Psyllid ID: psy4300

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------
Protein Sequence
MRKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNFCYLQDDVVEEIITHPIENQMHQRGPGGLRTSSRISQA
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHcccccHHHHHHHHcccHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHHcccccEEEEEEccEEEEEcccccccccccccccccEEEEEEEcccccEEEEEEccccccccHHHHccccccccccccccccccccccEEEEEcccccccccEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccHHHcc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHcccccccccccccccHHHHHHHHHHHHHccccHHHHHHHccccHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHccccccccccEEEEEccEEEEEccccccccccccccccEEEEEEEEccccEEEEEEEcccccccHHHHHHHcHHHHHHHccccccccccccEEEEEcccccccccEEccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHHHcccccHHHcccccccccccccccHHHHHHHHHcc
Coil and Loop (DISEMBL)
MRKTTFGFLVEALAAINGYETlyergvpfvpveKKTLVALSYMATQLSMrkigdqfnladstVWSCIDSFLTamsqpqiqcqyikwpteeeSVIIERNFRALakfpgvigaidgchiegkfskdirndynnrkctqSMILqgvctsnklltnihvgctgrnhdakvlstsqigrridaygptsllyrdeyhllgdsayplrtwcmvpyknfghmtEEEKKYNTalsktrvpieNVFGLIKGRWRrlkyidvgdpKRMAYIISAACVLHNFCYLQDDVVEEIIThpienqmhqrgpgglrtssrisqa
Flexible Loop (DISEMBL)
MRKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHvgctgrnhdakvlstsqigrriDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYntalsktrvpienvfglikgrwrrLKYIDVGDPKRMAYIISAACVLHNFCYLQDDVVEEIITHpienqmhqrgpgglrtssrisqa
Low Complexity Region (SEG)
MRKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNFCYLQDDVVEEIITHPIENQMHQRGPGGLRTSSRISQA
Disordered region (IsUnstruct)
****TFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNFCYLQDDVVEEIITHPI*********************
Disordered Region (DISOPRED)
MRKTTFGFLVEALAAINGYE********FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNFCYLQDDVVEEIITHPIE********************
Disordered Region (DISEMBL)
MRKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNFCYLQDDVVEEIITHPIENQM*****************
Disordered Region (DISPRO)
*RKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNFCYLQDDVVEE*I*************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNFCYLQDDVVEEIITHPIENQMHQRGPGGLRTSSRISQA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	307	2.2.26 [Sep-21-2011]
Q96MB7	349	Putative nuclease HARBI1	yes	N/A	0.866	0.762	0.295	1e-21
Q17QR8	349	Putative nuclease HARBI1	yes	N/A	0.853	0.750	0.294	2e-21
B0BN95	349	Putative nuclease HARBI1	yes	N/A	0.853	0.750	0.287	8e-20
Q8BR93	349	Putative nuclease HARBI1	yes	N/A	0.801	0.704	0.287	3e-18
Q6AZB8	349	Putative nuclease HARBI1	no	N/A	0.817	0.719	0.269	5e-15
Q5U538	347	Putative nuclease HARBI1	N/A	N/A	0.833	0.737	0.255	2e-13

>sp|Q96MB7|HARB1_HUMAN Putative nuclease HARBI1 OS=Homo sapiens GN=HARBI1 PE=1 SV=1

 Score =  104 bits (259), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 85/288 (29%), Positives = 132/288 (45%), Gaps = 22/288 (7%)

Query: 8   FLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCI 67
           +LVE L A     T   R +     E + L AL +  +     ++GD   ++ +++  C+
Sbjct: 48  YLVELLGANLSRPTQRSRAIS---PETQVLAALGFYTSGSFQTRMGDAIGISQASMSRCV 104

Query: 68  DSFLTAMSQPQIQCQYIKWPTEEESV-IIERNFRALAKFPGVIGAIDGCHIEGKFSKDIR 126
            +   A+ +     Q+I++P +E S+  ++  F  LA  PGV+G +D  H+  K      
Sbjct: 105 ANVTEALVERA--SQFIRFPADEASIQALKDEFYGLAGMPGVMGVVDCIHVAIKAPNAED 162

Query: 127 NDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLY 186
             Y NRK   S+    VC     L  +     G   D  VL  S +  + +A      ++
Sbjct: 163 LSYVNRKGLHSLNCLMVCDIRGTLMTVETNWPGSLQDCAVLQQSSLSSQFEAG-----MH 217

Query: 187 RDEYHLLGDSAYPLRTWCMVPYKNFGHMTE--EEKKYNTALSKTRVPIENVFGLIKGRWR 244
           +D + LLGDS++ LRTW M P     H+ E   E +YN A S T   IE  F  +  R+R
Sbjct: 218 KDSW-LLGDSSFFLRTWLMTPL----HIPETPAEYRYNMAHSATHSVIEKTFRTLCSRFR 272

Query: 245 RL---KYIDVGDPKRMAYIISAACVLHNFCYLQD-DVVEEIITHPIEN 288
            L   K      P++ ++II A CVLHN       DV    +T P+E 
Sbjct: 273 CLDGSKGALQYSPEKSSHIILACCVLHNISLEHGMDVWSSPMTGPMEQ 320

Transposase-derived protein that may have nuclease activity (Potential). Does not have transposase activity.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -

>sp|Q17QR8|HARB1_BOVIN Putative nuclease HARBI1 OS=Bos taurus GN=HARBI1 PE=2 SV=1

 Score =  103 bits (256), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/292 (29%), Positives = 132/292 (45%), Gaps = 30/292 (10%)

Query: 8   FLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCI 67
           +LVE L A     T   R +     E + L AL +  +     ++GD   ++ +++  C+
Sbjct: 48  YLVELLGASLSRPTQRSRAIS---PETQILAALGFYTSGSFQTRMGDAIGISQASMSRCV 104

Query: 68  DSFLTAMSQPQIQCQYIKWPTEEESV-IIERNFRALAKFPGVIGAIDGCHIEGKFSKDIR 126
            +   A+ +     Q+I +P +E SV  ++  F  LA  PGVIG +D  H+  K      
Sbjct: 105 ANVTEALVERA--SQFIHFPADEASVQALKDEFYGLAGIPGVIGVVDCMHVAIKAPNAED 162

Query: 127 NDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLY 186
             Y NRK   S+    VC     L  +     G   D  VL  S +  + +A      ++
Sbjct: 163 LSYVNRKGLHSLNCLMVCDIRGALMTVETSWPGSLQDCVVLQQSSLSSQFEAG-----MH 217

Query: 187 RDEYHLLGDSAYPLRTWCMVPYKNFGHMTE--EEKKYNTALSKTRVPIENVFGLIKGRWR 244
           ++ + LLGDS++ LRTW M P     H+ E   E +YN A S T   IE  F  +  R+R
Sbjct: 218 KESW-LLGDSSFFLRTWLMTPL----HIPETPAEYRYNMAHSATHSVIEKTFRTLCSRFR 272

Query: 245 -------RLKYIDVGDPKRMAYIISAACVLHNFCYLQD-DVVEEIITHPIEN 288
                   L+Y     P++ ++II A CVLHN       DV    +T P+E 
Sbjct: 273 CLDGSKGALQY----SPEKSSHIILACCVLHNISLEHGMDVWSSPVTGPVEQ 320

Transposase-derived protein that may have nuclease activity (Potential). Does not have transposase activity.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|B0BN95|HARB1_RAT Putative nuclease HARBI1 OS=Rattus norvegicus GN=Harbi1 PE=2 SV=1

 Score = 97.8 bits (242), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 84/292 (28%), Positives = 129/292 (44%), Gaps = 30/292 (10%)

Query: 8   FLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCI 67
           +LVE L A     T   R +     E + L AL +  +     ++GD   ++ +++  C+
Sbjct: 48  YLVELLGASLSRPTQRSRAIS---PETQILAALGFYTSGSFQTRMGDAIGISQASMSRCV 104

Query: 68  DSFLTAMSQPQIQCQYIKWPTEEESV-IIERNFRALAKFPGVIGAIDGCHIEGKFSKDIR 126
            +   A+ +     Q+I +P +E ++  ++  F  LA  PGVIGA+D  H+  K      
Sbjct: 105 ANVTEALVERA--SQFIHFPADEAAIQSLKDEFYGLAGMPGVIGAVDCIHVAIKAPNAED 162

Query: 127 NDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLY 186
             Y NRK   S+    VC     L  +     G   D  VL  S +  + +   P     
Sbjct: 163 LSYVNRKGLHSLNCLVVCDIRGALMTVETSWPGSLQDCAVLQQSSLSSQFETGMP----- 217

Query: 187 RDEYHLLGDSAYPLRTWCMVPYKNFGHMTE--EEKKYNTALSKTRVPIENVFGLIKGRWR 244
           +D + LLGDS++ L TW + P     H+ E   E +YN A S T   IE     +  R+R
Sbjct: 218 KDSW-LLGDSSFFLHTWLLTPL----HIPETPAEYRYNRAHSATHSVIEKTLRTLCCRFR 272

Query: 245 -------RLKYIDVGDPKRMAYIISAACVLHNFCYLQD-DVVEEIITHPIEN 288
                   L+Y     P++ ++II A CVLHN       DV    +T PIE 
Sbjct: 273 CLDGSKGALQY----SPEKSSHIILACCVLHNISLEHGMDVWSSPVTGPIEQ 320

Transposase-derived protein that may have nuclease activity (Potential). Does not have transposase activity.

Rattus norvegicus (taxid: 10116)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q8BR93|HARB1_MOUSE Putative nuclease HARBI1 OS=Mus musculus GN=Harbi1 PE=2 SV=1

 Score = 92.8 bits (229), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 78/271 (28%), Positives = 119/271 (43%), Gaps = 25/271 (9%)

Query: 8   FLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCI 67
           FLVE L A     T   R +     E + L AL +  +     ++GD   ++ +++  C+
Sbjct: 48  FLVELLGASLSRPTQRSRAIS---PETQILAALGFYTSGSFQTRMGDAIGISQASMSRCV 104

Query: 68  DSFLTAMSQPQIQCQYIKWPTEEESV-IIERNFRALAKFPGVIGAIDGCHIEGKFSKDIR 126
            +   A+ +     Q+I +P +E +V  ++  F  LA  PGVIG  D  H+  K      
Sbjct: 105 ANVTEALVERA--SQFIHFPVDEAAVQSLKDEFYGLAGMPGVIGVADCIHVAIKAPNAED 162

Query: 127 NDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLY 186
             Y NRK   S+    VC     L  +     G   D  VL  S +  + +   P     
Sbjct: 163 LSYVNRKGLHSLNCLVVCDIRGALMTVETSWPGSLQDCAVLQRSSLTSQFETGMP----- 217

Query: 187 RDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWR-- 244
           +D + LLGDS++ LR+W + P       T  E +YN A S T   IE     +  R+R  
Sbjct: 218 KDSW-LLGDSSFFLRSWLLTPLPI--PETAAEYRYNRAHSATHSVIERTLQTLCCRFRCL 274

Query: 245 -----RLKYIDVGDPKRMAYIISAACVLHNF 270
                 L+Y     P++ ++II A CVLHN 
Sbjct: 275 DGSKGALQY----SPEKCSHIILACCVLHNI 301

Transposase-derived protein that may have nuclease activity (Potential). Does not have transposase activity.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q6AZB8|HARB1_DANRE Putative nuclease HARBI1 OS=Danio rerio GN=harbi1 PE=2 SV=1

 Score = 82.0 bits (201), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 75/278 (26%), Positives = 122/278 (43%), Gaps = 27/278 (9%)

Query: 5   TFGF-------LVEALAAINGYETLYERGV-PFVPVEKKTLVALSYMATQLSMRKIGDQF 56
           TFGF       LVE L       T   R + P V +    L AL +  +     K+GD  
Sbjct: 38  TFGFPREFIYYLVELLKDSLLRRTQRSRAISPDVQI----LAALGFYTSGSFQSKMGDAI 93

Query: 57  NLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEES-VIIERNFRALAKFPGVIGAIDGC 115
            ++ +++  C+ +   A+ +   +  +I +  +E +    +  F  +A  P V G +D  
Sbjct: 94  GISQASMSRCVSNVTKALIEKAPE--FIGFTRDEATKQQFKDEFYRIAGIPNVTGVVDCA 151

Query: 116 HIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRR 175
           HI  K      + Y N+K   S+  Q VC +  LL +      G   D  V   S + + 
Sbjct: 152 HIAIKAPNADDSSYVNKKGFHSINCQLVCDARGLLLSAETHWPGSLTDRAVFKQSNVAKL 211

Query: 176 IDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIENV 235
            +          DE  LLGD+ YPL+ W M P ++    +  + +YN A + T   ++  
Sbjct: 212 FEEQEND-----DEGWLLGDNRYPLKKWLMTPVQS--PESPADYRYNLAHTTTHEIVDRT 264

Query: 236 FGLIKGRWRRLK----YIDVGDPKRMAYIISAACVLHN 269
           F  I+ R+R L     Y+    P++ ++II A CVLHN
Sbjct: 265 FRAIQTRFRCLDGAKGYLQYS-PEKCSHIIQACCVLHN 301

Transposase-derived protein that may have nuclease activity (Potential). Does not have transposase activity.

Danio rerio (taxid: 7955)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

>sp|Q5U538|HARB1_XENLA Putative nuclease HARBI1 OS=Xenopus laevis GN=harbi1 PE=2 SV=1

 Score = 77.0 bits (188), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 76/297 (25%), Positives = 124/297 (41%), Gaps = 41/297 (13%)

Query: 4   TTFGF-------LVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQF 56
           TT+GF       LV+ L A     T   R +     E + + AL +  +     ++GD  
Sbjct: 37  TTYGFPRPFIDYLVDLLGASLSRPTHRSRAIS---PETQIMAALGFYTSGSFQTRMGDTI 93

Query: 57  NLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVI-IERNFRALAKFPGVIGAIDGC 115
            ++ +++  C+ +   A+ +     Q+I +P +E SV  ++  F  LA  PGV+G +D  
Sbjct: 94  GISQASMSRCVTNVTEALVERA--SQFISFPRDERSVQGLKDEFYNLAGVPGVLGVVDCT 151

Query: 116 HIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRR 175
            +  K        Y N +   S+    VC +   L        G   D  VL  S++   
Sbjct: 152 QVNIKAPNSEDLSYVNSRGLHSLNCLLVCDARGSLLWAETSRLGSMQDNAVLHQSEL--- 208

Query: 176 IDAYGPTSLLYRDEYH----LLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVP 231
                  S L+  + H    LL D+A+ LR W M P +     +  + +YN A + T   
Sbjct: 209 -------SGLFETKMHKQGWLLADNAFILRPWLMTPVQI--PESPSDYRYNMAHTATHSV 259

Query: 232 IENV-------FGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNFCYLQD-DVVEE 280
           +E         F  + G    L+Y     P++ A I+ A C+LHN     D D+V E
Sbjct: 260 MERTQRSLRLRFRCLDGSRATLQY----SPEKSAQIVLACCILHNIALQHDLDIVSE 312

Transposase-derived protein that may have nuclease activity (Potential). Does not have transposase activity.

