-binding prote	83.24
3g5g_A	99	Regulatory protein; transcriptional regulator, hel	83.2
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	83.2
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	83.16
1pb6_A	212	Hypothetical transcriptional regulator YCDC; helix	83.15
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	83.12
1u8b_A	133	ADA polyprotein; protein-DNA complex, methylation,	83.1
2eh3_A	179	Transcriptional regulator; all alpha proteins, tet	83.09
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	83.08
2guh_A	214	Putative TETR-family transcriptional regulator; he	83.08
3pas_A	195	TETR family transcription regulator; structural ge	83.07
2g7l_A	243	TETR-family transcriptional regulator; APC6062, pr	83.06
3onq_A	262	Regulator of polyketide synthase expression; struc	83.05
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	83.04
2dg7_A	195	Putative transcriptional regulator; helix-turn-hel	83.03
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	83.02
3vib_A	210	MTRR; helix-turn-helix motif, DNA binding, DNA bin	83.01
3col_A	196	Putative transcription regulator; structural genom	82.94
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	82.91
3bja_A	139	Transcriptional regulator, MARR family, putative;	82.89
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	82.88
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	82.87
2vpr_A	207	Tetracycline resistance repressor protein; transcr	82.87
3f0c_A	216	TETR-molecule A, transcriptional regulator; MCSG,P	82.83
2o7t_A	199	Transcriptional regulator; transcription regulator	82.83
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	82.82
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	82.79
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	82.73
2iu5_A	195	DHAS, YCEG, HTH-type dhaklm operon transcriptional	82.72
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	82.69
3mvp_A	217	TETR/ACRR transcriptional regulator; PSI, MCSG, st	82.65
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	82.62
1mkm_A	249	ICLR transcriptional regulator; structural genomic	82.6
1mkm_A	249	ICLR transcriptional regulator; structural genomic	82.6
3rd3_A	197	Probable transcriptional regulator; 2.40A {Pseudom	82.54
2ijl_A	135	AGR_C_4647P, molybdenum-binding transcriptional re	82.53
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	82.5
3bqy_A	209	Putative TETR family transcriptional regulator; st	82.48
3mnl_A	203	KSTR, transcriptional regulatory protein (probably	82.4
3cec_A	104	Putative antidote protein of plasmid maintenance;	82.39
3dpj_A	194	Transcription regulator, TETR family; APC88616, si	82.39
3bni_A	229	Putative TETR-family transcriptional regulator; st	82.39
3mlf_A	111	Transcriptional regulator; structural genomics, he	82.37
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	82.34
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	82.34
1t33_A	224	Putative transcriptional repressor (TETR/ACRR FAM;	82.32
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	82.31
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	82.31
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	82.27
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	82.18
2q24_A	194	Putative TETR family transcriptional regulator; st	82.15
3bru_A	222	Regulatory protein, TETR family; structural genomi	82.12
2gen_A	197	Probable transcriptional regulator; APC6095, TETR	82.11
1u8b_A	133	ADA polyprotein; protein-DNA complex, methylation,	82.11
2eby_A	113	Putative HTH-type transcriptional regulator YBAQ;	82.11
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	82.08
2fq4_A	192	Transcriptional regulator, TETR family; DNA-bindin	82.08
2q0o_A	236	Probable transcriptional activator protein TRAR; h	82.05
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	82.03
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	82.02
2ict_A	94	Antitoxin HIGA; helix-turn-helix, structural genom	82.01
3anp_C	204	Transcriptional repressor, TETR family; all alpha	82.0
2q0o_A	236	Probable transcriptional activator protein TRAR; h	81.85
3vk0_A	114	NHTF, transcriptional regulator; HTH motif, XRE tr	81.81
3kkc_A	177	TETR family transcriptional regulator; APC20805, s	81.68
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	81.67
3nnr_A	228	Transcriptional regulator, TETR family; TETR-famil	81.64
3frq_A	195	Repressor protein MPHR(A); macrolide antibiotic. r	81.57
3by6_A	126	Predicted transcriptional regulator; structural ge	81.54
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	81.52
3knw_A	212	Putative transcriptional regulator (TETR/ACRR FAM;	81.47
2xdn_A	210	HTH-type transcriptional regulator TTGR; transcrip	81.47
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	81.45
3trb_A	104	Virulence-associated protein I; mobIle and extrach	81.44
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	81.44
3qkx_A	188	Uncharacterized HTH-type transcriptional regulato;	81.42
2id3_A	225	Putative transcriptional regulator; structural gen	81.4
3rqi_A	184	Response regulator protein; structural genomics, s	81.38
2gxg_A	146	146AA long hypothetical transcriptional regulator;	81.36
3m8j_A	111	FOCB protein; all-alpha, helix-turn-helix, transcr	81.31
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	81.27
2ibd_A	204	Possible transcriptional regulator; probable trans	81.19
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	81.14
1j1v_A	94	Chromosomal replication initiator protein DNAA, 5'	81.14
3cwr_A	208	Transcriptional regulator, TETR family; YP_425770.	81.11
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	81.11
3sqn_A	485	Conserved domain protein; structural genomics, PSI	81.09
2zb9_A	214	Putative transcriptional regulator; transcription	81.09
3rh2_A	212	Hypothetical TETR-like transcriptional regulator;	81.07
3b81_A	203	Transcriptional regulator, ACRR family; NP_350189.	81.06
2f07_A	197	YVDT; helix-turn-helix, transcription; HET: BTB; 2	80.99
2pg4_A	95	Uncharacterized protein; structural genomics, join	80.98
3s5r_A	216	Transcriptional regulator TETR family; DNA/RNA-bin	80.95
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	80.84
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	80.8

>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=99.38  E-value=9.1e-12  Score=96.83  Aligned_cols=99  Identities=8%  Similarity=-0.069  Sum_probs=81.8

Q ss_pred             cCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCc
Q psy17316        113 YGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTT  192 (229)
Q Consensus       113 ~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s  192 (229)
                      +|+++.|+.+++..++.++.+|. |..+||+.+||+.+|+++|++.+.........++++++++++...+++.+.++..+
T Consensus         1 Mgr~~~~s~~~r~~i~~~~~~G~-s~~~ia~~lgis~~Tv~r~~~~~~~~g~~~~~gr~~~l~~~~~~~i~~~~~~~~~s   79 (141)
T 1u78_A            1 MPRGSALSDTERAQLDVMKLLNV-SLHEMSRKISRSRHCIRVYLKDPVSYGTSKRAPRRKALSVRDERNVIRAASNSCKT   79 (141)
T ss_dssp             -CCSCCCCHHHHHHHHHHHHTTC-CHHHHHHHHTCCHHHHHHHHHSGGGTTCCCCCCCCCSSCHHHHHHHHHHHHHCCCC
T ss_pred             CCCcccCCHHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHcccccCCcCCCCCCCcCCHHHHHHHHHHHhCCCCC
Confidence            36778899999999999997775 99999999999999999999865211111113556788999998898887778899


Q ss_pred             HHHHHHHhC--CChHHHHHHHH
Q psy17316        193 VQRASAEYG--IPSGTLYGRCK  212 (229)
Q Consensus       193 ~~eAA~~fg--Vp~~tv~~~vk  212 (229)
                      +.+++..||  ||++|||+|++
T Consensus        80 ~~~i~~~lg~~~s~~tV~r~l~  101 (141)
T 1u78_A           80 ARDIRNELQLSASKRTILNVIK  101 (141)
T ss_dssp             HHHHHHHTTCCSCHHHHHHHHH
T ss_pred             HHHHHHHHCCCccHHHHHHHHH
Confidence            999999999  89999999998

>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=99.37  E-value=6.5e-12  Score=100.82  Aligned_cols=114  Identities=14%  Similarity=0.097  Sum_probs=90.2

Q ss_pred             hhcchhhhhhhhccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccCCCCCC-CCCCC
Q psy17316        100 RAGSISANKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQPFNAS-PTAWK  175 (229)
Q Consensus       100 ~~G~ls~~~~~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~~~~~~-~r~~t  175 (229)
                      .+|..-.++.+...|..++|+.+++.+++.++.+|. |+.+||+.|||+.+||++|++++   |.....+..++ +++++
T Consensus         7 ~~~~~~~~~~g~~~~~~~~~s~e~r~~ii~l~~~G~-s~~~IA~~lgis~~TV~rwl~r~~~~G~~~~~~r~gr~~~~~~   85 (159)
T 2k27_A            7 RSGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQGV-RPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVAT   85 (159)
T ss_dssp             CCSCSSCCCCCCTTSSSCSSCHHHHHHHHHHHHHTC-CHHHHHHHHTCCSHHHHHHHCCSSTTSCCCCCCCCCCCCCCCC
T ss_pred             hhcchhhhhcCCcCCCCCCCCHHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHHHhcCCccCCCCCCCCCCCCC
Confidence            456666677777777788999999999999998775 99999999999999999999865   32111122222 56788


Q ss_pred             HHHHHHHHHHHHh-CCCcHHHHHHHh----------CCChHHHHHHHHhh
Q psy17316        176 PEDLEIALEGIRS-GQTTVQRASAEY----------GIPSGTLYGRCKLS  214 (229)
Q Consensus       176 ~e~r~eaV~~~~~-~~~s~~eAA~~f----------gVp~~tv~~~vk~~  214 (229)
                      +++...|++++.+ ..+++.+++..+          .||++|||+|++..
T Consensus        86 ~~~~~~I~~~~~~~~~~s~~~i~~~l~~~~~~~~~~~~S~sTV~r~L~~~  135 (159)
T 2k27_A           86 PKVVEKIGDYKRQNPTMFAWEIRDRLLAEGVCDNDTVPSVSSINRIIRTK  135 (159)
T ss_dssp             TTHHHHHHHHHHHCSSSCHHHHHHHHHHHTCSCTTTSCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCccchHHHHHHHHHHhcccccCCccCHHHHHHHHHHH
Confidence            8888889888875 469999999887          59999999999833

>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=99.31  E-value=3e-11  Score=93.85  Aligned_cols=126  Identities=9%  Similarity=-0.014  Sum_probs=79.4

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhh
Q psy17316         30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKA  109 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~  109 (229)
                      ...||.+++..++..+.+ |+|..+||+.+||+++||++|++++...+....                            
T Consensus         4 ~~~~s~~~r~~i~~~~~~-G~s~~~ia~~lgis~~Tv~r~~~~~~~~g~~~~----------------------------   54 (141)
T 1u78_A            4 GSALSDTERAQLDVMKLL-NVSLHEMSRKISRSRHCIRVYLKDPVSYGTSKR----------------------------   54 (141)
T ss_dssp             SCCCCHHHHHHHHHHHHT-TCCHHHHHHHHTCCHHHHHHHHHSGGGTTCCCC----------------------------
T ss_pred             cccCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHcccccCCcCC----------------------------
Confidence            368999999999988755 689999999999999999999998754432211                            


Q ss_pred             hhccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhC--CChHHHHHHHHHhCC-cccCCCCCCCCCCCHHHHHHHHHHH
Q psy17316        110 SKAYGPTKSWNEEILNVALDALRAGSISANKASKAYG--IPSSTLYKIARKEGI-RLAQPFNASPTAWKPEDLEIALEGI  186 (229)
Q Consensus       110 ~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~g--Ip~sTL~~~ik~~g~-k~~~~~~~~~r~~t~e~r~eaV~~~  186 (229)
                         .|++.+++++.....+....++..|..+|+..+|  |+.+|+++|+++.|+ ....+.  .....++..+..=+++|
T Consensus        55 ---~gr~~~l~~~~~~~i~~~~~~~~~s~~~i~~~lg~~~s~~tV~r~l~~~g~~~~~k~~--~~~~l~~~~~~~R~~~~  129 (141)
T 1u78_A           55 ---APRRKALSVRDERNVIRAASNSCKTARDIRNELQLSASKRTILNVIKRSGVIVRQKLR--PAPLLSADHKLKRLEFA  129 (141)
T ss_dssp             ---CCCCCSSCHHHHHHHHHHHHHCCCCHHHHHHHTTCCSCHHHHHHHHHHTC---------------------------
T ss_pred             ---CCCCCcCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCccHHHHHHHHHHCCCceeeecC--CCCCCCHHHHHHHHHHH
Confidence               2345667777766666665667789999999999  788999999998887 443321  12233445555556666


Q ss_pred             HhC
Q psy17316        187 RSG  189 (229)
Q Consensus       187 ~~~  189 (229)
                      ..+
T Consensus       130 ~~~  132 (141)
T 1u78_A          130 KNN  132 (141)
T ss_dssp             ---
T ss_pred             HHH
Confidence            553

>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=99.29  E-value=7.2e-11  Score=93.43  Aligned_cols=97  Identities=11%  Similarity=0.103  Sum_probs=78.9

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccCCCCCC-CCCCCHHHHHHHHHHHHhC-C
Q psy17316        116 TKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQPFNAS-PTAWKPEDLEIALEGIRSG-Q  190 (229)
Q Consensus       116 ~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~~~~~~-~r~~t~e~r~eaV~~~~~~-~  190 (229)
                      .+.|+.+++.++|.++.+| .|+.+||+.+||+.+|+++|++++   |.....+..++ ++.+++++...|++++.++ .
T Consensus        30 ~~~~s~e~r~~iv~~~~~G-~s~~~iA~~lgis~~TV~rw~~~~~~~G~~~~~~r~gr~~~~~~~~~~~~I~~~~~~~~~  108 (149)
T 1k78_A           30 GRPLPDVVRQRIVELAHQG-VRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPKVATPKVVEKIAEYKRQNPT  108 (149)
T ss_dssp             TSCCCHHHHHHHHHHHHTT-CCHHHHHHHHTCCHHHHHHHHHHHHHHSCCCCCCCCCCCCSSSCHHHHHHHHHHHHHCTT
T ss_pred             CCCCCHHHHHHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHHHHHHcCCCCccCCCCCCCCCCCHHHHHHHHHHHHhCcc
Confidence            4689999999999999876 599999999999999999999865   43222222232 5678898899999988764 6


Q ss_pred             CcHHHHHHHh--------C--CChHHHHHHHHh
Q psy17316        191 TTVQRASAEY--------G--IPSGTLYGRCKL  213 (229)
Q Consensus       191 ~s~~eAA~~f--------g--Vp~~tv~~~vk~  213 (229)
                      .++.+++..+        |  ||++||++|++.
T Consensus       109 ~s~~~i~~~l~~~~~~~~g~~~S~sTV~r~L~~  141 (149)
T 1k78_A          109 MFAWEIRDRLLAERVCDNDTVPSVSSINRIIRT  141 (149)
T ss_dssp             CCHHHHHHHHHHTTSSCTTTSCCHHHHHHHHHC
T ss_pred             hhHHHHHHHHHHhcccccCCCcCHHHHHHHHHH
Confidence            8999999988        6  899999999983

>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=99.22  E-value=9.3e-11  Score=88.98  Aligned_cols=96  Identities=14%  Similarity=0.061  Sum_probs=76.6

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccCCCCC-CCCCCCHHHHHHHHHHHHh-CC
Q psy17316        116 TKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQPFNA-SPTAWKPEDLEIALEGIRS-GQ  190 (229)
Q Consensus       116 ~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~~~~~-~~r~~t~e~r~eaV~~~~~-~~  190 (229)
                      .++|+.+++.+++.++.+|. |+.+||+.|||+.+|+++|++.+   |.....+..+ .++.++++++..|++++.+ ..
T Consensus        15 ~~~~s~~~r~~i~~~~~~g~-s~~~ia~~lgis~~Tv~~w~~~~~~~g~~~~~~~~g~~~~~l~~~~~~~i~~~~~~~~~   93 (128)
T 1pdn_C           15 GRPLPNNIRLKIVEMAADGI-RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYKRSSPG   93 (128)
T ss_dssp             TSCCCHHHHHHHHHHHHTTC-CHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTHHHHHHHTTTTCTT
T ss_pred             CCcCCHHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHHHhhCCcccccCCCCCCCcCCHHHHHHHHHHHHhCcc
Confidence            45899999999999998764 99999999999999999999865   5322222222 4567788888888888765 46


Q ss_pred             CcHHHHHHHh---C-------CChHHHHHHHH
Q psy17316        191 TTVQRASAEY---G-------IPSGTLYGRCK  212 (229)
Q Consensus       191 ~s~~eAA~~f---g-------Vp~~tv~~~vk  212 (229)
                      +++.+++..+   |       +|++|||+|++
T Consensus        94 ~s~~~i~~~l~~~g~~~~~~~~s~~tv~r~l~  125 (128)
T 1pdn_C           94 MFSWEIREKLIREGVCDRSTAPSVSAISRLVR  125 (128)
T ss_dssp             CCHHHHHHHHHHTSSSCSTTCCCHHHHHHHC-
T ss_pred             hHHHHHHHHHHHcCCccccCCcCHHHHHHHHH
Confidence            8999999999   7       59999999986

>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=99.17  E-value=3e-10  Score=89.87  Aligned_cols=118  Identities=13%  Similarity=0.084  Sum_probs=79.3

Q ss_pred             CCCCCCCcccccCCCC-CCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHH
Q psy17316         13 SSNYSDGETDKAGSLT-VTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEI   91 (229)
Q Consensus        13 ~~~~~~~~~~~~~~~~-~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~   91 (229)
                      +|---++.....|... ..+.||.+++..++..+.+ |+|+.+||+.+||+++||++|+++|...|.....+        
T Consensus        12 ~~~~~~~~~~~~gg~~~~~~~~s~e~r~~iv~~~~~-G~s~~~iA~~lgis~~TV~rw~~~~~~~G~~~~~~--------   82 (149)
T 1k78_A           12 TSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQ-GVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGV--------   82 (149)
T ss_dssp             -------CBCTTSCBCCTTSCCCHHHHHHHHHHHHT-TCCHHHHHHHHTCCHHHHHHHHHHHHHHSCCCCCC--------
T ss_pred             cccCCCCCccCCCceecCCCCCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHcCCCCccC--------
Confidence            3333334444444432 3578999999999999865 68999999999999999999999873222111100        


Q ss_pred             HHHHHHHHhhcchhhhhhhhccCC-CCCCCHHHHHHHHHHHHc-CCCCHHHHHHHh--------C--CChHHHHHHHHHh
Q psy17316         92 LNVALDALRAGSISANKASKAYGP-TKSWNEEILNVALDALRA-GSISANKASKAY--------G--IPSSTLYKIARKE  159 (229)
Q Consensus        92 ~~~a~~ll~~G~ls~~~~~~~~G~-~~kYs~e~k~~AV~~~~~-g~~S~~~~a~k~--------g--Ip~sTL~~~ik~~  159 (229)
                                          ..|+ +.++++++...+++.+.+ ...|..+++..+        |  ++.+||++|+++.
T Consensus        83 --------------------r~gr~~~~~~~~~~~~I~~~~~~~~~~s~~~i~~~l~~~~~~~~g~~~S~sTV~r~L~~~  142 (149)
T 1k78_A           83 --------------------IGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTK  142 (149)
T ss_dssp             --------------------CCCCCCSSSCHHHHHHHHHHHHHCTTCCHHHHHHHHHHTTSSCTTTSCCHHHHHHHHHCC
T ss_pred             --------------------CCCCCCCCCCHHHHHHHHHHHHhCcchhHHHHHHHHHHhcccccCCCcCHHHHHHHHHHH
Confidence                                0122 456676666666666654 357999999887        7  7889999999864

>2cob_A LCOR protein; MLR2, KIAA1795, helix-turn-helix, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.15

Probab=99.16  E-value=1.3e-10  Score=81.77  Aligned_cols=50  Identities=26%  Similarity=0.355  Sum_probs=46.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         27 LTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        27 ~~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      |..+++|++|++++||++|.+|.||+.+||+.||||++||.++++.....
T Consensus         8 ~~ryr~Yte~~L~~Ai~aVr~g~mS~~~Aak~yGVP~sTL~~RVk~~~~~   57 (70)
T 2cob_A            8 RGRYRQYNSEILEEAISVVMSGKMSVSKAQSIYGIPHSTLEYKVKERLGT   57 (70)
T ss_dssp             SSCSCCCCHHHHHHHHHHHHTTSSCHHHHHHHHTCCHHHHHHHHHHHTTT
T ss_pred             cccccccCHHHHHHHHHHHHcCCccHHHHHHHhCCChHHHHHHHHhhccc
Confidence            66789999999999999999998999999999999999999999976443

>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=99.11  E-value=2.2e-10  Score=86.84  Aligned_cols=99  Identities=13%  Similarity=0.079  Sum_probs=71.1

Q ss_pred             CCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh---CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchh
Q psy17316         29 VTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL---GIHTPKKEGPTKSWNEEILNVALDALRAGSIS  105 (229)
Q Consensus        29 ~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~---gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls  105 (229)
                      ..++|+.+++..++..+.+ |+|+.+||+.+||+++||++|+++|   |...+...                        
T Consensus        14 m~~~~s~~~r~~i~~~~~~-g~s~~~ia~~lgis~~Tv~~w~~~~~~~g~~~~~~~------------------------   68 (128)
T 1pdn_C           14 NGRPLPNNIRLKIVEMAAD-GIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI------------------------   68 (128)
T ss_dssp             TTSCCCHHHHHHHHHHHHT-TCCHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCC------------------------
T ss_pred             CCCcCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHhhCCcccccC------------------------
Confidence            3568999999999998864 6899999999999999999999997   33222111                        


Q ss_pred             hhhhhhccC-CCCCCCHHHHHHHHHHHHc-CCCCHHHHHHHh---CC-------ChHHHHHHHHHh
Q psy17316        106 ANKASKAYG-PTKSWNEEILNVALDALRA-GSISANKASKAY---GI-------PSSTLYKIARKE  159 (229)
Q Consensus       106 ~~~~~~~~G-~~~kYs~e~k~~AV~~~~~-g~~S~~~~a~k~---gI-------p~sTL~~~ik~~  159 (229)
                             .| .+.+++++.....++.+.+ ...|..+++..+   |+       +.+|+++|+++.
T Consensus        69 -------~g~~~~~l~~~~~~~i~~~~~~~~~~s~~~i~~~l~~~g~~~~~~~~s~~tv~r~l~~~  127 (128)
T 1pdn_C           69 -------GGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISRLVRGR  127 (128)
T ss_dssp             -------SCCCCCSSCSTHHHHHHHTTTTCTTCCHHHHHHHHHHTSSSCSTTCCCHHHHHHHC---
T ss_pred             -------CCCCCCcCCHHHHHHHHHHHHhCcchHHHHHHHHHHHcCCccccCCcCHHHHHHHHHhc
Confidence                   11 2445555555555555443 457999999988   75       778999998764

>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=99.04  E-value=2.3e-09  Score=85.75  Aligned_cols=101  Identities=11%  Similarity=0.026  Sum_probs=76.1

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhh
Q psy17316         30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKA  109 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~  109 (229)
                      .++||.+++..++..+.+ |+|+.+||+.+||+++||++|+++|...+.....+                          
T Consensus        23 ~~~~s~e~r~~ii~l~~~-G~s~~~IA~~lgis~~TV~rwl~r~~~~G~~~~~~--------------------------   75 (159)
T 2k27_A           23 GRPLPEVVRQRIVDLAHQ-GVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGV--------------------------   75 (159)
T ss_dssp             SCSSCHHHHHHHHHHHHH-TCCHHHHHHHHTCCSHHHHHHHCCSSTTSCCCCCC--------------------------
T ss_pred             CCCCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHhcCCccCCC--------------------------
Confidence            468999999999998865 67999999999999999999999875443211110                          


Q ss_pred             hhccCC-CCCCCHHHHHHHHHHHHc-CCCCHHHHHHHh----------CCChHHHHHHHHHh
Q psy17316        110 SKAYGP-TKSWNEEILNVALDALRA-GSISANKASKAY----------GIPSSTLYKIARKE  159 (229)
Q Consensus       110 ~~~~G~-~~kYs~e~k~~AV~~~~~-g~~S~~~~a~k~----------gIp~sTL~~~ik~~  159 (229)
                        ..|. +.++++++...+++.+.+ ...|..+++..+          .++.+|+++|++++
T Consensus        76 --r~gr~~~~~~~~~~~~I~~~~~~~~~~s~~~i~~~l~~~~~~~~~~~~S~sTV~r~L~~~  135 (159)
T 2k27_A           76 --IGGSKPKVATPKVVEKIGDYKRQNPTMFAWEIRDRLLAEGVCDNDTVPSVSSINRIIRTK  135 (159)
T ss_dssp             --CCCCCCCCCCTTHHHHHHHHHHHCSSSCHHHHHHHHHHHTCSCTTTSCCHHHHHHHHHHH
T ss_pred             --CCCCCCCCCCHHHHHHHHHHHHHCccchHHHHHHHHHHhcccccCCccCHHHHHHHHHHH
Confidence              0122 456676666666666654 457999998877          47889999999876

>2cob_A LCOR protein; MLR2, KIAA1795, helix-turn-helix, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.15

Probab=98.90  E-value=4.4e-09  Score=73.99  Aligned_cols=53  Identities=34%  Similarity=0.474  Sum_probs=46.9

Q ss_pred             cCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccC
Q psy17316        113 YGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQ  165 (229)
Q Consensus       113 ~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~  165 (229)
                      .|..+.|+++++++||++|.+|.+|+..+|.+||||++||+++++........
T Consensus         8 ~~ryr~Yte~~L~~Ai~aVr~g~mS~~~Aak~yGVP~sTL~~RVk~~~~~~~~   60 (70)
T 2cob_A            8 RGRYRQYNSEILEEAISVVMSGKMSVSKAQSIYGIPHSTLEYKVKERLGTLKN   60 (70)
T ss_dssp             SSCSCCCCHHHHHHHHHHHHTTSSCHHHHHHHHTCCHHHHHHHHHHHTTTTSS
T ss_pred             cccccccCHHHHHHHHHHHHcCCccHHHHHHHhCCChHHHHHHHHhhcccccC
Confidence            45678999999999999999998999999999999999999999976544444

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

Probab=98.70  E-value=2.4e-08  Score=73.65  Aligned_cols=52  Identities=23%  Similarity=0.217  Sum_probs=46.2

Q ss_pred             CCCCCCHHHHHHHHHHHHcC-CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCC
Q psy17316         29 VTKTWTHEDMDAALEALRAG-QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKK   80 (229)
Q Consensus        29 ~~~kyt~e~~~~AI~~~~~g-~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~   80 (229)
                      .+++||.+.+..+|+.+.++ +.|+.+||+.|||+++||++|+++|...+...
T Consensus         2 ~r~~ys~e~k~~~v~~~~~~~g~s~~~ia~~~gIs~~tl~rW~~~~~~~g~~~   54 (97)
T 2jn6_A            2 PTKTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKYGSNHNVQ   54 (97)
T ss_dssp             CCCCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHHCCCSTTC
T ss_pred             CCCCCCHHHHHHHHHHHHHcCCChHHHHHHHHCcCHHHHHHHHHHHhhcCccc
Confidence            35789999999999999877 89999999999999999999999997766543

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

Probab=98.61  E-value=4.3e-08  Score=66.31  Aligned_cols=45  Identities=16%  Similarity=0.255  Sum_probs=38.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCCC----HHHHHHHhCCChHHHHHHHHHh
Q psy17316        114 GPTKSWNEEILNVALDALRAGSIS----ANKASKAYGIPSSTLYKIARKE  159 (229)
Q Consensus       114 G~~~kYs~e~k~~AV~~~~~g~~S----~~~~a~k~gIp~sTL~~~ik~~  159 (229)
                      |+.++||+|||++|++.+..| .|    +.++|++|||+.+||++|++.+
T Consensus         1 g~r~~ys~efK~~~~~~~~~g-~s~~~~~~~vA~~~gIs~~tl~~W~~~~   49 (59)
T 2glo_A            1 GSRRIFTPHFKLQVLESYRND-NDCKGNQRATARKYNIHRRQIQKWLQCE   49 (59)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHC-TTTTTCHHHHHHHTTSCHHHHHHHHTTH
T ss_pred             CCCCcCCHHHHHHHHHHHHcC-CCcchHHHHHHHHHCcCHHHHHHHHHHH
Confidence            567899999999996555444 58    9999999999999999999754

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

Probab=98.52  E-value=9.7e-08  Score=64.52  Aligned_cols=43  Identities=9%  Similarity=0.000  Sum_probs=37.7

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCC----HHHHHHHcCCChhhHHHHHHHh
Q psy17316         30 TKTWTHEDMDAALEALRAGQMS----LTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~~S----~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +++||.|.+++|+ ++.+++.|    +.++|++|||+++||++|++++
T Consensus         3 r~~ys~efK~~~~-~~~~~g~s~~~~~~~vA~~~gIs~~tl~~W~~~~   49 (59)
T 2glo_A            3 RRIFTPHFKLQVL-ESYRNDNDCKGNQRATARKYNIHRRQIQKWLQCE   49 (59)
T ss_dssp             CCCCCHHHHHHHH-HHHHHCTTTTTCHHHHHHHTTSCHHHHHHHHTTH
T ss_pred             CCcCCHHHHHHHH-HHHHcCCCcchHHHHHHHHHCcCHHHHHHHHHHH
Confidence            5789999999995 55566779    9999999999999999999865

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=98.51  E-value=2.9e-07  Score=66.94  Aligned_cols=46  Identities=17%  Similarity=0.200  Sum_probs=41.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         28 TVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        28 ~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      ..+++||.+.+..|++.+. ++.|+.+||++|||+++||++|++++.
T Consensus        18 ~~~~~ys~e~k~~~v~~~~-~g~s~~~iA~~~gIs~sTl~rW~k~~~   63 (87)
T 2elh_A           18 RPLRSLTPRDKIHAIQRIH-DGESKASVARDIGVPESTLRGWCKNED   63 (87)
T ss_dssp             SCCSSCCHHHHHHHHHHHH-HTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4567999999999999885 468999999999999999999999864

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

Probab=98.49  E-value=2e-07  Score=68.62  Aligned_cols=44  Identities=25%  Similarity=0.273  Sum_probs=40.4

Q ss_pred             CCCCHHHHHHHHHHHHcC-CCCHHHHHHHhCCChHHHHHHHHHhC
Q psy17316        117 KSWNEEILNVALDALRAG-SISANKASKAYGIPSSTLYKIARKEG  160 (229)
Q Consensus       117 ~kYs~e~k~~AV~~~~~g-~~S~~~~a~k~gIp~sTL~~~ik~~g  160 (229)
                      ++||.+++.+||..|.++ +.|+.+||+.|||+.+|||+|++.+.
T Consensus         4 ~~ys~e~k~~~v~~~~~~~g~s~~~ia~~~gIs~~tl~rW~~~~~   48 (97)
T 2jn6_A            4 KTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKYG   48 (97)
T ss_dssp             CCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHcCCChHHHHHHHHCcCHHHHHHHHHHHh
Confidence            579999999999999876 67999999999999999999999874

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

Probab=98.48  E-value=4.9e-07  Score=67.50  Aligned_cols=57  Identities=16%  Similarity=0.173  Sum_probs=51.4

Q ss_pred             CCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCC
Q psy17316         27 LTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGP   83 (229)
Q Consensus        27 ~~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~   83 (229)
                      ..-+++|+.++++.+|.++..|++|+.++|++|||+.++|++|.+.|...|..++..
T Consensus        27 ~~~~rrWs~~~Kl~VV~~~~~g~~s~~e~arry~Is~s~i~~W~r~~~~~G~~~L~~   83 (95)
T 2jrt_A           27 PLDTRRWVASRKAAVVKAVIHGLITEREALDRYSLSEEEFALWRSAVAAHGEKALKV   83 (95)
T ss_dssp             CSSCCCCCHHHHHHHHHHHHTTSSCHHHHHHHTTCCHHHHHHHHHHTTTCCTTSCCT
T ss_pred             hHhhhccCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhHHHHhh
Confidence            445788999999999999999999999999999999999999999997777777654

>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri}

Probab=98.47  E-value=2e-07  Score=69.85  Aligned_cols=45  Identities=20%  Similarity=0.201  Sum_probs=40.6

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCC-------CcHHHHHHHhCCChHHHHHHHHh
Q psy17316        169 ASPTAWKPEDLEIALEGIRSGQ-------TTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       169 ~~~r~~t~e~r~eaV~~~~~~~-------~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      ..+++||+|++.+||+.+.+++       .++.++|.+|||+.+|||+|++.
T Consensus         2 ~~~~~ys~e~K~~~v~~~~~~~~~~~s~g~s~~~va~~~gIs~~tl~~W~~~   53 (108)
T 2rn7_A            2 TKNTRFSPEVRQRAVRMVLESQGEYDSQWATICSIAPKIGCTPETLRVWVRQ   53 (108)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHhcccccccccccHHHHHHHHCcCHHHHHHHHHH
Confidence            3467899999999999998765       89999999999999999999993

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=98.35  E-value=7.8e-07  Score=64.63  Aligned_cols=43  Identities=23%  Similarity=0.302  Sum_probs=39.0

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh
Q psy17316        116 TKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE  159 (229)
Q Consensus       116 ~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~  159 (229)
                      +++|+.+++.+||+.+.+| .|+.+||++|||+.+|||+|++++
T Consensus        20 ~~~ys~e~k~~~v~~~~~g-~s~~~iA~~~gIs~sTl~rW~k~~   62 (87)
T 2elh_A           20 LRSLTPRDKIHAIQRIHDG-ESKASVARDIGVPESTLRGWCKNE   62 (87)
T ss_dssp             CSSCCHHHHHHHHHHHHHT-CCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHCC-CCHHHHHHHHCcCHHHHHHHHHHH
Confidence            5689999999999999665 599999999999999999999865

>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri}

Probab=98.30  E-value=3.3e-07  Score=68.63  Aligned_cols=48  Identities=15%  Similarity=0.135  Sum_probs=42.7

Q ss_pred             CCCCCHHHHHHHHHHHHcCC-------CCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         30 TKTWTHEDMDAALEALRAGQ-------MSLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~-------~S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      +++||.|.+..||+.+.+++       .|+.+||++|||+.+||++|++++...+
T Consensus         4 ~~~ys~e~K~~~v~~~~~~~~~~~s~g~s~~~va~~~gIs~~tl~~W~~~~~~~~   58 (108)
T 2rn7_A            4 NTRFSPEVRQRAVRMVLESQGEYDSQWATICSIAPKIGCTPETLRVWVRQHERDT   58 (108)
T ss_dssp             SCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTSCHHHHHHHHHHHHTTS
T ss_pred             CCCCCHHHHHHHHHHHHhcccccccccccHHHHHHHHCcCHHHHHHHHHHHHhcc
Confidence            56899999999999997765       8999999999999999999999985543

>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=98.28  E-value=2.7e-06  Score=53.57  Aligned_cols=44  Identities=7%  Similarity=-0.154  Sum_probs=38.5

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        170 SPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       170 ~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      ++..++++++..|+..+.+| +++.++|..||||.+||++|++..
T Consensus         2 R~~~l~~~~~~~i~~~~~~g-~s~~~IA~~lgis~~Tv~~~~~~~   45 (51)
T 1tc3_C            2 RGSALSDTERAQLDVMKLLN-VSLHEMSRKISRSRHCIRVYLKDP   45 (51)
T ss_dssp             CSCCCCHHHHHHHHHHHHTT-CCHHHHHHHHTCCHHHHHHHHHCS
T ss_pred             CCCCCCHHHHHHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHhhH
Confidence            45678899999999987665 999999999999999999999843

>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=98.26  E-value=2.1e-06  Score=54.06  Aligned_cols=45  Identities=4%  Similarity=-0.093  Sum_probs=40.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh
Q psy17316        114 GPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE  159 (229)
Q Consensus       114 G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~  159 (229)
                      |++..++++++..++.++.+| +|+.+||+.+||+.+|+++|++.+
T Consensus         1 GR~~~l~~~~~~~i~~~~~~g-~s~~~IA~~lgis~~Tv~~~~~~~   45 (51)
T 1tc3_C            1 PRGSALSDTERAQLDVMKLLN-VSLHEMSRKISRSRHCIRVYLKDP   45 (51)
T ss_dssp             CCSCCCCHHHHHHHHHHHHTT-CCHHHHHHHHTCCHHHHHHHHHCS
T ss_pred             CCCCCCCHHHHHHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHhhH
Confidence            567889999999999988776 599999999999999999999854

>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=98.24  E-value=7e-07  Score=57.18  Aligned_cols=47  Identities=23%  Similarity=0.313  Sum_probs=40.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCC
Q psy17316        114 GPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGI  161 (229)
Q Consensus       114 G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~  161 (229)
                      |++++++++++..++.++.+| .|+.+||+.+||+.+|+++|++..+.
T Consensus         1 GRp~~~~~~~~~~i~~l~~~g-~s~~~ia~~lgvs~~Tv~r~l~~~~~   47 (52)
T 1jko_C            1 GRPRAINKHEQEQISRLLEKG-HPRQQLAIIFGIGVSTLYRYFPASSI   47 (52)
T ss_dssp             CCCCSSCTTHHHHHHHHHHTT-CCHHHHHHTTSCCHHHHHHHSCTTC-
T ss_pred             CCCCCCCHHHHHHHHHHHHcC-CCHHHHHHHHCCCHHHHHHHHHHccc
Confidence            567788888888888888777 69999999999999999999987654

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

Probab=98.21  E-value=3.5e-06  Score=62.81  Aligned_cols=45  Identities=11%  Similarity=0.159  Sum_probs=42.1

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        170 SPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       170 ~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      +.+.|+.+++.+||+.+..|++++.+||.+|+|+.++++.|.+..
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            457899999999999999999999999999999999999999944

>3hot_A Transposable element mariner, complete CDS; protein-DNA complex, synaptic complex, transposase, inverted DNA, DNA binding protein-DNA complex; HET: 5IU; 3.25A {Drosophila mauritiana} PDB: 3hos_A*

Probab=98.20  E-value=3.4e-05  Score=67.85  Aligned_cols=124  Identities=10%  Similarity=0.051  Sum_probs=79.6

Q ss_pred             CHHHH-HHHHHHHHcCCCCHHHHHHHcC-------CChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchh
Q psy17316         34 THEDM-DAALEALRAGQMSLTKASVSYG-------IPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSIS  105 (229)
Q Consensus        34 t~e~~-~~AI~~~~~g~~S~~~aA~~~g-------Ip~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls  105 (229)
                      +..++ ..+|..+.+ |.|..+||+.++       |+++|+++|++++.- |...+..                      
T Consensus         7 ~~~~~R~~i~~~~~~-G~s~~~~~~~l~~~~g~~~vs~~tv~~w~~r~~~-g~~~l~~----------------------   62 (345)
T 3hot_A            7 NKEQTRTVLIFCFHL-KKTAAESHRMLVEAFGEQVPTVKTCERWFQRFKS-GDFDVDD----------------------   62 (345)
T ss_dssp             CHHHHHHHHHHHHHT-TCCHHHHHHHHHHHTCSCSCCHHHHHHHHHHHTT-CCCCCSC----------------------
T ss_pred             cHHHHHHHHHHHHHc-CCCHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhC-CCccccC----------------------
Confidence            34444 445555555 779999999976       999999999999853 3222210                      


Q ss_pred             hhhhhhccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHH
Q psy17316        106 ANKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEG  185 (229)
Q Consensus       106 ~~~~~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~  185 (229)
                          ....|++.+.+.+.+.+.|+  .+...|+++++..++|+.+|+++++++.|+....+. ..+...+++.+..-++.
T Consensus        63 ----~~r~grp~~~~~~~i~~~v~--~~~~~t~~~ia~~l~vs~~tV~r~L~~~g~~~k~~~-~~~~~l~~~~~~~r~~~  135 (345)
T 3hot_A           63 ----KEHGKPPKRYEDAELQALLD--EDDAQTQKQLAEQLEVSQQAVSNRLREMGKIQKVGR-WVPHELNERQMERRKNT  135 (345)
T ss_dssp             ----CCCCCCCCSSCHHHHHHHHH--HCSCCCHHHHHHHTTSCHHHHHHHHHHTTCEEEECC-EESSCCCHHHHHHHHHH
T ss_pred             ----CCCCCCCCcccHHHHHHHHH--hCccchHHHHHHHHCCCHHHHHHHHHHhCCeeeccc-cccccCChhhhhhhHHH
Confidence                01124566666655555443  255679999999999999999999999887643211 11223455555544554


Q ss_pred             HHh
Q psy17316        186 IRS  188 (229)
Q Consensus       186 ~~~  188 (229)
                      |..
T Consensus       136 ~~~  138 (345)
T 3hot_A          136 CEI  138 (345)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

>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=98.05  E-value=4.2e-06  Score=53.41  Aligned_cols=43  Identities=23%  Similarity=0.273  Sum_probs=37.1

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316        170 SPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       170 ~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      +++.++++++..|++++.+| +++.++|..||||.+|||+|++.
T Consensus         2 Rp~~~~~~~~~~i~~l~~~g-~s~~~ia~~lgvs~~Tv~r~l~~   44 (52)
T 1jko_C            2 RPRAINKHEQEQISRLLEKG-HPRQQLAIIFGIGVSTLYRYFPA   44 (52)
T ss_dssp             CCCSSCTTHHHHHHHHHHTT-CCHHHHHHTTSCCHHHHHHHSCT
T ss_pred             CCCCCCHHHHHHHHHHHHcC-CCHHHHHHHHCCCHHHHHHHHHH
Confidence            45677888888888887666 99999999999999999999973

>3hot_A Transposable element mariner, complete CDS; protein-DNA complex, synaptic complex, transposase, inverted DNA, DNA binding protein-DNA complex; HET: 5IU; 3.25A {Drosophila mauritiana} PDB: 3hos_A*

Probab=98.05  E-value=4.3e-05  Score=67.24  Aligned_cols=91  Identities=11%  Similarity=0.134  Sum_probs=68.6

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHhC-------CChHHHHHHHHHh--CCcccC--CCCCCCCCCCHHHHHHHHHHHH
Q psy17316        119 WNEEILNVALDALRAGSISANKASKAYG-------IPSSTLYKIARKE--GIRLAQ--PFNASPTAWKPEDLEIALEGIR  187 (229)
Q Consensus       119 Ys~e~k~~AV~~~~~g~~S~~~~a~k~g-------Ip~sTL~~~ik~~--g~k~~~--~~~~~~r~~t~e~r~eaV~~~~  187 (229)
                      ...+.+..++.++.+|. |..++++.++       |+.+|+++|++++  |.....  +..+++++.+.++..++|+  .
T Consensus         7 ~~~~~R~~i~~~~~~G~-s~~~~~~~l~~~~g~~~vs~~tv~~w~~r~~~g~~~l~~~~r~grp~~~~~~~i~~~v~--~   83 (345)
T 3hot_A            7 NKEQTRTVLIFCFHLKK-TAAESHRMLVEAFGEQVPTVKTCERWFQRFKSGDFDVDDKEHGKPPKRYEDAELQALLD--E   83 (345)
T ss_dssp             CHHHHHHHHHHHHHTTC-CHHHHHHHHHHHTCSCSCCHHHHHHHHHHHTTCCCCCSCCCCCCCCCSSCHHHHHHHHH--H
T ss_pred             cHHHHHHHHHHHHHcCC-CHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhCCCccccCCCCCCCCCcccHHHHHHHHH--h
Confidence            34556677777788876 9999988855       9999999999875  322222  3346677777766655553  3


Q ss_pred             hCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        188 SGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       188 ~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +...++.++|..++||.+||++.++
T Consensus        84 ~~~~t~~~ia~~l~vs~~tV~r~L~  108 (345)
T 3hot_A           84 DDAQTQKQLAEQLEVSQQAVSNRLR  108 (345)
T ss_dssp             CSCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             CccchHHHHHHHHCCCHHHHHHHHH
Confidence            5668999999999999999999998

>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=98.05  E-value=7e-06  Score=63.02  Aligned_cols=45  Identities=11%  Similarity=0.188  Sum_probs=39.5

Q ss_pred             CCCCCCHHHHHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         29 VTKTWTHEDMDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        29 ~~~kyt~e~~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .+..||.|++.++|+.+ .+|..+..++|+.|||+++||++|++..
T Consensus         4 ~r~~~t~e~K~~iv~~~~~~g~~~~~~~A~~~gvs~stl~~~~~~~   49 (131)
T 1hlv_A            4 KRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNK   49 (131)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTH
T ss_pred             cceeCCHHHHHHHHHHHHHCCCCcHHHHHHHhCCCHHHHHHHHhch
Confidence            57889999999999998 5566666799999999999999999964

>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=97.95  E-value=2.9e-05  Score=58.42  Aligned_cols=57  Identities=18%  Similarity=0.257  Sum_probs=51.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCC
Q psy17316         27 LTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGP   83 (229)
Q Consensus        27 ~~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~   83 (229)
                      ..-.++|+...++++|.++..|.+|+.+||++|||+.++|.+|.+.|.-.|..+++.
T Consensus        28 ~~~~rRWva~rK~~VV~~v~~g~lS~~EAa~ry~Is~~ei~~W~r~y~~~G~~aLr~   84 (101)
T 2oa4_A           28 PANTRRWVASRKIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVSALAEHGKDALKV   84 (101)
T ss_dssp             CSCCSCCCHHHHHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHHHHHCCCSSSSCC
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhHHHhcc
Confidence            345689999999999999999999999999999999999999999997777777754

>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=97.90  E-value=2.4e-05  Score=60.01  Aligned_cols=42  Identities=12%  Similarity=0.135  Sum_probs=36.7

Q ss_pred             CCCCCHHHHHHHHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        171 PTAWKPEDLEIALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       171 ~r~~t~e~r~eaV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+.||.|++.+||+++. .|..+..++|..||||.+||++|++
T Consensus         5 r~~~t~e~K~~iv~~~~~~g~~~~~~~A~~~gvs~stl~~~~~   47 (131)
T 1hlv_A            5 RRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILK   47 (131)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHH
T ss_pred             ceeCCHHHHHHHHHHHHHCCCCcHHHHHHHhCCCHHHHHHHHh
Confidence            56799999999999994 5545556999999999999999998

>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=97.78  E-value=4.5e-05  Score=57.38  Aligned_cols=55  Identities=13%  Similarity=0.203  Sum_probs=45.9

Q ss_pred             HHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhcC
Q psy17316        143 KAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRS  216 (229)
Q Consensus       143 ~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~~  216 (229)
                      .+||||.+++++|+..                   .+.+||++++.|.+|+.|||++|+||.+++.+|.+.-+.
T Consensus        22 ~~~dlp~~~~rRWva~-------------------rK~~VV~~v~~g~lS~~EAa~ry~Is~~ei~~W~r~y~~   76 (101)
T 2oa4_A           22 TRADLPPANTRRWVAS-------------------RKIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVSALAE   76 (101)
T ss_dssp             ETTSSCCSCCSCCCHH-------------------HHHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHHHHHC
T ss_pred             hhcCCChHHHHHHHHH-------------------HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            6677777666666553                   499999999999999999999999999999999994433

>2ao9_A Phage protein; structural genomics, nine-fold NCS., PSI, protein structure initiative, midwest center for structural genomics, MCSG, U function; 1.90A {Bacillus cereus} SCOP: a.4.1.17

Probab=97.66  E-value=4e-05  Score=61.93  Aligned_cols=43  Identities=21%  Similarity=0.343  Sum_probs=38.5

Q ss_pred             CCCCCHHHHHHHHHHHHcC--------CCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         30 TKTWTHEDMDAALEALRAG--------QMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g--------~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +++||.+.+.+|+..+..+        ++|+.+||+++||+++|||+|.+.
T Consensus        21 ~r~yt~EfK~aAv~l~~~~~~~p~~~~~lTv~eIA~~LGIS~~TLyrW~k~   71 (155)
T 2ao9_A           21 KQKLTAKQIQAAYLLVENELMESNNEEKRTQDEMANELGINRTTLWEWRTK   71 (155)
T ss_dssp             HTTSCHHHHHHHHHHHHHHHCC---CCCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hhhcCHHHHHHHHHHHHccccccccccCCCHHHHHHHhCCCHHHHHHHHHc
Confidence            6789999999998766554        789999999999999999999995

>4dyq_A Gene 1 protein; GP1, octamer, DNA-binding, viral protein; 1.50A {Shigella phage SF6} PDB: 4dyc_A 4dyr_A 3hef_A 4dzj_A 4dzp_A

Probab=97.66  E-value=3.2e-05  Score=61.02  Aligned_cols=48  Identities=25%  Similarity=0.349  Sum_probs=39.5

Q ss_pred             hccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCC-hHHHHHHHHHh
Q psy17316        111 KAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIP-SSTLYKIARKE  159 (229)
Q Consensus       111 ~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp-~sTL~~~ik~~  159 (229)
                      ++.|++++|+++...+..+.+..|. |+.+||+.+||| .+|||+|++++
T Consensus         5 ~k~GRPtk~t~e~~e~I~~~i~~G~-sl~~i~~~~~~ps~~T~~~W~~~~   53 (140)
T 4dyq_A            5 PKAGRPSDYMPEVADDICSLLSSGE-SLLKVCKRPGMPDKSTVFRWLAKH   53 (140)
T ss_dssp             -----CCSCCTTHHHHHHHHHHTTC-CHHHHHTSTTCCCHHHHHHHHHHC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHCCC-cHHHHHhcCCCCCHHHHHHHHHcC
Confidence            3468999999999999999999886 999999999995 79999999853

>2ao9_A Phage protein; structural genomics, nine-fold NCS., PSI, protein structure initiative, midwest center for structural genomics, MCSG, U function; 1.90A {Bacillus cereus} SCOP: a.4.1.17

Probab=97.47  E-value=0.00014  Score=58.73  Aligned_cols=42  Identities=17%  Similarity=0.201  Sum_probs=38.2

Q ss_pred             CCCCCHHHHHHHHHHHHhC--------CCcHHHHHHHhCCChHHHHHHHH
Q psy17316        171 PTAWKPEDLEIALEGIRSG--------QTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       171 ~r~~t~e~r~eaV~~~~~~--------~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+.|++|++.+||..+.++        ++|+.++|...|||++|+|+|.+
T Consensus        21 ~r~yt~EfK~aAv~l~~~~~~~p~~~~~lTv~eIA~~LGIS~~TLyrW~k   70 (155)
T 2ao9_A           21 KQKLTAKQIQAAYLLVENELMESNNEEKRTQDEMANELGINRTTLWEWRT   70 (155)
T ss_dssp             HTTSCHHHHHHHHHHHHHHHCC---CCCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             hhhcCHHHHHHHHHHHHccccccccccCCCHHHHHHHhCCCHHHHHHHHH
Confidence            5789999999999887665        68999999999999999999998

>3oou_A LIN2118 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; HET: BTB; 1.57A {Listeria innocua}

Probab=97.36  E-value=0.0042  Score=45.80  Aligned_cols=89  Identities=19%  Similarity=0.162  Sum_probs=65.3

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGP  115 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~  115 (229)
                      .+...|+.-....+++.++|+.+||++++|.+..++. |...           .+..+                      
T Consensus         9 ~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~-----------~~~~~----------------------   55 (108)
T 3oou_A            9 NVLSYITEHFSEGMSLKTLGNDFHINAVYLGQLFQKEMGEHF-----------TDYLN----------------------   55 (108)
T ss_dssp             HHHHHHHHHTTSCCCHHHHHHHHTSCHHHHHHHHHHHHSSCH-----------HHHHH----------------------
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH-----------HHHHH----------------------
Confidence            3445555555668999999999999999999999985 6531           01110                      


Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        116 TKSWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       116 ~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                           .--+..|.+++.++.+|+.+||...|-+..+ +.+..++. |+.+
T Consensus        56 -----~~Rl~~A~~lL~~~~~si~~IA~~~Gf~~~s~F~r~Fk~~~G~tP  100 (108)
T 3oou_A           56 -----RYRVNYAKEELLQTKDNLTIIAGKSGYTDMAYFYRQFKKHTGETP  100 (108)
T ss_dssp             -----HHHHHHHHHHHHHCCCCHHHHHHHTTCCCHHHHHHHHHHHHSSCH
T ss_pred             -----HHHHHHHHHHHHcCCCCHHHHHHHcCCCChHHHHHHHHHHhCcCH
Confidence                 1124677788888888999999999997755 88888765 7544

>3uj3_X DNA-invertase; helix-turn-helix, site-specific recombinase, recombination; 3.51A {Enterobacteria phage MU} PDB: 3plo_X

Probab=97.36  E-value=2.5e-05  Score=64.15  Aligned_cols=60  Identities=22%  Similarity=0.219  Sum_probs=0.8

Q ss_pred             hhcchhhhhhhhccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhC
Q psy17316        100 RAGSISANKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEG  160 (229)
Q Consensus       100 ~~G~ls~~~~~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g  160 (229)
                      .+|...+++.|++.|+++.|+++....+.+++.+|. |+.+||+.+||+++|+|+|++..+
T Consensus       124 ~~g~~~~~~~G~~~Gr~~~~~~~~~~~i~~l~~~G~-s~~~Ia~~l~vs~~Tvyr~l~~~~  183 (193)
T 3uj3_X          124 MAGLAAARNKGRIGGRPPKLTKAEWEQAGRLLAQGI-PRKQVALIYDVALSTLYKKHPAKR  183 (193)
T ss_dssp             TC-----------------------------------------------------------
T ss_pred             HHHHHHHHHhcccCCCCCCCCHHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHhh
Confidence            346667777888889999999999889999998874 999999999999999999998653

>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}

Probab=97.35  E-value=0.0049  Score=44.93  Aligned_cols=89  Identities=16%  Similarity=0.113  Sum_probs=65.3

Q ss_pred             HHHHHHHHHHc-CCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccC
Q psy17316         37 DMDAALEALRA-GQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYG  114 (229)
Q Consensus        37 ~~~~AI~~~~~-g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G  114 (229)
                      .+...|+.-.. +.+++.++|+.+||++++|.+..++. |...           .+..+                     
T Consensus         6 ~i~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~g~s~-----------~~~~~---------------------   53 (103)
T 3lsg_A            6 LIQNIIEESYTDSQFTLSVLSEKLDLSSGYLSIMFKKNFGIPF-----------QDYLL---------------------   53 (103)
T ss_dssp             HHHHHHHHHTTCTTCCHHHHHHHTTCCHHHHHHHHHHHHSSCH-----------HHHHH---------------------
T ss_pred             HHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH-----------HHHHH---------------------
Confidence            44555655444 48999999999999999999999986 6531           01110                     


Q ss_pred             CCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        115 PTKSWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       115 ~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                            .--+..|.+++.++..|+.+||...|-+... +.+..++. |..+
T Consensus        54 ------~~Rl~~A~~lL~~~~~si~~iA~~~Gf~~~s~F~r~Fk~~~G~tP   98 (103)
T 3lsg_A           54 ------QKRMEKAKLLLLTTELKNYEIAEQVGFEDVNYFITKFKKYYQITP   98 (103)
T ss_dssp             ------HHHHHHHHHHHHHCCCCHHHHHHHTTCSCHHHHHHHHHHHHSSCH
T ss_pred             ------HHHHHHHHHHHHCCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence                  1124677888888888999999999998755 88888765 7543

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

Probab=97.23  E-value=0.00068  Score=46.02  Aligned_cols=38  Identities=24%  Similarity=0.352  Sum_probs=30.7

Q ss_pred             HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      .+.+++...+..+.++|+.+||+++||+++++++|+..
T Consensus        23 ~i~~aL~~~~gn~~~aA~~LGisr~tL~rklkk~gi~~   60 (63)
T 3e7l_A           23 FIEEKLREYDYDLKRTAEEIGIDLSNLYRKIKSLNIRV   60 (63)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHTCCHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHhCCCC
Confidence            33445545556899999999999999999999999863

>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=97.20  E-value=0.0086  Score=43.99  Aligned_cols=89  Identities=18%  Similarity=0.231  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGP  115 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~  115 (229)
                      .+...|+.-....+++.++|+.+||++++|.+..++. |...            ...   +                   
T Consensus         6 ~~~~~i~~~~~~~~~~~~lA~~~~~s~~~l~r~fk~~~G~s~------------~~~---~-------------------   51 (108)
T 3mn2_A            6 QVEEYIEANWMRPITIEKLTALTGISSRGIFKAFQRSRGYSP------------MAF---A-------------------   51 (108)
T ss_dssp             HHHHHHHHHTTSCCCHHHHHHHHTCCHHHHHHHHHHHTSSCH------------HHH---H-------------------
T ss_pred             HHHHHHHHcccCCCCHHHHHHHHCCCHHHHHHHHHHHhCcCH------------HHH---H-------------------
Confidence            3445555555677999999999999999999999985 5531            111   0                   


Q ss_pred             CCCCCHHHHHHHHHHHHcCC--CCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        116 TKSWNEEILNVALDALRAGS--ISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       116 ~~kYs~e~k~~AV~~~~~g~--~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                          ..--+..|.+++.++.  +|+.+||...|-+..+ +.+..++. |+.+
T Consensus        52 ----~~~Rl~~A~~lL~~~~~~~si~~IA~~~Gf~~~s~F~r~Fk~~~G~tP   99 (108)
T 3mn2_A           52 ----KRVRLQHAHNLLSDGATPTTVTAAALSCGFSNLGHFARDYRDMFGEKP   99 (108)
T ss_dssp             ----HHHHHHHHHHHHHSSSSCCCHHHHHHHTTCCCHHHHHHHHHHHHSSCH
T ss_pred             ----HHHHHHHHHHHHHcCCCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCh
Confidence                0113577888888877  6999999999998866 88887765 7544

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

Probab=97.18  E-value=0.0012  Score=44.52  Aligned_cols=39  Identities=15%  Similarity=0.134  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      +...+.+.+... .+..++|+.+||+++||+++++++|+.
T Consensus        22 Er~~I~~aL~~~-gn~~~aA~~LGIsr~tL~rklkk~gi~   60 (61)
T 1g2h_A           22 EAQVLKLFYAEY-PSTRKLAQRLGVSHTAIANKLKQYGIG   60 (61)
T ss_dssp             HHHHHHHHHHHS-CSHHHHHHHTTSCTHHHHHHHHTTTCC
T ss_pred             HHHHHHHHHHHh-CCHHHHHHHhCCCHHHHHHHHHHhCCC
Confidence            333333344444 489999999999999999999999874

>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}

Probab=97.14  E-value=0.0058  Score=45.93  Aligned_cols=87  Identities=15%  Similarity=0.142  Sum_probs=62.5

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCC
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKS  118 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~k  118 (229)
                      ...|+.-....+++.++|..+||++++|.+.+++.|..            +...   +                      
T Consensus        13 ~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~G~s------------~~~~---~----------------------   55 (120)
T 3mkl_A           13 CTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETS------------YSQL---L----------------------   55 (120)
T ss_dssp             HHHHHTSTTSCCCHHHHHHHTTCCHHHHHHHHHHTTCC------------HHHH---H----------------------
T ss_pred             HHHHHHhccCCCCHHHHHHHHCcCHHHHHHHHHHcCCC------------HHHH---H----------------------
Confidence            33443333457999999999999999999999975332            1111   1                      


Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        119 WNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       119 Ys~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                       ..--+..|.+++.++..|+.+||...|-.... +.+..++. |+.+
T Consensus        56 -~~~Rl~~A~~lL~~~~~si~eIA~~~Gf~~~s~F~r~Fk~~~G~tP  101 (120)
T 3mkl_A           56 -TECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVFRNYYGMTP  101 (120)
T ss_dssp             -HHHHHHHHHHHHTSTTCCHHHHHHHTTCSCHHHHHHHHHHHHSSCH
T ss_pred             -HHHHHHHHHHHHHcCCCCHHHHHHHHCCCCHHHHHHHHHHHHCcCH
Confidence             01124677888877888999999999998755 88888765 7544

>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}

Probab=97.11  E-value=0.0058  Score=45.38  Aligned_cols=88  Identities=19%  Similarity=0.169  Sum_probs=64.1

Q ss_pred             HHHHHHHHH---cCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhcc
Q psy17316         38 MDAALEALR---AGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAY  113 (229)
Q Consensus        38 ~~~AI~~~~---~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~  113 (229)
                      +..+++.+.   ...+++.++|..+||++++|.+..++. |...            .....                   
T Consensus         9 i~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~------------~~~~~-------------------   57 (113)
T 3oio_A            9 LTEAVSLMEANIEEPLSTDDIAYYVGVSRRQLERLFKQYLGTVP------------SKYYL-------------------   57 (113)
T ss_dssp             HHHHHHHHHTCSSSCCCHHHHHHHHTSCHHHHHHHHHHHTSSCH------------HHHHH-------------------
T ss_pred             HHHHHHHHHhhhcCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH------------HHHHH-------------------
Confidence            344444443   356999999999999999999999985 5531            11100                   


Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        114 GPTKSWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       114 G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                             .--+..|.+++.++..|+.+||...|-+... +.+..++. |+.+
T Consensus        58 -------~~Rl~~A~~lL~~~~~~i~eIA~~~Gf~~~s~F~r~Fk~~~G~tP  102 (113)
T 3oio_A           58 -------ELRLNRARQLLQQTSKSIVQIGLACGFSSGPHFSSTYRNHFNITP  102 (113)
T ss_dssp             -------HHHHHHHHHHHHHCCCCHHHHHHHTTCSCHHHHHHHHHHHHSSCH
T ss_pred             -------HHHHHHHHHHHHcCCCCHHHHHHHHCCCCHHHHHHHHHHHHCcCH
Confidence                   1125778888888888999999999998866 88888765 7644

>4dyq_A Gene 1 protein; GP1, octamer, DNA-binding, viral protein; 1.50A {Shigella phage SF6} PDB: 4dyc_A 4dyr_A 3hef_A 4dzj_A 4dzp_A

Probab=97.09  E-value=0.00041  Score=54.57  Aligned_cols=44  Identities=16%  Similarity=0.286  Sum_probs=38.1

Q ss_pred             CCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCC-ChHHHHHHHH
Q psy17316        168 NASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGI-PSGTLYGRCK  212 (229)
Q Consensus       168 ~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgV-p~~tv~~~vk  212 (229)
                      .+++++|+++.-.+|.++|..| ++..+++..+|| +++|||+|++
T Consensus         7 ~GRPtk~t~e~~e~I~~~i~~G-~sl~~i~~~~~~ps~~T~~~W~~   51 (140)
T 4dyq_A            7 AGRPSDYMPEVADDICSLLSSG-ESLLKVCKRPGMPDKSTVFRWLA   51 (140)
T ss_dssp             ---CCSCCTTHHHHHHHHHHTT-CCHHHHHTSTTCCCHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHCC-CcHHHHHhcCCCCCHHHHHHHHH
Confidence            4678899999999999998877 899999999999 6999999997

>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}

Probab=97.07  E-value=0.01  Score=43.58  Aligned_cols=87  Identities=10%  Similarity=0.106  Sum_probs=63.2

Q ss_pred             HHHHHHHHc-CCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCC
Q psy17316         39 DAALEALRA-GQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPT  116 (229)
Q Consensus        39 ~~AI~~~~~-g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~  116 (229)
                      ...|+.-.. ..+++.++|+.+||++++|.+..++. |...            .....                      
T Consensus         9 ~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~------------~~~~~----------------------   54 (107)
T 2k9s_A            9 CQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQQLGISV------------LSWRE----------------------   54 (107)
T ss_dssp             HHHHHHTSSCSSCCHHHHHHHTTSCHHHHHHHHHHHHSSCH------------HHHHH----------------------
T ss_pred             HHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCH------------HHHHH----------------------
Confidence            333433333 68999999999999999999999984 6531            11100                      


Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        117 KSWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       117 ~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                          .--+..|.+++.+..+|+.+||...|-+..+ +.+..++. |..+
T Consensus        55 ----~~Rl~~A~~lL~~~~~si~~IA~~~Gf~~~s~F~r~Fk~~~G~tP   99 (107)
T 2k9s_A           55 ----DQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASP   99 (107)
T ss_dssp             ----HHHHHHHHHHHHHCCCCHHHHHHHTTCCCHHHHHHHHHHHHSSCH
T ss_pred             ----HHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCH
Confidence                1124777888887888999999999999866 88887765 7544

>1gdt_A GD resolvase, protein (gamma delta resolvase); protein-DNA complex, double helix, overhanging base, DNA binding protein/DNA complex; 3.00A {Escherichia coli} SCOP: a.4.1.2 c.53.1.1 PDB: 1zr4_A 1zr2_A 2gm4_A 1res_A 1ret_A

Probab=97.06  E-value=0.0016  Score=52.81  Aligned_cols=64  Identities=22%  Similarity=0.335  Sum_probs=49.9

Q ss_pred             HHHHHHHHHhhcchhhhhhhhccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHH
Q psy17316         91 ILNVALDALRAGSISANKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARK  158 (229)
Q Consensus        91 ~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~  158 (229)
                      +++...+-..+|...+++.|+..|.++.|+++   .+.+.+.+|. |+.+||+.+||+++|+|+++++
T Consensus       118 E~~~i~~R~~~g~~~~~~~G~~~Gr~~~~~~~---~i~~~~~~G~-s~~~Ia~~l~is~~tv~r~l~~  181 (183)
T 1gdt_A          118 ERQRILERTNEGRQEAMAKGVVFGRKRKIDRD---AVLNMWQQGL-GASHISKTMNIARSTVYKVINE  181 (183)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCCCSSCCCSCHH---HHHHHHHTTC-CHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHcCCcCCCCCCCCHH---HHHHHHHCCC-CHHHHHHHHCcCHHHHHHHHhh
Confidence            33334444556877888888889999999765   3456777765 9999999999999999999874

>2r0q_C Putative transposon TN552 DNA-invertase BIN3; site-specific recombinase, resolvase, DNA-binding protein, protein-DNA complex, DNA integration, DNA invertase, DNA recombination; 3.20A {Staphylococcus aureus}

Probab=97.02  E-value=0.00065  Score=56.38  Aligned_cols=60  Identities=18%  Similarity=0.280  Sum_probs=47.5

Q ss_pred             HhhcchhhhhhhhccCCCCCCCHHH--------HHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh
Q psy17316         99 LRAGSISANKASKAYGPTKSWNEEI--------LNVALDALRAGSISANKASKAYGIPSSTLYKIARKE  159 (229)
Q Consensus        99 l~~G~ls~~~~~~~~G~~~kYs~e~--------k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~  159 (229)
                      .++|...+++.|++.|++..|..+.        ...+.+.+.+|. |+.+||+.+||+++|+|+++++.
T Consensus       132 ~~~g~~~~~~~G~~~Grp~gy~~~~~~~~~a~iv~~i~~~~~~G~-s~~~Ia~~l~is~~tv~r~l~~~  199 (209)
T 2r0q_C          132 QAQGIQVAKEKGVYKGRPLLYSPNAKDPQKRVIYHRVVEMLEEGQ-AISKIAKEVNITRQTVYRIKHDN  199 (209)
T ss_dssp             HHHHHHHHHHHTCCCCCCCSSSTTCSSHHHHHHHHHHHHHHHTTC-CHHHHHHHHTCCHHHHHHHHTTC
T ss_pred             HHHHHHHHHHcCCcCCCCCCCCccccchHHHHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHhcc
Confidence            3456667777888888887887542        456777888775 99999999999999999998754

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

Probab=96.89  E-value=0.001  Score=43.26  Aligned_cols=36  Identities=8%  Similarity=0.106  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         35 HEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        35 ~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +++...++..+ ..|+|+.+||+.+||+++||++|++
T Consensus        18 ~~~~~~i~~l~-~~g~s~~eIA~~lgis~~TV~~~l~   53 (55)
T 2x48_A           18 DDLVSVAHELA-KMGYTVQQIANALGVSERKVRRYLE   53 (55)
T ss_dssp             HHHHHHHHHHH-HTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            56666666554 5678999999999999999999986

>1bl0_A Protein (multiple antibiotic resistance protein), DNA (5'- D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP *AP*AP*TP* CP*C)-3')...; transcriptional activator; HET: DNA; 2.30A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 PDB: 1xs9_A

Probab=96.83  E-value=0.012  Score=44.85  Aligned_cols=92  Identities=14%  Similarity=0.159  Sum_probs=66.0

Q ss_pred             CHHHHHHHHHHHH---cCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhh
Q psy17316         34 THEDMDAALEALR---AGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKA  109 (229)
Q Consensus        34 t~e~~~~AI~~~~---~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~  109 (229)
                      ..+.+..+++.+.   ...+++.++|+.+||+.++|.+..++. |...           .+..+                
T Consensus         9 ~~~~i~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~G~s~-----------~~~l~----------------   61 (129)
T 1bl0_A            9 DAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSL-----------GQYIR----------------   61 (129)
T ss_dssp             CHHHHHHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHHHHHSSCH-----------HHHHH----------------
T ss_pred             hHHHHHHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH-----------HHHHH----------------
Confidence            3444455554443   346999999999999999999999985 6531           01110                


Q ss_pred             hhccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        110 SKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       110 ~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                                 .--+..|.+++.++..|+.+||...|-+... +.+..++. |+.+
T Consensus        62 -----------~~Rl~~A~~lL~~~~~si~~IA~~~Gf~~~s~F~r~Fk~~~G~tP  106 (129)
T 1bl0_A           62 -----------SRKMTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPP  106 (129)
T ss_dssp             -----------HHHHHHHHHHHHHCCCCHHHHHHHTTCSCHHHHHHHHHHHHSSCH
T ss_pred             -----------HHHHHHHHHHHHcCCCCHHHHHHHHCCCCHHHHHHHHHHHHCcCH
Confidence                       1124678888888888999999999999866 88887765 7644

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

Probab=96.71  E-value=0.0032  Score=40.79  Aligned_cols=36  Identities=17%  Similarity=0.116  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++....|+.+ ...++++.++|..+|||.+||++|++
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            5656666666 45669999999999999999999985

>1ntc_A Protein (nitrogen regulation protein (NTRC)); helix-turn-helix, FIS, four-helix bundle, transcription regulation; NMR {Salmonella typhimurium} SCOP: a.4.1.12

Probab=96.68  E-value=0.0011  Score=48.26  Aligned_cols=33  Identities=30%  Similarity=0.304  Sum_probs=27.2

Q ss_pred             HHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         43 EALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        43 ~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      +.+...+.++.++|+.+||+++||+++++++|+
T Consensus        58 ~aL~~~~gn~~~aA~~LGIsr~tL~rklkk~~i   90 (91)
T 1ntc_A           58 TALRHTQGHKQEAARLLGWGAATLTAKLKELGM   90 (91)
T ss_dssp             HHHHHTTTCTTHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHCcCHHHHHHHHHHhCc
Confidence            344444557889999999999999999999876

>4ich_A Transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, transcription RE; 1.95A {Saccharomonospora viridis}

Probab=96.65  E-value=0.0018  Score=56.04  Aligned_cols=34  Identities=9%  Similarity=0.172  Sum_probs=0.0

Q ss_pred             HHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         38 MDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        38 ~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +-+.|+.+ ..-|+|+.++|++.||+++||.+|-.
T Consensus        31 ~~~~l~~~r~~~g~t~~~la~~~g~s~~~is~~e~   65 (311)
T 4ich_A           31 LRRRVRGLIHSRPGAQREFAAAIGLDESKLSKSLN   65 (311)
T ss_dssp             -----------------------------------
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHc
Confidence            33444443 45689999999999999999999976

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=96.56  E-value=0.0047  Score=43.70  Aligned_cols=30  Identities=23%  Similarity=0.369  Sum_probs=25.9

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~   78 (229)
                      .+++.++|+.+||+..||+.|-+..|+-.|
T Consensus         5 ~~~i~e~A~~~gvs~~tlR~ye~~~gl~~p   34 (81)
T 2jml_A            5 TLRIRTIARMTGIREATLRAWERRYGFPRP   34 (81)
T ss_dssp             CEEHHHHHHTTSTTHHHHHHHHHHTCCSCC
T ss_pred             cccHHHHHHHHCcCHHHHHHHHHhCCCCCC
Confidence            368999999999999999999998776544

>1vz0_A PARB, chromosome partitioning protein PARB; nuclear protein, chromosome segregation, DNA-binding, helix-turn-helix; 2.3A {Thermus thermophilus} SCOP: a.4.14.1 d.268.1.1

Probab=96.53  E-value=0.015  Score=49.37  Aligned_cols=92  Identities=20%  Similarity=0.168  Sum_probs=67.6

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhh
Q psy17316         30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKA  109 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~  109 (229)
                      +..+++-+...++..+.+.|+|..+||+.+|+++++|.+.++-.++            +++    ..+++.+|.++..++
T Consensus       115 R~~L~~~E~a~~~~~l~~~g~t~~~iA~~lG~s~~~V~~~l~l~~l------------~~~----v~~~l~~g~is~~~A  178 (230)
T 1vz0_A          115 REDLSPVEEARGYQALLEMGLTQEEVARRVGKARSTVANALRLLQL------------PPE----ALEALERGEITAGHA  178 (230)
T ss_dssp             STTCCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHGGGS------------CHH----HHHHHHTTSSCHHHH
T ss_pred             cCCCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHcC------------CHH----HHHHHHcCCCCHHHH
Confidence            6788999998888888788999999999999999999999885422            333    556777888776665


Q ss_pred             hhccCCCCCCCHHHHHHHHHHHHcCCCCHHHH
Q psy17316        110 SKAYGPTKSWNEEILNVALDALRAGSISANKA  141 (229)
Q Consensus       110 ~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~  141 (229)
                      -...+..    .+..+.+.+.+..+++|++++
T Consensus       179 ~~L~~l~----~~~q~~l~~~i~~~~lsv~~~  206 (230)
T 1vz0_A          179 RALLMLE----PEDRLWGLKEILEKGLSVRQA  206 (230)
T ss_dssp             HHHHTSC----GGGHHHHHHHHHHTCCCHHHH
T ss_pred             HHHHcCC----cHHHHHHHHHHHHcCCCHHHH
Confidence            4443332    223333677777777888776

>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}

Probab=96.44  E-value=0.013  Score=42.61  Aligned_cols=71  Identities=13%  Similarity=0.118  Sum_probs=53.8

Q ss_pred             cCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHH-HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHH
Q psy17316        133 AGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPE-DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGR  210 (229)
Q Consensus       133 ~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e-~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~  210 (229)
                      ++.+++.++|+.+||+.++|.+..++. |....        .|=.. -...|.+.+.+.++++.++|...|-+.++-...
T Consensus        17 ~~~~~~~~lA~~~~~S~~~l~r~fk~~~g~s~~--------~~~~~~Rl~~A~~lL~~~~~si~~iA~~~Gf~~~s~F~r   88 (103)
T 3lsg_A           17 DSQFTLSVLSEKLDLSSGYLSIMFKKNFGIPFQ--------DYLLQKRMEKAKLLLLTTELKNYEIAEQVGFEDVNYFIT   88 (103)
T ss_dssp             CTTCCHHHHHHHTTCCHHHHHHHHHHHHSSCHH--------HHHHHHHHHHHHHHHHHCCCCHHHHHHHTTCSCHHHHHH
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHCCCCCHHHHHHHhCCCCHHHHHH
Confidence            347899999999999999999999977 75543        23223 345566777778899999999999966554444


Q ss_pred             H
Q psy17316        211 C  211 (229)
Q Consensus       211 v  211 (229)
                      +
T Consensus        89 ~   89 (103)
T 3lsg_A           89 K   89 (103)
T ss_dssp             H
T ss_pred             H
Confidence            3

>1eto_A FIS, factor for inversion stimulation; transcriptional activation region, DNA-binding protein, transcription activator; 1.90A {Escherichia coli} SCOP: a.4.1.12 PDB: 1etq_A 1ety_A 1fia_A 3fis_A 3iv5_A* 3jr9_A* 3jra_A* 3jrb_A* 3jrc_A* 3jrd_A* 3jre_A* 3jrf_A* 3jrg_A* 3jrh_A* 3jri_A* 1f36_A 1etv_A 1etk_A 1etx_A 1fip_A ...

Probab=96.42  E-value=0.0047  Score=45.87  Aligned_cols=32  Identities=22%  Similarity=0.344  Sum_probs=27.1

Q ss_pred             HHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         44 ALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      .+...+-.+..+|+.+||+++||+++++++|+
T Consensus        66 aL~~~~gn~~~AA~~LGIsR~TL~rkLkk~gi   97 (98)
T 1eto_A           66 VMQYTLGNQTRAALMMGINRGTLRKKLKKYGM   97 (98)
T ss_dssp             HHHHTTTCHHHHHHHHTSCHHHHHHHHHHTTC
T ss_pred             HHHHhCCCHHHHHHHhCCCHHHHHHHHHHhCC
Confidence            34344448999999999999999999999986

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=96.38  E-value=0.0077  Score=42.56  Aligned_cols=65  Identities=15%  Similarity=0.169  Sum_probs=47.2

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCC-CCCCCCCHHHH--HHHHHHHH-hCCCcHHHHHHHh
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFN-ASPTAWKPEDL--EIALEGIR-SGQTTVQRASAEY  200 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~-~~~r~~t~e~r--~eaV~~~~-~~~~s~~eAA~~f  200 (229)
                      +++.++|+.+||+..||+.|.+..|+-...... +..|.|+.++.  +..|..+. +-+++..++...+
T Consensus         6 ~~i~e~A~~~gvs~~tlR~ye~~~gl~~p~r~~~~g~R~Y~~~dl~~l~~I~~l~~~~G~sl~ei~~~l   74 (81)
T 2jml_A            6 LRIRTIARMTGIREATLRAWERRYGFPRPLRSEGNNYRVYSREEVEAVRRVARLIQEEGLSVSEAIAQV   74 (81)
T ss_dssp             EEHHHHHHTTSTTHHHHHHHHHHTCCSCCBSSSCSSSCEECHHHHHHHHHHHHHHHHTSTHHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHHhCCCCCCcCCCCCCeeecCHHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence            589999999999999999999865643221112 34577887754  45577777 7779988887754

>3oou_A LIN2118 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; HET: BTB; 1.57A {Listeria innocua}

Probab=96.34  E-value=0.015  Score=42.63  Aligned_cols=71  Identities=14%  Similarity=0.192  Sum_probs=53.4

Q ss_pred             HcCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHH-HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHH
Q psy17316        132 RAGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPE-DLEIALEGIRSGQTTVQRASAEYGIPSGTLYG  209 (229)
Q Consensus       132 ~~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e-~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~  209 (229)
                      ....+++.++|+.+||+.++|.+..++. |....        .|-.. -...|.+.+.+.++++.++|...|-+.++-..
T Consensus        18 ~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~~--------~~~~~~Rl~~A~~lL~~~~~si~~IA~~~Gf~~~s~F~   89 (108)
T 3oou_A           18 FSEGMSLKTLGNDFHINAVYLGQLFQKEMGEHFT--------DYLNRYRVNYAKEELLQTKDNLTIIAGKSGYTDMAYFY   89 (108)
T ss_dssp             TTSCCCHHHHHHHHTSCHHHHHHHHHHHHSSCHH--------HHHHHHHHHHHHHHHHHCCCCHHHHHHHTTCCCHHHHH
T ss_pred             hcCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHcCCCChHHHH
Confidence            3456899999999999999999999876 75443        23223 34556667777889999999999996655444


Q ss_pred             H
Q psy17316        210 R  210 (229)
Q Consensus       210 ~  210 (229)
                      .
T Consensus        90 r   90 (108)
T 3oou_A           90 R   90 (108)
T ss_dssp             H
T ss_pred             H
Confidence            3

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

Probab=96.31  E-value=0.0098  Score=40.11  Aligned_cols=35  Identities=26%  Similarity=0.398  Sum_probs=28.7

Q ss_pred             HHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCccc
Q psy17316        130 ALRAGSISANKASKAYGIPSSTLYKIARKEGIRLA  164 (229)
Q Consensus       130 ~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~  164 (229)
                      ++...+.++.++|+..||+++|||++++++|+...
T Consensus        27 aL~~~~gn~~~aA~~LGisr~tL~rklkk~gi~~~   61 (63)
T 3e7l_A           27 KLREYDYDLKRTAEEIGIDLSNLYRKIKSLNIRVK   61 (63)
T ss_dssp             HHHHTTTCHHHHHHHHTCCHHHHHHHHHHTTCCCC
T ss_pred             HHHHhCCCHHHHHHHHCcCHHHHHHHHHHhCCCCC
Confidence            33333458999999999999999999999998653

>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=96.22  E-value=0.0036  Score=49.17  Aligned_cols=46  Identities=9%  Similarity=0.014  Sum_probs=41.9

Q ss_pred             CCCCCCCCHHHHHHHHHHH--HcCCCCHHHHHH----Hc--CCChhhHHHHHHH
Q psy17316         27 LTVTKTWTHEDMDAALEAL--RAGQMSLTKASV----SY--GIPSTTLWQRAHR   72 (229)
Q Consensus        27 ~~~~~kyt~e~~~~AI~~~--~~g~~S~~~aA~----~~--gIp~sTL~~~i~~   72 (229)
                      ...+..+|.+++.++++.+  .+++++..++|+    +|  ||+++||.+|++.
T Consensus         6 ~~~R~~lT~~qK~~i~~~~~~~~~~~~q~~la~wa~~~f~~~is~stis~ilk~   59 (144)
T 1iuf_A            6 KIKRRAITEHEKRALRHYFFQLQNRSGQQDLIEWFREKFGKDISQPSVSQILSS   59 (144)
T ss_dssp             CCSSSCCCSHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHSSCCSSSSTTHHHHH
T ss_pred             CCcCccCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCCCCcHHHHHHHHhh
Confidence            4568899999999999998  568999999999    99  9999999999986

>3gbg_A TCP pilus virulence regulatory protein; cupin, helix-turn-helix, ARAC family, activator, DNA-binding transcription, transcription regulation; HET: PAM; 1.90A {Vibrio cholerae}

Probab=96.18  E-value=0.043  Score=46.32  Aligned_cols=90  Identities=8%  Similarity=0.131  Sum_probs=64.7

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPT  116 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~  116 (229)
                      .....|+.-....+|+.++|+.+||++++|.+..+..|..            +...   +                    
T Consensus       173 ~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~G~t------------~~~~---l--------------------  217 (276)
T 3gbg_A          173 KISCLVKSDITRNWRWADICGELRTNRMILKKELESRGVK------------FREL---I--------------------  217 (276)
T ss_dssp             HHHHHHHHTTTSCCCHHHHHHHHTCCHHHHHHHHHTTTCC------------HHHH---H--------------------
T ss_pred             HHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHcCCC------------HHHH---H--------------------
Confidence            3344444444567999999999999999999999744332            1111   0                    


Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCccc
Q psy17316        117 KSWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRLA  164 (229)
Q Consensus       117 ~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~~  164 (229)
                         ..--+.+|.+++.++.+|+.+||...|-+..+ ..+..|++ |+.+.
T Consensus       218 ---~~~Rl~~A~~lL~~~~~si~eIA~~~Gf~~~s~F~r~Fkk~~G~tP~  264 (276)
T 3gbg_A          218 ---NSIRISYSISLMKTGEFKIKQIAYQSGFASVSYFSTVFKSTMNVAPS  264 (276)
T ss_dssp             ---HHHHHHHHHHHHHHTCCCHHHHHHHTTCSCHHHHHHHHHHHHSSCHH
T ss_pred             ---HHHHHHHHHHHHhCCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHH
Confidence               01235788888888889999999999998866 87777765 76543

>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}

Probab=96.18  E-value=0.017  Score=42.71  Aligned_cols=80  Identities=16%  Similarity=0.258  Sum_probs=58.0

Q ss_pred             HHHHHHHHHc---CCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHH-HHHHHHHHHHhCCCcHHHHHH
Q psy17316        124 LNVALDALRA---GSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPE-DLEIALEGIRSGQTTVQRASA  198 (229)
Q Consensus       124 k~~AV~~~~~---g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e-~r~eaV~~~~~~~~s~~eAA~  198 (229)
                      ..++++.+.+   ..+++.++|+.+||+.++|.+..++. |....        .|-.. -...|.+.+...++++.++|.
T Consensus         9 i~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~~--------~~~~~~Rl~~A~~lL~~~~~~i~eIA~   80 (113)
T 3oio_A            9 LTEAVSLMEANIEEPLSTDDIAYYVGVSRRQLERLFKQYLGTVPS--------KYYLELRLNRARQLLQQTSKSIVQIGL   80 (113)
T ss_dssp             HHHHHHHHHTCSSSCCCHHHHHHHHTSCHHHHHHHHHHHTSSCHH--------HHHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_pred             HHHHHHHHHhhhcCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHH
Confidence            4455555544   34799999999999999999999976 75443        23223 345567777777899999999


Q ss_pred             HhCCChHHHHHHH
Q psy17316        199 EYGIPSGTLYGRC  211 (229)
Q Consensus       199 ~fgVp~~tv~~~v  211 (229)
                      ..|-+..+-...+
T Consensus        81 ~~Gf~~~s~F~r~   93 (113)
T 3oio_A           81 ACGFSSGPHFSST   93 (113)
T ss_dssp             HTTCSCHHHHHHH
T ss_pred             HHCCCCHHHHHHH
Confidence            9998766544443

>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=96.16  E-value=0.021  Score=41.78  Aligned_cols=72  Identities=24%  Similarity=0.282  Sum_probs=53.9

Q ss_pred             HcCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHH-HHHHHHHHHhCC--CcHHHHHHHhCCChHHH
Q psy17316        132 RAGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPED-LEIALEGIRSGQ--TTVQRASAEYGIPSGTL  207 (229)
Q Consensus       132 ~~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~-r~eaV~~~~~~~--~s~~eAA~~fgVp~~tv  207 (229)
                      ....+++.++|+.+|++.++|.+..++. |....        .|-... ...|.+.+..++  +++.++|...|-+.++-
T Consensus        15 ~~~~~~~~~lA~~~~~s~~~l~r~fk~~~G~s~~--------~~~~~~Rl~~A~~lL~~~~~~~si~~IA~~~Gf~~~s~   86 (108)
T 3mn2_A           15 WMRPITIEKLTALTGISSRGIFKAFQRSRGYSPM--------AFAKRVRLQHAHNLLSDGATPTTVTAAALSCGFSNLGH   86 (108)
T ss_dssp             TTSCCCHHHHHHHHTCCHHHHHHHHHHHTSSCHH--------HHHHHHHHHHHHHHHHSSSSCCCHHHHHHHTTCCCHHH
T ss_pred             ccCCCCHHHHHHHHCCCHHHHHHHHHHHhCcCHH--------HHHHHHHHHHHHHHHHcCCCCCCHHHHHHHhCCCCHHH
Confidence            3456899999999999999999999976 75443        232233 455667777776  69999999999987665


Q ss_pred             HHHH
Q psy17316        208 YGRC  211 (229)
Q Consensus       208 ~~~v  211 (229)
                      ...+
T Consensus        87 F~r~   90 (108)
T 3mn2_A           87 FARD   90 (108)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5544

>4fcy_A Transposase; rnaseh, DDE transposase, DNA binding protein-DNA complex; HET: DNA; 3.71A {Enterobacteria phage MU} PDB: 2ezk_A 2ezl_A 2ezh_A 2ezi_A

Probab=96.14  E-value=0.029  Score=52.21  Aligned_cols=33  Identities=12%  Similarity=0.208  Sum_probs=26.0

Q ss_pred             HHHHHcCCCCHH----HHHHHcCCChhhHHHHHHHhC
Q psy17316         42 LEALRAGQMSLT----KASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        42 I~~~~~g~~S~~----~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      +..+..+|.+..    .+|+++||+.+||++|+++|.
T Consensus        41 v~~l~~~g~~~~~a~~~~a~~~gvS~~Tl~rW~~~y~   77 (529)
T 4fcy_A           41 ADEMLNQGISTKTAFATVAGHYQVSASTLRDKYYQVQ   77 (529)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence            344556777854    459999999999999999873

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

Probab=95.95  E-value=0.033  Score=41.42  Aligned_cols=70  Identities=11%  Similarity=0.137  Sum_probs=45.8

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV  126 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~  126 (229)
                      ++++.++|+.+|||..||+.|-+. |.-.|.....                              |....|+.++  ++.
T Consensus         1 ~~~i~e~A~~~gvs~~tLR~ye~~-Gll~p~~r~~------------------------------~g~R~Y~~~dl~~l~   49 (108)
T 2vz4_A            1 SYSVGQVAGFAGVTVRTLHHYDDI-GLLVPSERSH------------------------------AGHRRYSDADLDRLQ   49 (108)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHH-TSSCCSEECS------------------------------SCCEEBCHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCC------------------------------CCCeecCHHHHHHHH
Confidence            378999999999999999999886 5433321111                              0123344444  344


Q ss_pred             HHHHHHcCCCCHHHHHHHhCCCh
Q psy17316        127 ALDALRAGSISANKASKAYGIPS  149 (229)
Q Consensus       127 AV~~~~~g~~S~~~~a~k~gIp~  149 (229)
                      .|..+.+-++|+.+|......+.
T Consensus        50 ~I~~lr~~G~sl~~I~~~l~~~~   72 (108)
T 2vz4_A           50 QILFYRELGFPLDEVAALLDDPA   72 (108)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTC--
T ss_pred             HHHHHHHCCCCHHHHHHHHhCCc
Confidence            56666676789999988877653

>3uj3_X DNA-invertase; helix-turn-helix, site-specific recombinase, recombination; 3.51A {Enterobacteria phage MU} PDB: 3plo_X

Probab=95.91  E-value=0.0013  Score=53.80  Aligned_cols=51  Identities=18%  Similarity=0.236  Sum_probs=0.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhcCCCCC
Q psy17316        169 ASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRSTPRP  220 (229)
Q Consensus       169 ~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~~~~~~  220 (229)
                      +++..++++...+|.+++.+| +++.++|..+|||.+|||+|++.....+.+
T Consensus       138 Gr~~~~~~~~~~~i~~l~~~G-~s~~~Ia~~l~vs~~Tvyr~l~~~~~~~~~  188 (193)
T 3uj3_X          138 GRPPKLTKAEWEQAGRLLAQG-IPRKQVALIYDVALSTLYKKHPAKRAHIEN  188 (193)
T ss_dssp             ----------------------------------------------------
T ss_pred             CCCCCCCHHHHHHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHHHhhhcCCC
Confidence            445567777778888887766 899999999999999999999865544433

>1bl0_A Protein (multiple antibiotic resistance protein), DNA (5'- D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP *AP*AP*TP* CP*C)-3')...; transcriptional activator; HET: DNA; 2.30A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 PDB: 1xs9_A

Probab=95.84  E-value=0.028  Score=42.65  Aligned_cols=82  Identities=18%  Similarity=0.256  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHHc---CCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHHH-HHHHHHHHhCCCcHHH
Q psy17316        121 EEILNVALDALRA---GSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPEDL-EIALEGIRSGQTTVQR  195 (229)
Q Consensus       121 ~e~k~~AV~~~~~---g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~r-~eaV~~~~~~~~s~~e  195 (229)
                      .+...++++.+.+   ..+++.++|+.+|++.++|.+..++. |....        .|-.+.| ..|.+.+...++++.+
T Consensus        10 ~~~i~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~G~s~~--------~~l~~~Rl~~A~~lL~~~~~si~~   81 (129)
T 1bl0_A           10 AITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHSLG--------QYIRSRKMTEIAQKLKESNEPILY   81 (129)
T ss_dssp             HHHHHHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHHHHHSSCHH--------HHHHHHHHHHHHHHHHHCCCCHHH
T ss_pred             HHHHHHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHH
Confidence            3445555555544   35799999999999999999999876 75443        2323334 4567777778899999


Q ss_pred             HHHHhCCChHHHHHH
Q psy17316        196 ASAEYGIPSGTLYGR  210 (229)
Q Consensus       196 AA~~fgVp~~tv~~~  210 (229)
                      +|...|-+.++-...
T Consensus        82 IA~~~Gf~~~s~F~r   96 (129)
T 1bl0_A           82 LAERYGFESQQTLTR   96 (129)
T ss_dssp             HHHHTTCSCHHHHHH
T ss_pred             HHHHHCCCCHHHHHH
Confidence            999999886655444

>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}

Probab=95.79  E-value=0.03  Score=40.97  Aligned_cols=79  Identities=13%  Similarity=0.280  Sum_probs=57.4

Q ss_pred             CCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHH-HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHH
Q psy17316        134 GSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPED-LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRC  211 (229)
Q Consensus       134 g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~-r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~v  211 (229)
                      ..+++.++|+.+|++.++|.+..++. |....        .|-... ...|.+.+...++++.++|...|-+.++-...+
T Consensus        19 ~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~~--------~~~~~~Rl~~A~~lL~~~~~si~~IA~~~Gf~~~s~F~r~   90 (107)
T 2k9s_A           19 SNFDIASVAQHVCLSPSRLSHLFRQQLGISVL--------SWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRV   90 (107)
T ss_dssp             SSCCHHHHHHHTTSCHHHHHHHHHHHHSSCHH--------HHHHHHHHHHHHHHHHHCCCCHHHHHHHTTCCCHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHH
Confidence            56799999999999999999999876 75543        232233 455666777788999999999999876655544


Q ss_pred             HhhcCCCCC
Q psy17316        212 KLSRSTPRP  220 (229)
Q Consensus       212 k~~~~~~~~  220 (229)
                      =...-|-+|
T Consensus        91 Fk~~~G~tP   99 (107)
T 2k9s_A           91 FKKCTGASP   99 (107)
T ss_dssp             HHHHHSSCH
T ss_pred             HHHHHCcCH
Confidence            333334444

>4fcy_A Transposase; rnaseh, DDE transposase, DNA binding protein-DNA complex; HET: DNA; 3.71A {Enterobacteria phage MU} PDB: 2ezk_A 2ezl_A 2ezh_A 2ezi_A

Probab=95.73  E-value=0.13  Score=47.83  Aligned_cols=86  Identities=16%  Similarity=0.192  Sum_probs=48.3

Q ss_pred             HHHHHHcCCCC----HHHHHHHhCCChHHHHHHHHHh-CC------cccCCCC------CCCCCCCHHHHHHHHHHHHhC
Q psy17316        127 ALDALRAGSIS----ANKASKAYGIPSSTLYKIARKE-GI------RLAQPFN------ASPTAWKPEDLEIALEGIRSG  189 (229)
Q Consensus       127 AV~~~~~g~~S----~~~~a~k~gIp~sTL~~~ik~~-g~------k~~~~~~------~~~r~~t~e~r~eaV~~~~~~  189 (229)
                      +|..+..++.+    +..+|+++||+.+|||+|.+++ +.      ..+.|..      .....++++....++......
T Consensus        40 ~v~~l~~~g~~~~~a~~~~a~~~gvS~~Tl~rW~~~y~~~~~~~gl~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~yl~~  119 (529)
T 4fcy_A           40 AADEMLNQGISTKTAFATVAGHYQVSASTLRDKYYQVQKFAKPDWAAALVDGRGASRRNVHKSEFDEDAWQFLIADYLRP  119 (529)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHTTSCHHHHHHHHHHHHTSCGGGHHHHHC------------CCCCHHHHHHHHHHHTST
T ss_pred             HHHHHHhcCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHhhCcccCceecccCCCCCCCCCCcCcCCHHHHHHHHHHHhCc
Confidence            33434455556    4556999999999999999765 21      1222221      112345666555555544443


Q ss_pred             -CCcHHH-------HHHHhC--C-ChHHHHHHHH
Q psy17316        190 -QTTVQR-------ASAEYG--I-PSGTLYGRCK  212 (229)
Q Consensus       190 -~~s~~e-------AA~~fg--V-p~~tv~~~vk  212 (229)
                       ..+...       .+..-|  | |+.||+++++
T Consensus       120 ~~~s~~~~~~~~~~~~~~~g~~~PS~~tv~r~l~  153 (529)
T 4fcy_A          120 EKPAFRKCYERLELAAREHGWSIPSRATAFRRIQ  153 (529)
T ss_dssp             TCCCHHHHHHHHHHHHHHHTCCCCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence             334332       333444  4 7999999987

>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=95.65  E-value=0.014  Score=43.60  Aligned_cols=33  Identities=21%  Similarity=0.224  Sum_probs=26.9

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ......+..|.+|+++||+.+||+++||.|--+
T Consensus        48 ~~l~~~L~~ge~TQREIA~~lGiS~stISRi~r   80 (101)
T 1jhg_A           48 VRIIEELLRGEMSQRELKNELGAGIATITRGSN   80 (101)
T ss_dssp             HHHHHHHHHCCSCHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCCChhhhhHHHH
Confidence            445555567779999999999999999999833

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=95.60  E-value=0.019  Score=39.21  Aligned_cols=40  Identities=15%  Similarity=0.159  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHh--CCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        178 DLEIALEGIRS--GQTTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       178 ~r~eaV~~~~~--~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      .+.+|++.+.+  ..++..++|..+|||.++|++.++ +...|
T Consensus        11 ~~~~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L~~~G   53 (67)
T 2heo_A           11 LEQKILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLKKED   53 (67)
T ss_dssp             HHHHHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            46678888765  358999999999999999999998 44444

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

Probab=95.57  E-value=0.043  Score=40.79  Aligned_cols=68  Identities=7%  Similarity=0.071  Sum_probs=43.8

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      +++.++|+.+|||..||+.|-+. |.-.|.....                              |....|++++  +...
T Consensus         3 ~~i~e~A~~~gvs~~tLR~ye~~-Gll~p~~~~~------------------------------~g~R~Y~~~dl~~l~~   51 (109)
T 1r8d_A            3 YQVKQVAEISGVSIRTLHHYDNI-ELLNPSALTD------------------------------AGYRLYSDADLERLQQ   51 (109)
T ss_dssp             BCHHHHHHHHSCCHHHHHHHHHT-TSSCCSEECT------------------------------TCCEEBCHHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHHC-CCCCCCeECC------------------------------CCCeeeCHHHHHHHHH
Confidence            68999999999999999999874 5433321100                              1123344444  2344


Q ss_pred             HHHHHcCCCCHHHHHHHhCCC
Q psy17316        128 LDALRAGSISANKASKAYGIP  148 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gIp  148 (229)
                      |..+.+-++|+.+|......+
T Consensus        52 I~~l~~~G~~l~~I~~~l~~~   72 (109)
T 1r8d_A           52 ILFFKEIGFRLDEIKEMLDHP   72 (109)
T ss_dssp             HHHHHHTTCCHHHHHHHHHCT
T ss_pred             HHHHHHCCCCHHHHHHHHhCC
Confidence            555666667888888776554

>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=95.53  E-value=0.009  Score=46.84  Aligned_cols=43  Identities=7%  Similarity=-0.013  Sum_probs=38.7

Q ss_pred             CCCCCCHHHHHHHHHHH--HhCCCcHHHHHH----Hh--CCChHHHHHHHH
Q psy17316        170 SPTAWKPEDLEIALEGI--RSGQTTVQRASA----EY--GIPSGTLYGRCK  212 (229)
Q Consensus       170 ~~r~~t~e~r~eaV~~~--~~~~~s~~eAA~----~f--gVp~~tv~~~vk  212 (229)
                      ....+|.+++.+|+++.  .+++++..++|.    +|  +||.+||.+|++
T Consensus         8 ~R~~lT~~qK~~i~~~~~~~~~~~~q~~la~wa~~~f~~~is~stis~ilk   58 (144)
T 1iuf_A            8 KRRAITEHEKRALRHYFFQLQNRSGQQDLIEWFREKFGKDISQPSVSQILS   58 (144)
T ss_dssp             SSSCCCSHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHSSCCSSSSTTHHHH
T ss_pred             cCccCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCCCCcHHHHHHHHh
Confidence            45678999999999999  457899999999    99  999999999998

>4fe7_A Xylose operon regulatory protein; HTH_ARAC, helix-turn-helix, PBP, periplasmic binding protein binding transcription regulator, DNA xylose; HET: XYS; 2.90A {Escherichia coli} PDB: 4fe4_A

Probab=95.48  E-value=0.15  Score=45.64  Aligned_cols=87  Identities=20%  Similarity=0.246  Sum_probs=63.9

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCC
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTK  117 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~  117 (229)
                      ...|+.-....+++.++|+.+|+++++|.+.+++. |...           .+..+                        
T Consensus       311 ~~~i~~~~~~~~~~~~~a~~~~~s~~~l~r~f~~~~g~s~-----------~~~~~------------------------  355 (412)
T 4fe7_A          311 MHYIRNHACKGIKVDQVLDAVGISRSNLEKRFKEEVGETI-----------HAMIH------------------------  355 (412)
T ss_dssp             HHHHHHHGGGTCCHHHHHHHTTCCHHHHHHHHHHHHSSCH-----------HHHHH------------------------
T ss_pred             HHHHHhhccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH-----------HHHHH------------------------
Confidence            34444444578999999999999999999999986 6531           01111                        


Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        118 SWNEEILNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       118 kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                         .--+..|.+++.++.+|+.+||...|-+..+ +.+..|+. |..+
T Consensus       356 ---~~r~~~a~~~L~~~~~~i~~ia~~~Gf~~~~~f~~~Fk~~~g~tP  400 (412)
T 4fe7_A          356 ---AEKLEKARSLLISTTLSINEISQMCGYPSLQYFYSVFKKAYDTTP  400 (412)
T ss_dssp             ---HHHHHHHHHHHHHCCCCHHHHHHHTTCSCHHHHHHHHHHHSSSCH
T ss_pred             ---HHHHHHHHHHHhcCCCCHHHHHHHcCCCCHHHHHHHHHHHHCcCH
Confidence               1124677888888888999999999997755 88888875 6544

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

Probab=95.34  E-value=0.058  Score=40.08  Aligned_cols=68  Identities=15%  Similarity=0.095  Sum_probs=49.1

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCC-CCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHhCCCh
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQP-FNASPTAWKPED--LEIALEGIRSGQTTVQRASAEYGIPS  204 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~-~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~fgVp~  204 (229)
                      +++.++|+.+|||..||+.|.+. |.-.... ..+..|.|+.++  ++..|..+.+-+++..++...+..+.
T Consensus         2 ~~i~e~A~~~gvs~~tLR~ye~~-Gll~p~~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~~I~~~l~~~~   72 (108)
T 2vz4_A            2 YSVGQVAGFAGVTVRTLHHYDDI-GLLVPSERSHAGHRRYSDADLDRLQQILFYRELGFPLDEVAALLDDPA   72 (108)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHH-TSSCCSEECSSCCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHTC--
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHhCCc
Confidence            58899999999999999999884 5422111 123457787764  45666777777899999999887764

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

Probab=95.32  E-value=0.033  Score=37.15  Aligned_cols=41  Identities=24%  Similarity=0.274  Sum_probs=31.1

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ...++.+.. ++....-.|+|..+||..+||+.+|+++++++
T Consensus        14 ~~L~~~~r~-il~l~~~~g~s~~eIA~~lgis~~tv~~~~~r   54 (70)
T 2o8x_A           14 ADLTTDQRE-ALLLTQLLGLSYADAAAVCGCPVGTIRSRVAR   54 (70)
T ss_dssp             TSSCHHHHH-HHHHHHTSCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HhCCHHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            345666654 44443344789999999999999999999886

>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}

Probab=95.31  E-value=0.053  Score=40.50  Aligned_cols=78  Identities=15%  Similarity=0.072  Sum_probs=54.4

Q ss_pred             HHHHHHHHHc---CCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHH-HHHHHHHhCCCcHHHHHHH
Q psy17316        124 LNVALDALRA---GSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLE-IALEGIRSGQTTVQRASAE  199 (229)
Q Consensus       124 k~~AV~~~~~---g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~-eaV~~~~~~~~s~~eAA~~  199 (229)
                      ..++++.+.+   ..+++.++|+.+||+.++|.+..++.|....        .|-...|+ .|.+.+...++++.++|..
T Consensus         9 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~G~s~~--------~~~~~~Rl~~A~~lL~~~~~si~eIA~~   80 (120)
T 3mkl_A            9 RTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYS--------QLLTECRMQRALQLIVIHGFSIKRVAVS   80 (120)
T ss_dssp             HHHHHHHHHTSTTSCCCHHHHHHHTTCCHHHHHHHHHHTTCCHH--------HHHHHHHHHHHHHHHTSTTCCHHHHHHH
T ss_pred             HHHHHHHHHHhccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHH--------HHHHHHHHHHHHHHHHcCCCCHHHHHHH
Confidence            3444444433   4579999999999999999999987664332        23233344 4555665688999999999


Q ss_pred             hCCChHHHHH
Q psy17316        200 YGIPSGTLYG  209 (229)
Q Consensus       200 fgVp~~tv~~  209 (229)
                      .|-+-++-..
T Consensus        81 ~Gf~~~s~F~   90 (120)
T 3mkl_A           81 CGYHSVSYFI   90 (120)
T ss_dssp             TTCSCHHHHH
T ss_pred             HCCCCHHHHH
Confidence            9987554433

>1q06_A Transcriptional regulator CUER; MERR family transcriptional regulator, copper efflux regulator; 2.07A {Escherichia coli} SCOP: a.6.1.3 PDB: 1q05_A 1q07_A

Probab=95.30  E-value=0.06  Score=41.72  Aligned_cols=24  Identities=13%  Similarity=0.192  Sum_probs=21.8

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      |++.++|+.+||+..||+.|-+..
T Consensus         1 ~~I~e~A~~~gvs~~tLR~ye~~G   24 (135)
T 1q06_A            1 MNISDVAKITGLTSKAIRFYEEKG   24 (135)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHTT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            688999999999999999998863

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=95.29  E-value=0.018  Score=41.48  Aligned_cols=41  Identities=7%  Similarity=0.024  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      +....+|+.+..+++|..++|+++||+++++++.+.++.-+
T Consensus        17 ~~~~~IL~lL~~~g~sa~eLAk~LgiSk~aVr~~L~~Le~e   57 (82)
T 1oyi_A           17 EIVCEAIKTIGIEGATAAQLTRQLNMEKREVNKALYDLQRS   57 (82)
T ss_dssp             HHHHHHHHHHSSSTEEHHHHHHHSSSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            34466666666677999999999999999999999986433

>3gp4_A Transcriptional regulator, MERR family; structural genomics, DNA-BI transcription regulator, PSI-2; 1.85A {Listeria monocytogenes str}

Probab=95.04  E-value=0.11  Score=40.60  Aligned_cols=27  Identities=19%  Similarity=0.319  Sum_probs=23.5

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      .+++.++|+.+||+..||+.|-+. |.-
T Consensus         2 ~~~I~e~A~~~gvs~~tLR~Ye~~-GLl   28 (142)
T 3gp4_A            2 SLNIKEASEKSGVSADTIRYYERI-GLI   28 (142)
T ss_dssp             CBCHHHHHHHHTSCHHHHHHHHHH-TSS
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence            368999999999999999999888 443

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=95.01  E-value=0.029  Score=40.43  Aligned_cols=37  Identities=11%  Similarity=0.032  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+-+..|++.+..+++++.++|+++|||+++|++.++
T Consensus        16 ~~~~~~IL~lL~~~g~sa~eLAk~LgiSk~aVr~~L~   52 (82)
T 1oyi_A           16 AEIVCEAIKTIGIEGATAAQLTRQLNMEKREVNKALY   52 (82)
T ss_dssp             HHHHHHHHHHHSSSTEEHHHHHHHSSSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4568889999888889999999999999999999998

>1d5y_A ROB transcription factor; protein-DNA complex, DNA, transcription/DNA complex; HET: DNA; 2.70A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 d.60.1.2

Probab=95.01  E-value=0.13  Score=43.68  Aligned_cols=75  Identities=17%  Similarity=0.125  Sum_probs=54.9

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHHh-CCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHRL-GIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEILN  125 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~~-gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~k~  125 (229)
                      +..+|+.++|+.+|+++++|.+..++. |...            -.....                          --+.
T Consensus        17 ~~~~~~~~la~~~~~s~~~l~r~f~~~~g~s~------------~~~~~~--------------------------~Rl~   58 (292)
T 1d5y_A           17 DQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAI------------GAYIRA--------------------------RRLS   58 (292)
T ss_dssp             SSSCCCHHHHTTTSSCHHHHHHHHHHHHSSCH------------HHHHHH--------------------------HHHH
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH------------HHHHHH--------------------------HHHH
Confidence            467999999999999999999999975 5431            111001                          1246


Q ss_pred             HHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh
Q psy17316        126 VALDALRAGSISANKASKAYGIPSST-LYKIARKE  159 (229)
Q Consensus       126 ~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~  159 (229)
                      .|..++.+.+.|+.+||..+|-+... +.+..++.
T Consensus        59 ~a~~~L~~~~~~i~~ia~~~Gf~~~~~f~r~fk~~   93 (292)
T 1d5y_A           59 KSAVALRLTARPILDIALQYRFDSQQTFTRAFKKQ   93 (292)
T ss_dssp             HHHHHHHHCCCCHHHHHHHTTCSCHHHHHHHHHHH
T ss_pred             HHHHHHhcCCCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            67777777778999999999988755 66666543

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

Probab=95.01  E-value=0.057  Score=40.13  Aligned_cols=68  Identities=9%  Similarity=0.024  Sum_probs=48.9

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHhCCCh
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPED--LEIALEGIRSGQTTVQRASAEYGIPS  204 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~fgVp~  204 (229)
                      +++.++|+.+|||..||+.|.+ .|.- ......+..|.|+.++  ++..|..+.+-+++..++...+..+.
T Consensus         3 ~~i~e~A~~~gvs~~tLR~ye~-~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~l~~~G~~l~~I~~~l~~~~   73 (109)
T 1r8d_A            3 YQVKQVAEISGVSIRTLHHYDN-IELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRLDEIKEMLDHPN   73 (109)
T ss_dssp             BCHHHHHHHHSCCHHHHHHHHH-TTSSCCSEECTTCCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHHCTT
T ss_pred             ccHHHHHHHHCcCHHHHHHHHH-CCCCCCCeECCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHhCCC
Confidence            5889999999999999999987 4532 2110123456788764  44566667777799999988886653

>1ntc_A Protein (nitrogen regulation protein (NTRC)); helix-turn-helix, FIS, four-helix bundle, transcription regulation; NMR {Salmonella typhimurium} SCOP: a.4.1.12

Probab=94.99  E-value=0.025  Score=40.87  Aligned_cols=35  Identities=23%  Similarity=0.234  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++.-|.+.+...+.|..+||+.+||+++|||++++
T Consensus        52 E~~~i~~aL~~~~gn~~~aA~~LGIsr~tL~rklk   86 (91)
T 1ntc_A           52 ERTLLTTALRHTQGHKQEAARLLGWGAATLTAKLK   86 (91)
T ss_dssp             HHHHHHHHHHHTTTCTTHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence            46667777777777899999999999999999987

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=94.97  E-value=0.042  Score=39.48  Aligned_cols=35  Identities=9%  Similarity=-0.044  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+..|+..+ ++.++..++|..+|||.+||++.++
T Consensus        31 ~~r~~Il~~L-~~~~~~~eLa~~l~is~~tv~~~L~   65 (96)
T 1y0u_A           31 PVRRKILRML-DKGRSEEEIMQTLSLSKKQLDYHLK   65 (96)
T ss_dssp             HHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4578899999 8999999999999999999999998

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

Probab=94.95  E-value=0.042  Score=36.77  Aligned_cols=37  Identities=5%  Similarity=0.029  Sum_probs=30.7

Q ss_pred             CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..-++.-|.+.+... -|..+||...|||++|+|++++
T Consensus        19 ~~~Er~~I~~aL~~~-gn~~~aA~~LGIsr~tL~rklk   55 (61)
T 1g2h_A           19 GFYEAQVLKLFYAEY-PSTRKLAQRLGVSHTAIANKLK   55 (61)
T ss_dssp             SHHHHHHHHHHHHHS-CSHHHHHHHTTSCTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHh-CCHHHHHHHhCCCHHHHHHHHH
Confidence            444566677777777 6899999999999999999988

>1j9i_A GPNU1 DBD;, terminase small subunit; DNA binding domain, homodimer, viral assembly, winged helix-turn-helix, viral protein; NMR {Enterobacteria phage lambda} SCOP: a.6.1.5

Probab=94.95  E-value=0.018  Score=39.25  Aligned_cols=46  Identities=9%  Similarity=0.130  Sum_probs=30.4

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCC--CCCCCcHHHHHHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEG--PTKSWNEEILNVAL   96 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~--~~k~~s~e~~~~a~   96 (229)
                      ++..++|+.+||+++||++|++. |........  +..-|..++..+-+
T Consensus         3 lt~~e~a~~LgvS~~Tl~rw~~~-G~P~~~~~g~~~~~~y~~~dv~~wl   50 (68)
T 1j9i_A            3 VNKKQLADIFGASIRTIQNWQEQ-GMPVLRGGGKGNEVLYDSAAVIKWY   50 (68)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHTTT-TCCCSSCCCSSSCCEEEHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHC-CCCeEeeCCCcceEEECHHHHHHHH
Confidence            57899999999999999999987 552222222  12246666554433

>2l1p_A DNA-binding protein SATB1; PSI-biology, NESG, structural genomics, protein structure in northeast structural genomics consortium; NMR {Homo sapiens} PDB: 3nzl_A*

Probab=94.95  E-value=0.062  Score=38.63  Aligned_cols=46  Identities=13%  Similarity=0.271  Sum_probs=40.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         26 SLTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        26 ~~~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +-.+-.+|+.+.....|..++. |+++.++|++.||+++||...++.
T Consensus        10 ~~~~~~~~~~~~~~~kLK~il~-GikQ~eLAK~iGIsqsTLSaIenG   55 (83)
T 2l1p_A           10 HMLPPEQWSHTTVRNALKDLLK-DMNQSSLAKECPLSQSMISSIVNS   55 (83)
T ss_dssp             CTTTTSCCCHHHHHHHHHHHHT-TSCHHHHHHHSSSCHHHHHHHHTC
T ss_pred             ccCCHHHhhHHHHHHHHHHHHH-hcCHHHHHHHcCCCHHHHHHHHcC
Confidence            4455678999999999998888 999999999999999999998873

>1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli}

Probab=94.90  E-value=0.02  Score=38.93  Aligned_cols=46  Identities=13%  Similarity=0.065  Sum_probs=31.0

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHH
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNV   94 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~   94 (229)
                      -+++.++|..+||+++|||+|++.-.+..|....+..-|..++.++
T Consensus        10 ~l~~~eva~~lgvsrstiy~~~~~g~fP~piklG~~~~w~~~ev~~   55 (66)
T 1z4h_A           10 LVDLKFIMADTGFGKTFIYDRIKSGDLPKAKVIHGRARWLYRDHCE   55 (66)
T ss_dssp             EECHHHHHHHHSSCHHHHHHHHHHHHCCCSEESSSCEEEEHHHHHH
T ss_pred             ccCHHHHHHHHCcCHHHHHHHHHCCCCCCCEEeCCCeEEeHHHHHH
Confidence            3688999999999999999999986554333333222244444433

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

Probab=94.84  E-value=0.06  Score=36.26  Aligned_cols=40  Identities=13%  Similarity=0.109  Sum_probs=31.9

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ...|+.+. +++..+ ..|+|..+||..+||+.+|++.++++
T Consensus        10 ~~L~~~e~-~il~~~-~~g~s~~eIA~~l~is~~tV~~~~~~   49 (74)
T 1fse_A           10 PLLTKRER-EVFELL-VQDKTTKEIASELFISEKTVRNHISN   49 (74)
T ss_dssp             CCCCHHHH-HHHHHH-TTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCHHHH-HHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            45666666 445456 55779999999999999999999886

>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=94.83  E-value=0.046  Score=40.81  Aligned_cols=33  Identities=15%  Similarity=0.153  Sum_probs=29.5

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRC  211 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~v  211 (229)
                      |..++..+..|+++|+++|..+|||.+||-+.-
T Consensus        47 R~~l~~~L~~ge~TQREIA~~lGiS~stISRi~   79 (101)
T 1jhg_A           47 RVRIIEELLRGEMSQRELKNELGAGIATITRGS   79 (101)
T ss_dssp             HHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCChhhhhHHH
Confidence            388888888999999999999999999998873

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=94.80  E-value=0.09  Score=41.38  Aligned_cols=70  Identities=6%  Similarity=0.037  Sum_probs=47.2

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV  126 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~  126 (229)
                      .+++.++|+.+|||..||+.|-+. |.-.|.....                              |....|++++  ++.
T Consensus         4 ~~tI~evA~~~Gvs~~tLR~ye~~-GLl~p~~r~~------------------------------~g~R~Y~~~dl~~l~   52 (146)
T 3hh0_A            4 AWLISEFASVGDVTVRALRYYDKI-NLLKPSDYTE------------------------------GGHRLYTKDDLYVLQ   52 (146)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHT-TSSCCSEECT------------------------------TSCEEBCHHHHHHHH
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHHC-CCCCCCeECC------------------------------CCCEeeCHHHHHHHH
Confidence            579999999999999999999887 4432321111                              1123444444  345


Q ss_pred             HHHHHHcCCCCHHHHHHHhCCCh
Q psy17316        127 ALDALRAGSISANKASKAYGIPS  149 (229)
Q Consensus       127 AV~~~~~g~~S~~~~a~k~gIp~  149 (229)
                      .|..+.+-++|+.+|...+.-..
T Consensus        53 ~I~~lr~~G~sl~~I~~~l~~~~   75 (146)
T 3hh0_A           53 QIQSFKHLGFSLGEIQNIILQRD   75 (146)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSSE
T ss_pred             HHHHHHHcCCCHHHHHHHHHccC
Confidence            56666777789999888776654

>1q06_A Transcriptional regulator CUER; MERR family transcriptional regulator, copper efflux regulator; 2.07A {Escherichia coli} SCOP: a.6.1.3 PDB: 1q05_A 1q07_A

Probab=94.73  E-value=0.091  Score=40.68  Aligned_cols=65  Identities=9%  Similarity=0.103  Sum_probs=46.8

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCC-cccCCCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHhC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGI-RLAQPFNASPTAWKPED--LEIALEGIRSGQTTVQRASAEYG  201 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~-k~~~~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~fg  201 (229)
                      +++.++|+.+||+..||+.|.+ .|. .......+..|.|+.++  ++..|..+.+-+++..++...+.
T Consensus         1 ~~I~e~A~~~gvs~~tLR~ye~-~Gll~p~~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~   68 (135)
T 1q06_A            1 MNISDVAKITGLTSKAIRFYEE-KGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVN   68 (135)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH-TTCSCCCEECTTSCEECCHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH-CCCCCCCccCCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            4789999999999999999987 343 22111123457788764  55666777777799999988774

>3gp4_A Transcriptional regulator, MERR family; structural genomics, DNA-BI transcription regulator, PSI-2; 1.85A {Listeria monocytogenes str}

Probab=94.65  E-value=0.15  Score=39.94  Aligned_cols=65  Identities=12%  Similarity=0.168  Sum_probs=48.4

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCccc-CCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLA-QPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYG  201 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~-~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fg  201 (229)
                      +++.++|+.+||+..||+-|.+. |.-.. ....+..|.|+++  +++..|..+.+-+++..++...+.
T Consensus         3 ~~I~e~A~~~gvs~~tLR~Ye~~-GLl~p~~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sL~eIk~~l~   70 (142)
T 3gp4_A            3 LNIKEASEKSGVSADTIRYYERI-GLIPPIHRNESGVRKFGAEDLRWILFTRQMRRAGLSIEALIDYLA   70 (142)
T ss_dssp             BCHHHHHHHHTSCHHHHHHHHHH-TSSCCCCBCTTSCBCBCHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            58999999999999999999885 53222 1112346778766  456778888888899999987665

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=94.53  E-value=0.059  Score=37.54  Aligned_cols=39  Identities=28%  Similarity=0.464  Sum_probs=32.3

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +..|..+++..++.   .-|+|+.++|++.||+++||.+|..
T Consensus         6 ~~~~~~~ri~~~l~---~~glT~~~LA~~~Gvs~stls~~~~   44 (74)
T 1neq_A            6 ARDWHRADVIAGLK---KRKLSLSALSRQFGYAPTTLANALE   44 (74)
T ss_dssp             SSSCCHHHHHHHHH---TTSCCHHHHHHHHSSCHHHHHHTTT
T ss_pred             cCCCCHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            45778777777764   5689999999999999999998844

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=94.50  E-value=0.026  Score=40.34  Aligned_cols=27  Identities=15%  Similarity=0.110  Sum_probs=24.5

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      .++..++|+++||+++||++.+.++.-
T Consensus        27 ~~t~~eLA~~Lgvsr~tV~~~L~~Le~   53 (81)
T 1qbj_A           27 ATTAHDLSGKLGTPKKEINRVLYSLAK   53 (81)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            699999999999999999999998643

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=94.44  E-value=0.063  Score=40.05  Aligned_cols=36  Identities=14%  Similarity=0.127  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .+..+..+|...|+++.+||+++||++.++.+-+++
T Consensus        22 ~~~~~A~lyYv~g~tQ~eIA~~lGiSR~~VsrlL~~   57 (101)
T 2w7n_A           22 QTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVHR   57 (101)
T ss_dssp             HHHHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            456777788888999999999999999999998875

>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=94.43  E-value=0.062  Score=40.50  Aligned_cols=40  Identities=15%  Similarity=0.263  Sum_probs=31.4

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..++.+..-....+.+ |+|+.+||..+|||.+||+.++++
T Consensus        22 ~L~~~~r~vl~l~y~~-g~s~~EIA~~lgiS~~tV~~~l~r   61 (113)
T 1s7o_A           22 LLTDKQMNYIELYYAD-DYSLAEIADEFGVSRQAVYDNIKR   61 (113)
T ss_dssp             GSCHHHHHHHHHHHHT-CCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4666666444433445 789999999999999999999986

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

Probab=94.43  E-value=0.044  Score=35.75  Aligned_cols=32  Identities=13%  Similarity=0.017  Sum_probs=26.8

Q ss_pred             HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +++..+. .|+|..+||..+||+.+|++.++++
T Consensus         5 ~vl~l~~-~g~s~~eIA~~l~is~~tV~~~~~~   36 (61)
T 2jpc_A            5 QVLKLID-EGYTNHGISEKLHISIKTVETHRMN   36 (61)
T ss_dssp             HHHHHHH-TSCCSHHHHHHTCSCHHHHHHHHHH
T ss_pred             HHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            4555554 4789999999999999999998886

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

Probab=94.42  E-value=0.041  Score=40.39  Aligned_cols=40  Identities=8%  Similarity=0.142  Sum_probs=31.2

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +..+-...+++.+...++++.++|+.+||+.+||++.+..
T Consensus         4 ~~~~R~~~I~~~l~~~~~ti~dlA~~~gVS~~TVsR~L~~   43 (93)
T 2l0k_A            4 YIKERTIKIGKYIVETKKTVRVIAKEFGVSKSTVHKDLTE   43 (93)
T ss_dssp             THHHHHHHHHHHHHHHCCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             cHHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence            3444445566666666799999999999999999999863

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=94.41  E-value=0.11  Score=40.86  Aligned_cols=69  Identities=3%  Similarity=-0.047  Sum_probs=51.2

Q ss_pred             CCCHHHHHHHhCCChHHHHHHHHHhCCcccC-CCCCCCCCCCHHH--HHHHHHHHHhCCCcHHHHHHHhCCCh
Q psy17316        135 SISANKASKAYGIPSSTLYKIARKEGIRLAQ-PFNASPTAWKPED--LEIALEGIRSGQTTVQRASAEYGIPS  204 (229)
Q Consensus       135 ~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~-~~~~~~r~~t~e~--r~eaV~~~~~~~~s~~eAA~~fgVp~  204 (229)
                      .+++.++|+.+|||.+||+.|-+. |.-... ...+..|.|++++  ++..|..+.+-+++..++...+.-..
T Consensus         4 ~~tI~evA~~~Gvs~~tLR~ye~~-GLl~p~~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~~I~~~l~~~~   75 (146)
T 3hh0_A            4 AWLISEFASVGDVTVRALRYYDKI-NLLKPSDYTEGGHRLYTKDDLYVLQQIQSFKHLGFSLGEIQNIILQRD   75 (146)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHT-TSSCCSEECTTSCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHTSSE
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHHC-CCCCCCeECCCCCEeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHccC
Confidence            469999999999999999999885 532211 1123467787764  56667777788899999999887653

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=94.35  E-value=0.029  Score=39.50  Aligned_cols=35  Identities=20%  Similarity=0.216  Sum_probs=28.2

Q ss_pred             HHHHHHHH-cC---CCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEALR-AG---QMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~~-~g---~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..+++.+. ++   ++|+.++|+++||+++||++.+.++
T Consensus        17 ~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L   55 (77)
T 1qgp_A           17 QRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSL   55 (77)
T ss_dssp             HHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            44444443 45   6999999999999999999999986

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=94.32  E-value=0.063  Score=37.44  Aligned_cols=30  Identities=17%  Similarity=0.353  Sum_probs=25.0

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..||+.+   + |+.++|+.+||++.||++|+..
T Consensus         4 ~~ai~~~---G-~~~~lA~~lGVs~~aVs~W~~g   33 (71)
T 2hin_A            4 EELVRHF---G-DVEKAAVGVGVTPGAVYQWLQA   33 (71)
T ss_dssp             HHHHHHH---S-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHH---C-CHHHHHHHHCCCHHHHHHHHhC
Confidence            4566554   2 6999999999999999999986

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

Probab=94.21  E-value=0.054  Score=35.31  Aligned_cols=32  Identities=22%  Similarity=0.093  Sum_probs=27.5

Q ss_pred             HHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        180 EIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       180 ~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+|+.++..| +++.++|..+|||..||+.+++
T Consensus         4 ~~vl~l~~~g-~s~~eIA~~l~is~~tV~~~~~   35 (61)
T 2jpc_A            4 RQVLKLIDEG-YTNHGISEKLHISIKTVETHRM   35 (61)
T ss_dssp             HHHHHHHHTS-CCSHHHHHHTCSCHHHHHHHHH
T ss_pred             HHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHH
Confidence            4677775555 9999999999999999999886

>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian}

Probab=94.16  E-value=0.13  Score=40.50  Aligned_cols=67  Identities=7%  Similarity=0.034  Sum_probs=43.7

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHH
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNV  126 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~  126 (229)
                      .+++.++|+.+||+..||+.|-+..-+..+... .                              +....|++++  ++.
T Consensus        16 ~~~I~evA~~~gvs~~tLR~Ye~~Gll~p~~r~-~------------------------------~g~R~Y~~~dl~~l~   64 (148)
T 3gpv_A           16 YYTIGQVAKMQHLTISQIRYYDKQGLFPFLQRN-E------------------------------KGDRIFNEEALKYLE   64 (148)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHHHTTCCTTCEEC-T------------------------------TCCEEBCHHHHHHHH
T ss_pred             ceeHHHHHHHHCcCHHHHHHHHHCCCCCCCcCC-C------------------------------CCCeecCHHHHHHHH
Confidence            478999999999999999999876433222111 1                              1123444444  345


Q ss_pred             HHHHHHcCCCCHHHHHHHhC
Q psy17316        127 ALDALRAGSISANKASKAYG  146 (229)
Q Consensus       127 AV~~~~~g~~S~~~~a~k~g  146 (229)
                      .|..+.+-++|+.+|.....
T Consensus        65 ~I~~lr~~G~sL~eIk~~l~   84 (148)
T 3gpv_A           65 MILCLKNTGMPIQKIKQFID   84 (148)
T ss_dssp             HHHHHHTTTCCHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHH
Confidence            56666777778888877654

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=94.16  E-value=0.069  Score=37.25  Aligned_cols=34  Identities=6%  Similarity=-0.122  Sum_probs=29.8

Q ss_pred             HHHHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +..|++.+.. +.++..++|..+|||.+||++.++
T Consensus         2 r~~Il~~L~~~~~~s~~eLa~~lgvs~~tv~r~L~   36 (81)
T 2htj_A            2 KNEILEFLNRHNGGKTAEIAEALAVTDYQARYYLL   36 (81)
T ss_dssp             HHHHHHHHHHSCCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4567777765 679999999999999999999998

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=94.16  E-value=0.044  Score=39.32  Aligned_cols=36  Identities=14%  Similarity=0.065  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|..|+..+.+|.+++.++|..+|||.+||...++
T Consensus        23 ~~r~~Il~~L~~~~~~~~ela~~l~is~~tvs~~L~   58 (98)
T 3jth_A           23 ERRLQILCMLHNQELSVGELCAKLQLSQSALSQHLA   58 (98)
T ss_dssp             HHHHHHHHHTTTSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            458899999988999999999999999999999998

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=94.12  E-value=0.073  Score=38.47  Aligned_cols=36  Identities=17%  Similarity=0.112  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|..|+..+.+|.+++.++|..+|||.+||...++
T Consensus        23 ~~r~~Il~~L~~~~~~~~ela~~l~is~~tvs~~L~   58 (102)
T 3pqk_A           23 PVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLG   58 (102)
T ss_dssp             HHHHHHHHHHHTCCBCHHHHHHHHTCCTTHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            458999999999999999999999999999999998

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=94.09  E-value=0.058  Score=36.72  Aligned_cols=36  Identities=25%  Similarity=0.285  Sum_probs=28.0

Q ss_pred             HHHHHHH-c-CCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         40 AALEALR-A-GQMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        40 ~AI~~~~-~-g~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      .+++.+. + +.+|..++|+.+|||++|+++.++.+.-
T Consensus        14 ~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L~~   51 (67)
T 2heo_A           14 KILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLKK   51 (67)
T ss_dssp             HHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3444443 3 4699999999999999999999997633

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

Probab=94.01  E-value=0.094  Score=34.84  Aligned_cols=38  Identities=24%  Similarity=0.176  Sum_probs=30.1

Q ss_pred             CCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        174 WKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       174 ~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .++.++ +|+....-.++++.++|..+|||.+||+.+++
T Consensus        16 L~~~~r-~il~l~~~~g~s~~eIA~~lgis~~tv~~~~~   53 (70)
T 2o8x_A           16 LTTDQR-EALLLTQLLGLSYADAAAVCGCPVGTIRSRVA   53 (70)
T ss_dssp             SCHHHH-HHHHHHHTSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            445544 56666545559999999999999999999887

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

Probab=93.93  E-value=0.093  Score=37.39  Aligned_cols=40  Identities=18%  Similarity=0.164  Sum_probs=29.8

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..++.+.. +|.++.-.|+|+.+||+.+||+.+||+.++++
T Consensus        37 ~L~~~~r~-vl~l~~~~g~s~~eIA~~lgis~~tV~~~l~r   76 (92)
T 3hug_A           37 QLSAEHRA-VIQRSYYRGWSTAQIATDLGIAEGTVKSRLHY   76 (92)
T ss_dssp             TSCHHHHH-HHHHHHTSCCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             cCCHHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            34444444 34443345889999999999999999999886

>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=93.91  E-value=0.15  Score=35.82  Aligned_cols=54  Identities=11%  Similarity=0.072  Sum_probs=36.8

Q ss_pred             HHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCC
Q psy17316        125 NVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQ  190 (229)
Q Consensus       125 ~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~  190 (229)
                      .+++.++.+| +|..+||+.+||+..|++.++++.-.++..           ..+.+++.++..++
T Consensus        27 ~~vl~l~~~g-~s~~eIA~~l~is~~tV~~~l~r~~~kL~~-----------~~~~~l~~~a~~~g   80 (82)
T 1je8_A           27 RDILKLIAQG-LPNKMIARRLDITESTVKVHVKHMLKKMKL-----------KSRVEAAVWVHQER   80 (82)
T ss_dssp             HHHHHHHTTT-CCHHHHHHHHTSCHHHHHHHHHHHHHHTTC-----------SSHHHHHHHHHHTT
T ss_pred             HHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHHHHHHHHcC-----------CCHHHHHHHHHHcC
Confidence            3556666666 599999999999999999887643222221           11567777766654

>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=93.90  E-value=0.094  Score=35.20  Aligned_cols=39  Identities=10%  Similarity=0.153  Sum_probs=29.9

Q ss_pred             CCHHHHHHHHHHHH----cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         33 WTHEDMDAALEALR----AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        33 yt~e~~~~AI~~~~----~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .++.+. +++...-    ..++|..+||+.+|||.+|+++++++
T Consensus         6 L~~~er-~il~l~~~l~~~~g~s~~eIA~~lgis~~tV~~~~~r   48 (68)
T 2p7v_B            6 LTAREA-KVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAK   48 (68)
T ss_dssp             CCHHHH-HHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCHHHH-HHHHHHHccCCCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            455554 4444443    35899999999999999999999886

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

Probab=93.86  E-value=0.12  Score=35.27  Aligned_cols=32  Identities=9%  Similarity=0.042  Sum_probs=27.3

Q ss_pred             HHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        180 EIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       180 ~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+|+.++ ..++++.++|..+|||..||+.+++
T Consensus        22 ~~vl~l~-~~g~s~~eIA~~l~is~~tV~~~~~   53 (79)
T 1x3u_A           22 RQVLSAV-VAGLPNKSIAYDLDISPRTVEVHRA   53 (79)
T ss_dssp             HHHHHHH-TTTCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4666666 5669999999999999999999886

>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian}

Probab=93.81  E-value=0.15  Score=40.11  Aligned_cols=66  Identities=9%  Similarity=0.069  Sum_probs=49.0

Q ss_pred             CCCHHHHHHHhCCChHHHHHHHHHhCCcc-cCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhC
Q psy17316        135 SISANKASKAYGIPSSTLYKIARKEGIRL-AQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYG  201 (229)
Q Consensus       135 ~~S~~~~a~k~gIp~sTL~~~ik~~g~k~-~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fg  201 (229)
                      .+++.++|+.+||+..||+-|.+. |.-. .....+..|.|+++  +++..|..+.+-+++..++...+.
T Consensus        16 ~~~I~evA~~~gvs~~tLR~Ye~~-Gll~p~~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sL~eIk~~l~   84 (148)
T 3gpv_A           16 YYTIGQVAKMQHLTISQIRYYDKQ-GLFPFLQRNEKGDRIFNEEALKYLEMILCLKNTGMPIQKIKQFID   84 (148)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHHHT-TCCTTCEECTTCCEEBCHHHHHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             ceeHHHHHHHHCcCHHHHHHHHHC-CCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            368999999999999999999873 4321 11112345778766  456777888888899999988876

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

Probab=93.80  E-value=0.12  Score=38.01  Aligned_cols=39  Identities=15%  Similarity=0.135  Sum_probs=32.3

Q ss_pred             CCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        172 TAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       172 r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...++.++ +|+.++..| +++.|+|..+|||..||+.+++
T Consensus        33 ~~Lt~re~-~Vl~l~~~G-~s~~EIA~~L~iS~~TV~~~l~   71 (99)
T 1p4w_A           33 KRLSPKES-EVLRLFAEG-FLVTEIAKKLNRSIKTISSQKK   71 (99)
T ss_dssp             SSCCHHHH-HHHHHHHHT-CCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCCCHHHH-HHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHH
Confidence            34666666 677887765 9999999999999999999886

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

Probab=93.78  E-value=0.12  Score=34.74  Aligned_cols=38  Identities=13%  Similarity=0.082  Sum_probs=30.7

Q ss_pred             CCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        173 AWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       173 ~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..++.++ +|+.++ ..++++.++|..+|||.+||+.+++
T Consensus        11 ~L~~~e~-~il~~~-~~g~s~~eIA~~l~is~~tV~~~~~   48 (74)
T 1fse_A           11 LLTKRER-EVFELL-VQDKTTKEIASELFISEKTVRNHIS   48 (74)
T ss_dssp             CCCHHHH-HHHHHH-TTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCCHHHH-HHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3555444 677776 5558999999999999999999987

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=93.77  E-value=0.096  Score=37.51  Aligned_cols=35  Identities=14%  Similarity=0.018  Sum_probs=30.3

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ...++..+ +|.+++.++|+.+||+++||++.++.+
T Consensus        33 r~~Il~~L-~~~~~~~eLa~~l~is~~tv~~~L~~L   67 (96)
T 1y0u_A           33 RRKILRML-DKGRSEEEIMQTLSLSKKQLDYHLKVL   67 (96)
T ss_dssp             HHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            34566666 889999999999999999999999875

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=93.76  E-value=0.079  Score=36.85  Aligned_cols=36  Identities=14%  Similarity=0.053  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHh---CCCcHHHHHHHh-----CCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRS---GQTTVQRASAEY-----GIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~---~~~s~~eAA~~f-----gVp~~tv~~~vk  212 (229)
                      ..|..|++.+.+   +.++..+++..+     +||.+|||+.++
T Consensus        17 ~~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~   60 (83)
T 2fu4_A           17 LPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLN   60 (83)
T ss_dssp             HHHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHH
Confidence            358899999876   469999999999     999999999998

>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=93.74  E-value=0.12  Score=38.87  Aligned_cols=38  Identities=13%  Similarity=0.283  Sum_probs=29.5

Q ss_pred             CCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        174 WKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       174 ~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .++.++ +|+....-.++|+.++|..+|||.+||+.++.
T Consensus        23 L~~~~r-~vl~l~y~~g~s~~EIA~~lgiS~~tV~~~l~   60 (113)
T 1s7o_A           23 LTDKQM-NYIELYYADDYSLAEIADEFGVSRQAVYDNIK   60 (113)
T ss_dssp             SCHHHH-HHHHHHHHTCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            445555 55555544459999999999999999999986

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=93.67  E-value=0.11  Score=37.89  Aligned_cols=36  Identities=11%  Similarity=0.103  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|..|+..+.++.+++.++|..+|||.+||...++
T Consensus        26 ~~r~~IL~~L~~~~~~~~ela~~l~is~stvs~~L~   61 (106)
T 1r1u_A           26 YNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLK   61 (106)
T ss_dssp             HHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            458899999988999999999999999999999998

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

Probab=93.67  E-value=0.08  Score=38.81  Aligned_cols=38  Identities=18%  Similarity=0.111  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      .+-+..|++++..++.+..++|..+|||.+||.+.++.
T Consensus         6 ~~R~~~I~~~l~~~~~ti~dlA~~~gVS~~TVsR~L~~   43 (93)
T 2l0k_A            6 KERTIKIGKYIVETKKTVRVIAKEFGVSKSTVHKDLTE   43 (93)
T ss_dssp             HHHHHHHHHHHHHHCCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence            45566788888888899999999999999999999874

>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=93.65  E-value=0.13  Score=35.05  Aligned_cols=42  Identities=7%  Similarity=0.126  Sum_probs=31.0

Q ss_pred             CCCCHHHHHHHHHHHH-c--CCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         31 KTWTHEDMDAALEALR-A--GQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~-~--g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ...++.+..-....+. +  .++|..+||..+|||.+|+++++.+
T Consensus         9 ~~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~r   53 (73)
T 1ku3_A            9 SKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENK   53 (73)
T ss_dssp             TTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            3456666644443442 1  5799999999999999999998875

>1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli}

Probab=93.51  E-value=0.052  Score=36.76  Aligned_cols=49  Identities=10%  Similarity=0.072  Sum_probs=31.7

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEG  185 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~  185 (229)
                      +++.+++..+||+++|+|+|++.-.+..... -+....|..++..+-|+.
T Consensus        11 l~~~eva~~lgvsrstiy~~~~~g~fP~pik-lG~~~~w~~~ev~~Wl~~   59 (66)
T 1z4h_A           11 VDLKFIMADTGFGKTFIYDRIKSGDLPKAKV-IHGRARWLYRDHCEFKNK   59 (66)
T ss_dssp             ECHHHHHHHHSSCHHHHHHHHHHHHCCCSEE-SSSCEEEEHHHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHCCCCCCCEE-eCCCeEEeHHHHHHHHHH
Confidence            6899999999999999999998533222111 122223766555555444

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=93.48  E-value=0.085  Score=42.18  Aligned_cols=42  Identities=17%  Similarity=0.139  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH-hhcCCC
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-LSRSTP  218 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~~  218 (229)
                      |-|..|+++++.|..+..++|+..|+||++++..+. +.+.|-
T Consensus        11 erk~~ILE~Lk~G~~~t~~Iak~LGlShg~aq~~Ly~LeREG~   53 (165)
T 2vxz_A           11 VRLRDILALLADGCKTTSLIQQRLGLSHGRAKALIYVLEKEGR   53 (165)
T ss_dssp             HHHHHHHHHHTTCCEEHHHHHHHHTCCHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHhCCccHHHHHHHhCCcHHHHHHHHHHHHhcCc
Confidence            568899999999999999999999999999999988 776663

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=93.46  E-value=0.12  Score=36.84  Aligned_cols=37  Identities=16%  Similarity=0.120  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHhCC----CcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRSGQ----TTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~----~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+...+|++.+.++.    +++.++|.++|||+.+|.+.+.
T Consensus         9 ~~~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~   49 (81)
T 1qbj_A            9 QDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLY   49 (81)
T ss_dssp             HHHHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            344556777776644    8999999999999999999987

>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=93.40  E-value=0.11  Score=36.40  Aligned_cols=38  Identities=16%  Similarity=0.099  Sum_probs=30.5

Q ss_pred             CCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        173 AWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       173 ~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..++.++ +|+.++ ..++++.++|..+|||..||+.+++
T Consensus        21 ~Lt~~e~-~vl~l~-~~g~s~~eIA~~l~is~~tV~~~l~   58 (82)
T 1je8_A           21 QLTPRER-DILKLI-AQGLPNKMIARRLDITESTVKVHVK   58 (82)
T ss_dssp             GSCHHHH-HHHHHH-TTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             cCCHHHH-HHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3455544 677776 4559999999999999999999887

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=93.39  E-value=0.42  Score=35.51  Aligned_cols=53  Identities=6%  Similarity=0.033  Sum_probs=37.5

Q ss_pred             CCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHH
Q psy17316         86 SWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIAR  157 (229)
Q Consensus        86 ~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik  157 (229)
                      .++++..+.++.                  ....++ ...+|..+|...+++..+||+++||+++++.+-++
T Consensus         4 rmT~~eFe~~~~------------------~l~~~~-~~~~~A~lyYv~g~tQ~eIA~~lGiSR~~VsrlL~   56 (101)
T 2w7n_A            4 RLTESQFQEAIQ------------------GLEVGQ-QTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVH   56 (101)
T ss_dssp             CCCHHHHHHHHT------------------TCCCCH-HHHHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCHHHHHHHHc------------------cCChHH-HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            467777777762                  224544 34555556655556999999999999999888765

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=93.37  E-value=0.13  Score=37.45  Aligned_cols=36  Identities=6%  Similarity=0.029  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+..|+..+.+|.++..++|..+|||.+||++.++
T Consensus        21 ~~r~~IL~~L~~~~~~~~ela~~l~is~~tv~~~l~   56 (114)
T 2oqg_A           21 ETRWEILTELGRADQSASSLATRLPVSRQAIAKHLN   56 (114)
T ss_dssp             HHHHHHHHHHHHSCBCHHHHHHHSSSCHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            457889998888899999999999999999999998

>3gbg_A TCP pilus virulence regulatory protein; cupin, helix-turn-helix, ARAC family, activator, DNA-binding transcription, transcription regulation; HET: PAM; 1.90A {Vibrio cholerae}

Probab=93.31  E-value=0.19  Score=42.19  Aligned_cols=81  Identities=7%  Similarity=0.137  Sum_probs=58.2

Q ss_pred             HHHHHHHHHH---cCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCC-CHHHHHHHHHHHHhCCCcHHHHHH
Q psy17316        123 ILNVALDALR---AGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAW-KPEDLEIALEGIRSGQTTVQRASA  198 (229)
Q Consensus       123 ~k~~AV~~~~---~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~-t~e~r~eaV~~~~~~~~s~~eAA~  198 (229)
                      ...++++.+.   ....|+.++|+.+||+.++|.+..|..|....        .| ..--..+|.+++..+++++.++|.
T Consensus       170 ~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~G~t~~--------~~l~~~Rl~~A~~lL~~~~~si~eIA~  241 (276)
T 3gbg_A          170 AMEKISCLVKSDITRNWRWADICGELRTNRMILKKELESRGVKFR--------ELINSIRISYSISLMKTGEFKIKQIAY  241 (276)
T ss_dssp             HHHHHHHHHHHTTTSCCCHHHHHHHHTCCHHHHHHHHHTTTCCHH--------HHHHHHHHHHHHHHHHHTCCCHHHHHH
T ss_pred             HHHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHH--------HHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence            3444444443   34579999999999999999999975454332        23 223456677777788899999999


Q ss_pred             HhCCChHHHHHHH
Q psy17316        199 EYGIPSGTLYGRC  211 (229)
Q Consensus       199 ~fgVp~~tv~~~v  211 (229)
                      ..|-+.++-...+
T Consensus       242 ~~Gf~~~s~F~r~  254 (276)
T 3gbg_A          242 QSGFASVSYFSTV  254 (276)
T ss_dssp             HTTCSCHHHHHHH
T ss_pred             HhCCCCHHHHHHH
Confidence            9999776655554

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=93.28  E-value=0.12  Score=36.85  Aligned_cols=42  Identities=14%  Similarity=0.208  Sum_probs=32.8

Q ss_pred             CCCHHHHHHHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         32 TWTHEDMDAALEALR-AGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        32 kyt~e~~~~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..+..+....+..+. ++++|+.++|+.+||+++|+++.++.+
T Consensus        18 ~l~~~~~~~l~~l~~~~~~~t~~ela~~l~is~~tv~~~l~~L   60 (109)
T 2d1h_A           18 KITDTDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKL   60 (109)
T ss_dssp             TCCHHHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            345555544444444 788999999999999999999999986

>2zhg_A Redox-sensitive transcriptional activator SOXR; oxidative stress, MERR family, activator; HET: DNA; 2.80A {Escherichia coli} PDB: 2zhh_A

Probab=93.27  E-value=0.11  Score=41.19  Aligned_cols=26  Identities=8%  Similarity=0.135  Sum_probs=23.2

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ...+++.++|+.+||+..||+.|-+.
T Consensus         9 ~~~~~i~e~A~~~gvs~~TLR~ye~~   34 (154)
T 2zhg_A            9 KALLTPGEVAKRSGVAVSALHFYESK   34 (154)
T ss_dssp             -CCBCHHHHHHHHTSCHHHHHHHHHT
T ss_pred             ccCCCHHHHHHHHCcCHHHHHHHHHc
Confidence            34689999999999999999999887

>1gdt_A GD resolvase, protein (gamma delta resolvase); protein-DNA complex, double helix, overhanging base, DNA binding protein/DNA complex; 3.00A {Escherichia coli} SCOP: a.4.1.2 c.53.1.1 PDB: 1zr4_A 1zr2_A 2gm4_A 1res_A 1ret_A

Probab=93.26  E-value=0.14  Score=41.02  Aligned_cols=40  Identities=15%  Similarity=0.138  Sum_probs=31.1

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316        170 SPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       170 ~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      ++..++++   .|.++..+| +++.++|..+|||.+|||++++.
T Consensus       142 r~~~~~~~---~i~~~~~~G-~s~~~Ia~~l~is~~tv~r~l~~  181 (183)
T 1gdt_A          142 RKRKIDRD---AVLNMWQQG-LGASHISKTMNIARSTVYKVINE  181 (183)
T ss_dssp             SCCCSCHH---HHHHHHHTT-CCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             CCCCCCHH---HHHHHHHCC-CCHHHHHHHHCcCHHHHHHHHhh
Confidence            34456653   466666655 89999999999999999999874

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=93.26  E-value=0.062  Score=37.01  Aligned_cols=25  Identities=8%  Similarity=0.033  Sum_probs=23.2

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-++|+.++|+.+||+++||.+|..
T Consensus        23 ~~gltq~~lA~~~gvs~~~is~~e~   47 (80)
T 3kz3_A           23 ELGLSYESVADKMGMGQSAVAALFN   47 (80)
T ss_dssp             HHTCCHHHHHHHTTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHHc
Confidence            4689999999999999999999986

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=93.21  E-value=0.13  Score=35.75  Aligned_cols=27  Identities=4%  Similarity=-0.122  Sum_probs=24.9

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +|.+|..++|+.+||+++|+++.+..+
T Consensus        12 ~~~~s~~eLa~~lgvs~~tv~r~L~~L   38 (81)
T 2htj_A           12 HNGGKTAEIAEALAVTDYQARYYLLLL   38 (81)
T ss_dssp             SCCCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            478999999999999999999998875

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=93.19  E-value=0.074  Score=37.37  Aligned_cols=37  Identities=16%  Similarity=0.127  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHhC----CCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRSG----QTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~~----~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++....|++.+.++    .+++.++|.++|||+.||.+.+.
T Consensus        13 ~~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~   53 (77)
T 1qgp_A           13 QDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLY   53 (77)
T ss_dssp             HHHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            44456777777765    48999999999999999999987

>1eto_A FIS, factor for inversion stimulation; transcriptional activation region, DNA-binding protein, transcription activator; 1.90A {Escherichia coli} SCOP: a.4.1.12 PDB: 1etq_A 1ety_A 1fia_A 3fis_A 3iv5_A* 3jr9_A* 3jra_A* 3jrb_A* 3jrc_A* 3jrd_A* 3jre_A* 3jrf_A* 3jrg_A* 3jrh_A* 3jri_A* 1f36_A 1etv_A 1etk_A 1etx_A 1fip_A ...