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 1

EC: .

EC: -

EC: .

EC: -

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	307
270004721	319	hypothetical protein TcasGA2_TC010492 [T	0.879	0.846	0.393	8e-47
241573389	275	transposase, putative [Ixodes scapularis	0.745	0.832	0.395	4e-42
291233883	389	PREDICTED: hypothetical protein [Saccogl	0.872	0.688	0.338	1e-36
340382901	418	PREDICTED: putative nuclease HARBI1-like	0.938	0.688	0.335	1e-36
270016593	393	hypothetical protein TcasGA2_TC010570 [T	0.872	0.681	0.320	3e-36
328724776	275	PREDICTED: putative nuclease HARBI1-like	0.732	0.818	0.367	5e-36
322786153	313	hypothetical protein SINV_12000 [Solenop	0.798	0.782	0.338	1e-35
432951686	360	PREDICTED: putative nuclease HARBI1-like	0.928	0.791	0.332	6e-35
326667245	349	PREDICTED: putative nuclease HARBI1-like	0.899	0.790	0.357	5e-34
328699306	395	PREDICTED: putative nuclease HARBI1-like	0.850	0.660	0.327	2e-33

>gi|270004721|gb|EFA01169.1| hypothetical protein TcasGA2_TC010492 [Tribolium castaneum]

 Score =  193 bits (490), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 114/290 (39%), Positives = 165/290 (56%), Gaps = 20/290 (6%)

Query: 1   MRKTTFGFLVEALAAINGYETLYER------GVPFVPVEKKTLVALSYMATQLSMRKIGD 54
           M +TTF  +V  +    G+  L+ +      G   +  EK  LV L  +AT  S R IG+
Sbjct: 1   MSRTTFEIVVNHI----GHSHLFHKRDKELGGRKQIGPEKALLVTLWTLATPDSYRSIGE 56

Query: 55  QFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDG 114
           +F +A S+V+ C+ + +  +   ++  ++IKWPTE+E+V +   F A    P VIG IDG
Sbjct: 57  RFGIAKSSVYFCLQTVINVILH-ELTHRFIKWPTEDETVYVANRF-AKYGLPKVIGVIDG 114

Query: 115 CHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGR 174
           CHI  K   +   DY NRK   SM+LQGVC  +    +  +   G  HD +VL TS    
Sbjct: 115 CHIPIKKPVENSIDYFNRKKFYSMVLQGVCKPDLTFIDCDIRWPGSVHDGRVLRTS---- 170

Query: 175 RIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIEN 234
             D Y     L R  Y+++GDSAYPL+ W + PY+N GH+  ++  +N  L+KTRV IEN
Sbjct: 171 --DIYPIAEQLCRPNYYVIGDSAYPLKKWLITPYRNNGHLLPQQVYFNRMLAKTRVVIEN 228

Query: 235 VFGLIKGRWRRLK-YIDVGDPKRMAYIISAACVLHNFCYLQ-DDVVEEII 282
            F L+KGR+RRLK Y+D   P+ +   + AAC LHN C ++ +D VE+ I
Sbjct: 229 TFALLKGRFRRLKDYLDRDKPEDIIQTVMAACTLHNICLVEGEDEVEQYI 278

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|241573389|ref|XP_002403173.1| transposase, putative [Ixodes scapularis] gi|215500182|gb|EEC09676.1| transposase, putative [Ixodes scapularis]

 Score =  177 bits (450), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 139/240 (57%), Gaps = 11/240 (4%)

Query: 30  VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTE 89
           +PVE K L+ L  +  Q S R + D+F +    ++   +  +   +   +   +I+W  +
Sbjct: 25  IPVETKVLMTLWLLGNQESFRGVVDRFGVNKGVLFYVANQMIETWAN--LAVDFIRWLMQ 82

Query: 90  EESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKL 149
            + V   R F    +FPGV+GA+DGCHI  K  ++ ++ Y NRK   S+ILQG C S  +
Sbjct: 83  LQRV--SRAFTRKWRFPGVVGAVDGCHIAIKAPEEEQDAYYNRKEFHSIILQGCCNSEMV 140

Query: 150 LTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYK 209
            T++HVG  GR HDA+V S S +   ID   P SL      H+LGDSAY LR   M PY+
Sbjct: 141 FTHVHVGSPGRMHDARVFSISGLDEIIDNL-PLSL------HVLGDSAYSLRLGLMRPYR 193

Query: 210 NFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHN 269
           N GH++EE+  +N  LS  R  IE  F  +KG++RRLKY+D+   + M+  + A+CVLHN
Sbjct: 194 NNGHLSEEQVTFNETLSAARSVIERAFAQLKGKFRRLKYLDMEATEMMSKYVLASCVLHN 253

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|291233883|ref|XP_002736880.1| PREDICTED: hypothetical protein [Saccoglossus kowalevskii]

 Score =  159 bits (403), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 94/278 (33%), Positives = 148/278 (53%), Gaps = 10/278 (3%)

Query: 4   TTFGFLVEALAA-INGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADST 62
           + F +L + L   +   E ++  G P +  +KK  + L  + +  ++  I   FN+ +S+
Sbjct: 68  SVFEYLADILTGPLIENEPIHCGGRPAILPDKKIAIFLKCVGSMETILDIAQLFNITESS 127

Query: 63  VWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRAL--AKFPGVIGAIDGCHIEGK 120
           V   +   +T +    +    I WP   E   I   F  +  +  P +IGA+DG HI   
Sbjct: 128 VIK-VRRQVTNVILIHLLNNTIHWPLRRELQGISACFNDMHTSNLPNIIGAVDGSHIPIS 186

Query: 121 FSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYG 180
              +  + Y NRK  +S++LQGVC  +    ++ VGC GR HDA+VL  S +       G
Sbjct: 187 TPHEQPDAYYNRKKFRSVVLQGVCREDLQFIDVSVGCPGRMHDARVLRNSTLWN--TGMG 244

Query: 181 PTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIENVFGLIK 240
                 R +YH++GD+AYPL  W M PY++ GH+ E ++ +NT+LS+ RV IE  FG +K
Sbjct: 245 NCQ---RGQYHVIGDAAYPLTNWLMTPYRDNGHLDEHQRLFNTSLSRRRVIIERAFGSLK 301

Query: 241 GRWRR-LKYIDVGDPKRMAYIISAACVLHNFCYLQDDV 277
            R+RR L  ID+ D   +  I+ AAC++HN C   DD+
Sbjct: 302 RRFRRLLNGIDITDVNEINKIVLAACIIHNICIKHDDI 339

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|340382901|ref|XP_003389956.1| PREDICTED: putative nuclease HARBI1-like [Amphimedon queenslandica]

 Score =  159 bits (403), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 101/301 (33%), Positives = 157/301 (52%), Gaps = 13/301 (4%)

Query: 1   MRKTTFGFLVEAL-AAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLA 59
           M KTTF  +   L +++    T   + +P   VEK+  ++L +MAT    R IG  F ++
Sbjct: 98  MSKTTFVMICNELRSSLKKSSTTMRQPIP---VEKRVAISLWFMATGTDYRTIGHLFGVS 154

Query: 60  DSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEG 119
            ++V   I     A+    ++ +YIKWP+ E    I   F+    FP  +GA+DG HI  
Sbjct: 155 KASVCLAIRQVCRAILTTLLE-RYIKWPSGENLKNIISGFKHKFGFPQCVGAVDGTHIPI 213

Query: 120 KFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTS------QIG 173
              +D   DY NRK   S+++QG      +  +I++G  GR HDA+V   S      Q G
Sbjct: 214 ISPEDYPADYYNRKGWHSVLMQGTVDHLGIFIDIYIGWPGRVHDARVFVNSSLYKKGQEG 273

Query: 174 RRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIE 233
             +  +  +         LLGD AYPL  W M PY + GH+T ++K++N  LSK RV +E
Sbjct: 274 TLLPNWKESIEGQEVPLVLLGDPAYPLLPWLMKPYSDNGHLTRDQKRFNYRLSKGRVVVE 333

Query: 234 NVFGLIKGRWR-RLKYIDVGDPKRMAYIISAACVLHNFCYLQDDVVEEIITHPIENQMHQ 292
           + +G +KGRWR  LK +DV   + +  +++A CVLHN C +  +     +   I++ + Q
Sbjct: 334 HAYGRLKGRWRCLLKRLDVS-VEFVPDVVAACCVLHNICEIHGETFNNELLDGIDDTLVQ 392

Query: 293 R 293
           R
Sbjct: 393 R 393

Source: Amphimedon queenslandica

Species: Amphimedon queenslandica

Genus: Amphimedon

Family: Niphatidae

Order: Haplosclerida

Class: Demospongiae

Phylum: Porifera

Superkingdom: Eukaryota

>gi|270016593|gb|EFA13039.1| hypothetical protein TcasGA2_TC010570 [Tribolium castaneum]

 Score =  158 bits (399), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 91/284 (32%), Positives = 145/284 (51%), Gaps = 16/284 (5%)

Query: 16  INGYETLYERGVPF-----------VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVW 64
           I  YE L +   P+           V VEK+ L  +  + T  S R +G++F LA S++ 
Sbjct: 78  IEAYEQLLQTVGPYLMRQAATGRSTVQVEKQLLSVIWILVTPDSYRSVGERFGLAKSSLS 137

Query: 65  SCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKD 124
            C    +  ++   +    IKWP   +   +ER F A A+ P  IGAIDG ++E K  K+
Sbjct: 138 QCFKRVVKILNA--VAPTIIKWPEGMQLQNVERRFHAFARMPHCIGAIDGTYVEIKAPKE 195

Query: 125 IRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSL 184
               Y  RKC  +  LQ +   +   T+  +G  G   D+++   S     ++A      
Sbjct: 196 DPQSYITRKCNYAFTLQAIAVPSLKFTDAFIGYPGSVSDSRIFKNSDFYNAVNA--NMGH 253

Query: 185 LYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWR 244
            + +E++L+GD AYP   WC+ PY N G++   +  +NT  ++TR  IE  F L+ GR+R
Sbjct: 254 YFAEEHYLIGDKAYPNLPWCIAPYINRGNLNAAQVYFNTVHAQTRQVIERSFALLFGRFR 313

Query: 245 RLKYIDVGDPKRMAYIISAACVLHNFCY-LQDDVVEEIITHPIE 287
           RLK++D+ D K +   + AACVLHN C    D  +++ I + I+
Sbjct: 314 RLKFLDMNDTKLIPATVIAACVLHNVCLDFHDLHIDDYINNGID 357

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328724776|ref|XP_003248249.1| PREDICTED: putative nuclease HARBI1-like [Acyrthosiphon pisum]

 Score =  157 bits (397), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 85/231 (36%), Positives = 130/231 (56%), Gaps = 6/231 (2%)

Query: 51  KIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRAL--AKFPGV 108
           +IGD+F+L+       I  F+   S+  +   ++ WP       I ++F++L     P  
Sbjct: 4   QIGDRFDLSRGLACRTILKFIRVFSK--LLDNFVLWPKGSSDAAIIKDFKSLRFNYMPST 61

Query: 109 IGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLS 168
           IG IDGCHI     +D R+DY NRK  QS++L  VC +    T +  G  G +HDA+V  
Sbjct: 62  IGCIDGCHIRIHAPRDKRSDYTNRKMFQSIVLLAVCNAKFEFTYMFSGWPGSSHDARVFK 121

Query: 169 TSQIGRRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKT 228
            S +G  +    P  ++ +++ H+LGDSA+PL    MVPYK    +TE+EK +N  LS T
Sbjct: 122 NSSLGHTL-INSPQEIISKNQ-HILGDSAFPLLENLMVPYKATHILTEKEKSFNRRLSST 179

Query: 229 RVPIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNFCYLQDDVVE 279
           RV IE  FGL+ GR+ RLK ++    + M+  +++AC+LHN     +D +E
Sbjct: 180 RVVIEQAFGLLLGRFWRLKILEAKSIELMSLTVTSACILHNLALQNNDFIE 230

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322786153|gb|EFZ12759.1| hypothetical protein SINV_12000 [Solenopsis invicta]

 Score =  156 bits (394), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 85/251 (33%), Positives = 136/251 (54%), Gaps = 6/251 (2%)

Query: 30  VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTE 89
           +  EK+ L+A+ +M+T  S R +  +F +  +T +  +     A+    I  Q+I+WP  
Sbjct: 35  ISAEKQLLIAIWFMSTPDSYRSVSTKFGVGKATAFRALRRVTYALHC--IAPQFIQWPKG 92

Query: 90  EESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKL 149
             +  + R F  +  FP VIG IDG HI+ +  K+    Y NRK   S+ +Q VC S  L
Sbjct: 93  AIATNVMRKFEQVCGFPNVIGCIDGTHIKIRAPKEDPVSYINRKGFHSINVQVVCESRGL 152

Query: 150 LTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYK 209
            T+ + G  G  HDA+V   S +    D        + D  H++GD+AY +   CMVP++
Sbjct: 153 FTHCYAGHVGSVHDARVFRNSPVA---DFLQLPETYFPDNSHIIGDAAYSIHPHCMVPFR 209

Query: 210 NFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWR-RLKYIDVGDPKRMAYIISAACVLH 268
           + GH+T  +K +N  LS TR+ IE   G +K R+R  L  + + + +++   I A CVLH
Sbjct: 210 DNGHLTNAQKNFNYCLSSTRMTIERAIGHLKVRFRILLDCLPLTNIRKIPEFILACCVLH 269

Query: 269 NFCYLQDDVVE 279
           N C L++D++E
Sbjct: 270 NICILKNDIIE 280

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|432951686|ref|XP_004084885.1| PREDICTED: putative nuclease HARBI1-like [Oryzias latipes]

 Score =  154 bits (388), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 102/307 (33%), Positives = 153/307 (49%), Gaps = 22/307 (7%)

Query: 1   MRKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLAD 60
           MR+ TF  L   L+ +  YE    R    +PV+K+  V L ++AT    R +   F ++D
Sbjct: 39  MRQETFEMLSVRLSPMLSYEDTTFRQA--IPVQKRVGVGLWWLATGAGYRTLAHLFGISD 96

Query: 61  STVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGK 120
           ++V   +  F  A+   +++ +YIK P  EE   +   F+    FP   GAIDG HI   
Sbjct: 97  ASVCLIVREFCHAVRHERMR-EYIKLPEGEELQTVLLGFKNRWGFPQCAGAIDGSHIPVI 155

Query: 121 FSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYG 180
              +   DY NRK   S+ILQ V        NI++G  G  HD++VL  S++  + +   
Sbjct: 156 APHENHADYFNRKGCHSVILQAVVDHKYCFKNINIGWPGSVHDSRVLRNSEMYEKAE--- 212

Query: 181 PTSLLYRDEYH----------LLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRV 230
            + +L+ +             LLGD AYPLR+W M  Y   G++ E+++++N  LS  R+
Sbjct: 213 -SGVLFPNTTEEIQGTQVPIMLLGDPAYPLRSWLMKGYPETGNLNEQQRQFNNRLSGARM 271

Query: 231 PIENVFGLIKGRWRRL-KYIDVGDPKRMAYIISAACVLHNFCYLQDDVVEEIITHPIENQ 289
             E  FG +KGRWR L K +DV D   +  +ISA C LHN C   ++   E   HP    
Sbjct: 272 TAECAFGRLKGRWRCLSKRLDV-DISLVPTVISACCTLHNICEKHNEAYSE---HPSAAG 327

Query: 290 MHQRGPG 296
           +    PG
Sbjct: 328 LPDVPPG 334

Source: Oryzias latipes

Species: Oryzias latipes

Genus: Oryzias

Family: Adrianichthyidae

Order: Beloniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|326667245|ref|XP_003198536.1| PREDICTED: putative nuclease HARBI1-like [Danio rerio]

 Score =  150 bits (380), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 105/294 (35%), Positives = 146/294 (49%), Gaps = 18/294 (6%)

Query: 1   MRKTTFGFLVEALAA-INGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLA 59
           M +++F  L + L   +    T Y + VP   VE +  + +  +AT L  R I   F + 
Sbjct: 29  MERSSFILLCDTLRPWLTRQNTRYRKPVP---VEIRVAICIWRLATNLEYRSISHLFGVG 85

Query: 60  DSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEG 119
            ST        +TA++   ++ QYIK P+  E  +I + FR    FP V GAIDG HI  
Sbjct: 86  VSTCCIITQEVVTAINVI-MKPQYIKKPSAAEFKMIVQGFRDRWGFPQVAGAIDGTHINI 144

Query: 120 KFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQI------G 173
           K   +   DY NRK   S++LQ V  +     +I+VG  G+ HDA+V   S +      G
Sbjct: 145 KAPSNTPADYYNRKGNYSIVLQAVVDNKMKFWDINVGQPGKVHDARVFCLSSLFDGGSSG 204

Query: 174 RRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIE 233
             +  +  T         LLGDSAYPL  W M PY     +T E+ K+N  LS+ R+ +E
Sbjct: 205 TLLPTWTETFEAIDVPLFLLGDSAYPLSHWLMKPYPEGRGVTPEQIKFNHRLSQARMTVE 264

Query: 234 NVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNFC-------YLQDDVVEE 280
             FG +KGRWR L          ++ I+SA CVLHNFC       Y +DDV EE
Sbjct: 265 RAFGRLKGRWRCLLKQCEAHITLVSRIVSACCVLHNFCEVRNEEFYGRDDVREE 318

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|328699306|ref|XP_003240898.1| PREDICTED: putative nuclease HARBI1-like [Acyrthosiphon pisum]

 Score =  149 bits (376), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 90/275 (32%), Positives = 136/275 (49%), Gaps = 14/275 (5%)

Query: 26  GVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTV----WSCIDSFLTAMSQPQIQC 81
           G P +P+ K+ L  L  +AT  S R +G++F++  S++    +  I+  +   S      
Sbjct: 98  GRPEIPIVKQLLSVLWILATPDSYRSVGEKFDMGKSSLSVSFFRIINLLIMNASN----- 152

Query: 82  QYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQ 141
             I WP  EE    +  F  +A  P VIGA+DG  I  K  K     Y  RKC  ++ LQ
Sbjct: 153 -VIIWPHGEEMERQKELFFRMASIPNVIGAVDGTFIPIKAPKQDAEVYVTRKCNYAITLQ 211

Query: 142 GVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRDEYHLLGDSAYPLR 201
            +  +    T++ VG  G   D ++   S I   I+        + ++ H+LGD AYP  
Sbjct: 212 AITNAELKFTDVFVGYPGSVSDTRIFRNSDIF--INIMRNQKFYFPNDEHILGDKAYPPL 269

Query: 202 TWCMVPYKNFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWRRLKYIDVGDPKRMAYII 261
           TWC+ PY N G +TE +K +N  +S+TR  +E  F L  GR+RR KY+D+     +   +
Sbjct: 270 TWCVEPYINRGRLTEAQKNFNFNISRTRQTVERSFALFFGRFRRFKYLDMSRTDFIPSTV 329

Query: 262 SAACVLHNFCYLQ--DDVVEEIITHPIENQMHQRG 294
            AACVLHN C     D  +++ I   +    HQR 
Sbjct: 330 LAACVLHNLCLKNKSDANIKDYIEEGMNFLRHQRS 364

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

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	307
ZFIN|ZDB-GENE-050327-32	415	zgc:113227 "zgc:113227" [Danio	0.775	0.573	0.318	8.4e-26
UNIPROTKB|Q17QR8	349	HARBI1 "Putative nuclease HARB	0.863	0.759	0.306	7.8e-23
UNIPROTKB|Q96MB7	349	HARBI1 "Putative nuclease HARB	0.863	0.759	0.303	7.8e-23
UNIPROTKB|E2RCW9	349	HARBI1 "Uncharacterized protei	0.863	0.759	0.306	1.3e-22
UNIPROTKB|F1SIA2	349	HARBI1 "Uncharacterized protei	0.863	0.759	0.299	2.6e-22
TAIR|locus:2123874	540	AT4G29780 "AT4G29780" [Arabido	0.876	0.498	0.253	3.3e-22
UNIPROTKB|E1BQ99	348	HARBI1 "Uncharacterized protei	0.804	0.709	0.305	1.9e-21
TAIR|locus:2143104	502	AT5G12010 [Arabidopsis thalian	0.915	0.559	0.251	2e-21
RGD|1584007	349	Harbi1 "harbinger transposase	0.863	0.759	0.296	6.3e-21
ZFIN|ZDB-GENE-081022-77	394	zgc:194221 "zgc:194221" [Danio	0.794	0.619	0.296	4.3e-20

ZFIN|ZDB-GENE-050327-32 zgc:113227 "zgc:113227" [Danio rerio (taxid:7955)]

 Score = 292 (107.8 bits), Expect = 8.4e-26, P = 8.4e-26
 Identities = 80/251 (31%), Positives = 126/251 (50%)

Query:    30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTE 89
             VPV+K+  +AL  +AT    R +   F +  STV++C+  F +A+ +  +   ++K+P+ 
Sbjct:   114 VPVKKRVAIALCKLATGSEYRYVSQLFGVGVSTVFNCVQDFCSAVIKILVPV-HMKFPSP 172

Query:    90 EESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKL 149
             E+   +   F      P  IG+ID  HI     +     Y NRK   S++LQ V   N L
Sbjct:   173 EKLKEMADVFENCWNVPQCIGSIDAHHIPIIAPEKNPRGYLNRKGWHSVVLQAVVDGNGL 232

Query:   150 LTNIHVGCTGRNHDAKVLSTSQIG-----RRIDAYGPTSLLYRDE-YHLLGDSAYPLRTW 203
               ++ VG +G   DA+VL  S +      R +  +    +   D  Y+L+GDSAYPL+ W
Sbjct:   233 FWDLCVGFSGNLSDARVLRQSYLWSLLSERDLLNHNKVDISGCDVGYYLIGDSAYPLQNW 292

Query:   204 CMVPYKNFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWR---RLKYIDVGDPKRMAYI 260
              M P+ + G +T +++ +N+ LS  R   +  F  +K RW+   R     V   K+MA  
Sbjct:   293 LMKPFPDIGGLTPQQESFNSRLSSARSVSDLSFKKLKARWQCLFRRNDCKVELVKKMAL- 351

Query:   261 ISAACVLHNFC 271
                 CVLHN C
Sbjct:   352 --TCCVLHNIC 360

GO:0005575 "cellular_component" evidence=ND

UNIPROTKB|Q17QR8 HARBI1 "Putative nuclease HARBI1" [Bos taurus (taxid:9913)]

 Score = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 88/287 (30%), Positives = 133/287 (46%)

Query:     8 FLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCI 67
             +LVE L A     T   R +   P E + L AL +  +     ++GD   ++ +++  C+
Sbjct:    48 YLVELLGASLSRPTQRSRAIS--P-ETQILAALGFYTSGSFQTRMGDAIGISQASMSRCV 104

Query:    68 DSFLTAMSQPQIQCQYIKWPTEEESV-IIERNFRALAKFPGVIGAIDGCHIEGKFSKDIR 126
              +   A+ +     Q+I +P +E SV  ++  F  LA  PGVIG +D  H+  K      
Sbjct:   105 ANVTEALVERA--SQFIHFPADEASVQALKDEFYGLAGIPGVIGVVDCMHVAIKAPNAED 162

Query:   127 NDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLY 186
               Y NRK   S+    VC     L  +     G   D  VL  S +  + +A G    ++
Sbjct:   163 LSYVNRKGLHSLNCLMVCDIRGALMTVETSWPGSLQDCVVLQQSSLSSQFEA-G----MH 217

Query:   187 RDEYHLLGDSAYPLRTWCMVPYKNFGHMTEE--EKKYNTALSKTRVPIENVFGLIKGRWR 244
             ++ + LLGDS++ LRTW M P     H+ E   E +YN A S T   IE  F  +  R+R
Sbjct:   218 KESW-LLGDSSFFLRTWLMTPL----HIPETPAEYRYNMAHSATHSVIEKTFRTLCSRFR 272

Query:   245 RL---KYIDVGDPKRMAYIISAACVLHNFCYLQD-DVVEEIITHPIE 287
              L   K      P++ ++II A CVLHN       DV    +T P+E
Sbjct:   273 CLDGSKGALQYSPEKSSHIILACCVLHNISLEHGMDVWSSPVTGPVE 319

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005813 "centrosome" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

UNIPROTKB|Q96MB7 HARBI1 "Putative nuclease HARBI1" [Homo sapiens (taxid:9606)]

 Score = 264 (98.0 bits), Expect = 7.8e-23, P = 7.8e-23
 Identities = 87/287 (30%), Positives = 134/287 (46%)

Query:     8 FLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCI 67
             +LVE L A     T   R +   P E + L AL +  +     ++GD   ++ +++  C+
Sbjct:    48 YLVELLGANLSRPTQRSRAIS--P-ETQVLAALGFYTSGSFQTRMGDAIGISQASMSRCV 104

Query:    68 DSFLTAMSQPQIQCQYIKWPTEEESV-IIERNFRALAKFPGVIGAIDGCHIEGKFSKDIR 126
              +   A+ +     Q+I++P +E S+  ++  F  LA  PGV+G +D  H+  K      
Sbjct:   105 ANVTEALVERA--SQFIRFPADEASIQALKDEFYGLAGMPGVMGVVDCIHVAIKAPNAED 162

Query:   127 NDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLY 186
               Y NRK   S+    VC     L  +     G   D  VL  S +  + +A G    ++
Sbjct:   163 LSYVNRKGLHSLNCLMVCDIRGTLMTVETNWPGSLQDCAVLQQSSLSSQFEA-G----MH 217

Query:   187 RDEYHLLGDSAYPLRTWCMVPYKNFGHMTEE--EKKYNTALSKTRVPIENVFGLIKGRWR 244
             +D + LLGDS++ LRTW M P     H+ E   E +YN A S T   IE  F  +  R+R
Sbjct:   218 KDSW-LLGDSSFFLRTWLMTPL----HIPETPAEYRYNMAHSATHSVIEKTFRTLCSRFR 272

Query:   245 RL---KYIDVGDPKRMAYIISAACVLHNFCYLQD-DVVEEIITHPIE 287
              L   K      P++ ++II A CVLHN       DV    +T P+E
Sbjct:   273 CLDGSKGALQYSPEKSSHIILACCVLHNISLEHGMDVWSSPMTGPME 319

GO:0004518 "nuclease activity" evidence=IEA

GO:0046872 "metal ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005813 "centrosome" evidence=IDA

UNIPROTKB|E2RCW9 HARBI1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 262 (97.3 bits), Expect = 1.3e-22, P = 1.3e-22
 Identities = 88/287 (30%), Positives = 133/287 (46%)

Query:     8 FLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCI 67
             +LVE L A     T   R +   P E + L AL +  +     ++GD   ++ +++  C+
Sbjct:    48 YLVELLGASLSRPTQRSRAIS--P-ETQILAALGFYTSGSFQTRMGDAIGISQASMSRCV 104

Query:    68 DSFLTAMSQPQIQCQYIKWPTEEESV-IIERNFRALAKFPGVIGAIDGCHIEGKFSKDIR 126
              +   A+ +   Q  +I++P +E S+  ++  F  LA  PGVIG +D  H+  K      
Sbjct:   105 ANVTEALVERATQ--FIRFPADEASMQALKDEFYGLAGMPGVIGVVDCIHVAIKAPNAED 162

Query:   127 NDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLY 186
               Y NRK   S+    VC     L  +     G   D  VL  S +    +A G    ++
Sbjct:   163 LSYVNRKGLHSLNCLMVCDIRGALMTVETNWPGSLQDYAVLQQSSLNSHFEA-G----MH 217