Probab=93.19  E-value=0.14  Score=37.70  Aligned_cols=36  Identities=22%  Similarity=0.159  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      ++.-|.+.+...+-+..+||...||+++|||++++.
T Consensus        59 Er~~I~~aL~~~~gn~~~AA~~LGIsR~TL~rkLkk   94 (98)
T 1eto_A           59 EQPLLDMVMQYTLGNQTRAALMMGINRGTLRKKLKK   94 (98)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            455566667677778999999999999999999873

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

Probab=93.19  E-value=0.13  Score=35.17  Aligned_cols=37  Identities=11%  Similarity=0.128  Sum_probs=29.0

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      |+.+. +++..+ -.|+|..+||..+||+.+|++.++++
T Consensus        18 ~~~e~-~vl~l~-~~g~s~~eIA~~l~is~~tV~~~~~r   54 (79)
T 1x3u_A           18 SERER-QVLSAV-VAGLPNKSIAYDLDISPRTVEVHRAN   54 (79)
T ss_dssp             CHHHH-HHHHHH-TTTCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred             CHHHH-HHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            34443 445555 56889999999999999999998886

>2r0q_C Putative transposon TN552 DNA-invertase BIN3; site-specific recombinase, resolvase, DNA-binding protein, protein-DNA complex, DNA integration, DNA invertase, DNA recombination; 3.20A {Staphylococcus aureus}

Probab=93.13  E-value=0.35  Score=39.57  Aligned_cols=32  Identities=19%  Similarity=0.301  Sum_probs=27.0

Q ss_pred             HHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        180 EIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       180 ~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+|.+++.+| +++.++|..+|||.+|||++++
T Consensus       166 ~~i~~~~~~G-~s~~~Ia~~l~is~~tv~r~l~  197 (209)
T 2r0q_C          166 HRVVEMLEEG-QAISKIAKEVNITRQTVYRIKH  197 (209)
T ss_dssp             HHHHHHHHTT-CCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHh
Confidence            3555666555 8999999999999999999987

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=93.12  E-value=0.16  Score=35.32  Aligned_cols=51  Identities=14%  Similarity=0.138  Sum_probs=37.7

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCc
Q psy17316        124 LNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTT  192 (229)
Q Consensus       124 k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s  192 (229)
                      +.+||+.+    .|+.++|+..||+++++++|+...++              +..+...|+.+-+|...
T Consensus         3 ~~~ai~~~----G~~~~lA~~lGVs~~aVs~W~~g~~i--------------P~~~~~~Ie~~T~G~vk   53 (71)
T 2hin_A            3 PEELVRHF----GDVEKAAVGVGVTPGAVYQWLQAGEI--------------PPLRQSDIEVRTAYKLK   53 (71)
T ss_dssp             HHHHHHHH----SSHHHHHHHHTSCHHHHHHHHHHTSC--------------CHHHHHHHHHHTTTSSC
T ss_pred             HHHHHHHH----CCHHHHHHHHCCCHHHHHHHHhCCCC--------------CHHHHHHHHHHhCCcch
Confidence            35667776    37999999999999999999975332              24466677777777665

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=93.04  E-value=0.081  Score=39.54  Aligned_cols=42  Identities=14%  Similarity=0.200  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      ...|..|+..+.+|.+++.++|..+|||.+||...++ +.+.|
T Consensus        17 ~~~R~~Il~~L~~~~~~~~eLa~~l~is~~tvs~hL~~L~~~G   59 (118)
T 3f6o_A           17 DPTRRAVLGRLSRGPATVSELAKPFDMALPSFMKHIHFLEDSG   59 (118)
T ss_dssp             SHHHHHHHHHHHTCCEEHHHHHTTCCSCHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHhCCCCHHHHHHHhCcCHHHHHHHHHHHHHCC
Confidence            3568999999999999999999999999999999998 44333

>2dg6_A Putative transcriptional regulator; winged-helix motif, MERR family, gene regulation; 2.20A {Streptomyces coelicolor}

Probab=93.04  E-value=0.35  Score=40.72  Aligned_cols=65  Identities=17%  Similarity=0.241  Sum_probs=44.1

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCC-cccCCCCCCCCCCCHH--HHHHHHHHHHhC-CCcHHHHHHHhC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGI-RLAQPFNASPTAWKPE--DLEIALEGIRSG-QTTVQRASAEYG  201 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~-k~~~~~~~~~r~~t~e--~r~eaV~~~~~~-~~s~~eAA~~fg  201 (229)
                      +++.++|+.+||+.+||+-|-+. |. .......+..|.|+++  .++..|..+.+- +++..++...+.
T Consensus         1 ~~IgevA~~~Gvs~~TLRyYE~~-GLl~p~~R~~~gyR~Y~~~dl~~L~~I~~lr~~~G~sL~eIk~~l~   69 (222)
T 2dg6_A            1 MRLADLSKRSGVSTATIKYYLRE-GLLPPGRQVNATTAEYDEDHLRRLRLVRALIQVGKVPVATAREVLG   69 (222)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHH-TSSCCC---------CCHHHHHHHHHHHHHHHTTCCCHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC-CCCCCCeeCCCCceeeCHHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence            47899999999999999999885 53 2211112345778766  566777788776 899999988664

>2dg6_A Putative transcriptional regulator; winged-helix motif, MERR family, gene regulation; 2.20A {Streptomyces coelicolor}

Probab=93.01  E-value=0.32  Score=40.98  Aligned_cols=24  Identities=21%  Similarity=0.173  Sum_probs=22.0

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      |++.++|+.+||+..||+.|-+..
T Consensus         1 ~~IgevA~~~Gvs~~TLRyYE~~G   24 (222)
T 2dg6_A            1 MRLADLSKRSGVSTATIKYYLREG   24 (222)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            688999999999999999998873

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=93.00  E-value=0.16  Score=42.05  Aligned_cols=43  Identities=9%  Similarity=0.156  Sum_probs=32.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .+|.-++-..+..+...|+|+.+||+++||++.+|.++++.-.
T Consensus         7 e~sl~eiG~ria~~y~~g~tQ~eIA~~lGiSr~~VSR~L~~A~   49 (192)
T 1zx4_A            7 QHSIREIGLRLMRMKNDGMSQKDIAAKEGLSQAKVTRALQAAS   49 (192)
T ss_dssp             SSCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHT
T ss_pred             cccHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHhc
Confidence            4455556333333455679999999999999999999998743

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

Probab=92.99  E-value=0.22  Score=36.49  Aligned_cols=41  Identities=10%  Similarity=0.108  Sum_probs=33.8

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..+.|+.++ +++..+.+ |+|..+||..+||+.+||+.++.+
T Consensus        32 ~~~Lt~re~-~Vl~l~~~-G~s~~EIA~~L~iS~~TV~~~l~r   72 (99)
T 1p4w_A           32 DKRLSPKES-EVLRLFAE-GFLVTEIAKKLNRSIKTISSQKKS   72 (99)
T ss_dssp             SSSCCHHHH-HHHHHHHH-TCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             cCCCCHHHH-HHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHH
Confidence            567888887 44556655 789999999999999999998886

>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=92.94  E-value=0.12  Score=37.25  Aligned_cols=40  Identities=13%  Similarity=0.094  Sum_probs=31.3

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ...|+.+. +++..+ ..|+|..+||..+||+.+||+.++++
T Consensus        26 ~~Lt~~e~-~vl~l~-~~g~s~~eIA~~l~is~~tV~~~l~r   65 (95)
T 3c57_A           26 SGLTDQER-TLLGLL-SEGLTNKQIADRMFLAEKTVKNYVSR   65 (95)
T ss_dssp             -CCCHHHH-HHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hcCCHHHH-HHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45677666 444456 45789999999999999999998886

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=92.90  E-value=0.13  Score=38.85  Aligned_cols=93  Identities=8%  Similarity=0.049  Sum_probs=59.7

Q ss_pred             HHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCC-CCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHH
Q psy17316         44 ALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTP-KKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEE  122 (229)
Q Consensus        44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~-~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e  122 (229)
                      .+.....++.++|..+||+..++.+|++..--.|. .......-|.++...++.+.+                       
T Consensus        15 ~~~~~p~~~~~la~~~~~~~~~~~~~l~~l~~~G~l~~i~~~~~~~~~~~~~~~~~l-----------------------   71 (121)
T 2pjp_A           15 LFGDEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVKDRYYRNDRIVEFANMI-----------------------   71 (121)
T ss_dssp             GCSSSCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEETTEEEEHHHHHHHHHHH-----------------------
T ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCceECHHHHHHHHHHH-----------------------
Confidence            44346779999999999999999999887533321 111111123444333333211                       


Q ss_pred             HHHHHHHHH-HcCCCCHHHHHHHhCCChH---HHHHHHHHhCCccc
Q psy17316        123 ILNVALDAL-RAGSISANKASKAYGIPSS---TLYKIARKEGIRLA  164 (229)
Q Consensus       123 ~k~~AV~~~-~~g~~S~~~~a~k~gIp~s---TL~~~ik~~g~k~~  164 (229)
                           .+.+ .+|.+++.++-..+|+++.   +|-...-+.|+...
T Consensus        72 -----~~~~~~~~~it~ae~Rd~lg~sRK~ai~lLE~~Dr~g~TrR  112 (121)
T 2pjp_A           72 -----RDLDQECGSTCAADFRDRLGVGRKLAIQILEYFDRIGFTRR  112 (121)
T ss_dssp             -----HHHHHHHSSEEHHHHHHHHTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             -----HHHHHHCCCccHHHHHHHHCCcHHHHHHHHHHHhhcCCeEe
Confidence                 1111 2577999999999999998   68787777776543

>1d5y_A ROB transcription factor; protein-DNA complex, DNA, transcription/DNA complex; HET: DNA; 2.70A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 d.60.1.2

Probab=92.89  E-value=0.19  Score=42.61  Aligned_cols=79  Identities=15%  Similarity=0.199  Sum_probs=57.0

Q ss_pred             HHHHHHHHHc---CCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHHH-HHHHHHHHHhCCCcHHHHHH
Q psy17316        124 LNVALDALRA---GSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPED-LEIALEGIRSGQTTVQRASA  198 (229)
Q Consensus       124 k~~AV~~~~~---g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e~-r~eaV~~~~~~~~s~~eAA~  198 (229)
                      ..++++.+.+   ..+|+.++|+.+|++.++|.+..++. |....        .|-... +..|.+++...++++.++|.
T Consensus         5 ~~~~~~~i~~~~~~~~~~~~la~~~~~s~~~l~r~f~~~~g~s~~--------~~~~~~Rl~~a~~~L~~~~~~i~~ia~   76 (292)
T 1d5y_A            5 IRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIG--------AYIRARRLSKSAVALRLTARPILDIAL   76 (292)
T ss_dssp             HHHHHHHHHTTSSSSCCCHHHHTTTSSCHHHHHHHHHHHHSSCHH--------HHHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHhcCCCCHHHHHH
Confidence            4455555543   45799999999999999999999876 75443        232333 45566677778899999999


Q ss_pred             HhCCChHHHHHH
Q psy17316        199 EYGIPSGTLYGR  210 (229)
Q Consensus       199 ~fgVp~~tv~~~  210 (229)
                      .+|-+.++-...
T Consensus        77 ~~Gf~~~~~f~r   88 (292)
T 1d5y_A           77 QYRFDSQQTFTR   88 (292)
T ss_dssp             HTTCSCHHHHHH
T ss_pred             HcCCCCHHHHHH
Confidence            999776554443

>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=92.86  E-value=0.15  Score=34.22  Aligned_cols=37  Identities=5%  Similarity=0.038  Sum_probs=29.0

Q ss_pred             CHHHHHHHHHHHH----hCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        175 KPEDLEIALEGIR----SGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       175 t~e~r~eaV~~~~----~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++.++ +|+...-    ..++++.++|..+|||.+||..++.
T Consensus         7 ~~~er-~il~l~~~l~~~~g~s~~eIA~~lgis~~tV~~~~~   47 (68)
T 2p7v_B            7 TAREA-KVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEA   47 (68)
T ss_dssp             CHHHH-HHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHH-HHHHHHHccCCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            44444 5666555    3569999999999999999999886

>2p5k_A Arginine repressor; DNA-binding domain, winged helix-turn-helix (WHTH), DNA binding protein; 1.00A {Bacillus subtilis} SCOP: a.4.5.3 PDB: 2p5l_C*

Probab=92.85  E-value=0.27  Score=32.10  Aligned_cols=36  Identities=14%  Similarity=0.080  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHh--CCCcHHHHHHHh-----CCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRS--GQTTVQRASAEY-----GIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~--~~~s~~eAA~~f-----gVp~~tv~~~vk  212 (229)
                      ..|..+|..+..  +.++..+++..|     +||..|||+.++
T Consensus         4 ~~R~~~i~~ll~~~~~~t~~el~~~l~~~~~~vs~~Tv~R~L~   46 (64)
T 2p5k_A            4 GQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIK   46 (64)
T ss_dssp             HHHHHHHHHHHHHSCCCSHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCcCHHHHHHHHH
Confidence            457776665543  568999999999     999999999988

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=92.85  E-value=0.13  Score=37.41  Aligned_cols=37  Identities=11%  Similarity=0.068  Sum_probs=31.2

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      ...++..+.+|.+++.++|+.+||+++|+++.++.+.
T Consensus        23 r~~IL~~L~~~~~~~~ela~~l~is~~tv~~~l~~L~   59 (114)
T 2oqg_A           23 RWEILTELGRADQSASSLATRLPVSRQAIAKHLNALQ   59 (114)
T ss_dssp             HHHHHHHHHHSCBCHHHHHHHSSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3455555678899999999999999999999999863

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=92.80  E-value=0.14  Score=37.34  Aligned_cols=39  Identities=13%  Similarity=0.116  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .....++..+.+|.+++.++|+.+||+++||.+.++.+.
T Consensus        26 ~~r~~IL~~L~~~~~~~~ela~~l~is~stvs~~L~~L~   64 (106)
T 1r1u_A           26 YNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLK   64 (106)
T ss_dssp             HHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            334566666678899999999999999999999999753

>3m8j_A FOCB protein; all-alpha, helix-turn-helix, transcription; 1.40A {Escherichia coli}

Probab=92.78  E-value=0.2  Score=37.99  Aligned_cols=43  Identities=12%  Similarity=0.082  Sum_probs=39.1

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ++.+.+++..|+++++-.|+|.+++|.+|||+.+-+.+.++++
T Consensus        42 S~IrSekII~ALrdyLV~G~srkeaCe~~gV~~syfS~~L~rL   84 (111)
T 3m8j_A           42 SSIHSDRVILAMKDYLVSGHSRKDVCEKYQMNNGYFSTTLGRL   84 (111)
T ss_dssp             SCCCCHHHHHHHHHHHTTCCCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHH
Confidence            5566789999999999999999999999999999999988874

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

Probab=92.77  E-value=0.19  Score=35.47  Aligned_cols=41  Identities=7%  Similarity=0.042  Sum_probs=30.3

Q ss_pred             CCCHHHHHHHHHHHH-c--CCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALR-A--GQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~-~--g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..++.+..-....+. .  .++|+.+||..+|||.+||+.++.+
T Consensus        18 ~L~~~er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~r   61 (87)
T 1tty_A           18 TLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVK   61 (87)
T ss_dssp             TSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            345555544443342 1  5799999999999999999999886

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=92.69  E-value=0.16  Score=36.68  Aligned_cols=38  Identities=24%  Similarity=0.155  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ...+.++..+.+|.+++.++|+.+||+++||.+.++.+
T Consensus        23 ~~r~~Il~~L~~~~~~~~ela~~l~is~~tvs~~L~~L   60 (102)
T 3pqk_A           23 PVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVL   60 (102)
T ss_dssp             HHHHHHHHHHHTCCBCHHHHHHHHTCCTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            34456777777899999999999999999999999986

>3fmy_A HTH-type transcriptional regulator MQSA (YGIT/B3021); helix-turn-helix, DNA-binding, transcription regulation, DNA binding protein; HET: MEQ; 1.40A {Escherichia coli k-12}

Probab=92.64  E-value=0.16  Score=34.54  Aligned_cols=37  Identities=14%  Similarity=0.019  Sum_probs=29.5

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .++.+.+..+-+   .-++|+.++|+.+||+.+||.+|-.
T Consensus        10 ~~~g~~lr~~R~---~~gltq~elA~~~gvs~~tis~~E~   46 (73)
T 3fmy_A           10 TVAPEFIVKVRK---KLSLTQKEASEIFGGGVNAFSRYEK   46 (73)
T ss_dssp             CCCHHHHHHHHH---HTTCCHHHHHHHHCSCTTHHHHHHT
T ss_pred             CCCHHHHHHHHH---HcCCCHHHHHHHhCcCHHHHHHHHc
Confidence            456666655443   3489999999999999999999966

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=92.64  E-value=0.083  Score=38.93  Aligned_cols=34  Identities=15%  Similarity=0.143  Sum_probs=31.6

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      |..|+..+.++.+++.++|..+|||.+||...++
T Consensus        27 r~~IL~~L~~~~~s~~eLa~~lgis~stvs~~L~   60 (108)
T 2kko_A           27 RLQILDLLAQGERAVEAIATATGMNLTTASANLQ   60 (108)
T ss_dssp             THHHHHHHTTCCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            6788888888999999999999999999999998

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=92.61  E-value=0.15  Score=35.99  Aligned_cols=36  Identities=8%  Similarity=0.020  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHhC-CCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSG-QTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~-~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+..|+..+..+ .++..++|..+|||.+||.+.++
T Consensus        24 ~~~~~il~~l~~~~~~s~~ela~~l~is~~tvs~~l~   60 (99)
T 3cuo_A           24 PKRLLILCMLSGSPGTSAGELTRITGLSASATSQHLA   60 (99)
T ss_dssp             HHHHHHHHHHTTCCSEEHHHHHHHHCCCHHHHHHHHH
T ss_pred             hHHHHHHHHHHhCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            4578889888777 79999999999999999999998

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

Probab=92.61  E-value=0.19  Score=37.83  Aligned_cols=35  Identities=11%  Similarity=0.006  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|.+|++.+.+| ++|++++..+|||..||-+..+
T Consensus        46 aqR~~Ia~lL~~G-~SyreIa~~tG~StaTIsRv~r   80 (107)
T 3frw_A           46 SQRFEVAKMLTDK-RTYLDISEKTGASTATISRVNR   80 (107)
T ss_dssp             HHHHHHHHHHHTT-CCHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcC-CCHHHHHHHHCccHHHHHHHHH
Confidence            3588999998888 9999999999999999988766

>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=92.59  E-value=0.21  Score=33.88  Aligned_cols=38  Identities=11%  Similarity=0.194  Sum_probs=29.2

Q ss_pred             CCHHHHHHHHHHHHh----CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        174 WKPEDLEIALEGIRS----GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       174 ~t~e~r~eaV~~~~~----~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .++.++ +|+...--    .++++.++|..+|||.+||+.+..
T Consensus        11 L~~~er-~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~   52 (73)
T 1ku3_A           11 LSEREA-MVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIEN   52 (73)
T ss_dssp             SCHHHH-HHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHH-HHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            445555 55555443    569999999999999999999876

>2zhg_A Redox-sensitive transcriptional activator SOXR; oxidative stress, MERR family, activator; HET: DNA; 2.80A {Escherichia coli} PDB: 2zhh_A

Probab=92.53  E-value=0.2  Score=39.69  Aligned_cols=68  Identities=12%  Similarity=0.197  Sum_probs=49.1

Q ss_pred             cCCCCHHHHHHHhCCChHHHHHHHHHhCC-cccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCC
Q psy17316        133 AGSISANKASKAYGIPSSTLYKIARKEGI-RLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGI  202 (229)
Q Consensus       133 ~g~~S~~~~a~k~gIp~sTL~~~ik~~g~-k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgV  202 (229)
                      ...+++.++|+.+||+..||+.|.+. |. ...+ ..+..|.|+.+  +++..|..+.+-+++..++...+..
T Consensus         9 ~~~~~i~e~A~~~gvs~~TLR~ye~~-Gll~p~r-~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~~   79 (154)
T 2zhg_A            9 KALLTPGEVAKRSGVAVSALHFYESK-GLITSIR-NSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGV   79 (154)
T ss_dssp             -CCBCHHHHHHHHTSCHHHHHHHHHT-TSSCCEE-CTTSCEEBCTTHHHHHHHHHHHHHHTCCHHHHHHHHCC
T ss_pred             ccCCCHHHHHHHHCcCHHHHHHHHHc-CCCCccc-CCCCCEEeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            44579999999999999999999884 53 2211 11335667654  4566677777777999999998875

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=92.51  E-value=0.14  Score=35.04  Aligned_cols=30  Identities=13%  Similarity=0.193  Sum_probs=25.6

Q ss_pred             HHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         42 LEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        42 I~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      |..+.... |+.++|+.+||++++|.+|++.
T Consensus         7 Lk~l~~~~-sq~~~A~~Lgvsq~aVS~~~~~   36 (65)
T 2cw1_A            7 LKKFVEDK-NQEYAARALGLSQKLIEEVLKR   36 (65)
T ss_dssp             HHHHHTTS-CHHHHHHHSSSCHHHHHHHHHT
T ss_pred             HHHHHHHc-CHHHHHHHhCCCHHHHHHHHHh
Confidence            44455655 9999999999999999999985

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

Probab=92.51  E-value=0.2  Score=35.65  Aligned_cols=34  Identities=15%  Similarity=0.206  Sum_probs=27.6

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -.+|+.+..-.++++.+||..+|||.+||+.++.
T Consensus        42 ~r~vl~l~~~~g~s~~eIA~~lgis~~tV~~~l~   75 (92)
T 3hug_A           42 HRAVIQRSYYRGWSTAQIATDLGIAEGTVKSRLH   75 (92)
T ss_dssp             HHHHHHHHHTSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4455666555559999999999999999999876

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=92.49  E-value=0.23  Score=33.70  Aligned_cols=23  Identities=22%  Similarity=0.143  Sum_probs=21.1

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +++.++|+..||+++||.+.+..
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLng   23 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVING   23 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcC
Confidence            57899999999999999999983

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}

Probab=92.42  E-value=0.17  Score=38.43  Aligned_cols=39  Identities=8%  Similarity=0.027  Sum_probs=28.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..++.+..-.+ .+. .|+|+.+||+.+|||.+||+.++++
T Consensus       109 ~L~~~~r~v~~-~~~-~g~s~~EIA~~lgis~~tV~~~~~r  147 (164)
T 3mzy_A          109 NFSKFEKEVLT-YLI-RGYSYREIATILSKNLKSIDNTIQR  147 (164)
T ss_dssp             HSCHHHHHHHH-HHT-TTCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hCCHHHHHHHH-HHH-cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            34444443333 444 5889999999999999999999886

>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=92.39  E-value=0.22  Score=37.26  Aligned_cols=40  Identities=15%  Similarity=0.303  Sum_probs=30.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..++.+.. ++..+.-.|+|+.+||..+|||.+|++.++++
T Consensus        25 ~L~~~~r~-vl~l~~~~g~s~~EIA~~lgiS~~tV~~~l~r   64 (113)
T 1xsv_A           25 LLTNKQRN-YLELFYLEDYSLSEIADTFNVSRQAVYDNIRR   64 (113)
T ss_dssp             GSCHHHHH-HHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             cCCHHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            34555543 44444355889999999999999999999886

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=92.38  E-value=0.19  Score=35.55  Aligned_cols=34  Identities=12%  Similarity=0.112  Sum_probs=29.4

Q ss_pred             HHHHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +.+|++++.. |..++.+.|.+|+||..||.+-+.
T Consensus         4 L~~Il~~L~~~g~vsv~eLa~~l~VS~~TIRrdL~   38 (78)
T 1xn7_A            4 LIQVRDLLALRGRMEAAQISQTLNTPQPMINAMLQ   38 (78)
T ss_dssp             HHHHHHHHHHSCSBCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHH
Confidence            4577777765 779999999999999999999876

>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=92.22  E-value=0.2  Score=35.95  Aligned_cols=38  Identities=13%  Similarity=0.198  Sum_probs=30.8

Q ss_pred             CCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        173 AWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       173 ~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|+.+ .+|+.++..| +++.++|..+|||..||...++
T Consensus        29 ~Lt~rE-~~Vl~l~~~G-~s~~eIA~~L~iS~~TV~~~~~   66 (90)
T 3ulq_B           29 VLTPRE-CLILQEVEKG-FTNQEIADALHLSKRSIEYSLT   66 (90)
T ss_dssp             CCCHHH-HHHHHHHHTT-CCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHH-HHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHH
Confidence            445544 4677777755 9999999999999999999887

>1r71_A Transcriptional repressor protein KORB; INCP, plasmid partitioning, protein-DNA complex, heilx-turn- helix motif, transcription factor; HET: BRU; 2.20A {Escherichia coli} SCOP: a.4.14.1

Probab=92.21  E-value=0.64  Score=37.80  Aligned_cols=44  Identities=11%  Similarity=0.022  Sum_probs=39.7

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +...++-+...++..+.+.|+|..+||+++|+++++|.+.++-.
T Consensus        33 RedL~piE~A~a~~~L~~~G~t~eeiA~~lG~s~s~V~~~LrLl   76 (178)
T 1r71_A           33 RNELTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVTLL   76 (178)
T ss_dssp             TTCCCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHGGG
T ss_pred             cCCCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            67888999999999888889999999999999999999998854

>2p5k_A Arginine repressor; DNA-binding domain, winged helix-turn-helix (WHTH), DNA binding protein; 1.00A {Bacillus subtilis} SCOP: a.4.5.3 PDB: 2p5l_C*

Probab=92.20  E-value=0.38  Score=31.36  Aligned_cols=40  Identities=5%  Similarity=0.033  Sum_probs=30.9

Q ss_pred             HHHHHHHHHH-H-cCCCCHHHHHHHc-----CCChhhHHHHHHHhCC
Q psy17316         36 EDMDAALEAL-R-AGQMSLTKASVSY-----GIPSTTLWQRAHRLGI   75 (229)
Q Consensus        36 e~~~~AI~~~-~-~g~~S~~~aA~~~-----gIp~sTL~~~i~~~gi   75 (229)
                      .+....|..+ . ++.+|+.+++..+     +|+.+||++.++..|+
T Consensus         4 ~~R~~~i~~ll~~~~~~t~~el~~~l~~~~~~vs~~Tv~R~L~~lg~   50 (64)
T 2p5k_A            4 GQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKELHL   50 (64)
T ss_dssp             HHHHHHHHHHHHHSCCCSHHHHHHHHHHTTCCCCHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCcCHHHHHHHHHHcCC
Confidence            3444444433 2 5679999999999     9999999999997764

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

Probab=92.18  E-value=0.22  Score=38.19  Aligned_cols=35  Identities=17%  Similarity=0.124  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|.+|++.+.+| ++|+++|..+|||-.||-+-.+
T Consensus        63 s~R~eV~klL~~G-~syreIA~~~g~S~aTIsRv~r   97 (119)
T 3kor_A           63 SQRLQVAKMIKQG-YTYATIEQESGASTATISRVKR   97 (119)
T ss_dssp             HHHHHHHHHHHHT-CCHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcC-CCHHHHHHHHCCCHHHHHHHHH
Confidence            3479999999999 9999999999999999988665

>3qao_A LMO0526 protein, MERR-like transcriptional regulator; structural genomics, the center for structural genomics of I diseases, csgid; 1.87A {Listeria monocytogenes}

Probab=92.14  E-value=0.37  Score=41.15  Aligned_cols=30  Identities=20%  Similarity=0.333  Sum_probs=25.2

Q ss_pred             CCCCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316         48 GQMSLTKASVSYGIPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        48 g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~   78 (229)
                      +.+++.++|+.+||+..||+.|-+. |+-.|
T Consensus         2 ~~~tI~evA~~~gvs~~TLRyYe~~-GLL~p   31 (249)
T 3qao_A            2 NAMQIKELAELTGVSVRTLHHYDKI-GLLVP   31 (249)
T ss_dssp             CCBCHHHHHHHHCCCHHHHHHHHHT-TSSCC
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHC-CCCCC
Confidence            4689999999999999999999884 55434

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=92.12  E-value=0.21  Score=37.57  Aligned_cols=41  Identities=10%  Similarity=0.048  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        177 EDLEIALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       177 e~r~eaV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      ..|.+|+..+. .+.+++.++|..+|||.+||...++ +...|
T Consensus        42 ~~rl~IL~~L~~~~~~s~~eLa~~l~is~stvs~~L~~L~~~G   84 (122)
T 1u2w_A           42 ENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQG   84 (122)
T ss_dssp             HHHHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            44788999887 6889999999999999999999998 33333

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=92.05  E-value=0.1  Score=37.31  Aligned_cols=38  Identities=16%  Similarity=0.109  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      ....++..+.+|.+++.++|+.+||+++|+++.++.+.
T Consensus        24 ~r~~Il~~L~~~~~~~~ela~~l~is~~tvs~~L~~L~   61 (98)
T 3jth_A           24 RRLQILCMLHNQELSVGELCAKLQLSQSALSQHLAWLR   61 (98)
T ss_dssp             HHHHHHHHTTTSCEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            34566777777899999999999999999999999863

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=92.05  E-value=0.22  Score=37.62  Aligned_cols=36  Identities=8%  Similarity=0.084  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|..|+..+.++.+++.++|..+|||.++|...++
T Consensus        46 ~~rl~IL~~L~~~~~s~~ela~~lgis~stvs~~L~   81 (122)
T 1r1t_A           46 PNRLRLLSLLARSELCVGDLAQAIGVSESAVSHQLR   81 (122)
T ss_dssp             HHHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            347889999888889999999999999999999998

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=91.99  E-value=0.12  Score=37.99  Aligned_cols=35  Identities=20%  Similarity=0.214  Sum_probs=29.8

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..++..+.+|.+++.++|+.+||+++|+.+.++.+
T Consensus        28 ~~IL~~L~~~~~s~~eLa~~lgis~stvs~~L~~L   62 (108)
T 2kko_A           28 LQILDLLAQGERAVEAIATATGMNLTTASANLQAL   62 (108)
T ss_dssp             HHHHHHHTTCCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            34555566789999999999999999999999975

>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=91.97  E-value=0.27  Score=35.40  Aligned_cols=38  Identities=11%  Similarity=0.017  Sum_probs=30.1

Q ss_pred             CCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        173 AWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       173 ~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..++.++ +|+.++ ..++++.++|..+|||..||+.+++
T Consensus        27 ~Lt~~e~-~vl~l~-~~g~s~~eIA~~l~is~~tV~~~l~   64 (95)
T 3c57_A           27 GLTDQER-TLLGLL-SEGLTNKQIADRMFLAEKTVKNYVS   64 (95)
T ss_dssp             CCCHHHH-HHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCHHHH-HHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3455444 667777 4559999999999999999999886

>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription complex, serine kinase, DNA-bindin mercury derivative, repressor; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B*

Probab=91.97  E-value=0.31  Score=33.61  Aligned_cols=40  Identities=13%  Similarity=0.239  Sum_probs=32.1

Q ss_pred             CCCHHHHHHHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         32 TWTHEDMDAALEALR-AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        32 kyt~e~~~~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .++..++-..|..+. ..|+|+.++|+..||++++|.+|..
T Consensus         7 ~~~~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   47 (88)
T 2wiu_B            7 IYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFEN   47 (88)
T ss_dssp             BCSHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            345566666666553 5789999999999999999999988

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

Probab=91.95  E-value=0.27  Score=37.67  Aligned_cols=33  Identities=9%  Similarity=0.155  Sum_probs=28.5

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .++++.+.+| +|+++||+++|++.+||.|-.+.
T Consensus        66 ~eV~klL~~G-~syreIA~~~g~S~aTIsRv~r~   98 (119)
T 3kor_A           66 LQVAKMIKQG-YTYATIEQESGASTATISRVKRS   98 (119)
T ss_dssp             HHHHHHHHHT-CCHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHHHHcC-CCHHHHHHHHCCCHHHHHHHHHH
Confidence            6777777776 89999999999999999986664

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

Probab=91.92  E-value=0.14  Score=36.48  Aligned_cols=41  Identities=15%  Similarity=0.097  Sum_probs=31.8

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ....|+.++. ++..+. .|+|..+||..+||+.+||+.++++
T Consensus        27 l~~Lt~~e~~-vl~l~~-~g~s~~eIA~~l~is~~tV~~~l~r   67 (91)
T 2rnj_A           27 YEMLTEREME-ILLLIA-KGYSNQEIASASHITIKTVKTHVSN   67 (91)
T ss_dssp             GGGCCSHHHH-HHHHHH-TTCCTTHHHHHHTCCHHHHHHHHHH
T ss_pred             HhcCCHHHHH-HHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3456666653 444564 4789999999999999999999886

>1j9i_A GPNU1 DBD;, terminase small subunit; DNA binding domain, homodimer, viral assembly, winged helix-turn-helix, viral protein; NMR {Enterobacteria phage lambda} SCOP: a.6.1.5

Probab=91.92  E-value=0.12  Score=34.96  Aligned_cols=23  Identities=9%  Similarity=0.101  Sum_probs=21.2

Q ss_pred             CcHHHHHHHhCCChHHHHHHHHh
Q psy17316        191 TTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       191 ~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      ++..|+|..+|||..|||+|++.
T Consensus         3 lt~~e~a~~LgvS~~Tl~rw~~~   25 (68)
T 1j9i_A            3 VNKKQLADIFGASIRTIQNWQEQ   25 (68)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHTTT
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHC
Confidence            57899999999999999999984

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

Probab=91.90  E-value=0.15  Score=36.24  Aligned_cols=37  Identities=14%  Similarity=0.012  Sum_probs=29.4

Q ss_pred             CCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        174 WKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       174 ~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .++.++ +|+.++. .++++.++|..+|||..||+.+++
T Consensus        30 Lt~~e~-~vl~l~~-~g~s~~eIA~~l~is~~tV~~~l~   66 (91)
T 2rnj_A           30 LTEREM-EILLLIA-KGYSNQEIASASHITIKTVKTHVS   66 (91)
T ss_dssp             CCSHHH-HHHHHHH-TTCCTTHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHH-HHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344444 5666665 459999999999999999999986

>4fe7_A Xylose operon regulatory protein; HTH_ARAC, helix-turn-helix, PBP, periplasmic binding protein binding transcription regulator, DNA xylose; HET: XYS; 2.90A {Escherichia coli} PDB: 4fe4_A

Probab=91.87  E-value=0.51  Score=42.00  Aligned_cols=92  Identities=23%  Similarity=0.221  Sum_probs=64.3

Q ss_pred             HHHHHHHHHHHH---cCCCCHHHHHHHhCCChHHHHHHHHHh-CCcccCCCCCCCCCCCHH-HHHHHHHHHHhCCCcHHH
Q psy17316        121 EEILNVALDALR---AGSISANKASKAYGIPSSTLYKIARKE-GIRLAQPFNASPTAWKPE-DLEIALEGIRSGQTTVQR  195 (229)
Q Consensus       121 ~e~k~~AV~~~~---~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k~~~~~~~~~r~~t~e-~r~eaV~~~~~~~~s~~e  195 (229)
                      .....++++.+.   ...+++.++|+.+|++.++|.+..+++ |....        .|-.. ....|.+++...++++.+
T Consensus       304 d~~~~~~~~~i~~~~~~~~~~~~~a~~~~~s~~~l~r~f~~~~g~s~~--------~~~~~~r~~~a~~~L~~~~~~i~~  375 (412)
T 4fe7_A          304 DPAVIQAMHYIRNHACKGIKVDQVLDAVGISRSNLEKRFKEEVGETIH--------AMIHAEKLEKARSLLISTTLSINE  375 (412)
T ss_dssp             CHHHHHHHHHHHHHGGGTCCHHHHHHHTTCCHHHHHHHHHHHHSSCHH--------HHHHHHHHHHHHHHHHHCCCCHHH
T ss_pred             cHHHHHHHHHHHhhccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHH--------HHHHHHHHHHHHHHHhcCCCCHHH
Confidence            445555555553   456899999999999999999999977 75443        23223 345577777788899999


Q ss_pred             HHHHhCCChHHHHHHHHhhcCCCCC
Q psy17316        196 ASAEYGIPSGTLYGRCKLSRSTPRP  220 (229)
Q Consensus       196 AA~~fgVp~~tv~~~vk~~~~~~~~  220 (229)
                      +|...|-+.++-...+=.+.-|-+|
T Consensus       376 ia~~~Gf~~~~~f~~~Fk~~~g~tP  400 (412)
T 4fe7_A          376 ISQMCGYPSLQYFYSVFKKAYDTTP  400 (412)
T ss_dssp             HHHHTTCSCHHHHHHHHHHHSSSCH
T ss_pred             HHHHcCCCCHHHHHHHHHHHHCcCH
Confidence            9999999766655544333333333

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

Probab=91.80  E-value=0.28  Score=36.97  Aligned_cols=34  Identities=15%  Similarity=0.105  Sum_probs=27.0

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .+++..+.+ |+|+++||+.+|++.+||.|..+.+
T Consensus        49 ~~Ia~lL~~-G~SyreIa~~tG~StaTIsRv~r~L   82 (107)
T 3frw_A           49 FEVAKMLTD-KRTYLDISEKTGASTATISRVNRSL   82 (107)
T ss_dssp             HHHHHHHHT-TCCHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHc-CCCHHHHHHHHCccHHHHHHHHHHH
Confidence            455555555 5899999999999999999876653

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=91.79  E-value=0.14  Score=36.19  Aligned_cols=43  Identities=5%  Similarity=-0.005  Sum_probs=33.5

Q ss_pred             CCCHHHHHHHHHHH-H---cCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         32 TWTHEDMDAALEAL-R---AGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        32 kyt~e~~~~AI~~~-~---~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      +...+++++.|+.. .   .+-.|+++||+.+||+.+|+++-+..+.
T Consensus         3 ~~r~~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~Le   49 (77)
T 2jt1_A            3 ESIVTKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQLH   49 (77)
T ss_dssp             CTHHHHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            34456677777655 1   2567999999999999999999998763

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=91.74  E-value=0.21  Score=35.25  Aligned_cols=34  Identities=3%  Similarity=-0.007  Sum_probs=28.1

Q ss_pred             HHHHHHHHHh-------CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRS-------GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~-------~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+|++++..       +..++.|+|..||||.+||.+.++
T Consensus         6 ~~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~   46 (77)
T 2jt1_A            6 VTKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLE   46 (77)
T ss_dssp             HHHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            5566666655       356899999999999999999988

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

Probab=91.71  E-value=0.29  Score=36.57  Aligned_cols=30  Identities=10%  Similarity=0.126  Sum_probs=28.3

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~   78 (229)
                      .+|+.++|++.||+.+||.|-+++.|..|.
T Consensus        39 ~~si~elA~~~~vS~aTv~Rf~kklG~~gf   68 (111)
T 2o3f_A           39 ESTVNEISALANSSDAAVIRLCXSLGLKGF   68 (111)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHHHHHTTCSSH
T ss_pred             hcCHHHHHHHHCCCHHHHHHHHHHcCCCCH
Confidence            799999999999999999999999999873

>1rzs_A Antirepressor, regulatory protein CRO; helix-turn-helix, DNA-binding protein, structural evolution, transcription; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=91.69  E-value=0.06  Score=35.86  Aligned_cols=22  Identities=14%  Similarity=0.089  Sum_probs=20.3

Q ss_pred             CCCHHHHHHHcCCChhhHHHHH
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRA   70 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i   70 (229)
                      ++|+.++|+.+||++++|.+|.
T Consensus        10 ~~tq~~lA~~lGvs~~~Vs~we   31 (61)
T 1rzs_A           10 FGTQRAVAKALGISDAAVSQWK   31 (61)
T ss_dssp             HSSHHHHHHHHTCCHHHHHHCC
T ss_pred             cCCHHHHHHHhCCCHHHHHHHH
Confidence            3499999999999999999996

>2xi8_A Putative transcription regulator; HTH DNA-binding motif; HET: GOL; 1.21A {Enterococcus faecalis} PDB: 2gzu_A 1utx_A* 2xj3_A 2xiu_A

Probab=91.62  E-value=0.15  Score=33.06  Aligned_cols=26  Identities=8%  Similarity=0.073  Sum_probs=23.7

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ...++|+.++|+..||+++||.+|..
T Consensus        11 ~~~g~s~~~lA~~~gis~~~i~~~e~   36 (66)
T 2xi8_A           11 EKKKISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             HHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            35689999999999999999999976

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}

Probab=91.54  E-value=0.25  Score=37.49  Aligned_cols=35  Identities=3%  Similarity=-0.085  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +.+|.-+ .... .++|+.++|..+|||.+||+.++.
T Consensus       112 ~~~r~v~-~~~~-~g~s~~EIA~~lgis~~tV~~~~~  146 (164)
T 3mzy_A          112 KFEKEVL-TYLI-RGYSYREIATILSKNLKSIDNTIQ  146 (164)
T ss_dssp             HHHHHHH-HHHT-TTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHH-HHHH-cCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4455544 4544 559999999999999999999876

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=91.50  E-value=0.24  Score=35.88  Aligned_cols=34  Identities=15%  Similarity=0.126  Sum_probs=29.3

Q ss_pred             HHHHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +.+|++++.. |..++.+.|.+|+||..||.+-+.
T Consensus         4 L~~Il~~L~~~g~vsv~eLA~~l~VS~~TIRrDL~   38 (87)
T 2k02_A            4 LMEVRDMLALQGRMEAKQLSARLQTPQPLIDAMLE   38 (87)
T ss_dssp             THHHHHHHHHSCSEEHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHH
Confidence            3567777764 779999999999999999999887

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=91.47  E-value=0.19  Score=35.40  Aligned_cols=35  Identities=17%  Similarity=0.100  Sum_probs=29.2

Q ss_pred             HHHHHHHHcC-CCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEALRAG-QMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~~~g-~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..++..+.++ .+|+.++|+.+||+++|+.+.++.+
T Consensus        27 ~~il~~l~~~~~~s~~ela~~l~is~~tvs~~l~~L   62 (99)
T 3cuo_A           27 LLILCMLSGSPGTSAGELTRITGLSASATSQHLARM   62 (99)
T ss_dssp             HHHHHHHTTCCSEEHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4555555555 7999999999999999999999986

>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=91.46  E-value=0.29  Score=36.61  Aligned_cols=34  Identities=9%  Similarity=0.160  Sum_probs=28.1

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -.+|+.+..-.++|+.++|..+|||.+||+.++.
T Consensus        30 ~r~vl~l~~~~g~s~~EIA~~lgiS~~tV~~~l~   63 (113)
T 1xsv_A           30 QRNYLELFYLEDYSLSEIADTFNVSRQAVYDNIR   63 (113)
T ss_dssp             HHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3456666655669999999999999999999876

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=91.45  E-value=0.33  Score=34.42  Aligned_cols=37  Identities=14%  Similarity=0.194  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +..+..++..+. .+.++..++|..+|||.+||++.++
T Consensus        21 ~~~~~~l~~l~~~~~~~t~~ela~~l~is~~tv~~~l~   58 (109)
T 2d1h_A           21 DTDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLK   58 (109)
T ss_dssp             HHHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            333333334444 5779999999999999999999998

>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434} SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A 2r63_A 1sq8_A

Probab=91.42  E-value=0.37  Score=31.42  Aligned_cols=35  Identities=3%  Similarity=-0.169  Sum_probs=28.9

Q ss_pred             HHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhcC
Q psy17316        182 ALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRS  216 (229)
Q Consensus       182 aV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~~  216 (229)
                      +-+.....+++..+.|...|||.++|.+|.++...
T Consensus         6 l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~   40 (69)
T 1r69_A            6 VKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTK   40 (69)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSCS
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCC
Confidence            34455667799999999999999999999887554

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

Probab=91.17  E-value=0.35  Score=34.05  Aligned_cols=37  Identities=8%  Similarity=0.115  Sum_probs=28.3

Q ss_pred             CHHHHHHHHHHHHh----CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        175 KPEDLEIALEGIRS----GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       175 t~e~r~eaV~~~~~----~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++.+| +|+....-    .++|+.++|..+|||.+||+.+..
T Consensus        20 ~~~er-~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~   60 (87)
T 1tty_A           20 SPREA-MVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEV   60 (87)
T ss_dssp             CHHHH-HHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHH-HHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34444 45555443    569999999999999999999876

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

Probab=91.16  E-value=0.27  Score=36.28  Aligned_cols=35  Identities=20%  Similarity=0.315  Sum_probs=29.4

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +.++..+.++.+|+.++|+.+||+++|+.+.++.+
T Consensus        35 ~~il~~L~~~~~s~~ela~~l~is~stvsr~l~~L   69 (119)
T 2lkp_A           35 LMILTQLRNGPLPVTDLAEAIGMEQSAVSHQLRVL   69 (119)
T ss_dssp             HHHHHHHHHCCCCHHHHHHHHSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            34555555678999999999999999999999985

>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens}

Probab=91.14  E-value=0.24  Score=32.63  Aligned_cols=27  Identities=11%  Similarity=0.197  Sum_probs=23.5

Q ss_pred             HHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         45 LRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        45 ~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +...+ |+.++|+.+||++++|.+|++.
T Consensus        10 ~~~~g-s~~~~A~~lgis~~~vs~~~~~   36 (67)
T 2pij_A           10 LEEHG-TQSALAAALGVNQSAISQMVRA   36 (67)
T ss_dssp             HHHTC-CHHHHHHHHTSCHHHHHHHHHT
T ss_pred             HHHcC-CHHHHHHHHCcCHHHHHHHHcC
Confidence            34456 9999999999999999999974

>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix, transcription/DNA complex; HET: DNA; 1.80A {Enterobacteria phage lambda} SCOP: a.35.1.2 PDB: 1lrp_A 1rio_A 1lli_A*

Probab=91.07  E-value=0.29  Score=34.20  Aligned_cols=42  Identities=17%  Similarity=0.196  Sum_probs=29.8

Q ss_pred             CCCCCHHHHH--HHHHHH-----HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         30 TKTWTHEDMD--AALEAL-----RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        30 ~~kyt~e~~~--~AI~~~-----~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +..++.+++.  ..|..+     ..-|+|+.++|+.+||+++||.+|..
T Consensus         4 ~~~~~~~~~~~~~~l~~~l~~~R~~~glsq~~lA~~~gis~~~is~~e~   52 (92)
T 1lmb_3            4 KKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFN   52 (92)
T ss_dssp             --CCCHHHHHHHHHHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4456666542  222222     45689999999999999999999987

>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=90.98  E-value=0.31  Score=34.93  Aligned_cols=42  Identities=5%  Similarity=0.006  Sum_probs=31.6

Q ss_pred             CCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         29 VTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        29 ~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .....|+.++. ++..+. .|+|..+||..+||+..||+..+++
T Consensus        26 ~~~~Lt~rE~~-Vl~l~~-~G~s~~eIA~~L~iS~~TV~~~~~~   67 (90)
T 3ulq_B           26 EQDVLTPRECL-ILQEVE-KGFTNQEIADALHLSKRSIEYSLTS   67 (90)
T ss_dssp             ---CCCHHHHH-HHHHHH-TTCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             cccCCCHHHHH-HHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            34556776663 555665 5889999999999999999998886

>3qao_A LMO0526 protein, MERR-like transcriptional regulator; structural genomics, the center for structural genomics of I diseases, csgid; 1.87A {Listeria monocytogenes}

Probab=90.96  E-value=0.54  Score=40.06  Aligned_cols=70  Identities=9%  Similarity=0.048  Sum_probs=51.6

Q ss_pred             CCCCHHHHHHHhCCChHHHHHHHHHhCCc-ccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCCh
Q psy17316        134 GSISANKASKAYGIPSSTLYKIARKEGIR-LAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIPS  204 (229)
Q Consensus       134 g~~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp~  204 (229)
                      +.+++.++|+.+|||..||+-|-+ .|.- +.....+..|-|+++  .++..|..+.+-+++..++...+..+.
T Consensus         2 ~~~tI~evA~~~gvs~~TLRyYe~-~GLL~p~~~~~~GyR~Y~~~dl~~L~~I~~lr~~G~sL~eIk~~l~~~~   74 (249)
T 3qao_A            2 NAMQIKELAELTGVSVRTLHHYDK-IGLLVPQKDDWNGYRIYSEKDVDKLQQILFFKELDFPLKKIQQILDDPL   74 (249)
T ss_dssp             CCBCHHHHHHHHCCCHHHHHHHHH-TTSSCCEECTTTCCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHHCTT
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH-CCCCCCceECCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHhccCc
Confidence            357999999999999999999988 5532 211012345778766  456677788888899999998887654

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=90.80  E-value=0.62  Score=31.13  Aligned_cols=37  Identities=19%  Similarity=0.152  Sum_probs=30.2

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      ...+-+.....++|..+.|...|||.++|.+|.++..
T Consensus         9 ~~~l~~~r~~~g~sq~~lA~~~gis~~~i~~~e~g~~   45 (78)
T 3b7h_A            9 SEHLMELITQQNLTINRVATLAGLNQSTVNAMFEGRS   45 (78)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHCTTC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCC
Confidence            3444555666789999999999999999999988654

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=90.80  E-value=0.15  Score=34.19  Aligned_cols=25  Identities=8%  Similarity=-0.118  Sum_probs=23.2

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..++|+.++|+.+||+++||.+|..
T Consensus        19 ~~glsq~~lA~~~gis~~~is~~e~   43 (73)
T 3omt_A           19 EKGKTNLWLTETLDKNKTTVSKWCT   43 (73)
T ss_dssp             HHTCCHHHHHHHTTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4589999999999999999999987

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=90.73  E-value=0.44  Score=37.99  Aligned_cols=44  Identities=18%  Similarity=0.268  Sum_probs=31.8

Q ss_pred             CCCCCCHHHHHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         29 VTKTWTHEDMDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        29 ~~~kyt~e~~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .....++-+. .++..+ .++.+|+.++|+++||+++|++++++++
T Consensus        11 ~~~~ld~~d~-~IL~~L~~~~~~s~~eLA~~lglS~~tv~~~l~~L   55 (171)
T 2ia0_A           11 SEIHLDDLDR-NILRLLKKDARLTISELSEQLKKPESTIHFRIKKL   55 (171)
T ss_dssp             ---CCCHHHH-HHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CcCCCCHHHH-HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3344444444 344444 3678999999999999999999999986

>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434} SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A 2r63_A 1sq8_A

Probab=90.71  E-value=0.2  Score=32.75  Aligned_cols=26  Identities=8%  Similarity=0.019  Sum_probs=23.6

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ...++|+.++|+..||+++||.+|..
T Consensus        11 ~~~glsq~~lA~~~gis~~~i~~~e~   36 (69)
T 1r69_A           11 IQLGLNQAELAQKVGTTQQSIEQLEN   36 (69)
T ss_dssp             HHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            35689999999999999999999976

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=90.70  E-value=0.33  Score=36.59  Aligned_cols=28  Identities=14%  Similarity=0.171  Sum_probs=25.2

Q ss_pred             HcCC--CCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         46 RAGQ--MSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        46 ~~g~--~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .+++  +|+.++|+.+|++++|+++.+.++
T Consensus        37 ~~~~~~~t~~eLa~~l~~s~sTV~r~L~~L   66 (123)
T 3r0a_A           37 NEPDRWIDTDALSKSLKLDVSTVQRSVKKL   66 (123)
T ss_dssp             HSTTCCEEHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HCCCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3566  899999999999999999999986

>1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L*

Probab=90.64  E-value=0.52  Score=30.82  Aligned_cols=34  Identities=6%  Similarity=-0.125  Sum_probs=28.3

Q ss_pred             HHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhcC
Q psy17316        183 LEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRS  216 (229)
Q Consensus       183 V~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~~  216 (229)
                      -+.....+++..+.|...|||.++|.+|.++...
T Consensus         9 ~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~   42 (71)
T 1zug_A            9 KKRRIALKMTQTELATKAGVKQQSIQLIEAGVTK   42 (71)
T ss_dssp             HHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTCCS
T ss_pred             HHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCC
Confidence            3445567799999999999999999999987654

>2l8n_A Transcriptional repressor CYTR; bacterial gene repressor, helix turn helix binding domain, L family, transcription regulation, binding protein; NMR {Escherichia coli} PDB: 2lcv_A

Probab=90.63  E-value=0.33  Score=33.09  Aligned_cols=40  Identities=10%  Similarity=0.130  Sum_probs=29.2

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHH
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDAL   99 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll   99 (229)
                      .+++.++|+..||+.+||.+++..     ..      ..+++.++..++..
T Consensus         9 ~~t~~diA~~aGVS~sTVSr~ln~-----~~------~vs~~t~~rV~~~a   48 (67)
T 2l8n_A            9 AATMKDVALKAKVSTATVSRALMN-----PD------KVSQATRNRVEKAA   48 (67)
T ss_dssp             CCCHHHHHHHTTCCHHHHHHTTTC-----CC------CSCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHcC-----CC------CCCHHHHHHHHHHH
Confidence            369999999999999999998752     11      23677776665433

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=90.61  E-value=0.22  Score=35.18  Aligned_cols=38  Identities=13%  Similarity=0.099  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHcCC-CCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         36 EDMDAALEALRAGQ-MSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        36 e~~~~AI~~~~~g~-~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +.+..||..+-+|+ .+...||+++|++++.+.+-+-.+
T Consensus        15 ~~v~~~i~~L~~~~~~Ta~~IAkkLg~sK~~vNr~LY~L   53 (75)
T 1sfu_A           15 SLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKL   53 (75)
T ss_dssp             HHHHHHHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCcchHHHHHHHHHCCCHHHHHHHHHHH
Confidence            34466676666777 999999999999999999988765

>3osg_A MYB21; transcription-DNA complex, MYB2, R2R3 domain, DNA binding PR transcription factor; 2.00A {Trichomonas vaginalis} PDB: 3osf_A

Probab=90.60  E-value=3.1  Score=31.38  Aligned_cols=88  Identities=15%  Similarity=0.130  Sum_probs=60.6

Q ss_pred             CCCCHHH---HHHHHHHHHcCCCCHHHHHHHhCCChH-HHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCc
Q psy17316        117 KSWNEEI---LNVALDALRAGSISANKASKAYGIPSS-TLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTT  192 (229)
Q Consensus       117 ~kYs~e~---k~~AV~~~~~g~~S~~~~a~k~gIp~s-TL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s  192 (229)
                      .+||+|.   +.++|+.+  |. .-..||..++-... ..+.+-.++-    .|. .....||+||-..+++++...+.+
T Consensus        12 ~~WT~eED~~L~~~v~~~--G~-~W~~Ia~~~~~Rt~~qcr~Rw~~~l----~p~-~~~~~WT~eEd~~L~~~v~~~G~~   83 (126)
T 3osg_A           12 QKFTPEEDEMLKRAVAQH--GS-DWKMIAATFPNRNARQCRDRWKNYL----APS-ISHTPWTAEEDALLVQKIQEYGRQ   83 (126)
T ss_dssp             CCCCHHHHHHHHHHHHHH--TT-CHHHHHHTCTTCCHHHHHHHHHHHT----STT-SCCSCCCHHHHHHHHHHHHHHCSC
T ss_pred             CCCCHHHHHHHHHHHHHh--CC-CHHHHHHHcCCCCHHHHHHHHhhhc----ccc-cccccCCHHHHHHHHHHHHHHCcC
Confidence            4555555   34455554  44 88899988743333 3555444331    111 123579999999999999887788


Q ss_pred             HHHHHHHh-CCChHHHHHHHH
Q psy17316        193 VQRASAEY-GIPSGTLYGRCK  212 (229)
Q Consensus       193 ~~eAA~~f-gVp~~tv~~~vk  212 (229)
                      -..+|..| |-+..++.+++.
T Consensus        84 W~~Ia~~l~gRt~~~~k~rw~  104 (126)
T 3osg_A           84 WAIIAKFFPGRTDIHIKNRWV  104 (126)
T ss_dssp             HHHHHTTSTTCCHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHH
Confidence            99999999 899999999887

>1b0n_A Protein (SINR protein); transcription regulator, antagonist, sporulation; 1.90A {Bacillus subtilis} SCOP: a.34.1.1 a.35.1.3 PDB: 2yal_A

Probab=90.57  E-value=0.4  Score=34.50  Aligned_cols=26  Identities=15%  Similarity=0.181  Sum_probs=23.7

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ...|+|+.++|+..||+++||.+|..
T Consensus        11 ~~~gltq~~lA~~~gis~~~i~~~e~   36 (111)
T 1b0n_A           11 KEKGYSLSELAEKAGVAKSYLSSIER   36 (111)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            35689999999999999999999976

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=90.51  E-value=0.18  Score=43.83  Aligned_cols=34  Identities=26%  Similarity=0.267  Sum_probs=26.6

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +..+.+.+...+.++.++|+.+||+++|||++++
T Consensus       270 ~~~i~~~l~~~~gn~~~aA~~Lgi~r~tl~~kl~  303 (304)
T 1ojl_A          270 KEVILAALEKTGGNKTEAARQLGITRKTLLAKLS  303 (304)
T ss_dssp             HHHHHHHHHTTTTCHHHHHHHHTSCHHHHHHHTC
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence            3344455555556899999999999999999975

>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28

Probab=90.48  E-value=0.34  Score=34.08  Aligned_cols=36  Identities=6%  Similarity=-0.034  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+..|+..+. .+.++..++|..+|||.+||+..++
T Consensus        16 ~~~~~iL~~L~~~~~~~~~ela~~l~is~~tvs~~l~   52 (100)
T 1ub9_A           16 PVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIR   52 (100)
T ss_dssp             HHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHH
T ss_pred             hHHHHHHHHHHhcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            34778888775 6779999999999999999999998

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=90.40  E-value=0.28  Score=38.58  Aligned_cols=34  Identities=18%  Similarity=0.498  Sum_probs=29.1

Q ss_pred             HHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         40 AALEALR-AGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        40 ~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .+++.+. +|.+|..++|+++|++.+|++++++++
T Consensus         7 ~il~~L~~~~~~s~~~la~~lg~s~~tv~~rl~~L   41 (162)
T 3i4p_A            7 KILRILQEDSTLAVADLAKKVGLSTTPCWRRIQKM   41 (162)
T ss_dssp             HHHHHHTTCSCSCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4455553 688999999999999999999999986

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=90.37  E-value=0.38  Score=41.91  Aligned_cols=38  Identities=16%  Similarity=0.071  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +.+..+...+..+++++.++|+++||++.|++|-+...
T Consensus         8 ~~~~~ia~l~~~~~~~~~ela~~l~vS~~tIrRdL~~l   45 (315)
T 2w48_A            8 RLIVKIAQLYYEQDMTQAQIARELGIYRTTISRLLKRG   45 (315)
T ss_dssp             HHHHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            34466777888999999999999999999999988864

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=90.36  E-value=0.22  Score=33.25  Aligned_cols=26  Identities=12%  Similarity=0.001  Sum_probs=23.7

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ...++|+.++|+..||+++||.+|..
T Consensus        20 ~~~g~s~~~lA~~~gis~~~i~~~e~   45 (76)
T 3bs3_A           20 AEKQRTNRWLAEQMGKSENTISRWCS   45 (76)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            35689999999999999999999976

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=90.36  E-value=0.38  Score=34.70  Aligned_cols=36  Identities=8%  Similarity=-0.023  Sum_probs=31.6

Q ss_pred             HHHHHHHHH-HHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEG-IRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~-~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|.+|+.. +..|.+++.++|..+|+|.+||...++
T Consensus        27 ~~Rl~IL~~l~~~~~~~~~ela~~l~is~stvs~hL~   63 (99)
T 2zkz_A           27 PMRLKIVNELYKHKALNVTQIIQILKLPQSTVSQHLC   63 (99)
T ss_dssp             HHHHHHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            468899954 456889999999999999999999998

>2ofy_A Putative XRE-family transcriptional regulator; transcription regulator, structural genomics, PS protein structure initiative; 1.70A {Rhodococcus SP} SCOP: a.35.1.3

Probab=90.34  E-value=0.55  Score=32.28  Aligned_cols=32  Identities=22%  Similarity=0.270  Sum_probs=27.6

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      -..|..+.... |+.++|+..||+++||.+|-.
T Consensus        18 g~~l~~~R~~~-sq~~lA~~~gis~~~is~~E~   49 (86)
T 2ofy_A           18 GELLRSARGDM-SMVTVAFDAGISVETLRKIET   49 (86)
T ss_dssp             HHHHHHHHTTS-CHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHC-CHHHHHHHhCCCHHHHHHHHc
Confidence            45677777766 999999999999999999976

>1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L*

Probab=90.30  E-value=0.23  Score=32.67  Aligned_cols=26  Identities=15%  Similarity=0.116  Sum_probs=23.6

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..-++|+.++|+..||+++||.+|..
T Consensus        13 ~~~glsq~~lA~~~gis~~~i~~~e~   38 (71)
T 1zug_A           13 IALKMTQTELATKAGVKQQSIQLIEA   38 (71)
T ss_dssp             HHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            35689999999999999999999976

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=90.28  E-value=0.37  Score=36.32  Aligned_cols=34  Identities=12%  Similarity=0.255  Sum_probs=29.4

Q ss_pred             HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .++..+.+|.+++.++|+.+||+++|+.+.++.+
T Consensus        50 ~IL~~L~~~~~s~~ela~~lgis~stvs~~L~~L   83 (122)
T 1r1t_A           50 RLLSLLARSELCVGDLAQAIGVSESAVSHQLRSL   83 (122)
T ss_dssp             HHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4555566788999999999999999999999986

>3trb_A Virulence-associated protein I; mobIle and extrachromosomal element functions, DNA binding P; 2.00A {Coxiella burnetii}

Probab=90.22  E-value=0.66  Score=34.07  Aligned_cols=27  Identities=15%  Similarity=0.097  Sum_probs=24.5

Q ss_pred             HHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         45 LRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        45 ~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ...-|+|+.++|+.+||+++||.+|..
T Consensus        23 r~~~gltq~eLA~~lGis~~~is~ie~   49 (104)
T 3trb_A           23 GFLDKMSANQLAKHLAIPTNRVTAILN   49 (104)
T ss_dssp             HHTTSCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            356789999999999999999999986

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=90.16  E-value=0.32  Score=35.42  Aligned_cols=35  Identities=17%  Similarity=0.210  Sum_probs=29.0

Q ss_pred             HHHHHHH-HcC-CCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEAL-RAG-QMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~-~~g-~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +.++..+ ..| .+|..++|+.+||+++|+++.++.+
T Consensus        21 l~Il~~l~~~g~~~s~~eLa~~lgvs~~tV~~~L~~L   57 (110)
T 1q1h_A           21 IDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLL   57 (110)
T ss_dssp             HHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4555544 466 7999999999999999999999875

>2ovg_A Phage lambda CRO; transcription factor, helix-turn-helix, bacteriophage, flexi transcription; 1.35A {Enterobacteria phage lambda} PDB: 2ecs_A 1cop_D 4cro_A* 5cro_O 1orc_A 2orc_A 2a63_A 1d1l_A 6cro_A* 3orc_A* 1d1m_B

Probab=90.15  E-value=0.16  Score=34.70  Aligned_cols=30  Identities=20%  Similarity=0.234  Sum_probs=24.5

Q ss_pred             HHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         42 LEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        42 I~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      |..+.... |+.++|+++||+.++|.+|++.
T Consensus         7 L~~~~~~~-s~t~aA~~L~vtQ~AVS~~ir~   36 (66)
T 2ovg_A            7 LKDYAMRF-GQTKTAKDLGVYPSSINQAIHA   36 (66)
T ss_dssp             HHHHHHHH-CHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHC-CHHHHHHHhCCCHHHHHHHHHh
Confidence            33344444 9999999999999999999985

>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, transcription regulat; HET: MSE; 1.90A {Listeria innocua}

Probab=90.08  E-value=0.39  Score=35.09  Aligned_cols=25  Identities=4%  Similarity=-0.052  Sum_probs=23.2

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-|+|+.++|+..||+++||.+|-+
T Consensus        20 ~~glsq~~lA~~~gis~~~i~~~e~   44 (114)
T 3op9_A           20 EHGLKNHQIAELLNVQTRTVAYYMS   44 (114)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            3589999999999999999999988

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=90.07  E-value=0.32  Score=36.47  Aligned_cols=35  Identities=11%  Similarity=0.096  Sum_probs=29.9

Q ss_pred             HHHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEALR-AGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +.++..+. +|.+++.++|+.+||+++|+.+.++.+
T Consensus        45 l~IL~~L~~~~~~s~~eLa~~l~is~stvs~~L~~L   80 (122)
T 1u2w_A           45 AKITYALCQDEELCVCDIANILGVTIANASHHLRTL   80 (122)
T ss_dssp             HHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            35555555 688999999999999999999999985

>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens}

Probab=90.00  E-value=0.37  Score=31.66  Aligned_cols=32  Identities=13%  Similarity=0.146  Sum_probs=26.3

Q ss_pred             HHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        183 LEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       183 V~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      ...+...+ ++.++|..+|||.++|..|+++.+
T Consensus         7 ~~~~~~~g-s~~~~A~~lgis~~~vs~~~~~~~   38 (67)
T 2pij_A            7 SKYLEEHG-TQSALAAALGVNQSAISQMVRAGR   38 (67)
T ss_dssp             HHHHHHTC-CHHHHHHHHTSCHHHHHHHHHTTC
T ss_pred             HHHHHHcC-CHHHHHHHHCcCHHHHHHHHcCCC
Confidence            34556666 999999999999999999998543

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

Probab=89.97  E-value=0.48  Score=34.88  Aligned_cols=36  Identities=14%  Similarity=0.247  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+..|+..+.++.+++.++|..+|||.+||.+.++
T Consensus        32 ~~~~~il~~L~~~~~s~~ela~~l~is~stvsr~l~   67 (119)
T 2lkp_A           32 PSRLMILTQLRNGPLPVTDLAEAIGMEQSAVSHQLR   67 (119)
T ss_dssp             HHHHHHHHHHHHCCCCHHHHHHHHSSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            347788888888789999999999999999999998

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=89.95  E-value=0.63  Score=32.79  Aligned_cols=28  Identities=14%  Similarity=0.260  Sum_probs=25.8

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .++.+|+.++|+.+||+++|+++.++++
T Consensus        31 ~~~~~s~~ela~~l~is~~tv~~~l~~L   58 (109)
T 1sfx_A           31 ERGGMRVSEIARELDLSARFVRDRLKVL   58 (109)
T ss_dssp             HHCCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3688999999999999999999999985

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=89.93  E-value=0.3  Score=42.34  Aligned_cols=37  Identities=19%  Similarity=0.272  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .-++..|.+.+...+.|..+||+..|||++|||++++
T Consensus       267 ~~e~~~i~~~l~~~~gn~~~aA~~Lgi~r~tl~~kl~  303 (304)
T 1ojl_A          267 DVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKLS  303 (304)
T ss_dssp             HHHHHHHHHHHHTTTTCHHHHHHHHTSCHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence            3467777888888888999999999999999999875

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12

Probab=89.92  E-value=0.48  Score=33.13  Aligned_cols=34  Identities=0%  Similarity=0.003  Sum_probs=27.3

Q ss_pred             HHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         38 MDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        38 ~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +-..|..+ ..-++|+.++|+..||+++||.+|..
T Consensus        14 ~~~~l~~~r~~~glsq~~lA~~~gis~~~is~~e~   48 (91)
T 1x57_A           14 VGKVIQQGRQSKGLTQKDLATKINEKPQVIADYES   48 (91)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            44444433 45689999999999999999999987

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=89.87  E-value=0.58  Score=32.96  Aligned_cols=27  Identities=19%  Similarity=0.300  Sum_probs=24.3

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +|.+|+.++|+.|||+..||++=+...
T Consensus        14 ~g~vsv~eLa~~l~VS~~TIRrdL~~L   40 (78)
T 1xn7_A           14 RGRMEAAQISQTLNTPQPMINAMLQQL   40 (78)
T ss_dssp             SCSBCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             cCCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence            689999999999999999999877654

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=89.85  E-value=0.23  Score=36.99  Aligned_cols=39  Identities=15%  Similarity=0.274  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      ...+.++..+.+|.+++.++|+.+||+++|+.+.++.+.
T Consensus        18 ~~R~~Il~~L~~~~~~~~eLa~~l~is~~tvs~hL~~L~   56 (118)
T 3f6o_A           18 PTRRAVLGRLSRGPATVSELAKPFDMALPSFMKHIHFLE   56 (118)
T ss_dssp             HHHHHHHHHHHTCCEEHHHHHTTCCSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence            345667777778999999999999999999999999863

>3ivp_A Putative transposon-related DNA-binding protein; APC62618, clostridium diffic structural genomics, PSI-2, protein structure initiative; HET: PG4; 2.02A {Clostridium difficile}

Probab=89.77  E-value=1.2  Score=33.03  Aligned_cols=38  Identities=8%  Similarity=0.090  Sum_probs=29.7

Q ss_pred             CHHHHHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDMDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ....+-..|..+ ..-|+|+.++|+..||++++|.+|-.
T Consensus         9 ~~~~~g~~lk~~R~~~glsq~~lA~~~gis~~~is~~E~   47 (126)
T 3ivp_A            9 DFRALGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIEN   47 (126)
T ss_dssp             CTHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHC
Confidence            334454555544 35789999999999999999999987

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=89.72  E-value=0.43  Score=31.97  Aligned_cols=34  Identities=12%  Similarity=0.207  Sum_probs=26.9

Q ss_pred             HHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         38 MDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        38 ~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +...|..+ ...|+|+.++|+..||+++||.+|..
T Consensus         8 ~~~~l~~~r~~~g~sq~~lA~~~gis~~~i~~~e~   42 (78)
T 3b7h_A            8 VSEHLMELITQQNLTINRVATLAGLNQSTVNAMFE   42 (78)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            33444433 45689999999999999999999976

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=89.71  E-value=0.4  Score=32.48  Aligned_cols=53  Identities=8%  Similarity=0.120  Sum_probs=35.2

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRAS  197 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA  197 (229)
                      +++.++|+..||+.+|+.+++......         ...+++-+..|.+.+.+-+...+..|
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLng~~~~---------~~vs~et~~rI~~aa~~lgY~pn~~a   53 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVINGKAKQ---------YRVSDKTVEKVMAVVREHNYHPNAVA   53 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHTCTTT---------TTCTTHHHHHHHHHHHHHTCCCC---
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCCCC---------CCCCHHHHHHHHHHHHHhCCCccHHH
Confidence            478999999999999999988732100         13556777777777666545444443

>2xi8_A Putative transcription regulator; HTH DNA-binding motif; HET: GOL; 1.21A {Enterococcus faecalis} PDB: 2gzu_A 1utx_A* 2xj3_A 2xiu_A

Probab=89.68  E-value=0.5  Score=30.37  Aligned_cols=32  Identities=13%  Similarity=-0.041  Sum_probs=27.1

Q ss_pred             HHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        184 EGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       184 ~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      +.....++|..+.|...|||.++|.+|.++..
T Consensus         8 ~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~   39 (66)
T 2xi8_A            8 LIREKKKISQSELAALLEVSRQTINGIEKNKY   39 (66)
T ss_dssp             HHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSC
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCC
Confidence            34556779999999999999999999998653

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=89.68  E-value=0.31  Score=35.13  Aligned_cols=40  Identities=10%  Similarity=0.079  Sum_probs=32.0

Q ss_pred             HHHHHHH-HHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         37 DMDAALE-ALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        37 ~~~~AI~-~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      ..+.++. .+.+|.+++.++|+.+||+++|+.+.++...-.
T Consensus        28 ~Rl~IL~~l~~~~~~~~~ela~~l~is~stvs~hL~~L~~~   68 (99)
T 2zkz_A           28 MRLKIVNELYKHKALNVTQIIQILKLPQSTVSQHLCKMRGK   68 (99)
T ss_dssp             HHHHHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHHHHBTT
T ss_pred             HHHHHHHHHHHCCCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            3455663 445788999999999999999999999986543

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=89.61  E-value=0.37  Score=33.35  Aligned_cols=38  Identities=18%  Similarity=0.415  Sum_probs=29.6

Q ss_pred             CCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        172 TAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       172 r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|..+...+   .+...++|..+.|.+.|||.+||.+|.+
T Consensus         7 ~~~~~~ri~~---~l~~~glT~~~LA~~~Gvs~stls~~~~   44 (74)
T 1neq_A            7 RDWHRADVIA---GLKKRKLSLSALSRQFGYAPTTLANALE   44 (74)
T ss_dssp             SSCCHHHHHH---HHHTTSCCHHHHHHHHSSCHHHHHHTTT
T ss_pred             CCCCHHHHHH---HHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4676554444   4446679999999999999999998865

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=89.59  E-value=0.22  Score=39.18  Aligned_cols=42  Identities=14%  Similarity=0.215  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      ..-|..|+..+..+.+++.++|..+|||.+||...++ +.+.|
T Consensus        57 ~p~R~~IL~~L~~~~~t~~eLa~~lgls~stvs~hL~~L~~aG   99 (151)
T 3f6v_A           57 EPTRRRLVQLLTSGEQTVNNLAAHFPASRSAISQHLRVLTEAG   99 (151)
T ss_dssp             SHHHHHHHHHGGGCCEEHHHHHTTSSSCHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            3569999999999999999999999999999999998 44433

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=89.52  E-value=0.44  Score=36.03  Aligned_cols=33  Identities=27%  Similarity=0.439  Sum_probs=27.7

Q ss_pred             HHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         41 ALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        41 AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ++..+ .+|.+|..++|+.+||+++|+++.++++
T Consensus         9 il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L   42 (141)
T 1i1g_A            9 ILEILEKDARTPFTEIAKKLGISETAVRKRVKAL   42 (141)
T ss_dssp             HHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            34444 3678999999999999999999999975

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=89.51  E-value=0.69  Score=32.58  Aligned_cols=34  Identities=15%  Similarity=0.070  Sum_probs=29.4

Q ss_pred             HHHHHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...|+..+. .+.++..++|..+|||.+||++.++
T Consensus        22 ~~~il~~l~~~~~~s~~ela~~l~is~~tv~~~l~   56 (109)
T 1sfx_A           22 DVRIYSLLLERGGMRVSEIARELDLSARFVRDRLK   56 (109)
T ss_dssp             HHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            556677665 4789999999999999999999998

>1h89_C C-MYB, MYB proto-oncogene protein; transcription/DNA; 2.45A {Mus musculus} SCOP: a.4.1.3 a.4.1.3 a.4.1.3 PDB: 1h88_C

Probab=89.47  E-value=6.3  Score=30.72  Aligned_cols=144  Identities=10%  Similarity=0.066  Sum_probs=61.1

Q ss_pred             CCCCCCHHHHHHHHHHHHcCC-CCHHHHHHHc-CCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhh
Q psy17316         29 VTKTWTHEDMDAALEALRAGQ-MSLTKASVSY-GIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISA  106 (229)
Q Consensus        29 ~~~kyt~e~~~~AI~~~~~g~-~S~~~aA~~~-gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~  106 (229)
                      .+.+||+|+-...+++|...| ..-..||..+ |=+....+.+...+-    .+.....++++|+-..            
T Consensus         5 ~k~~Wt~eED~~L~~~v~~~g~~~W~~Ia~~l~~Rt~~qcr~Rw~~~l----~p~~~~~~Wt~eEd~~------------   68 (159)
T 1h89_C            5 GKTRWTREEDEKLKKLVEQNGTDDWKVIANYLPNRTDVQCQHRWQKVL----NPELIKGPWTKEEDQR------------   68 (159)
T ss_dssp             --------------------------------------CHHHHHHTTT----CTTCCCSCCCHHHHHH------------
T ss_pred             CCCCCCHHHHHHHHHHHHHhCCCCHHHHHHHcCCCCHHHHHHHHHHcc----CCCcCCCCCChHHHHH------------
Confidence            467899888776666665433 3567778776 333333443333221    1111112344443322            