Query:   187 RDEYHLLGDSAYPLRTWCMVPYKNFGHMTEE--EKKYNTALSKTRVPIENVFGLIKGRWR 244
             +D + LLGDS++ LRTW M P     H+ E   E +YN A S T   IE  F  +  R+R
Sbjct:   218 KDSW-LLGDSSFFLRTWLMTPL----HIPETPAEYRYNMAHSATHSVIEKTFRTLCSRFR 272

Query:   245 RL---KYIDVGDPKRMAYIISAACVLHNFCYLQD-DVVEEIITHPIE 287
              L   K      P++ ++II A CVLHN       DV    +T P+E
Sbjct:   273 CLDGSKGALQYSPEKSSHIILACCVLHNISLEHGMDVWSSPMTGPME 319

GO:0005813 "centrosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|F1SIA2 HARBI1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 259 (96.2 bits), Expect = 2.6e-22, P = 2.6e-22
 Identities = 86/287 (29%), Positives = 134/287 (46%)

Query:     8 FLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCI 67
             +LVE L +     T   R +   P E + L AL +  +     ++GD   ++ +++  C+
Sbjct:    48 YLVELLGSSLSRPTQRSRAIS--P-ETQILAALGFYTSGSFQTRMGDAIGISQASMSRCV 104

Query:    68 DSFLTAMSQPQIQCQYIKWPTEEESV-IIERNFRALAKFPGVIGAIDGCHIEGKFSKDIR 126
              +   A+ +     Q+I++P +E SV  ++  F  LA  PGVIG +D  H+  K      
Sbjct:   105 TNVTEALVERA--SQFIRFPADEASVQALKDEFYGLAGMPGVIGVVDCIHVAIKAPNAED 162

Query:   127 NDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLY 186
               Y NRK   S+    VC     L  +     G   D  VL  S +  + +A G    ++
Sbjct:   163 LSYVNRKGLHSLNCLMVCDIRGTLMTVETNWPGSLQDCVVLQQSSLSSQFEA-G----MH 217

Query:   187 RDEYHLLGDSAYPLRTWCMVPYKNFGHMTEE--EKKYNTALSKTRVPIENVFGLIKGRWR 244
             ++ + LLGDS++ LR+W M P     H+ E   E +YN A S T   IE  F  +  R+R
Sbjct:   218 KESW-LLGDSSFFLRSWLMTPL----HIPETPAEYRYNMAHSATHSVIEKTFRTLCSRFR 272

Query:   245 RL---KYIDVGDPKRMAYIISAACVLHNFCYLQD-DVVEEIITHPIE 287
              L   K      P++ ++II A CVLHN       DV    +T P+E
Sbjct:   273 CLDGSKGALQYSPEKCSHIILACCVLHNISLEHGMDVWSSPVTGPME 319

GO:0005813 "centrosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

TAIR|locus:2123874 AT4G29780 "AT4G29780" [Arabidopsis thaliana (taxid:3702)]

 Score = 265 (98.3 bits), Expect = 3.3e-22, P = 3.3e-22
 Identities = 74/292 (25%), Positives = 144/292 (49%)

Query:     1 MRKTTFGFLVEAL-AAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLA 59
             M K+TF  + E L   +    T+    +P  P  K+  V +  +AT   +R + ++F L 
Sbjct:   219 MSKSTFNLICEELDTTVTKKNTMLRDAIP-AP--KRVGVCVWRLATGAPLRHVSERFGLG 275

Query:    60 DSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAI------- 112
              ST    +     A+    +  +Y+ WP++ E    +  F ++ K P V+G+I       
Sbjct:   276 ISTCHKLVIEVCRAIYDV-LMPKYLLWPSDSEINSTKAKFESVHKIPNVVGSIYTTHIPI 334

Query:   113 --DGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTS 170
                  H+   F+K  R+   N+K + S+ +QGV  ++ + T++ +G  G   D ++L  S
Sbjct:   335 IAPKVHVAAYFNK--RHTERNQKTSYSITVQGVVNADGIFTDVCIGNPGSLTDDQILEKS 392

Query:   171 QIGRRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRV 230
              + R+  A G    + RD + ++G+S +PL  + +VPY    ++T  +  +N ++ + + 
Sbjct:   393 SLSRQRAARG----MLRDSW-IVGNSGFPLTDYLLVPYTR-QNLTWTQHAFNESIGEIQG 446

Query:   231 PIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNFCYLQ-DDVVEEI 281
                  F  +KGRW  L+       + + Y++ A CVLHN C ++ ++++ E+
Sbjct:   447 IATAAFERLKGRWACLQKRTEVKLQDLPYVLGACCVLHNICEMRKEEMLPEL 498

GO:0009611 "response to wounding" evidence=RCA

GO:0009612 "response to mechanical stimulus" evidence=RCA

GO:0009873 "ethylene mediated signaling pathway" evidence=RCA

GO:0010200 "response to chitin" evidence=RCA

UNIPROTKB|E1BQ99 HARBI1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 251 (93.4 bits), Expect = 1.9e-21, P = 1.9e-21
 Identities = 82/268 (30%), Positives = 129/268 (48%)

Query:     8 FLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCI 67
             +LV+ L A     T   R +   P E + L AL +  +     ++GD   ++ +++  C+
Sbjct:    48 YLVDLLGASLSRPTQRSRAIS--P-ETQVLAALGFYTSGSFQTRMGDAIGISQASMSRCV 104

Query:    68 DSFLTAMSQPQIQCQYIKWPTEEESV-IIERNFRALAKFPGVIGAIDGCHIEGKFSKDIR 126
              +   A+ +   Q  +I +P +E +V  ++ +F ALA  PGV+G +D  H+  K      
Sbjct:   105 ANVTEALVERAPQ--FIHFPEDEAAVQSLKDDFYALAGMPGVLGVVDCTHVAIKAPNAED 162

Query:   127 NDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLY 186
               Y NRK   S+    VC +   L +      G   D  VL  + +  + +     + LY
Sbjct:   163 LSYVNRKGLHSLNCLMVCDARGALLSAETHWPGSMPDCNVLQQAALTSQFE-----NELY 217

Query:   187 RDEYHLLGDSAYPLRTWCMVPYKNFGHMTEE--EKKYNTALSKTRVPIENVFGLIKGRWR 244
             +D + LLGDS++ LRTW M P     H+ E   E +YN A S T   IE  F  I+ R+R
Sbjct:   218 KDGW-LLGDSSFFLRTWLMTPL----HIPETPAEYRYNMAHSATHNVIERTFRTIRSRFR 272

Query:   245 RL---KYIDVGDPKRMAYIISAACVLHN 269
              L   K      P++ ++II A CVLHN
Sbjct:   273 CLDGSKGTLQYSPEKSSHIILACCVLHN 300

GO:0005737 "cytoplasm" evidence=IEA

GO:0005813 "centrosome" evidence=IEA

TAIR|locus:2143104 AT5G12010 [Arabidopsis thaliana (taxid:3702)]

 Score = 257 (95.5 bits), Expect = 2.0e-21, P = 2.0e-21
 Identities = 75/298 (25%), Positives = 143/298 (47%)

Query:     1 MRKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLAD 60
             M K+TF  + + L +    E    R    +PV ++  V +  +AT   +R +  +F L  
Sbjct:   181 MSKSTFELICDELNSAVAKEDTALRNA--IPVRQRVAVCIWRLATGEPLRLVSKKFGLGI 238

Query:    61 STVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIE-- 118
             ST    +     A+    +  +Y++WP +E    I   F +++  P V+G++   HI   
Sbjct:   239 STCHKLVLEVCKAIKDV-LMPKYLQWPDDESLRNIRERFESVSGIPNVVGSMYTTHIPII 297

Query:   119 -GKFSK----DIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIG 173
               K S     + R+   N+K + S+ +Q V     + T++ +G  G   D KVL  S + 
Sbjct:   298 APKISVASYFNKRHTERNQKTSYSITIQAVVNPKGVFTDLCIGWPGSMPDDKVLEKSLLY 357

Query:   174 RRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIE 233
             +R +  G    L +  + + G   +PL  W +VPY    ++T  +  +N  +S+ +   +
Sbjct:   358 QRANNGG----LLKGMW-VAGGPGHPLLDWVLVPYTQ-QNLTWTQHAFNEKMSEVQGVAK 411

Query:   234 NVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNFCYLQDDVVE-EIITHPIENQM 290
               FG +KGRW  L+       + +  ++ A CVLHN C ++++ +E E++   I++++
Sbjct:   412 EAFGRLKGRWACLQKRTEVKLQDLPTVLGACCVLHNICEMREEKMEPELMVEVIDDEV 469

GO:0005634 "nucleus" evidence=ISM

GO:0005886 "plasma membrane" evidence=IDA

GO:0005774 "vacuolar membrane" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0009507 "chloroplast" evidence=IDA

GO:0015824 "proline transport" evidence=RCA

RGD|1584007 Harbi1 "harbinger transposase derived 1" [Rattus norvegicus (taxid:10116)]

 Score = 246 (91.7 bits), Expect = 6.3e-21, P = 6.3e-21
 Identities = 85/287 (29%), Positives = 129/287 (44%)

Query:     8 FLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCI 67
             +LVE L A     T   R +   P E + L AL +  +     ++GD   ++ +++  C+
Sbjct:    48 YLVELLGASLSRPTQRSRAIS--P-ETQILAALGFYTSGSFQTRMGDAIGISQASMSRCV 104

Query:    68 DSFLTAMSQPQIQCQYIKWPTEEESV-IIERNFRALAKFPGVIGAIDGCHIEGKFSKDIR 126
              +   A+ +     Q+I +P +E ++  ++  F  LA  PGVIGA+D  H+  K      
Sbjct:   105 ANVTEALVERA--SQFIHFPADEAAIQSLKDEFYGLAGMPGVIGAVDCIHVAIKAPNAED 162

Query:   127 NDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLY 186
               Y NRK   S+    VC     L  +     G   D  VL  S +  + +   P     
Sbjct:   163 LSYVNRKGLHSLNCLVVCDIRGALMTVETSWPGSLQDCAVLQQSSLSSQFETGMP----- 217

Query:   187 RDEYHLLGDSAYPLRTWCMVPYKNFGHMTEE--EKKYNTALSKTRVPIENVFGLIKGRWR 244
             +D + LLGDS++ L TW + P     H+ E   E +YN A S T   IE     +  R+R
Sbjct:   218 KDSW-LLGDSSFFLHTWLLTPL----HIPETPAEYRYNRAHSATHSVIEKTLRTLCCRFR 272

Query:   245 RL---KYIDVGDPKRMAYIISAACVLHNFCYLQD-DVVEEIITHPIE 287
              L   K      P++ ++II A CVLHN       DV    +T PIE
Sbjct:   273 CLDGSKGALQYSPEKSSHIILACCVLHNISLEHGMDVWSSPVTGPIE 319

GO:0004518 "nuclease activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0005813 "centrosome" evidence=IEA;ISO

GO:0046872 "metal ion binding" evidence=IEA

ZFIN|ZDB-GENE-081022-77 zgc:194221 "zgc:194221" [Danio rerio (taxid:7955)]

 Score = 241 (89.9 bits), Expect = 4.3e-20, P = 4.3e-20
 Identities = 78/263 (29%), Positives = 124/263 (47%)

Query:    20 ETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQI 79
             +T Y + +   P E+   + L ++AT  S R I   + +  STV   + +   A+     
Sbjct:    79 DTNYRQSIE--PAERLA-ICLRFLATGDSYRTIAFSYRVGVSTVAGIVAAVTRAIWDTLA 135

Query:    80 QCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMI 139
             Q + +  PT E+   I  +F     FP  +G+IDG H+  K   +  + + N K T S++
Sbjct:   136 Q-EVMPVPTTEDWRNISTDFLHRWNFPNCLGSIDGKHVVIKAPDNSGSLFYNYKGTYSVV 194

Query:   140 LQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGR--RIDAYG-PTSLLYRDEYHL---- 192
             L  V  S      + VG  GR  D  VL+ S  G+  R  A G P   L     H     
Sbjct:   195 LLAVVDSQYRFRVVDVGSYGRMSDGGVLANSIFGQALRDGALGLPQDALLSGAEHFGPQP 254

Query:   193 ---LGDSAYPLRTWCMVPYKNFGH-MTEEEKKYNTALSKTRVPIENVFGLIKGRWRRLK- 247
                + D A+PLR   M P+   GH ++  ++ +N  LS+ R+ +EN FG++  +WR  + 
Sbjct:   255 HVFVADEAFPLRRDLMRPFP--GHNLSGRQRIFNYRLSRARLIVENTFGILTAQWRMYRG 312

Query:   248 YIDVGDPKRMAYIISAACVLHNF 270
              I++  P  +   + A CVLHNF
Sbjct:   313 AIEIS-PANVDACVKATCVLHNF 334

GO:0005575 "cellular_component" evidence=ND

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

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	307
pfam13359	155	pfam13359, DDE_4, DDE superfamily endonuclease	1e-29
pfam04827	205	pfam04827, Plant_tran, Plant transposon protein	7e-04

>gnl|CDD|222071 pfam13359, DDE_4, DDE superfamily endonuclease

 Score =  109 bits (275), Expect = 1e-29
 Identities = 38/165 (23%), Positives = 70/165 (42%), Gaps = 17/165 (10%)

Query: 112 IDGCHIEGKFSKDI---RNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLS 168
           IDG  I  +  K +      Y+  K   ++ +  V   +  +  + VG  G   D ++L 
Sbjct: 1   IDGTEIPIERPKSLEEQAQTYSGYKKHNTLKVLIVVDPDGRIIFVSVGWPGSVSDKRILE 60

Query: 169 TSQIGRRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFGH---MTEEEKKYNTAL 225
            S +  ++              ++L D  +PL    + P         +TEEE ++N  +
Sbjct: 61  NSGLLEKLPPG----------DYVLADRGFPLSDSLLAPPAKKPGGAQLTEEEVEFNRRI 110

Query: 226 SKTRVPIENVFGLIKGRWRRLK-YIDVGDPKRMAYIISAACVLHN 269
           +  R+ +E V G +KGR+R L+  + +     +  I+   C LHN
Sbjct: 111 ASARIHVERVIGRLKGRFRILRGRLRISKLTTLDKIVLVCCALHN 155

This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Length = 155

>gnl|CDD|203098 pfam04827, Plant_tran, Plant transposon protein

 Score = 39.6 bits (92), Expect = 7e-04
 Identities = 44/201 (21%), Positives = 87/201 (43%), Gaps = 18/201 (8%)