Q ss_pred             hhhhhccCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChH-HHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHH
Q psy17316        107 NKASKAYGPTKSWNEEILNVALDALRAGSISANKASKAYGIPSS-TLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEG  185 (229)
Q Consensus       107 ~~~~~~~G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~s-TL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~  185 (229)
                                       +.++|+.+  |...-..||..+.-... .++.+-..+    ..|. .....||+||-..+++.
T Consensus        69 -----------------L~~~v~~~--g~~~W~~Ia~~l~~Rt~~qcr~Rw~~~----l~p~-~~~~~WT~eEd~~L~~~  124 (159)
T 1h89_C           69 -----------------VIKLVQKY--GPKRWSVIAKHLKGRIGKQCRERWHNH----LNPE-VKKTSWTEEEDRIIYQA  124 (159)
T ss_dssp             -----------------HHHHHHHH--CSCCHHHHHHTSTTCCHHHHHHHHHHT----TCTT-SCCSCCCHHHHHHHHHH
T ss_pred             -----------------HHHHHHHh--CcccHHHHHHHcCCCCHHHHHHHHHHH----hCcc-ccccCCChHHHHHHHHH
Confidence                             23344443  33357778877632222 244443332    1121 23467999999999999


Q ss_pred             HHhCCCcHHHHHHHh-CCChHHHHHHHH
Q psy17316        186 IRSGQTTVQRASAEY-GIPSGTLYGRCK  212 (229)
Q Consensus       186 ~~~~~~s~~eAA~~f-gVp~~tv~~~vk  212 (229)
                      +...+..-.++|..| |-+-.+|.+.++
T Consensus       125 ~~~~g~~W~~Ia~~l~gRt~~~~knr~~  152 (159)
T 1h89_C          125 HKRLGNRWAEIAKLLPGRTDNAIKNHWN  152 (159)
T ss_dssp             HHHHCSCHHHHHTTSTTCCHHHHHHHHH
T ss_pred             HHHHCCCHHHHHHHCCCCCHHHHHHHHH
Confidence            988778899999988 888888888876

>1on2_A Transcriptional regulator MNTR; helix-turn-helix, DNA-binding protein, metalloregulatory protein; 1.61A {Bacillus subtilis} SCOP: a.4.5.24 a.76.1.1 PDB: 2ev0_A 1on1_A 2ev5_A 2ev6_A* 2f5c_A 2f5d_A 2f5e_A 2f5f_A 2hyf_A* 2hyg_D 3r60_A* 3r61_A*

Probab=89.43  E-value=0.45  Score=35.98  Aligned_cols=43  Identities=9%  Similarity=0.127  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHH--HcCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         35 HEDMDAALEAL--RAGQMSLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        35 ~e~~~~AI~~~--~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      .++.+.+|-.+  ..+++++.++|+.+||+++|+.+.++++.-.|
T Consensus         6 ~~~~L~~i~~l~~~~~~~~~~ela~~l~vs~~tvs~~l~~Le~~G   50 (142)
T 1on2_A            6 MEMYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDE   50 (142)
T ss_dssp             HHHHHHHHHHHHHHHSSCCHHHHHHHHTSCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhhcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            34455555544  35889999999999999999999999864333

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=89.41  E-value=0.17  Score=42.84  Aligned_cols=39  Identities=18%  Similarity=0.233  Sum_probs=31.6

Q ss_pred             HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH-hhcCCCC
Q psy17316        181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCK-LSRSTPR  219 (229)
Q Consensus       181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~~~  219 (229)
                      .++-.+.+|.++..++|..+|+|.++|...++ +...|+-
T Consensus       169 ~l~~~l~~~~~t~~~la~~~~l~~~~V~~~l~~L~~~~~v  208 (232)
T 2qlz_A          169 ILHYLLLNGRATVEELSDRLNLKEREVREKISEMARFVPV  208 (232)
T ss_dssp             HHHHHHHSSEEEHHHHHHHHTCCHHHHHHHHHHHTTTSCE
T ss_pred             HHHHHHhcCCCCHHHHHHHhCcCHHHHHHHHHHHHhcCCe
Confidence            34445556889999999999999999999988 6666654

>2a6c_A Helix-turn-helix motif; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: CIT; 1.90A {Nitrosomonas europaea} SCOP: a.35.1.13

Probab=89.41  E-value=0.71  Score=31.85  Aligned_cols=37  Identities=16%  Similarity=0.121  Sum_probs=30.3

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      ...+-+.....+++..+.|...||+.++|.+|.++..
T Consensus        20 ~~~l~~~r~~~glsq~elA~~~gis~~~is~~e~g~~   56 (83)
T 2a6c_A           20 LIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKI   56 (83)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHTTCG
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCC
Confidence            3445555666789999999999999999999998654

>2a6c_A Helix-turn-helix motif; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: CIT; 1.90A {Nitrosomonas europaea} SCOP: a.35.1.13

Probab=89.34  E-value=0.4  Score=33.17  Aligned_cols=32  Identities=16%  Similarity=0.180  Sum_probs=26.4

Q ss_pred             HHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         40 AALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        40 ~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|+.+ ...++|+.++|+.+||+++||.+|..
T Consensus        21 ~~l~~~r~~~glsq~elA~~~gis~~~is~~e~   53 (83)
T 2a6c_A           21 IVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMR   53 (83)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            344433 45789999999999999999999987

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=89.31  E-value=0.76  Score=35.29  Aligned_cols=34  Identities=9%  Similarity=0.183  Sum_probs=28.2

Q ss_pred             HHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         40 AALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        40 ~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .++..+ .++.+|..++|+.+|++++|++++++++
T Consensus        13 ~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L   47 (151)
T 2dbb_A           13 QLVKILSENSRLTYRELADILNTTRQRIARRIDKL   47 (151)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            344444 3688999999999999999999999985

>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix, DNA-binding, transcription, transcription regulation; 1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB: 3jxb_C 3jxc_L 3jxd_L

Probab=89.26  E-value=0.33  Score=31.45  Aligned_cols=25  Identities=8%  Similarity=0.074  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-++|+.++|+..||+++||.+|..
T Consensus        16 ~~g~s~~~lA~~~gis~~~i~~~e~   40 (68)
T 2r1j_L           16 KLKIRQAALGKMVGVSNVAISQWER   40 (68)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            4479999999999999999999976

>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A

Probab=89.25  E-value=0.42  Score=36.01  Aligned_cols=25  Identities=12%  Similarity=0.069  Sum_probs=23.3

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-++|+.++|+.+||+++||.+|-.
T Consensus        82 ~~glsq~~la~~~g~s~~~i~~~E~  106 (133)
T 3o9x_A           82 KLSLTQKEASEIFGGGVNAFSRYEK  106 (133)
T ss_dssp             HTTCCHHHHHHHHCSCTTHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHC
Confidence            4589999999999999999999977

>1j5y_A Transcriptional regulator, biotin repressor famil; structural genomics, TM1602, BIOT repressor family, JCSG, conserved hypothetical protein; 2.30A {Thermotoga maritima} SCOP: a.4.5.1 d.94.2.1

Probab=89.21  E-value=0.46  Score=38.27  Aligned_cols=41  Identities=10%  Similarity=0.101  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHh-CC-CcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        177 EDLEIALEGIRS-GQ-TTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       177 e~r~eaV~~~~~-~~-~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      +.+.+|++.+.+ ++ ++..+.|.+||||..||++.++ +...|
T Consensus        21 ~R~~~Il~~L~~~~~~~s~~eLa~~l~vS~~Ti~rdi~~L~~~G   64 (187)
T 1j5y_A           21 ERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLG   64 (187)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            456778888875 34 9999999999999999999998 44444

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=89.19  E-value=0.22  Score=40.36  Aligned_cols=36  Identities=11%  Similarity=-0.017  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhC-CChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYG-IPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fg-Vp~~tv~~~vk  212 (229)
                      .-|..||+.+..|.+++.++|..++ +|.+||+.+++
T Consensus        23 P~Rl~il~~L~~~~~~~~~l~~~l~~~~~~~~s~Hl~   59 (182)
T 4g6q_A           23 PLRWRITQLLIGRSLTTRELAELLPDVATTTLYRQVG   59 (182)
T ss_dssp             HHHHHHHHHTTTSCEEHHHHHHHCTTBCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhcCCCHHHHHHHHH
Confidence            4699999999999999999999996 99999999988

>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A

Probab=89.18  E-value=0.58  Score=36.71  Aligned_cols=31  Identities=16%  Similarity=0.196  Sum_probs=25.6

Q ss_pred             HHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         42 LEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        42 I~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.+..-.|+|+.+||..+|||.+||+.++.+
T Consensus       149 l~l~~~~g~s~~EIA~~lgis~~tV~~~l~r  179 (194)
T 1or7_A          149 ITLRELDGLSYEEIAAIMDCPVGTVRSRIFR  179 (194)
T ss_dssp             HHHHHTTCCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred             hHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            3333345889999999999999999999886

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=89.00  E-value=0.35  Score=35.25  Aligned_cols=35  Identities=14%  Similarity=0.153  Sum_probs=31.0

Q ss_pred             HHHHHHHHHH-hC-CCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIR-SG-QTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~-~~-~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+.+|+..+. .| .++..++|..||||.++|+..++
T Consensus        19 ~~l~Il~~l~~~g~~~s~~eLa~~lgvs~~tV~~~L~   55 (110)
T 1q1h_A           19 DVIDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLN   55 (110)
T ss_dssp             TTHHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4778888874 56 79999999999999999999998

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=88.99  E-value=0.49  Score=31.23  Aligned_cols=32  Identities=16%  Similarity=0.113  Sum_probs=26.0

Q ss_pred             HHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         40 AALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        40 ~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|..+ ...|+|+.++|+..||++++|.+|..
T Consensus        16 ~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~   48 (74)
T 1y7y_A           16 QRLRELRTAKGLSQETLAFLSGLDRSYVGGVER   48 (74)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            334433 35789999999999999999999976

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

Probab=88.95  E-value=0.26  Score=36.74  Aligned_cols=30  Identities=10%  Similarity=0.070  Sum_probs=28.4

Q ss_pred             CCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         48 GQMSLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        48 g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      ..+|+.++|++.||+.+||.|-+++.|..|
T Consensus        34 ~~~si~elA~~~~vS~aTv~Rf~kkLGf~g   63 (107)
T 3iwf_A           34 VNMTSQEIANQLETSSTSIIRLSKKVTPGG   63 (107)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHHHHSTTH
T ss_pred             HHCCHHHHHHHHCCCHHHHHHHHHHhCCCC
Confidence            479999999999999999999999999886

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=88.94  E-value=0.5  Score=36.35  Aligned_cols=34  Identities=21%  Similarity=0.400  Sum_probs=28.3

Q ss_pred             HHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         40 AALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        40 ~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .++..+ .+|.+|+.++|+.+|++++|++++++++
T Consensus        11 ~iL~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L   45 (150)
T 2w25_A           11 ILVRELAADGRATLSELATRAGLSVSAVQSRVRRL   45 (150)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            344444 3688999999999999999999999986

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=88.87  E-value=0.86  Score=35.53  Aligned_cols=40  Identities=18%  Similarity=0.324  Sum_probs=30.9

Q ss_pred             CCHHHHHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         33 WTHEDMDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        33 yt~e~~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .++-+. ..++.+ .++.+|+.++|+.+|++++|++++++++
T Consensus         8 ld~~~~-~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L   48 (162)
T 2p5v_A            8 LDKTDI-KILQVLQENGRLTNVELSERVALSPSPCLRRLKQL   48 (162)
T ss_dssp             CCHHHH-HHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCHHHH-HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            344333 444444 3688999999999999999999999986

>3ppb_A Putative TETR family transcription regulator; DNA-binding, helix-turn-helix motif, HTH motif, DNA/RNA-BIND helical bundle fold; HET: MSE PG4; 2.10A {Shewanella loihica}

Probab=88.80  E-value=0.47  Score=36.27  Aligned_cols=42  Identities=17%  Similarity=0.196  Sum_probs=30.2

Q ss_pred             CCCCCHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         30 TKTWTHEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        30 ~~kyt~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ++.-+.+.++ .|++.+.+.   +.|+++||++.||+++|||+...
T Consensus         6 ~~~~~r~~Il~aa~~l~~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~   51 (195)
T 3ppb_A            6 SKRTKKQAILETALQLFVSQGFHGTSTATIAREAGVATGTLFHHFP   51 (195)
T ss_dssp             --CCHHHHHHHHHHHHHHHTCSTTSCHHHHHHHHTCCHHHHHHHCS
T ss_pred             chhhHHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCChhHHHHHcC
Confidence            4445666664 445555553   58999999999999999998744

>1j5y_A Transcriptional regulator, biotin repressor famil; structural genomics, TM1602, BIOT repressor family, JCSG, conserved hypothetical protein; 2.30A {Thermotoga maritima} SCOP: a.4.5.1 d.94.2.1

Probab=88.75  E-value=0.57  Score=37.74  Aligned_cols=37  Identities=11%  Similarity=0.143  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHc-CC-CCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         37 DMDAALEALRA-GQ-MSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        37 ~~~~AI~~~~~-g~-~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .....++.+.+ ++ +|..++|+++||+++|+++.++..
T Consensus        22 R~~~Il~~L~~~~~~~s~~eLa~~l~vS~~Ti~rdi~~L   60 (187)
T 1j5y_A           22 RLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYL   60 (187)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            34566666663 44 999999999999999999999864

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei}

Probab=88.70  E-value=1.8  Score=31.46  Aligned_cols=35  Identities=17%  Similarity=0.190  Sum_probs=28.3

Q ss_pred             HHHHHHHHHH---cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         37 DMDAALEALR---AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        37 ~~~~AI~~~~---~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+-..|..++   .-++|+.++|+.+||+++||.+|..
T Consensus        34 ~~g~~lk~~R~~~~~glsq~elA~~~gis~~~is~~E~   71 (107)
T 2jvl_A           34 EVGKAIEQGRQKFEPTMTQAELGKEIGETAATVASYER   71 (107)
T ss_dssp             HHHHHHHHHHTTSSSCCCHHHHHHHHTCCHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4455566554   4689999999999999999999965

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=88.64  E-value=0.53  Score=31.40  Aligned_cols=32  Identities=13%  Similarity=0.102  Sum_probs=26.1

Q ss_pred             HHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         40 AALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        40 ~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|..+ ..-|+|+.++|+..||++++|.+|..
T Consensus        13 ~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   45 (77)
T 2b5a_A           13 RTLKKIRTQKGVSQEELADLAGLHRTYISEVER   45 (77)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHC
Confidence            344433 35689999999999999999999976

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=88.56  E-value=0.9  Score=34.75  Aligned_cols=34  Identities=15%  Similarity=0.335  Sum_probs=28.4

Q ss_pred             HHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         40 AALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        40 ~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..++.+ .++.+|+.++|+++||+++|++++++++
T Consensus         9 ~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L   43 (144)
T 2cfx_A            9 NIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQL   43 (144)
T ss_dssp             HHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            344444 3678999999999999999999999986

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=88.54  E-value=1  Score=34.68  Aligned_cols=34  Identities=24%  Similarity=0.429  Sum_probs=28.5

Q ss_pred             HHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         40 AALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        40 ~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..++.+ .+|.+|+.++|+++|++++|++++++++
T Consensus        11 ~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L   45 (151)
T 2cyy_A           11 KIIKILQNDGKAPLREISKITGLAESTIHERIRKL   45 (151)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            444444 3688999999999999999999999986

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=88.42  E-value=0.4  Score=31.87  Aligned_cols=25  Identities=8%  Similarity=0.074  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..++|+.++|+..||++++|.+|..
T Consensus        16 ~~gls~~~lA~~~gis~~~i~~~e~   40 (76)
T 1adr_A           16 KLKIRQAALGKMVGVSNVAISQWER   40 (76)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4589999999999999999999976

>1uly_A Hypothetical protein PH1932; helix-turn-helix, structural genomics, DNA binding protein; 2.50A {Pyrococcus horikoshii} SCOP: a.4.5.58 PDB: 2cwe_A

Probab=88.39  E-value=0.6  Score=38.10  Aligned_cols=36  Identities=19%  Similarity=0.272  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +.+..|+..+.+|.+++.++|..+|||.+||++.++
T Consensus        20 ~~~~~IL~~L~~~~~s~~eLA~~lglS~stv~~~l~   55 (192)
T 1uly_A           20 DTRRKILKLLRNKEMTISQLSEILGKTPQTIYHHIE   55 (192)
T ss_dssp             HHHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            446788888888999999999999999999999998

>2qko_A Possible transcriptional regulator, TETR family P; TETR family protein, structural genomics, P protein structure initiative; 2.35A {Rhodococcus SP}

Probab=88.37  E-value=0.38  Score=38.07  Aligned_cols=41  Identities=17%  Similarity=0.166  Sum_probs=29.9

Q ss_pred             CCCCHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         31 KTWTHEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        31 ~kyt~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.-+.+.++ .|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        26 ~~~~r~~Il~aa~~lf~~~G~~~~tv~~IA~~agvs~~t~Y~~F~   70 (215)
T 2qko_A           26 NPERRAALVNAAIEVLAREGARGLTFRAVDVEANVPKGTASNYFP   70 (215)
T ss_dssp             -CHHHHHHHHHHHHHHHHTCTTTCCHHHHHHHSSSTTTCHHHHCS
T ss_pred             cHHHHHHHHHHHHHHHHHhChhhccHHHHHHHcCCCcchHHHhCC
Confidence            444556664 455555553   58999999999999999998754

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=88.30  E-value=0.69  Score=31.84  Aligned_cols=37  Identities=16%  Similarity=0.136  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHc---CCCCHHHHHHHc-----CCChhhHHHHHHHh
Q psy17316         37 DMDAALEALRA---GQMSLTKASVSY-----GIPSTTLWQRAHRL   73 (229)
Q Consensus        37 ~~~~AI~~~~~---g~~S~~~aA~~~-----gIp~sTL~~~i~~~   73 (229)
                      ....+++.+.+   +.+|+.+++..+     +|+.+|||+-+..+
T Consensus        18 ~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L   62 (83)
T 2fu4_A           18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQF   62 (83)
T ss_dssp             HHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHH
Confidence            44556665543   579999999999     99999999998875

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=88.29  E-value=0.63  Score=35.67  Aligned_cols=35  Identities=29%  Similarity=0.367  Sum_probs=29.1

Q ss_pred             HHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         40 AALEALR-AGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        40 ~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .++..+. ++.+|..++|+.+||+++|++++++++.
T Consensus         7 ~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~   42 (150)
T 2pn6_A            7 RILKILQYNAKYSLDEIAREIRIPKATLSYRIKKLE   42 (150)
T ss_dssp             HHHHHHTTCTTSCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4555554 5779999999999999999999999863

>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28

Probab=88.24  E-value=0.38  Score=33.84  Aligned_cols=35  Identities=9%  Similarity=0.022  Sum_probs=28.9

Q ss_pred             HHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..++..+ .++.+|+.++|+.+||+++||++.++++
T Consensus        19 ~~iL~~L~~~~~~~~~ela~~l~is~~tvs~~l~~L   54 (100)
T 1ub9_A           19 LGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVL   54 (100)
T ss_dssp             HHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3444444 3688999999999999999999999986

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=88.21  E-value=0.66  Score=35.52  Aligned_cols=35  Identities=23%  Similarity=0.147  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+.+|++.+.. +.+++.++|..+|||.+||.+.++
T Consensus         4 ~~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~   39 (150)
T 2pn6_A            4 IDLRILKILQYNAKYSLDEIAREIRIPKATLSYRIK   39 (150)
T ss_dssp             HHHHHHHHHTTCTTSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45678887764 569999999999999999999998

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=88.21  E-value=0.76  Score=34.46  Aligned_cols=42  Identities=5%  Similarity=0.108  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHH--cCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         36 EDMDAALEALR--AGQMSLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        36 e~~~~AI~~~~--~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      .+.+.+|..+.  ++.+|+.++|+.+||+++|+.+.++++.-.|
T Consensus        16 ~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~~~l~~Le~~G   59 (139)
T 2x4h_A           16 FSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVFEEVSHLEEKG   59 (139)
T ss_dssp             HHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHHHHHHHHHHCC
Confidence            34455655442  4688999999999999999999999864333

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=88.21  E-value=0.9  Score=30.85  Aligned_cols=30  Identities=10%  Similarity=0.086  Sum_probs=24.5

Q ss_pred             HHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        184 EGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       184 ~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      +.+.+.. ++.++|+.+||+.++|..|++..
T Consensus         8 k~l~~~~-sq~~~A~~Lgvsq~aVS~~~~~~   37 (65)
T 2cw1_A            8 KKFVEDK-NQEYAARALGLSQKLIEEVLKRG   37 (65)
T ss_dssp             HHHHTTS-CHHHHHHHSSSCHHHHHHHHHTT
T ss_pred             HHHHHHc-CHHHHHHHhCCCHHHHHHHHHhc
Confidence            3345554 99999999999999999999743

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=88.12  E-value=0.49  Score=34.18  Aligned_cols=30  Identities=17%  Similarity=0.204  Sum_probs=26.2

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      .|.+|+.++|+.|||+..||++=+..+.-.
T Consensus        14 ~g~vsv~eLA~~l~VS~~TIRrDL~~Le~~   43 (87)
T 2k02_A           14 QGRMEAKQLSARLQTPQPLIDAMLERMEAM   43 (87)
T ss_dssp             SCSEEHHHHHHHTTCCHHHHHHHHHHHHTT
T ss_pred             cCCCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            689999999999999999999988875433

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=88.06  E-value=0.64  Score=34.43  Aligned_cols=42  Identities=24%  Similarity=0.275  Sum_probs=31.3

Q ss_pred             HHHH-HHHHHHHcCCC-------CHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         36 EDMD-AALEALRAGQM-------SLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        36 e~~~-~AI~~~~~g~~-------S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      +++. ...+.|.+|.+       |.+++|++|||+++|+++-+..+.-.|
T Consensus        12 ~~i~~~i~~~I~~g~~~~G~~lPs~~~La~~~~vSr~tvr~al~~L~~~G   61 (113)
T 3tqn_A           12 QQLRDKIVEAIIDGSYVEGEMIPSIRKISTEYQINPLTVSKAYQSLLDDN   61 (113)
T ss_dssp             HHHHHHHHHHHHHTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            4444 33446667665       899999999999999999888764443

>2opt_A Actii protein; helical protein, TETR family, APO-protein, transcriptional R transcription; 2.05A {Streptomyces coelicolor} PDB: 3b6a_A* 3b6c_A*

Probab=88.01  E-value=0.65  Score=38.50  Aligned_cols=42  Identities=17%  Similarity=0.234  Sum_probs=32.8

Q ss_pred             CCCCCHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         30 TKTWTHEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        30 ~~kyt~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +...+.+.++ .|++.+.+.   ++|+++||++.||+++|||+...
T Consensus         3 r~~~tr~~Il~AA~~l~~~~G~~~~S~r~IA~~aGvs~~tlY~hF~   48 (234)
T 2opt_A            3 MAPLTQDRIVVTALGILDAEGLDALSMRRLAQELKTGHASLYAHVG   48 (234)
T ss_dssp             CCCCCHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHHhCCccccCHHHHHHHHCCChhHHHHHcC
Confidence            4566778774 555555543   58999999999999999999866

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=87.98  E-value=0.75  Score=30.54  Aligned_cols=33  Identities=15%  Similarity=0.133  Sum_probs=27.5

Q ss_pred             HHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        183 LEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       183 V~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      -+.....+++..+.|...|||.++|.+|.++.+
T Consensus        16 ~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~   48 (76)
T 3bs3_A           16 KVVLAEKQRTNRWLAEQMGKSENTISRWCSNKS   48 (76)
T ss_dssp             HHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSS
T ss_pred             HHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCC
Confidence            344556779999999999999999999998654

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=87.93  E-value=0.38  Score=34.03  Aligned_cols=34  Identities=12%  Similarity=0.164  Sum_probs=27.4

Q ss_pred             HHHHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         38 MDAALEALR-AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        38 ~~~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +-..|+.++ ..++|+.++|+.+||+++||.+|..
T Consensus        10 ~~~~lk~~r~~~glsq~~lA~~~gis~~~is~~e~   44 (94)
T 2kpj_A           10 FSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCK   44 (94)
T ss_dssp             HHHHHHHHHTTSSSCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence            344455444 5689999999999999999999976

>1uly_A Hypothetical protein PH1932; helix-turn-helix, structural genomics, DNA binding protein; 2.50A {Pyrococcus horikoshii} SCOP: a.4.5.58 PDB: 2cwe_A

Probab=87.93  E-value=0.5  Score=38.61  Aligned_cols=35  Identities=23%  Similarity=0.410  Sum_probs=30.3

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..++..+.+|.+|+.++|+.+||+++|+++.++++
T Consensus        23 ~~IL~~L~~~~~s~~eLA~~lglS~stv~~~l~~L   57 (192)
T 1uly_A           23 RKILKLLRNKEMTISQLSEILGKTPQTIYHHIEKL   57 (192)
T ss_dssp             HHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            34555666899999999999999999999999985

>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix, DNA-binding, transcription, transcription regulation; 1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB: 3jxb_C 3jxc_L 3jxd_L

Probab=87.89  E-value=0.66  Score=29.96  Aligned_cols=32  Identities=3%  Similarity=-0.088  Sum_probs=26.6

Q ss_pred             HHHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        183 LEGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       183 V~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      -+.....+++..+.|...|||.++|.+|.++.
T Consensus        11 ~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~   42 (68)
T 2r1j_L           11 RARRKKLKIRQAALGKMVGVSNVAISQWERSE   42 (68)
T ss_dssp             HHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTS
T ss_pred             HHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCC
Confidence            34445566999999999999999999998864

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=87.82  E-value=1  Score=34.67  Aligned_cols=34  Identities=21%  Similarity=0.429  Sum_probs=28.5

Q ss_pred             HHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         40 AALEALR-AGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        40 ~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..++.+. +|.+|+.++|+++|++++|++++++++
T Consensus        12 ~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L   46 (152)
T 2cg4_A           12 GILEALMGNARTAYAELAKQFGVSPETIHVRVEKM   46 (152)
T ss_dssp             HHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4444443 578999999999999999999999985

>3dcf_A Transcriptional regulator of the TETR/ACRR family; YP_290855.1, structural genomics, joint center for structural genomics, JCSG; 2.50A {Thermobifida fusca YX}

Probab=87.76  E-value=0.67  Score=36.16  Aligned_cols=40  Identities=15%  Similarity=0.144  Sum_probs=29.8

Q ss_pred             CCCHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         32 TWTHEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        32 kyt~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-+.+.++ .|++.+.+.   +.|+.+||++.||+++|||++..
T Consensus        30 ~~~r~~Il~aa~~l~~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~   73 (218)
T 3dcf_A           30 NDRRTQIIKVATELFREKGYYATSLDDIADRIGFTKPAIYYYFK   73 (218)
T ss_dssp             CHHHHHHHHHHHHHHHHTCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             cchHHHHHHHHHHHHHHcCcccCcHHHHHHHhCCCHHHHHHHcC
Confidence            34556664 555555543   48999999999999999998754

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=87.74  E-value=0.82  Score=34.30  Aligned_cols=40  Identities=20%  Similarity=0.204  Sum_probs=34.1

Q ss_pred             CCCHHHHHHHHHHHHh-CCCcHHHHHHHh--CCChHHHHHHHH
Q psy17316        173 AWKPEDLEIALEGIRS-GQTTVQRASAEY--GIPSGTLYGRCK  212 (229)
Q Consensus       173 ~~t~e~r~eaV~~~~~-~~~s~~eAA~~f--gVp~~tv~~~vk  212 (229)
                      .|-......|++.+.. |.+++.++|..+  +||.++|..+++
T Consensus         9 ~~md~~d~~IL~~L~~~g~~s~~eLA~~l~~giS~~aVs~rL~   51 (111)
T 3b73_A            9 SWMTIWDDRILEIIHEEGNGSPKELEDRDEIRISKSSVSRRLK   51 (111)
T ss_dssp             TTCCHHHHHHHHHHHHHSCBCHHHHHTSTTCCSCHHHHHHHHH
T ss_pred             hhcCHHHHHHHHHHHHcCCCCHHHHHHHHhcCCCHHHHHHHHH
Confidence            3434456888998865 999999999999  999999999998

>2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2, protein struct initiative, northeast structural genomics consortium, NESG; 1.63A {Escherichia coli} SCOP: a.35.1.3 PDB: 2icp_A

Probab=87.70  E-value=0.39  Score=33.81  Aligned_cols=25  Identities=16%  Similarity=0.056  Sum_probs=23.2

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-++|+.++|+..||+++||.+|..
T Consensus        19 ~~gltq~~lA~~~gis~~~is~~e~   43 (94)
T 2ict_A           19 ELNVSLREFARAMEIAPSTASRLLT   43 (94)
T ss_dssp             HHTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            4479999999999999999999988

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=87.67  E-value=0.58  Score=31.16  Aligned_cols=31  Identities=10%  Similarity=-0.003  Sum_probs=26.4

Q ss_pred             HHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        184 EGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       184 ~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      +.+...+++..+.|.+.|||.+||.+|.++.
T Consensus        15 ~~r~~~glsq~~lA~~~gis~~~is~~e~g~   45 (73)
T 3omt_A           15 SVLAEKGKTNLWLTETLDKNKTTVSKWCTND   45 (73)
T ss_dssp             HHHHHHTCCHHHHHHHTTCCHHHHHHHHTTS
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence            3344566999999999999999999999865

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=87.56  E-value=0.72  Score=34.81  Aligned_cols=42  Identities=12%  Similarity=0.156  Sum_probs=31.4

Q ss_pred             HHHHHH-HHHHHcCCC-------CHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         36 EDMDAA-LEALRAGQM-------SLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        36 e~~~~A-I~~~~~g~~-------S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      +++... .+.|.+|.+       |.+++|++|||+++||++-+..+.-+|
T Consensus        16 ~~i~~~i~~~I~~g~~~~g~~Lps~~~La~~~~vSr~tvr~Al~~L~~~G   65 (125)
T 3neu_A           16 SQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAG   65 (125)
T ss_dssp             HHHHHHHHHHHHTTSSCTTCBCCCHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            445444 446677665       799999999999999999888764433

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=87.54  E-value=0.36  Score=32.70  Aligned_cols=25  Identities=12%  Similarity=0.150  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..++|+.++|++.||+++||.+|..
T Consensus        13 ~~glsq~~lA~~~gis~~~i~~~e~   37 (77)
T 2k9q_A           13 RLSLTAKSVAEEMGISRQQLCNIEQ   37 (77)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            4589999999999999999999976

>3qkx_A Uncharacterized HTH-type transcriptional regulato; structural genomics, joint center for structural genomics; HET: MSE; 2.35A {Haemophilus influenzae}

Probab=87.54  E-value=0.73  Score=35.04  Aligned_cols=36  Identities=17%  Similarity=0.217  Sum_probs=27.2

Q ss_pred             HHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         36 EDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        36 e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        11 ~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   50 (188)
T 3qkx_A           11 EQIFSATDRLMAREGLNQLSMLKLAKEANVAAGTIYLYFK   50 (188)
T ss_dssp             HHHHHHHHHHHHHSCSTTCCHHHHHHHHTCCHHHHHHHSS
T ss_pred             HHHHHHHHHHHHhcCcccCCHHHHHHHhCCCcchHHHHcC
Confidence            344 4455555553   58999999999999999998744

>3nxc_A HTH-type protein SLMA; nucleoid occlusion, cell division, TETR family member, DNA B protein; 2.50A {Escherichia coli}

Probab=87.53  E-value=0.5  Score=36.85  Aligned_cols=41  Identities=20%  Similarity=0.324  Sum_probs=30.3

Q ss_pred             CCCCHHHHHHH-HHHH-Hc-C--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         31 KTWTHEDMDAA-LEAL-RA-G--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        31 ~kyt~e~~~~A-I~~~-~~-g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.-+.+.++.| ++.+ .+ |  +.|+++||++.||+++|||+...
T Consensus        22 ~~~~r~~Il~aA~~~lf~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   67 (212)
T 3nxc_A           22 KRNRREEILQSLALMLESSDGSQRITTAKLAASVGVSEAALYRHFP   67 (212)
T ss_dssp             -CTTHHHHHHHHHHHHHC------CCHHHHHHHTTSCHHHHHTTCS
T ss_pred             chHHHHHHHHHHHHHHHhcCChhhcCHHHHHHHhCCChhHHHHHCC
Confidence            55677888766 6645 44 3  69999999999999999998743

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=87.49  E-value=0.4  Score=32.90  Aligned_cols=25  Identities=16%  Similarity=0.153  Sum_probs=23.2

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-++|+.++|+.+||++++|.+|.+
T Consensus        21 ~~gltq~elA~~~gis~~~is~~E~   45 (78)
T 3qq6_A           21 EKGYSLSELAEKAGVAKSYLSSIER   45 (78)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4689999999999999999999976

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=87.44  E-value=0.29  Score=33.48  Aligned_cols=23  Identities=17%  Similarity=0.281  Sum_probs=21.8

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      | |+.++|+.+||+++||.+|.+.
T Consensus        12 g-sq~~lA~~lgvs~~~is~~e~g   34 (79)
T 3bd1_A           12 G-SVSALAASLGVRQSAISNWRAR   34 (79)
T ss_dssp             S-SHHHHHHHHTCCHHHHHHHHHH
T ss_pred             C-CHHHHHHHHCCCHHHHHHHHHC
Confidence            5 9999999999999999999985

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=87.43  E-value=1.3  Score=29.37  Aligned_cols=34  Identities=6%  Similarity=-0.102  Sum_probs=27.6

Q ss_pred             HHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        182 ALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       182 aV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      +-+.....+++..+.|...|||.++|.+|.++.+
T Consensus        15 l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~   48 (77)
T 2b5a_A           15 LKKIRTQKGVSQEELADLAGLHRTYISEVERGDR   48 (77)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCS
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCC
Confidence            3344455779999999999999999999988653

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36

Probab=87.38  E-value=0.4  Score=35.81  Aligned_cols=35  Identities=14%  Similarity=0.130  Sum_probs=28.8

Q ss_pred             HHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         39 DAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      +.++ .+.+|++|+.++|+.+||+++|+++.++++.
T Consensus        32 l~~L-~~~~~~~t~~ela~~l~~~~stvs~~l~~L~   66 (152)
T 1ku9_A           32 YAIL-YLSDKPLTISDIMEELKISKGNVSMSLKKLE   66 (152)
T ss_dssp             HHHH-HHCSSCEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHH-HHcCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4444 3346889999999999999999999999863

>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=87.35  E-value=0.77  Score=33.68  Aligned_cols=25  Identities=8%  Similarity=0.222  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         48 GQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        48 g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .++|+.+||..+|||..||++++.+
T Consensus        38 e~~s~~EIA~~lgiS~~tVr~~~~r   62 (99)
T 3t72_q           38 TDYTLEEVGKQFDVTRERIRQIEAK   62 (99)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            5799999999999999999998875

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=87.34  E-value=1.4  Score=28.96  Aligned_cols=33  Identities=9%  Similarity=-0.096  Sum_probs=27.2

Q ss_pred             HHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        182 ALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       182 aV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      +-+.....+++..+.|...|||.++|.+|.++.
T Consensus        18 l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~   50 (74)
T 1y7y_A           18 LRELRTAKGLSQETLAFLSGLDRSYVGGVERGQ   50 (74)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTC
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCC
Confidence            334445577999999999999999999998865

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2}

Probab=87.28  E-value=0.52  Score=32.02  Aligned_cols=33  Identities=12%  Similarity=0.232  Sum_probs=26.8

Q ss_pred             HHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      -..|..+ ..-|+|+.++|+..||++++|.+|..
T Consensus        12 ~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   45 (84)
T 2ef8_A           12 VQLLTKLRKEASLSQSELAIFLGLSQSDISKIES   45 (84)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            3444444 35689999999999999999999976

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=87.13  E-value=1  Score=34.56  Aligned_cols=34  Identities=15%  Similarity=0.328  Sum_probs=29.4

Q ss_pred             HHHHHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...|+..+. ++.+++.++|..+|+|.+||.+.++
T Consensus         9 ~~~iL~~L~~~~~~s~~ela~~lg~s~~tv~~~l~   43 (150)
T 2w25_A            9 DRILVRELAADGRATLSELATRAGLSVSAVQSRVR   43 (150)
T ss_dssp             HHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            446777765 4679999999999999999999998

>2l1p_A DNA-binding protein SATB1; PSI-biology, NESG, structural genomics, protein structure in northeast structural genomics consortium; NMR {Homo sapiens} PDB: 3nzl_A*

Probab=87.03  E-value=1.2  Score=31.96  Aligned_cols=41  Identities=17%  Similarity=0.329  Sum_probs=34.9

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHH
Q psy17316        116 TKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIAR  157 (229)
Q Consensus       116 ~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik  157 (229)
                      ...|+-+.....+..++. ++++.++|++.||+++||..+++
T Consensus        14 ~~~~~~~~~~~kLK~il~-GikQ~eLAK~iGIsqsTLSaIen   54 (83)
T 2l1p_A           14 PEQWSHTTVRNALKDLLK-DMNQSSLAKECPLSQSMISSIVN   54 (83)
T ss_dssp             TSCCCHHHHHHHHHHHHT-TSCHHHHHHHSSSCHHHHHHHHT
T ss_pred             HHHhhHHHHHHHHHHHHH-hcCHHHHHHHcCCCHHHHHHHHc
Confidence            456777777777788888 67999999999999999999876

>1r8e_A Multidrug-efflux transporter regulator; protein-DNA complex, MERR-family transcription activator, MU binding protein; HET: P4P; 2.40A {Bacillus subtilis} SCOP: a.6.1.3 d.60.1.1 PDB: 1exi_A* 1exj_A* 3iao_A 3q5p_A* 3d71_A* 3q3d_A* 3q1m_A* 3q2y_A* 3q5r_A* 3q5s_A* 3d70_A 3d6z_A* 3d6y_A* 1bow_A 2bow_A*

Probab=86.98  E-value=1  Score=37.93  Aligned_cols=27  Identities=11%  Similarity=0.026  Sum_probs=23.5

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      -+++.++|+.+||+..||+.|-+. |+-
T Consensus         5 ~~~i~e~a~~~gvs~~tlr~y~~~-gll   31 (278)
T 1r8e_A            5 YYSIGEVSKLANVSIKALRYYDKI-DLF   31 (278)
T ss_dssp             EEEHHHHHHHHTCCHHHHHHHHHT-TSS
T ss_pred             cEeHHHHHHHHCcCHHHHHHHHHC-CCC
Confidence            478999999999999999999876 543

>2yve_A Transcriptional regulator; helix-turn-helix, TETR-family; HET: MBT; 1.40A {Corynebacterium glutamicum} PDB: 1v7b_A 2zoy_A 2yvh_A 2dh0_A* 2zoz_A*

Probab=86.90  E-value=0.79  Score=35.56  Aligned_cols=38  Identities=13%  Similarity=0.159  Sum_probs=28.7

Q ss_pred             CHHHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+.+ ..|++.+.+.   +.|+++||++.||+++|||++..
T Consensus         5 ~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   46 (185)
T 2yve_A            5 KKEMILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFP   46 (185)
T ss_dssp             HHHHHHHHHHHHHHHSCSTTCCHHHHHHHHCCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHcChhhccHHHHHHHhCCChHHHHHhCc
Confidence            44555 4555555553   48999999999999999999854

>3s8q_A R-M controller protein; protein-DNA complex, helix-turn-helix; HET: DNA; 2.10A {Enterobacter SP} SCOP: a.35.1.0 PDB: 3clc_A* 3ufd_A*

Probab=86.86  E-value=0.56  Score=31.94  Aligned_cols=33  Identities=6%  Similarity=0.019  Sum_probs=26.6

Q ss_pred             HHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      -..|..+ ..-++|+.++|+..||+++||.+|-.
T Consensus        13 g~~lk~~R~~~glsq~~lA~~~gis~~~i~~~e~   46 (82)
T 3s8q_A           13 SFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIER   46 (82)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHC
Confidence            3444444 35789999999999999999999976

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=86.86  E-value=0.26  Score=38.28  Aligned_cols=37  Identities=11%  Similarity=-0.068  Sum_probs=28.7

Q ss_pred             CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++..| +|+....-.++|+.|+|..+|||..||..++.
T Consensus        95 p~~~r-~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~  131 (157)
T 2lfw_A           95 TPLSR-QALLLTAMEGFSPEDAAYLIEVDTSEVETLVT  131 (157)
T ss_dssp             CTTHH-HHHTTTSSSCCCHHHHHHTTTSCHHHHHHHHH
T ss_pred             CHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34434 55655545569999999999999999999885

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=86.84  E-value=0.88  Score=35.67  Aligned_cols=39  Identities=10%  Similarity=0.175  Sum_probs=31.6

Q ss_pred             HHHHHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        179 LEIALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       179 r~eaV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      -.+|++.+. ++.+++.++|..+|+|.+||+++++ +...|
T Consensus         5 d~~il~~L~~~~~~s~~~la~~lg~s~~tv~~rl~~L~~~g   45 (162)
T 3i4p_A            5 DRKILRILQEDSTLAVADLAKKVGLSTTPCWRRIQKMEEDG   45 (162)
T ss_dssp             HHHHHHHHTTCSCSCHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            456777775 4679999999999999999999998 44444

>2g7g_A RHA04620, putative transcriptional regulator; helix-turn-helix, structural genomics, PSI, protein structur initiative; 2.01A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=86.82  E-value=0.68  Score=37.37  Aligned_cols=42  Identities=14%  Similarity=0.333  Sum_probs=30.7

Q ss_pred             CCCCCHHHHHH-HHHHHH-cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         30 TKTWTHEDMDA-ALEALR-AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        30 ~~kyt~e~~~~-AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +...+.+.++. |++.+. +|++|+++||++.||+++|||+...
T Consensus         8 ~~~~~r~~Il~aA~~l~~~~G~~s~~~IA~~aGvs~~tlY~hF~   51 (213)
T 2g7g_A            8 VARLDRERIAEAALELVDRDGDFRMPDLARHLNVQVSSIYHHAK   51 (213)
T ss_dssp             ---CCHHHHHHHHHHHHHHHSSCCHHHHHHHTTSCHHHHHTTSC
T ss_pred             CCCCCHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCHhHHHHHcC
Confidence            34567777754 454443 4689999999999999999998654

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=86.82  E-value=1.1  Score=30.00  Aligned_cols=37  Identities=16%  Similarity=0.176  Sum_probs=29.3

Q ss_pred             HHHHHHHhCC--CcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        181 IALEGIRSGQ--TTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       181 eaV~~~~~~~--~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      +++.++.+++  +++...|++|||++..|+.-++ +..-|
T Consensus        14 ~lL~yIr~sGGildI~~~a~kygV~kdeV~~~LrrLe~KG   53 (59)
T 2xvc_A           14 ELLDYIVNNGGFLDIEHFSKVYGVEKQEVVKLLEALKNKG   53 (59)
T ss_dssp             HHHHHHHHTTSEEEHHHHHHHHCCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCEEeHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            5666776643  8999999999999999999987 44433

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=86.81  E-value=0.73  Score=30.23  Aligned_cols=32  Identities=16%  Similarity=0.084  Sum_probs=26.2

Q ss_pred             HHHHHH-HcCCCCHHHHHHHcC--CChhhHHHHHH
Q psy17316         40 AALEAL-RAGQMSLTKASVSYG--IPSTTLWQRAH   71 (229)
Q Consensus        40 ~AI~~~-~~g~~S~~~aA~~~g--Ip~sTL~~~i~   71 (229)
                      ..|..+ ...|+|+.++|+..|  |++++|.+|..
T Consensus        11 ~~l~~~r~~~glsq~~lA~~~g~~is~~~i~~~e~   45 (71)
T 2ewt_A           11 AKLRAIRTQQGLSLHGVEEKSQGRWKAVVVGSYER   45 (71)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHTTTSSCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCcCCHHHHHHHHC
Confidence            344433 356899999999999  99999999987

>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response E family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV}

Probab=86.78  E-value=0.41  Score=32.69  Aligned_cols=32  Identities=13%  Similarity=0.169  Sum_probs=25.9

Q ss_pred             HHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         40 AALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        40 ~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|..+ ..-|+|+.++|+..||++++|.+|..
T Consensus        17 ~~l~~~R~~~gltq~elA~~~gis~~~is~~e~   49 (83)
T 3f6w_A           17 DLLLEARSAAGITQKELAARLGRPQSFVSKTEN   49 (83)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            344433 34689999999999999999999976

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=86.77  E-value=1.1  Score=34.96  Aligned_cols=35  Identities=17%  Similarity=0.117  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...++++.+.. +.+++.++|..+|+|.+||+++++
T Consensus        11 ~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~   46 (162)
T 2p5v_A           11 TDIKILQVLQENGRLTNVELSERVALSPSPCLRRLK   46 (162)
T ss_dssp             HHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34577877754 679999999999999999999998

>2hxi_A Putative transcriptional regulator; structural genomics, APC6293, TET streptomyces coelicolor A3(2), PSI-2; 1.70A {Streptomyces coelicolor}

Probab=86.77  E-value=0.79  Score=37.99  Aligned_cols=43  Identities=30%  Similarity=0.476  Sum_probs=31.6

Q ss_pred             CCCCCCHHHHHH-HHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         29 VTKTWTHEDMDA-ALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        29 ~~~kyt~e~~~~-AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+...+.+.++. |++.+.+.   ++|+++||++.||+++|||+...
T Consensus        25 ~~~~~tr~~Il~aA~~l~~~~G~~~~s~~~IA~~aGvs~~tlY~hF~   71 (241)
T 2hxi_A           25 GRRRWSTEQILDAAAELLLAGDAETFSVRKLAASLGTDSSSLYRHFR   71 (241)
T ss_dssp             ---CCCHHHHHHHHHHHHSSSSCCCCCHHHHHHHTTSCHHHHHHHTS
T ss_pred             cchhhHHHHHHHHHHHHHHhcCcccCCHHHHHHHhCcCHHHHHHHcC
Confidence            356678888854 55555443   58999999999999999999754

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=86.76  E-value=1.1  Score=34.06  Aligned_cols=43  Identities=12%  Similarity=0.085  Sum_probs=32.0

Q ss_pred             HHHHHHH-HHHHcCCC-------CHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316         36 EDMDAAL-EALRAGQM-------SLTKASVSYGIPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        36 e~~~~AI-~~~~~g~~-------S~~~aA~~~gIp~sTL~~~i~~~gi~~~   78 (229)
                      +++...| +.|.+|.+       |.+++|++|||+++||++-+..+...|.
T Consensus         7 ~~i~~~i~~~I~~g~l~~G~~LPse~~La~~~gvSr~tVr~Al~~L~~~Gl   57 (129)
T 2ek5_A            7 KQIASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGI   57 (129)
T ss_dssp             HHHHHHHHHHHHTTSSCTTSCBCCHHHHHHHTTCCHHHHHHHHHHHHTTTS
T ss_pred             HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCc
Confidence            4444333 46666654       8999999999999999998888755543

>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription complex, serine kinase, DNA-bindin mercury derivative, repressor; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B*

Probab=86.68  E-value=1.5  Score=29.94  Aligned_cols=38  Identities=18%  Similarity=0.104  Sum_probs=28.7

Q ss_pred             HHHHHHHH-HHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316        176 PEDLEIAL-EGIRSGQTTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       176 ~e~r~eaV-~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      ....-+.| +.....+++..+.|...|||.++|.+|.++
T Consensus        10 ~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g   48 (88)
T 2wiu_B           10 PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENN   48 (88)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence            33333334 444457799999999999999999999884

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae}

Probab=86.68  E-value=1.5  Score=33.75  Aligned_cols=26  Identities=12%  Similarity=0.197  Sum_probs=24.1

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..-|+|+.++|+.+||++++|.+|-+
T Consensus        78 ~~~glTq~elA~~lGis~s~is~~E~  103 (141)
T 3kxa_A           78 MKKGFTQSELATAAGLPQPYLSRIEN  103 (141)
T ss_dssp             HHTTCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            45789999999999999999999987

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A

Probab=86.65  E-value=0.98  Score=36.40  Aligned_cols=40  Identities=3%  Similarity=0.003  Sum_probs=29.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.++.+.. +|.+..-.++|+.+||+.+|||.+||++++++
T Consensus       187 ~L~~~~r~-vl~l~~~~g~s~~EIA~~lgis~~~V~~~~~r  226 (239)
T 1rp3_A          187 KLPEREKL-VIQLIFYEELPAKEVAKILETSVSRVSQLKAK  226 (239)
T ss_dssp             TSCHHHHH-HHHHHHTSCCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred             cCCHHHHH-HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            34444443 33343345889999999999999999998875

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=86.63  E-value=1.2  Score=33.46  Aligned_cols=34  Identities=9%  Similarity=-0.003  Sum_probs=28.7

Q ss_pred             HHHHHHHHHh-CC--CcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRS-GQ--TTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~-~~--~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...|+..+.+ ++  ++..++|..+++|.+|||+.++
T Consensus        28 e~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L~   64 (123)
T 3r0a_A           28 DLNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSVK   64 (123)
T ss_dssp             HHHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            4567776664 45  7999999999999999999998

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi}

Probab=86.63  E-value=1.2  Score=30.99  Aligned_cols=34  Identities=6%  Similarity=0.031  Sum_probs=27.3

Q ss_pred             HHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         38 MDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        38 ~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +-..|..+ ..-|+|+.++|+..||++++|.+|-.
T Consensus        15 ~g~~l~~~R~~~gltq~elA~~~gis~~~is~~E~   49 (86)
T 3eus_A           15 LCQRLRQARLDAGLTQADLAERLDKPQSFVAKVET   49 (86)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHC
Confidence            34445544 35789999999999999999999965

>4hku_A LMO2814 protein, TETR transcriptional regulator; structural genomics, PSI-biology; 2.30A {Listeria monocytogenes}

Probab=86.62  E-value=0.54  Score=36.35  Aligned_cols=41  Identities=10%  Similarity=0.133  Sum_probs=31.4

Q ss_pred             CCCCCHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHH
Q psy17316         30 TKTWTHEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRA   70 (229)
Q Consensus        30 ~~kyt~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i   70 (229)
                      +++.|.+.++ .|++.+.+.   +.|+++||++.||+++|||+..
T Consensus         4 ~a~~tRe~Il~aA~~lf~~~G~~~~s~~~IA~~aGvs~~tlY~~F   48 (178)
T 4hku_A            4 MARLSQEIILNMAEKIIYEKGMEKTTLYDIASNLNVTHAALYKHY   48 (178)
T ss_dssp             -CCCCHHHHHHHHHHHHHHHCGGGCCHHHHHHHTTSCGGGGGGTC
T ss_pred             hHHHHHHHHHHHHHHHHHHhCcccccHHHHHHHhCcCHhHHHHHC
Confidence            5677888875 455555543   5899999999999999999863

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=86.60  E-value=0.35  Score=37.52  Aligned_cols=41  Identities=12%  Similarity=-0.028  Sum_probs=30.9

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ...++.+.. ++.+..-.|+|+.+||..+|||.+||+.++.+
T Consensus        92 ~~Lp~~~r~-vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~r  132 (157)
T 2lfw_A           92 ARMTPLSRQ-ALLLTAMEGFSPEDAAYLIEVDTSEVETLVTE  132 (157)
T ss_dssp             TTSCTTHHH-HHTTTSSSCCCHHHHHHTTTSCHHHHHHHHHH
T ss_pred             HhCCHHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            445555554 34344345889999999999999999998886

>2l8n_A Transcriptional repressor CYTR; bacterial gene repressor, helix turn helix binding domain, L family, transcription regulation, binding protein; NMR {Escherichia coli} PDB: 2lcv_A

Probab=86.60  E-value=0.57  Score=31.87  Aligned_cols=51  Identities=8%  Similarity=0.006  Sum_probs=35.9

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASA  198 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~  198 (229)
                      .++.++|+..||+.+|+.+++..            ....+++-+..|.+.+.+-+...+..|.
T Consensus        10 ~t~~diA~~aGVS~sTVSr~ln~------------~~~vs~~t~~rV~~~a~~lgY~pn~~a~   60 (67)
T 2l8n_A           10 ATMKDVALKAKVSTATVSRALMN------------PDKVSQATRNRVEKAAREVGYLPQPMGR   60 (67)
T ss_dssp             CCHHHHHHHTTCCHHHHHHTTTC------------CCCSCHHHHHHHHHHHHHHCCCC-----
T ss_pred             CCHHHHHHHHCCCHHHHHHHHcC------------CCCCCHHHHHHHHHHHHHhCCCccHHHH
Confidence            59999999999999999996642            1235678888888887776665555554

>2pz9_A Putative regulatory protein; structural genomics, transcriptional regulator, PSI, protein structure initiative; 2.80A {Streptomyces coelicolor A3}

Probab=86.59  E-value=0.56  Score=37.62  Aligned_cols=45  Identities=9%  Similarity=-0.003  Sum_probs=29.8

Q ss_pred             CCCCCCCCHHHHHH-HHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         27 LTVTKTWTHEDMDA-ALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        27 ~~~~~kyt~e~~~~-AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +..+..-+.+.++. |++.+.+.   +.|+++||++.||+++|||+...
T Consensus        24 r~~~~~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvs~~tlY~~F~   72 (226)
T 2pz9_A           24 GGGSTDSTRQRIVAAAKEEFARHGIAGARVDRIAKQARTSKERVYAYFR   72 (226)
T ss_dssp             ------CCHHHHHHHHHHHHHHHHHHHCCHHHHHHHTTSCHHHHHHHCS
T ss_pred             cccchhHHHHHHHHHHHHHHHHhCcccCcHHHHHHHHCCChHHHHHHcC
Confidence            33455567777754 44455443   58999999999999999998744

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=86.58  E-value=0.98  Score=34.76  Aligned_cols=34  Identities=15%  Similarity=0.264  Sum_probs=29.6

Q ss_pred             HHHHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+|++.+.. +.+++.++|..+|+|.+||++.++
T Consensus         9 ~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~   43 (151)
T 2cyy_A            9 DKKIIKILQNDGKAPLREISKITGLAESTIHERIR   43 (151)
T ss_dssp             HHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4577877764 679999999999999999999998

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=86.56  E-value=0.98  Score=34.73  Aligned_cols=34  Identities=18%  Similarity=0.262  Sum_probs=29.5

Q ss_pred             HHHHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..++++.+.. +.+++.++|..+|+|.+||+++++
T Consensus        10 d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~   44 (152)
T 2cg4_A           10 DRGILEALMGNARTAYAELAKQFGVSPETIHVRVE   44 (152)
T ss_dssp             HHHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4577777755 679999999999999999999998

>1sgm_A Putative HTH-type transcriptional regulator YXAF; structural genomics, PSI, protein structure initiative; 2.00A {Bacillus subtilis} SCOP: a.4.1.9 a.121.1.1

Probab=86.40  E-value=0.73  Score=35.12  Aligned_cols=40  Identities=15%  Similarity=0.105  Sum_probs=29.5

Q ss_pred             CCCHHHHH-HHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         32 TWTHEDMD-AALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        32 kyt~e~~~-~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-+.+.++ .|++.+.+   .+.|+++||++.||+++|||+...
T Consensus         5 ~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   48 (191)
T 1sgm_A            5 GDSREKILHTASRLSQLQGYHATGLNQIVKESGAPKGSLYHFFP   48 (191)
T ss_dssp             CCHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHCCCSCHHHHSTT
T ss_pred             cchHHHHHHHHHHHHHHcCccccCHHHHHHHHCCCchhHHHHcc
Confidence            34555564 45555544   258999999999999999998854

>3dew_A Transcriptional regulator, TETR family; S genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; HET: MSE; 1.75A {Geobacter sulfurreducens}

Probab=86.38  E-value=0.69  Score=35.55  Aligned_cols=39  Identities=13%  Similarity=0.087  Sum_probs=28.8

Q ss_pred             CCHHHHH-HHHHHHHc-C--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         33 WTHEDMD-AALEALRA-G--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        33 yt~e~~~-~AI~~~~~-g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      -+.+.++ .|++.+.+ |  +.|+++||++.||+++|||+...
T Consensus         8 ~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   50 (206)
T 3dew_A            8 DCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFG   50 (206)
T ss_dssp             CHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHhcCCcccCcHHHHHHHhCCCHHHHHHHcC
Confidence            3445554 45555544 3  58999999999999999998754

>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=86.38  E-value=1.1  Score=32.86  Aligned_cols=24  Identities=4%  Similarity=0.106  Sum_probs=22.1

Q ss_pred             CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        189 GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       189 ~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +++|+.++|..+|||.+||..+..
T Consensus        38 e~~s~~EIA~~lgiS~~tVr~~~~   61 (99)
T 3t72_q           38 TDYTLEEVGKQFDVTRERIRQIEA   61 (99)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            569999999999999999999875

>2xpw_A Tetracycline repressor protein class D; transcription, transcription regulator, helix-turn-helix, ME coordination; HET: OTC MES; 1.44A {Escherichia coli} PDB: 1bjy_A* 1bj0_A 1du7_A* 1ork_A* 2fj1_A* 1bjz_A* 2o7o_A* 2x6o_A* 2x9d_A* 2xps_A* 2xpt_A* 2vke_A* 2xpu_A* 2xpv_A* 2tct_A* 2xb5_A* 2trt_A* 2xrl_A* 1qpi_A* 1a6i_A ...

Probab=86.37  E-value=0.61  Score=37.63  Aligned_cols=40  Identities=28%  Similarity=0.331  Sum_probs=30.3

Q ss_pred             CCCHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         32 TWTHEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        32 kyt~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|.+.++ .|++.+.+.   ++|+++||++.||+++|||+...
T Consensus         2 ~ltr~~Il~aA~~l~~~~G~~~~s~~~IA~~~Gvs~~slY~hF~   45 (207)
T 2xpw_A            2 RLNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVK   45 (207)
T ss_dssp             CCSHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTCCHHHHHHHCC
T ss_pred             CCCHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCCcchHHHhcC
Confidence            45667764 455555443   58999999999999999998754

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=86.35  E-value=1.2  Score=33.95  Aligned_cols=34  Identities=6%  Similarity=0.143  Sum_probs=29.1

Q ss_pred             HHHHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...+++.+.. +.+++.++|..+|||.+||.+.++
T Consensus         7 d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~   41 (144)
T 2cfx_A            7 DLNIIEELKKDSRLSMRELGRKIKLSPPSVTERVR   41 (144)
T ss_dssp             HHHHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3467777654 679999999999999999999998

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=86.35  E-value=0.77  Score=34.63  Aligned_cols=34  Identities=24%  Similarity=0.304  Sum_probs=28.9

Q ss_pred             HHHHHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...|+..+. ++.+++.++|..+|||.+||++.++
T Consensus         6 ~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~   40 (141)
T 1i1g_A            6 DKIILEILEKDARTPFTEIAKKLGISETAVRKRVK   40 (141)
T ss_dssp             HHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            346777665 4679999999999999999999998

>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR, heat shock, transcriptional regulation, winged DNA binding; 2.60A {Pyrococcus furiosus} SCOP: a.4.5.64

Probab=86.33  E-value=0.91  Score=37.40  Aligned_cols=36  Identities=17%  Similarity=0.098  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+..|+..+..|.+++.++|..+|||.+||+..++
T Consensus        15 ~~rl~IL~~L~~~~~s~~eLa~~l~is~stvs~hLk   50 (202)
T 2p4w_A           15 ETRRRILFLLTKRPYFVSELSRELGVGQKAVLEHLR   50 (202)
T ss_dssp             HHHHHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            458889999989999999999999999999999998

>2ev1_A Hypothetical protein RV1264/MT1302; alpha-helical, regulatory domain of adenylyl cyclase, oleic lyase; HET: OLA 1PE; 1.60A {Mycobacterium tuberculosis} PDB: 2ev2_A* 2ev3_A* 2ev4_A*

Probab=86.32  E-value=1.7  Score=36.69  Aligned_cols=48  Identities=19%  Similarity=0.246  Sum_probs=38.9

Q ss_pred             CCCCHHHHHHHH-------HHHHcCC--C-CHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316         31 KTWTHEDMDAAL-------EALRAGQ--M-SLTKASVSYGIPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        31 ~kyt~e~~~~AI-------~~~~~g~--~-S~~~aA~~~gIp~sTL~~~i~~~gi~~~   78 (229)
                      ..||.+++..+.       +.++.|.  + |..++|+..|||.-++++|.+.+|+..+
T Consensus        50 ~G~t~~~i~~a~~~l~l~~~~LLGg~~~yvT~~eVAe~aGv~~e~~rr~wRalGfp~~  107 (222)
T 2ev1_A           50 QGITPDEIRATNPPLLLATRHLVGDDGTYVSAREISENYGVDLELLQRVQRAVGLARV  107 (222)
T ss_dssp             TTCCHHHHHHSSSCTTHHHHHHTTCCSCEECHHHHHHHHTCCHHHHHHHHHHHCCCCC
T ss_pred             cCCCHHHHHHHhhhhhhHHHHHhCCCcCcCCHHHHHHHHCcCHHHHHHHHHHhCCCCC
Confidence            567777777644       5665544  4 9999999999999999999999998765

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=86.30  E-value=0.88  Score=30.09  Aligned_cols=32  Identities=3%  Similarity=-0.067  Sum_probs=26.4

Q ss_pred             HHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        184 EGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       184 ~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      +.....+++..+.|...|||.++|.+|.++..
T Consensus        12 ~~r~~~gls~~~lA~~~gis~~~i~~~e~g~~   43 (76)
T 1adr_A           12 ARRKKLKIRQAALGKMVGVSNVAISQWERSET   43 (76)
T ss_dssp             HHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSS
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCC
Confidence            34445669999999999999999999988643

>3fiw_A Putative TETR-family transcriptional regulator; TETR-family transcriptional regulator streptomyces, structur genomics, PSI-2; 2.20A {Streptomyces coelicolor}

Probab=86.25  E-value=0.53  Score=38.13  Aligned_cols=45  Identities=13%  Similarity=0.159  Sum_probs=31.6

Q ss_pred             CCCCCCCCHHHHHHH-HHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         27 LTVTKTWTHEDMDAA-LEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        27 ~~~~~kyt~e~~~~A-I~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ...+...+.+.++.| ++.+.+.   +.|+++||++.||+++|||+...
T Consensus        19 ~~~r~~~tr~~Il~aA~~l~~~~G~~~~s~~~IA~~aGvs~~tlY~~F~   67 (211)
T 3fiw_A           19 FQGMTKMNRETVITEALDLLDEVGLDGVSTRRLAKRLGVEQPSLYWYFR   67 (211)
T ss_dssp             -----CCCHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTSCTHHHHTTCS
T ss_pred             cccccccCHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCChhHHHHHcC
Confidence            344677888888554 5455443   58999999999999999998743

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=86.25  E-value=1.1  Score=30.48  Aligned_cols=29  Identities=3%  Similarity=-0.017  Sum_probs=25.2

Q ss_pred             HhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        187 RSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       187 ~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      .+.+++..+.|...|||.++|.+|.++.+
T Consensus        22 ~~~gltq~~lA~~~gvs~~~is~~e~g~~   50 (80)
T 3kz3_A           22 NELGLSYESVADKMGMGQSAVAALFNGIN   50 (80)
T ss_dssp             HHHTCCHHHHHHHTTSCHHHHHHHHTTSS
T ss_pred             HHcCCCHHHHHHHhCcCHHHHHHHHcCCC
Confidence            34669999999999999999999998653

>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A

Probab=86.16  E-value=1  Score=35.28  Aligned_cols=32  Identities=19%  Similarity=0.154  Sum_probs=26.1

Q ss_pred             HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +|+....-.++|+.++|..+|||.+||+.++.
T Consensus       147 ~vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~  178 (194)
T 1or7_A          147 MAITLRELDGLSYEEIAAIMDCPVGTVRSRIF  178 (194)
T ss_dssp             HHHHHHHTTCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHhHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            44544444569999999999999999999886

>3egq_A TETR family transcriptional regulator; DNA-binding, transcription regulation, bacterial regulatory DNA/RNA-binding 3-helical bundle fold; HET: MSE PE8; 2.55A {Archaeoglobus fulgidus}

Probab=85.99  E-value=0.9  Score=34.31  Aligned_cols=36  Identities=11%  Similarity=0.183  Sum_probs=27.5

Q ss_pred             HHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         36 EDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        36 e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus         7 ~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   46 (170)
T 3egq_A            7 VRIIEAALRLYMKKPPHEVSIEEIAREAKVSKSLIFYHFE   46 (170)
T ss_dssp             HHHHHHHHHHHTTSCGGGCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHhcCCccCcHHHHHHHhCCCchhHHHHcC
Confidence            344 4555566554   48999999999999999999744

>2f2e_A PA1607; transcription factor, helix-TRUN-helix, APC5613, structural genomics, PSI, protein structure initiative; HET: GLC; 1.85A {Pseudomonas aeruginosa} SCOP: a.4.5.69

Probab=85.96  E-value=0.78  Score=35.55  Aligned_cols=36  Identities=19%  Similarity=0.184  Sum_probs=29.9

Q ss_pred             HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      +|..+.+|.+++.++++.+||+++||.+.++++.-.
T Consensus        29 IL~~L~~g~~~~~eLa~~lgis~~tls~~L~~Le~~   64 (146)
T 2f2e_A           29 IVRDAFEGLTRFGEFQKSLGLAKNILAARLRNLVEH   64 (146)
T ss_dssp             HHHHHHTTCCSHHHHHHHHCCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            444445889999999999999999999999986433

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A

Probab=85.91  E-value=0.92  Score=32.19  Aligned_cols=25  Identities=24%  Similarity=0.219  Sum_probs=22.4

Q ss_pred             cCCCCHHHHHHHcCCChhh----HHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTT----LWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sT----L~~~i~   71 (229)
                      .-|+|+.++|+..||+++|    |.+|-.
T Consensus        12 ~~glsq~~lA~~~gis~~~~~~~is~~E~   40 (98)
T 3lfp_A           12 RAGISQEKLGVLAGIDEASASARMNQYEK   40 (98)
T ss_dssp             HHTCCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHhCCCcchhhhHHHHHHC
Confidence            4589999999999999999    888876

>1zk8_A Transcriptional regulator, TETR family; TETR member,transcriptional regulator, STRU genomics, PSI, protein structure initiative; 2.15A {Bacillus cereus atcc 14579} SCOP: a.4.1.9 a.121.1.1

Probab=85.91  E-value=0.58  Score=35.78  Aligned_cols=42  Identities=19%  Similarity=0.285  Sum_probs=30.9

Q ss_pred             CCCCCHHHHHH-HHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         30 TKTWTHEDMDA-ALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        30 ~~kyt~e~~~~-AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +..-+.+.+++ |++.+.+.   +.|+++||++.||+++|||+...
T Consensus         5 r~~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   50 (183)
T 1zk8_A            5 RIGLTLQKIVETAAEIADANGVQEVTLASLAQTLGVRSPSLYNHVK   50 (183)
T ss_dssp             -CCCCHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTSCHHHHTTTCS
T ss_pred             hhHHHHHHHHHHHHHHHHhcCccccCHHHHHHHcCCCchHHHHHcC
Confidence            34557777754 55555443   58999999999999999998643

>2ppx_A AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif, XRE-family, structural genomics, PSI-2, protein structure initiative; 2.00A {Agrobacterium tumefaciens str} SCOP: a.35.1.3

Probab=85.83  E-value=0.81  Score=32.67  Aligned_cols=25  Identities=28%  Similarity=0.312  Sum_probs=23.0

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-++|+.++|+.+||+++||.+|-.
T Consensus        41 ~~glsq~elA~~lgvs~~~is~~E~   65 (99)
T 2ppx_A           41 ALKLTQEEFSARYHIPLGTLRDWEQ   65 (99)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHHc
Confidence            4689999999999999999999965

>2dg7_A Putative transcriptional regulator; helix-turn-helix motif, TETR family, gene regulation; 2.30A {Streptomyces coelicolor}

Probab=85.79  E-value=1.1  Score=34.73  Aligned_cols=41  Identities=15%  Similarity=0.215  Sum_probs=30.6

Q ss_pred             CCCHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         32 TWTHEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        32 kyt~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .-+.+.++ .|++.+.+.   +.|+++||++.||+++|||+....
T Consensus         6 ~~~r~~Il~aA~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~s   50 (195)
T 2dg7_A            6 PGAEQRLKRAALELYSEHGYDNVTVTDIAERAGLTRRSYFRYFPD   50 (195)
T ss_dssp             TTHHHHHHHHHHHHHHHSCGGGCCHHHHHHHTTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHHHHHHHhcCccccCHHHHHHHhCCCHHHHHHHcCC
Confidence            34556664 455555554   489999999999999999998763

>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69

Probab=85.74  E-value=1  Score=33.05  Aligned_cols=33  Identities=18%  Similarity=0.233  Sum_probs=28.1

Q ss_pred             HHHHHHcCCCCHHHHHHHc-CCChhhHHHHHHHh
Q psy17316         41 ALEALRAGQMSLTKASVSY-GIPSTTLWQRAHRL   73 (229)
Q Consensus        41 AI~~~~~g~~S~~~aA~~~-gIp~sTL~~~i~~~   73 (229)
                      ++..+.+|.+++.++|+.+ ||+++||.+.++++
T Consensus        27 IL~~L~~~~~~~~eLa~~l~~is~~tvs~~L~~L   60 (112)
T 1z7u_A           27 LMDELFQGTKRNGELMRALDGITQRVLTDRLREM   60 (112)
T ss_dssp             HHHHHHHSCBCHHHHHHHSTTCCHHHHHHHHHHH
T ss_pred             HHHHHHhCCCCHHHHHHHhccCCHHHHHHHHHHH
Confidence            3444446899999999999 99999999999986

>1r8e_A Multidrug-efflux transporter regulator; protein-DNA complex, MERR-family transcription activator, MU binding protein; HET: P4P; 2.40A {Bacillus subtilis} SCOP: a.6.1.3 d.60.1.1 PDB: 1exi_A* 1exj_A* 3iao_A 3q5p_A* 3d71_A* 3q3d_A* 3q1m_A* 3q2y_A* 3q5r_A* 3q5s_A* 3d70_A 3d6z_A* 3d6y_A* 1bow_A 2bow_A*

Probab=85.74  E-value=1.3  Score=37.34  Aligned_cols=68  Identities=10%  Similarity=-0.018  Sum_probs=50.3

Q ss_pred             CCCHHHHHHHhCCChHHHHHHHHHhCCc-ccCC-CCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCC
Q psy17316        135 SISANKASKAYGIPSSTLYKIARKEGIR-LAQP-FNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIP  203 (229)
Q Consensus       135 ~~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~~-~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp  203 (229)
                      .+++.++|+.+||+..||+.|-+. |.- .... ..+..|-|+.+  .++..|..+.+-+++..++...+...
T Consensus         5 ~~~i~e~a~~~gvs~~tlr~y~~~-gll~p~~~d~~~g~R~y~~~~~~~l~~i~~l~~~g~~l~~i~~~~~~~   76 (278)
T 1r8e_A            5 YYSIGEVSKLANVSIKALRYYDKI-DLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLE   76 (278)
T ss_dssp             EEEHHHHHHHHTCCHHHHHHHHHT-TSSCCSEECTTTCCEEEETGGGGHHHHHHHHHHTTCCHHHHHHHTTSC
T ss_pred             cEeHHHHHHHHCcCHHHHHHHHHC-CCCCCCccCCCCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhC
Confidence            468999999999999999999874 532 2110 11234556543  57788888888889999999998876

>2qwt_A Transcriptional regulator, TETR family; structural genomics, PSI-2, protein structure initiative; 2.30A {Mycobacterium vanbaalenii pyr-1}

Probab=85.73  E-value=1  Score=35.16  Aligned_cols=33  Identities=12%  Similarity=0.280  Sum_probs=26.2

Q ss_pred             HHHHHHHHcC--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRAG--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+.  +.|+++||++.||+++|||+...
T Consensus        20 ~aA~~lf~~~G~~~t~~~IA~~agvs~~tlY~~F~   54 (196)
T 2qwt_A           20 EVAYDTFAAEGLGVPMDEIARRAGVGAGTVYRHFP   54 (196)
T ss_dssp             HHHHHHHHHTCTTSCHHHHHHHTTSCHHHHHHHCS
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHCC
Confidence            4555566554  48999999999999999999754

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=85.68  E-value=1.2  Score=32.82  Aligned_cols=35  Identities=23%  Similarity=0.273  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHhCCC-------cHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQT-------TVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~-------s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -...+.+.+..|.+       |..+.|..||||.+||+..++
T Consensus        14 i~~~i~~~I~~g~~~~G~~lPs~~~La~~~~vSr~tvr~al~   55 (113)
T 3tqn_A           14 LRDKIVEAIIDGSYVEGEMIPSIRKISTEYQINPLTVSKAYQ   55 (113)
T ss_dssp             HHHHHHHHHHHTSSCTTCEECCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHH
Confidence            34456666666665       789999999999999999987

>3iuo_A ATP-dependent DNA helicase RECQ; C-terminal, GI PSI, MCSG, structural genomics, midwest center for structur genomics; 1.60A {Porphyromonas gingivalis}

Probab=85.41  E-value=4.7  Score=30.37  Aligned_cols=85  Identities=12%  Similarity=0.142  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccCCCCCCCCCCCHHHHHHHHHHHHh-CCCcHHHHHH
Q psy17316        123 ILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQPFNASPTAWKPEDLEIALEGIRS-GQTTVQRASA  198 (229)
Q Consensus       123 ~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~~~~~~~r~~t~e~r~eaV~~~~~-~~~s~~eAA~  198 (229)
                      .+...++++..|. |+.+||..-|++.+|++.++-..   |.+.....- -..-.+.+...+|.+++.. +..++..+-.
T Consensus        21 t~~~t~~l~~~G~-sleeIA~~R~L~~~TI~~Hl~~~v~~G~~l~i~~~-i~~~l~~~~~~~I~~~~~~~~~~~Lk~i~e   98 (122)
T 3iuo_A           21 MKVSIVQQIDRKV-ALDDIAVSHGLDFPELLSEVETIVYSGTRINIDYF-INEVMDEDHLEDIFEYFKESTTDSLEEAMQ   98 (122)
T ss_dssp             HHHHHHHHHHTTC-CHHHHHHHTTCCHHHHHHHHHHHHHTTCCCCCHHH-HHHHSCHHHHHHHHHHHHHCSCCCHHHHHH
T ss_pred             cHHHHHHHHHcCC-CHHHHHHHcCCCHHHHHHHHHHHHHcCCccCHHHH-cccccCHHHHHHHHHHHHHcCcccHHHHHH
Confidence            4577788888886 99999999999999999987543   422221000 0001225666777777776 4457888889


Q ss_pred             HhC--CChHHHHH
Q psy17316        199 EYG--IPSGTLYG  209 (229)
Q Consensus       199 ~fg--Vp~~tv~~  209 (229)
                      .|+  ++|..++-
T Consensus        99 ~l~~~~sy~eIRl  111 (122)
T 3iuo_A           99 ELGKDYSEEEIRL  111 (122)
T ss_dssp             HHTTTSCHHHHHH
T ss_pred             HccCcCCHHHHHH
Confidence            995  88888765

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=85.40  E-value=0.75  Score=34.51  Aligned_cols=85  Identities=14%  Similarity=0.078  Sum_probs=54.5

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccCCCCCCCCCCCHHHHHHHHHHHH-----hCCCcHHH
Q psy17316        124 LNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQPFNASPTAWKPEDLEIALEGIR-----SGQTTVQR  195 (229)
Q Consensus       124 k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~~~~~~~r~~t~e~r~eaV~~~~-----~~~~s~~e  195 (229)
                      +.+.+..+.....++.+++..+|++..++.+|++..   |.-...+   ...-+..+...++++.+.     +|..++.+
T Consensus         9 ~~~i~~~~~~~p~~~~~la~~~~~~~~~~~~~l~~l~~~G~l~~i~---~~~~~~~~~~~~~~~~l~~~~~~~~~it~ae   85 (121)
T 2pjp_A            9 WQKAEPLFGDEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIV---KDRYYRNDRIVEFANMIRDLDQECGSTCAAD   85 (121)
T ss_dssp             HHHHGGGCSSSCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE---TTEEEEHHHHHHHHHHHHHHHHHHSSEEHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec---CCceECHHHHHHHHHHHHHHHHHCCCccHHH
Confidence            344445554344599999999999999999987643   4211111   122334444444444444     36799999


Q ss_pred             HHHHhCCChHHHHHHH
Q psy17316        196 ASAEYGIPSGTLYGRC  211 (229)
Q Consensus       196 AA~~fgVp~~tv~~~v  211 (229)
                      +-..+|+|+--..-.+
T Consensus        86 ~Rd~lg~sRK~ai~lL  101 (121)
T 2pjp_A           86 FRDRLGVGRKLAIQIL  101 (121)
T ss_dssp             HHHHHTSCHHHHHHHH
T ss_pred             HHHHHCCcHHHHHHHH
Confidence            9999999999444333

>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69

Probab=85.36  E-value=0.79  Score=33.36  Aligned_cols=36  Identities=19%  Similarity=0.183  Sum_probs=29.9

Q ss_pred             HHHHHHHcCCCCHHHHHHHc-CCChhhHHHHHHHhCC
Q psy17316         40 AALEALRAGQMSLTKASVSY-GIPSTTLWQRAHRLGI   75 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~-gIp~sTL~~~i~~~gi   75 (229)
                      .+|..+.+|.+++.++|+.+ ||+++||.+.++++.-
T Consensus        18 ~IL~~L~~~~~~~~eLa~~l~~is~~tls~~L~~Le~   54 (107)
T 2hzt_A           18 VILXHLTHGKKRTSELKRLMPNITQKMLTQQLRELEA   54 (107)
T ss_dssp             HHHHHHTTCCBCHHHHHHHCTTSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence            34545557899999999999 9999999999998643

>3kz9_A SMCR; transcriptional regulator, quorum S DNA-binding, transcription regulation, transcription regula; HET: MSE; 2.10A {Vibrio vulnificus} PDB: 2pbx_A

Probab=85.28  E-value=1.1  Score=34.50  Aligned_cols=33  Identities=12%  Similarity=0.096  Sum_probs=25.8

Q ss_pred             HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        24 ~aa~~l~~~~G~~~~s~~~Ia~~agvs~~t~Y~~F~   59 (206)
T 3kz9_A           24 EIALEVFARRGIGRGGHADIAEIAQVSVATVFNYFP   59 (206)
T ss_dssp             HHHHHHHHHSCCSSCCHHHHHHHHTSCHHHHHHHCC
T ss_pred             HHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHcC
Confidence            3455555553   48999999999999999999744

>3bqz_B HTH-type transcriptional regulator QACR; multidrug resistance, TETR, malachite green, DNA- binding, plasmid, repressor; HET: MGR; 2.17A {Staphylococcus aureus} PDB: 3br1_B* 3br3_B* 3pm1_B* 1rkw_B* 1jt0_A* 1jty_B* 1jum_B* 1jup_B* 1jtx_B* 1jus_B* 2dtz_B 2gby_B* 2hq5_B 3br2_B* 3br5_B* 1qvt_B* 1qvu_B* 3br0_B* 3br6_B* 1jt6_B* ...