Query: 81  CQYIKWPTEEESVIIER--NFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNR--KCTQ 136
             Y++ PT +    ++R  +      FPG++G++D  H + K           R    + 
Sbjct: 1   ASYLRAPTAKN---VDRLLHIGESRGFPGMLGSLDCMHWKWKNCPTAWKGQYTRGDSKSP 57

Query: 137 SMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSL---LYRDEYHL- 192
           ++IL+ V + +  + +   GC G N+D  VL+ S I   I       +   +   +Y++ 
Sbjct: 58  TIILEAVASYDLWIWHAFFGCPGSNNDINVLNQSPIFDDILQGTAPRVRYTVNGRQYNMG 117

Query: 193 --LGDSAYPLRTWCMVPYKNFGHMTEEEKK-YNTALSKTRVPIENVFGLIKGRWRRLKYI 249
             L D  YP   W     K+      E+ K +       R  +E  FG+++ R++ +   
Sbjct: 118 YYLADGIYP--EWATF-VKSIRLPQLEKHKLFAQQQEACRKDVERAFGVLQARFKIVATP 174

Query: 250 D-VGDPKRMAYIISAACVLHN 269
             + +   ++ I++A  +LHN
Sbjct: 175 ARLWNQSDLSNIMTACIILHN 195

This family contains plant transposases which are putative members of the PIF / Ping-Pong family. Length = 205

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	307
PF13359	158	DDE_Tnp_4: DDE superfamily endonuclease	100.0
KOG4585|consensus	326		100.0
PF04827	205	Plant_tran: Plant transposon protein; InterPro: IP	100.0
PF13612	155	DDE_Tnp_1_3: Transposase DDE domain	99.25
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	99.24
PF01609	213	DDE_Tnp_1: Transposase DDE domain; InterPro: IPR00	98.23
PF13586	88	DDE_Tnp_1_2: Transposase DDE domain	97.97
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	97.21
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	97.19
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	97.08
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	96.87
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	96.66
PF13518	52	HTH_28: Helix-turn-helix domain	96.51
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	96.44
PF13340	75	DUF4096: Putative transposase of IS4/5 family (DUF	96.39
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	96.33
smart00351	125	PAX Paired Box domain.	96.2
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	95.96
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	95.87
PRK09413	121	IS2 repressor TnpA; Reviewed	95.85
cd00131	128	PAX Paired Box domain	95.84
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	95.71
COG3415	138	Transposase and inactivated derivatives [DNA repli	95.6
PF12116	82	SpoIIID: Stage III sporulation protein D; InterPro	95.31
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	95.18
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	95.16
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	94.9
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	94.78
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	94.74
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	94.72
PRK00118	104	putative DNA-binding protein; Validated	94.54
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	94.53
PRK04217	110	hypothetical protein; Provisional	94.47
PRK06030	124	hypothetical protein; Provisional	93.94
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	93.9
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	93.79
PHA00675	78	hypothetical protein	93.71
TIGR02844	80	spore_III_D sporulation transcriptional regulator	93.53
PRK12529	178	RNA polymerase sigma factor; Provisional	93.36
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	93.28
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	93.25
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	93.1
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	93.09
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	93.09
PRK03975	141	tfx putative transcriptional regulator; Provisiona	93.09
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	92.98
COG2963	116	Transposase and inactivated derivatives [DNA repli	92.83
PF13730	55	HTH_36: Helix-turn-helix domain	92.77
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	92.63
PRK12515	189	RNA polymerase sigma factor; Provisional	92.54
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	92.25
PHA00542	82	putative Cro-like protein	92.22
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	92.18
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	92.12
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	91.97
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	91.9
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	91.86
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	91.8
PRK15320	251	transcriptional activator SprB; Provisional	91.77
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	91.76
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	91.69
PF13551	112	HTH_29: Winged helix-turn helix	91.52
PRK12514	179	RNA polymerase sigma factor; Provisional	91.39
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	91.35
PF08299	70	Bac_DnaA_C: Bacterial dnaA protein helix-turn-heli	91.3
COG3316	215	Transposase and inactivated derivatives [DNA repli	91.23
PRK11924	179	RNA polymerase sigma factor; Provisional	91.17
PRK09047	161	RNA polymerase factor sigma-70; Validated	91.1
PF13610	140	DDE_Tnp_IS240: DDE domain	91.06
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	91.04
PRK12530	189	RNA polymerase sigma factor; Provisional	90.97
PRK05803	233	sporulation sigma factor SigK; Reviewed	90.96
PRK12547	164	RNA polymerase sigma factor; Provisional	90.92
PRK08301	234	sporulation sigma factor SigE; Reviewed	90.91
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	90.81
PRK12511	182	RNA polymerase sigma factor; Provisional	90.79
PRK12524	196	RNA polymerase sigma factor; Provisional	90.75
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	90.66
PRK12533	216	RNA polymerase sigma factor; Provisional	90.65
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	90.61
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	90.56
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	90.55
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	90.54
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	90.51
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	90.35
PRK12528	161	RNA polymerase sigma factor; Provisional	90.26
PRK01381	99	Trp operon repressor; Provisional	90.22
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	90.21
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	90.15
PRK12537	182	RNA polymerase sigma factor; Provisional	90.11
PRK12516	187	RNA polymerase sigma factor; Provisional	90.08
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	90.08
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	90.07
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	90.02
PRK12519	194	RNA polymerase sigma factor; Provisional	89.97
PRK06759	154	RNA polymerase factor sigma-70; Validated	89.97
PRK12532	195	RNA polymerase sigma factor; Provisional	89.94
PF00126	60	HTH_1: Bacterial regulatory helix-turn-helix prote	89.91
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	89.8
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	89.76
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	89.75
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	89.71
PRK05572	252	sporulation sigma factor SigF; Validated	89.66
PRK06811	189	RNA polymerase factor sigma-70; Validated	89.57
PRK12512	184	RNA polymerase sigma factor; Provisional	89.42
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	89.42
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	89.42
PRK05602	186	RNA polymerase sigma factor; Reviewed	89.37
PRK12531	194	RNA polymerase sigma factor; Provisional	89.33
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	89.31
PRK06704	228	RNA polymerase factor sigma-70; Validated	89.21
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	89.19
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	89.05
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	89.02
PRK09415	179	RNA polymerase factor sigma C; Reviewed	89.01
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	88.98
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	88.95
PRK12534	187	RNA polymerase sigma factor; Provisional	88.94
PRK08215	258	sporulation sigma factor SigG; Reviewed	88.94
PRK08583	257	RNA polymerase sigma factor SigB; Validated	88.94
PRK12525	168	RNA polymerase sigma factor; Provisional	88.91
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	88.81
PRK12520	191	RNA polymerase sigma factor; Provisional	88.62
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	88.62
PF13751	125	DDE_Tnp_1_6: Transposase DDE domain	88.5
PRK12523	172	RNA polymerase sigma factor; Reviewed	88.49
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	88.49
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	88.48
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	88.27
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	88.19
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	88.19
PRK12540	182	RNA polymerase sigma factor; Provisional	88.17
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	88.07
PRK12546	188	RNA polymerase sigma factor; Provisional	88.03
PRK12544	206	RNA polymerase sigma factor; Provisional	88.0
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	87.86
PRK12539	184	RNA polymerase sigma factor; Provisional	87.85
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	87.84
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	87.82
PRK10402	226	DNA-binding transcriptional activator YeiL; Provis	87.81
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	87.8
PRK12536	181	RNA polymerase sigma factor; Provisional	87.68
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	87.67
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	87.66
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	87.64
PRK06930	170	positive control sigma-like factor; Validated	87.63
PRK13919	186	putative RNA polymerase sigma E protein; Provision	87.61
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	87.6
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	87.57
PRK07405	317	RNA polymerase sigma factor SigD; Validated	87.28
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	87.09
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	87.06
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	86.92
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	86.83
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	86.75
PHA02591	83	hypothetical protein; Provisional	86.66
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	86.65
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	86.58
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	86.52
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	86.51
PRK12541	161	RNA polymerase sigma factor; Provisional	86.44
PRK12545	201	RNA polymerase sigma factor; Provisional	86.42
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	86.38
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	86.29
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	86.27
PRK15418	318	transcriptional regulator LsrR; Provisional	86.23
PRK07670	251	RNA polymerase sigma factor SigD; Validated	86.21
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	86.04
PRK12522	173	RNA polymerase sigma factor; Provisional	85.94
PRK12543	179	RNA polymerase sigma factor; Provisional	85.93
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	85.9
PRK12527	159	RNA polymerase sigma factor; Reviewed	85.88
PF05344	65	DUF746: Domain of Unknown Function (DUF746); Inter	85.83
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	85.71
PF13309	64	HTH_22: HTH domain	85.66
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	85.6
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	85.59
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	85.54
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	85.51
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	85.48
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	85.31
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	85.22
PRK12526	206	RNA polymerase sigma factor; Provisional	85.06
PRK15201	198	fimbriae regulatory protein FimW; Provisional	84.99
PF07638	185	Sigma70_ECF: ECF sigma factor	84.93
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	84.86
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	84.84
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	84.75
PRK12538	233	RNA polymerase sigma factor; Provisional	84.73
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	84.65
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	84.48
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	84.44
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	84.41
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	84.31
PRK08295	208	RNA polymerase factor sigma-70; Validated	84.21
PRK12542	185	RNA polymerase sigma factor; Provisional	84.21
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	84.19
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	84.15
PRK08241	339	RNA polymerase factor sigma-70; Validated	83.96
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	83.91
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	83.8
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	83.55
PRK14086	617	dnaA chromosomal replication initiation protein; P	83.55
PRK03573	144	transcriptional regulator SlyA; Provisional	83.51
PF09607	58	BrkDBD: Brinker DNA-binding domain; InterPro: IPR0	83.38
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	83.37
PRK00149	450	dnaA chromosomal replication initiation protein; R	83.29
PRK11922	231	RNA polymerase sigma factor; Provisional	83.29
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	83.12
COG2522	119	Predicted transcriptional regulator [General funct	83.07
PRK07598	415	RNA polymerase sigma factor SigC; Validated	83.05
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	83.05
PRK13413	200	mpi multiple promoter invertase; Provisional	83.02
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	83.02
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	82.67
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	82.66
PRK12535	196	RNA polymerase sigma factor; Provisional	82.6
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	82.54
PHA00738	108	putative HTH transcription regulator	82.46
PRK14088	440	dnaA chromosomal replication initiation protein; P	82.42
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	82.28
PF00292	125	PAX: 'Paired box' domain; InterPro: IPR001523 The	81.86
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	81.83
PRK05949	327	RNA polymerase sigma factor; Validated	81.74
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	81.7
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	81.55
smart00352	75	POU Found in Pit-Oct-Unc transcription factors.	81.54
PRK09391	230	fixK transcriptional regulator FixK; Provisional	81.53
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	81.52
PRK05901	509	RNA polymerase sigma factor; Provisional	81.39
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	81.32
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	81.3
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	81.18
PRK12517	188	RNA polymerase sigma factor; Provisional	80.53
PRK13870	234	transcriptional regulator TraR; Provisional	80.37
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	80.29
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	80.19
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	80.16

>PF13359 DDE_Tnp_4: DDE superfamily endonuclease

Probab=100.00  E-value=5.2e-40  Score=270.21  Aligned_cols=152  Identities=35%  Similarity=0.603  Sum_probs=141.2

Q ss_pred             ecceeEEeecCCC---CccccccccCCcceeEEeeeCCCcceEeeeeccccccCCCcccccchhhcchhhcCCCCCCCCC
Q psy4300         112 IDGCHIEGKFSKD---IRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRD  188 (307)
Q Consensus       112 iDgt~i~i~~P~~---~~~~y~~~k~~~s~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~S~l~~~l~~~~~~~~~~~~  188 (307)
                      ||||||+|++|.+   ....|+++|+.|++|+|++||++|+|++++.++||++||+.+|++|++...+..      .++.
T Consensus         1 iDgt~v~i~~P~~~~~~~~~y~~~k~~~~~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~s~~~~~l~~------~~~~   74 (158)
T PF13359_consen    1 IDGTHVPIQRPSDKEEQREFYSGKKKNHSLKVQIVCDPDGRIIYVSVGWPGSVHDSTIFRQSGLLDRLEQ------AFPP   74 (158)
T ss_pred             CccEEEEEEeCCccccccccccCCCCcceEeEEEEEeccceeEeeecccccccccccccccccccceeec------cccc
Confidence            7999999999998   688999999999999999999999999999999999999999999998887763      1446


Q ss_pred             CeEEEecCCCCCCcccccccc--CCCCCCHHHHHHhHHHHhhhhHHHHHHHHHHhhccccc-ccccCChhhHHHHHHHHH
Q psy4300         189 EYHLLGDSAYPLRTWCMVPYK--NFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWRRLK-YIDVGDPKRMAYIISAAC  265 (307)
Q Consensus       189 ~~~llgD~gY~~~~~l~~P~~--~~~~lt~~q~~fN~~~s~~R~~VE~~fg~LK~rf~iL~-~~~~~~~~~~~~ii~a~~  265 (307)
                      ++++|||+||++.+++++||+  ...+++++|+.||+.|++.|.+||++||+||+||++|+ +++....+.+..+|.|||
T Consensus        75 ~~~~l~D~gy~~~~~~~~P~~~~~~~~l~~~e~~~N~~~s~~R~~vE~~~~~lK~rf~~l~~~~~~~~~~~~~~ii~~~~  154 (158)
T PF13359_consen   75 GEYLLGDSGYPLSPYLLTPYKKPKGRELTPEEKEFNRRHSSARIIVERAFGRLKSRFRILRGRLRLSRPEKAPQIILACC  154 (158)
T ss_pred             CccccccccccccccccccccccccccccccccchhccccceeeeeHHHHHHHHHhcccCCcccCCCcHhHHHHHHheeE
Confidence            799999999999999999997  44578999999999999999999999999999999999 888834999999999999


Q ss_pred             Hhhh
Q psy4300         266 VLHN  269 (307)
Q Consensus       266 ~LhN  269 (307)
                      +|||
T Consensus       155 ~LhN  158 (158)
T PF13359_consen  155 VLHN  158 (158)
T ss_pred             EEEC
Confidence            9999

>KOG4585|consensus

Probab=100.00  E-value=1.1e-36  Score=274.52  Aligned_cols=264  Identities=29%  Similarity=0.423  Sum_probs=219.4

Q ss_pred             CCHHHHHHHHHHHhhhcCcccccCCC-CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccccc
Q psy4300           1 MRKTTFGFLVEALAAINGYETLYERG-VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQI   79 (307)
Q Consensus         1 ms~~~F~~L~~~l~~~~~~~~~~~~~-~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~   79 (307)
                      +++.+|++++..........+ .... ...++....+++.++.++++.+.+.++..||..++|+     .+.......  
T Consensus        10 ~s~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~-----~~~~~~~~~--   81 (326)
T KOG4585|consen   10 KSYTTFDKICSLVQSLNVVKN-SGFMLSSLLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC-----KFLEEKEDL--   81 (326)
T ss_pred             HHHHHHHHHhhhhhhhhhhcc-cchhhhccccHHhhhhhhhccccccchHHHHHHHcCCcchhh-----hHHHhhhcc--
Confidence            367889999988766543223 2111 2222289999999999999999999999999999998     555566666  


Q ss_pred             ccccccCCChHHHHHHHHHHHHhhCCCCcceeecceeEEeecCCCCccccccccCCcceeEEeeeCCCcceEeeeecccc
Q psy4300          80 QCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTG  159 (307)
Q Consensus        80 ~~~~i~~P~~~~~~~~~~~f~~~~~~p~~~g~iDgt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d~~g~i~~v~~~~~G  159 (307)
                      ++.++.||....+..+.+.++.   +|+|+|++|+||+++..|+.....|.|+  .++.|+|+|||.+++|+++.+|+||
T Consensus        82 ~~~~~~~p~~~~~~~i~~~~~~---~~~~~g~~d~~hi~~~~~~~~~~~~~n~--~~~~Nvlav~n~d~~f~~v~vg~~G  156 (326)
T KOG4585|consen   82 APHFLKWPSRRILYEIRERFES---LPNCVGAIDTTHIPIRVPPKSGSVYFNK--EQSKNLLAVCNFDMRFIYVDVGWPG  156 (326)
T ss_pred             cchhhcCchhhhhhhhcccccc---ccchhccccccccceecCcccccccccc--ccchhhhheecCCceEEEEEccCCC
Confidence            8999999998777788888875   9999999999999999999998888888  8889999999999999999999999


Q ss_pred             ccCCCcccccchhhcchhhcCCCCC-----CCCCCeEEEecCCCCCCccccccccCCCCCCHHHHHHhHHHHhhhhHHHH
Q psy4300         160 RNHDAKVLSTSQIGRRIDAYGPTSL-----LYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIEN  234 (307)
Q Consensus       160 s~~D~~i~~~S~l~~~l~~~~~~~~-----~~~~~~~llgD~gY~~~~~l~~P~~~~~~lt~~q~~fN~~~s~~R~~VE~  234 (307)
                      +.||+.+++.+.+......++|..+     ..+...+++|+.+||+.+++++|+..+. .+..++.||.+|+..|.++|+
T Consensus       157 s~~D~kvl~~~~~~~~~~~~~~~k~yl~d~~~~~~~~~~g~~~~~~~~~~~~~~~~~~-~~~~~elFN~rh~~~r~v~e~  235 (326)
T KOG4585|consen  157 SAHDTKVLQDSLLYKRNFPHPPLKYYLVDSGYPLRPGLLGPIGFPLYSLLMFPYGGPQ-PTNSQELFNKRHSSLRSVAER  235 (326)
T ss_pred             CccHHHHHHhhcccccccccCCccccccccCcccccccccccccccchhhhcccCCCC-CCchHHHHhhhhhhHHHHHHH
Confidence            9999999999988776666444211     1124567777777778888888888764 478889999999999999999


Q ss_pred             HHHHHHhhccccc-ccccCChhhHHHHHHHHHHhhhhhcccCCcch
Q psy4300         235 VFGLIKGRWRRLK-YIDVGDPKRMAYIISAACVLHNFCYLQDDVVE  279 (307)
Q Consensus       235 ~fg~LK~rf~iL~-~~~~~~~~~~~~ii~a~~~LhN~~~~~~~~~~  279 (307)
                      +||++|.||+||. . ...+.++..++|.+||+|||+|++.++...
T Consensus       236 ~fg~lk~rw~il~~~-~~~~~~~~~~iV~a~caLHN~~~~~~~~~~  280 (326)
T KOG4585|consen  236 AFGVLKAKWRILQRR-EKYDLKKLPKIVTACCALHNIIRDSDEEDP  280 (326)
T ss_pred             HHHHhhhhhHHHhhc-ccccccchHHHHHHHHHHHHHHHhhccccc
Confidence            9999999999999 6 555899999999999999999998887443

>PF04827 Plant_tran: Plant transposon protein; InterPro: IPR006912 This entry represents a putative Harbinger transposase-derived nuclease, which is thought to have nuclease activity

Probab=100.00  E-value=2.4e-36  Score=245.79  Aligned_cols=193  Identities=23%  Similarity=0.341  Sum_probs=171.0

Q ss_pred             ccccCCChHHHHHHHHHHHHhhCCCCcceeecceeEEee-cCCCCccccc-cccCCcceeEEeeeCCCcceEeeeecccc
Q psy4300          82 QYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGK-FSKDIRNDYN-NRKCTQSMILQGVCTSNKLLTNIHVGCTG  159 (307)
Q Consensus        82 ~~i~~P~~~~~~~~~~~f~~~~~~p~~~g~iDgt~i~i~-~P~~~~~~y~-~~k~~~s~~~q~v~d~~g~i~~v~~~~~G  159 (307)
                      +|++-|+.++.+++.+.++. .|||+.+|+|||+|+.++ +|......|. |++|.+++.+++|+++|.+|+++..|.||
T Consensus         2 ~YLr~P~~~d~~rll~~~e~-rGFpGmlGSIDCmHw~WkncP~aw~g~~~~G~~g~pTiiLEaVAs~dlwIWhaffG~~G   80 (205)
T PF04827_consen    2 EYLRRPTNEDLERLLQIGEA-RGFPGMLGSIDCMHWEWKNCPTAWKGQYTRGKEGVPTIILEAVASHDLWIWHAFFGMPG   80 (205)
T ss_pred             cccCCCChhHHHHHHHhhhh-cCCCccccceeEEEeehhcchHHhhhcccCCCCCCCeehhhhhhccchhhhheeeccCC
Confidence            67889999999999977776 699999999999999997 5666666676 99999999999999999999999999999


Q ss_pred             ccCCCcccccchhhcchhhc-CCCCCCCC-----CCeEEEecCCCCCCccccccccCCCCCCHHHHHHhHHHHhhhhHHH
Q psy4300         160 RNHDAKVLSTSQIGRRIDAY-GPTSLLYR-----DEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIE  233 (307)
Q Consensus       160 s~~D~~i~~~S~l~~~l~~~-~~~~~~~~-----~~~~llgD~gY~~~~~l~~P~~~~~~lt~~q~~fN~~~s~~R~~VE  233 (307)
                      |.+|..+++.|+++..+..+ .|..-..-     +-.|.|+|..||.+..++.+++.|.  +++++.|.+++.++|..||
T Consensus        81 S~NDiNVL~~Splf~~~~~G~ap~v~f~VNg~~Y~~gYYLaDGiYP~watfvktI~~p~--~~k~k~fa~~QE~~RKDVE  158 (205)
T PF04827_consen   81 SNNDINVLDRSPLFDDLLQGQAPRVQFTVNGHEYNMGYYLADGIYPEWATFVKTISLPQ--GEKRKLFAKHQESARKDVE  158 (205)
T ss_pred             cccccccccccHHHHHHhcCcCCceEEEecCeecccceeeccCcCcchHhHhhhcchhh--chhhHHHHHhCHHHHHHHH
Confidence            99999999999999877775 23221111     2358889999999999999999864  8899999999999999999


Q ss_pred             HHHHHHHhhccccc-ccccCChhhHHHHHHHHHHhhhhhcccCCc
Q psy4300         234 NVFGLIKGRWRRLK-YIDVGDPKRMAYIISAACVLHNFCYLQDDV  277 (307)
Q Consensus       234 ~~fg~LK~rf~iL~-~~~~~~~~~~~~ii~a~~~LhN~~~~~~~~  277 (307)
                      ++||.|++||+|++ +.+.++.+.+..|+.||++||||+++.+.+
T Consensus       159 rAFGVLQaRfaIi~~p~r~w~~~~l~~Im~aCiILHNMIvEDEr~  203 (205)
T PF04827_consen  159 RAFGVLQARFAIIRGPARLWDREDLANIMRACIILHNMIVEDERD  203 (205)
T ss_pred             HHHHHHHHHHHHhcCchhccCHHHHHHHHHHHHHhhheeEecccc
Confidence            99999999999999 899989999999999999999999987754

However it does not have transposase activity [, ]. ; GO: 0016788 hydrolase activity, acting on ester bonds

>PF13612 DDE_Tnp_1_3: Transposase DDE domain

Probab=99.25  E-value=5.1e-12  Score=102.50  Aligned_cols=126  Identities=19%  Similarity=0.178  Sum_probs=94.2

Q ss_pred             CCcceeecceeEEeecCCCC-------ccc---cccccCCcceeEEeeeCCCcceEeeeeccccccCCCcccccchhhcc
Q psy4300         106 PGVIGAIDGCHIEGKFSKDI-------RND---YNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRR  175 (307)
Q Consensus       106 p~~~g~iDgt~i~i~~P~~~-------~~~---y~~~k~~~s~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~S~l~~~  175 (307)
                      +..+.+||+|.+|++.+...       +..   |+..+-+|++|++++|+.+|.++.+.. .||+.||..++..      
T Consensus         4 ~~~i~~iDS~Pi~vC~~~R~~r~k~~~~~a~~G~~a~~~fyGfKlHllv~~~G~i~~~~l-T~an~~D~~~~~~------   76 (155)
T PF13612_consen    4 CTGIYIIDSFPIPVCHNIRIKRHKVFKGLAYRGYCAMGWFYGFKLHLLVNDSGEIVAFTL-TPANVHDRKVLEE------   76 (155)
T ss_pred             ccEEEEEecCChhHhCccchhhhccccCccccceeccceeEeeeeeeEEccCCcEEEEEE-ccccccccccccc------
Confidence            56788999999999876532       122   233344699999999999999999877 7999999988732      


Q ss_pred             hhhcCCCCCCCCCCeEEEecCCCCCCc----------cccccccCCCCCCHHHHHHhHHHHhhhhHHHHHHHHHHhhccc
Q psy4300         176 IDAYGPTSLLYRDEYHLLGDSAYPLRT----------WCMVPYKNFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWRR  245 (307)
Q Consensus       176 l~~~~~~~~~~~~~~~llgD~gY~~~~----------~l~~P~~~~~~lt~~q~~fN~~~s~~R~~VE~~fg~LK~rf~i  245 (307)
                      +..        .....++||+||-...          .++||.+++- .......+++.+.+.|.+||.+|+.||..|.+
T Consensus        77 l~~--------~~~g~l~gDkGYis~~L~~~L~~~gI~L~t~~RkNm-k~~~~~~~~~~l~~~R~~IETvfs~Lk~~~~i  147 (155)
T PF13612_consen   77 LSE--------NLKGKLFGDKGYISKELKDELKEQGIKLITPRRKNM-KNKLMPLFDKLLLRKRRIIETVFSQLKNQFNI  147 (155)
T ss_pred             ccc--------ccccceecchhhhcchHHhhhhhceEEEeccccccc-cccccchhhhhhhheeeEeehHHHHHHHhhce
Confidence            211        1134799999996433          3799998752 12223457889999999999999999998877


Q ss_pred             cc
Q psy4300         246 LK  247 (307)
Q Consensus       246 L~  247 (307)
                      =+
T Consensus       148 e~  149 (155)
T PF13612_consen  148 EH  149 (155)
T ss_pred             Ee
Confidence            54

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

Probab=99.24  E-value=1.5e-11  Score=81.52  Aligned_cols=50  Identities=20%  Similarity=0.383  Sum_probs=48.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      +++.+++++++|.||+.|.++.++|..||||+||++++++++++.|+..+
T Consensus         2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l   51 (53)
T PF13613_consen    2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL   51 (53)
T ss_pred             CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence            68999999999999999999999999999999999999999999999874

>PF01609 DDE_Tnp_1: Transposase DDE domain; InterPro: IPR002559 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element

Probab=98.23  E-value=2e-08  Score=85.21  Aligned_cols=150  Identities=23%  Similarity=0.234  Sum_probs=88.0

Q ss_pred             cceeecceeEEeecCCCC-ccccccccCCcceeEEeee-CCCcceEeeeeccccccCCCcccccchhhcchhhcCCCCCC
Q psy4300         108 VIGAIDGCHIEGKFSKDI-RNDYNNRKCTQSMILQGVC-TSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLL  185 (307)
Q Consensus       108 ~~g~iDgt~i~i~~P~~~-~~~y~~~k~~~s~~~q~v~-d~~g~i~~v~~~~~Gs~~D~~i~~~S~l~~~l~~~~~~~~~  185 (307)
                      .+.+||+|.++.. +... ...+.+++...+.++++++ +..|.++.+... +|+.+|...+..  +.+.  .      .
T Consensus         5 ~~~~iD~T~i~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~d~~~~~~--ll~~--~------~   72 (213)
T PF01609_consen    5 RVVAIDGTTIRTP-HDKSARRYKKGKKRGFGYKLHLAVDDNSGLPLSVKVT-PGNVHDSKALPE--LLER--K------P   72 (213)
T ss_dssp             EEEEEETTT--EE-EEEEE-B-SSGGGHSSHGGHHHHHHHHHGGGGGGEEE-EEEGG-HHHHHH--HHTT----------
T ss_pred             eEEEEECcEEEee-cchhhhcccCCCCcCCCEeEEEEEeecccceeeeecc-ccccceeecccc--cccc--c------c
Confidence            4679999999988 1111 3344456667888999999 567788888885 999999988764  2222  1      2