Probab=85.24  E-value=0.9  Score=34.78  Aligned_cols=34  Identities=9%  Similarity=0.002  Sum_probs=26.9

Q ss_pred             HHHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         38 MDAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        38 ~~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +..|++.+.+   .+.|+++||++.||+++|||+...
T Consensus         8 l~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   44 (194)
T 3bqz_B            8 LGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFK   44 (194)
T ss_dssp             HHHHHHHHHHHTTTTCCHHHHHHHTTCCHHHHHHHTS
T ss_pred             HHHHHHHHHHcCCccCCHHHHHHHhCCCchhHHHhCC
Confidence            3556666654   358999999999999999999754

>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A

Probab=85.19  E-value=0.74  Score=32.44  Aligned_cols=25  Identities=20%  Similarity=0.131  Sum_probs=23.0

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-++|+.++|+.+||+++||.+|..
T Consensus        15 ~~gltq~~lA~~~gis~~~is~~e~   39 (99)
T 2l49_A           15 SEYLSRQQLADLTGVPYGTLSYYES   39 (99)
T ss_dssp             HTTCCHHHHHHHHCCCHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4589999999999999999999966

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=85.18  E-value=1.2  Score=30.24  Aligned_cols=29  Identities=17%  Similarity=0.186  Sum_probs=24.5

Q ss_pred             HHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        186 IRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       186 ~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      +...+ +..+.|.+.||+.++|.+|.++.+
T Consensus         8 r~~~g-sq~~lA~~lgvs~~~is~~e~g~~   36 (79)
T 3bd1_A            8 INKLG-SVSALAASLGVRQSAISNWRARGR   36 (79)
T ss_dssp             HHHHS-SHHHHHHHHTCCHHHHHHHHHHTC
T ss_pred             HHHhC-CHHHHHHHHCCCHHHHHHHHHCCC
Confidence            34445 899999999999999999998754

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus}

Probab=85.17  E-value=1.2  Score=32.53  Aligned_cols=42  Identities=14%  Similarity=0.158  Sum_probs=30.5

Q ss_pred             CCCCCHHHHH----HHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         30 TKTWTHEDMD----AALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        30 ~~kyt~e~~~----~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +...+...+.    +-|+.+ +.-|+|+.++|++.||+++||.+|=+
T Consensus        25 ~~~~~~~~l~~~lG~~ir~~R~~~glTQ~eLA~~~gvs~~~is~~E~   71 (101)
T 4ghj_A           25 MKHVTAAALAEEIGDRLKQARLNRDLTQSEVAEIAGIARKTVLNAEK   71 (101)
T ss_dssp             -CCCCHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             hhhccHHHHHHHHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHC
Confidence            4556655554    334444 35799999999999999999999943

>2fq4_A Transcriptional regulator, TETR family; DNA-binding protein, bacillu structural genomics, PSI, protein structure initiative; 1.79A {Bacillus cereus} SCOP: a.4.1.9 a.121.1.1

Probab=85.01  E-value=1.1  Score=34.68  Aligned_cols=38  Identities=16%  Similarity=0.228  Sum_probs=28.0

Q ss_pred             CHHHH-HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDM-DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~-~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+.+ ..|++.+.+   .+.|+.+||++.||+++|||++..
T Consensus        13 ~r~~Il~aA~~lf~e~G~~~~t~~~IA~~agvsk~tlY~~F~   54 (192)
T 2fq4_A           13 TQKAILSASYELLLESGFKAVTVDKIAERAKVSKATIYKWWP   54 (192)
T ss_dssp             HHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHcCcccccHHHHHHHcCCCHHHHHHHCC
Confidence            34444 345555544   368999999999999999999754

>1b0n_A Protein (SINR protein); transcription regulator, antagonist, sporulation; 1.90A {Bacillus subtilis} SCOP: a.34.1.1 a.35.1.3 PDB: 2yal_A

Probab=84.97  E-value=1.6  Score=31.12  Aligned_cols=30  Identities=7%  Similarity=0.029  Sum_probs=26.1

Q ss_pred             HHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316        184 EGIRSGQTTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       184 ~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      +.....++|..+.|...|||.++|.+|.++
T Consensus         8 ~~r~~~gltq~~lA~~~gis~~~i~~~e~g   37 (111)
T 1b0n_A            8 QYRKEKGYSLSELAEKAGVAKSYLSSIERN   37 (111)
T ss_dssp             HHHHHTTCCHHHHHHHHTCCHHHHHHHHTT
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            445567799999999999999999999886

>3gzi_A Transcriptional regulator, TETR family; TETR family transcriptional regulator, structural genomics, center for structural genomics, JCSG; 2.05A {Shewanella loihica pv-4}

Probab=84.90  E-value=1.2  Score=34.73  Aligned_cols=33  Identities=15%  Similarity=-0.002  Sum_probs=26.3

Q ss_pred             HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        24 ~aA~~l~~~~G~~~~t~~~IA~~agvs~~t~Y~~F~   59 (218)
T 3gzi_A           24 LAARNLFIERPYAQVSIREIASLAGTDPGLIRYYFG   59 (218)
T ss_dssp             HHHHHHHHTSCCSCCCHHHHHHHHTSCTHHHHHHHS
T ss_pred             HHHHHHHHHCCCCcCCHHHHHHHhCCCHHHHHHHcC
Confidence            3455555554   47999999999999999999865

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=84.89  E-value=2.1  Score=35.29  Aligned_cols=41  Identities=7%  Similarity=0.171  Sum_probs=30.3

Q ss_pred             CCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        174 WKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       174 ~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      .+.-+.-.-+.++...+++..++|..+|||+++|-++++.+
T Consensus         8 ~sl~eiG~ria~~y~~g~tQ~eIA~~lGiSr~~VSR~L~~A   48 (192)
T 1zx4_A            8 HSIREIGLRLMRMKNDGMSQKDIAAKEGLSQAKVTRALQAA   48 (192)
T ss_dssp             SCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHh
Confidence            34433444444445566999999999999999999998843

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=84.86  E-value=1.2  Score=33.69  Aligned_cols=42  Identities=10%  Similarity=0.139  Sum_probs=31.5

Q ss_pred             HHHHHHHH-HHHcCCC-------CHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         36 EDMDAALE-ALRAGQM-------SLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        36 e~~~~AI~-~~~~g~~-------S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      +++...|. .|.+|.+       |.+++|++|||+++||++-+..+...|
T Consensus        14 ~~i~~~l~~~I~~g~~~~G~~lPse~~La~~~~vSr~tvr~Al~~L~~~G   63 (126)
T 3by6_A           14 LQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQK   63 (126)
T ss_dssp             HHHHHHHHHHHHTTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            45544444 5666654       999999999999999999888764443

>1rzs_A Antirepressor, regulatory protein CRO; helix-turn-helix, DNA-binding protein, structural evolution, transcription; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=84.84  E-value=0.44  Score=31.48  Aligned_cols=21  Identities=14%  Similarity=0.140  Sum_probs=19.8

Q ss_pred             CcHHHHHHHhCCChHHHHHHH
Q psy17316        191 TTVQRASAEYGIPSGTLYGRC  211 (229)
Q Consensus       191 ~s~~eAA~~fgVp~~tv~~~v  211 (229)
                      .+..+.|...||+.++|..|.
T Consensus        11 ~tq~~lA~~lGvs~~~Vs~we   31 (61)
T 1rzs_A           11 GTQRAVAKALGISDAAVSQWK   31 (61)
T ss_dssp             SSHHHHHHHHTCCHHHHHHCC
T ss_pred             CCHHHHHHHhCCCHHHHHHHH
Confidence            589999999999999999995

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=84.83  E-value=1.8  Score=31.80  Aligned_cols=44  Identities=14%  Similarity=0.059  Sum_probs=32.8

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      ..|..+..-......++++++.++|+.+||+++|+.+.+++..-
T Consensus        35 ~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~L~~   78 (140)
T 2nnn_A           35 GLTPTQWAALVRLGETGPCPQNQLGRLTAMDAATIKGVVERLDK   78 (140)
T ss_dssp             CCCHHHHHHHHHHHHHSSBCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            56666543222223467899999999999999999999998643

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=84.80  E-value=1.6  Score=30.66  Aligned_cols=31  Identities=19%  Similarity=0.212  Sum_probs=25.6

Q ss_pred             HHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        184 EGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       184 ~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      +.....+++..+.|...|||.++|.+|.++.
T Consensus        16 ~~r~~~glsq~~lA~~~gis~~~is~~e~G~   46 (94)
T 2kpj_A           16 SYIAKSEKTQLEIAKSIGVSPQTFNTWCKGI   46 (94)
T ss_dssp             HHHTTSSSCHHHHHHHHTCCHHHHHHHHTTS
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHHhCC
Confidence            3344567999999999999999999998753

>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A*

Probab=84.78  E-value=1.3  Score=36.58  Aligned_cols=38  Identities=13%  Similarity=0.130  Sum_probs=31.7

Q ss_pred             CCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        173 AWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       173 ~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|+.++ +|+.++. .++++.|+|...|||..||...++
T Consensus       173 ~Lt~~e~-~vl~~~~-~g~s~~eIa~~l~is~~tV~~~~~  210 (234)
T 1l3l_A          173 WLDPKEA-TYLRWIA-VGKTMEEIADVEGVKYNSVRVKLR  210 (234)
T ss_dssp             CCCHHHH-HHHHHHT-TTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHH-HHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4666655 7788865 559999999999999999999886

>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 3jso_A* 3jsp_A* 3k3r_E* 1jhc_A 1jhe_A 1lea_A 1leb_A

Probab=84.72  E-value=1.1  Score=36.13  Aligned_cols=42  Identities=10%  Similarity=0.072  Sum_probs=31.5

Q ss_pred             CCCHHH--HHHHHHHH-HcCCC--CHHHHHHHcCCC-hhhHHHHHHHh
Q psy17316         32 TWTHED--MDAALEAL-RAGQM--SLTKASVSYGIP-STTLWQRAHRL   73 (229)
Q Consensus        32 kyt~e~--~~~AI~~~-~~g~~--S~~~aA~~~gIp-~sTL~~~i~~~   73 (229)
                      ..|..+  +.+.|+.+ .+.++  |+.++|+.+||+ ++|+.+|+...
T Consensus         3 ~lt~~q~~i~~~i~~~~~~~g~~ps~~elA~~lgiss~~tv~~~~~~l   50 (202)
T 1jhf_A            3 ALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKAL   50 (202)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHHHhCCCccHHHHHHHhCCCChHHHHHHHHHH
Confidence            345543  45666654 34577  999999999999 99999998863

>3vp5_A Transcriptional regulator; heme, sensor protein, TETR superf transcription; HET: HEM; 1.90A {Lactococcus lactis} PDB: 3vox_A 3vok_A*

Probab=84.68  E-value=1.2  Score=34.71  Aligned_cols=36  Identities=17%  Similarity=0.334  Sum_probs=26.8

Q ss_pred             HHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         36 EDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        36 e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        15 ~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   54 (189)
T 3vp5_A           15 NRVYDACLNEFQTHSFHEAKIMHIVKALDIPRGSFYQYFE   54 (189)
T ss_dssp             HHHHHHHHHHHHHSCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHCCcccccHHHHHHHhCCChHHHHHHCC
Confidence            444 3455555543   57999999999999999998744

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=84.65  E-value=0.83  Score=36.92  Aligned_cols=41  Identities=12%  Similarity=0.082  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHH-c-C-CCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         36 EDMDAALEALR-A-G-QMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        36 e~~~~AI~~~~-~-g-~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      .+++++|..+. + | ..|++++|+.+|++++|++++++++.-.
T Consensus         8 ~~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~l~~Le~~   51 (196)
T 3k2z_A            8 RKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHLIALEKK   51 (196)
T ss_dssp             HHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHHHHHHHHC
Confidence            45577777653 2 3 4899999999999999999999986433

>2rae_A Transcriptional regulator, ACRR family protein; TETR/ACRR family transcriptional regulator, structural genom 2, RHA08332, MCSG; 2.20A {Rhodococcus SP}

Probab=84.65  E-value=1.4  Score=34.21  Aligned_cols=43  Identities=16%  Similarity=0.240  Sum_probs=31.9

Q ss_pred             CCCCCCHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         29 VTKTWTHEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        29 ~~~kyt~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .++.-+.+.++ .|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        13 ~~~~~~r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   59 (207)
T 2rae_A           13 RRPSTTQDRISTVGIELFTEQGFDATSVDEVAEASGIARRTLFRYFP   59 (207)
T ss_dssp             CSCCCHHHHHHHHHHHHHHHHCTTTSCHHHHHHHTTSCHHHHHHHCS
T ss_pred             cchHhHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCcchHhhhCC
Confidence            34455667665 445555442   58999999999999999999865

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=84.64  E-value=1.5  Score=33.50  Aligned_cols=42  Identities=19%  Similarity=0.301  Sum_probs=31.2

Q ss_pred             HHHHHHHHHH-H-cCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         36 EDMDAALEAL-R-AGQMSLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        36 e~~~~AI~~~-~-~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      ++....|..+ . .|++++.++|+.+||+++||.+-++++.-.|
T Consensus        39 ~~~~~~i~~~l~~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~G   82 (155)
T 2h09_A           39 DDYVELISDLIREVGEARQVDMAARLGVSQPTVAKMLKRLATMG   82 (155)
T ss_dssp             HHHHHHHHHHHHHHSCCCHHHHHHHHTSCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCCCcCHHHHHHHhCcCHHHHHHHHHHHHHCC
Confidence            3444444333 2 4789999999999999999999999864444

>3f1b_A TETR-like transcriptional regulator; APC5888, rhodococcus SP. RHA1, structural genomics, PS protein structure initiative; 2.40A {Rhodococcus}

Probab=84.63  E-value=0.98  Score=34.75  Aligned_cols=37  Identities=22%  Similarity=0.342  Sum_probs=27.3

Q ss_pred             HHHH-HHHHHHHHc-C--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         35 HEDM-DAALEALRA-G--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        35 ~e~~-~~AI~~~~~-g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+.+ ..|++.+.+ |  +.|+++||++.||+++|||+...
T Consensus        16 r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   56 (203)
T 3f1b_A           16 EQQMLDAAVDVFSDRGFHETSMDAIAAKAEISKPMLYLYYG   56 (203)
T ss_dssp             HHHHHHHHHHHHHHHCTTTCCHHHHHHHTTSCHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHcCcccccHHHHHHHhCCchHHHHHHhC
Confidence            3444 345555544 3  68999999999999999999743

>4ac0_A Tetracycline repressor protein class B from trans TN1 0; transcription; HET: MIY; 2.45A {Escherichia coli}

Probab=84.59  E-value=0.64  Score=37.64  Aligned_cols=41  Identities=20%  Similarity=0.257  Sum_probs=30.9

Q ss_pred             CCCCHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         31 KTWTHEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        31 ~kyt~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ++.|.+.++ .|++.+.+.   ++|+++||++.||+++|||+...
T Consensus         1 s~~tr~~Il~aA~~l~~~~G~~~~s~~~IA~~aGvs~~tlY~~F~   45 (202)
T 4ac0_A            1 SRLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVK   45 (202)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTSCHHHHHTTCS
T ss_pred             CcCCHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCCchhHHhhcC
Confidence            356778775 455555443   58999999999999999998643

>1z0x_A Transcriptional regulator, TETR family; structural genomics, PSI, P structure initiative; 2.40A {Enterococcus faecalis} SCOP: a.4.1.9 a.121.1.1

Probab=84.56  E-value=0.9  Score=36.77  Aligned_cols=41  Identities=17%  Similarity=0.336  Sum_probs=31.0

Q ss_pred             CCCCHHHH-HHHHHHHHcC----CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         31 KTWTHEDM-DAALEALRAG----QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        31 ~kyt~e~~-~~AI~~~~~g----~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..-+.+.+ ..|++.+.+.    +.|+++||++.||+++|||+...
T Consensus         3 ~~~tr~~Il~aA~~l~~~~~G~~~~s~~~IA~~aGvs~~tlY~~F~   48 (220)
T 1z0x_A            3 PKLSKDTIIAAAFSLLEKSPTLEQLSMRKVAKQLGVQAPAIYWYFK   48 (220)
T ss_dssp             -CCSHHHHHHHHHHHHHHSCCGGGCCHHHHHHHHTSCHHHHHTTCS
T ss_pred             ccchHHHHHHHHHHHHHhcCCcccCCHHHHHHHcCCCHHHHHHhcC
Confidence            34566766 4566666666    48999999999999999998544

>1vz0_A PARB, chromosome partitioning protein PARB; nuclear protein, chromosome segregation, DNA-binding, helix-turn-helix; 2.3A {Thermus thermophilus} SCOP: a.4.14.1 d.268.1.1

Probab=84.54  E-value=5.8  Score=33.11  Aligned_cols=42  Identities=14%  Similarity=0.105  Sum_probs=33.9

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHH
Q psy17316        117 KSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARK  158 (229)
Q Consensus       117 ~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~  158 (229)
                      ...++-.+..++..+...+.|..++|+.+|++.+++.+.++-
T Consensus       116 ~~L~~~E~a~~~~~l~~~g~t~~~iA~~lG~s~~~V~~~l~l  157 (230)
T 1vz0_A          116 EDLSPVEEARGYQALLEMGLTQEEVARRVGKARSTVANALRL  157 (230)
T ss_dssp             TTCCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHG
T ss_pred             CCCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            356666777777777666779999999999999999998763

>3lwj_A Putative TETR-family transcriptional regulator; structural G joint center for structural genomics, JCSG, protein structu initiative; 2.07A {Syntrophomonas wolfei subsp}

Probab=84.46  E-value=0.96  Score=34.96  Aligned_cols=37  Identities=11%  Similarity=0.162  Sum_probs=27.0

Q ss_pred             HHHHH-HHHHHHHc-C--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         35 HEDMD-AALEALRA-G--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        35 ~e~~~-~AI~~~~~-g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+.++ .|++.+.+ |  +.|+++||++.||+++|||+...
T Consensus        14 r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   54 (202)
T 3lwj_A           14 RQKILTCSLDLFIEKGYYNTSIRDIIALSEVGTGTFYNYFV   54 (202)
T ss_dssp             HHHHHHHHHHHHHHHCTTTCCHHHHHHHHCSCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCchhHHHHcC
Confidence            33443 44444543 3  58999999999999999999744

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=84.40  E-value=1.9  Score=31.65  Aligned_cols=42  Identities=14%  Similarity=0.178  Sum_probs=31.1

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .|..+..-......++++++.++|+.+||+++|+.+.+++..
T Consensus        27 l~~~~~~iL~~l~~~~~~~~~ela~~l~~s~~tvs~~l~~L~   68 (138)
T 3bpv_A           27 LTDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLE   68 (138)
T ss_dssp             CCHHHHHHHHHHHHSTTCBHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            455554322222346889999999999999999999999863

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=84.40  E-value=0.55  Score=39.96  Aligned_cols=29  Identities=17%  Similarity=0.131  Sum_probs=25.3

Q ss_pred             CCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         48 GQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        48 g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      +..++.++|+.+||+++||++|++++++.
T Consensus       263 ~~~~~~~~a~~lgi~~~tl~~~l~~~~i~  291 (324)
T 1hqc_A          263 GPVGLATLATALSEDPGTLEEVHEPYLIR  291 (324)
T ss_dssp             SCCCHHHHHHHTTSCHHHHHHHTHHHHHH
T ss_pred             CCchHHHHHHHhCCCHHHHHHHHhHHHHH
Confidence            34679999999999999999999997654

>3lhq_A Acrab operon repressor (TETR/ACRR family); structural genomics, IDP02616, csgid, DNA-binding, transcription, transcription regulation; 1.56A {Salmonella enterica subsp} PDB: 3bcg_A 2qop_A

Probab=84.40  E-value=0.97  Score=35.09  Aligned_cols=36  Identities=17%  Similarity=0.298  Sum_probs=26.8

Q ss_pred             HHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         36 EDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        36 e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        17 ~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   56 (220)
T 3lhq_A           17 QHILDVALRLFSQQGVSATSLAEIANAAGVTRGAIYWHFK   56 (220)
T ss_dssp             HHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHcCcccCCHHHHHHHhCCCceeehhhcC
Confidence            444 3455555443   58999999999999999999744

>3ljl_A Transcriptional regulator LUXT; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: MES; 3.20A {Vibrio parahaemolyticus}

Probab=84.31  E-value=1  Score=34.10  Aligned_cols=37  Identities=24%  Similarity=0.257  Sum_probs=27.7

Q ss_pred             HHHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         35 HEDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        35 ~e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        16 r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   56 (156)
T 3ljl_A           16 IQKIMDAVVDQLLRLGYDKMSYTTLSQQTGVSRTGISHHFP   56 (156)
T ss_dssp             HHHHHHHHHHHHHHTHHHHCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHhChhhcCHHHHHHHHCCCHHHHHHHCC
Confidence            3444 3455555554   48999999999999999999854

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=84.29  E-value=0.66  Score=36.38  Aligned_cols=39  Identities=10%  Similarity=0.196  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      ...+.+|..+.+|.+++.++|+.+||+++||.+.++.+.
T Consensus        58 p~R~~IL~~L~~~~~t~~eLa~~lgls~stvs~hL~~L~   96 (151)
T 3f6v_A           58 PTRRRLVQLLTSGEQTVNNLAAHFPASRSAISQHLRVLT   96 (151)
T ss_dssp             HHHHHHHHHGGGCCEEHHHHHTTSSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            445777877778999999999999999999999999863

>2zcm_A Biofilm operon icaabcd HTH-type negative transcri regulator ICAR; helix-turn-helix, TETR family, repressor; 1.33A {Staphylococcus epidermidis} PDB: 2zcn_A

Probab=84.27  E-value=1.5  Score=33.81  Aligned_cols=38  Identities=18%  Similarity=0.274  Sum_probs=28.7

Q ss_pred             CHHHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..+.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus         8 ~~~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tlY~~F~   49 (192)
T 2zcm_A            8 MKDKIIDNAITLFSEKGYDGTTLDDISKSVNIKKASLYYHYD   49 (192)
T ss_dssp             CHHHHHHHHHHHHHHHCTTTCCHHHHHHHTTCCHHHHHHHTC
T ss_pred             hHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCChHHHHHHCC
Confidence            44555 4556555543   58999999999999999999754

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2}

Probab=84.24  E-value=2.3  Score=28.63  Aligned_cols=32  Identities=6%  Similarity=0.047  Sum_probs=26.7

Q ss_pred             HHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        184 EGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       184 ~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      +.....+++..+.|...|||.++|.+|.++.+
T Consensus        17 ~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~   48 (84)
T 2ef8_A           17 KLRKEASLSQSELAIFLGLSQSDISKIESFER   48 (84)
T ss_dssp             HHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSS
T ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC
Confidence            34445779999999999999999999988653

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=84.15  E-value=1  Score=32.43  Aligned_cols=27  Identities=15%  Similarity=0.236  Sum_probs=24.0

Q ss_pred             CHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         51 SLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        51 S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      |..++|++|||+++||++-++.+.-.|
T Consensus        37 s~~eLa~~~~vSr~tvr~al~~L~~~G   63 (102)
T 1v4r_A           37 SVADIRAQFGVAAKTVSRALAVLKSEG   63 (102)
T ss_dssp             CHHHHHHHSSSCTTHHHHHTTTTTTSS
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            999999999999999999998865444

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=84.10  E-value=1.5  Score=33.57  Aligned_cols=34  Identities=6%  Similarity=-0.044  Sum_probs=28.9

Q ss_pred             HHHHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...|++.+.. +..++.++|..+|+|.+||++.++
T Consensus        11 d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~   45 (151)
T 2dbb_A           11 DMQLVKILSENSRLTYRELADILNTTRQRIARRID   45 (151)
T ss_dssp             HHHHHHHHHHCTTCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3467776654 679999999999999999999998

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=83.95  E-value=1.6  Score=32.81  Aligned_cols=35  Identities=9%  Similarity=0.116  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHhCCC-------cHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQT-------TVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~-------s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -...+.+.+..|.+       |..+.|.+||||.+||...++
T Consensus        18 i~~~i~~~I~~g~~~~g~~Lps~~~La~~~~vSr~tvr~Al~   59 (125)
T 3neu_A           18 ISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQ   59 (125)
T ss_dssp             HHHHHHHHHHTTSSCTTCBCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34455566666665       699999999999999999987

>4aci_A HTH-type transcriptional repressor ACNR; aconitase, citrate, TETR superfamily; HET: CIT; 1.65A {Corynebacterium glutamicum} PDB: 4ac6_A*

Probab=83.82  E-value=0.87  Score=34.95  Aligned_cols=40  Identities=8%  Similarity=0.124  Sum_probs=29.6

Q ss_pred             CCCHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         32 TWTHEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        32 kyt~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-+.+.++ .|++.+.+.   +.|+.+||++.||+++|||+...
T Consensus        13 ~~~r~~Il~aA~~l~~~~G~~~~t~~~IA~~agvs~~t~Y~~F~   56 (191)
T 4aci_A           13 TNSRQEILEGARRCFAEHGYEGATVRRLEEATGKSRGAIFHHFG   56 (191)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTCCHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCCCchHHHHHCC
Confidence            34555554 555555543   48999999999999999999865

>2qtq_A Transcriptional regulator, TETR family; transcription regulator, DNA/RNA-binding 3-helical bundle FO turn helix motif, HTH motif; HET: MSE; 1.85A {Novosphingobium aromaticivorans} PDB: 2rha_A*

Probab=83.77  E-value=1.7  Score=33.68  Aligned_cols=42  Identities=17%  Similarity=0.141  Sum_probs=31.3

Q ss_pred             CCCCCHHHHH-HHHHHHHc-C--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         30 TKTWTHEDMD-AALEALRA-G--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        30 ~~kyt~e~~~-~AI~~~~~-g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ++.-+.+.++ .|++.+.+ |  +.|+++||++.||+++|||+...
T Consensus        13 ~~~~~r~~Il~aa~~lf~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   58 (213)
T 2qtq_A           13 ETPGARDLLLQTASNIMREGDVVDISLSELSLRSGLNSALVKYYFG   58 (213)
T ss_dssp             CCTTHHHHHHHHHHHHHHHHTSSCCCHHHHHHHHCCCHHHHHHHHS
T ss_pred             CChhHHHHHHHHHHHHHHHcCcccccHHHHHHHhCCChhhHhHhcC
Confidence            4445666664 44555544 3  58999999999999999999865

>3vpr_A Transcriptional regulator, TETR family; all alpha, helix-turn-helix, transcriptional repressor, DNA protein; 2.27A {Thermus thermophilus}

Probab=83.73  E-value=1.4  Score=33.91  Aligned_cols=37  Identities=11%  Similarity=0.280  Sum_probs=28.4

Q ss_pred             HHHH-HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         35 HEDM-DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        35 ~e~~-~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+.+ ..|++.+.+   .+.|+.+||++.||+++|||+...
T Consensus         5 r~~Il~aA~~lf~~~G~~~~s~~~IA~~agvsk~t~Y~~F~   45 (190)
T 3vpr_A            5 RDRILEEAAKLFTEKGYEATSVQDLAQALGLSKAALYHHFG   45 (190)
T ss_dssp             HHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHcC
Confidence            3444 455655654   358999999999999999999865

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=83.65  E-value=1.9  Score=29.34  Aligned_cols=32  Identities=6%  Similarity=-0.003  Sum_probs=26.9

Q ss_pred             HHHHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316        182 ALEGIRSGQTTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       182 aV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      +-++-...+++..+.|...|||.++|.+|-++
T Consensus        15 ik~~R~~~gltq~elA~~~gis~~~is~~E~G   46 (78)
T 3qq6_A           15 IKQYRKEKGYSLSELAEKAGVAKSYLSSIERN   46 (78)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTT
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            33444667799999999999999999999886

>3on4_A Transcriptional regulator, TETR family; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics; HET: MSE; 1.85A {Legionella pneumophila subsp}

Probab=83.59  E-value=1.4  Score=33.39  Aligned_cols=40  Identities=13%  Similarity=0.145  Sum_probs=29.7

Q ss_pred             CCCHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         32 TWTHEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        32 kyt~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-+.+.++ .|++.+.+.   +.|+++||++.||+++|||+...
T Consensus         9 ~~~r~~Il~aa~~l~~~~G~~~~t~~~IA~~agvs~~t~Y~~F~   52 (191)
T 3on4_A            9 SNTKERILAVAEALIQKDGYNAFSFKDIATAINIKTASIHYHFP   52 (191)
T ss_dssp             CCHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             hhHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCcchhhhcCC
Confidence            34556664 455555442   58999999999999999999844

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=83.56  E-value=2.9  Score=27.16  Aligned_cols=32  Identities=3%  Similarity=-0.162  Sum_probs=26.8

Q ss_pred             HHHHhCCCcHHHHHHHhC--CChHHHHHHHHhhc
Q psy17316        184 EGIRSGQTTVQRASAEYG--IPSGTLYGRCKLSR  215 (229)
Q Consensus       184 ~~~~~~~~s~~eAA~~fg--Vp~~tv~~~vk~~~  215 (229)
                      +.....++|..+.|...|  ||.++|.+|-++..
T Consensus        15 ~~r~~~glsq~~lA~~~g~~is~~~i~~~e~g~~   48 (71)
T 2ewt_A           15 AIRTQQGLSLHGVEEKSQGRWKAVVVGSYERGDR   48 (71)
T ss_dssp             HHHHHTTCCHHHHHHHTTTSSCHHHHHHHHHTCS
T ss_pred             HHHHHcCCCHHHHHHHHCCcCCHHHHHHHHCCCC
Confidence            344557799999999999  99999999988653

>1y6u_A XIS, excisionase from transposon TN916; structure, DNA architectural protein, tyrosine recombinase, winged-helix protein; NMR {Enterococcus faecalis}

Probab=83.56  E-value=0.59  Score=32.27  Aligned_cols=25  Identities=20%  Similarity=0.247  Sum_probs=22.8

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      -+++.+||..+||++++|++.++..
T Consensus        16 ~LTi~EaAeylgIg~~~l~~L~~~~   40 (70)
T 1y6u_A           16 TLTIEEASKYFRIGENKLRRLAEEN   40 (70)
T ss_dssp             EEEHHHHHHHTCSCHHHHHHHHHHC
T ss_pred             eeCHHHHHHHHCcCHHHHHHHHHcC
Confidence            4789999999999999999999874

>3o60_A LIN0861 protein; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative, unknown function; 2.80A {Listeria innocua}

Probab=83.48  E-value=1.2  Score=35.11  Aligned_cols=39  Identities=13%  Similarity=0.227  Sum_probs=29.7

Q ss_pred             CCHHHHHHHHHHH--Hc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         33 WTHEDMDAALEAL--RA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        33 yt~e~~~~AI~~~--~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      -|.+.+++|...+  .+   .+.|+++||++.||+++|+|+...
T Consensus        19 ~tr~~I~~Aa~~lF~~~~g~~~~tv~~Ia~~Agvs~~t~Y~~F~   62 (185)
T 3o60_A           19 KTQTKLYTVLERFYVEDRTFESISIKDLCEQARVSRATFYRHHK   62 (185)
T ss_dssp             HHHHHHHHHHHHHHHTTCCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHhcCCcccCCHHHHHHHhCCCHHHHHHHcC
Confidence            3556676665555  33   368999999999999999999744

>2hxo_A Putative TETR-family transcriptional regulator; TETR transcriptional regulator, structural genomics, PSI-2, structure initiative; 2.40A {Streptomyces coelicolor}

Probab=83.45  E-value=0.96  Score=37.29  Aligned_cols=44  Identities=11%  Similarity=0.137  Sum_probs=30.8

Q ss_pred             CCCCCCCHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         28 TVTKTWTHEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        28 ~~~~kyt~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..+...+.+.++ .|++.+.+.   ++|+++||++.||+++|||+...
T Consensus        11 ~~~~~~~r~~Il~aA~~l~~~~G~~~~s~~~IA~~aGvs~~tlY~hF~   58 (237)
T 2hxo_A           11 RRQEPLSRERIVGAAVELLDTVGERGLTFRALAERLATGPGAIYWHIT   58 (237)
T ss_dssp             -----CCHHHHHHHHHHHHHHTTTTTCCHHHHHHHHTSCGGGGGGTCC
T ss_pred             CCCCccCHHHHHHHHHHHHHhcCcccCCHHHHHHHHCCChHHHHHhcC
Confidence            345567788775 555555544   58999999999999999998644

>2g7s_A Transcriptional regulator, TETR family; APC5906, PSI, protein structure initiat midwest center for structural genomics, MCSG; HET: MSE; 1.40A {Agrobacterium tumefaciens str} SCOP: a.4.1.9 a.121.1.1

Probab=83.40  E-value=1.2  Score=33.94  Aligned_cols=37  Identities=19%  Similarity=0.288  Sum_probs=27.3

Q ss_pred             HHHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         35 HEDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        35 ~e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        10 r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   50 (194)
T 2g7s_A           10 ADDILQCARTLIIRGGYNSFSYADISQVVGIRNASIHHHFP   50 (194)
T ss_dssp             HHHHHHHHHHHHHHHCGGGCCHHHHHHHHCCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCchHHHHHcC
Confidence            3444 3445555443   58999999999999999999744

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=83.37  E-value=2.1  Score=31.93  Aligned_cols=43  Identities=14%  Similarity=0.080  Sum_probs=33.4

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      ..|..+..-.......|++++.++|+.+||+++|+.+.+++..
T Consensus        37 ~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le   79 (148)
T 3nrv_A           37 GIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLE   79 (148)
T ss_dssp             TCCHHHHHHHHHHHHSSSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4666665333333457899999999999999999999999863

>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28

Probab=83.34  E-value=2.2  Score=31.61  Aligned_cols=29  Identities=24%  Similarity=0.226  Sum_probs=26.2

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .+|++++.++|+.+||+++|+.+.++++.
T Consensus        44 ~~~~~~~~~la~~l~~s~~tvs~~l~~L~   72 (145)
T 2a61_A           44 FEGPKRPGELSVLLGVAKSTVTGLVKRLE   72 (145)
T ss_dssp             HHCCBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHHCCCchhHHHHHHHHH
Confidence            36889999999999999999999999863

>2dg8_A Putative TETR-family transcriptional regulatory P; helix-turn-helix motif, gene regulation; 2.21A {Streptomyces coelicolor}

Probab=83.34  E-value=1.1  Score=34.68  Aligned_cols=38  Identities=16%  Similarity=0.259  Sum_probs=28.3

Q ss_pred             CHHHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        10 ~r~~Il~aa~~l~~~~G~~~~ti~~IA~~agvs~~t~Y~~F~   51 (193)
T 2dg8_A           10 RRERILAATLDLIAEEGIARVSHRRIAQRAGVPLGSMTYHFT   51 (193)
T ss_dssp             HHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTSCTHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHhChhhccHHHHHHHhCCCchhhheeCC
Confidence            44555 4455555443   58999999999999999998744

>2d6y_A Putative TETR family regulatory protein; helix-turn-helix, gene regulation; HET: TLA; 2.30A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=83.29  E-value=1.2  Score=35.01  Aligned_cols=39  Identities=8%  Similarity=0.086  Sum_probs=29.4

Q ss_pred             CCHHHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         33 WTHEDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        33 yt~e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      -+.+.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus         8 ~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvs~~tiY~~F~   50 (202)
T 2d6y_A            8 ATKARIFEAAVAEFARHGIAGARIDRIAAEARANKQLIYAYYG   50 (202)
T ss_dssp             CHHHHHHHHHHHHHHHHTTTSCCHHHHHHHHTCCHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCHHHHHHHcC
Confidence            344555 4555555543   58999999999999999999865

>3bjb_A Probable transcriptional regulator, TETR family P; APC7331, rhodococcus SP. RHA1, structural genomics, PS protein structure initiative; 2.50A {Rhodococcus SP}

Probab=83.27  E-value=1.5  Score=34.71  Aligned_cols=33  Identities=18%  Similarity=0.287  Sum_probs=26.4

Q ss_pred             HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+.   +.|+.+||++.||+++|||+...
T Consensus        29 ~AA~~lf~e~G~~~~s~~~IA~~AGVsk~tlY~~F~   64 (207)
T 3bjb_A           29 EAAIELATEKELARVQMHEVAKRAGVAIGTLYRYFP   64 (207)
T ss_dssp             HHHHHHHHHSCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHcCcccCCHHHHHHHhCCCHHHHHHHCC
Confidence            4555566554   48999999999999999999754

>2np5_A Transcriptional regulator; TETR family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; HET: MSE LMT NDS; 1.80A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=83.26  E-value=0.97  Score=35.53  Aligned_cols=41  Identities=10%  Similarity=0.128  Sum_probs=29.7

Q ss_pred             CCCCHHHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         31 KTWTHEDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        31 ~kyt~e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +..+.+.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus         7 ~~~tr~~Il~AA~~lf~~~G~~~~s~~~IA~~AGvs~gtlY~~F~   51 (203)
T 2np5_A            7 SSTSPERLAAALFDVAAESGLEGASVREVAKRAGVSIGAVQHHFS   51 (203)
T ss_dssp             --CHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             cchhHHHHHHHHHHHHHHhChhhccHHHHHHHhCCCHHHHHHHcC
Confidence            34456666 4555565543   58999999999999999999744

>2hku_A A putative transcriptional regulator; structural genomics, APC6040, TET rhodococcus SP. RHA1, PSI-2, protein structure initiative; HET: PG4; 2.00A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=83.25  E-value=1.2  Score=35.10  Aligned_cols=40  Identities=18%  Similarity=0.136  Sum_probs=29.3

Q ss_pred             CCCHHHHH-HHHHHHHc-C-CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         32 TWTHEDMD-AALEALRA-G-QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        32 kyt~e~~~-~AI~~~~~-g-~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-+.+.++ .|++.+.+ | +.|+++||++.||+++|||+...
T Consensus        19 ~~~r~~Il~aA~~lf~~~G~~~s~~~IA~~aGvs~~tlY~~F~   61 (215)
T 2hku_A           19 RQTRDALFTAATELFLEHGEGVPITQICAAAGAHPNQVTYYYG   61 (215)
T ss_dssp             -CHHHHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHHcC
Confidence            34555564 44445544 3 69999999999999999999865

>2jj7_A Hemolysin II regulatory protein; DNA-binding protein, transcription regulation, DNA-binding, family, transcription, transcriptional regulator; 2.10A {Bacillus cereus} PDB: 2wv1_A 2jk3_A 2fx0_A

Probab=83.24  E-value=0.93  Score=34.69  Aligned_cols=36  Identities=11%  Similarity=0.044  Sum_probs=27.1

Q ss_pred             HHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         36 EDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        36 e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        10 ~~Il~aa~~l~~~~G~~~~t~~~IA~~agvs~~tlY~~F~   49 (186)
T 2jj7_A           10 ENILKAAKKKFGERGYEGTSIQEIAKEAKVNVAMASYYFN   49 (186)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCHHHHHHHHTSCHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHcCCccCCHHHHHHHhCCChhhhhhhcC
Confidence            444 3445555443   48999999999999999999765

>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A

Probab=83.20  E-value=1.8  Score=31.17  Aligned_cols=33  Identities=6%  Similarity=0.019  Sum_probs=26.9

Q ss_pred             HHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      -..|..+ ..-++|+.++|+..||++++|.+|-.
T Consensus        30 g~~lr~~R~~~gltq~elA~~~gis~~~is~iE~   63 (99)
T 3g5g_A           30 SFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIER   63 (99)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            3445444 35789999999999999999999976

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=83.20  E-value=1.3  Score=29.68  Aligned_cols=29  Identities=17%  Similarity=0.059  Sum_probs=22.9

Q ss_pred             HHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316        185 GIRSGQTTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       185 ~~~~~~~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      .....+++..+.|...||+.++|.+|.++
T Consensus        10 ~r~~~glsq~~lA~~~gis~~~i~~~e~g   38 (77)
T 2k9q_A           10 ERIRLSLTAKSVAEEMGISRQQLCNIEQS   38 (77)
T ss_dssp             HHHHHTCCHHHHHHHHTSCHHHHHHHHTC
T ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence            34455688999999999999998888764

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=83.16  E-value=1.8  Score=32.73  Aligned_cols=35  Identities=14%  Similarity=0.094  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHh--CCCcHHHHHHHh-----CCChHHHHHHHH
Q psy17316        178 DLEIALEGIRS--GQTTVQRASAEY-----GIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~--~~~s~~eAA~~f-----gVp~~tv~~~vk  212 (229)
                      .|..|++.+.+  +.+|..++...+     +||.+|||+.++
T Consensus        12 qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~is~~TVYR~L~   53 (131)
T 2o03_A           12 QRAAISTLLETLDDFRSAQELHDELRRRGENIGLTTVYRTLQ   53 (131)
T ss_dssp             HHHHHHHHHHHCCSCEEHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHH
Confidence            58999999985  358999999988     999999999998

>1pb6_A Hypothetical transcriptional regulator YCDC; helix-loop-helix, dimer, structural genomics, PSI, protein structure initiative; 2.50A {Escherichia coli} PDB: 3loc_A*

Probab=83.15  E-value=1.2  Score=34.54  Aligned_cols=38  Identities=21%  Similarity=0.245  Sum_probs=27.4

Q ss_pred             CHHHHH-HHHHHHHc-C--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDMD-AALEALRA-G--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~~-~AI~~~~~-g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+.++ .|++.+.+ |  +.|+++||++.||+++|||+...
T Consensus        19 ~r~~Il~aa~~l~~~~G~~~~s~~~Ia~~agvs~~t~Y~~F~   60 (212)
T 1pb6_A           19 KKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFP   60 (212)
T ss_dssp             HHHHHHHHHHHHHHHHCTTTCCHHHHHHHTTSCHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHcCcchhhHHHHHHHHCCChhHHHHhCC
Confidence            344443 44444444 2  58999999999999999999744

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}

Probab=83.12  E-value=1.6  Score=33.19  Aligned_cols=42  Identities=14%  Similarity=0.241  Sum_probs=30.0

Q ss_pred             HHHHHHHH-HHHcCC------C-CHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         36 EDMDAALE-ALRAGQ------M-SLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        36 e~~~~AI~-~~~~g~------~-S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      +++...|. .|.+|.      + |.+++|++|||+++||++=++.+..+|
T Consensus        17 ~QI~~~i~~~I~~G~l~pG~~LPser~La~~~gVSr~tVReAl~~L~~eG   66 (134)
T 4ham_A           17 EQIVQKIKEQVVKGVLQEGEKILSIREFASRIGVNPNTVSKAYQELERQE   66 (134)
T ss_dssp             HHHHHHHHHHHHHTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHcCCCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence            44544443 555543      4 899999999999999999888764443

>1u8b_A ADA polyprotein; protein-DNA complex, methylation, zinc, helix-turn-helix, metal binding protein/DNA complex; 2.10A {Escherichia coli} PDB: 1zgw_A* 1wpk_A* 1adn_A 1eyf_A

Probab=83.10  E-value=1.4  Score=33.15  Aligned_cols=36  Identities=11%  Similarity=0.074  Sum_probs=30.2

Q ss_pred             HHHHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         38 MDAALEALR-AGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        38 ~~~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +..|++.+. +..+|+.++|..+|++.++|.+..++.
T Consensus        81 l~~a~~~i~~~~~~sl~~lA~~~g~S~~~f~r~Fk~~  117 (133)
T 1u8b_A           81 ITHACRLLEQETPVTLEALADQVAMSPFHLHRLFKAT  117 (133)
T ss_dssp             HHHHHHHTCSSSCCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            455665565 678999999999999999999999874

>2eh3_A Transcriptional regulator; all alpha proteins, tetracyclin repressor-like, C-terminal D homeodomain-like, DNA/RNA-binding 3-helical bundle; 1.55A {Aquifex aeolicus}

Probab=83.09  E-value=1.6  Score=33.36  Aligned_cols=33  Identities=6%  Similarity=0.055  Sum_probs=26.4

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+   .+.|+.+||++.||+++|||+...
T Consensus         9 ~aA~~lf~~~Gy~~~s~~~Ia~~agvskgtlY~~F~   44 (179)
T 2eh3_A            9 EVSKELFFEKGYQGTSVEEIVKRANLSKGAFYFHFK   44 (179)
T ss_dssp             HHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHcCCccCCHHHHHHHhCCCcHHHHHHcC
Confidence            456666654   358999999999999999999743

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=83.08  E-value=1.8  Score=36.61  Aligned_cols=45  Identities=18%  Similarity=0.234  Sum_probs=32.9

Q ss_pred             CCCHHHHHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         32 TWTHEDMDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        32 kyt~e~~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      ..+..+. .+++.+ .++++|+.++|+.+|++++|+++.++.+.-.|
T Consensus       149 ~L~~~~~-~IL~~L~~~~~~s~~eLA~~lglsksTv~r~L~~Le~~G  194 (244)
T 2wte_A          149 DYSREEM-KLLNVLYETKGTGITELAKMLDKSEKTLINKIAELKKFG  194 (244)
T ss_dssp             CCCHHHH-HHHHHHHHHTCBCHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred             CCCHHHH-HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            3454443 233332 57899999999999999999999999864333

>2guh_A Putative TETR-family transcriptional regulator; helix-turn-helix, TETR fold, structural genomics, PSI, prote structure initiative; HET: MSE; 1.52A {Rhodococcus SP}

Probab=83.08  E-value=1.5  Score=34.97  Aligned_cols=38  Identities=16%  Similarity=0.193  Sum_probs=28.9

Q ss_pred             CHHHH-HHHHHHHHcCC---CCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDM-DAALEALRAGQ---MSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~-~~AI~~~~~g~---~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+.+ ..|++.+.+.|   .|+++||++.||+++|||+...
T Consensus        40 ~r~~Il~AA~~lf~e~G~~~~tv~~IA~~AGvs~~tlY~~F~   81 (214)
T 2guh_A           40 SRSLIVDAAGRAFATRPYREITLKDIAEDAGVSAPLIIKYFG   81 (214)
T ss_dssp             HHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHcChhhcCHHHHHHHhCCCHHHHHHHcC
Confidence            34444 34555665544   8999999999999999999865

>3pas_A TETR family transcription regulator; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.90A {Marinobacter aquaeolei}

Probab=83.07  E-value=0.89  Score=34.65  Aligned_cols=33  Identities=18%  Similarity=0.265  Sum_probs=25.8

Q ss_pred             HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        15 ~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   50 (195)
T 3pas_A           15 EATVREVADHGFSATSVGKIAKAAGLSPATLYIYYE   50 (195)
T ss_dssp             HHHHHHHHHHHHHHCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             HHHHHHHHHcChHhcCHHHHHHHhCCCchHHHHHcC
Confidence            3455555543   48999999999999999999744

>2g7l_A TETR-family transcriptional regulator; APC6062, protein structure initiativ midwest center for structural genomics, MCSG; 2.10A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=83.06  E-value=0.94  Score=37.61  Aligned_cols=43  Identities=12%  Similarity=0.231  Sum_probs=32.3

Q ss_pred             CCCCCCHHHHH-HHHHHHHc-C--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         29 VTKTWTHEDMD-AALEALRA-G--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        29 ~~~kyt~e~~~-~AI~~~~~-g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+...+.+.++ .|++.+.+ |  ++|+++||++.||+++|||+...
T Consensus        15 ~r~~~tr~~Il~AA~~l~~e~G~~~~S~~~IA~~aGvs~~tlY~hF~   61 (243)
T 2g7l_A           15 AKPALSRRWIVDTAVALMRAEGLEKVTMRRLAQELDTGPASLYVYVA   61 (243)
T ss_dssp             -CCCCCHHHHHHHHHHHHHHHCSSSCCHHHHHHHTTSCHHHHTTTCC
T ss_pred             CCcccCHHHHHHHHHHHHHhcCchhcCHHHHHHHHCCChhHHHHHcC
Confidence            35567888885 45555544 3  58999999999999999998644

>3onq_A Regulator of polyketide synthase expression; structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Bifidobacterium adolescentis}

Probab=83.05  E-value=1.4  Score=37.63  Aligned_cols=38  Identities=13%  Similarity=0.113  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .++++.++.|.+.+.++.++|++++|.+.||+.++++.
T Consensus       196 ~~ll~TL~~yl~~~~~~~~tA~~L~iHrNTl~yRL~ri  233 (262)
T 3onq_A          196 DPTYLTVSTFLKYGSSLENTAKELNVHPNTVRYRLKRA  233 (262)
T ss_dssp             CHHHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence            36889999999989999999999999999999999984

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=83.04  E-value=2.2  Score=31.41  Aligned_cols=28  Identities=7%  Similarity=0.048  Sum_probs=25.7

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .++++++.++|+.+||+++|+.+.+++.
T Consensus        42 ~~~~~~~~ela~~l~is~~~vs~~l~~L   69 (142)
T 3bdd_A           42 KDAPLHQLALQERLQIDRAAVTRHLKLL   69 (142)
T ss_dssp             HHCSBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             hCCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            3588999999999999999999999985

>2dg7_A Putative transcriptional regulator; helix-turn-helix motif, TETR family, gene regulation; 2.30A {Streptomyces coelicolor}

Probab=83.03  E-value=1.7  Score=33.58  Aligned_cols=23  Identities=13%  Similarity=0.226  Sum_probs=21.4

Q ss_pred             CCcHHHHHHHhCCChHHHHHHHH
Q psy17316        190 QTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       190 ~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +.|+.++|..-|||..|+|+...
T Consensus        27 ~~t~~~Ia~~agvs~~t~Y~~F~   49 (195)
T 2dg7_A           27 NVTVTDIAERAGLTRRSYFRYFP   49 (195)
T ss_dssp             GCCHHHHHHHTTCCHHHHHHHCS
T ss_pred             ccCHHHHHHHhCCCHHHHHHHcC
Confidence            48999999999999999999876

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=83.02  E-value=1.9  Score=37.49  Aligned_cols=37  Identities=16%  Similarity=-0.010  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+....|......+.+++.++|.+||||..||.+-++
T Consensus         7 ~~~~~~ia~l~~~~~~~~~ela~~l~vS~~tIrRdL~   43 (315)
T 2w48_A            7 IRLIVKIAQLYYEQDMTQAQIARELGIYRTTISRLLK   43 (315)
T ss_dssp             HHHHHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4456677777778889999999999999999999988

>3vib_A MTRR; helix-turn-helix motif, DNA binding, DNA binding protein; HET: CXS; 2.40A {Neisseria gonorrhoeae}

Probab=83.01  E-value=1.9  Score=33.73  Aligned_cols=37  Identities=16%  Similarity=0.205  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHh-------CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRS-------GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~-------~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+.|.+|++....       ++.|+.++|..-|||..|+|...+
T Consensus         9 ~~tR~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvs~~t~Y~~F~   52 (210)
T 3vib_A            9 LKTKEHLMLAALETFYRKGIARTSLNEIAQAAGVTRDALYWHFK   52 (210)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCcCHHHHHHHCC
Confidence            4445556554443       468999999999999999999865

>3col_A Putative transcription regulator; structural genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; HET: MSE; 2.10A {Lactobacillus plantarum WCFS1}

Probab=82.94  E-value=0.92  Score=34.60  Aligned_cols=41  Identities=20%  Similarity=0.238  Sum_probs=28.8

Q ss_pred             CCCCHHHHH-HHHHHHHc-C--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         31 KTWTHEDMD-AALEALRA-G--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        31 ~kyt~e~~~-~AI~~~~~-g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.-+.+.++ .|++.+.+ |  +.|+++||++.||+++|||+...
T Consensus         8 ~~~~r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   52 (196)
T 3col_A            8 DMNKQVKIQDAVAAIILAEGPAGVSTTKVAKRVGIAQSNVYLYFK   52 (196)
T ss_dssp             --CHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTSCHHHHHTTCS
T ss_pred             HHHHHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCcHHHHHHHhC
Confidence            344556664 44555544 3  58999999999999999998643

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=82.91  E-value=2  Score=34.07  Aligned_cols=33  Identities=21%  Similarity=0.225  Sum_probs=28.7

Q ss_pred             HHHHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        180 EIALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       180 ~eaV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+|+..+. ++.+++.++|..+|||.+||++.++
T Consensus        20 ~~IL~~L~~~~~~s~~eLA~~lglS~~tv~~~l~   53 (171)
T 2ia0_A           20 RNILRLLKKDARLTISELSEQLKKPESTIHFRIK   53 (171)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            36777765 4679999999999999999999998

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}

Probab=82.89  E-value=1.7  Score=31.85  Aligned_cols=41  Identities=12%  Similarity=0.182  Sum_probs=30.8

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .|..+..-......++++++.++|+.+||+++|+.+.+++.
T Consensus        31 l~~~~~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L   71 (139)
T 3bja_A           31 ISYVQFGVIQVLAKSGKVSMSKLIENMGCVPSNMTTMIQRM   71 (139)
T ss_dssp             CCHHHHHHHHHHHHSCSEEHHHHHHHCSSCCTTHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCCChhHHHHHHHHH
Confidence            45555432222234688999999999999999999999986

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=82.88  E-value=1.3  Score=33.14  Aligned_cols=38  Identities=24%  Similarity=0.279  Sum_probs=31.3

Q ss_pred             HHHHHHHH-cCCCCHHHHHHHc--CCChhhHHHHHHHhCCC
Q psy17316         39 DAALEALR-AGQMSLTKASVSY--GIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        39 ~~AI~~~~-~g~~S~~~aA~~~--gIp~sTL~~~i~~~gi~   76 (229)
                      ..+++.+. +|.+|+.++|+.+  ||++.+++++++++.-.
T Consensus        16 ~~IL~~L~~~g~~s~~eLA~~l~~giS~~aVs~rL~~Le~~   56 (111)
T 3b73_A           16 DRILEIIHEEGNGSPKELEDRDEIRISKSSVSRRLKKLADH   56 (111)
T ss_dssp             HHHHHHHHHHSCBCHHHHHTSTTCCSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHhcCCCHHHHHHHHHHHHHC
Confidence            45566664 4999999999999  99999999999986433

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=82.87  E-value=1.5  Score=36.76  Aligned_cols=40  Identities=13%  Similarity=0.210  Sum_probs=32.3

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ...++.++. ++.++. .|+|..+||..+|||.+||+.++++
T Consensus       196 ~~L~~~ere-vl~L~~-~G~s~~EIA~~L~iS~~TVk~~l~r  235 (258)
T 3clo_A          196 NILSEREKE-ILRCIR-KGLSSKEIAATLYISVNTVNRHRQN  235 (258)
T ss_dssp             TSSCHHHHH-HHHHHH-TTCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             ccCCHHHHH-HHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            567777664 444554 6899999999999999999999886

>2vpr_A Tetracycline resistance repressor protein; transcription, metal-binding, antibiotic resistance, transcr regulator; HET: TDC; 2.49A {Pasteurella multocida}

Probab=82.87  E-value=0.61  Score=37.73  Aligned_cols=40  Identities=20%  Similarity=0.227  Sum_probs=30.0

Q ss_pred             CCCHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         32 TWTHEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        32 kyt~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..+.+.++ .|++.+.+.   ++|+++||++.||+++|||+...
T Consensus         3 ~~tr~~Il~aA~~l~~~~G~~~~s~~~IA~~agvs~~tlY~~f~   46 (207)
T 2vpr_A            3 KLDKEQVIDNALILLNEVGIEGLTTRKLAQKIGVEQPTLYWHVK   46 (207)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTCCHHHHTTTCC
T ss_pred             cccHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCChhHHHHHcC
Confidence            45677775 455555443   58999999999999999998643

>3f0c_A TETR-molecule A, transcriptional regulator; MCSG,PSI, SAD, structural genomics, protein structure initiative; 2.96A {Cytophaga hutchinsonii}

Probab=82.83  E-value=1.2  Score=34.74  Aligned_cols=40  Identities=15%  Similarity=0.169  Sum_probs=29.4

Q ss_pred             CCCHHHHH-HHHHHHHc-C--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         32 TWTHEDMD-AALEALRA-G--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        32 kyt~e~~~-~AI~~~~~-g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-+.+.++ .|++.+.+ |  +.|+++||++.||+++|||+...
T Consensus        10 ~~~r~~Il~aA~~lf~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   53 (216)
T 3f0c_A           10 DGKLELIINAAQKRFAHYGLCKTTMNEIASDVGMGKASLYYYFP   53 (216)
T ss_dssp             CCHHHHHHHHHHHHHHHHCSSSCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHhCCCHHHHHHHcC
Confidence            34555564 45555544 3  58999999999999999999744

>2o7t_A Transcriptional regulator; transcription regulator, DNA/RNA-binding 3-helical bundle FO turn helix motif, HTH motif; HET: UNL; 2.10A {Corynebacterium glutamicum} SCOP: a.4.1.9 a.121.1.1

Probab=82.83  E-value=1.6  Score=33.88  Aligned_cols=33  Identities=12%  Similarity=0.248  Sum_probs=26.4

Q ss_pred             HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        15 ~aA~~lf~~~G~~~~t~~~IA~~agvs~~tlY~~F~   50 (199)
T 2o7t_A           15 TTTCNLYRTHHHDSLTMENIAEQAGVGVATLYRNFP   50 (199)
T ss_dssp             HHHHHHHHHSCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHcC
Confidence            4555566554   48999999999999999999854

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=82.82  E-value=2.3  Score=31.62  Aligned_cols=45  Identities=9%  Similarity=-0.020  Sum_probs=30.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      ..|..+..-......+|++++.++|+.+||+++|+.+.+++..-.
T Consensus        34 ~lt~~~~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~   78 (142)
T 3ech_A           34 DLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGR   78 (142)
T ss_dssp             CCCHHHHHHHHHHHHTTTCCHHHHHHHHC---CHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            345555432222344689999999999999999999999986433

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=82.79  E-value=1.2  Score=31.33  Aligned_cols=31  Identities=13%  Similarity=0.097  Sum_probs=23.9

Q ss_pred             HHHHHHHhCC-CcHHHHHHHhCCChHHHHHHH
Q psy17316        181 IALEGIRSGQ-TTVQRASAEYGIPSGTLYGRC  211 (229)
Q Consensus       181 eaV~~~~~~~-~s~~eAA~~fgVp~~tv~~~v  211 (229)
                      .+|..+-.|+ .+..++|+++|+|++.|-+.+
T Consensus        19 ~~i~~L~~~~~~Ta~~IAkkLg~sK~~vNr~L   50 (75)
T 1sfu_A           19 KEVLSLNTNDYTTAISLSNRLKINKKKINQQL   50 (75)
T ss_dssp             HHHHTSCTTCEECHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHhCCCCcchHHHHHHHHHCCCHHHHHHHH
Confidence            3444444577 889999999999999877765

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=82.73  E-value=1.8  Score=34.28  Aligned_cols=38  Identities=13%  Similarity=-0.076  Sum_probs=33.5

Q ss_pred             CHHHHHHHHHHHHhC---CCcHHHHHHHhC-CChHHHHHHHH
Q psy17316        175 KPEDLEIALEGIRSG---QTTVQRASAEYG-IPSGTLYGRCK  212 (229)
Q Consensus       175 t~e~r~eaV~~~~~~---~~s~~eAA~~fg-Vp~~tv~~~vk  212 (229)
                      ....|..|++.+..+   ..++.+++..++ ||.+|||+.++
T Consensus        27 ~~~tR~~IL~~Ll~~p~~~~ta~eL~~~l~~lS~aTVyrhL~   68 (151)
T 3u1d_A           27 LHETRLDVLHQILAQPDGVLSVEELLYRNPDETEANLRYHVD   68 (151)
T ss_dssp             CCHHHHHHHHHHHHSTTSCBCHHHHHHHCTTSCHHHHHHHHH
T ss_pred             cchHHHHHHHHHHcCCCCCCCHHHHHHhcCCCCHHHHHHHHH
Confidence            345799999999885   378999999999 99999999998

>2iu5_A DHAS, YCEG, HTH-type dhaklm operon transcriptional activator; synthase, TETR family; 1.6A {Lactococcus lactis subsp} SCOP: a.4.1.9 a.121.1.1

Probab=82.72  E-value=1  Score=35.00  Aligned_cols=38  Identities=16%  Similarity=0.183  Sum_probs=28.2

Q ss_pred             CCHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHH
Q psy17316         33 WTHEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRA   70 (229)
Q Consensus        33 yt~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i   70 (229)
                      -+.+.++ .|++.+.+.   +.|+++||++.||+++|||+..
T Consensus        13 ~~r~~Il~aa~~lf~~~G~~~~tv~~Ia~~agvs~~t~Y~~F   54 (195)
T 2iu5_A           13 ITQKIIAKAFKDLMQSNAYHQISVSDIMQTAKIRRQTFYNYF   54 (195)
T ss_dssp             HHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCGGGGGGTC
T ss_pred             HHHHHHHHHHHHHHHhCCCCeeCHHHHHHHhCCCHHHHHHHc
Confidence            3556664 445555543   4899999999999999999864

>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response E family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV}

Probab=82.69  E-value=2.1  Score=28.98  Aligned_cols=32  Identities=19%  Similarity=0.183  Sum_probs=26.5

Q ss_pred             HHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        184 EGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       184 ~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      +.....+++..+.|...|||.++|.+|-++.+
T Consensus        21 ~~R~~~gltq~elA~~~gis~~~is~~e~g~~   52 (83)
T 3f6w_A           21 EARSAAGITQKELAARLGRPQSFVSKTENAER   52 (83)
T ss_dssp             HHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSS
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCC
Confidence            34445669999999999999999999988653

>3mvp_A TETR/ACRR transcriptional regulator; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 1.85A {Streptococcus mutans}

Probab=82.65  E-value=1.2  Score=34.57  Aligned_cols=37  Identities=8%  Similarity=0.141  Sum_probs=27.5

Q ss_pred             HHHH-HHHHHHHHc-C--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         35 HEDM-DAALEALRA-G--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        35 ~e~~-~~AI~~~~~-g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+.+ ..|++.+.+ |  +.|+++||++.||+++|||+...
T Consensus        28 r~~Il~aA~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   68 (217)
T 3mvp_A           28 RNKILQVAKDLFSDKTYFNVTTNEIAKKADVSVGTLYAYFA   68 (217)
T ss_dssp             HHHHHHHHHHHHHHHCGGGCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHcCccccCHHHHHHHhCCChhHHHHHcC
Confidence            3444 345555544 3  58999999999999999999754

>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda}

Probab=82.62  E-value=0.97  Score=37.05  Aligned_cols=43  Identities=16%  Similarity=0.130  Sum_probs=32.4

Q ss_pred             CCCCCCHHHH------HHHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         29 VTKTWTHEDM------DAALEALR-AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        29 ~~~kyt~e~~------~~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+.+.|..++      .+.|+.+. .-++|+.++|+.+||+++||.+|.+
T Consensus         3 ~~~~lt~~~~~~~~~~~~~l~~~r~~~g~t~~~lA~~~gis~~~i~~~~~   52 (236)
T 3bdn_A            3 KKKPLTQEQLEDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFN   52 (236)
T ss_dssp             SSCCCCSHHHHHHHHHHHHHHHHTTTTTCCSHHHHHHHTSCHHHHHHHTT
T ss_pred             CcccCCHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            3555665544      34555443 4688999999999999999999976

>1mkm_A ICLR transcriptional regulator; structural genomics, winged helix-turn-helix, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.33 d.110.2.2

Probab=82.60  E-value=2.1  Score=35.78  Aligned_cols=42  Identities=12%  Similarity=0.127  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHHhC--CCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        176 PEDLEIALEGIRSG--QTTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       176 ~e~r~eaV~~~~~~--~~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      -+.-..|++.+..+  .+++.++|..+|+|++||++.++ +...|
T Consensus         7 l~r~l~iL~~l~~~~~~~~~~ela~~~gl~~stv~r~l~~L~~~G   51 (249)
T 1mkm_A            7 LKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKG   51 (249)
T ss_dssp             HHHHHHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            45567888888763  59999999999999999999998 44433

>1mkm_A ICLR transcriptional regulator; structural genomics, winged helix-turn-helix, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.33 d.110.2.2

Probab=82.60  E-value=1.8  Score=36.15  Aligned_cols=39  Identities=8%  Similarity=0.139  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHHc-C-CCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         35 HEDMDAALEALRA-G-QMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        35 ~e~~~~AI~~~~~-g-~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      -+.-+.+++.+.. + .+|+.++|+.+|+|++|+++.++.+
T Consensus         7 l~r~l~iL~~l~~~~~~~~~~ela~~~gl~~stv~r~l~~L   47 (249)
T 1mkm_A            7 LKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVL   47 (249)
T ss_dssp             HHHHHHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3444666766654 3 6999999999999999999999975

>3rd3_A Probable transcriptional regulator; 2.40A {Pseudomonas aeruginosa}

Probab=82.54  E-value=0.9  Score=34.80  Aligned_cols=41  Identities=15%  Similarity=0.247  Sum_probs=28.6

Q ss_pred             CCCCHHHHH-HHHHHHHc-C--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         31 KTWTHEDMD-AALEALRA-G--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        31 ~kyt~e~~~-~AI~~~~~-g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.-+.+.++ .|++.+.+ |  +.|+++||++.||+++|||+...
T Consensus         8 ~~~~r~~Il~aa~~lf~~~G~~~~t~~~IA~~agvs~~tlY~~F~   52 (197)
T 3rd3_A            8 YDDTRQHLLDTGYRIMAVKGFSGVGLNEILQSAGVPKGSFYHYFK   52 (197)
T ss_dssp             --CHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHTTTCS
T ss_pred             hHhHHHHHHHHHHHHHHHCCcccCCHHHHHHHhCCChhhHHHHcC
Confidence            344556664 44445544 3  57999999999999999998643

>2ijl_A AGR_C_4647P, molybdenum-binding transcriptional repressor; structural GE DNA-binding protein, PSI-2, PROT structure initiative; 2.30A {Agrobacterium tumefaciens str}

Probab=82.53  E-value=1.4  Score=34.10  Aligned_cols=39  Identities=13%  Similarity=0.252  Sum_probs=30.1

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ++..++ .++..+.+.+ |+..||+.+||+.++|++.+++.
T Consensus        24 ~~~~~L-~~f~av~e~g-S~s~AA~~L~iSqsavS~~I~~L   62 (135)
T 2ijl_A           24 LGHGKV-ELMQLIAETG-SISAAGRAMDMSYRRAWLLVDAL   62 (135)
T ss_dssp             ESHHHH-HHHHHHHHHS-CHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCHHHH-HHHHHHHHhC-CHHHHHHHHCcCHHHHHHHHHHH
Confidence            344444 4455666655 99999999999999999999985

>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69

Probab=82.50  E-value=1.7  Score=31.53  Aligned_cols=34  Identities=12%  Similarity=0.168  Sum_probs=31.0

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHh-CCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEY-GIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~f-gVp~~tv~~~vk  212 (229)
                      +..|+..+.+|.+++.+++..+ ||+.++|...++
T Consensus        16 ~~~IL~~L~~~~~~~~eLa~~l~~is~~tls~~L~   50 (107)
T 2hzt_A           16 KXVILXHLTHGKKRTSELKRLMPNITQKMLTQQLR   50 (107)
T ss_dssp             HHHHHHHHTTCCBCHHHHHHHCTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHhcCCCHHHHHHHHH
Confidence            6678888778889999999999 999999999998

>3bqy_A Putative TETR family transcriptional regulator; structural genomics, strept coelicolor, PSI-2, protein structure initiative; 1.95A {Streptomyces coelicolor A3}

Probab=82.48  E-value=1.3  Score=35.70  Aligned_cols=38  Identities=11%  Similarity=0.240  Sum_probs=29.0

Q ss_pred             CHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      |.+.++ .|++.+.+.   ++|+++||++.||+++|||+...
T Consensus         3 tr~~Il~aA~~l~~~~G~~~~s~~~IA~~aGvs~~tlY~hf~   44 (209)
T 3bqy_A            3 DRARTVQTALDLLNESGLDTLTMRRLAQAMDVQAGALYRYFA   44 (209)
T ss_dssp             CHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             CHHHHHHHHHHHHHhCCcccCCHHHHHHHhCCCcchHHhhcC
Confidence            456664 555555443   58999999999999999999754

>3mnl_A KSTR, transcriptional regulatory protein (probably TETR; TETR family of transcriptional regulator, all-helical; 1.80A {Mycobacterium tuberculosis}

Probab=82.40  E-value=0.99  Score=34.81  Aligned_cols=37  Identities=14%  Similarity=0.240  Sum_probs=27.4

Q ss_pred             HHHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         35 HEDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        35 ~e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        22 r~~Il~aA~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   62 (203)
T 3mnl_A           22 RKRILDATMAIASKGGYEAVQMRAVADRADVAVGTLYRYFP   62 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHcCCccCCHHHHHHHcCCChhHHHHHcC
Confidence            3444 3455555443   58999999999999999999754

>3cec_A Putative antidote protein of plasmid maintenance; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.60A {Nostoc punctiforme}

Probab=82.39  E-value=0.75  Score=32.97  Aligned_cols=25  Identities=8%  Similarity=0.116  Sum_probs=23.0

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..++|+.++|+.+||+++||.+|..
T Consensus        29 ~~gltq~~lA~~~gis~~~is~~e~   53 (104)
T 3cec_A           29 DLDINTANFAEILGVSNQTIQEVIN   53 (104)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            3489999999999999999999987

>3dpj_A Transcription regulator, TETR family; APC88616, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; HET: MES; 1.90A {Silicibacter pomeroyi}

Probab=82.39  E-value=1.3  Score=33.96  Aligned_cols=33  Identities=27%  Similarity=0.314  Sum_probs=25.5

Q ss_pred             HHHHHHHHc-C--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA-G--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~-g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+ |  +.|+++||++.||+++|||+...
T Consensus        15 ~aA~~l~~~~G~~~~t~~~IA~~Agvs~~tly~~F~   50 (194)
T 3dpj_A           15 AAADELFYRQGFAQTSFVDISAAVGISRGNFYYHFK   50 (194)
T ss_dssp             HHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHcCcccCCHHHHHHHHCCChHHHHHHcC
Confidence            344555544 3  68999999999999999999743

>3bni_A Putative TETR-family transcriptional regulator; structural genomics, APC7281; HET: PG4; 2.30A {Streptomyces coelicolor A3}

Probab=82.39  E-value=1.3  Score=35.63  Aligned_cols=37  Identities=14%  Similarity=0.199  Sum_probs=27.1

Q ss_pred             HHHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         35 HEDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        35 ~e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        45 r~~Il~aA~~l~~~~G~~~~tv~~IA~~AGvs~~t~Y~~F~   85 (229)
T 3bni_A           45 LTRILDACADLLDEVGYDALSTRAVALRADVPIGSVYRFFG   85 (229)
T ss_dssp             HHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHhcChhhccHHHHHHHHCCCchhHHHHcC
Confidence            3444 3444455442   58999999999999999999844