Q ss_pred             CCCCeEEEecCCCCCCcc----------ccccccCCCCC---------------------------------CHHHHHHh
Q psy4300         186 YRDEYHLLGDSAYPLRTW----------CMVPYKNFGHM---------------------------------TEEEKKYN  222 (307)
Q Consensus       186 ~~~~~~llgD~gY~~~~~----------l~~P~~~~~~l---------------------------------t~~q~~fN  222 (307)
                      ...+.++++|+||...+.          .+.|.+.+...                                 ...++...
T Consensus        73 ~~~~~~vv~D~gy~s~~~~~~l~~~~~~~vi~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (213)
T PF01609_consen   73 GRKPDLVVADRGYDSAENLEALKERGIHFVIRLKKNRKKKIQKIENKFWKSFDRRSARKKPKQKSKRVRVVIRKEQKKKG  152 (213)
T ss_dssp             ---EEEEEE-S--BBTTHHHHHHTS---EEEEE--EEEE-TTS-EEEE--EEEEEEEEEEETGGGEEEEEEEEEECS--T
T ss_pred             cccccceeecccccceeccccccccccccccccccccccccccchhhccccccccccccccccccccccccccccccccc
Confidence            335789999999974331          24444432111                                 00111111


Q ss_pred             HH--------------HHhhhhHHHHHHHHHHhhcccccccccCChhhHHHHHHHHHHhhhh
Q psy4300         223 TA--------------LSKTRVPIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNF  270 (307)
Q Consensus       223 ~~--------------~s~~R~~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~a~~~LhN~  270 (307)
                      ..              +.+.|+.||+.|..||+.|. +.+++....+.+...+.++++-.|+
T Consensus       153 ~~~~~~~~~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~-l~~~~~~~~~~~~~~~~~~~la~nl  213 (213)
T PF01609_consen  153 YFLVTNITTLPRDTAALYRRRWQIERFFRELKQFLG-LERLRVRSPERIEAHLFLTLLAYNL  213 (213)
T ss_dssp             TS---EEEEEESS--SHHHCGGHHHHHHHHHTTTTT-GGGS--SSHHHHHHHHHHHHHH---
T ss_pred             ccccccccccccccceeecccchhhHHHHHHHhcCC-CchhcccCHHHHHHHHHHHHhhCcC
Confidence            22              89999999999999999644 4566666788888888888877775

Transposases have been grouped into various families [, , ]. This family includes the IS4 transposase. 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: 3ECP_A 4DM0_A 1MUS_A 1MUH_A 1MM8_A 1B7E_A.

>PF13586 DDE_Tnp_1_2: Transposase DDE domain

Probab=97.97  E-value=3.9e-06  Score=61.69  Aligned_cols=48  Identities=25%  Similarity=0.357  Sum_probs=37.5

Q ss_pred             HHHHHhHHHHhhhhHHHHHHHHHHhhccccc-ccccCChhhHHHHH-HHHHH
Q psy4300         217 EEKKYNTALSKTRVPIENVFGLIKGRWRRLK-YIDVGDPKRMAYII-SAACV  266 (307)
Q Consensus       217 ~q~~fN~~~s~~R~~VE~~fg~LK~rf~iL~-~~~~~~~~~~~~ii-~a~~~  266 (307)
                      .+..+...+.+.|++||++|+.||. |+.|. ++.. .+......+ +||++
T Consensus        35 ~~~~~d~~~~~~Rw~VEr~f~wlk~-~Rrl~~ryek-~~~s~~~~v~la~~~   84 (88)
T PF13586_consen   35 RPRKFDFRLYKRRWVVERTFAWLKR-FRRLATRYEK-LASSFLAFVHLACIV   84 (88)
T ss_pred             ccCccchhhhccceehhhhhHHHHH-cCcccccccc-CHHHHHHHHHHHHHH
Confidence            4667889999999999999999998 88888 8888 555444444 55544

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

Probab=97.21  E-value=0.00053  Score=43.30  Aligned_cols=41  Identities=17%  Similarity=0.287  Sum_probs=23.7

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      +.++.+++..+.- ++..|.|.+.||..+|+|+|||++.+++
T Consensus         3 ~~Lt~~eR~~I~~-l~~~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen    3 KHLTPEERNQIEA-LLEQGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             ---------HHHH-HHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred             cchhhhHHHHHHH-HHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            4677888877774 4789999999999999999999999875

>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=97.19  E-value=0.00057  Score=43.38  Aligned_cols=40  Identities=25%  Similarity=0.379  Sum_probs=30.3

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      +.++.+ ++.-++..+..|.+..++|..||||++||+|+++
T Consensus         4 ~~~~~~-~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen    4 PKLSKE-QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             SSSSHC-CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             CCCCHH-HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence            334444 5677778889999999999999999999999875

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 ....

>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=97.08  E-value=0.0024  Score=41.33  Aligned_cols=45  Identities=20%  Similarity=0.437  Sum_probs=38.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAM   74 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l   74 (307)
                      .+|++++-.+.++| ..+.++.++|..+|+|.+||+++.++.+.-|
T Consensus         4 ~L~~~er~vi~~~y-~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL   48 (50)
T PF04545_consen    4 QLPPREREVIRLRY-FEGLTLEEIAERLGISRSTVRRILKRALKKL   48 (50)
T ss_dssp             TS-HHHHHHHHHHH-TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHh-cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence            68899999999999 6689999999999999999999999877654

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 ....

>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=96.87  E-value=0.0023  Score=42.10  Aligned_cols=42  Identities=21%  Similarity=0.259  Sum_probs=32.0

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      +..+++++++-+.-. +..|.+..++|..|||++||++.|+..
T Consensus         4 R~~LTl~eK~~iI~~-~e~g~s~~~ia~~fgv~~sTv~~I~K~   45 (53)
T PF04218_consen    4 RKSLTLEEKLEIIKR-LEEGESKRDIAREFGVSRSTVSTILKN   45 (53)
T ss_dssp             SSS--HHHHHHHHHH-HHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred             CccCCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence            578999999987655 678889999999999999999999874

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.

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

Probab=96.66  E-value=0.0022  Score=41.46  Aligned_cols=38  Identities=21%  Similarity=0.378  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300          33 EKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFL   71 (307)
Q Consensus        33 ~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~   71 (307)
                      +.++.+...+.. |.+..++|..+|+|++||+++++++.
T Consensus         5 ~~R~~ii~l~~~-G~s~~~ia~~lgvs~~Tv~~w~kr~~   42 (50)
T PF13384_consen    5 ERRAQIIRLLRE-GWSIREIAKRLGVSRSTVYRWIKRYR   42 (50)
T ss_dssp             -----HHHHHHH-T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred             hHHHHHHHHHHC-CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence            444554444444 99999999999999999999998864

>PF13518 HTH_28: Helix-turn-helix domain

Probab=96.51  E-value=0.0055  Score=39.75  Aligned_cols=37  Identities=24%  Similarity=0.447  Sum_probs=31.6

Q ss_pred             HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ++.+...++ .|.+..++|..||||.+|+++++.++-.
T Consensus         2 r~~iv~~~~-~g~s~~~~a~~~gis~~tv~~w~~~y~~   38 (52)
T PF13518_consen    2 RLQIVELYL-EGESVREIAREFGISRSTVYRWIKRYRE   38 (52)
T ss_pred             HHHHHHHHH-cCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence            456677777 6779999999999999999999998765

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=96.44  E-value=0.011  Score=42.55  Aligned_cols=51  Identities=4%  Similarity=0.128  Sum_probs=46.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH----cccc
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA----MSQP   77 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~----l~~~   77 (307)
                      +-.+++..++.++-..+..|.+...+|..||||..|+++|+.++-..    |.+.
T Consensus         6 nA~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DR   60 (85)
T PF13011_consen    6 NARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDR   60 (85)
T ss_pred             CCCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCccccccc
Confidence            57899999999999999999999999999999999999999998753    5555

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

Probab=96.39  E-value=0.0044  Score=43.91  Aligned_cols=65  Identities=15%  Similarity=0.220  Sum_probs=49.2

Q ss_pred             CCHHHHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300           1 MRKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFL   71 (307)
Q Consensus         1 ms~~~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~   71 (307)
                      ||.+++..|-..|.+.    .. .++++..+..+.+-..|+.+++|+++++|...|| +.+||++.+++..
T Consensus         1 lsD~~W~~i~p~lp~~----~~-~~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~   65 (75)
T PF13340_consen    1 LSDEEWALIEPLLPPR----KP-RGGRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWS   65 (75)
T ss_pred             CCHHHHHHHHhhCCCC----CC-CCCCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHH
Confidence            3455555555444433    22 3356789999999999999999999999999999 7888888877654

>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=96.33  E-value=0.011  Score=37.37  Aligned_cols=37  Identities=19%  Similarity=0.311  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHhcC-CcHHHHHhhhCCChhhHHHHHHH
Q psy4300          33 EKKTLVALSYMATQ-LSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        33 ~~~l~i~L~~L~~g-~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      ++.+..+|..+.+| .|++..|..|||++||+++.++.
T Consensus         2 ee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g   39 (45)
T PF05225_consen    2 EEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLRG   39 (45)
T ss_dssp             HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            57788888888898 99999999999999999987764

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.

>smart00351 PAX Paired Box domain

Probab=96.20  E-value=0.016  Score=45.35  Aligned_cols=45  Identities=11%  Similarity=0.098  Sum_probs=40.1

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+++.+.+.-+.+.+. .|.+..++|..||||++||+++++++-.
T Consensus        15 ~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~   59 (125)
T smart00351       15 GRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYE   59 (125)
T ss_pred             CCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            45699999998888775 8999999999999999999999999854

>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=95.96  E-value=0.023  Score=37.22  Aligned_cols=44  Identities=18%  Similarity=0.323  Sum_probs=33.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .+|+.++-++.|.|+. |.++.++|..+|+|.+||...+.+....
T Consensus        10 ~L~~~~r~i~~l~~~~-g~s~~eIa~~l~~s~~~v~~~l~ra~~~   53 (54)
T PF08281_consen   10 QLPERQREIFLLRYFQ-GMSYAEIAEILGISESTVKRRLRRARKK   53 (54)
T ss_dssp             CS-HHHHHHHHHHHTS----HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH-CcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence            5788888888887765 7999999999999999999998876543

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.

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

Probab=95.87  E-value=0.014  Score=41.08  Aligned_cols=49  Identities=14%  Similarity=0.208  Sum_probs=39.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMS   75 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~   75 (307)
                      +...|++.++-++-.++..|.+..+++..+||+.+|+++|+........
T Consensus         4 r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~~~~~   52 (76)
T PF01527_consen    4 RRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYREGQS   52 (76)
T ss_dssp             S----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH--ST
T ss_pred             CCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHhcCCC
Confidence            5789999999999999999999999999999999999999999973333

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.

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=95.85  E-value=0.03  Score=43.58  Aligned_cols=46  Identities=9%  Similarity=0.125  Sum_probs=43.4

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ++..+.+.++-++...+..|.+..++|..||||.+|+++|++.+..
T Consensus        10 rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~   55 (121)
T PRK09413         10 RRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE   55 (121)
T ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence            5789999999999999999999999999999999999999999865

>cd00131 PAX Paired Box domain

Probab=95.84  E-value=0.028  Score=44.18  Aligned_cols=46  Identities=9%  Similarity=0.102  Sum_probs=40.8

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..++|.+.+.-+.+.+ ..|.+.+++|..||||++||+++++++-+.
T Consensus        15 ~~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~   60 (128)
T cd00131          15 GRPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYYET   60 (128)
T ss_pred             CCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence            4789998888888776 689999999999999999999999998753

>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=95.71  E-value=0.032  Score=32.58  Aligned_cols=39  Identities=18%  Similarity=0.272  Sum_probs=29.5

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCI   67 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v   67 (307)
                      ..++.++...+.. .+..|.+..+++..||+|++|+++++
T Consensus         4 ~~~~~~~~~~i~~-~~~~~~s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569           4 PKLTPEQIEEARR-LLAAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CcCCHHHHHHHHH-HHHcCCCHHHHHHHHCCCHHHHHHhC
Confidence            4566655554444 45678899999999999999998863

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

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

Probab=95.60  E-value=0.024  Score=44.97  Aligned_cols=44  Identities=18%  Similarity=0.243  Sum_probs=40.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      +.+...+..++-.++..|.|.+.+|..||||.+|+.+++++.-.
T Consensus         4 ~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e   47 (138)
T COG3415           4 PFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRE   47 (138)
T ss_pred             hhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhcc
Confidence            45678888999999999999999999999999999999999875

>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=95.31  E-value=0.018  Score=40.59  Aligned_cols=44  Identities=18%  Similarity=0.214  Sum_probs=31.0

Q ss_pred             HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+-++-+.+.+..+.+..|..||||+|||++=+.+=+.-+...|
T Consensus         8 ~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~L   51 (82)
T PF12116_consen    8 VIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINPEL   51 (82)
T ss_dssp             HHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHH
T ss_pred             HHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHH
Confidence            45566677899999999999999999999998877666665554

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.

>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=95.18  E-value=0.077  Score=33.90  Aligned_cols=44  Identities=20%  Similarity=0.336  Sum_probs=36.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .++..++-++.+.|+ .|.++.++|..+|+|.+|+++++.+...-
T Consensus        10 ~l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~~~~   53 (55)
T cd06171          10 KLPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRALKK   53 (55)
T ss_pred             hCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            466777777777665 78999999999999999999999887543

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

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=95.16  E-value=0.088  Score=34.25  Aligned_cols=47  Identities=11%  Similarity=0.319  Sum_probs=36.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .++..++-.+  .++..|.++.++|..+|+|.+|+.+.+.+....+-..
T Consensus         3 ~l~~~e~~i~--~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~~~   49 (58)
T smart00421        3 SLTPREREVL--RLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVR   49 (58)
T ss_pred             CCCHHHHHHH--HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence            4666666543  3357899999999999999999999999887666433

lux regulon (activates the bioluminescence operon

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=94.90  E-value=0.11  Score=38.05  Aligned_cols=50  Identities=20%  Similarity=0.264  Sum_probs=45.4

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhC-CChhhHHHHHHHHHHHccc
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFN-LADSTVWSCIDSFLTAMSQ   76 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fg-vs~stv~r~v~~~~~~l~~   76 (307)
                      ...+...-+++|.|..-..|.|+.++|..|| .+.|||+..++++-..+.+
T Consensus        25 ~~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~   75 (90)
T cd06571          25 KKEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE   75 (90)
T ss_pred             CcCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence            4578889999999999999999999999999 9999999999999887755

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.