>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp}

Probab=82.37  E-value=1.2  Score=32.69  Aligned_cols=25  Identities=8%  Similarity=0.064  Sum_probs=23.4

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-|+|+.++|+.+||+++||.+|-.
T Consensus        34 ~~gltq~elA~~~gis~~~is~~E~   58 (111)
T 3mlf_A           34 DYGLTQKELGDLFKVSSRTIQNMEK   58 (111)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            4689999999999999999999987

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=82.34  E-value=2.3  Score=32.34  Aligned_cols=33  Identities=15%  Similarity=0.099  Sum_probs=26.5

Q ss_pred             HHHHHHHHhCCC-------cHHHHHHHhCCChHHHHHHHH
Q psy17316        180 EIALEGIRSGQT-------TVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       180 ~eaV~~~~~~~~-------s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+.+.+..|.+       +..+.|..||||++||+..++
T Consensus        11 ~~i~~~I~~g~l~~G~~LPse~~La~~~gvSr~tVr~Al~   50 (129)
T 2ek5_A           11 SLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLT   50 (129)
T ss_dssp             HHHHHHHHTTSSCTTSCBCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHH
Confidence            345555666654       789999999999999999987

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=82.34  E-value=2.7  Score=31.82  Aligned_cols=43  Identities=9%  Similarity=-0.085  Sum_probs=31.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      ..|..+..-......++++++.++|+.+||+++|+.+.+++..
T Consensus        46 ~lt~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le   88 (162)
T 2fa5_A           46 GMAIPEWRVITILALYPGSSASEVSDRTAMDKVAVSRAVARLL   88 (162)
T ss_dssp             CCCHHHHHHHHHHHHSTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3455544222222336899999999999999999999999863

>1t33_A Putative transcriptional repressor (TETR/ACRR FAM; structural genomics, TETR/CCRR FA helix turn helix DNA binding domain, PSI; 2.20A {Salmonella typhimurium} SCOP: a.4.1.9 a.121.1.1

Probab=82.32  E-value=1.2  Score=35.14  Aligned_cols=37  Identities=11%  Similarity=0.003  Sum_probs=28.0

Q ss_pred             HHHH-HHHHHHHHcCC--CCHHHHHHHcCCChhhHHHHHH
Q psy17316         35 HEDM-DAALEALRAGQ--MSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        35 ~e~~-~~AI~~~~~g~--~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+.+ ..|++.+.+.|  .|+++||++.||+++|||++..
T Consensus        14 r~~Il~aA~~lf~~~G~~~s~~~IA~~agvs~~tiY~~F~   53 (224)
T 1t33_A           14 KSQLIAAALAQFGEYGLHATTRDIAALAGQNIAAITYYFG   53 (224)
T ss_dssp             HHHHHHHHHHHHHHHGGGSCHHHHHHHHTSCHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHhCccccHHHHHHHhCCCHHHHHHhcC
Confidence            3444 45555555433  8999999999999999999865

>3s8q_A R-M controller protein; protein-DNA complex, helix-turn-helix; HET: DNA; 2.10A {Enterobacter SP} SCOP: a.35.1.0 PDB: 3clc_A* 3ufd_A*

Probab=82.31  E-value=3  Score=28.11  Aligned_cols=33  Identities=9%  Similarity=-0.104  Sum_probs=27.2

Q ss_pred             HHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        182 ALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       182 aV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      +-+.....++|..+.|...|||.++|.+|-++.
T Consensus        16 lk~~R~~~glsq~~lA~~~gis~~~i~~~e~g~   48 (82)
T 3s8q_A           16 IKKIRLEKGMTQEDLAYKSNLDRTYISGIERNS   48 (82)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTC
T ss_pred             HHHHHHHcCCCHHHHHHHhCcCHHHHHHHHCCC
Confidence            334445577999999999999999999998865

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=82.31  E-value=1.8  Score=32.93  Aligned_cols=35  Identities=11%  Similarity=0.072  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHh---CCCcHHHHHHHh-----CCChHHHHHHHH
Q psy17316        178 DLEIALEGIRS---GQTTVQRASAEY-----GIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~---~~~s~~eAA~~f-----gVp~~tv~~~vk  212 (229)
                      .|..|++.+.+   +.+|..++...+     +||.+|||+.++
T Consensus        19 qR~~Il~~L~~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~   61 (136)
T 1mzb_A           19 PRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLT   61 (136)
T ss_dssp             HHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHH
Confidence            49999999986   458999999988     899999999998

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A

Probab=82.27  E-value=1.8  Score=34.81  Aligned_cols=37  Identities=3%  Similarity=-0.058  Sum_probs=28.2

Q ss_pred             CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++.+| +|+....-.++++.++|..+|||.+||+.++.
T Consensus       189 ~~~~r-~vl~l~~~~g~s~~EIA~~lgis~~~V~~~~~  225 (239)
T 1rp3_A          189 PEREK-LVIQLIFYEELPAKEVAKILETSVSRVSQLKA  225 (239)
T ss_dssp             CHHHH-HHHHHHHTSCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             CHHHH-HHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            34444 44444444569999999999999999999876

>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A

Probab=82.18  E-value=2.1  Score=33.75  Aligned_cols=36  Identities=14%  Similarity=0.074  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         35 HEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        35 ~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+.+.+-|..+..-. |+.++|+.+||+++||.+|.+
T Consensus         7 ~~~~~~rl~~~r~~~-tq~elA~~~Gis~~~i~~~e~   42 (189)
T 2fjr_A            7 NVDVLDRICEAYGFS-QKIQLANHFDIASSSLSNRYT   42 (189)
T ss_dssp             HHHHHHHHHHHHTCS-SHHHHHHHTTCCHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhhc-CHHHHHHHhCcCHHHHHHHHh
Confidence            345556666665544 999999999999999999988

>2q24_A Putative TETR family transcriptional regulator; structural genomics, PSI, protein structure initiative; 1.80A {Streptomyces coelicolor A3}

Probab=82.15  E-value=1.4  Score=33.99  Aligned_cols=39  Identities=18%  Similarity=0.245  Sum_probs=28.4

Q ss_pred             CCHHHHH-HHHHHHHcCC--CCHHHHHHHcCCChhhHHHHHH
Q psy17316         33 WTHEDMD-AALEALRAGQ--MSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        33 yt~e~~~-~AI~~~~~g~--~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      -+.+.++ .|++.+.+.|  .|+++||++.||+++|||+...
T Consensus        15 ~~r~~Il~aA~~lf~~~G~~~s~~~IA~~agvs~~tlY~~F~   56 (194)
T 2q24_A           15 RNRDKILAAAVRVFSEEGLDAHLERIAREAGVGSGTLYRNFP   56 (194)
T ss_dssp             -CHHHHHHHHHHHHHHHCTTCCHHHHHHHTTCCHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHHhcCcCCCHHHHHHHhCCChHHHHHHcC
Confidence            3556664 5555555432  7999999999999999998744

>3bru_A Regulatory protein, TETR family; structural genomics, APC88928, PSI-2, protein structur initiative; 2.30A {Rhodobacter sphaeroides 2}

Probab=82.12  E-value=1.7  Score=34.00  Aligned_cols=38  Identities=16%  Similarity=0.328  Sum_probs=28.8

Q ss_pred             CHHHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        31 ~r~~Il~aA~~l~~~~G~~~~t~~~IA~~aGvs~~t~Y~~F~   72 (222)
T 3bru_A           31 AHQSLIRAGLEHLTEKGYSSVGVDEILKAARVPKGSFYHYFR   72 (222)
T ss_dssp             HHHHHHHHHHHHHHHSCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHcCCCcCcHHHHHHHhCCCcchhhhhCC
Confidence            45555 4555555553   58999999999999999999854

>2gen_A Probable transcriptional regulator; APC6095, TETR family, structural genomics, PSI, protein structure initiative; 1.70A {Pseudomonas aeruginosa PAO1} SCOP: a.4.1.9 a.121.1.1

Probab=82.11  E-value=1.9  Score=33.62  Aligned_cols=40  Identities=13%  Similarity=0.215  Sum_probs=29.4

Q ss_pred             CCCHHHH-HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         32 TWTHEDM-DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        32 kyt~e~~-~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-+.+.+ ..|++.+.+   .+.|+++||++.||+++|||+...
T Consensus         6 ~~~r~~Il~aA~~lf~~~G~~~ts~~~IA~~aGvs~gtlY~~F~   49 (197)
T 2gen_A            6 SSRKDEILQAALACFSEHGVDATTIEMIRDRSGASIGSLYHHFG   49 (197)
T ss_dssp             --CHHHHHHHHHHHHHHHCTTTCCHHHHHHHHCCCHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHcCcccCCHHHHHHHHCCChHHHHHHCC
Confidence            3455666 455666654   257999999999999999999854

>1u8b_A ADA polyprotein; protein-DNA complex, methylation, zinc, helix-turn-helix, metal binding protein/DNA complex; 2.10A {Escherichia coli} PDB: 1zgw_A* 1wpk_A* 1adn_A 1eyf_A

Probab=82.11  E-value=2.1  Score=32.04  Aligned_cols=39  Identities=10%  Similarity=0.209  Sum_probs=31.0

Q ss_pred             HHHHHHHHH-cCCCCHHHHHHHhCCChHHHHHHHHHh-CCc
Q psy17316        124 LNVALDALR-AGSISANKASKAYGIPSSTLYKIARKE-GIR  162 (229)
Q Consensus       124 k~~AV~~~~-~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k  162 (229)
                      +..|++.+. ...+|+.++|...|++.++|.+..+++ |..
T Consensus        81 l~~a~~~i~~~~~~sl~~lA~~~g~S~~~f~r~Fk~~~G~t  121 (133)
T 1u8b_A           81 ITHACRLLEQETPVTLEALADQVAMSPFHLHRLFKATTGMT  121 (133)
T ss_dssp             HHHHHHHTCSSSCCCHHHHHHHHTSCHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence            455566655 567899999999999999999999875 643

>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli}

Probab=82.11  E-value=0.76  Score=33.40  Aligned_cols=26  Identities=0%  Similarity=-0.005  Sum_probs=23.8

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..-|+|+.++|+.+||+++||.+|..
T Consensus        21 ~~~glsq~~lA~~~gis~~~is~~e~   46 (113)
T 2eby_A           21 EPLDLKINELAELLHVHRNSVSALIN   46 (113)
T ss_dssp             TTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            45689999999999999999999987

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12

Probab=82.08  E-value=3.6  Score=28.43  Aligned_cols=38  Identities=11%  Similarity=-0.037  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      ..-..+-+.....+++..+.|...||+.++|.+|.++.
T Consensus        13 ~~~~~l~~~r~~~glsq~~lA~~~gis~~~is~~e~g~   50 (91)
T 1x57_A           13 EVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGR   50 (91)
T ss_dssp             HHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence            34444555556678999999999999999999998854

>2fq4_A Transcriptional regulator, TETR family; DNA-binding protein, bacillu structural genomics, PSI, protein structure initiative; 1.79A {Bacillus cereus} SCOP: a.4.1.9 a.121.1.1

Probab=82.08  E-value=2.4  Score=32.77  Aligned_cols=37  Identities=16%  Similarity=0.171  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHh-------CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRS-------GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~-------~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+.|..|++...+       ++.|+.++|..-|||+.|+|++..
T Consensus        11 ~~~r~~Il~aA~~lf~e~G~~~~t~~~IA~~agvsk~tlY~~F~   54 (192)
T 2fq4_A           11 IETQKAILSASYELLLESGFKAVTVDKIAERAKVSKATIYKWWP   54 (192)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             hHHHHHHHHHHHHHHHHcCcccccHHHHHHHcCCCHHHHHHHCC
Confidence            4455555555444       568999999999999999999876

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=82.05  E-value=1.7  Score=35.91  Aligned_cols=38  Identities=18%  Similarity=0.222  Sum_probs=31.4

Q ss_pred             CCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        173 AWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       173 ~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|+.++ +|+.++.+| +++.|+|...|||..||..+++
T Consensus       175 ~Lt~~e~-~vl~~~~~g-~s~~eIa~~l~is~~tV~~~~~  212 (236)
T 2q0o_A          175 MLSPREM-LCLVWASKG-KTASVTANLTGINARTVQHYLD  212 (236)
T ss_dssp             SCCHHHH-HHHHHHHTT-CCHHHHHHHHCCCHHHHHHHHH
T ss_pred             CCCHHHH-HHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHH
Confidence            4566655 578887655 9999999999999999999886

>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69

Probab=82.03  E-value=1.8  Score=31.63  Aligned_cols=34  Identities=15%  Similarity=0.150  Sum_probs=30.7

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHh-CCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEY-GIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~f-gVp~~tv~~~vk  212 (229)
                      +..|+..+..|.+++.++|..+ +|+.++|...++
T Consensus        24 ~~~IL~~L~~~~~~~~eLa~~l~~is~~tvs~~L~   58 (112)
T 1z7u_A           24 KLSLMDELFQGTKRNGELMRALDGITQRVLTDRLR   58 (112)
T ss_dssp             HHHHHHHHHHSCBCHHHHHHHSTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCHHHHHHHhccCCHHHHHHHHH
Confidence            5677777778999999999999 999999999998

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=82.02  E-value=2.4  Score=31.58  Aligned_cols=43  Identities=16%  Similarity=0.111  Sum_probs=31.6

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      ..|..+..-......+|++++.++|+.+||+++|+.+.+++..
T Consensus        39 ~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le   81 (150)
T 2rdp_A           39 PITPPQFVALQWLLEEGDLTVGELSNKMYLACSTTTDLVDRME   81 (150)
T ss_dssp             SSCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHH
Confidence            3455554222222346889999999999999999999999863

>2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2, protein struct initiative, northeast structural genomics consortium, NESG; 1.63A {Escherichia coli} SCOP: a.35.1.3 PDB: 2icp_A

Probab=82.01  E-value=1.8  Score=30.21  Aligned_cols=31  Identities=10%  Similarity=0.013  Sum_probs=26.4

Q ss_pred             HHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        184 EGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       184 ~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      +.+...+++..+.|...|||.++|.+|.++.
T Consensus        15 ~~r~~~gltq~~lA~~~gis~~~is~~e~g~   45 (94)
T 2ict_A           15 ESLDELNVSLREFARAMEIAPSTASRLLTGK   45 (94)
T ss_dssp             HHHHHHTCCHHHHHHHHTCCHHHHHHHHHTS
T ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence            3445566999999999999999999999864

>3anp_C Transcriptional repressor, TETR family; all alpha protein, DNA, acyl-COA; HET: DCC DAO; 1.95A {Thermus thermophilus} PDB: 3ang_C*

Probab=82.00  E-value=1.3  Score=34.47  Aligned_cols=33  Identities=21%  Similarity=0.303  Sum_probs=25.9

Q ss_pred             HHHHHHHHc-C--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA-G--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~-g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+ |  +.|+.+||++.||+++|||+...
T Consensus        16 ~aA~~lf~~~G~~~~t~~~Ia~~Agvs~gt~Y~yF~   51 (204)
T 3anp_C           16 RAAMELFRNRGFQETTATEIAKAAHVSRGTFFNYYP   51 (204)
T ss_dssp             HHHHHHHHHHCTTTCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             HHHHHHHHHcCcccccHHHHHHHcCCchHHHHHHcC
Confidence            455555554 3  58999999999999999999744

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=81.85  E-value=2.8  Score=34.51  Aligned_cols=40  Identities=18%  Similarity=0.175  Sum_probs=30.7

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh
Q psy17316        118 SWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE  159 (229)
Q Consensus       118 kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~  159 (229)
                      ..++..+ +++..+.+|. |.++||+..||+..|++.++++.
T Consensus       175 ~Lt~~e~-~vl~~~~~g~-s~~eIa~~l~is~~tV~~~~~~~  214 (236)
T 2q0o_A          175 MLSPREM-LCLVWASKGK-TASVTANLTGINARTVQHYLDKA  214 (236)
T ss_dssp             SCCHHHH-HHHHHHHTTC-CHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             CCCHHHH-HHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHHH
Confidence            3455444 4667777765 99999999999999988887643

>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}

Probab=81.81  E-value=1.2  Score=32.65  Aligned_cols=34  Identities=9%  Similarity=0.041  Sum_probs=26.8

Q ss_pred             HHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         38 MDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        38 ~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +-..|..+ ...|+|+.++|+..||++++|.+|-.
T Consensus        22 ~g~~lr~~R~~~gltq~elA~~~gis~~~is~~E~   56 (114)
T 3vk0_A           22 LAYNMRLFRVNKGWSQEELARQCGLDRTYVSAVER   56 (114)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            33444433 45789999999999999999999965

>3kkc_A TETR family transcriptional regulator; APC20805, structural genomics, PSI-2, protein structure initiative; 2.50A {Streptococcus agalactiae 2603V}

Probab=81.68  E-value=0.9  Score=34.38  Aligned_cols=38  Identities=8%  Similarity=0.134  Sum_probs=27.0

Q ss_pred             CHHHHHH-HHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDMDA-ALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~~~-AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+.+++ |++.+.+.   +.|+++||++.||+++|||+...
T Consensus        13 tr~~Il~aa~~l~~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~   54 (177)
T 3kkc_A           13 TKVAIYNAFISLLQENDYSKITVQDVIGLANVGRSTFYSHYE   54 (177)
T ss_dssp             HHHHHHHHHHHHTTTSCTTTCCHHHHHHHHCCCHHHHTTTCS
T ss_pred             HHHHHHHHHHHHHHhCChhHhhHHHHHHHhCCcHhhHHHHcC
Confidence            4455544 44444443   57999999999999999998643

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=81.67  E-value=2.4  Score=32.63  Aligned_cols=35  Identities=14%  Similarity=0.207  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHh--CCCcHHHHHHHh-----CCChHHHHHHHH
Q psy17316        178 DLEIALEGIRS--GQTTVQRASAEY-----GIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~--~~~s~~eAA~~f-----gVp~~tv~~~vk  212 (229)
                      .|..|++.+.+  +.+|..++...+     +||.+|||+.++
T Consensus        23 qR~~Il~~L~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~   64 (145)
T 2fe3_A           23 QRHAILEYLVNSMAHPTADDIYKALEGKFPNMSVATVYNNLR   64 (145)
T ss_dssp             HHHHHHHHHHHCSSCCCHHHHHHHHGGGCTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCChhhHHHHHH
Confidence            49999999976  458999999999     999999999998

>3nnr_A Transcriptional regulator, TETR family; TETR-family transcriptional regulator, structural genomics, center for structural genomics, JCSG; HET: MSE; 2.49A {Marinobacter aquaeolei}

Probab=81.64  E-value=1.3  Score=35.23  Aligned_cols=38  Identities=13%  Similarity=0.256  Sum_probs=28.2

Q ss_pred             CHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+.++ .|++.+.+.   +.|+++||++.||+++|||+...
T Consensus         6 tr~~Il~aA~~lf~~~G~~~~t~~~IA~~Agvs~~t~Y~~F~   47 (228)
T 3nnr_A            6 TRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR   47 (228)
T ss_dssp             HHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHhChhhcCHHHHHHHhCCCCccchhcCC
Confidence            445554 455555543   58999999999999999998643

>3frq_A Repressor protein MPHR(A); macrolide antibiotic. repressor, biosensor, erythromycin, STRPTOMYCES, natural products, biosynthesis, DNA-binding; HET: ERY; 1.76A {Escherichia coli} PDB: 3g56_A

Probab=81.57  E-value=1.5  Score=33.88  Aligned_cols=41  Identities=17%  Similarity=0.207  Sum_probs=0.0

Q ss_pred             CCCCCHHHHHHHHHHHHc----CCCCHHHHHHHcCCChhhHHHHH
Q psy17316         30 TKTWTHEDMDAALEALRA----GQMSLTKASVSYGIPSTTLWQRA   70 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~----g~~S~~~aA~~~gIp~sTL~~~i   70 (229)
                      .+.-+.+.++.|...+..    .+.|+++||++.||+++|||+..
T Consensus         5 ~~~~tr~~Il~AA~~l~~~~G~~~~t~~~IA~~agvs~~t~Y~~F   49 (195)
T 3frq_A            5 PKLKSDDEVLEAATVVLKRCGPIEFTLSGVAKEVGLSRAALIQRF   49 (195)
T ss_dssp             -CCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CccCcHHHHHHHHHHHHHhhCcccCCHHHHHHHhCCCHHHHHHHc

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=81.54  E-value=2.3  Score=32.10  Aligned_cols=33  Identities=12%  Similarity=0.113  Sum_probs=26.5

Q ss_pred             HHHHHHHHhCCC-------cHHHHHHHhCCChHHHHHHHH
Q psy17316        180 EIALEGIRSGQT-------TVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       180 ~eaV~~~~~~~~-------s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+.+.+..|.+       +..+.|..||||++||...++
T Consensus        18 ~~l~~~I~~g~~~~G~~lPse~~La~~~~vSr~tvr~Al~   57 (126)
T 3by6_A           18 DRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYK   57 (126)
T ss_dssp             HHHHHHHHTTSSCTTCEECCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHH
Confidence            344455666654       899999999999999999887

>3fmy_A HTH-type transcriptional regulator MQSA (YGIT/B3021); helix-turn-helix, DNA-binding, transcription regulation, DNA binding protein; HET: MEQ; 1.40A {Escherichia coli k-12}

Probab=81.52  E-value=1.9  Score=28.97  Aligned_cols=30  Identities=17%  Similarity=-0.012  Sum_probs=25.8

Q ss_pred             HHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        186 IRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       186 ~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      ....++|..+.|...|||.+||.+|-++.+
T Consensus        20 R~~~gltq~elA~~~gvs~~tis~~E~G~~   49 (73)
T 3fmy_A           20 RKKLSLTQKEASEIFGGGVNAFSRYEKGNA   49 (73)
T ss_dssp             HHHTTCCHHHHHHHHCSCTTHHHHHHTTSS
T ss_pred             HHHcCCCHHHHHHHhCcCHHHHHHHHcCCC
Confidence            345679999999999999999999988654

>3knw_A Putative transcriptional regulator (TETR/ACRR FAM; TETR-like protein, MCSG, PSI, structural genomics, protein S initiative; 2.45A {Acinetobacter SP}

Probab=81.47  E-value=1.5  Score=34.04  Aligned_cols=38  Identities=11%  Similarity=0.285  Sum_probs=27.6

Q ss_pred             CHHHHH-HHHHHHHc-C--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDMD-AALEALRA-G--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~~-~AI~~~~~-g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+.++ .|++.+.+ |  +.|+++||++.||+++|||+...
T Consensus        15 ~r~~Il~aa~~l~~~~G~~~~ti~~IA~~agvs~~t~Y~~F~   56 (212)
T 3knw_A           15 KRQHILDSGFHLVLRKGFVGVGLQEILKTSGVPKGSFYHYFE   56 (212)
T ss_dssp             HHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             hHHHHHHHHHHHHHHcCCccCCHHHHHHHhCCChHHHHHHCC
Confidence            344443 44444543 3  68999999999999999998744

>2xdn_A HTH-type transcriptional regulator TTGR; transcription regulation, TETR family; 2.20A {Pseudomonas putida} PDB: 2uxu_A* 2uxi_A* 2uxo_A* 2uxp_A* 2uxh_A*

Probab=81.47  E-value=1.9  Score=33.70  Aligned_cols=33  Identities=15%  Similarity=0.226  Sum_probs=26.0

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+   .+.|+.+||++.||+++|||+...
T Consensus        18 ~aA~~lf~~~G~~~~s~~~IA~~aGvskgtlY~~F~   53 (210)
T 2xdn_A           18 EAAERAFYKRGVARTTLADIAELAGVTRGAIYWHFN   53 (210)
T ss_dssp             HHHHHHHHHHCSTTCCHHHHHHHHTCCTTHHHHHCS
T ss_pred             HHHHHHHHHcCcccCcHHHHHHHHCCChHHHHHHhC
Confidence            445555554   368999999999999999999854

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=81.45  E-value=2.2  Score=31.41  Aligned_cols=42  Identities=14%  Similarity=0.043  Sum_probs=31.0

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .|..+..-.......+++++.++|+.+||+++|+.+.+++..
T Consensus        34 lt~~~~~iL~~l~~~~~~t~~ela~~l~~s~~~vs~~l~~Le   75 (142)
T 2fbi_A           34 LTEQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLE   75 (142)
T ss_dssp             CCHHHHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence            455544222223346789999999999999999999999863

>3trb_A Virulence-associated protein I; mobIle and extrachromosomal element functions, DNA binding P; 2.00A {Coxiella burnetii}

Probab=81.44  E-value=2.1  Score=31.28  Aligned_cols=31  Identities=10%  Similarity=0.035  Sum_probs=27.8

Q ss_pred             HHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        185 GIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       185 ~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      .+...+++..+.|...|||.++|..|.++.+
T Consensus        22 lr~~~gltq~eLA~~lGis~~~is~ie~G~~   52 (104)
T 3trb_A           22 LGFLDKMSANQLAKHLAIPTNRVTAILNGAR   52 (104)
T ss_dssp             HHHTTSCCHHHHHHHHTSCHHHHHHHHTTSS
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHcCCC
Confidence            4677889999999999999999999998764

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=81.44  E-value=13  Score=30.23  Aligned_cols=64  Identities=11%  Similarity=0.051  Sum_probs=43.5

Q ss_pred             CHHHHHHHHHHHH--cCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCC--CCcHHHHHHHHH
Q psy17316         34 THEDMDAALEALR--AGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTK--SWNEEILNVALD   97 (229)
Q Consensus        34 t~e~~~~AI~~~~--~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k--~~s~e~~~~a~~   97 (229)
                      +.||-+++|-.+.  .+.+++.++|+.+||+++|+.+-++++.-.|.-...+++  ..+++=+..+.+
T Consensus         3 ~~edYL~~I~~l~~~~~~~~~~~lA~~l~vs~~tvs~~l~~Le~~GlV~r~~~~~i~LT~~G~~~~~~   70 (214)
T 3hrs_A            3 NKEDYLKCLYELGTRHNKITNKEIAQLMQVSPPAVTEMMKKLLAEELLIKDKKAGYLLTDLGLKLVSD   70 (214)
T ss_dssp             CHHHHHHHHHHTTSSCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTEEEECHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCEEEecCCCeEECHHHHHHHHH
Confidence            4677777776554  467999999999999999999999987554432222211  235555544443

>3qkx_A Uncharacterized HTH-type transcriptional regulato; structural genomics, joint center for structural genomics; HET: MSE; 2.35A {Haemophilus influenzae}

Probab=81.42  E-value=2.2  Score=32.26  Aligned_cols=32  Identities=16%  Similarity=0.213  Sum_probs=26.3

Q ss_pred             HHHHHHHHHcCC---CCHHHHHHHhCCChHHHHHH
Q psy17316        124 LNVALDALRAGS---ISANKASKAYGIPSSTLYKI  155 (229)
Q Consensus       124 k~~AV~~~~~g~---~S~~~~a~k~gIp~sTL~~~  155 (229)
                      +..|++.+.+.+   .|+.+||+.-||+++|+|+.
T Consensus        14 l~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~   48 (188)
T 3qkx_A           14 FSATDRLMAREGLNQLSMLKLAKEANVAAGTIYLY   48 (188)
T ss_dssp             HHHHHHHHHHSCSTTCCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHhcCcccCCHHHHHHHhCCCcchHHHH
Confidence            456667766544   69999999999999999997

>2id3_A Putative transcriptional regulator; structural genomics, PSI-2, prote structure initiative; 1.70A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=81.40  E-value=1.5  Score=35.00  Aligned_cols=38  Identities=29%  Similarity=0.315  Sum_probs=28.3

Q ss_pred             CHHHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        41 ~r~~Il~aA~~lf~~~G~~~~t~~~IA~~Agvs~~t~Y~~F~   82 (225)
T 2id3_A           41 IREAVLLAAGDALAADGFDALDLGEIARRAGVGKTTVYRRWG   82 (225)
T ss_dssp             HHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHhCcccCCHHHHHHHHCCCHHHHHHHCC
Confidence            34444 3555555543   58999999999999999998765

>3rqi_A Response regulator protein; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: PHD CIT; 1.70A {Burkholderia pseudomallei}

Probab=81.38  E-value=1.2  Score=34.66  Aligned_cols=32  Identities=9%  Similarity=0.184  Sum_probs=25.6

Q ss_pred             HHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         44 ALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      .+...+.+...+|+++|+++.|++++++++++
T Consensus       151 ~~~~~~~~~~~ia~~l~is~~tv~~~l~~~~~  182 (184)
T 3rqi_A          151 VLAENNNNISATARALNMHRRTLQRKLAKKPV  182 (184)
T ss_dssp             HHHHTTSCHHHHHHHHTSCHHHHHHHHCC---
T ss_pred             HHHhccccHHHHHHHcCCcHHHHHHHHHhcCC
Confidence            44456789999999999999999999987765

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=81.36  E-value=2.4  Score=31.44  Aligned_cols=28  Identities=11%  Similarity=0.221  Sum_probs=25.9

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .+++++.++|+.+||+++|+.+.+++..
T Consensus        48 ~~~~~~~ela~~l~~s~~tvs~~l~~Le   75 (146)
T 2gxg_A           48 DGPKTMAYLANRYFVTQSAITASVDKLE   75 (146)
T ss_dssp             TSCBCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             cCCcCHHHHHHHhCCCchhHHHHHHHHH
Confidence            7889999999999999999999999863

>3m8j_A FOCB protein; all-alpha, helix-turn-helix, transcription; 1.40A {Escherichia coli}

Probab=81.31  E-value=4.8  Score=30.30  Aligned_cols=42  Identities=10%  Similarity=0.135  Sum_probs=35.9

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHH
Q psy17316        117 KSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARK  158 (229)
Q Consensus       117 ~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~  158 (229)
                      .+..-+....|+.+|+-.+.+-+++|.+|||+.+-+...+++
T Consensus        42 S~IrSekII~ALrdyLV~G~srkeaCe~~gV~~syfS~~L~r   83 (111)
T 3m8j_A           42 SSIHSDRVILAMKDYLVSGHSRKDVCEKYQMNNGYFSTTLGR   83 (111)
T ss_dssp             SCCCCHHHHHHHHHHHTTCCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHH
Confidence            345557889999999998899999999999999998887664

>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix, transcription/DNA complex; HET: DNA; 1.80A {Enterobacteria phage lambda} SCOP: a.35.1.2 PDB: 1lrp_A 1rio_A 1lli_A*

Probab=81.27  E-value=2.2  Score=29.39  Aligned_cols=28  Identities=4%  Similarity=-0.067  Sum_probs=25.0

Q ss_pred             HhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        187 RSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       187 ~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      ...+++..+.|...|||.++|.+|.++.
T Consensus        27 ~~~glsq~~lA~~~gis~~~is~~e~g~   54 (92)
T 1lmb_3           27 NELGLSQESVADKMGMGQSGVGALFNGI   54 (92)
T ss_dssp             HHHTCCHHHHHHHHTSCHHHHHHHHTTS
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence            4567999999999999999999999864

>2ibd_A Possible transcriptional regulator; probable transcriptional regulatory protein, rhodococcus SP. structural genomics, PSI-2; 1.50A {Rhodococcus SP}

Probab=81.19  E-value=2  Score=33.45  Aligned_cols=38  Identities=16%  Similarity=0.247  Sum_probs=28.3

Q ss_pred             CHHHH-HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDM-DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~-~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+.+ ..|++.+.+   .+.|+++||++.||+++|||+...
T Consensus        15 ~r~~Il~aA~~lf~~~G~~~~s~~~IA~~agvs~~tlY~~F~   56 (204)
T 2ibd_A           15 RRTELLDIAATLFAERGLRATTVRDIADAAGILSGSLYHHFD   56 (204)
T ss_dssp             HHHHHHHHHHHHHHHHCSTTCCHHHHHHHTTSCHHHHHHHCS
T ss_pred             hHHHHHHHHHHHHHHcCchhcCHHHHHHHhCCCchhHHHhcC
Confidence            33444 455555554   368999999999999999999744

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=81.14  E-value=1.9  Score=32.05  Aligned_cols=43  Identities=9%  Similarity=0.074  Sum_probs=32.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      ..|..+. .++..+..+++++.++|+.+||+++|+.+.+.+..-
T Consensus        35 ~lt~~~~-~iL~~l~~~~~t~~eLa~~l~~s~~tvs~~l~~L~~   77 (146)
T 3tgn_A           35 ALTNTQE-HILMLLSEESLTNSELARRLNVSQAAVTKAIKSLVK   77 (146)
T ss_dssp             CCCHHHH-HHHHHHTTCCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHH-HHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3466654 344444455599999999999999999999998643

>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=81.14  E-value=4.5  Score=29.17  Aligned_cols=60  Identities=12%  Similarity=0.251  Sum_probs=43.6

Q ss_pred             HHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHh-CCCcHHHHHHHh-CCChHHHHHHHH
Q psy17316        139 NKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRS-GQTTVQRASAEY-GIPSGTLYGRCK  212 (229)
Q Consensus       139 ~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~-~~~s~~eAA~~f-gVp~~tv~~~vk  212 (229)
                      ..+|+.|||+..-|..             .++.+.. ...|.-|.=+|.. .++|+.+++..| |..++||..-++
T Consensus         8 ~~Va~~f~i~~~dl~s-------------~~R~~~i-~~aRqiamyL~r~~t~~Sl~~IG~~fggrdHsTV~ha~~   69 (94)
T 1j1v_A            8 KTVAEYYKIKVADLLS-------------KRRSRSV-ARPRQMAMALAKELTNHSLPEIGDAFGGRDHTTVLHACR   69 (94)
T ss_dssp             HHHHHHTTCCHHHHHS-------------CCCCHHH-HHHHHHHHHHHHHHSCCCHHHHHHHTTSCCHHHHHHHHH
T ss_pred             HHHHHHhCCCHHHHhC-------------CCCCchh-HHHHHHHHHHHHHHHCcCHHHHHHHhCCCCHHHHHHHHH
Confidence            4578888888877643             0112222 2347777777776 679999999999 899999998876

>3cwr_A Transcriptional regulator, TETR family; YP_425770.1, transcriptional regulator of TETR family, bacterial regulatory proteins; 1.50A {Rhodospirillum rubrum atcc 11170}

Probab=81.11  E-value=1.6  Score=33.61  Aligned_cols=38  Identities=26%  Similarity=0.350  Sum_probs=27.7

Q ss_pred             CHHHHH-HHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDMD-AALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~~-~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+.++ .|++.+.+   .+.|+++||++.||+++|||+...
T Consensus        18 ~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   59 (208)
T 3cwr_A           18 VRESIVGAAQRLLSSGGAAAMTMEGVASEAGIAKKTLYRFAS   59 (208)
T ss_dssp             HHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHcCHHhccHHHHHHHhCCCHHHHHHHcC
Confidence            444453 44445544   358999999999999999998744

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=81.11  E-value=2.9  Score=31.13  Aligned_cols=42  Identities=10%  Similarity=0.112  Sum_probs=31.1

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .|..+..-.......+++++.++|+.+||+++|+.+.+.++.
T Consensus        29 lt~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le   70 (145)
T 3g3z_A           29 LNYNLFAVLYTLATEGSRTQKHIGEKWSLPKQTVSGVCKTLA   70 (145)
T ss_dssp             CCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            455554222222356789999999999999999999999863

>3sqn_A Conserved domain protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, MGA family; 2.31A {Enterococcus faecalis}

Probab=81.09  E-value=1.8  Score=40.19  Aligned_cols=106  Identities=12%  Similarity=0.084  Sum_probs=60.3

Q ss_pred             HHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCC---CCCCCC----cHHHH-HHHHHHHhhcchhhhhh
Q psy17316         39 DAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKE---GPTKSW----NEEIL-NVALDALRAGSISANKA  109 (229)
Q Consensus        39 ~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~---~~~k~~----s~e~~-~~a~~ll~~G~ls~~~~  109 (229)
                      ...++.+ .++.+|..++|+.+||+..||++-++..+-..+...   ++.+.|    ++... +...             
T Consensus        21 ~~IL~~L~~~~~it~~eLA~~L~VS~RTIr~dI~~In~~L~~~~~I~~~~~Gy~L~~~~~~~~~~~~-------------   87 (485)
T 3sqn_A           21 IRLLEQLLNVPQLTAKRLAAQIQTTERTVFSDLQYIRSQLPADWSIETDSSGIRLRNQGNAQTNELW-------------   87 (485)
T ss_dssp             HHHHHHHHHCCSCBCGGGHHHHTSCHHHHHHHHHHHHTTCCTTEEEEEETTEEEEEEC---CTHHHH-------------
T ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHHHHHHHHhcccCcEEEEcCCEEEEecCcHHHHHHHH-------------
Confidence            3444433 366799999999999999999999987543321110   111222    11100 0000             


Q ss_pred             hhccCCCCCCCHHH-HHHHHH-HHHcCCCCHHHHHHHhCCChHHHHHH-------HHHhCCccc
Q psy17316        110 SKAYGPTKSWNEEI-LNVALD-ALRAGSISANKASKAYGIPSSTLYKI-------ARKEGIRLA  164 (229)
Q Consensus       110 ~~~~G~~~kYs~e~-k~~AV~-~~~~g~~S~~~~a~k~gIp~sTL~~~-------ik~~g~k~~  164 (229)
                             ..++++. ....+. .+.++..++.++|..+.||++|+.+-       ++++++...
T Consensus        88 -------~~~~~~eR~~~Il~~LL~~~~isi~~Lae~l~VS~sTi~~DLk~i~~~L~~y~L~L~  144 (485)
T 3sqn_A           88 -------SLFLPQSISIQLLKELLFTKELVTTSFLSTSGVSYETLKRHIKKMNQALRDFHLTIQ  144 (485)
T ss_dssp             -------HHHGGGSHHHHHHHHHHHCSEEEHHHHHHHHTCCHHHHHHHHHHHHHHHGGGTCEEE
T ss_pred             -------HhcCHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHCCeEEE
Confidence                   0112222 222333 33456689999999999999996554       445666554

>2zb9_A Putative transcriptional regulator; transcription regulator, TETR family, helix-turn-helix, DNA- binding, transcription regulation; 2.25A {Streptomyces coelicolor}

Probab=81.09  E-value=1.5  Score=34.30  Aligned_cols=33  Identities=24%  Similarity=0.294  Sum_probs=25.6

Q ss_pred             HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+.   +.|+.+||++.||+++|||+...
T Consensus        30 ~aA~~lf~~~G~~~~t~~~IA~~agvs~~t~Y~~F~   65 (214)
T 2zb9_A           30 HAVGELLLTEGTAQLTFERVARVSGVSKTTLYKWWP   65 (214)
T ss_dssp             HHHHHHHHHHCGGGCCHHHHHHHHCCCHHHHHHHCS
T ss_pred             HHHHHHHHHhCcccCCHHHHHHHHCCCHHHHHHHCC
Confidence            3455555543   58999999999999999998744

>3rh2_A Hypothetical TETR-like transcriptional regulator; DNA/RNA-binding 3-helical bundle, structural genomics, joint for structural genomics; 2.42A {Shewanella amazonensis}

Probab=81.07  E-value=1.5  Score=34.26  Aligned_cols=36  Identities=14%  Similarity=0.289  Sum_probs=27.0

Q ss_pred             HHH-HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         36 EDM-DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        36 e~~-~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+ ..|++.+.+.   +.|+++||++.||+++|||+...
T Consensus         6 ~~Il~aA~~lf~~~G~~~~s~~~IA~~Agvs~~t~Y~~F~   45 (212)
T 3rh2_A            6 DKIIQASLELFNEHGERTITTNHIAAHLDISPGNLYYHFR   45 (212)
T ss_dssp             HHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHcCcccCCHHHHHHHhCCCHHHHHHHCC
Confidence            444 4555555543   58999999999999999998643

>3b81_A Transcriptional regulator, ACRR family; NP_350189.1, predicted DNA-binding transcriptional regulator TETR/ACRR family; 2.10A {Clostridium acetobutylicum atcc 824}

Probab=81.06  E-value=1.2  Score=34.31  Aligned_cols=33  Identities=18%  Similarity=0.250  Sum_probs=24.9

Q ss_pred             HHHHHHHHc-C--CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA-G--QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~-g--~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+ |  +.|+++||++.||+++|||+...
T Consensus        18 ~aA~~lf~~~G~~~~s~~~Ia~~agvs~~t~Y~~F~   53 (203)
T 3b81_A           18 NKIWDIFIANGYENTTLAFIINKLGISKGALYHYFS   53 (203)
T ss_dssp             HHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHTTCS
T ss_pred             HHHHHHHHHcCcccCcHHHHHHHhCCCchhHHHHcC
Confidence            344444443 3  58999999999999999998643

>2f07_A YVDT; helix-turn-helix, transcription; HET: BTB; 2.30A {Bacillus subtilis subsp}

Probab=80.99  E-value=2.1  Score=33.33  Aligned_cols=39  Identities=18%  Similarity=0.221  Sum_probs=29.1

Q ss_pred             CCHHHH-HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         33 WTHEDM-DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        33 yt~e~~-~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      -+.+.+ ..|++.+.+   .+.|+.+||++.||+++|||+...
T Consensus        10 ~~r~~Il~aA~~lf~~~G~~~~s~~~Ia~~Agvskgt~Y~yF~   52 (197)
T 2f07_A           10 GKYEKILQAAIEVISEKGLDKASISDIVKKAGTAQGTFYLYFS   52 (197)
T ss_dssp             SHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCchHHHHhCC
Confidence            344555 455555654   357999999999999999999754

>2pg4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, DNA binding protein; HET: MSE CIT; 2.21A {Aeropyrum pernix} SCOP: a.4.5.48

Probab=80.98  E-value=1.6  Score=30.71  Aligned_cols=35  Identities=23%  Similarity=0.274  Sum_probs=27.6

Q ss_pred             HHHHHHH-cC-CCCHHHHHHHcCCChhh-HHHHHHHhC
Q psy17316         40 AALEALR-AG-QMSLTKASVSYGIPSTT-LWQRAHRLG   74 (229)
Q Consensus        40 ~AI~~~~-~g-~~S~~~aA~~~gIp~sT-L~~~i~~~g   74 (229)
                      .++..+. +| ++++.++|+.+||+++| +.+.++++.
T Consensus        19 ~~L~~l~~~~~~~t~~eLa~~l~is~~t~vs~~l~~Le   56 (95)
T 2pg4_A           19 PTLLEFEKKGYEPSLAEIVKASGVSEKTFFMGLKDRLI   56 (95)
T ss_dssp             HHHHHHHHTTCCCCHHHHHHHHCCCHHHHHTTHHHHHH
T ss_pred             HHHHHHHhcCCCCCHHHHHHHHCCCchHHHHHHHHHHH
Confidence            3444443 45 79999999999999999 999988763

>3s5r_A Transcriptional regulator TETR family; DNA/RNA-binding 3-helical bundle, tetracyclin repressor-like structural genomics; 2.60A {Syntrophus aciditrophicus}

Probab=80.95  E-value=1.5  Score=34.16  Aligned_cols=39  Identities=15%  Similarity=0.116  Sum_probs=28.8

Q ss_pred             CCHHHHH-HHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         33 WTHEDMD-AALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        33 yt~e~~~-~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      -+.+.++ .|++.+.+.   +.|+++||++.||+++|||+...
T Consensus        10 ~~r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   52 (216)
T 3s5r_A           10 NTRELLLDAATTLFAEQGIAATTMAEIAASVGVNPAMIHYYFK   52 (216)
T ss_dssp             CHHHHHHHHHHHHHHHHCTTTCCHHHHHHTTTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHcCcccCCHHHHHHHHCCCHHHHHHHcC
Confidence            3455554 455555543   58999999999999999999744

>3k0l_A Repressor protein; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.35A {Acinetobacter SP}

Probab=80.84  E-value=3.5  Score=31.42  Aligned_cols=43  Identities=12%  Similarity=-0.090  Sum_probs=32.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      ..|..+..-.......|++++.++|+.+||+++|+.+.+.+..
T Consensus        43 glt~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le   85 (162)
T 3k0l_A           43 EISLPQFTALSVLAAKPNLSNAKLAERSFIKPQSANKILQDLL   85 (162)
T ss_dssp             TCCHHHHHHHHHHHHCTTCCHHHHHHHHTSCGGGHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4555554322223346899999999999999999999999863

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=80.80  E-value=2.9  Score=30.66  Aligned_cols=42  Identities=12%  Similarity=0.003  Sum_probs=31.3

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .|..+..-......++++++.++|+.+||+++|+.+.+++..
T Consensus        32 lt~~~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~~L~   73 (138)
T 1jgs_A           32 ITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLV   73 (138)
T ss_dssp             SCHHHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcCCCCHHHHHHHHCCChHHHHHHHHHHH
Confidence            455554322222346889999999999999999999999863

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	229
d2coba1	63	a.4.1.15 (A:8-70) Ligand-dependent corepressor (LC	8e-05
d2coba1	63	a.4.1.15 (A:8-70) Ligand-dependent corepressor (LC	3e-04

>d2coba1 a.4.1.15 (A:8-70) Ligand-dependent corepressor (LCoR) {Human (Homo sapiens) [TaxId: 9606]} Length = 63

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Psq domain
domain: Ligand-dependent corepressor (LCoR)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 37.7 bits (87), Expect = 8e-05
 Identities = 18/55 (32%), Positives = 33/55 (60%), Gaps = 2/55 (3%)

Query: 31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTL-WQRAHRLG-IHTPKKEGP 83
          + +  E ++ A+  + +G+MS++KA   YGIP +TL ++   RLG +  P K+  
Sbjct: 5  RQYNSEILEEAISVVMSGKMSVSKAQSIYGIPHSTLEYKVKERLGTLKNPPKKKM 59

>d2coba1 a.4.1.15 (A:8-70) Ligand-dependent corepressor (LCoR) {Human (Homo sapiens) [TaxId: 9606]} Length = 63

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Psq domain
domain: Ligand-dependent corepressor (LCoR)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.8 bits (82), Expect = 3e-04
 Identities = 20/48 (41%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 114 GPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTL-YKIARKEG 160
           G  + +N EIL  A+  + +G +S +KA   YGIP STL YK+  + G
Sbjct: 2   GRYRQYNSEILEEAISVVMSGKMSVSKAQSIYGIPHSTLEYKVKERLG 49

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	229
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	98.84
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	98.76
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	98.46
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	98.44
d1hlva1	66	DNA-binding domain of centromere binding protein B	98.29
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	98.27
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	98.17
d2coba1	63	Ligand-dependent corepressor (LCoR) {Human (Homo s	98.11
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	98.11
d2coba1	63	Ligand-dependent corepressor (LCoR) {Human (Homo s	98.06
d1hlva1	66	DNA-binding domain of centromere binding protein B	97.98
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	97.93
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	97.68
d2oa4a1	93	Uncharacterized protein SPO1678 {Silicibacter pome	97.56
d1g2ha_	61	Transcriptional regulator TyrR, C-terminal domain	97.37
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	97.0
d1etxa_	89	FIS protein {Escherichia coli [TaxId: 562]}	96.92
d2oa4a1	93	Uncharacterized protein SPO1678 {Silicibacter pome	96.8
d1ntca_	91	DNA-binding domain of NTRC {Salmonella typhimurium	96.79
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	96.52
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	96.45
d1g2ha_	61	Transcriptional regulator TyrR, C-terminal domain	96.21
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	95.93
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	95.79
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	95.22
d1q06a_	127	Transcriptional regulator CueR {Escherichia coli [	95.09
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	95.08
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	95.04
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	94.9
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	94.89
d1q06a_	127	Transcriptional regulator CueR {Escherichia coli [	94.86
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	94.79
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	94.65
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.55
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	94.46
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	94.44
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	94.44
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	94.42
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	94.38
d1etxa_	89	FIS protein {Escherichia coli [TaxId: 562]}	94.35
d1jhga_	101	Trp repressor, TrpR {Escherichia coli [TaxId: 562]	94.15
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	94.14
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	93.79
d1r8ea1	118	Transcription activator BmrR {Bacillus subtilis [T	93.74
d1jhga_	101	Trp repressor, TrpR {Escherichia coli [TaxId: 562]	93.71
d1r8ea1	118	Transcription activator BmrR {Bacillus subtilis [T	93.51
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	93.49
d2ezla_	99	Ibeta subdomain of the mu end DNA-binding domain o	93.47
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	93.44
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	93.39
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	93.36
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	93.32
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	93.21
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	93.17
d2ao9a1	120	Phage protein BC1890 {Bacillus cereus [TaxId: 1396	92.87
d2ezla_	99	Ibeta subdomain of the mu end DNA-binding domain o	92.85
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	92.82
d1ntca_	91	DNA-binding domain of NTRC {Salmonella typhimurium	92.74
d1z0xa1	68	Transcriptional regulator EF0787 {Enterococcus fae	92.73
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	92.56
d2g7la1	68	Putative transcriptional regulator SCO7704 {Strept	92.52
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	92.51
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.48
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	92.48
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	92.4
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	92.32
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	92.24
d2g7ga1	65	Putative transcriptional regulator Rha04620 {Rhodo	92.24
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	92.14
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	91.92
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	91.85
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	91.85
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	91.8
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	91.53
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	91.49
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	91.43
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	91.33
d2np5a1	69	Transcriptional regulator RHA1_ro04179 {Rhodococcu	91.27
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	91.24
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	91.2
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	91.05
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	90.79
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	90.64
d2i10a1	69	Putative transcriptional regulator RHA1_ro09068 {R	90.62
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	90.6
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	90.58
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	90.52
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	90.5
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	90.47
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	90.36
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	90.34
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	90.22
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	90.15
d2fbqa1	79	Transcriptional regulator PsrA {Pseudomonas aerugi	90.02
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	89.94
d1t56a1	73	Ethr repressor {Mycobacterium tuberculosis [TaxId:	89.88
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	89.85
d2gfna1	77	Probable transcriptional regulator RHA1_ro04631 {R	89.8
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	89.67
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	89.63
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	89.59
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	89.5
d1jt6a1	71	Multidrug binding protein QacR {Staphylococcus aur	89.46
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	89.37
d2iu5a1	71	Transcriptional activator DhaS {Lactococcus lactis	89.34
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	89.33
d2gena1	70	Probable transcriptional regulator PA1836 {Pseudom	89.24
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	89.13
d1zk8a1	72	Transcriptional regulator BC5000 {Bacillus cereus	89.01
d2fq4a1	69	Transcriptional regulator BC3163 {Bacillus cereus	89.0
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	88.91
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	88.85
d1nera_	74	Ner {Bacteriophage mu [TaxId: 10677]}	88.8
d1v7ba1	74	Transcriptional regulator Cgl2612 {Corynebacterium	88.8
d2vkva1	62	Tetracyclin repressor (Tet-repressor, TetR) {Esche	88.76
d1pb6a1	72	Hypothetical transcriptional regulator YcdC {Esche	88.75
d2hkua1	70	Putative transcriptional regulator RHA1_ro03468 {R	88.73
d2g7sa1	74	Putative transcriptional regulator Atu0279 {Agroba	88.66
d1ui5a1	71	A-factor receptor homolog CprB {Streptomyces coeli	88.63
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	88.51
d1y7ya1	69	Restriction-modification controller protein C.AhdI	88.43
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	88.43
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	88.38
d3c07a1	75	Putative transcriptional regulator SCO4850 {Strept	88.25
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	88.08
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	88.07
d2o7ta1	78	Transcriptional regulator Cgl1640/Cg1846 {Coryneba	87.96
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	87.92
d2i10a1	69	Putative transcriptional regulator RHA1_ro09068 {R	87.84
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	87.78
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	87.76
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	87.67
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	87.53
d2d6ya1	68	Putative regulator SCO4008 {Streptomyces coelicolo	87.51
d1sgma1	73	Putative transcriptional regulator YxaF {Bacillus	87.51
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	87.44
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	87.36
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	87.36
d2fx0a1	73	Hemolysin II regulatory protein, HlyIIR {Bacillus	87.21
d2esna1	89	Probable LysR-type transcriptional regulator PA047	87.16
d2gena1	70	Probable transcriptional regulator PA1836 {Pseudom	87.11
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	87.06
d1t56a1	73	Ethr repressor {Mycobacterium tuberculosis [TaxId:	86.99
d2id3a1	68	Putative transcriptional regulator SCO5951 {Strept	86.95
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	86.88
d1bl0a2	62	MarA {Escherichia coli [TaxId: 562]}	86.68
d1pb6a1	72	Hypothetical transcriptional regulator YcdC {Esche	86.62
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	86.51
d1jt6a1	71	Multidrug binding protein QacR {Staphylococcus aur	86.23
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	86.19
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	85.76
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	85.73
d3c07a1	75	Putative transcriptional regulator SCO4850 {Strept	85.69
d2g3ba1	72	Putative transcriptional regulator {Rhodococcus sp	85.65
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	85.61
d2ao9a1	120	Phage protein BC1890 {Bacillus cereus [TaxId: 1396	85.52
d1b9ma1	127	N-terminal domain of molybdate-dependent transcrip	85.48
d2g7ga1	65	Putative transcriptional regulator Rha04620 {Rhodo	85.34
d2o7ta1	78	Transcriptional regulator Cgl1640/Cg1846 {Coryneba	85.31
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	85.24
d2hkua1	70	Putative transcriptional regulator RHA1_ro03468 {R	85.14
d2hyja1	75	Putative transcriptional regulator SCO4940 {Strept	85.14
d1vi0a1	72	Hypothetical transcriptional regulator YsiA {Bacil	84.84
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	84.83
d2gfna1	77	Probable transcriptional regulator RHA1_ro04631 {R	84.76
d1v7ba1	74	Transcriptional regulator Cgl2612 {Corynebacterium	84.58
d2g7sa1	74	Putative transcriptional regulator Atu0279 {Agroba	84.55
d2id6a1	75	Transcriptional regulator TM1030 {Thermotoga marit	84.33
d2oi8a1	79	Putative regulatory protein Sco4313 {Streptomyces	84.28
d1ixca1	89	LysR-type regulatory protein CbnR {Ralstonia eutro	84.28
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	84.26
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	84.0
d1j9ia_	68	Terminase gpNU1 subunit domain {Bacteriophage lamb	83.93
d2fd5a1	76	Probable transcriptional regulator PA3133 {Pseudom	83.71
d2vkva1	62	Tetracyclin repressor (Tet-repressor, TetR) {Esche	83.7
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	83.66
d2d6ya1	68	Putative regulator SCO4008 {Streptomyces coelicolo	83.49
d2fq4a1	69	Transcriptional regulator BC3163 {Bacillus cereus	83.08
d1rr7a_	94	Middle operon regulator, Mor {Bacteriophage Mu [Ta	82.99
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	82.96
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	82.88
d2fx0a1	73	Hemolysin II regulatory protein, HlyIIR {Bacillus	82.86
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	82.63
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	82.61
d2fbqa1	79	Transcriptional regulator PsrA {Pseudomonas aerugi	82.59
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	82.55
d2np5a1	69	Transcriptional regulator RHA1_ro04179 {Rhodococcu	82.53
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	82.41
d1vi0a1	72	Hypothetical transcriptional regulator YsiA {Bacil	82.39
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	82.21
d1y7ya1	69	Restriction-modification controller protein C.AhdI	82.08
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	82.01
d1ui5a1	71	A-factor receptor homolog CprB {Streptomyces coeli	81.99
d1bl0a2	62	MarA {Escherichia coli [TaxId: 562]}	81.98
d2g3ba1	72	Putative transcriptional regulator {Rhodococcus sp	81.86
d1z0xa1	68	Transcriptional regulator EF0787 {Enterococcus fae	81.78
d1rkta1	81	Hypothetical transcriptional regulator YfiR {Bacil	81.77
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	81.68
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	81.5
d1sgma1	73	Putative transcriptional regulator YxaF {Bacillus	81.44
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	81.14
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	81.13
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	80.93
d2id6a1	75	Transcriptional regulator TM1030 {Thermotoga marit	80.82
d1ic8a2	94	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (H	80.76
d1rr7a_	94	Middle operon regulator, Mor {Bacteriophage Mu [Ta	80.3
d2id3a1	68	Putative transcriptional regulator SCO5951 {Strept	80.28
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	80.1

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=98.84  E-value=5.6e-09  Score=75.02  Aligned_cols=54  Identities=22%  Similarity=0.195  Sum_probs=47.1

Q ss_pred             CCCCCCHHHHHHHHHHHHc-CCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCC
Q psy17316         29 VTKTWTHEDMDAALEALRA-GQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEG   82 (229)
Q Consensus        29 ~~~kyt~e~~~~AI~~~~~-g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~   82 (229)
                      .+++||.|.+.+||+++.+ +|.|+.++|++|||+.+||++|+++|+..+.....
T Consensus         2 ~rk~Ys~EfK~~aV~l~~~~~g~s~~~vA~~lGIs~~tl~~W~k~~~~~~~~~~~   56 (89)
T d2jn6a1           2 PTKTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKYGSNHNVQGT   56 (89)
T ss_dssp             CCCCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHHCCCSTTCSC
T ss_pred             cCCCCCHHHHHHHHHHHHHcCCCcHHHHHHHHCCCHHHHHHHHHHHhhcccccCC
Confidence            4678999999999999986 47899999999999999999999999877654443

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=98.76  E-value=4.9e-09  Score=75.33  Aligned_cols=48  Identities=23%  Similarity=0.225  Sum_probs=42.0

Q ss_pred             CCCCHHHHHHHHHHHHcC-CCCHHHHHHHhCCChHHHHHHHHHhCCccc
Q psy17316        117 KSWNEEILNVALDALRAG-SISANKASKAYGIPSSTLYKIARKEGIRLA  164 (229)
Q Consensus       117 ~kYs~e~k~~AV~~~~~g-~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~  164 (229)
                      ++||+|||.+||.+|+++ +.|+.++|++|||+.+||++|+++++....
T Consensus         4 k~Ys~EfK~~aV~l~~~~~g~s~~~vA~~lGIs~~tl~~W~k~~~~~~~   52 (89)
T d2jn6a1           4 KTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKYGSNHN   52 (89)
T ss_dssp             CCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHHCCCST
T ss_pred             CCCCHHHHHHHHHHHHHcCCCcHHHHHHHHCCCHHHHHHHHHHHhhccc
Confidence            479999999999999874 469999999999999999999999864443

>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=98.46  E-value=1.3e-07  Score=60.18  Aligned_cols=42  Identities=24%  Similarity=0.339  Sum_probs=39.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHH
Q psy17316        114 GPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIA  156 (229)
Q Consensus       114 G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~i  156 (229)
                      |++++.+++.+.+|.+++.+|. |+.+||+.|||+++|||+|+
T Consensus         1 GR~~~lt~~q~~~a~~l~~~G~-s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           1 GRPRAINKHEQEQISRLLEKGH-PRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             CCCCSSCHHHHHHHHHHHHTTC-CHHHHHHHHTCCHHHHHHHS
T ss_pred             CCCCcCCHHHHHHHHHHHHCCC-CHHHHHHHHCcCHHHHHhhC
Confidence            6889999999999999999986 99999999999999999985

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=98.44  E-value=8e-07  Score=67.27  Aligned_cols=94  Identities=13%  Similarity=0.044  Sum_probs=71.2

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHh---CCcccCCC-CCCCCCCCHHHHHHHHHHHHhC-CC
Q psy17316        117 KSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKE---GIRLAQPF-NASPTAWKPEDLEIALEGIRSG-QT  191 (229)
Q Consensus       117 ~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~---g~k~~~~~-~~~~r~~t~e~r~eaV~~~~~~-~~  191 (229)
                      +-|+.+.+.++|+++.+|. |..+||+.|+|+.+|+++|++++   |--...|. ..+++..+++....|++++.++ ..
T Consensus        15 rpLs~dlR~rIv~~~~~G~-s~r~iA~~~~VS~~tV~k~l~r~~~~G~~~~~~~~~~rpr~~t~~~~~~I~~~~~~~P~~   93 (123)
T d1pdnc_          15 RPLPNNIRLKIVEMAADGI-RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIENRIEEYKRSSPGM   93 (123)
T ss_dssp             SCCCHHHHHHHHHHHHTTC-CHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTHHHHHHHTTTTCTTC
T ss_pred             cCCCHHHHHHHHHHHHhcC-CHHHHHHHHCcCHHHHHHHHHHHHccCCcCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCc
Confidence            4588899999999998775 99999999999999999999865   43222232 2355667777778888887774 47


Q ss_pred             cHHHHHHHh----------CCChHHHHHHH
Q psy17316        192 TVQRASAEY----------GIPSGTLYGRC  211 (229)
Q Consensus       192 s~~eAA~~f----------gVp~~tv~~~v  211 (229)
                      +..|+...+          -+|.+|+.+++
T Consensus        94 t~~El~~~L~~egv~~~~~~pSvStI~RiL  123 (123)
T d1pdnc_          94 FSWEIREKLIREGVCDRSTAPSVSAISRLV  123 (123)
T ss_dssp             CHHHHHHHHHHTSSSCSTTCCCHHHHHHHC
T ss_pred             cHHHHHHHHHHcCCCCCCCCCChhhHhhcC
Confidence            788887766          34777887653

>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=98.29  E-value=6.6e-07  Score=60.76  Aligned_cols=45  Identities=11%  Similarity=0.213  Sum_probs=41.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCC-CCHHHHHHHcCCChhhHHHHHHH
Q psy17316         28 TVTKTWTHEDMDAALEALRAGQ-MSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        28 ~~~~kyt~e~~~~AI~~~~~g~-~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.++.+|.+++.++|+.+.+|. +++.+||+.||||++||..|+++
T Consensus         3 ~kRk~LT~~eK~~ii~~~e~g~k~sq~eIA~~fGv~~STvs~IlKn   48 (66)
T d1hlva1           3 PKRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKN   48 (66)
T ss_dssp             CSSCCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHT
T ss_pred             cccccCCHHHHHHHHHHHHcCCcchHHHHHHHhCCChhHHHHHHHH
Confidence            3467799999999999999976 79999999999999999999985

>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=98.27  E-value=8.7e-07  Score=56.26  Aligned_cols=42  Identities=24%  Similarity=0.298  Sum_probs=36.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHH
Q psy17316        169 ASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRC  211 (229)
Q Consensus       169 ~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~v  211 (229)
                      +++++.|+|...+|.+.+.+| ++..++|..||||.+|||+|+
T Consensus         1 GR~~~lt~~q~~~a~~l~~~G-~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           1 GRPRAINKHEQEQISRLLEKG-HPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             CCCCSSCHHHHHHHHHHHHTT-CCHHHHHHHHTCCHHHHHHHS
T ss_pred             CCCCcCCHHHHHHHHHHHHCC-CCHHHHHHHHCcCHHHHHhhC
Confidence            357788998888888888776 899999999999999999997

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=98.17  E-value=5e-06  Score=62.72  Aligned_cols=44  Identities=7%  Similarity=-0.047  Sum_probs=39.9

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .+.++.|....+|+++.+ |+|.++||++|||+++|+++|+++|.
T Consensus        14 GrpLs~dlR~rIv~~~~~-G~s~r~iA~~~~VS~~tV~k~l~r~~   57 (123)
T d1pdnc_          14 GRPLPNNIRLKIVEMAAD-GIRPCVISRQLRVSHGCVSKILNRYQ   57 (123)
T ss_dssp             TSCCCHHHHHHHHHHHHT-TCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CcCCCHHHHHHHHHHHHh-cCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            467899999999999865 78999999999999999999999973

>d2coba1 a.4.1.15 (A:8-70) Ligand-dependent corepressor (LCoR) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Psq domain
domain: Ligand-dependent corepressor (LCoR)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.11  E-value=9.8e-06  Score=52.74  Aligned_cols=44  Identities=34%  Similarity=0.461  Sum_probs=42.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        169 ASPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       169 ~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++.|.|+.+.+.+||..+..|+||+..|...||||.+||-..||
T Consensus         2 GrYR~Yd~d~l~eAv~~V~~G~MSV~rA~~~ygvPHSTLEYKVK   45 (63)
T d2coba1           2 GRYRQYNSEILEEAISVVMSGKMSVSKAQSIYGIPHSTLEYKVK   45 (63)
T ss_dssp             SCSCCCCHHHHHHHHHHHHTTSSCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CcccccCHHHHHHHHHHHHhcceeehhcCccccCCchhhhhhHH
Confidence            46789999999999999999999999999999999999999998

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.11  E-value=2.9e-06  Score=57.01  Aligned_cols=46  Identities=9%  Similarity=-0.064  Sum_probs=41.0

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhcC
Q psy17316        170 SPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRS  216 (229)
Q Consensus       170 ~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~~  216 (229)
                      .+|.|+-|.|..||+++.+| ++..+||++|+||.++|..|++..+.
T Consensus        11 ~GrPls~DLR~Riv~~~~~G-~s~r~aA~rf~VS~s~v~k~l~r~re   56 (63)
T d1k78a1          11 NGRPLPDVVRQRIVELAHQG-VRPCDISRQLRVSHGCVSKILGRYYE   56 (63)
T ss_dssp             TTSCCCHHHHHHHHHHHHTT-CCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCcCCHHHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            46789999999999998866 99999999999999999999995444

>d2coba1 a.4.1.15 (A:8-70) Ligand-dependent corepressor (LCoR) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Psq domain
domain: Ligand-dependent corepressor (LCoR)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.06  E-value=1.3e-05  Score=52.23  Aligned_cols=52  Identities=35%  Similarity=0.495  Sum_probs=45.7

Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCcccC
Q psy17316        114 GPTKSWNEEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIRLAQ  165 (229)
Q Consensus       114 G~~~kYs~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~  165 (229)
                      |+..+|+.+.+.+||.+|..|++|+..+..-||||.|||-=.+|+....+..
T Consensus         2 GrYR~Yd~d~l~eAv~~V~~G~MSV~rA~~~ygvPHSTLEYKVKER~~~Lk~   53 (63)
T d2coba1           2 GRYRQYNSEILEEAISVVMSGKMSVSKAQSIYGIPHSTLEYKVKERLGTLKN   53 (63)
T ss_dssp             SCSCCCCHHHHHHHHHHHHTTSSCHHHHHHHHTCCHHHHHHHHHHHTTTTSS
T ss_pred             CcccccCHHHHHHHHHHHHhcceeehhcCccccCCchhhhhhHHhhhhhhcc
Confidence            5678999999999999999999999999999999999988888876444444

>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=97.98  E-value=9.5e-06  Score=54.87  Aligned_cols=43  Identities=12%  Similarity=0.134  Sum_probs=39.6

Q ss_pred             CCCCCCHHHHHHHHHHHHhCC-CcHHHHHHHhCCChHHHHHHHH
Q psy17316        170 SPTAWKPEDLEIALEGIRSGQ-TTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       170 ~~r~~t~e~r~eaV~~~~~~~-~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+..|.+++.+|++.+..|. ++..++|+.||||.+||-.|+|
T Consensus         4 kRk~LT~~eK~~ii~~~e~g~k~sq~eIA~~fGv~~STvs~IlK   47 (66)
T d1hlva1           4 KRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILK   47 (66)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHH
T ss_pred             ccccCCHHHHHHHHHHHHcCCcchHHHHHHHhCCChhHHHHHHH
Confidence            356789999999999999997 6899999999999999999998

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.93  E-value=1.2e-05  Score=53.90  Aligned_cols=47  Identities=6%  Similarity=-0.055  Sum_probs=41.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         27 LTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        27 ~~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      ...-+.||.|-...+|+++.+ |+|.++||++|+|+++|+.+|++++-
T Consensus         9 ~~~GrPls~DLR~Riv~~~~~-G~s~r~aA~rf~VS~s~v~k~l~r~r   55 (63)
T d1k78a1           9 FVNGRPLPDVVRQRIVELAHQ-GVRPCDISRQLRVSHGCVSKILGRYY   55 (63)
T ss_dssp             CCTTSCCCHHHHHHHHHHHHT-TCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             ccCCCcCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            344578999999999998865 78999999999999999999999974

>d1umqa_ a.4.1.12 (A:) Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain {Rhodobacter sphaeroides [TaxId: 1063]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=97.68  E-value=2.8e-05  Score=51.38  Aligned_cols=39  Identities=5%  Similarity=0.004  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGI   75 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi   75 (229)
                      ++..+++.+...+-.+.++|+.+||+++|||+++++|++
T Consensus        21 Er~~I~~aL~~~~gn~~~aA~~LGIsR~TL~rkmkky~~   59 (60)
T d1umqa_          21 RWEHIQRIYEMCDRNVSETARRLNMHRRTLQRILAKRSP   59 (60)
T ss_dssp             HHHHHHHHHHHTTSCHHHHHHHHTSCHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHhcCcHHHHHHHHCCCHHHHHHHHHHcCC
Confidence            445555566655668999999999999999999999976

>d2oa4a1 a.4.12.3 (A:1-93) Uncharacterized protein SPO1678 {Silicibacter pomeroyi [TaxId: 89184]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: SPO1678-like
domain: Uncharacterized protein SPO1678
species: Silicibacter pomeroyi [TaxId: 89184]

Probab=97.56  E-value=0.00012  Score=52.28  Aligned_cols=57  Identities=18%  Similarity=0.257  Sum_probs=52.5

Q ss_pred             CCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCC
Q psy17316         27 LTVTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGP   83 (229)
Q Consensus        27 ~~~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~   83 (229)
                      +.-++.|+...|.+.|.++..|.+|+.+|+++|||+..-++.|.+.+.-.|..+++.
T Consensus        28 ~~~trRWva~RKaaVV~av~~Gl~S~~EAcrrY~LS~eEf~~W~~a~~~hGe~aLr~   84 (93)
T d2oa4a1          28 PANTRRWVASRKIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVSALAEHGKDALKV   84 (93)
T ss_dssp             CSCCSCCCHHHHHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHHHHHCCCSSSSCC
T ss_pred             CcccccccHHHHHHHHHHHHcCcCCHHHHHHHhCCCHHHHHHHHHHHHHHhHHHHHH
Confidence            455799999999999999999999999999999999999999999998888777764

>d1g2ha_ a.4.1.12 (A:) Transcriptional regulator TyrR, C-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Transcriptional regulator TyrR, C-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=97.37  E-value=0.00028  Score=46.52  Aligned_cols=41  Identities=15%  Similarity=0.122  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         35 HEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        35 ~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      .-++..+.+++...| +..++|+.+||+++||++++++|||.
T Consensus        20 ~~Er~~I~~aL~~~g-n~~~aA~~Lgisr~tL~rKlkk~gi~   60 (61)
T d1g2ha_          20 FYEAQVLKLFYAEYP-STRKLAQRLGVSHTAIANKLKQYGIG   60 (61)
T ss_dssp             HHHHHHHHHHHHHSC-SHHHHHHHTTSCTHHHHHHHHTTTCC
T ss_pred             HHHHHHHHHHHHHCC-CHHHHHHHHCCCHHHHHHHHHHhCCC
Confidence            334443344444444 78899999999999999999999984

>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=97.00  E-value=0.0031  Score=44.73  Aligned_cols=88  Identities=20%  Similarity=0.174  Sum_probs=62.4

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhcc
Q psy17316         34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAY  113 (229)
Q Consensus        34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~  113 (229)
                      ++=+-..|+..+.+-++|..+||+++|.++++|.++++-.+.            +++    +.++|.+|.++..++=...
T Consensus         4 ~piEeA~a~~~L~e~g~t~~~iA~~~Gks~~~V~~~LrLl~L------------~~~----v~~~l~~g~Is~ghAr~L~   67 (93)
T d1vz0a1           4 SPVEEARGYQALLEMGLTQEEVARRVGKARSTVANALRLLQL------------PPE----ALEALERGEITAGHARALL   67 (93)
T ss_dssp             CHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHGGGS------------CHH----HHHHHHTTSSCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCCHHHHHHHHccchHHHHHHHHHHHH------------HHH----HHHHHHcCCccHHHHHHHH
Confidence            344555677777777899999999999999999999995433            233    5577788888876655444


Q ss_pred             CCCCCCCHHHHHHHHHHHHcCCCCHHHH
Q psy17316        114 GPTKSWNEEILNVALDALRAGSISANKA  141 (229)
Q Consensus       114 G~~~kYs~e~k~~AV~~~~~g~~S~~~~  141 (229)
                      +.+.    +....+++.+..+++|++++
T Consensus        68 ~l~~----~~q~~~~~~ii~~~lSVR~~   91 (93)
T d1vz0a1          68 MLEP----EDRLWGLKEILEKGLSVRQA   91 (93)
T ss_dssp             TSCG----GGHHHHHHHHHHTCCCHHHH
T ss_pred             CCCh----HHHHHHHHHHHHcCCCHHHh
Confidence            4442    23345566677777888875

>d1etxa_ a.4.1.12 (A:) FIS protein {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: FIS protein
species: Escherichia coli [TaxId: 562]

Probab=96.92  E-value=0.00062  Score=48.06  Aligned_cols=36  Identities=19%  Similarity=0.283  Sum_probs=29.4

Q ss_pred             HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      +..++...+-.+.++|+.+||+++|||+++++||+.
T Consensus        54 i~~aL~~~~gn~~~aA~~LGisR~tL~~klk~~gi~   89 (89)
T d1etxa_          54 LDMVMQYTRGNATRAALMMGINRGTLRKKLKKYGMN   89 (89)
T ss_dssp             HHHHHHHTTTCHHHHHHHHTSCHHHHHHHHHHTTCC
T ss_pred             HHHHHHHcCCcHHHHHHHHCCCHHHHHHHHHHhCcC
Confidence            333444455589999999999999999999999974

>d2oa4a1 a.4.12.3 (A:1-93) Uncharacterized protein SPO1678 {Silicibacter pomeroyi [TaxId: 89184]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: SPO1678-like
domain: Uncharacterized protein SPO1678
species: Silicibacter pomeroyi [TaxId: 89184]

Probab=96.80  E-value=0.0015  Score=46.44  Aligned_cols=43  Identities=16%  Similarity=0.333  Sum_probs=41.4

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        170 SPTAWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       170 ~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..+.|+.+.+.+||..+..|..|..||+..|+||-+-.+.|.+
T Consensus        30 ~trRWva~RKaaVV~av~~Gl~S~~EAcrrY~LS~eEf~~W~~   72 (93)
T d2oa4a1          30 NTRRWVASRKIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVS   72 (93)
T ss_dssp             CCSCCCHHHHHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHH
T ss_pred             ccccccHHHHHHHHHHHHcCcCCHHHHHHHhCCCHHHHHHHHH
Confidence            4678999999999999999999999999999999999999998

>d1ntca_ a.4.1.12 (A:) DNA-binding domain of NTRC {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: DNA-binding domain of NTRC
species: Salmonella typhimurium [TaxId: 90371]

Probab=96.79  E-value=0.00039  Score=48.99  Aligned_cols=33  Identities=30%  Similarity=0.309  Sum_probs=27.2

Q ss_pred             HHHcCCCCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         44 ALRAGQMSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      .+...+-.+.++|+.+||+|+||++++++||++
T Consensus        59 aL~~~~Gn~~~AA~~LGI~R~TL~~Klk~~gid   91 (91)
T d1ntca_          59 ALRHTQGHKQEAARLLGWGAATLTAKLKELGME   91 (91)
T ss_dssp             HHHHTTTCTTHHHHHTTCCHHHHHHHHHHHHHC
T ss_pred             HHHHhCCcHHHHHHHHCCCHHHHHHHHHHHCcC
Confidence            333344478899999999999999999999874

>d1umqa_ a.4.1.12 (A:) Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain {Rhodobacter sphaeroides [TaxId: 1063]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=96.52  E-value=0.0021  Score=41.94  Aligned_cols=41  Identities=10%  Similarity=-0.078  Sum_probs=36.2

Q ss_pred             CCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316        173 AWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       173 ~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      ...+-|+..|++.+..++-|..+||...|||+.|||++++.
T Consensus        16 ~l~~~Er~~I~~aL~~~~gn~~~aA~~LGIsR~TL~rkmkk   56 (60)
T d1umqa_          16 SADRVRWEHIQRIYEMCDRNVSETARRLNMHRRTLQRILAK   56 (60)
T ss_dssp             CHHHHHHHHHHHHHHHTTSCHHHHHHHHTSCHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHHHHhcCcHHHHHHHHCCCHHHHHHHHHH
Confidence            33456889999999999999999999999999999999873

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=96.45  E-value=0.0019  Score=39.41  Aligned_cols=31  Identities=10%  Similarity=0.190  Sum_probs=27.1

Q ss_pred             HHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         42 LEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        42 I~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      |..+.+.|++..+||+++||+++|||+-+..
T Consensus        11 V~~L~~~G~gat~IAk~lgI~R~SVYR~L~~   41 (43)
T d1gdta1          11 VLNMWQQGLGASHISKTMNIARSTVYKVINE   41 (43)
T ss_dssp             HHHHHHTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHHHHcCCCHHHHHHHHCCCHHHHHHHHhh
Confidence            5566677999999999999999999998864

>d1g2ha_ a.4.1.12 (A:) Transcriptional regulator TyrR, C-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Transcriptional regulator TyrR, C-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=96.21  E-value=0.0023  Score=41.87  Aligned_cols=38  Identities=16%  Similarity=0.304  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHHhCCc
Q psy17316        121 EEILNVALDALRAGSISANKASKAYGIPSSTLYKIARKEGIR  162 (229)
Q Consensus       121 ~e~k~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~~g~k  162 (229)
                      .+.+..|++..    .+..++|+..||+++|||+.++++|+.
T Consensus        23 r~~I~~aL~~~----gn~~~aA~~Lgisr~tL~rKlkk~gi~   60 (61)
T d1g2ha_          23 AQVLKLFYAEY----PSTRKLAQRLGVSHTAIANKLKQYGIG   60 (61)
T ss_dssp             HHHHHHHHHHS----CSHHHHHHHTTSCTHHHHHHHHTTTCC
T ss_pred             HHHHHHHHHHC----CCHHHHHHHHCCCHHHHHHHHHHhCCC
Confidence            34455555542    378899999999999999999999975

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=95.93  E-value=0.01  Score=36.02  Aligned_cols=33  Identities=12%  Similarity=0.096  Sum_probs=26.6

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +.+| ..+.+.++...++|++.||++.|||+.++
T Consensus         8 ~~~V-~~L~~~G~gat~IAk~lgI~R~SVYR~L~   40 (43)
T d1gdta1           8 RDAV-LNMWQQGLGASHISKTMNIARSTVYKVIN   40 (43)
T ss_dssp             HHHH-HHHHHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHH-HHHHHcCCCHHHHHHHHCCCHHHHHHHHh
Confidence            3344 44455569999999999999999999886

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.79  E-value=0.0068  Score=39.63  Aligned_cols=41  Identities=7%  Similarity=0.079  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHhCC-CcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        177 EDLEIALEGIRSGQ-TTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       177 e~r~eaV~~~~~~~-~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      +-+.++++.+.+++ .|..+.|.+||||..|||+.++ +...|
T Consensus         5 ~~~~~iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G   47 (63)
T d1biaa1           5 TVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWG   47 (63)
T ss_dssp             HHHHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            44677888887766 7999999999999999999998 55555

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=95.22  E-value=0.022  Score=36.93  Aligned_cols=29  Identities=10%  Similarity=0.276  Sum_probs=26.5

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .++.+|+.++|+.+|||.+|++++++++.
T Consensus        16 ~n~r~s~~~iA~~lgis~~tv~~Ri~~L~   44 (63)
T d2cfxa1          16 KDSRLSMRELGRKIKLSPPSVTERVRQLE   44 (63)
T ss_dssp             HCSCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            37899999999999999999999999863

>d1q06a_ a.6.1.3 (A:) Transcriptional regulator CueR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Transcriptional regulator CueR
species: Escherichia coli [TaxId: 562]

Probab=95.09  E-value=0.037  Score=40.37  Aligned_cols=24  Identities=13%  Similarity=0.192  Sum_probs=22.1

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      |.+.++|+.+|||..||+.|-+..
T Consensus         1 m~Ige~A~~~gvs~~TlR~Ye~~G   24 (127)
T d1q06a_           1 MNISDVAKITGLTSKAIRFYEEKG   24 (127)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHTT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcC
Confidence            688999999999999999998873

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=95.08  E-value=0.012  Score=38.31  Aligned_cols=33  Identities=21%  Similarity=0.444  Sum_probs=28.0

Q ss_pred             HHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         41 ALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        41 AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .|+.+ .++.+|+.++|+++|+|.+|++++++++
T Consensus        10 IL~~L~~~~r~s~~eiA~~l~ls~~~v~~Ri~rL   43 (63)
T d2cg4a1          10 ILEALMGNARTAYAELAKQFGVSPETIHVRVEKM   43 (63)
T ss_dssp             HHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            34433 4689999999999999999999999985

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.04  E-value=0.011  Score=38.51  Aligned_cols=38  Identities=13%  Similarity=0.129  Sum_probs=29.9

Q ss_pred             HHHHHHHHcCC-CCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         39 DAALEALRAGQ-MSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        39 ~~AI~~~~~g~-~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      .+.++.+.++. +|..++|+++||+++|+++.+....-.
T Consensus         8 ~~iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~   46 (63)
T d1biaa1           8 LKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDW   46 (63)
T ss_dssp             HHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHCCcCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            45555555544 899999999999999999999986433

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.90  E-value=0.025  Score=36.83  Aligned_cols=42  Identities=10%  Similarity=0.085  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHhCC--CcHHHHHHHhCCChHHHHHHHH-hhcCCC
Q psy17316        177 EDLEIALEGIRSGQ--TTVQRASAEYGIPSGTLYGRCK-LSRSTP  218 (229)
Q Consensus       177 e~r~eaV~~~~~~~--~s~~eAA~~fgVp~~tv~~~vk-~~~~~~  218 (229)
                      |-+.+|++.+.+++  .+..+.|.+||||..|||+-++ +...|-
T Consensus         7 eR~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L~~~G~   51 (65)
T d1j5ya1           7 ERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGY   51 (65)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence            44567888887643  7999999999999999999988 555553

>d1r8da_ a.6.1.3 (A:) Multidrug transporter activator MtaN {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Multidrug transporter activator MtaN
species: Bacillus subtilis [TaxId: 1423]

Probab=94.89  E-value=0.032  Score=39.65  Aligned_cols=68  Identities=7%  Similarity=0.029  Sum_probs=50.0

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCC-cccCCCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCCh
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGI-RLAQPFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIPS  204 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~-k~~~~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp~  204 (229)
                      .++.++|+.+|||..||+-|-+. |. .......+..|.|+++  .++..|..+.+-+++..++...++.+.
T Consensus         3 ytI~e~A~~~gvs~~tlR~Ye~~-GLl~p~~r~~~gyR~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~~~~   73 (109)
T d1r8da_           3 YQVKQVAEISGVSIRTLHHYDNI-ELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRLDEIKEMLDHPN   73 (109)
T ss_dssp             BCHHHHHHHHSCCHHHHHHHHHT-TSSCCSEECTTCCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHHCTT
T ss_pred             ccHHHHHHHHCcCHHHHHHHHHc-CCcCCcccCCcccccccHHHHHHHHHHHHHHHcCCCHHHHHHHHhccC
Confidence            47899999999999999999974 53 2221112346788876  455777778887799999988876543

>d1q06a_ a.6.1.3 (A:) Transcriptional regulator CueR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Transcriptional regulator CueR
species: Escherichia coli [TaxId: 562]

Probab=94.86  E-value=0.039  Score=40.23  Aligned_cols=65  Identities=11%  Similarity=0.122  Sum_probs=47.9

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccC-CCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQ-PFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYG  201 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~-~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fg  201 (229)
                      |.+.++|+.+|||..||+-|-+. |.-... ...+..|.|+++  .++..|..+..-+++..++...+.
T Consensus         1 m~Ige~A~~~gvs~~TlR~Ye~~-GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~   68 (127)
T d1q06a_           1 MNISDVAKITGLTSKAIRFYEEK-GLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVN   68 (127)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHT-TCSCCCEECTTSCEECCHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc-CCCCCCccCCcCcccchHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            57889999999999999999884 532211 112346778765  577788888888899999876553

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=94.79  E-value=0.02  Score=37.37  Aligned_cols=39  Identities=3%  Similarity=-0.056  Sum_probs=30.1

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .++.+..-.+ .+.-.++|+.+||..+|||.+|++.++++
T Consensus        22 L~~~~r~v~~-l~~~~~~s~~eIA~~lgis~~tv~~~~~r   60 (71)
T d1rp3a2          22 LPEREKLVIQ-LIFYEELPAKEVAKILETSVSRVSQLKAK   60 (71)
T ss_dssp             SCHHHHHHHH-HHHTSCCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred             CCHHHHHHHH-HHHhHhCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4455444444 44456899999999999999999999886

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=94.65  E-value=0.021  Score=40.34  Aligned_cols=36  Identities=8%  Similarity=0.084  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|.+|+..+..+++++.++|..+|+|.+||...++
T Consensus        23 p~Rl~Il~~L~~~~~~v~ela~~l~is~stvS~HL~   58 (98)
T d1r1ta_          23 PNRLRLLSLLARSELCVGDLAQAIGVSESAVSHQLR   58 (98)
T ss_dssp             HHHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            459999999999999999999999999999999998

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=94.55  E-value=0.03  Score=35.91  Aligned_cols=28  Identities=21%  Similarity=0.399  Sum_probs=26.0

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .++.+|+.++|++.|+|.+|++++++++
T Consensus        14 ~n~r~s~~~lA~~~gls~~~v~~Ri~~L   41 (60)
T d1i1ga1          14 KDARTPFTEIAKKLGISETAVRKRVKAL   41 (60)
T ss_dssp             HCTTCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4788999999999999999999999985

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=94.46  E-value=0.031  Score=39.16  Aligned_cols=37  Identities=11%  Similarity=0.094  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...|.+|++.+..|.+++.+++..+|+|.++|-..++
T Consensus        17 d~~Rl~Il~~L~~~~~~v~el~~~l~~s~~~vS~HL~   53 (94)
T d1r1ua_          17 DYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLK   53 (94)
T ss_dssp             SHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHH
Confidence            4569999999999999999999999999999999998

>d1r8da_ a.6.1.3 (A:) Multidrug transporter activator MtaN {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Multidrug transporter activator MtaN
species: Bacillus subtilis [TaxId: 1423]

Probab=94.44  E-value=0.055  Score=38.32  Aligned_cols=68  Identities=7%  Similarity=0.071  Sum_probs=45.4

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      .++.++|+.+||+..||+.|-+. |+-.|.....+                              ....|++++  ++..
T Consensus         3 ytI~e~A~~~gvs~~tlR~Ye~~-GLl~p~~r~~~------------------------------gyR~Y~~~~~~~l~~   51 (109)
T d1r8da_           3 YQVKQVAEISGVSIRTLHHYDNI-ELLNPSALTDA------------------------------GYRLYSDADLERLQQ   51 (109)
T ss_dssp             BCHHHHHHHHSCCHHHHHHHHHT-TSSCCSEECTT------------------------------CCEEBCHHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHHc-CCcCCcccCCc------------------------------ccccccHHHHHHHHH
Confidence            57899999999999999999977 44333222111                              133444444  3455


Q ss_pred             HHHHHcCCCCHHHHHHHhCCC
Q psy17316        128 LDALRAGSISANKASKAYGIP  148 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gIp  148 (229)
                      |..+.+-++|+.+|...+.-+
T Consensus        52 I~~lr~~G~sl~eI~~~l~~~   72 (109)
T d1r8da_          52 ILFFKEIGFRLDEIKEMLDHP   72 (109)
T ss_dssp             HHHHHHTTCCHHHHHHHHHCT
T ss_pred             HHHHHHcCCCHHHHHHHHhcc
Confidence            666677678999887766543

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=94.44  E-value=0.031  Score=36.39  Aligned_cols=34  Identities=3%  Similarity=-0.078  Sum_probs=28.2

Q ss_pred             HHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -.+|+..+--.++|+.++|..+|||.+||+.++.
T Consensus        26 ~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~~~   59 (71)
T d1rp3a2          26 EKLVIQLIFYEELPAKEVAKILETSVSRVSQLKA   59 (71)
T ss_dssp             HHHHHHHHHTSCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHhHhCCHHHHHHHHCCCHHHHHHHHH
Confidence            4455666566669999999999999999999876

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=94.42  E-value=0.028  Score=36.41  Aligned_cols=26  Identities=8%  Similarity=0.073  Sum_probs=24.2

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+.|+|+.++|+..||+.+|+.+|.+
T Consensus        11 ~~~g~tq~elA~~~gis~~~is~~e~   36 (66)
T d1utxa_          11 EKKKISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             HHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHhcccCHHHHHHHHc
Confidence            46799999999999999999999986

>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Regulatory protein C.BclI
species: Bacillus caldolyticus [TaxId: 1394]

Probab=94.38  E-value=0.046  Score=36.25  Aligned_cols=32  Identities=13%  Similarity=0.102  Sum_probs=26.0

Q ss_pred             HHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         40 AALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        40 ~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.|+.+ ...|+|+.++|+.+||++++|.+|..
T Consensus        13 ~~ik~~R~~~gltq~~lA~~~gis~~~i~~~e~   45 (77)
T d2b5aa1          13 RTLKKIRTQKGVSQEELADLAGLHRTYISEVER   45 (77)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            334433 35789999999999999999999976

>d1etxa_ a.4.1.12 (A:) FIS protein {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: FIS protein
species: Escherichia coli [TaxId: 562]

Probab=94.35  E-value=0.032  Score=38.79  Aligned_cols=37  Identities=22%  Similarity=0.195  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +-|+.-|.+.+...+-+..+||+..|||++|+|++++
T Consensus        48 e~E~~~i~~aL~~~~gn~~~aA~~LGisR~tL~~klk   84 (89)
T d1etxa_          48 EVEQPLLDMVMQYTRGNATRAALMMGINRGTLRKKLK   84 (89)
T ss_dssp             HHHHHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHCCCHHHHHHHHH
Confidence            3467778888888888899999999999999999987

>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=94.15  E-value=0.027  Score=40.29  Aligned_cols=35  Identities=20%  Similarity=0.193  Sum_probs=29.6

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ..+++..+..|.+|+++|++.+||+.+||.|-.+-
T Consensus        47 R~~ia~~L~~G~~s~reI~~~~gvs~aTItR~s~~   81 (101)
T d1jhga_          47 RVRIIEELLRGEMSQRELKNELGAGIATITRGSNS   81 (101)
T ss_dssp             HHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHhCCChHHHHHHHHH
Confidence            35677788899899999999999999999875553

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=94.14  E-value=0.046  Score=35.50  Aligned_cols=33  Identities=18%  Similarity=0.201  Sum_probs=27.2

Q ss_pred             HHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         40 AALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        40 ~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .++...--.++|+.+||..+|||.+|++.++++
T Consensus        25 ~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~r   57 (68)
T d1or7a1          25 MAITLRELDGLSYEEIAAIMDCPVGTVRSRIFR   57 (68)
T ss_dssp             HHHHHHHTTCCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            344444456899999999999999999999886

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF1790-like
domain: Transcriptional regulatory protein PF1790
species: Pyrococcus furiosus [TaxId: 2261]

Probab=93.79  E-value=0.035  Score=43.41  Aligned_cols=36  Identities=17%  Similarity=0.098  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .-|.+|++.+.+|.+++.++|..+|||.++|+.+++
T Consensus        15 ~~R~~Il~~L~~~~~~~~ela~~l~~s~~~v~~HL~   50 (194)
T d2p4wa1          15 ETRRRILFLLTKRPYFVSELSRELGVGQKAVLEHLR   50 (194)
T ss_dssp             HHHHHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            458999999999999999999999999999999998

>d1r8ea1 a.6.1.3 (A:3-120) Transcription activator BmrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Transcription activator BmrR
species: Bacillus subtilis [TaxId: 1423]

Probab=93.74  E-value=0.082  Score=37.84  Aligned_cols=78  Identities=12%  Similarity=0.143  Sum_probs=52.2

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHhhcchhhhhhhhccCCCCCCCHHH--HHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALRAGSISANKASKAYGPTKSWNEEI--LNVA  127 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~~G~ls~~~~~~~~G~~~kYs~e~--k~~A  127 (229)
                      .++.++|+.+||+..||+.|-+ .|+-.|.......                             ...-|++++  ++..
T Consensus         4 ytI~evA~~~gvs~~tlR~Ye~-~GLl~P~~~r~~~-----------------------------gyR~Y~~~~l~~l~~   53 (118)
T d1r8ea1           4 YSIGEVSKLANVSIKALRYYDK-IDLFKPAYVDPDT-----------------------------SYRYYTDSQLIHLDL   53 (118)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHH-TTSSCCSEECTTT-----------------------------CCEEEETGGGGHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHH-cCCcccccccCCC-----------------------------CcccccHHHHHHHHH
Confidence            4688999999999999999996 4765443321100                             112344433  4566


Q ss_pred             HHHHHcCCCCHHHHHHHhCCChHHHHHHHH
Q psy17316        128 LDALRAGSISANKASKAYGIPSSTLYKIAR  157 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gIp~sTL~~~ik  157 (229)
                      |..+.+-++|+.+|-...+.+...+..++.
T Consensus        54 I~~lr~~g~sl~eIk~~l~~~~~~~~~~l~   83 (118)
T d1r8ea1          54 IKSLKYIGTPLEEMKKAQDLEMEELFAFYT   83 (118)
T ss_dssp             HHHHHHTTCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHHHcCCCHHHHHHHHccCHHHHHHHHH
Confidence            777777788999998887776655555443

>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=93.71  E-value=0.057  Score=38.55  Aligned_cols=36  Identities=14%  Similarity=0.140  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|.+|++.+.+|+++|.+++.++|||-.||-+-.+
T Consensus        45 a~R~~ia~~L~~G~~s~reI~~~~gvs~aTItR~s~   80 (101)
T d1jhga_          45 GTRVRIIEELLRGEMSQRELKNELGAGIATITRGSN   80 (101)
T ss_dssp             HHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHhCCChHHHHHHHH
Confidence            358899999999999999999999999999987544

>d1r8ea1 a.6.1.3 (A:3-120) Transcription activator BmrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Transcription activator BmrR
species: Bacillus subtilis [TaxId: 1423]

Probab=93.51  E-value=0.094  Score=37.51  Aligned_cols=76  Identities=11%  Similarity=0.011  Sum_probs=56.0

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCc-ccC-CCCCCCCCCCHH--HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIR-LAQ-PFNASPTAWKPE--DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRC  211 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k-~~~-~~~~~~r~~t~e--~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~v  211 (229)
                      .++.++|+.+||+..||+-|-+ .|+- +.. ......|-|+++  .++..|..+.+-+++..++...++.+...+..++
T Consensus         4 ytI~evA~~~gvs~~tlR~Ye~-~GLl~P~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~g~sl~eIk~~l~~~~~~~~~~l   82 (118)
T d1r8ea1           4 YSIGEVSKLANVSIKALRYYDK-IDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEMEELFAFY   82 (118)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHH-TTSSCCSEECTTTCCEEEETGGGGHHHHHHHHHHTTCCHHHHHHHTTSCHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHH-cCCcccccccCCCCcccccHHHHHHHHHHHHHHHcCCCHHHHHHHHccCHHHHHHHH
Confidence            4789999999999999999996 5643 211 111224556443  6788888899888999999999988877776655


Q ss_pred             H
Q psy17316        212 K  212 (229)
Q Consensus       212 k  212 (229)
                      .
T Consensus        83 ~   83 (118)
T d1r8ea1          83 T   83 (118)
T ss_dssp             H
T ss_pred             H
Confidence            4

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=93.49  E-value=0.022  Score=36.75  Aligned_cols=25  Identities=28%  Similarity=0.312  Sum_probs=22.9

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .-|||+.++|+.+||+.+||.+|=.
T Consensus        10 ~~gltQ~elA~~lGvs~~tvs~~E~   34 (62)
T d2ppxa1          10 ALKLTQEEFSARYHIPLGTLRDWEQ   34 (62)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence            4589999999999999999999955

>d2ezla_ a.4.1.2 (A:) Ibeta subdomain of the mu end DNA-binding domain of phage mu transposase {Bacteriophage mu [TaxId: 10677]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: Ibeta subdomain of the mu end DNA-binding domain of phage mu transposase
species: Bacteriophage mu [TaxId: 10677]

Probab=93.47  E-value=0.054  Score=38.52  Aligned_cols=34  Identities=15%  Similarity=0.187  Sum_probs=27.9

Q ss_pred             HHHHHHHHcCCCCHH----HHHHHcCCChhhHHHHHHH
Q psy17316         39 DAALEALRAGQMSLT----KASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        39 ~~AI~~~~~g~~S~~----~aA~~~gIp~sTL~~~i~~   72 (229)
                      +.+|+.+.++|+|..    .+|.+|||+.+||++|..+
T Consensus        39 l~~V~~L~~~G~~~~~A~~~VA~~~~vs~~TL~nW~~~   76 (99)
T d2ezla_          39 VQAADEMLNQGISTKTAFATVAGHYQVSASTLRDKYYQ   76 (99)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHSSSCHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCcHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence            345666778898864    6789999999999999996

>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=93.44  E-value=0.057  Score=35.16  Aligned_cols=32  Identities=19%  Similarity=0.115  Sum_probs=28.8

Q ss_pred             HHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        180 EIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       180 ~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+|+.++..| ++..++|...+||..||...+.
T Consensus        12 ~~vl~ll~~G-~s~~eIA~~l~iS~~TV~~~~~   43 (67)
T d1a04a1          12 RDILKLIAQG-LPNKMIARRLDITESTVKVHVK   43 (67)
T ss_dssp             HHHHHHHHTT-CCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhC-CCHHHHHHHHCCCHHHHHHHHH
Confidence            5788888877 8999999999999999999886

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein PH1932
domain: Hypothetical protein PH1932
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=93.39  E-value=0.041  Score=42.59  Aligned_cols=36  Identities=19%  Similarity=0.272  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|.+|++.+..|.+++.++|..+|+|.++|+.+++
T Consensus        19 p~R~~Il~~L~~~~~s~~ela~~lg~s~~~v~~hl~   54 (190)
T d1ulya_          19 DTRRKILKLLRNKEMTISQLSEILGKTPQTIYHHIE   54 (190)
T ss_dssp             HHHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            458999999999999999999999999999999998

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=93.36  E-value=0.088  Score=33.45  Aligned_cols=34  Identities=24%  Similarity=0.440  Sum_probs=28.2

Q ss_pred             HHHHHHH-cCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         40 AALEALR-AGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        40 ~AI~~~~-~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..|+.+. ++.+|+.++|+++|++.+|++++++++
T Consensus         7 ~Il~~L~~n~r~s~~eiA~~l~ls~~~v~~Ri~~L   41 (60)
T d2cyya1           7 KIIKILQNDGKAPLREISKITGLAESTIHERIRKL   41 (60)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3444443 678999999999999999999999985

>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro 434
species: Bacteriophage 434 [TaxId: 10712]

Probab=93.32  E-value=0.12  Score=33.05  Aligned_cols=26  Identities=15%  Similarity=0.116  Sum_probs=23.6

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+-++|+.++|+..||+++|+.+|-+
T Consensus        13 ~~~gltq~~lA~~~gvs~~ti~~~E~   38 (65)
T d2croa_          13 IALKMTQTELATKAGVKQQSIQLIEA   38 (65)
T ss_dssp             HHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCcCHhHHHHHHC
Confidence            35689999999999999999999965

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

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

Probab=93.21  E-value=0.069  Score=38.22  Aligned_cols=44  Identities=11%  Similarity=0.022  Sum_probs=38.8

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         30 TKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        30 ~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +...|+-+...++..+.+-|.|..+||+++|+++++|.+.++-.
T Consensus        11 R~~L~p~e~A~a~~~l~~~g~s~~eiA~~~G~s~~~V~~~l~L~   54 (114)
T d1r71a_          11 RNELTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVTLL   54 (114)
T ss_dssp             TTCCCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHGGG
T ss_pred             ccCCCHHHHHHHHHHHHHhCCCHHHHHHHHCCcHHHHHHHHHHh
Confidence            45678889999999888878899999999999999999998843

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=93.17  E-value=0.074  Score=34.42  Aligned_cols=35  Identities=23%  Similarity=0.227  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .-.+|+....-.++|+.++|..+|||.+||..++.
T Consensus        22 ~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~   56 (68)
T d1or7a1          22 DLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIF   56 (68)
T ss_dssp             HHHHHHHHHHTTCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34456666666679999999999999999999886

>d2ao9a1 a.4.1.17 (A:13-132) Phage protein BC1890 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Nanomeric phage protein-like
domain: Phage protein BC1890
species: Bacillus cereus [TaxId: 1396]

Probab=92.87  E-value=0.087  Score=37.91  Aligned_cols=42  Identities=21%  Similarity=0.350  Sum_probs=31.8

Q ss_pred             CCCCHHHHHHHHHHHHc--------CCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         31 KTWTHEDMDAALEALRA--------GQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~--------g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ++.+.+++.+|.-++.+        ..-++.++|.++||++.|||+|-..
T Consensus        10 ~~L~~~q~~AA~~l~~Ne~~~~~~~ekktqeqiAeelGisr~tLyrWrt~   59 (120)
T d2ao9a1          10 QKLTAKQIQAAYLLVENELMESNNEEKRTQDEMANELGINRTTLWEWRTK   59 (120)
T ss_dssp             TTSCHHHHHHHHHHHHHHHCC---CCCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHhhHHHHHHHHHHhhchhccccchhhhhHHHHHHHhChhHHHHHHHhhc
Confidence            56677888766654432        2357889999999999999999843

>d2ezla_ a.4.1.2 (A:) Ibeta subdomain of the mu end DNA-binding domain of phage mu transposase {Bacteriophage mu [TaxId: 10677]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: Ibeta subdomain of the mu end DNA-binding domain of phage mu transposase
species: Bacteriophage mu [TaxId: 10677]

Probab=92.85  E-value=0.087  Score=37.41  Aligned_cols=36  Identities=14%  Similarity=0.215  Sum_probs=27.3

Q ss_pred             HHHHHHHHH---HHhCCCc----HHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEG---IRSGQTT----VQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~---~~~~~~s----~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +.|+++|..   +.+++.+    +.++|..||||..|||+|+.
T Consensus        33 k~RL~~l~~V~~L~~~G~~~~~A~~~VA~~~~vs~~TL~nW~~   75 (99)
T d2ezla_          33 EKWLPAVQAADEMLNQGISTKTAFATVAGHYQVSASTLRDKYY   75 (99)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHHHHSSSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCcHHHHHHHHHHHhCCCHHHHHHHHH
Confidence            445555544   4556676    67889999999999999987

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=92.82  E-value=0.09  Score=33.96  Aligned_cols=36  Identities=11%  Similarity=0.135  Sum_probs=28.6

Q ss_pred             HHHHHHHHHc--CCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         38 MDAALEALRA--GQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        38 ~~~AI~~~~~--g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ....++.+.+  +.+|..++|+++||++.|+++-+...
T Consensus         9 ~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L   46 (65)
T d1j5ya1           9 LKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYL   46 (65)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            4556666654  34899999999999999999988764

>d1ntca_ a.4.1.12 (A:) DNA-binding domain of NTRC {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: DNA-binding domain of NTRC
species: Salmonella typhimurium [TaxId: 90371]

Probab=92.74  E-value=0.058  Score=37.18  Aligned_cols=35  Identities=23%  Similarity=0.234  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      |+.-|.+.+..++-+..+||+..||++.|||++++
T Consensus        52 E~~lI~~aL~~~~Gn~~~AA~~LGI~R~TL~~Klk   86 (91)
T d1ntca_          52 ERTLLTTALRHTQGHKQEAARLLGWGAATLTAKLK   86 (91)
T ss_dssp             HHHHHHHHHHHTTTCTTHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCcHHHHHHHHCCCHHHHHHHHH
Confidence            45667777777778899999999999999999987

>d1z0xa1 a.4.1.9 (A:4-71) Transcriptional regulator EF0787 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator EF0787
species: Enterococcus faecalis [TaxId: 1351]

Probab=92.73  E-value=0.054  Score=35.22  Aligned_cols=40  Identities=18%  Similarity=0.346  Sum_probs=30.6

Q ss_pred             CCCHHHH-HHHHHHHH-cC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         32 TWTHEDM-DAALEALR-AG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        32 kyt~e~~-~~AI~~~~-~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.|.+.+ ..|++.+. ++   ++|+++||++.||+++|||+...
T Consensus         1 k~tr~~Ii~aa~~l~~e~~G~~~~t~~~Ia~~agvs~~~iy~hF~   45 (68)
T d1z0xa1           1 KLSKDTIIAAAFSLLEKSPTLEQLSMRKVAKQLGVQAPAIYWYFK   45 (68)
T ss_dssp             CCSHHHHHHHHHHHHHHSCCGGGCCHHHHHHHHTSCHHHHHTTCS
T ss_pred             CcCHHHHHHHHHHHHHHcCCccccCHHHHHHHHCcchhHHHHhcC
Confidence            3566776 46666664 33   68999999999999999998743

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=92.56  E-value=0.17  Score=32.52  Aligned_cols=36  Identities=8%  Similarity=0.213  Sum_probs=28.6

Q ss_pred             HHHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH-hhcC
Q psy17316        181 IALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK-LSRS  216 (229)
Q Consensus       181 eaV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk-~~~~  216 (229)
                      .|++.+. ++.+++.++|...|+|.+||+.+++ +...
T Consensus         9 ~IL~~L~~n~r~s~~~iA~~lgis~~tv~~Ri~~L~~~   46 (63)
T d2cfxa1           9 NIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQLESF   46 (63)
T ss_dssp             HHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            4444444 6779999999999999999999998 4433

>d2g7la1 a.4.1.9 (A:16-83) Putative transcriptional regulator SCO7704 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO7704
species: Streptomyces coelicolor [TaxId: 1902]

Probab=92.52  E-value=0.074  Score=34.49  Aligned_cols=40  Identities=8%  Similarity=0.128  Sum_probs=30.4

Q ss_pred             CCCCHHHHHHHHH-HHHc---CCCCHHHHHHHcCCChhhHHHHH
Q psy17316         31 KTWTHEDMDAALE-ALRA---GQMSLTKASVSYGIPSTTLWQRA   70 (229)
Q Consensus        31 ~kyt~e~~~~AI~-~~~~---g~~S~~~aA~~~gIp~sTL~~~i   70 (229)
                      +..+.++++++.. .+.+   .++|+++||++.||++++||+..
T Consensus         2 p~~tr~~Il~aa~~l~~~~g~~~~si~~ia~~~gvs~~~~y~hF   45 (68)
T d2g7la1           2 PALSRRWIVDTAVALMRAEGLEKVTMRRLAQELDTGPASLYVYV   45 (68)
T ss_dssp             CCCCHHHHHHHHHHHHHHHCSSSCCHHHHHHHTTSCHHHHTTTC
T ss_pred             ChhhHHHHHHHHHHHHHHhCcccCCHHHHHHHHCcCHhHhhHHC
Confidence            4567777755544 4443   46899999999999999999863

>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: P22 C2 repressor, DNA-binding domain
species: Salmonella bacteriophage P22 [TaxId: 10754]

Probab=92.51  E-value=0.065  Score=34.39  Aligned_cols=26  Identities=8%  Similarity=0.106  Sum_probs=23.7

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ...|+|+.++|+..||+.+||.+|..
T Consensus        13 ~~~g~tq~~lA~~~gvs~~~i~~~e~   38 (66)
T d2r1jl1          13 KKLKIRQAALGKMVGVSNVAISQWER   38 (66)
T ss_dssp             HHHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            35689999999999999999999986

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=92.48  E-value=0.088  Score=33.58  Aligned_cols=32  Identities=25%  Similarity=0.348  Sum_probs=27.0

Q ss_pred             HHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        181 IALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       181 eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +|++.+.+ +.+++.++|...|+|.++|+.+++
T Consensus         7 kIl~~L~~n~r~s~~~lA~~~gls~~~v~~Ri~   39 (60)
T d1i1ga1           7 IILEILEKDARTPFTEIAKKLGISETAVRKRVK   39 (60)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45555544 578999999999999999999998

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

Probab=92.48  E-value=0.23  Score=31.26  Aligned_cols=26  Identities=8%  Similarity=0.019  Sum_probs=23.6

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+-++|+.++|+..||+.+++.+|-+
T Consensus        11 ~~~g~sq~elA~~~gvs~~~is~~E~   36 (63)
T d1r69a_          11 IQLGLNQAELAQKVGTTQQSIEQLEN   36 (63)
T ss_dssp             HHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHcCCcHHHHHHHhCcCHHHHHHHHC
Confidence            35689999999999999999999965

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=92.40  E-value=0.083  Score=37.86  Aligned_cols=38  Identities=16%  Similarity=0.315  Sum_probs=31.0

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ++.+. .++.++.-.++|+.+||..+||++++|+..+++
T Consensus        20 pe~QR-~vl~L~~~e~ls~~EIA~~lgiS~~aV~~~l~R   57 (106)
T d1xsva_          20 TNKQR-NYLELFYLEDYSLSEIADTFNVSRQAVYDNIRR   57 (106)
T ss_dssp             CHHHH-HHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHH
T ss_pred             CHHHH-HHHHHHHHhCCcHHHHHHHHCcCHHHHHHHHHH
Confidence            34443 455576677999999999999999999999886

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=92.32  E-value=0.12  Score=36.51  Aligned_cols=42  Identities=14%  Similarity=0.169  Sum_probs=33.3

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      +|+.+..-..-.+..|.+|+.++|+..|||++|+++-+.+..
T Consensus        18 lt~~e~~v~~~L~~~g~~t~~eia~~~~i~~~~v~~~l~~L~   59 (109)
T d1sfxa_          18 FKPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLL   59 (109)
T ss_dssp             CCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcCCCCHHHHHHHhCCCcchHHHHHHHHH
Confidence            455555444445678999999999999999999999988763

>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=92.24  E-value=0.082  Score=34.27  Aligned_cols=32  Identities=16%  Similarity=0.111  Sum_probs=27.5

Q ss_pred             HHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        180 EIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       180 ~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+|++++.+| ++..++|..+|||..||...++
T Consensus        10 ~~vl~l~~~G-~s~~eIA~~L~is~~TV~~~~~   41 (67)
T d1fsea_          10 REVFELLVQD-KTTKEIASELFISEKTVRNHIS   41 (67)
T ss_dssp             HHHHHHHTTT-CCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHcc-CCHHHHHHHHCCCHHHHHHHHH
Confidence            4567776666 9999999999999999999886

>d2g7ga1 a.4.1.9 (A:9-73) Putative transcriptional regulator Rha04620 {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator Rha04620
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=92.24  E-value=0.085  Score=34.05  Aligned_cols=37  Identities=22%  Similarity=0.483  Sum_probs=27.8

Q ss_pred             HHHH-HHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         35 HEDM-DAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        35 ~e~~-~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      -+.+ ..|++.+ ..|+.|+++||++.||+++|||+...
T Consensus         3 R~~Il~aa~~l~~~~G~~ti~~Ia~~agvs~~~iY~~F~   41 (65)
T d2g7ga1           3 RERIAEAALELVDRDGDFRMPDLARHLNVQVSSIYHHAK   41 (65)
T ss_dssp             HHHHHHHHHHHHHHHSSCCHHHHHHHTTSCHHHHHTTSC
T ss_pred             HHHHHHHHHHHHHHcCCCCHHHHHHHhCccccchhhcCC
Confidence            3444 3444444 35899999999999999999998643

>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=92.14  E-value=0.089  Score=33.96  Aligned_cols=32  Identities=16%  Similarity=0.189  Sum_probs=27.2

Q ss_pred             HHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        180 EIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       180 ~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+|++++..| +|..++|..++||..||...++
T Consensus        10 ~~vl~l~~~G-~s~~eIA~~l~iS~~TV~~~~~   41 (65)
T d1l3la1          10 ATYLRWIAVG-KTMEEIADVEGVKYNSVRVKLR   41 (65)
T ss_dssp             HHHHHHHTTT-CCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHhc-CCHHHHHHHHCCCHHHHHHHHH
Confidence            4566666665 9999999999999999999886

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=91.92  E-value=0.15  Score=33.78  Aligned_cols=38  Identities=11%  Similarity=0.231  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHc--CCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         36 EDMDAALEALRA--GQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        36 e~~~~AI~~~~~--g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +.-+.+|+.+..  +.+|+.+||+..|+|++|+++-+..+
T Consensus         5 ~r~l~IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~tL   44 (75)
T d1mkma1           5 KKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVL   44 (75)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            344666666543  56899999999999999999999975

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=91.85  E-value=0.073  Score=36.35  Aligned_cols=31  Identities=10%  Similarity=0.088  Sum_probs=28.7

Q ss_pred             CCCCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316         48 GQMSLTKASVSYGIPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        48 g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~   78 (229)
                      ..+|+.++|++.||+.+||.|-+++.|..|.
T Consensus        35 ~~~si~~lA~~~~vS~sTi~Rf~kklG~~gf   65 (83)
T d2o3fa1          35 IESTVNEISALANSSDAAVIRLCKSLGLKGF   65 (83)
T ss_dssp             HTCCHHHHHHHTTCCHHHHHHHHHHTTCSSH
T ss_pred             HHccHHHHHHHHCCCHHHHHHHHHHhCCCCH
Confidence            4689999999999999999999999999873

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=91.85  E-value=0.14  Score=35.08  Aligned_cols=36  Identities=14%  Similarity=0.046  Sum_probs=29.9

Q ss_pred             HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhcC
Q psy17316        181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRS  216 (229)
Q Consensus       181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~~  216 (229)
                      .+-+...+.++|..++|.+.|||.++|.+|.++.-+
T Consensus        15 ~i~~~r~~~gltq~~lA~~~gis~~~is~ie~G~~~   50 (89)
T d2o38a1          15 ALNAVIDRARLSQAAAAARLGINQPKVSALRNYKLE   50 (89)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCT
T ss_pred             HHHHHHHHcCCCHHHHHHHHHhhHhHHHHHHcCCCC
Confidence            455566668899999999999999999999986533

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=91.80  E-value=0.098  Score=37.44  Aligned_cols=38  Identities=21%  Similarity=0.406  Sum_probs=30.2

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ++.+. .++.++--.++|+.+||..+|||.+||+..+++
T Consensus        18 p~~qR-~v~~L~y~~~ls~~EIA~~lgiS~~aV~~~l~R   55 (106)
T d1s7oa_          18 TDKQM-NYIELYYADDYSLAEIADEFGVSRQAVYDNIKR   55 (106)
T ss_dssp             CHHHH-HHHHHHHHTCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            44444 445555566999999999999999999999886

>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=91.53  E-value=0.13  Score=33.33  Aligned_cols=38  Identities=11%  Similarity=0.103  Sum_probs=28.8

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .|+-+ .+++..+.+ |+|..+||.++||+..|+...+.+
T Consensus         7 LT~rE-~~vl~ll~~-G~s~~eIA~~l~iS~~TV~~~~~~   44 (67)
T d1a04a1           7 LTPRE-RDILKLIAQ-GLPNKMIARRLDITESTVKVHVKH   44 (67)
T ss_dssp             SCHHH-HHHHHHHHT-TCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCHHH-HHHHHHHHh-CCCHHHHHHHHCCCHHHHHHHHHH
Confidence            34444 345555555 789999999999999999988875

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=91.49  E-value=0.06  Score=35.51  Aligned_cols=25  Identities=24%  Similarity=0.254  Sum_probs=22.8

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|+|+.++|+.+||++.|+.+|=.
T Consensus        12 ~~gltQ~elA~~LGvs~~ti~~yE~   36 (67)
T d2auwa1          12 RNNLSLTTAAEALGISRRMVSYYRT   36 (67)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            5699999999999999999999944

>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=91.43  E-value=0.21  Score=31.68  Aligned_cols=40  Identities=5%  Similarity=0.069  Sum_probs=30.6

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHH
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDAL   99 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll   99 (229)
                      +++++++|+..||+.+|+.+-+...     .      ..++|.++...+..
T Consensus         1 NvTi~dvA~~agvS~~TVSr~Ln~~-----~------~Vs~~tr~rV~~aa   40 (57)
T d2hsga1           1 NVTIYDVAREASVSMATVSRVVNGN-----P------NVKPSTRKKVLETI   40 (57)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHTTC-----T------TSCHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCcCHHHHHHHhCCC-----C------cCCHHHHHHHHHHH
Confidence            3689999999999999999998731     1      24778777776544

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=91.33  E-value=0.15  Score=36.50  Aligned_cols=35  Identities=9%  Similarity=0.160  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .-.+|+....-.++|+.|+|..+|||.++|+..+.
T Consensus        22 ~QR~vl~L~~~e~ls~~EIA~~lgiS~~aV~~~l~   56 (106)
T d1xsva_          22 KQRNYLELFYLEDYSLSEIADTFNVSRQAVYDNIR   56 (106)
T ss_dssp             HHHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCcHHHHHHHHCcCHHHHHHHHH
Confidence            34456666666779999999999999999999886

>d2np5a1 a.4.1.9 (A:9-77) Transcriptional regulator RHA1_ro04179 {Rhodococcus sp. [TaxId: 1831]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator RHA1 ro04179
species: Rhodococcus sp. [TaxId: 1831]

Probab=91.27  E-value=0.091  Score=33.85  Aligned_cols=38  Identities=11%  Similarity=0.144  Sum_probs=28.1

Q ss_pred             CHHHHHH-HHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDMDA-ALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~~~-AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      |.|.++. |++.+.+   .++|+++||++.||++++||+...
T Consensus         2 t~e~i~~aa~~l~~~~G~~~~ti~~Ia~~agvs~~~iy~~F~   43 (69)
T d2np5a1           2 SPERLAAALFDVAAESGLEGASVREVAKRAGVSIGAVQHHFS   43 (69)
T ss_dssp             HHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             hHHHHHHHHHHHHHHhCccccCHHHHHHHhCCCHHHHHHHCc
Confidence            3455544 4444443   468999999999999999999843

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=91.24  E-value=0.2  Score=31.97  Aligned_cols=32  Identities=19%  Similarity=0.321  Sum_probs=26.9

Q ss_pred             HHHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        181 IALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       181 eaV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +||+.+. ++.+++.++|.+.|+|.++|+.+++
T Consensus         9 ~IL~~L~~~~r~s~~eiA~~l~ls~~~v~~Ri~   41 (63)
T d2cg4a1           9 GILEALMGNARTAYAELAKQFGVSPETIHVRVE   41 (63)
T ss_dssp             HHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4555544 4679999999999999999999998

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=91.20  E-value=0.19  Score=33.00  Aligned_cols=35  Identities=9%  Similarity=0.021  Sum_probs=29.1

Q ss_pred             HHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhcC
Q psy17316        182 ALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRS  216 (229)
Q Consensus       182 aV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~~  216 (229)
                      +-++-...++|..++|..+|||..|+.+|=++.+.
T Consensus         6 ~k~~R~~~gltQ~elA~~LGvs~~ti~~yE~G~r~   40 (67)
T d2auwa1           6 FGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKI   40 (67)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSSC
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCC
Confidence            34566778899999999999999999999775543

>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=91.05  E-value=0.28  Score=31.39  Aligned_cols=33  Identities=12%  Similarity=0.186  Sum_probs=26.3

Q ss_pred             HHHHHHHHcCCCCHHHHHHHhCCChHHHHHHHHH
Q psy17316        125 NVALDALRAGSISANKASKAYGIPSSTLYKIARK  158 (229)
Q Consensus       125 ~~AV~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~  158 (229)
                      .+++..+.+|. |..+||++.+|+..|+...+++
T Consensus        10 ~~vl~l~~~G~-s~~eIA~~l~iS~~TV~~~~~~   42 (65)
T d1l3la1          10 ATYLRWIAVGK-TMEEIADVEGVKYNSVRVKLRE   42 (65)
T ss_dssp             HHHHHHHTTTC-CHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHHHHhcC-CHHHHHHHHCCCHHHHHHHHHH
Confidence            34556666665 9999999999999998887654

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=90.79  E-value=0.13  Score=35.93  Aligned_cols=38  Identities=11%  Similarity=0.193  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ...+.++..+.+|.+++.++|+.+||+++|+.+.++..
T Consensus        23 p~Rl~Il~~L~~~~~~v~ela~~l~is~stvS~HL~~L   60 (98)
T d1r1ta_          23 PNRLRLLSLLARSELCVGDLAQAIGVSESAVSHQLRSL   60 (98)
T ss_dssp             HHHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            45567888888999999999999999999999998875

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

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

Probab=90.64  E-value=0.1  Score=32.14  Aligned_cols=37  Identities=19%  Similarity=0.079  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .+...|+.-.+..+++.++|+..|+++++|.++.++.
T Consensus         7 ~v~~yI~~~~~~~~tl~~lA~~~~~s~~~l~r~Fk~~   43 (54)
T d1bl0a1           7 SILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKE   43 (54)
T ss_dssp             HHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHHHH
T ss_pred             HHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            4455555555678999999999999999999999974

>d2i10a1 a.4.1.9 (A:10-78) Putative transcriptional regulator RHA1_ro09068 {Rhodococcus sp. [TaxId: 1831]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator RHA1 ro09068
species: Rhodococcus sp. [TaxId: 1831]

Probab=90.62  E-value=0.21  Score=32.18  Aligned_cols=34  Identities=21%  Similarity=0.318  Sum_probs=27.8

Q ss_pred             HHHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         38 MDAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        38 ~~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +..|++.+.+   .+.|+++||++.||+++|||+...
T Consensus         6 L~aA~~lf~~~G~~~~ti~~Ia~~agvs~~~~Y~~F~   42 (69)
T d2i10a1           6 LQTAMELFWRQGYEGTSITDLTKALGINPPSLYAAFG   42 (69)
T ss_dssp             HHHHHHHHHHHTTTTCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             HHHHHHHHHHHCcccCCHHHHHHHhCCChhHHHHHCc
Confidence            4566666654   468999999999999999999865

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=90.60  E-value=0.17  Score=35.14  Aligned_cols=40  Identities=13%  Similarity=0.116  Sum_probs=35.4

Q ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         34 THEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        34 t~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +....+.++..+.+|.+++.++|..+|++++|+.+.++..
T Consensus        16 ~d~~Rl~Il~~L~~~~~~v~el~~~l~~s~~~vS~HL~~L   55 (94)
T d1r1ua_          16 GDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLL   55 (94)
T ss_dssp             CSHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHH
Confidence            3456678888889999999999999999999999999875

>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=90.58  E-value=0.16  Score=33.29  Aligned_cols=32  Identities=19%  Similarity=0.144  Sum_probs=26.7

Q ss_pred             HHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        180 EIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       180 ~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+|+.++..| ++..++|..+|||..||...+.
T Consensus        18 ~~vl~~l~~G-~s~~eIA~~l~iS~~TV~~~~~   49 (70)
T d1yioa1          18 QQVLQLTIRG-LMNKQIAGELGIAEVTVKVHRH   49 (70)
T ss_dssp             HHHHHHHTTT-CCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHcC-CCHHHHHHHHCCCHHHHHHHHH
Confidence            3566665555 8999999999999999999886

>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: HTH-motif protein NE1354
species: Nitrosomonas europaea [TaxId: 915]

Probab=90.52  E-value=0.21  Score=32.36  Aligned_cols=35  Identities=17%  Similarity=0.210  Sum_probs=28.5

Q ss_pred             HHHHHHH-HHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         37 DMDAALE-ALRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        37 ~~~~AI~-~~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ++...|. ...+.|+|+.++|+..||++++|.+|.+
T Consensus         6 ~l~~~i~~~r~~~gltq~elA~~~gv~~~~is~ie~   41 (69)
T d2a6ca1           6 QLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMR   41 (69)
T ss_dssp             HHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHcCHhHHHHHHc
Confidence            3444444 4467899999999999999999999976

>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=90.50  E-value=0.26  Score=31.27  Aligned_cols=51  Identities=10%  Similarity=0.110  Sum_probs=41.0

Q ss_pred             CHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHH
Q psy17316        137 SANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAE  199 (229)
Q Consensus       137 S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~  199 (229)
                      ++++||+..||+.+|+.+.+...            ...+++-|..|.+.+.+-+.-.+.+|.-
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~~------------~~vs~~tr~rV~~~a~~lgY~pn~~Ar~   52 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINKT------------RFVAEETRNAVWAAIKELHYSPSAVARS   52 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHTC------------SCCCHHHHHHHHHHHHHHTCCCCHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCC------------CccCHHHHHHHHHHHHHHCCCCCHHHHH
Confidence            68999999999999999988742            1356888999999998877766666654

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=90.47  E-value=0.19  Score=35.78  Aligned_cols=33  Identities=15%  Similarity=0.269  Sum_probs=27.1

Q ss_pred             HHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        180 EIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       180 ~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      -+|+.+..-+++|+.++|..+|||.+||+..+.
T Consensus        22 R~v~~L~y~~~ls~~EIA~~lgiS~~aV~~~l~   54 (106)
T d1s7oa_          22 MNYIELYYADDYSLAEIADEFGVSRQAVYDNIK   54 (106)
T ss_dssp             HHHHHHHHHTCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            445555555569999999999999999999886

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=90.36  E-value=0.28  Score=30.91  Aligned_cols=32  Identities=16%  Similarity=0.310  Sum_probs=27.6

Q ss_pred             HHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        181 IALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       181 eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++|+.+.. +.+++.++|.+.|+|.++|+.+++
T Consensus         7 ~Il~~L~~n~r~s~~eiA~~l~ls~~~v~~Ri~   39 (60)
T d2cyya1           7 KIIKILQNDGKAPLREISKITGLAESTIHERIR   39 (60)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            56666655 578999999999999999999997

>d1y9qa1 a.35.1.8 (A:4-82) Probable transcriptional regulator VC1968, N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Probable transcriptional regulator VC1968, N-terminal domain
domain: Probable transcriptional regulator VC1968, N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=90.34  E-value=0.16  Score=33.54  Aligned_cols=26  Identities=19%  Similarity=0.229  Sum_probs=24.0

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ...|+|+.++|+..||++++|.+|..
T Consensus        18 ~~~g~sq~~lA~~~gis~~~i~~~E~   43 (79)
T d1y9qa1          18 KSRGLSLDATAQLTGVSKAMLGQIER   43 (79)
T ss_dssp             HHTTCCHHHHHHHHSSCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCcchhHHHHHHc
Confidence            45799999999999999999999976

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=90.22  E-value=0.32  Score=32.02  Aligned_cols=41  Identities=15%  Similarity=0.199  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHh--CCCcHHHHHHHhCCChHHHHHHHH-hhcCC
Q psy17316        177 EDLEIALEGIRS--GQTTVQRASAEYGIPSGTLYGRCK-LSRST  217 (229)
Q Consensus       177 e~r~eaV~~~~~--~~~s~~eAA~~fgVp~~tv~~~vk-~~~~~  217 (229)
                      +.-.+|++.+-.  +.+++.++|+..|+|.+|+++.++ +.+.|
T Consensus         5 ~r~l~IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~tL~~~g   48 (75)
T d1mkma1           5 KKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKG   48 (75)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence            445678887765  358999999999999999999998 44443

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Cadmium efflux system accessory protein CadC
species: Staphylococcus aureus [TaxId: 1280]

Probab=90.15  E-value=0.2  Score=35.54  Aligned_cols=36  Identities=8%  Similarity=0.018  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHH-hCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIR-SGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~-~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|..|+..+. .|++++.++|..+|+|.+||...++
T Consensus        31 p~Rl~Il~~L~~~~~~~v~ela~~l~~s~s~vS~HL~   67 (108)
T d1u2wa1          31 ENRAKITYALCQDEELCVCDIANILGVTIANASHHLR   67 (108)
T ss_dssp             HHHHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCccHHHHHHHHccChhHHHHHHH
Confidence            45999999875 6889999999999999999999998

>d2fbqa1 a.4.1.9 (A:2-80) Transcriptional regulator PsrA {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator PsrA
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=90.02  E-value=0.17  Score=33.36  Aligned_cols=36  Identities=19%  Similarity=0.176  Sum_probs=27.4

Q ss_pred             HHH-HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         36 EDM-DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        36 e~~-~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+ ..|++.+.+   .++|+++||++.||++++||+...
T Consensus         7 e~Il~aa~~~~~~~G~~~~ti~~Ia~~agvs~~s~y~~F~   46 (79)
T d2fbqa1           7 ERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHFG   46 (79)
T ss_dssp             HHHHHHHHHHHHHHCSTTCCHHHHHHHHTSCHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHhCcccccHHHHHHHHCcChhHHHHHCc
Confidence            444 345555544   569999999999999999999854

>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: HTH-motif protein NE1354
species: Nitrosomonas europaea [TaxId: 915]

Probab=89.94  E-value=0.33  Score=31.31  Aligned_cols=40  Identities=15%  Similarity=0.072  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhcCC
Q psy17316        178 DLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRST  217 (229)
Q Consensus       178 ~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~~~  217 (229)
                      .-..+.+...+.++|..++|...||+.++|..|-++....
T Consensus         7 l~~~i~~~r~~~gltq~elA~~~gv~~~~is~ie~g~~~~   46 (69)
T d2a6ca1           7 LLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKIDL   46 (69)
T ss_dssp             HHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHTTCGGG
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHcCHhHHHHHHcccccc
Confidence            3455666677788999999999999999999998855333

>d1t56a1 a.4.1.9 (A:22-94) Ethr repressor {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Ethr repressor
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=89.88  E-value=0.24  Score=31.99  Aligned_cols=33  Identities=18%  Similarity=0.191  Sum_probs=25.7

Q ss_pred             HHHHHHHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+.   ++|+++||++.||+++|||+...
T Consensus        10 ~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   45 (73)
T d1t56a1          10 ATAENLLEDRPLADISVDDLAKGAGISRPTFYFYFP   45 (73)
T ss_dssp             HHHHHHHHHSCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHCc
Confidence            3455555543   58999999999999999999844

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=89.85  E-value=0.17  Score=34.61  Aligned_cols=28  Identities=14%  Similarity=0.214  Sum_probs=25.3

Q ss_pred             HHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         44 ALRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        44 ~~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .....|+|+.++|+.+||+++||.+|..
T Consensus        19 ~r~~~gltq~~lA~~~gis~~~is~ie~   46 (89)
T d2o38a1          19 VIDRARLSQAAAAARLGINQPKVSALRN   46 (89)
T ss_dssp             HHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHcCCCHHHHHHHHHhhHhHHHHHHc
Confidence            4456899999999999999999999977

>d2gfna1 a.4.1.9 (A:4-80) Probable transcriptional regulator RHA1_ro04631 {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator RHA1 ro04631
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=89.80  E-value=0.18  Score=33.15  Aligned_cols=33  Identities=15%  Similarity=0.126  Sum_probs=26.0

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+   .++|+++||++.||+++|||+...
T Consensus        13 ~aa~~l~~~~G~~~~s~~~Ia~~agvs~~~lY~~F~   48 (77)
T d2gfna1          13 DAVLALIAREGISAVTTRAVAEESGWSTGVLNHYFG   48 (77)
T ss_dssp             HHHHHHHHHHCGGGCCHHHHHHHHSSCHHHHHHHTS
T ss_pred             HHHHHHHHHhCccccCHHHHHHHHCCCHHHHHHHCc
Confidence            455555544   368999999999999999999854

>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=89.67  E-value=0.39  Score=30.39  Aligned_cols=39  Identities=15%  Similarity=0.209  Sum_probs=29.8

Q ss_pred             CHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHHh
Q psy17316         51 SLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDALR  100 (229)
Q Consensus        51 S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll~  100 (229)
                      ++++||+..||+.+|+.+-+...     .      ..+++.++..++..+
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~~-----~------~vs~~tr~rV~~~a~   40 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINKT-----R------FVAEETRNAVWAAIK   40 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHTC-----S------CCCHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCC-----C------ccCHHHHHHHHHHHH
Confidence            68999999999999999998732     1      236787877765443

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=89.63  E-value=0.37  Score=31.17  Aligned_cols=35  Identities=11%  Similarity=0.081  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHh-CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGIRS-GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~~~-~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+..|++.+.. |.+|..++|..+|+|.+||...++
T Consensus         7 N~~~Il~~l~~~g~~sr~eLa~~~glS~~Tv~~~l~   42 (71)
T d1z05a1           7 NAGRVYKLIDQKGPISRIDLSKESELAPASITKITR   42 (71)
T ss_dssp             HHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            45667777776 579999999999999999999998

>d1efaa1 a.35.1.5 (A:2-60) Lac repressor (LacR), 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: Lac repressor (LacR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.59  E-value=0.19  Score=32.16  Aligned_cols=53  Identities=8%  Similarity=0.115  Sum_probs=42.5

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHHHh
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASAEY  200 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~~f  200 (229)
                      .++.+||+..|++.+|+.+-+...            ...+++-+..|.+.+.+.+.-.+.+|.-+
T Consensus         3 ~Ti~diA~~agvS~sTVSr~l~~~------------~~vs~~tr~rI~~~a~~lgY~pn~~Ar~L   55 (59)
T d1efaa1           3 VTLYDVAEYAGVSYQTVSRVVNQA------------SHVSAKTREKVEAAMAELNYIPNRVAQQL   55 (59)
T ss_dssp             CCHHHHHHTTTSCHHHHHHHHTTC------------SSCCTHHHHHHHHHHHHHTCCCCHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCC------------CcCCHHHHHHHHHHHHHHCCCcCHHHHHH
Confidence            589999999999999999977532            23567889999999998777777776543

>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: SinR repressor, DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=89.50  E-value=0.35  Score=30.92  Aligned_cols=33  Identities=6%  Similarity=0.036  Sum_probs=27.9

Q ss_pred             HHHHhCCCcHHHHHHHhCCChHHHHHHHHhhcC
Q psy17316        184 EGIRSGQTTVQRASAEYGIPSGTLYGRCKLSRS  216 (229)
Q Consensus       184 ~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~~  216 (229)
                      +...+.+++..+.|...|||.++|..|-++.+.
T Consensus         8 ~~R~~~gltq~~la~~~gis~~~i~~~E~g~~~   40 (68)
T d1b0na2           8 QYRKEKGYSLSELAEKAGVAKSYLSSIERNLQT   40 (68)
T ss_dssp             HHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCS
T ss_pred             HHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCC
Confidence            345667799999999999999999999986543

>d1jt6a1 a.4.1.9 (A:2-72) Multidrug binding protein QacR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Multidrug binding protein QacR
species: Staphylococcus aureus [TaxId: 1280]

Probab=89.46  E-value=0.31  Score=31.36  Aligned_cols=33  Identities=9%  Similarity=-0.027  Sum_probs=26.4

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+   .++|+++||+..||+++|||+...
T Consensus         8 ~aa~~l~~~~G~~~~s~~~Ia~~agvs~~~~y~~F~   43 (71)
T d1jt6a1           8 GVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFK   43 (71)
T ss_dssp             HHHHHHHHHHCTTTCCHHHHHHHTTCCHHHHHHHHS
T ss_pred             HHHHHHHHHhCccccCHHHHHHHHCcCHhHHHHHCc
Confidence            345555544   468999999999999999999865

>d2icta1 a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Antitoxin HigA
species: Escherichia coli [TaxId: 562]

Probab=89.37  E-value=0.12  Score=35.22  Aligned_cols=26  Identities=15%  Similarity=0.050  Sum_probs=23.9

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..-|+|+.++|+.+||+++||.+|..
T Consensus        11 ~~~glsq~~LA~~lGvs~~~is~ie~   36 (87)
T d2icta1          11 DELNVSLREFARAMEIAPSTASRLLT   36 (87)
T ss_dssp             HHHTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHhhcHHHHHHHHH
Confidence            34589999999999999999999998

>d2iu5a1 a.4.1.9 (A:1-71) Transcriptional activator DhaS {Lactococcus lactis [TaxId: 1358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional activator DhaS
species: Lactococcus lactis [TaxId: 1358]

Probab=89.34  E-value=0.096  Score=34.13  Aligned_cols=42  Identities=14%  Similarity=0.207  Sum_probs=30.2

Q ss_pred             CCCCCHHHHHHHHH-HHHcC---CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         30 TKTWTHEDMDAALE-ALRAG---QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        30 ~~kyt~e~~~~AI~-~~~~g---~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ++..|.+.+++|.. .+.+.   +.|+++||++.||+++|+|+...
T Consensus         3 r~~~t~~~I~~aa~~l~~~~G~~~~sv~~Ia~~agvs~~t~Y~~F~   48 (71)
T d2iu5a1           3 KSIITQKIIAKAFKDLMQSNAYHQISVSDIMQTAKIRRQTFYNYFQ   48 (71)
T ss_dssp             TTSHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCGGGGGGTCS
T ss_pred             chHHHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCccccHHHHHcC
Confidence            34446666655554 44443   47999999999999999998743

>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Fructose repressor (FruR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.33  E-value=0.18  Score=32.25  Aligned_cols=23  Identities=22%  Similarity=0.143  Sum_probs=21.2

Q ss_pred             CCHHHHHHHcCCChhhHHHHHHH
Q psy17316         50 MSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        50 ~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      +++.+||+..||+.+|+.+-+..
T Consensus         1 vTl~diA~~agvS~sTVSrvLn~   23 (59)
T d1uxda_           1 MKLDEIARLAGVSRTTASYVING   23 (59)
T ss_dssp             CCHHHHHHHHTSCTTHHHHHHHT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcC
Confidence            57899999999999999999984

>d2gena1 a.4.1.9 (A:6-75) Probable transcriptional regulator PA1836 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator PA1836
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=89.24  E-value=0.29  Score=31.31  Aligned_cols=33  Identities=15%  Similarity=0.195  Sum_probs=26.3

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+   .++|+++||++.||+++|||+...
T Consensus         7 ~aa~~l~~~~G~~~~si~~Ia~~agvs~~t~Y~~F~   42 (70)
T d2gena1           7 QAALACFSEHGVDATTIEMIRDRSGASIGSLYHHFG   42 (70)
T ss_dssp             HHHHHHHHHHCTTTCCHHHHHHHHCCCHHHHHHHTC
T ss_pred             HHHHHHHHHhCcccCCHHHHHHHHCcCHHHHHHHCC
Confidence            455555544   468999999999999999999854

>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=89.13  E-value=0.45  Score=32.89  Aligned_cols=38  Identities=11%  Similarity=0.108  Sum_probs=33.4

Q ss_pred             CHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        175 KPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       175 t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++-+...+.+.+.+.+++..++|+++|.|.++|.+.++
T Consensus         4 ~piEeA~a~~~L~e~g~t~~~iA~~~Gks~~~V~~~Lr   41 (93)
T d1vz0a1           4 SPVEEARGYQALLEMGLTQEEVARRVGKARSTVANALR   41 (93)
T ss_dssp             CHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCCHHHHHHHHccchHHHHHHHH
Confidence            45566778888888889999999999999999999998

>d1zk8a1 a.4.1.9 (A:6-77) Transcriptional regulator BC5000 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator BC5000
species: Bacillus cereus [TaxId: 1396]

Probab=89.01  E-value=0.16  Score=32.95  Aligned_cols=38  Identities=18%  Similarity=0.311  Sum_probs=28.6

Q ss_pred             CCHHHHHHH-HHHHHc---CCCCHHHHHHHcCCChhhHHHHH
Q psy17316         33 WTHEDMDAA-LEALRA---GQMSLTKASVSYGIPSTTLWQRA   70 (229)
Q Consensus        33 yt~e~~~~A-I~~~~~---g~~S~~~aA~~~gIp~sTL~~~i   70 (229)
                      .|.+.++.| ++.+.+   .++|+++||++.||++++||+..
T Consensus         3 ~t~e~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~slY~yF   44 (72)
T d1zk8a1           3 LTLQKIVETAAEIADANGVQEVTLASLAQTLGVRSPSLYNHV   44 (72)
T ss_dssp             CCHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTSCHHHHTTTC
T ss_pred             ccHHHHHHHHHHHHHHhCCCcccHHHHHHHhCCCHHHHHHHC
Confidence            466777544 444443   45899999999999999999763

>d2fq4a1 a.4.1.9 (A:9-77) Transcriptional regulator BC3163 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator BC3163
species: Bacillus cereus [TaxId: 1396]

Probab=89.00  E-value=0.31  Score=31.39  Aligned_cols=33  Identities=15%  Similarity=0.191  Sum_probs=25.7

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..+++.+.+   .+.|+.+||++.||++++||+...
T Consensus        11 ~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~~y~~F~   46 (69)
T d2fq4a1          11 SASYELLLESGFKAVTVDKIAERAKVSKATIYKWWP   46 (69)
T ss_dssp             HHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHhCcccCCHHHHHHHHCcCHHHHHHHCC
Confidence            344545544   457999999999999999999854

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=88.91  E-value=0.25  Score=31.64  Aligned_cols=43  Identities=12%  Similarity=0.186  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHH--HcCCCCHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         35 HEDMDAALEAL--RAGQMSLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        35 ~e~~~~AI~~~--~~g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      .||-+++|-.+  ..|..+..+||+.+||+++|+.+-++++.-.|
T Consensus         5 ~EdYLk~I~~l~~~~~~v~~~~iA~~L~vs~~SVs~mikrL~~~G   49 (61)
T d2ev0a1           5 MEDYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDE   49 (61)
T ss_dssp             HHHHHHHHHHHHHHHSSCCHHHHHHHHTCCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhcCCCccHHHHHHHhCCCchhHHHHHHHHHHCC
Confidence            46667777544  36889999999999999999999999865444

>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=88.85  E-value=0.36  Score=30.97  Aligned_cols=38  Identities=13%  Similarity=0.113  Sum_probs=28.4

Q ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         33 WTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        33 yt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      .|+-+. +++..+. .|+|..+||.++||+.+|+...+++
T Consensus         5 LT~rE~-~vl~l~~-~G~s~~eIA~~L~is~~TV~~~~~~   42 (67)
T d1fsea_           5 LTKRER-EVFELLV-QDKTTKEIASELFISEKTVRNHISN   42 (67)
T ss_dssp             CCHHHH-HHHHHHT-TTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCHHHH-HHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHH
Confidence            444443 3444554 5789999999999999999988775

>d1nera_ a.35.1.2 (A:) Ner {Bacteriophage mu [TaxId: 10677]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: Ner
species: Bacteriophage mu [TaxId: 10677]

Probab=88.80  E-value=0.37  Score=32.20  Aligned_cols=40  Identities=28%  Similarity=0.451  Sum_probs=32.9

Q ss_pred             CCCCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         29 VTKTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        29 ~~~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ....|...|+..+|   ..-|+|+.++++++|++.+||..-+.
T Consensus         5 k~~dWh~adI~AaL---~krG~sLa~lsr~~gls~stl~naL~   44 (74)
T d1nera_           5 KARDWHRADVIAGL---KKRKLSLSALSRQFGYAPTTLANALE   44 (74)
T ss_dssp             CSSSCCHHHHHHHH---TTSSCCHHHHHHHHSCCHHHHHHTTT
T ss_pred             ccCCCCHHHHHHHH---HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            45678888877766   56688999999999999999987654

>d1v7ba1 a.4.1.9 (A:1-74) Transcriptional regulator Cgl2612 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator Cgl2612
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=88.80  E-value=0.3  Score=31.66  Aligned_cols=37  Identities=14%  Similarity=0.158  Sum_probs=27.5

Q ss_pred             HHHHH-HHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         35 HEDMD-AALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        35 ~e~~~-~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .+.++ .|++.+.+   .+.|+++||+..||+++|||+...
T Consensus         6 r~~Il~aa~~l~~~~G~~~~s~~~Ia~~agvs~~t~Y~~F~   46 (74)
T d1v7ba1           6 KEMILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFP   46 (74)
T ss_dssp             HHHHHHHHHHHHHHSCSTTCCHHHHHHHHCSCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHhCccccCHHHHHHHhCcCcchHhhhCC
Confidence            34453 44444544   468999999999999999999843

>d2vkva1 a.4.1.9 (A:6-67) Tetracyclin repressor (Tet-repressor, TetR) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Tetracyclin repressor (Tet-repressor, TetR)
species: Escherichia coli [TaxId: 562]

Probab=88.76  E-value=0.18  Score=31.93  Aligned_cols=33  Identities=21%  Similarity=0.299  Sum_probs=26.2

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+   .++|+++||++.||+++||+++..
T Consensus         6 ~aA~~l~~~~G~~~~s~~~Ia~~agvs~~tiy~~F~   41 (62)
T d2vkva1           6 NSALELGNEVGIEGLTTRKLAQKLGVEQPTLYWHVK   41 (62)
T ss_dssp             HHHHHHHHHHHHHHCCHHHHHHHHTSCHHHHHHHSC
T ss_pred             HHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHCC
Confidence            445555544   458999999999999999999854

>d1pb6a1 a.4.1.9 (A:14-85) Hypothetical transcriptional regulator YcdC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YcdC
species: Escherichia coli [TaxId: 562]

Probab=88.75  E-value=0.34  Score=31.36  Aligned_cols=33  Identities=21%  Similarity=0.205  Sum_probs=26.4

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+   .++|+++||++.||+++|||+...
T Consensus        11 ~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~y~~F~   46 (72)
T d1pb6a1          11 SAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFP   46 (72)
T ss_dssp             HHHHHHHHHHCTTTCCHHHHHHHTTSCHHHHHHHSS
T ss_pred             HHHHHHHHHhCccccCHHHHHHHhCCChHHHHHHCc
Confidence            455555554   468999999999999999999853

>d2hkua1 a.4.1.9 (A:18-87) Putative transcriptional regulator RHA1_ro03468 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator RHA1 ro03468
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=88.73  E-value=0.26  Score=31.95  Aligned_cols=33  Identities=18%  Similarity=0.156  Sum_probs=25.7

Q ss_pred             HHHHHHHHc-C-CCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA-G-QMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~-g-~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+ | +.|+++||++.||+++|||++..
T Consensus         8 ~aA~~l~~~~G~~~t~~~Ia~~agvs~~~~Y~~F~   42 (70)
T d2hkua1           8 TAATELFLEHGEGVPITQICAAAGAHPNQVTYYYG   42 (70)
T ss_dssp             HHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHS
T ss_pred             HHHHHHHHhcccCchHHHHHHHHCCChhhHHhcCC
Confidence            344554443 2 58999999999999999999975

>d2g7sa1 a.4.1.9 (A:3-76) Putative transcriptional regulator Atu0279 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator Atu0279
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=88.66  E-value=0.25  Score=32.17  Aligned_cols=33  Identities=15%  Similarity=0.169  Sum_probs=25.7

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+   .++|+++||++.||+++|||+...
T Consensus        11 ~aa~~l~~~~G~~~~s~~~Ia~~agvs~~~iY~~F~   46 (74)
T d2g7sa1          11 QCARTLIIRGGYNSFSYADISQVVGIRNASIHHHFP   46 (74)
T ss_dssp             HHHHHHHHHHCGGGCCHHHHHHHHCCCHHHHHHHCS
T ss_pred             HHHHHHHHHhCccccCHHHHHHHHCcCcchHHHHCc
Confidence            445555544   358999999999999999999843

>d1ui5a1 a.4.1.9 (A:5-75) A-factor receptor homolog CprB {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: A-factor receptor homolog CprB
species: Streptomyces coelicolor [TaxId: 1902]

Probab=88.63  E-value=0.34  Score=31.27  Aligned_cols=38  Identities=16%  Similarity=0.240  Sum_probs=28.4

Q ss_pred             CHHHH-HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         34 THEDM-DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        34 t~e~~-~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+.+ ..|++.+.+   .+.|+++||++.||+++|+|++..
T Consensus         6 ~r~~il~aa~~l~~~~G~~~~si~~Ia~~agvs~~~~y~~F~   47 (71)
T d1ui5a1           6 TRATIIGAAADLFDRRGYESTTLSEIVAHAGVTKGALYFHFA   47 (71)
T ss_dssp             HHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHhCccccCHHHHHHHHCcCHhHHHHHCc
Confidence            34555 345555544   568999999999999999999843

>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=88.51  E-value=0.38  Score=30.40  Aligned_cols=51  Identities=12%  Similarity=0.158  Sum_probs=40.1

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCCcHHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQTTVQRASA  198 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~s~~eAA~  198 (229)
                      .++.++|++.||+.+|+.+.+...            ...+++-|..|.+.+.+-+.-.+.+|.
T Consensus         2 vTi~dvA~~agvS~~TVSr~Ln~~------------~~Vs~~tr~rV~~aa~~lgY~pn~~A~   52 (57)
T d2hsga1           2 VTIYDVAREASVSMATVSRVVNGN------------PNVKPSTRKKVLETIERLGYRPNAVAR   52 (57)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHTTC------------TTSCHHHHHHHHHHHHHHTCCSCHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHhCCC------------CcCCHHHHHHHHHHHHHHCcCCCHHHH
Confidence            589999999999999999977631            136788899999988886666655554

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

Probab=88.43  E-value=0.19  Score=32.36  Aligned_cols=32  Identities=16%  Similarity=0.113  Sum_probs=26.4

Q ss_pred             HHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         40 AALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        40 ~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.|..+ ...|+|+.++|+..||+++++.+|-+
T Consensus        12 ~~ik~~R~~~gltq~~lA~~~gis~~~i~~~E~   44 (69)
T d1y7ya1          12 QRLRELRTAKGLSQETLAFLSGLDRSYVGGVER   44 (69)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHhHhCCCHHHHHHHHC
Confidence            344443 46799999999999999999999966

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=88.43  E-value=0.24  Score=34.02  Aligned_cols=35  Identities=6%  Similarity=-0.018  Sum_probs=31.6

Q ss_pred             HHHHHHHHH-HhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        178 DLEIALEGI-RSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       178 ~r~eaV~~~-~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+..|+..+ .+|.+++.++|..++|+.++|...++
T Consensus        17 ~r~~IL~~L~~~~~~~~~eLa~~l~is~~~vs~~l~   52 (100)
T d1ub9a_          17 VRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIR   52 (100)
T ss_dssp             HHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHhccCCCeeHHHHHHHHhhccccccHHHH
Confidence            378888888 46789999999999999999999998

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein PH1932
domain: Hypothetical protein PH1932
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=88.38  E-value=0.18  Score=38.65  Aligned_cols=37  Identities=22%  Similarity=0.372  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ....++..+.+|.+|+.++|+.+|++++|+++.++.+
T Consensus        20 ~R~~Il~~L~~~~~s~~ela~~lg~s~~~v~~hl~~L   56 (190)
T d1ulya_          20 TRRKILKLLRNKEMTISQLSEILGKTPQTIYHHIEKL   56 (190)
T ss_dssp             HHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3456777788999999999999999999999999975

>d3c07a1 a.4.1.9 (A:15-89) Putative transcriptional regulator SCO4850 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO4850
species: Streptomyces coelicolor [TaxId: 1902]

Probab=88.25  E-value=0.36  Score=31.19  Aligned_cols=33  Identities=6%  Similarity=0.179  Sum_probs=26.3

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+   .++|+++||++.||+++|||+...
T Consensus        12 ~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~~y~~F~   47 (75)
T d3c07a1          12 ETAMRLFQERGYDRTTMRAIAQEAGVSVGNAYYYFA   47 (75)
T ss_dssp             HHHHHHHHHTCSTTCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             HHHHHHHHHhCcccCCHHHHHHHHCcCHHHHHHHCc
Confidence            455555554   468999999999999999999844

>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: SinR repressor, DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=88.08  E-value=0.21  Score=32.02  Aligned_cols=26  Identities=15%  Similarity=0.181  Sum_probs=23.9

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ...|+|+.++|+..||+++||.+|-+
T Consensus        11 ~~~gltq~~la~~~gis~~~i~~~E~   36 (68)
T d1b0na2          11 KEKGYSLSELAEKAGVAKSYLSSIER   36 (68)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            35799999999999999999999976

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=88.07  E-value=0.34  Score=30.70  Aligned_cols=28  Identities=36%  Similarity=0.323  Sum_probs=24.6

Q ss_pred             HhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        187 RSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       187 ~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      ...++|..+.|..+||+.+||.+|=++.
T Consensus         9 ~~~gltQ~elA~~lGvs~~tvs~~E~G~   36 (62)
T d2ppxa1           9 RALKLTQEEFSARYHIPLGTLRDWEQGR   36 (62)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHTTS
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence            4566999999999999999999998753

>d2o7ta1 a.4.1.9 (A:1-78) Transcriptional regulator Cgl1640/Cg1846 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator Cgl1640/Cg1846
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=87.96  E-value=0.38  Score=31.62  Aligned_cols=32  Identities=13%  Similarity=0.271  Sum_probs=25.2

Q ss_pred             HHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         40 AALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        40 ~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      .|++.+.+   .++|+.+||++.||+++|||+...
T Consensus        15 aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~y~~F~   49 (78)
T d2o7ta1          15 TTCNLYRTHHHDSLTMENIAEQAGVGVATLYRNFP   49 (78)
T ss_dssp             HHHHHHHHSCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHhCccccCHHHHHHHhCCCHHHHHHHCc
Confidence            44555544   358999999999999999998843

>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Regulatory protein C.BclI
species: Bacillus caldolyticus [TaxId: 1394]

Probab=87.92  E-value=0.53  Score=30.63  Aligned_cols=34  Identities=3%  Similarity=-0.154  Sum_probs=28.6

Q ss_pred             HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      .+-+.+...++|..+.|...|||.++|.+|-++.
T Consensus        14 ~ik~~R~~~gltq~~lA~~~gis~~~i~~~e~g~   47 (77)
T d2b5aa1          14 TLKKIRTQKGVSQEELADLAGLHRTYISEVERGD   47 (77)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTC
T ss_pred             HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCC
Confidence            3445556688999999999999999999998865

>d2i10a1 a.4.1.9 (A:10-78) Putative transcriptional regulator RHA1_ro09068 {Rhodococcus sp. [TaxId: 1831]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator RHA1 ro09068
species: Rhodococcus sp. [TaxId: 1831]

Probab=87.84  E-value=0.33  Score=31.13  Aligned_cols=35  Identities=26%  Similarity=0.352  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHcC---CCCHHHHHHHhCCChHHHHHHHH
Q psy17316        123 ILNVALDALRAG---SISANKASKAYGIPSSTLYKIAR  157 (229)
Q Consensus       123 ~k~~AV~~~~~g---~~S~~~~a~k~gIp~sTL~~~ik  157 (229)
                      .+..|++.+.+.   ..|+++||+..||++.++|+...
T Consensus         5 iL~aA~~lf~~~G~~~~ti~~Ia~~agvs~~~~Y~~F~   42 (69)
T d2i10a1           5 ALQTAMELFWRQGYEGTSITDLTKALGINPPSLYAAFG   42 (69)
T ss_dssp             HHHHHHHHHHHHTTTTCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             HHHHHHHHHHHHCcccCCHHHHHHHhCCChhHHHHHCc
Confidence            345666666543   35999999999999999999653

>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=87.78  E-value=0.46  Score=30.82  Aligned_cols=31  Identities=16%  Similarity=0.157  Sum_probs=25.3

Q ss_pred             HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ++..+ ..|+|..+||..+||+..||...+.+
T Consensus        20 vl~~l-~~G~s~~eIA~~l~iS~~TV~~~~~~   50 (70)
T d1yioa1          20 VLQLT-IRGLMNKQIAGELGIAEVTVKVHRHN   50 (70)
T ss_dssp             HHHHH-TTTCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            44444 45789999999999999999988775

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=87.76  E-value=0.35  Score=30.79  Aligned_cols=33  Identities=12%  Similarity=-0.061  Sum_probs=28.4

Q ss_pred             HHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        183 LEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       183 V~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      -+...+.++|..+.|...|||++++..|.++.+
T Consensus         7 ~~lR~~~g~tq~elA~~~gis~~~is~~e~g~~   39 (66)
T d1utxa_           7 KLIREKKKISQSELAALLEVSRQTINGIEKNKY   39 (66)
T ss_dssp             HHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSC
T ss_pred             HHHHHHcCCCHHHHHHhcccCHHHHHHHHcCCC
Confidence            355667889999999999999999999998654

>d2icta1 a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Antitoxin HigA
species: Escherichia coli [TaxId: 562]

Probab=87.67  E-value=0.38  Score=32.59  Aligned_cols=32  Identities=9%  Similarity=0.007  Sum_probs=28.1

Q ss_pred             HHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        184 EGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       184 ~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      +.+...++|..+.|...|||.++|-.|.++.+
T Consensus         8 e~r~~~glsq~~LA~~lGvs~~~is~ie~g~~   39 (87)
T d2icta1           8 ESLDELNVSLREFARAMEIAPSTASRLLTGKA   39 (87)
T ss_dssp             HHHHHHTCCHHHHHHHHTCCHHHHHHHHHTSS
T ss_pred             HHHHHcCCCHHHHHHHHhhcHHHHHHHHHhcc
Confidence            55666789999999999999999999999764

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=87.53  E-value=0.33  Score=30.95  Aligned_cols=32  Identities=19%  Similarity=0.156  Sum_probs=29.3

Q ss_pred             HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .|++.+.+|.++-.|+|+..|+|.+||-..++
T Consensus         3 ~Il~~i~~~pisr~eLa~~~gls~~TVs~~v~   34 (62)
T d2hoea1           3 RILKRIMKSPVSRVELAEELGLTKTTVGEIAK   34 (62)
T ss_dssp             CSHHHHHHSCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            36778888999999999999999999999998

>d2d6ya1 a.4.1.9 (A:7-74) Putative regulator SCO4008 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative regulator SCO4008
species: Streptomyces coelicolor [TaxId: 1902]

Probab=87.51  E-value=0.36  Score=30.93  Aligned_cols=33  Identities=6%  Similarity=0.103  Sum_probs=26.0

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+   .+.|+++||++.||+++|||+...
T Consensus         9 ~aa~~l~~~~G~~~~ti~~Ia~~agvs~~~~Y~~F~   44 (68)
T d2d6ya1           9 EAAVAEFARHGIAGARIDRIAAEARANKQLIYAYYG   44 (68)
T ss_dssp             HHHHHHHHHHTTTSCCHHHHHHHHTCCHHHHHHHHS
T ss_pred             HHHHHHHHHhCccccCHHHHHHHHCcchhHHHHHCc
Confidence            345555544   458999999999999999999865

>d1sgma1 a.4.1.9 (A:5-77) Putative transcriptional regulator YxaF {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator YxaF
species: Bacillus subtilis [TaxId: 1423]

Probab=87.51  E-value=0.3  Score=31.62  Aligned_cols=32  Identities=16%  Similarity=0.162  Sum_probs=25.4

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRA   70 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i   70 (229)
                      ..|++.+..   .+.|+++||++.||++++||+..
T Consensus         9 ~aa~~l~~~~G~~~~si~~Ia~~agvs~~~iy~~F   43 (73)
T d1sgma1           9 HTASRLSQLQGYHATGLNQIVKESGAPKGSLYHFF   43 (73)
T ss_dssp             HHHHHHHHHHCTTTCCHHHHHHHHCCCSCHHHHST
T ss_pred             HHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHc
Confidence            445555543   56899999999999999999874

>d1efaa1 a.35.1.5 (A:2-60) Lac repressor (LacR), 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: Lac repressor (LacR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.44  E-value=0.41  Score=30.50  Aligned_cols=40  Identities=10%  Similarity=0.084  Sum_probs=29.1

Q ss_pred             CCCHHHHHHHcCCChhhHHHHHHHhCCCCCCCCCCCCCCcHHHHHHHHHHH
Q psy17316         49 QMSLTKASVSYGIPSTTLWQRAHRLGIHTPKKEGPTKSWNEEILNVALDAL   99 (229)
Q Consensus        49 ~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~~~~~~~k~~s~e~~~~a~~ll   99 (229)
                      .+++.+||+..||+.+|+.+-+...     ..      .+++.+....+..
T Consensus         2 ~~Ti~diA~~agvS~sTVSr~l~~~-----~~------vs~~tr~rI~~~a   41 (59)
T d1efaa1           2 PVTLYDVAEYAGVSYQTVSRVVNQA-----SH------VSAKTREKVEAAM   41 (59)
T ss_dssp             CCCHHHHHHTTTSCHHHHHHHHTTC-----SS------CCTHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHCCC-----Cc------CCHHHHHHHHHHH
Confidence            3689999999999999999998632     11      3566666555433

>d1lmb3_ a.35.1.2 (3:) lambda C1 repressor, DNA-binding domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: lambda C1 repressor, DNA-binding domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=87.36  E-value=0.32  Score=32.92  Aligned_cols=26  Identities=8%  Similarity=-0.012  Sum_probs=23.6

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.-|+|+.++|+.+||+.++|.+|-+
T Consensus        22 ~~~gltq~~lA~~lgis~~~is~~E~   47 (87)
T d1lmb3_          22 NELGLSQESVADKMGMGQSGVGALFN   47 (87)
T ss_dssp             HHHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHhCccHHHHHHHHh
Confidence            45789999999999999999999965

>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro 434
species: Bacteriophage 434 [TaxId: 10712]

Probab=87.36  E-value=0.47  Score=29.99  Aligned_cols=32  Identities=6%  Similarity=-0.131  Sum_probs=26.9

Q ss_pred             HHHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        183 LEGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       183 V~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      -+...+.+++..+.|...||+.+|+.+|-++.
T Consensus         9 r~~R~~~gltq~~lA~~~gvs~~ti~~~E~g~   40 (65)
T d2croa_           9 KKRRIALKMTQTELATKAGVKQQSIQLIEAGV   40 (65)
T ss_dssp             HHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTC
T ss_pred             HHHHHHcCCCHHHHHHHHCcCHhHHHHHHCCC
Confidence            33445677999999999999999999998764

>d2fx0a1 a.4.1.9 (A:4-76) Hemolysin II regulatory protein, HlyIIR {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hemolysin II regulatory protein, HlyIIR
species: Bacillus cereus [TaxId: 1396]

Probab=87.21  E-value=0.48  Score=30.78  Aligned_cols=33  Identities=9%  Similarity=-0.034  Sum_probs=26.3

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+   .++|+++||++.||+++|||+...
T Consensus        11 ~aa~~l~~~~G~~~~si~~Ia~~agvs~~~~Y~~F~   46 (73)
T d2fx0a1          11 KAAKKKFGERGYEGTSIQEIAKEAKVNVAMASYYFN   46 (73)
T ss_dssp             HHHHHHHHHHCTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHhCcccCcHHHHHHHHCcChhHHHHHCc
Confidence            445555543   568999999999999999999865

>d2esna1 a.4.5.37 (A:3-91) Probable LysR-type transcriptional regulator PA0477 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LysR-like transcriptional regulators
domain: Probable LysR-type transcriptional regulator PA0477
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=87.16  E-value=0.27  Score=33.40  Aligned_cols=41  Identities=15%  Similarity=0.095  Sum_probs=30.3

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ++.+-..+.-.+ .+.+.+ |+..||+++||+.++|.+.+++.
T Consensus         4 ~~ldl~~L~~f~-~v~~~g-s~t~AA~~l~isq~avs~~l~~l   44 (89)
T d2esna1           4 RRLDLNLLLVFD-ALYRHR-NVGTAASELAISASAFSHALGRL   44 (89)
T ss_dssp             TTSCTTHHHHHH-HHHHHS-SHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHH-HHHHhC-CHHHHHHHHCCCCcHhhHHHHHH
Confidence            344444544444 444435 99999999999999999999974

>d2gena1 a.4.1.9 (A:6-75) Probable transcriptional regulator PA1836 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator PA1836
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=87.11  E-value=0.4  Score=30.63  Aligned_cols=33  Identities=18%  Similarity=0.241  Sum_probs=25.4

Q ss_pred             HHHHHHHHHcC---CCCHHHHHHHhCCChHHHHHHH
Q psy17316        124 LNVALDALRAG---SISANKASKAYGIPSSTLYKIA  156 (229)
Q Consensus       124 k~~AV~~~~~g---~~S~~~~a~k~gIp~sTL~~~i  156 (229)
                      +..|++.+.+.   ..|+++||+..||+++|+|++.
T Consensus         6 l~aa~~l~~~~G~~~~si~~Ia~~agvs~~t~Y~~F   41 (70)
T d2gena1           6 LQAALACFSEHGVDATTIEMIRDRSGASIGSLYHHF   41 (70)
T ss_dssp             HHHHHHHHHHHCTTTCCHHHHHHHHCCCHHHHHHHT
T ss_pred             HHHHHHHHHHhCcccCCHHHHHHHHCcCHHHHHHHC
Confidence            45555555443   3599999999999999999954

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=87.06  E-value=0.33  Score=30.93  Aligned_cols=33  Identities=18%  Similarity=0.204  Sum_probs=28.6

Q ss_pred             HHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         41 ALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        41 AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +++.+.+|.+|..++|+..|++++|+.+.+..+
T Consensus         4 Il~~i~~~pisr~eLa~~~gls~~TVs~~v~~L   36 (62)
T d2hoea1           4 ILKRIMKSPVSRVELAEELGLTKTTVGEIAKIF   36 (62)
T ss_dssp             SHHHHHHSCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            355666789999999999999999999998874

>d1t56a1 a.4.1.9 (A:22-94) Ethr repressor {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Ethr repressor
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=86.99  E-value=0.47  Score=30.48  Aligned_cols=33  Identities=30%  Similarity=0.359  Sum_probs=25.8

Q ss_pred             HHHHHHHHHcCC---CCHHHHHHHhCCChHHHHHHH
Q psy17316        124 LNVALDALRAGS---ISANKASKAYGIPSSTLYKIA  156 (229)
Q Consensus       124 k~~AV~~~~~g~---~S~~~~a~k~gIp~sTL~~~i  156 (229)
                      +..|.+.+.+.+   .|+++||+..||+++|+|++.
T Consensus         9 l~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F   44 (73)
T d1t56a1           9 LATAENLLEDRPLADISVDDLAKGAGISRPTFYFYF   44 (73)
T ss_dssp             HHHHHHHHHHSCGGGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             HHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHC
Confidence            355566665544   599999999999999999953

>d2id3a1 a.4.1.9 (A:13-80) Putative transcriptional regulator SCO5951 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO5951
species: Streptomyces coelicolor [TaxId: 1902]

Probab=86.95  E-value=0.31  Score=31.17  Aligned_cols=36  Identities=31%  Similarity=0.332  Sum_probs=26.8

Q ss_pred             HHHH-HHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         36 EDMD-AALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        36 e~~~-~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.++ .+++.+.+   .+.|+.+||++.||+++|||+...
T Consensus         9 ~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~iY~~F~   48 (68)
T d2id3a1           9 EAVLLAAGDALAADGFDALDLGEIARRAGVGKTTVYRRWG   48 (68)
T ss_dssp             HHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHhCcccCCHHHHHHHHCcCHHHHHHHCc
Confidence            4443 44444443   458999999999999999999865

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF1790-like
domain: Transcriptional regulatory protein PF1790
species: Pyrococcus furiosus [TaxId: 2261]

Probab=86.88  E-value=0.23  Score=38.45  Aligned_cols=38  Identities=16%  Similarity=0.137  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         36 EDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        36 e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .....+|..+.+|.+++.++|..+||+.+++++.++.+
T Consensus        15 ~~R~~Il~~L~~~~~~~~ela~~l~~s~~~v~~HL~~L   52 (194)
T d2p4wa1          15 ETRRRILFLLTKRPYFVSELSRELGVGQKAVLEHLRIL   52 (194)
T ss_dssp             HHHHHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            34567777788899999999999999999999999986

>d1bl0a2 a.4.1.8 (A:63-124) MarA {Escherichia coli [TaxId: 562]}

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

Probab=86.68  E-value=0.61  Score=29.51  Aligned_cols=39  Identities=15%  Similarity=0.258  Sum_probs=33.5

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCC-ChhhHHHHHHH-hCCC
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGI-PSTTLWQRAHR-LGIH   76 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gI-p~sTL~~~i~~-~gi~   76 (229)
                      |.+|.+++.++++|+.+||..+|- +.+.+.+..++ +|..
T Consensus         3 l~~a~~lL~~t~~~i~~IA~~~Gf~~~~~F~r~Fk~~~g~t   43 (62)
T d1bl0a2           3 MTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVP   43 (62)
T ss_dssp             HHHHHHHHHHCCCCHHHHHHHTTCSCHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHccCCCHHHHHHHHCCCCHHHHHHHHHHHHCcC
Confidence            678899999999999999999999 57889998887 4553

>d1pb6a1 a.4.1.9 (A:14-85) Hypothetical transcriptional regulator YcdC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YcdC
species: Escherichia coli [TaxId: 562]

Probab=86.62  E-value=0.41  Score=30.91  Aligned_cols=33  Identities=18%  Similarity=0.235  Sum_probs=25.8

Q ss_pred             HHHHHHHHHcC---CCCHHHHHHHhCCChHHHHHHH
Q psy17316        124 LNVALDALRAG---SISANKASKAYGIPSSTLYKIA  156 (229)
Q Consensus       124 k~~AV~~~~~g---~~S~~~~a~k~gIp~sTL~~~i  156 (229)
                      +..|++.+.+.   ..|+++||+..||+++|||+..
T Consensus        10 l~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~y~~F   45 (72)
T d1pb6a1          10 LSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYF   45 (72)
T ss_dssp             HHHHHHHHHHHCTTTCCHHHHHHHTTSCHHHHHHHS
T ss_pred             HHHHHHHHHHhCccccCHHHHHHHhCCChHHHHHHC
Confidence            45556666553   3699999999999999999954

>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]}

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

Probab=86.51  E-value=0.17  Score=31.08  Aligned_cols=36  Identities=17%  Similarity=0.089  Sum_probs=29.4

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         38 MDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        38 ~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      +...|++-.+..+++.++|+.+|+++++|.+..++.
T Consensus         8 i~~yi~~~~~~~itl~~lA~~~~~S~~~l~r~Fk~~   43 (54)
T d1d5ya1           8 LLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDV   43 (54)
T ss_dssp             HHHHHHTTSSSSCCCHHHHTTTSSCHHHHHHHHHHH
T ss_pred             HHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            344555545678999999999999999999999873

>d1jt6a1 a.4.1.9 (A:2-72) Multidrug binding protein QacR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Multidrug binding protein QacR
species: Staphylococcus aureus [TaxId: 1280]

Probab=86.23  E-value=0.46  Score=30.49  Aligned_cols=34  Identities=18%  Similarity=0.182  Sum_probs=25.6

Q ss_pred             HHHHHHHHHcC---CCCHHHHHHHhCCChHHHHHHHH
Q psy17316        124 LNVALDALRAG---SISANKASKAYGIPSSTLYKIAR  157 (229)
Q Consensus       124 k~~AV~~~~~g---~~S~~~~a~k~gIp~sTL~~~ik  157 (229)
                      +..|++.+.+.   +.|+++||+..||+++|+|+...
T Consensus         7 l~aa~~l~~~~G~~~~s~~~Ia~~agvs~~~~y~~F~   43 (71)
T d1jt6a1           7 LGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFK   43 (71)
T ss_dssp             HHHHHHHHHHHCTTTCCHHHHHHHTTCCHHHHHHHHS
T ss_pred             HHHHHHHHHHhCccccCHHHHHHHHCcCHhHHHHHCc
Confidence            34555555442   36999999999999999999653

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=86.19  E-value=0.79  Score=31.91  Aligned_cols=27  Identities=19%  Similarity=0.283  Sum_probs=24.8

Q ss_pred             HHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        186 IRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       186 ~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +..|.++..++|...|||.++||..++
T Consensus        30 ~~~g~~t~~eia~~~~i~~~~v~~~l~   56 (109)
T d1sfxa_          30 LERGGMRVSEIARELDLSARFVRDRLK   56 (109)
T ss_dssp             HHHCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HhcCCCCHHHHHHHhCCCcchHHHHHH
Confidence            355889999999999999999999998

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=85.76  E-value=0.5  Score=30.33  Aligned_cols=45  Identities=13%  Similarity=-0.012  Sum_probs=35.4

Q ss_pred             CHHHHHHHHHHHHc--CCCCHHHHHHHcCCChhhHHHHHHHhCCCCC
Q psy17316         34 THEDMDAALEALRA--GQMSLTKASVSYGIPSTTLWQRAHRLGIHTP   78 (229)
Q Consensus        34 t~e~~~~AI~~~~~--g~~S~~~aA~~~gIp~sTL~~~i~~~gi~~~   78 (229)
                      |.|+-+++|-.+..  |..+..+||+.+||+++|+.+-++++.-.|.
T Consensus         6 s~EdYL~~I~~L~~~~~~v~~~~iA~~L~vs~~SVt~mvkrL~~~Gl   52 (63)
T d2isya1           6 TTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGL   52 (63)
T ss_dssp             HHHHHHHHHHHHHHTTCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCchhHHHHHHHHHHCCC
Confidence            45677777765543  6689999999999999999999998754443

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

Probab=85.73  E-value=0.74  Score=28.69  Aligned_cols=31  Identities=3%  Similarity=-0.169  Sum_probs=26.5

Q ss_pred             HHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        184 EGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       184 ~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      +.....++|..+.|...|||.+++..|-++.
T Consensus         8 ~~R~~~g~sq~elA~~~gvs~~~is~~E~g~   38 (63)
T d1r69a_           8 SKRIQLGLNQAELAQKVGTTQQSIEQLENGK   38 (63)
T ss_dssp             HHHHHTTCCHHHHHHHHTSCHHHHHHHHTTS
T ss_pred             HHHHHcCCcHHHHHHHhCcCHHHHHHHHCCC
Confidence            4445677999999999999999999998763

>d3c07a1 a.4.1.9 (A:15-89) Putative transcriptional regulator SCO4850 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO4850
species: Streptomyces coelicolor [TaxId: 1902]

Probab=85.69  E-value=0.67  Score=29.79  Aligned_cols=33  Identities=12%  Similarity=0.231  Sum_probs=26.3

Q ss_pred             HHHHHHHHHcCC---CCHHHHHHHhCCChHHHHHHH
Q psy17316        124 LNVALDALRAGS---ISANKASKAYGIPSSTLYKIA  156 (229)
Q Consensus       124 k~~AV~~~~~g~---~S~~~~a~k~gIp~sTL~~~i  156 (229)
                      +..|++.+.+.+   .|+.+||+.-||+++|+|++.
T Consensus        11 l~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~~y~~F   46 (75)
T d3c07a1          11 LETAMRLFQERGYDRTTMRAIAQEAGVSVGNAYYYF   46 (75)
T ss_dssp             HHHHHHHHHHTCSTTCCHHHHHHHHTSCHHHHHHHC
T ss_pred             HHHHHHHHHHhCcccCCHHHHHHHHCcCHHHHHHHC
Confidence            356666666533   699999999999999999953

>d2g3ba1 a.4.1.9 (A:2-73) Putative transcriptional regulator {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=85.65  E-value=0.35  Score=31.23  Aligned_cols=33  Identities=12%  Similarity=0.204  Sum_probs=26.2

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+   .+.|+..||++.||+++|||++..
T Consensus         9 ~aa~~l~~~~G~~~~ti~~Ia~~agvs~~~ly~~F~   44 (72)
T d2g3ba1           9 KASATAIAQRGIRGLRVNDVAEVAGVSPGLLYYHFK   44 (72)
T ss_dssp             HHHHHHHHHHHHHHCCHHHHHHHHTSCHHHHHHHHC
T ss_pred             HHHHHHHHHhCcccCCHHHHHHHhCcCHHHHHHHCc
Confidence            445555544   358999999999999999999865

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=85.61  E-value=0.36  Score=31.23  Aligned_cols=29  Identities=14%  Similarity=0.138  Sum_probs=26.2

Q ss_pred             HcCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         46 RAGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        46 ~~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .+|.+|..++|+.+|++++|+.+.+..+-
T Consensus        17 ~~g~~sr~eLa~~~glS~~Tv~~~l~~L~   45 (71)
T d1z05a1          17 QKGPISRIDLSKESELAPASITKITRELI   45 (71)
T ss_dssp             HHCSBCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HcCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            46899999999999999999999998753

>d2ao9a1 a.4.1.17 (A:13-132) Phage protein BC1890 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Nanomeric phage protein-like
domain: Phage protein BC1890
species: Bacillus cereus [TaxId: 1396]

Probab=85.52  E-value=0.81  Score=32.65  Aligned_cols=21  Identities=19%  Similarity=0.381  Sum_probs=19.6

Q ss_pred             CCHHHHHHHhCCChHHHHHHH
Q psy17316        136 ISANKASKAYGIPSSTLYKIA  156 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~i  156 (229)
                      -+..++|+..||++.|||+|-
T Consensus        37 ktqeqiAeelGisr~tLyrWr   57 (120)
T d2ao9a1          37 RTQDEMANELGINRTTLWEWR   57 (120)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHH
T ss_pred             hhHHHHHHHhChhHHHHHHHh
Confidence            478899999999999999997

>d2g7ga1 a.4.1.9 (A:9-73) Putative transcriptional regulator Rha04620 {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator Rha04620
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=85.34  E-value=0.53  Score=29.97  Aligned_cols=31  Identities=19%  Similarity=0.417  Sum_probs=24.2

Q ss_pred             HHHHHHH-HcCCCCHHHHHHHhCCChHHHHHH
Q psy17316        125 NVALDAL-RAGSISANKASKAYGIPSSTLYKI  155 (229)
Q Consensus       125 ~~AV~~~-~~g~~S~~~~a~k~gIp~sTL~~~  155 (229)
                      ..|++.+ ..|..|+++||+..||+.++||..
T Consensus         8 ~aa~~l~~~~G~~ti~~Ia~~agvs~~~iY~~   39 (65)
T d2g7ga1           8 EAALELVDRDGDFRMPDLARHLNVQVSSIYHH   39 (65)
T ss_dssp             HHHHHHHHHHSSCCHHHHHHHTTSCHHHHHTT
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCccccchhhc
Confidence            3444444 336789999999999999999984

>d2o7ta1 a.4.1.9 (A:1-78) Transcriptional regulator Cgl1640/Cg1846 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator Cgl1640/Cg1846
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=85.31  E-value=0.6  Score=30.57  Aligned_cols=24  Identities=21%  Similarity=0.344  Sum_probs=21.6

Q ss_pred             CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        189 GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       189 ~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++.|+.++|++.|||.+|+|....
T Consensus        26 ~~~t~~~Ia~~agvs~~t~y~~F~   49 (78)
T d2o7ta1          26 DSLTMENIAEQAGVGVATLYRNFP   49 (78)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             cccCHHHHHHHhCCCHHHHHHHCc
Confidence            458899999999999999999865

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=85.24  E-value=0.6  Score=31.57  Aligned_cols=38  Identities=16%  Similarity=0.109  Sum_probs=31.2

Q ss_pred             CCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        173 AWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       173 ~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ..|+- =.+|+.++.+| ++..++|..++||..||-...+
T Consensus        22 ~LT~r-E~~vl~ll~~G-~s~~eIA~~l~iS~~TV~~~~~   59 (87)
T d1p4wa_          22 RLSPK-ESEVLRLFAEG-FLVTEIAKKLNRSIKTISSQKK   59 (87)
T ss_dssp             SCCHH-HHHHHHHHHHT-CCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCCHH-HHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHH
Confidence            34553 35788888888 8899999999999999998876

>d2hkua1 a.4.1.9 (A:18-87) Putative transcriptional regulator RHA1_ro03468 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator RHA1 ro03468
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=85.14  E-value=0.56  Score=30.19  Aligned_cols=33  Identities=9%  Similarity=0.060  Sum_probs=24.7

Q ss_pred             HHHHHHHHcC--CCCHHHHHHHhCCChHHHHHHHH
Q psy17316        125 NVALDALRAG--SISANKASKAYGIPSSTLYKIAR  157 (229)
Q Consensus       125 ~~AV~~~~~g--~~S~~~~a~k~gIp~sTL~~~ik  157 (229)
                      ..|.+.+.++  +.|+++|++..||++.+||++..
T Consensus         8 ~aA~~l~~~~G~~~t~~~Ia~~agvs~~~~Y~~F~   42 (70)
T d2hkua1           8 TAATELFLEHGEGVPITQICAAAGAHPNQVTYYYG   42 (70)
T ss_dssp             HHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHS
T ss_pred             HHHHHHHHhcccCchHHHHHHHHCCChhhHHhcCC
Confidence            4444444332  26999999999999999999653

>d2hyja1 a.4.1.9 (A:8-82) Putative transcriptional regulator SCO4940 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO4940
species: Streptomyces coelicolor [TaxId: 1902]

Probab=85.14  E-value=0.37  Score=31.39  Aligned_cols=35  Identities=6%  Similarity=0.122  Sum_probs=26.6

Q ss_pred             HHH-HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHH
Q psy17316         36 EDM-DAALEALRA---GQMSLTKASVSYGIPSTTLWQRA   70 (229)
Q Consensus        36 e~~-~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i   70 (229)
                      +.+ ..|++.+.+   .++|+.+||+..||++++||+..
T Consensus         8 ~~il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~~Y~~F   46 (75)
T d2hyja1           8 GRILGRAAEIASEEGLDGITIGRLAEELEMSKSGVHKHF   46 (75)
T ss_dssp             HHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHTTC
T ss_pred             HHHHHHHHHHHHHhCcccCcHHHHHHHHCcCHHHHHHHC
Confidence            444 445555554   35899999999999999999874

>d1vi0a1 a.4.1.9 (A:6-77) Hypothetical transcriptional regulator YsiA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YsiA
species: Bacillus subtilis [TaxId: 1423]

Probab=84.84  E-value=0.52  Score=30.20  Aligned_cols=33  Identities=24%  Similarity=0.346  Sum_probs=26.2

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|++.+.+   .+.|+.+||++.||++++||+...
T Consensus         8 ~aa~~l~~~~G~~~~ti~~Ia~~agvs~~~~y~~F~   43 (72)
T d1vi0a1           8 DAAVEVIAENGYHQSQVSKIAKQAGVADGTIYLYFK   43 (72)
T ss_dssp             HHHHHHHHHHCGGGCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             HHHHHHHHHhCcccccHHHHHHHHCcCHHHHHHHCc
Confidence            455555554   358999999999999999999844

>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: P22 C2 repressor, DNA-binding domain
species: Salmonella bacteriophage P22 [TaxId: 10754]

Probab=84.83  E-value=0.55  Score=29.65  Aligned_cols=31  Identities=3%  Similarity=-0.067  Sum_probs=26.5

Q ss_pred             HHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        184 EGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       184 ~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      +...+.+++..+.|...|||.+|+..|-++.
T Consensus        10 ~~R~~~g~tq~~lA~~~gvs~~~i~~~e~g~   40 (66)
T d2r1jl1          10 ARRKKLKIRQAALGKMVGVSNVAISQWERSE   40 (66)
T ss_dssp             HHHHHHTCCHHHHHHHHTSCHHHHHHHHTTS
T ss_pred             HHHHHcCCCHHHHHHHHCCCHHHHHHHHcCC
Confidence            3345677999999999999999999999864

>d2gfna1 a.4.1.9 (A:4-80) Probable transcriptional regulator RHA1_ro04631 {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator RHA1 ro04631
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=84.76  E-value=0.5  Score=30.79  Aligned_cols=33  Identities=9%  Similarity=0.189  Sum_probs=25.4

Q ss_pred             HHHHHHHHHcC---CCCHHHHHHHhCCChHHHHHHH
Q psy17316        124 LNVALDALRAG---SISANKASKAYGIPSSTLYKIA  156 (229)
Q Consensus       124 k~~AV~~~~~g---~~S~~~~a~k~gIp~sTL~~~i  156 (229)
                      +..|++.+.+.   ..|+++||+.-||+++|||+..
T Consensus        12 l~aa~~l~~~~G~~~~s~~~Ia~~agvs~~~lY~~F   47 (77)
T d2gfna1          12 ADAVLALIAREGISAVTTRAVAEESGWSTGVLNHYF   47 (77)
T ss_dssp             HHHHHHHHHHHCGGGCCHHHHHHHHSSCHHHHHHHT
T ss_pred             HHHHHHHHHHhCccccCHHHHHHHHCCCHHHHHHHC
Confidence            35556665443   3599999999999999999954

>d1v7ba1 a.4.1.9 (A:1-74) Transcriptional regulator Cgl2612 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator Cgl2612
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=84.58  E-value=0.81  Score=29.43  Aligned_cols=33  Identities=27%  Similarity=0.268  Sum_probs=25.0

Q ss_pred             HHHHHHHHHcCC---CCHHHHHHHhCCChHHHHHHH
Q psy17316        124 LNVALDALRAGS---ISANKASKAYGIPSSTLYKIA  156 (229)
Q Consensus       124 k~~AV~~~~~g~---~S~~~~a~k~gIp~sTL~~~i  156 (229)
                      +..|++.+...+   .|+++||+..||+++|||+..
T Consensus        10 l~aa~~l~~~~G~~~~s~~~Ia~~agvs~~t~Y~~F   45 (74)
T d1v7ba1          10 LRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHF   45 (74)
T ss_dssp             HHHHHHHHHHSCSTTCCHHHHHHHHCSCHHHHHHHC
T ss_pred             HHHHHHHHHHhCccccCHHHHHHHhCcCcchHhhhC
Confidence            345555554433   599999999999999999943

>d2g7sa1 a.4.1.9 (A:3-76) Putative transcriptional regulator Atu0279 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator Atu0279
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=84.55  E-value=0.54  Score=30.38  Aligned_cols=33  Identities=21%  Similarity=0.239  Sum_probs=25.5

Q ss_pred             HHHHHHHHHcCC---CCHHHHHHHhCCChHHHHHHH
Q psy17316        124 LNVALDALRAGS---ISANKASKAYGIPSSTLYKIA  156 (229)
Q Consensus       124 k~~AV~~~~~g~---~S~~~~a~k~gIp~sTL~~~i  156 (229)
                      +..|.+.+.+.+   .|+++||+..||+++|+|+..
T Consensus        10 l~aa~~l~~~~G~~~~s~~~Ia~~agvs~~~iY~~F   45 (74)
T d2g7sa1          10 LQCARTLIIRGGYNSFSYADISQVVGIRNASIHHHF   45 (74)
T ss_dssp             HHHHHHHHHHHCGGGCCHHHHHHHHCCCHHHHHHHC
T ss_pred             HHHHHHHHHHhCccccCHHHHHHHHCcCcchHHHHC
Confidence            355566665433   599999999999999999953

>d2id6a1 a.4.1.9 (A:1-75) Transcriptional regulator TM1030 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator TM1030
species: Thermotoga maritima [TaxId: 2336]

Probab=84.33  E-value=0.45  Score=30.91  Aligned_cols=33  Identities=12%  Similarity=0.222  Sum_probs=26.2

Q ss_pred             HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         39 DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        39 ~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..+++.+.+   .+.|+++||++.||+++|||+...
T Consensus        10 ~aa~~l~~~~G~~~~ti~~Ia~~agvs~~~iY~~F~   45 (75)
T d2id6a1          10 KAAVEVFGKKGYDRATTDEIAEKAGVAKGLIFHYFK   45 (75)
T ss_dssp             HHHHHHHHHHHHHHCCHHHHHHHHTCCTHHHHHHHS
T ss_pred             HHHHHHHHHhCccccCHHHHHHHhCCCHHHHHHHCC
Confidence            445555544   358999999999999999999865

>d2oi8a1 a.4.1.9 (A:8-86) Putative regulatory protein Sco4313 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative regulatory protein Sco4313
species: Streptomyces coelicolor [TaxId: 1902]

Probab=84.28  E-value=0.46  Score=31.11  Aligned_cols=23  Identities=17%  Similarity=0.343  Sum_probs=20.6

Q ss_pred             CCCCHHHHHHHcCCChhhHHHHH
Q psy17316         48 GQMSLTKASVSYGIPSTTLWQRA   70 (229)
Q Consensus        48 g~~S~~~aA~~~gIp~sTL~~~i   70 (229)
                      .++|+++||++.||++++||+..
T Consensus        28 ~~~t~~~Ia~~agvs~~~~Y~~F   50 (79)
T d2oi8a1          28 SALSLNAIAKRMGMSGPALYRYF   50 (79)
T ss_dssp             TSCCHHHHHHHTTCCHHHHHTTC
T ss_pred             cccCHHHHHHHhCCCCCchhhhc
Confidence            35899999999999999999863

>d1ixca1 a.4.5.37 (A:1-89) LysR-type regulatory protein CbnR {Ralstonia eutropha [TaxId: 106590]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LysR-like transcriptional regulators
domain: LysR-type regulatory protein CbnR
species: Ralstonia eutropha [TaxId: 106590]

Probab=84.28  E-value=0.78  Score=30.97  Aligned_cols=41  Identities=10%  Similarity=0.206  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh----CCCCCC
Q psy17316         37 DMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL----GIHTPK   79 (229)
Q Consensus        37 ~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~----gi~~~~   79 (229)
                      ++...+ .+.+.+ |+..||+++||++++|.+.+++.    |.....
T Consensus         5 ~L~~f~-~v~e~g-s~~~AA~~L~isq~avs~~i~~LE~~lg~~Lf~   49 (89)
T d1ixca1           5 QLKYFI-AVAEAG-NMAAAAKRLHVSQPPITRQMQALEADLGVVLLE   49 (89)
T ss_dssp             HHHHHH-HHHHHS-SHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCBC
T ss_pred             HHHHHH-HHHHhC-CHHHHHHHhCCChHHHHHHHHHHHhcCCceeeE
Confidence            333344 444445 99999999999999999999974    655443

>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=84.26  E-value=0.67  Score=32.11  Aligned_cols=28  Identities=11%  Similarity=0.107  Sum_probs=25.1

Q ss_pred             cCCCCHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         47 AGQMSLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        47 ~g~~S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      .|.+|+.++|+.+||+++|+.+-+.++.
T Consensus        34 ~~~~t~~eLa~~~~i~~~tvs~~l~~L~   61 (109)
T d2d1ha1          34 EKPITSEELADIFKLSKTTVENSLKKLI   61 (109)
T ss_dssp             CSCEEHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCccHhHHHHHHHHHH
Confidence            4569999999999999999999999863

>d1x57a1 a.35.1.12 (A:8-85) Endothelial differentiation-related factor 1, EDF1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: EDF1-like
domain: Endothelial differentiation-related factor 1, EDF1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.00  E-value=0.71  Score=30.41  Aligned_cols=32  Identities=0%  Similarity=-0.015  Sum_probs=26.5

Q ss_pred             HHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         40 AALEAL-RAGQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        40 ~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      ..|..+ ..-++|+.++|+.+||+.++|.+|-.
T Consensus         9 ~~I~~~R~~~gltq~~lA~~~gis~~~is~~E~   41 (78)
T d1x57a1           9 KVIQQGRQSKGLTQKDLATKINEKPQVIADYES   41 (78)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCChhHHHHcCCCCHHHHHHHHc
Confidence            344433 35789999999999999999999977

>d1j9ia_ a.6.1.5 (A:) Terminase gpNU1 subunit domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: Terminase gpNU1 subunit domain
domain: Terminase gpNU1 subunit domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=83.93  E-value=0.31  Score=32.04  Aligned_cols=26  Identities=12%  Similarity=0.211  Sum_probs=21.9

Q ss_pred             CHHHHHHHcCCChhhHHHHHHHhCCCC
Q psy17316         51 SLTKASVSYGIPSTTLWQRAHRLGIHT   77 (229)
Q Consensus        51 S~~~aA~~~gIp~sTL~~~i~~~gi~~   77 (229)
                      ...++|+.|||+..||..|+++ |...
T Consensus         4 nk~~lA~iFGVS~~TI~~W~~~-G~Pv   29 (68)
T d1j9ia_           4 NKKQLADIFGASIRTIQNWQEQ-GMPV   29 (68)
T ss_dssp             EHHHHHHHTTCCHHHHHHHTTT-TCCC
T ss_pred             CHHHHHHHhCCCHHHHHHHHHC-CCCe
Confidence            4679999999999999999975 6543

>d2fd5a1 a.4.1.9 (A:1-76) Probable transcriptional regulator PA3133 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator PA3133
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=83.71  E-value=0.42  Score=31.05  Aligned_cols=36  Identities=17%  Similarity=0.167  Sum_probs=26.3

Q ss_pred             HHH-HHHHHHHHc---CCCCHHHHHHHcCCChhhHHHHHH
Q psy17316         36 EDM-DAALEALRA---GQMSLTKASVSYGIPSTTLWQRAH   71 (229)
Q Consensus        36 e~~-~~AI~~~~~---g~~S~~~aA~~~gIp~sTL~~~i~   71 (229)
                      +.+ ..|++.+.+   .+.|+++||++.||+++|||+...
T Consensus        10 ~~Il~aa~~l~~~~G~~~~si~~Ia~~agvs~~t~Y~~F~   49 (76)
T d2fd5a1          10 ARILGAATQALLERGAVEPSVGEVMGAAGLTVGGFYAHFQ   49 (76)
T ss_dssp             HHHHHHHHHHHHHHTTTSCCHHHHHHHTTCCGGGGGGTCS
T ss_pred             HHHHHHHHHHHHHhCcccccHHHHHHHhCCCccchhhcCC
Confidence            444 344444443   468999999999999999998743

>d2vkva1 a.4.1.9 (A:6-67) Tetracyclin repressor (Tet-repressor, TetR) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Tetracyclin repressor (Tet-repressor, TetR)
species: Escherichia coli [TaxId: 562]

Probab=83.70  E-value=0.53  Score=29.51  Aligned_cols=32  Identities=25%  Similarity=0.331  Sum_probs=23.9

Q ss_pred             HHHHHHHHcC---CCCHHHHHHHhCCChHHHHHHH
Q psy17316        125 NVALDALRAG---SISANKASKAYGIPSSTLYKIA  156 (229)
Q Consensus       125 ~~AV~~~~~g---~~S~~~~a~k~gIp~sTL~~~i  156 (229)
                      ..|++.+.+.   .+|+++||+..||+.+|||++.
T Consensus         6 ~aA~~l~~~~G~~~~s~~~Ia~~agvs~~tiy~~F   40 (62)
T d2vkva1           6 NSALELGNEVGIEGLTTRKLAQKLGVEQPTLYWHV   40 (62)
T ss_dssp             HHHHHHHHHHHHHHCCHHHHHHHHTSCHHHHHHHS
T ss_pred             HHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHC
Confidence            4444444332   3599999999999999999954

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=83.66  E-value=0.92  Score=29.50  Aligned_cols=34  Identities=12%  Similarity=0.159  Sum_probs=26.7

Q ss_pred             HHHHHHHHHhCC--CcHHHHHHHhCC-ChHHHHHHHH
Q psy17316        179 LEIALEGIRSGQ--TTVQRASAEYGI-PSGTLYGRCK  212 (229)
Q Consensus       179 r~eaV~~~~~~~--~s~~eAA~~fgV-p~~tv~~~vk  212 (229)
                      ..-|.+++..++  =|+.|+|..||+ |.+||+..++
T Consensus        11 L~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~   47 (71)
T d1jhfa1          11 FDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLK   47 (71)
T ss_dssp             HHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHH
Confidence            344555566666  459999999999 8999999998

>d2d6ya1 a.4.1.9 (A:7-74) Putative regulator SCO4008 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative regulator SCO4008
species: Streptomyces coelicolor [TaxId: 1902]

Probab=83.49  E-value=0.74  Score=29.35  Aligned_cols=33  Identities=6%  Similarity=0.084  Sum_probs=24.9

Q ss_pred             HHHHHHHHcC---CCCHHHHHHHhCCChHHHHHHHH
Q psy17316        125 NVALDALRAG---SISANKASKAYGIPSSTLYKIAR  157 (229)
Q Consensus       125 ~~AV~~~~~g---~~S~~~~a~k~gIp~sTL~~~ik  157 (229)
                      ..|++.+.+.   ..|+++||++.||+++++|+...
T Consensus         9 ~aa~~l~~~~G~~~~ti~~Ia~~agvs~~~~Y~~F~   44 (68)
T d2d6ya1           9 EAAVAEFARHGIAGARIDRIAAEARANKQLIYAYYG   44 (68)
T ss_dssp             HHHHHHHHHHTTTSCCHHHHHHHHTCCHHHHHHHHS
T ss_pred             HHHHHHHHHhCccccCHHHHHHHHCcchhHHHHHCc
Confidence            4445555443   35999999999999999999553

>d2fq4a1 a.4.1.9 (A:9-77) Transcriptional regulator BC3163 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator BC3163
species: Bacillus cereus [TaxId: 1396]

Probab=83.08  E-value=1.1  Score=28.60  Aligned_cols=24  Identities=17%  Similarity=0.259  Sum_probs=22.0

Q ss_pred             CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        189 GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       189 ~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+.++.++|.+-||+..++|+.+.
T Consensus        23 ~~~t~~~Ia~~agvs~~~~y~~F~   46 (69)
T d2fq4a1          23 KAVTVDKIAERAKVSKATIYKWWP   46 (69)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHCC
Confidence            458899999999999999999876

>d1rr7a_ a.4.1.14 (A:) Middle operon regulator, Mor {Bacteriophage Mu [TaxId: 10677]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Middle operon regulator, Mor
domain: Middle operon regulator, Mor
species: Bacteriophage Mu [TaxId: 10677]

Probab=82.99  E-value=0.61  Score=32.31  Aligned_cols=31  Identities=16%  Similarity=0.304  Sum_probs=25.2

Q ss_pred             HHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHh
Q psy17316        181 IALEGIRSGQTTVQRASAEYGIPSGTLYGRCKL  213 (229)
Q Consensus       181 eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~  213 (229)
                      +|.+..  ++.|+.+.|.+||+|..++|..++.
T Consensus        59 ~I~~ef--~G~n~~eLA~kY~lS~~~I~~Ii~~   89 (94)
T d1rr7a_          59 RIWNDF--NGRNVSELTTRYGVTFNTVYKAIRR   89 (94)
T ss_dssp             HHHHHC--CSSCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHHHh--CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            444443  4589999999999999999999873

>d1y9qa1 a.35.1.8 (A:4-82) Probable transcriptional regulator VC1968, N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Probable transcriptional regulator VC1968, N-terminal domain
domain: Probable transcriptional regulator VC1968, N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=82.96  E-value=0.92  Score=29.53  Aligned_cols=34  Identities=9%  Similarity=-0.048  Sum_probs=28.3

Q ss_pred             HHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        182 ALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       182 aV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      +-+.....++|..+.|...|||.+++..|-++..
T Consensus        13 lr~~R~~~g~sq~~lA~~~gis~~~i~~~E~g~~   46 (79)
T d1y9qa1          13 LKNLRKSRGLSLDATAQLTGVSKAMLGQIERGES   46 (79)
T ss_dssp             HHHHHHHTTCCHHHHHHHHSSCHHHHHHHHTTCS
T ss_pred             HHHHHHHcCCCHHHHHHHHCcchhHHHHHHcCCC
Confidence            3444556789999999999999999999998653

>d3bwga1 a.4.5.6 (A:5-82) Transcriptional regulator YydK {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional regulator YydK
species: Bacillus subtilis [TaxId: 1423]

Probab=82.88  E-value=1  Score=29.49  Aligned_cols=32  Identities=13%  Similarity=0.097  Sum_probs=25.5

Q ss_pred             HHHHHHHhCC------C-cHHHHHHHhCCChHHHHHHHH
Q psy17316        181 IALEGIRSGQ------T-TVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       181 eaV~~~~~~~------~-s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+.++|.+|.      + |..+.|..||||+.||...++
T Consensus         6 ~i~~~I~~g~l~~G~~LPse~~La~~~~vSr~tvr~Al~   44 (78)
T d3bwga1           6 EIETYIEEHQLQQGDKLPVLETLMAQFEVSKSTITKSLE   44 (78)
T ss_dssp             HHHHHHHHTTCCTTCBCCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHcCCCCCcCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            4555555544      4 689999999999999999987

>d2fx0a1 a.4.1.9 (A:4-76) Hemolysin II regulatory protein, HlyIIR {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hemolysin II regulatory protein, HlyIIR
species: Bacillus cereus [TaxId: 1396]

Probab=82.86  E-value=1.2  Score=28.72  Aligned_cols=24  Identities=13%  Similarity=0.014  Sum_probs=22.1

Q ss_pred             CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        189 GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       189 ~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ...|+.++|...|||.+++|+..+
T Consensus        23 ~~~si~~Ia~~agvs~~~~Y~~F~   46 (73)
T d2fx0a1          23 EGTSIQEIAKEAKVNVAMASYYFN   46 (73)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             ccCcHHHHHHHHCcChhHHHHHCc
Confidence            568999999999999999999876

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=82.63  E-value=1.2  Score=29.75  Aligned_cols=43  Identities=7%  Similarity=0.071  Sum_probs=34.5

Q ss_pred             CCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHh
Q psy17316        135 SISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRS  188 (229)
Q Consensus       135 ~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~  188 (229)
                      .+|+.++|++.||+.+|+.|-+++.|...-           .|++..+.+.+.+
T Consensus        36 ~~si~~lA~~~~vS~sTi~Rf~kklG~~gf-----------~e~k~~l~~el~~   78 (83)
T d2o3fa1          36 ESTVNEISALANSSDAAVIRLCKSLGLKGF-----------QDLKMRVAGDLAK   78 (83)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHHHHHTTCSSH-----------HHHHHHHHHHHHS
T ss_pred             HccHHHHHHHHCCCHHHHHHHHHHhCCCCH-----------HHHHHHHHHHHcc
Confidence            469999999999999999999998886553           3677777666544

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=82.61  E-value=0.74  Score=30.00  Aligned_cols=41  Identities=5%  Similarity=0.024  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHc-CC--CCHHHHHHHcCC-ChhhHHHHHHHhCCC
Q psy17316         36 EDMDAALEALRA-GQ--MSLTKASVSYGI-PSTTLWQRAHRLGIH   76 (229)
Q Consensus        36 e~~~~AI~~~~~-g~--~S~~~aA~~~gI-p~sTL~~~i~~~gi~   76 (229)
                      .+++.+|..+.. .|  -|+++||+.+|+ +.+|+++.+..+.-.
T Consensus         8 ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~k   52 (71)
T d1jhfa1           8 QEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARK   52 (71)
T ss_dssp             HHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHC
Confidence            455788887754 23  799999999999 799999999986433

>d2fbqa1 a.4.1.9 (A:2-80) Transcriptional regulator PsrA {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator PsrA
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=82.59  E-value=1.2  Score=28.91  Aligned_cols=24  Identities=8%  Similarity=0.155  Sum_probs=22.0

Q ss_pred             CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        189 GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       189 ~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .++++.++|..-|||..++|+...
T Consensus        23 ~~~ti~~Ia~~agvs~~s~y~~F~   46 (79)
T d2fbqa1          23 AETSLRLITSKAGVNLAAVNYHFG   46 (79)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHTC
T ss_pred             ccccHHHHHHHHCcChhHHHHHCc
Confidence            568999999999999999999875

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

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

Probab=82.55  E-value=1.4  Score=30.86  Aligned_cols=42  Identities=10%  Similarity=0.066  Sum_probs=36.1

Q ss_pred             CCCHHHHHHHHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhh
Q psy17316        173 AWKPEDLEIALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLS  214 (229)
Q Consensus       173 ~~t~e~r~eaV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~  214 (229)
                      ..++-+...+++.+...+.+..++|.++|+|.++|.+.+++.
T Consensus        13 ~L~p~e~A~a~~~l~~~g~s~~eiA~~~G~s~~~V~~~l~L~   54 (114)
T d1r71a_          13 ELTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVTLL   54 (114)
T ss_dssp             CCCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHGGG
T ss_pred             CCCHHHHHHHHHHHHHhCCCHHHHHHHHCCcHHHHHHHHHHh
Confidence            356777888888888877999999999999999999999843

>d2np5a1 a.4.1.9 (A:9-77) Transcriptional regulator RHA1_ro04179 {Rhodococcus sp. [TaxId: 1831]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator RHA1 ro04179
species: Rhodococcus sp. [TaxId: 1831]

Probab=82.53  E-value=0.8  Score=28.97  Aligned_cols=37  Identities=22%  Similarity=0.353  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHHh----CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        176 PEDLEIALEGIRS----GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       176 ~e~r~eaV~~~~~----~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +|..+++...+..    .+.++.++|...|||.+++|....
T Consensus         3 ~e~i~~aa~~l~~~~G~~~~ti~~Ia~~agvs~~~iy~~F~   43 (69)
T d2np5a1           3 PERLAAALFDVAAESGLEGASVREVAKRAGVSIGAVQHHFS   43 (69)
T ss_dssp             HHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHhCccccCHHHHHHHhCCCHHHHHHHCc
Confidence            3444444444443    458899999999999999999764

>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Putative transcriptional regulator RHA1 ro03477
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=82.41  E-value=0.78  Score=29.52  Aligned_cols=41  Identities=15%  Similarity=0.174  Sum_probs=29.4

Q ss_pred             HHHHHHH-HHHHcCC------CCHHHHHHHcCCChhhHHHHHHHhCCC
Q psy17316         36 EDMDAAL-EALRAGQ------MSLTKASVSYGIPSTTLWQRAHRLGIH   76 (229)
Q Consensus        36 e~~~~AI-~~~~~g~------~S~~~aA~~~gIp~sTL~~~i~~~gi~   76 (229)
                      +++...| ++|.+|.      ++.+++|++|||+++|+++=+..+..+
T Consensus         5 ~qi~~~l~~~I~~g~~~~G~~l~~~~La~~~~vSr~tvr~Al~~L~~~   52 (69)
T d2hs5a1           5 TRVAGILRDAIIDGTFRPGARLSEPDICAALDVSRNTVREAFQILIED   52 (69)
T ss_dssp             HHHHHHHHHHHHHTSSCTTCEECHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCCCcCccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            3444444 3555544      689999999999999999988775433

>d1vi0a1 a.4.1.9 (A:6-77) Hypothetical transcriptional regulator YsiA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YsiA
species: Bacillus subtilis [TaxId: 1423]

Probab=82.39  E-value=0.73  Score=29.43  Aligned_cols=33  Identities=18%  Similarity=0.382  Sum_probs=25.2

Q ss_pred             HHHHHHHHHcCC---CCHHHHHHHhCCChHHHHHHH
Q psy17316        124 LNVALDALRAGS---ISANKASKAYGIPSSTLYKIA  156 (229)
Q Consensus       124 k~~AV~~~~~g~---~S~~~~a~k~gIp~sTL~~~i  156 (229)
                      +..|++.+...+   .|+.+||+..||+++++|+..
T Consensus         7 l~aa~~l~~~~G~~~~ti~~Ia~~agvs~~~~y~~F   42 (72)
T d1vi0a1           7 IDAAVEVIAENGYHQSQVSKIAKQAGVADGTIYLYF   42 (72)
T ss_dssp             HHHHHHHHHHHCGGGCCHHHHHHHHTSCHHHHHHHC
T ss_pred             HHHHHHHHHHhCcccccHHHHHHHHCcCHHHHHHHC
Confidence            355555554433   599999999999999999943

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=82.21  E-value=0.85  Score=30.76  Aligned_cols=40  Identities=10%  Similarity=0.111  Sum_probs=30.7

Q ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHH
Q psy17316         31 KTWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHR   72 (229)
Q Consensus        31 ~kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~   72 (229)
                      ...|+-++ +++..+.. |++..+||..++|+..|+...+..
T Consensus        21 ~~LT~rE~-~vl~ll~~-G~s~~eIA~~l~iS~~TV~~~~~~   60 (87)
T d1p4wa_          21 KRLSPKES-EVLRLFAE-GFLVTEIAKKLNRSIKTISSQKKS   60 (87)
T ss_dssp             SSCCHHHH-HHHHHHHH-TCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCHHHH-HHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHH
Confidence            35666554 45556666 679999999999999999987774

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

Probab=82.08  E-value=1.4  Score=27.88  Aligned_cols=34  Identities=12%  Similarity=-0.047  Sum_probs=27.9

Q ss_pred             HHHHHHhCCCcHHHHHHHhCCChHHHHHHHHhhc
Q psy17316        182 ALEGIRSGQTTVQRASAEYGIPSGTLYGRCKLSR  215 (229)
Q Consensus       182 aV~~~~~~~~s~~eAA~~fgVp~~tv~~~vk~~~  215 (229)
                      +-+.....++|..+.|...||+.+++.+|-++..
T Consensus        14 ik~~R~~~gltq~~lA~~~gis~~~i~~~E~g~~   47 (69)
T d1y7ya1          14 LRELRTAKGLSQETLAFLSGLDRSYVGGVERGQR   47 (69)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCS
T ss_pred             HHHHHHHcCCCHHHHHhHhCCCHHHHHHHHCCCC
Confidence            3344556789999999999999999999987653

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

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

Probab=82.01  E-value=1.2  Score=26.79  Aligned_cols=36  Identities=17%  Similarity=0.159  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHHh---CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        177 EDLEIALEGIRS---GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       177 e~r~eaV~~~~~---~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      +...+|++++.+   ...++.+.|..+|+|..++.+..|
T Consensus         3 ~~i~~v~~yI~~~~~~~~tl~~lA~~~~~s~~~l~r~Fk   41 (54)
T d1bl0a1           3 ITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFK   41 (54)
T ss_dssp             HHHHHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            346677778777   458899999999999999999988

>d1ui5a1 a.4.1.9 (A:5-75) A-factor receptor homolog CprB {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: A-factor receptor homolog CprB
species: Streptomyces coelicolor [TaxId: 1902]

Probab=81.99  E-value=0.91  Score=29.05  Aligned_cols=32  Identities=19%  Similarity=0.200  Sum_probs=24.6

Q ss_pred             HHHHHHHHcC---CCCHHHHHHHhCCChHHHHHHH
Q psy17316        125 NVALDALRAG---SISANKASKAYGIPSSTLYKIA  156 (229)
Q Consensus       125 ~~AV~~~~~g---~~S~~~~a~k~gIp~sTL~~~i  156 (229)
                      ..|++.+.+.   ..|+.+||+.-||+++++|.+.
T Consensus        12 ~aa~~l~~~~G~~~~si~~Ia~~agvs~~~~y~~F   46 (71)
T d1ui5a1          12 GAAADLFDRRGYESTTLSEIVAHAGVTKGALYFHF   46 (71)
T ss_dssp             HHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             HHHHHHHHHhCccccCHHHHHHHHCcCHhHHHHHC
Confidence            4555555442   3599999999999999999953

>d1bl0a2 a.4.1.8 (A:63-124) MarA {Escherichia coli [TaxId: 562]}

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

Probab=81.98  E-value=1.4  Score=27.72  Aligned_cols=40  Identities=13%  Similarity=0.170  Sum_probs=33.1

Q ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCChHH-HHHHHHHh-CCcc
Q psy17316        124 LNVALDALRAGSISANKASKAYGIPSST-LYKIARKE-GIRL  163 (229)
Q Consensus       124 k~~AV~~~~~g~~S~~~~a~k~gIp~sT-L~~~ik~~-g~k~  163 (229)
                      +.+|.+++.++..|+.+||...|-+... +.++.++. |..+
T Consensus         3 l~~a~~lL~~t~~~i~~IA~~~Gf~~~~~F~r~Fk~~~g~tP   44 (62)
T d1bl0a2           3 MTEIAQKLKESNEPILYLAERYGFESQQTLTRTFKNYFDVPP   44 (62)
T ss_dssp             HHHHHHHHHHCCCCHHHHHHHTTCSCHHHHHHHHHHHHSSCH
T ss_pred             HHHHHHHHHccCCCHHHHHHHHCCCCHHHHHHHHHHHHCcCH
Confidence            4678889999999999999999998866 88887765 7544

>d2g3ba1 a.4.1.9 (A:2-73) Putative transcriptional regulator {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=81.86  E-value=0.72  Score=29.61  Aligned_cols=24  Identities=25%  Similarity=0.335  Sum_probs=21.7

Q ss_pred             CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        189 GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       189 ~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+.++.++|++.|||.+++|.+..
T Consensus        21 ~~~ti~~Ia~~agvs~~~ly~~F~   44 (72)
T d2g3ba1          21 RGLRVNDVAEVAGVSPGLLYYHFK   44 (72)
T ss_dssp             HHCCHHHHHHHHTSCHHHHHHHHC
T ss_pred             ccCCHHHHHHHhCcCHHHHHHHCc
Confidence            448899999999999999999875

>d1z0xa1 a.4.1.9 (A:4-71) Transcriptional regulator EF0787 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator EF0787
species: Enterococcus faecalis [TaxId: 1351]

Probab=81.78  E-value=0.78  Score=29.22  Aligned_cols=32  Identities=22%  Similarity=0.427  Sum_probs=25.3

Q ss_pred             HHHHHHHHH-c-C--CCCHHHHHHHhCCChHHHHHH
Q psy17316        124 LNVALDALR-A-G--SISANKASKAYGIPSSTLYKI  155 (229)
Q Consensus       124 k~~AV~~~~-~-g--~~S~~~~a~k~gIp~sTL~~~  155 (229)
                      +..|++.+. + |  ..|+++||++-||+++++|++
T Consensus         8 i~aa~~l~~e~~G~~~~t~~~Ia~~agvs~~~iy~h   43 (68)
T d1z0xa1           8 IAAAFSLLEKSPTLEQLSMRKVAKQLGVQAPAIYWY   43 (68)
T ss_dssp             HHHHHHHHHHSCCGGGCCHHHHHHHHTSCHHHHHTT
T ss_pred             HHHHHHHHHHcCCccccCHHHHHHHHCcchhHHHHh
Confidence            456666665 3 3  369999999999999999984

>d1rkta1 a.4.1.9 (A:2-82) Hypothetical transcriptional regulator YfiR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YfiR
species: Bacillus subtilis [TaxId: 1423]

Probab=81.77  E-value=0.79  Score=30.03  Aligned_cols=23  Identities=4%  Similarity=0.049  Sum_probs=20.9

Q ss_pred             CCCCHHHHHHHcCCChhhHHHHH
Q psy17316         48 GQMSLTKASVSYGIPSTTLWQRA   70 (229)
Q Consensus        48 g~~S~~~aA~~~gIp~sTL~~~i   70 (229)
                      .++|+.+||++.||+++|||+..
T Consensus        30 ~~~ti~~Ia~~agvs~~t~Y~~F   52 (81)
T d1rkta1          30 ELTTMKDVVEESGFSRGGVYLYF   52 (81)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHTTC
T ss_pred             ccCCHHHHHHHhCcCHHHHHHHC
Confidence            46899999999999999999874

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=81.68  E-value=0.54  Score=32.05  Aligned_cols=35  Identities=9%  Similarity=0.022  Sum_probs=29.2

Q ss_pred             HHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         39 DAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        39 ~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ..++..+ .+|.+++.++|+.+||+++||.+.+++.
T Consensus        19 ~~IL~~L~~~~~~~~~eLa~~l~is~~~vs~~l~~L   54 (100)
T d1ub9a_          19 LGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVL   54 (100)
T ss_dssp             HHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHhccCCCeeHHHHHHHHhhccccccHHHHHH
Confidence            3444444 4789999999999999999999999986

>d2etha1 a.4.5.28 (A:1-140) Putative transcriptional regulator TM0816 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator TM0816
species: Thermotoga maritima [TaxId: 2336]

Probab=81.50  E-value=1.1  Score=31.99  Aligned_cols=42  Identities=10%  Similarity=0.045  Sum_probs=34.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         32 TWTHEDMDAALEALRAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        32 kyt~e~~~~AI~~~~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      .+|..+..-......+|++++.++|..+||+++++.+-+++.
T Consensus        29 ~lt~~q~~iL~~l~~~~~~t~~~La~~l~i~~~~vs~~v~~L   70 (140)
T d2etha1          29 DMKTTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSL   70 (140)
T ss_dssp             HSBHHHHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence            456666544444567899999999999999999999999986

>d1sgma1 a.4.1.9 (A:5-77) Putative transcriptional regulator YxaF {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator YxaF
species: Bacillus subtilis [TaxId: 1423]

Probab=81.44  E-value=0.66  Score=29.80  Aligned_cols=24  Identities=29%  Similarity=0.427  Sum_probs=21.7

Q ss_pred             CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        189 GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       189 ~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      ++.|+.++|+.-|||.+++|....
T Consensus        21 ~~~si~~Ia~~agvs~~~iy~~F~   44 (73)
T d1sgma1          21 HATGLNQIVKESGAPKGSLYHFFP   44 (73)
T ss_dssp             TTCCHHHHHHHHCCCSCHHHHSTT
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHcC
Confidence            668999999999999999998763

>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Fructose repressor (FruR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=81.14  E-value=0.2  Score=32.01  Aligned_cols=47  Identities=9%  Similarity=0.140  Sum_probs=32.4

Q ss_pred             CCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhCCC
Q psy17316        136 ISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSGQT  191 (229)
Q Consensus       136 ~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~~~  191 (229)
                      +++.+||+..||+.+|+.+.+...+-.         ...+++-|..|.+.+.+-+.
T Consensus         1 vTl~diA~~agvS~sTVSrvLn~~~~~---------~~vs~~tr~rV~~~a~~lgY   47 (59)
T d1uxda_           1 MKLDEIARLAGVSRTTASYVINGKAKQ---------YRVSDKTVEKVMAVVREHNY   47 (59)
T ss_dssp             CCHHHHHHHHTSCTTHHHHHHHTCGGG---------TTCTTTTHHHHHHHHHHHTC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCCCc---------CcCCHHHHHHHHHHHHHHCC
Confidence            478999999999999999988743211         11344557777766666444

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Cadmium efflux system accessory protein CadC
species: Staphylococcus aureus [TaxId: 1280]

Probab=81.13  E-value=0.84  Score=32.09  Aligned_cols=38  Identities=13%  Similarity=0.157  Sum_probs=31.7

Q ss_pred             HHHHHHHHHH-HcCCCCHHHHHHHcCCChhhHHHHHHHh
Q psy17316         36 EDMDAALEAL-RAGQMSLTKASVSYGIPSTTLWQRAHRL   73 (229)
Q Consensus        36 e~~~~AI~~~-~~g~~S~~~aA~~~gIp~sTL~~~i~~~   73 (229)
                      ...+.++..+ .+|.+++.++|+.+|++.+|+.+.++.+
T Consensus        31 p~Rl~Il~~L~~~~~~~v~ela~~l~~s~s~vS~HL~~L   69 (108)
T d1u2wa1          31 ENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTL   69 (108)
T ss_dssp             HHHHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCccHHHHHHHHccChhHHHHHHHHH
Confidence            3456777665 4688999999999999999999998875

>d1hw1a1 a.4.5.6 (A:5-78) Fatty acid responsive transcription factor FadR, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Fatty acid responsive transcription factor FadR, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=80.93  E-value=0.9  Score=29.77  Aligned_cols=34  Identities=24%  Similarity=0.333  Sum_probs=26.6

Q ss_pred             HHHHHHcCC------C-CHHHHHHHcCCChhhHHHHHHHhC
Q psy17316         41 ALEALRAGQ------M-SLTKASVSYGIPSTTLWQRAHRLG   74 (229)
Q Consensus        41 AI~~~~~g~------~-S~~~aA~~~gIp~sTL~~~i~~~g   74 (229)
                      ..+.|.+|.      + |.+++|++|||+++|+++=++.+.
T Consensus        12 i~~~I~~g~~~~G~~LPs~~eLa~~~~vSr~tvr~Al~~L~   52 (74)
T d1hw1a1          12 IIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLA   52 (74)
T ss_dssp             HHHHHHTTSSCTTSBCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCCCcCCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence            344555543      5 899999999999999998877653

>d2id6a1 a.4.1.9 (A:1-75) Transcriptional regulator TM1030 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator TM1030
species: Thermotoga maritima [TaxId: 2336]

Probab=80.82  E-value=0.78  Score=29.64  Aligned_cols=34  Identities=9%  Similarity=0.317  Sum_probs=25.5

Q ss_pred             HHHHHHHHHcC---CCCHHHHHHHhCCChHHHHHHHH
Q psy17316        124 LNVALDALRAG---SISANKASKAYGIPSSTLYKIAR  157 (229)
Q Consensus       124 k~~AV~~~~~g---~~S~~~~a~k~gIp~sTL~~~ik  157 (229)
                      +..|++.+...   ..|+++||+..||++++||+...
T Consensus         9 l~aa~~l~~~~G~~~~ti~~Ia~~agvs~~~iY~~F~   45 (75)
T d2id6a1           9 LKAAVEVFGKKGYDRATTDEIAEKAGVAKGLIFHYFK   45 (75)
T ss_dssp             HHHHHHHHHHHHHHHCCHHHHHHHHTCCTHHHHHHHS
T ss_pred             HHHHHHHHHHhCccccCHHHHHHHhCCCHHHHHHHCC
Confidence            34555555442   25999999999999999999653

>d1ic8a2 a.35.1.1 (A:87-180) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=80.76  E-value=2.5  Score=29.15  Aligned_cols=57  Identities=9%  Similarity=0.039  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHc-CCCCHHHHHHHhCCChHHHHHHHHHhCCcccCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy17316        121 EEILNVALDALRA-GSISANKASKAYGIPSSTLYKIARKEGIRLAQPFNASPTAWKPEDLEIALEGIRSG  189 (229)
Q Consensus       121 ~e~k~~AV~~~~~-g~~S~~~~a~k~gIp~sTL~~~ik~~g~k~~~~~~~~~r~~t~e~r~eaV~~~~~~  189 (229)
                      +....+-|+.|+. ..+|...+|..+||+.|-|..|.. .|..++           .-.|-.+-.|....
T Consensus        26 ~~~v~~~IK~Fl~~h~I~Q~~Va~~TGlsQS~iSq~L~-~g~~M~-----------~~KR~alYtWylr~   83 (94)
T d1ic8a2          26 PWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLN-KGTPMK-----------TQKRAALYTWYVRK   83 (94)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHH-SBCCCC-----------HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHcccHHHHHHHHh-CCCCcc-----------HHHHHHHHHHHHHH
Confidence            3444455556654 568999999999999999999998 443332           23355556665554

>d1rr7a_ a.4.1.14 (A:) Middle operon regulator, Mor {Bacteriophage Mu [TaxId: 10677]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Middle operon regulator, Mor
domain: Middle operon regulator, Mor
species: Bacteriophage Mu [TaxId: 10677]

Probab=80.30  E-value=1.4  Score=30.39  Aligned_cols=29  Identities=24%  Similarity=0.564  Sum_probs=24.6

Q ss_pred             HHHHHcCCCCHHHHHHHhCCChHHHHHHHHH
Q psy17316        128 LDALRAGSISANKASKAYGIPSSTLYKIARK  158 (229)
Q Consensus       128 V~~~~~g~~S~~~~a~k~gIp~sTL~~~ik~  158 (229)
                      .+.| +|. ++.++|++||++..++|+++++
T Consensus        61 ~~ef-~G~-n~~eLA~kY~lS~~~I~~Ii~~   89 (94)
T d1rr7a_          61 WNDF-NGR-NVSELTTRYGVTFNTVYKAIRR   89 (94)
T ss_dssp             HHHC-CSS-CHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HHHh-CCC-CHHHHHHHHCCCHHHHHHHHHH
Confidence            3444 666 9999999999999999999875

>d2id3a1 a.4.1.9 (A:13-80) Putative transcriptional regulator SCO5951 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO5951
species: Streptomyces coelicolor [TaxId: 1902]

Probab=80.28  E-value=1.1  Score=28.41  Aligned_cols=24  Identities=17%  Similarity=0.259  Sum_probs=21.8

Q ss_pred             CCCcHHHHHHHhCCChHHHHHHHH
Q psy17316        189 GQTTVQRASAEYGIPSGTLYGRCK  212 (229)
Q Consensus       189 ~~~s~~eAA~~fgVp~~tv~~~vk  212 (229)
                      .+.|+.++|...|||..++|....
T Consensus        25 ~~~t~~~Ia~~agvs~~~iY~~F~   48 (68)
T d2id3a1          25 DALDLGEIARRAGVGKTTVYRRWG   48 (68)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHCc
Confidence            458899999999999999999875

>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]}

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

Probab=80.10  E-value=0.91  Score=27.50  Aligned_cols=39  Identities=15%  Similarity=0.127  Sum_probs=29.4

Q ss_pred             HHHHHHHH---HcCCCCHHHHHHHhCCChHHHHHHHHHh-CCc
Q psy17316        124 LNVALDAL---RAGSISANKASKAYGIPSSTLYKIARKE-GIR  162 (229)
Q Consensus       124 k~~AV~~~---~~g~~S~~~~a~k~gIp~sTL~~~ik~~-g~k  162 (229)
                      +.++++.+   ....+++.++|+.+|++.++|.+..++. |..
T Consensus         5 i~~i~~yi~~~~~~~itl~~lA~~~~~S~~~l~r~Fk~~~g~t   47 (54)
T d1d5ya1           5 IRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHA   47 (54)
T ss_dssp             HHHHHHHHHTTSSSSCCCHHHHTTTSSCHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence            34444444   3356899999999999999999998865 643