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

Probab=94.78  E-value=0.063  Score=34.78  Aligned_cols=33  Identities=18%  Similarity=0.307  Sum_probs=26.8

Q ss_pred             HHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300          38 VALSYMATQLSMRKIGDQFNLADSTVWSCIDSF   70 (307)
Q Consensus        38 i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~   70 (307)
                      ..+..|....++.++|..+|+|.+||.+++++.
T Consensus        19 ~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen   19 YILKLLRESRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             HHHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            334445555799999999999999999999874

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=94.74  E-value=0.062  Score=39.26  Aligned_cols=36  Identities=8%  Similarity=0.110  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          32 VEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        32 ~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      ..++ ...+.++..|.+..++|..+|+|++|++|+.+
T Consensus        37 Ls~R-~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~R   72 (88)
T TIGR02531        37 LAQR-LQVAKMLKQGKTYSDIEAETGASTATISRVKR   72 (88)
T ss_pred             hhHH-HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3444 56667799999999999999999999999553

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.

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=94.72  E-value=0.084  Score=37.01  Aligned_cols=42  Identities=14%  Similarity=0.209  Sum_probs=37.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      ..+|...+.+..|.+.-.|.|+.+||...|+|.+||...++.
T Consensus        14 ~~l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~   55 (73)
T TIGR03879        14 TWVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG   55 (73)
T ss_pred             hcCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            468888888999988889999999999999999999888764

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.

>PRK00118 putative DNA-binding protein; Validated

Probab=94.54  E-value=0.12  Score=38.88  Aligned_cols=50  Identities=16%  Similarity=0.392  Sum_probs=41.9

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      +.++..++-++.|+++ .|.|+.++|..+|+|++||++.+.+....+.+.+
T Consensus        16 ~~L~ekqRevl~L~y~-eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~   65 (104)
T PRK00118         16 SLLTEKQRNYMELYYL-DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE   65 (104)
T ss_pred             ccCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            5677888887766655 4899999999999999999999998887777764

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=94.53  E-value=0.076  Score=39.10  Aligned_cols=65  Identities=8%  Similarity=0.090  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHH------HhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300           4 TTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSY------MATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus         4 ~~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~------L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      +.++.+++++........-...-..-++++++-.+.++|      +..+.|++.++...|||++||+|+=+
T Consensus         7 ~~w~~~~~ll~~~~~~~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn   77 (94)
T TIGR01321         7 QAWEAFLKLLKKADSEDDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSN   77 (94)
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHh
Confidence            345666666654421000000012457888888888875      24679999999999999999988644

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.

>PRK04217 hypothetical protein; Provisional

Probab=94.47  E-value=0.11  Score=39.66  Aligned_cols=50  Identities=20%  Similarity=0.295  Sum_probs=40.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..++.+++-++.|+ ...|.++.++|..+|+|.+||++.+.+....|.+.+
T Consensus        41 ~~Lt~eereai~l~-~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L   90 (110)
T PRK04217         41 IFMTYEEFEALRLV-DYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQML   90 (110)
T ss_pred             ccCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            56778887544443 447899999999999999999999999887776664

>PRK06030 hypothetical protein; Provisional

Probab=93.94  E-value=0.39  Score=37.45  Aligned_cols=70  Identities=11%  Similarity=0.017  Sum_probs=53.6

Q ss_pred             HHHHHHHHHhhhcCccccc---CCC-CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHc
Q psy4300           5 TFGFLVEALAAINGYETLY---ERG-VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAM   74 (307)
Q Consensus         5 ~F~~L~~~l~~~~~~~~~~---~~~-~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l   74 (307)
                      +.+.|.+.+...+......   ..+ +..+...-+++|.|.+--++.|+.++|..||.+.|||...++.+-..+
T Consensus        24 t~d~Ii~~Va~~f~I~~~di~sk~R~rk~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~~   97 (124)
T PRK06030         24 LCEAVIDLLALAFGVSGAEIASPLRGRREVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDLR   97 (124)
T ss_pred             CHHHHHHHHHHHhCCCHHHHhCCCCCCcccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence            3466666666665432111   122 367899999999999999999999999999999999999999776655

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

Probab=93.90  E-value=0.24  Score=32.17  Aligned_cols=44  Identities=14%  Similarity=0.320  Sum_probs=34.1

Q ss_pred             CHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300          31 PVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ   76 (307)
Q Consensus        31 ~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~   76 (307)
                      +..++-++.+  +..|.++.++|..+++|.+|+.+.+++....+..
T Consensus         2 ~~~e~~i~~~--~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~   45 (57)
T cd06170           2 TPREREVLRL--LAEGKTNKEIADILGISEKTVKTHLRNIMRKLGV   45 (57)
T ss_pred             CHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence            3444444333  4689999999999999999999999988766554

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

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=93.79  E-value=0.35  Score=38.40  Aligned_cols=73  Identities=11%  Similarity=0.115  Sum_probs=53.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc---------ccccccccCCChHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP---------QIQCQYIKWPTEEESVIIER   97 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~---------l~~~~~i~~P~~~~~~~~~~   97 (307)
                      ...++..++-.+.|+  ..|.++.++|..+|+|++||+++.++...-|-..         +-++..+..|...++..+..
T Consensus         4 ~~~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~~~a~~~~~~~~g~~~~~~~~   81 (137)
T TIGR00721         4 KTFLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKFIKSPVRILCRRGDDLDEIPK   81 (137)
T ss_pred             cCCCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHHhcCCEEEEecCCCcHHHhHH
Confidence            356888888888883  6999999999999999999998888866666541         12455566666666665555


Q ss_pred             HHHH
Q psy4300          98 NFRA  101 (307)
Q Consensus        98 ~f~~  101 (307)
                      ...+
T Consensus        82 ~v~~   85 (137)
T TIGR00721        82 RLFK   85 (137)
T ss_pred             HHHH
Confidence            5443

Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.

>PHA00675 hypothetical protein

Probab=93.71  E-value=0.2  Score=35.13  Aligned_cols=43  Identities=5%  Similarity=-0.017  Sum_probs=34.8

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      ...|+..+.-.|...+-+.|.|+..||..||||+|||+.|-+.
T Consensus        20 ~AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~g   62 (78)
T PHA00675         20 NAKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRY   62 (78)
T ss_pred             CcccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHcc
Confidence            4567777766666666588999999999999999999987653

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=93.53  E-value=0.15  Score=36.48  Aligned_cols=37  Identities=22%  Similarity=0.386  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHhcC-CcHHHHHhhhCCChhhHHHHHH
Q psy4300          32 VEKKTLVALSYMATQ-LSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        32 ~~~~l~i~L~~L~~g-~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      .++++...+-+|..| .+..++|..||+|.+||++.++
T Consensus         4 ~~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~   41 (80)
T TIGR02844         4 IEERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVT   41 (80)
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhc
Confidence            355666677777654 6788999999999999999764

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.

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=93.36  E-value=0.22  Score=41.25  Aligned_cols=49  Identities=12%  Similarity=0.108  Sum_probs=43.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|++++.++.|.++ .|.++.++|..+|+|.+||...+.+-+..+.+.
T Consensus       126 ~~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~  174 (178)
T PRK12529        126 DTLRPRVKQAFLMATL-DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSL  174 (178)
T ss_pred             HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence            4688999999999888 789999999999999999999888877777665

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

Probab=93.28  E-value=0.53  Score=30.82  Aligned_cols=29  Identities=10%  Similarity=0.283  Sum_probs=25.2

Q ss_pred             CcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300          47 LSMRKIGDQFNLADSTVWSCIDSFLTAMS   75 (307)
Q Consensus        47 ~~~~~l~~~fgvs~stv~r~v~~~~~~l~   75 (307)
                      .+..+||..+|||++|++..+++...-|.
T Consensus        24 ~tl~elA~~lgis~st~~~~LRrae~kli   52 (53)
T PF04967_consen   24 ITLEELAEELGISKSTVSEHLRRAERKLI   52 (53)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence            67899999999999999999998766543

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

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=93.25  E-value=0.23  Score=40.37  Aligned_cols=48  Identities=13%  Similarity=0.259  Sum_probs=42.9

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|.+++-++.|.+  .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       111 ~~L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~  158 (166)
T PRK09639        111 AKMTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRKI  158 (166)
T ss_pred             HcCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            458889999999988  999999999999999999999999888877665

>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19

Probab=93.10  E-value=0.3  Score=36.53  Aligned_cols=43  Identities=14%  Similarity=0.415  Sum_probs=37.6

Q ss_pred             CHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHc
Q psy4300          31 PVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAM   74 (307)
Q Consensus        31 ~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l   74 (307)
                      ++.++..+.++|+ ++.+|.+++..+++|++|++|+-++.+..|
T Consensus        57 d~~~r~iL~~~Yi-~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L   99 (100)
T PF07374_consen   57 DPDERLILRMRYI-NKLTWEQIAEELNISRRTYYRIHKKALKEL   99 (100)
T ss_pred             ChhHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence            5788999999999 579999999999999999999988776544

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.

>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=93.09  E-value=0.34  Score=32.07  Aligned_cols=41  Identities=12%  Similarity=0.239  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          32 VEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        32 ~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+-.++...+=..+.+..+|+..++++++++++++++...
T Consensus         3 ~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~   43 (59)
T PF01047_consen    3 PSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEK   43 (59)
T ss_dssp             HHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence            34444444444455689999999999999999999998754

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 ....

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

Probab=93.09  E-value=0.085  Score=33.51  Aligned_cols=22  Identities=18%  Similarity=0.374  Sum_probs=19.4

Q ss_pred             cHHHHHhhhCCChhhHHHHHHH
Q psy4300          48 SMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        48 ~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      +..++|...|+|.+|||++++.
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~   22 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNG   22 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTT
T ss_pred             CHHHHHHHHCcCHHHHHHHHhC
Confidence            4579999999999999998874

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 ....

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=93.09  E-value=0.44  Score=38.02  Aligned_cols=73  Identities=12%  Similarity=0.118  Sum_probs=52.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc---------cccccccccCCChHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ---------PQIQCQYIKWPTEEESVIIER   97 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~---------~l~~~~~i~~P~~~~~~~~~~   97 (307)
                      ...+++.++-.+.|  ...|.++.++|..+|+|++||+.+.++...-|-.         .+-++..+..|...++..+..
T Consensus         4 ~~~Lt~rqreVL~l--r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl~~~~~l~a~~~v~~~~G~d~~~ip~   81 (141)
T PRK03975          4 ESFLTERQIEVLRL--RERGLTQQEIADILGTSRANVSSIEKRARENIEKARETLAFAETLNAPVRVTIPAGTDLFDIPK   81 (141)
T ss_pred             ccCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEEEecCCCcHHHhHH
Confidence            45788888888888  3699999999999999999999988875554332         222444566666666665555


Q ss_pred             HHHH
Q psy4300          98 NFRA  101 (307)
Q Consensus        98 ~f~~  101 (307)
                      ...+
T Consensus        82 ~v~~   85 (141)
T PRK03975         82 RIYK   85 (141)
T ss_pred             HHHH
Confidence            5444

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B

Probab=92.98  E-value=0.36  Score=32.20  Aligned_cols=26  Identities=15%  Similarity=0.335  Sum_probs=23.2

Q ss_pred             CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          47 LSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        47 ~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      .+..+|+..++++++|++++++++..
T Consensus        22 ~t~~~la~~l~~~~~~vs~~v~~L~~   47 (62)
T PF12802_consen   22 LTQSELAERLGISKSTVSRIVKRLEK   47 (62)
T ss_dssp             EEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            69999999999999999999998765

...

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

Probab=92.83  E-value=0.36  Score=37.03  Aligned_cols=51  Identities=8%  Similarity=0.061  Sum_probs=45.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCC-ChhhHHHHHHHHHHHcccc
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNL-ADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgv-s~stv~r~v~~~~~~l~~~   77 (307)
                      ++.+|.+.++-++-.++..|.++..+|..||| +.+++++|+.+....-...
T Consensus         5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~   56 (116)
T COG2963           5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLA   56 (116)
T ss_pred             cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHccccc
Confidence            57899999999999999999999999999995 9999999999887755333

>PF13730 HTH_36: Helix-turn-helix domain

Probab=92.77  E-value=0.35  Score=31.59  Aligned_cols=43  Identities=16%  Similarity=0.174  Sum_probs=32.7

Q ss_pred             CCH-HHHHHHHHHHHhc--C---CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          30 VPV-EKKTLVALSYMAT--Q---LSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        30 ~~~-~~~l~i~L~~L~~--g---~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      +++ +..|.+.|..+.+  +   .|+..+|...|+|+.||.+.+++..+
T Consensus         3 Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~   51 (55)
T PF13730_consen    3 LSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEE   51 (55)
T ss_pred             CCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            344 4556666766652  2   47899999999999999999998754

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

Probab=92.63  E-value=0.33  Score=38.85  Aligned_cols=48  Identities=19%  Similarity=0.262  Sum_probs=40.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ   76 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~   76 (307)
                      ..++..++-++.|+++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus       112 ~~L~~~~r~il~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~  159 (161)
T TIGR02985       112 EKLPEQCRKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKELRK  159 (161)
T ss_pred             HHCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence            3577888888888777 58999999999999999999998887666543

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.

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=92.54  E-value=0.27  Score=41.01  Aligned_cols=50  Identities=14%  Similarity=0.236  Sum_probs=43.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|++++-++.|.++ .|.++.++|..+|+|.+||...+.+....|...+
T Consensus       130 ~~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l  179 (189)
T PRK12515        130 AKLSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKLAELL  179 (189)
T ss_pred             HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            4678888888888887 7899999999999999999999988877776664

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

Probab=92.25  E-value=0.37  Score=35.07  Aligned_cols=38  Identities=16%  Similarity=0.171  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          32 VEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        32 ~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      ..+++.++=..|..|.+|++|+...|+|-.||+|+=+.
T Consensus        35 l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~   72 (87)
T PF01371_consen   35 LAQRWQVAKELLDEGKSYREIAEETGVSIATITRVSRC   72 (87)
T ss_dssp             HHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence            44555555557889999999999999999999886544

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 ....

>PHA00542 putative Cro-like protein

Probab=92.22  E-value=0.27  Score=35.41  Aligned_cols=53  Identities=13%  Similarity=0.080  Sum_probs=39.0

Q ss_pred             HHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHHHHh
Q psy4300          37 LVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRAL  102 (307)
Q Consensus        37 ~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f~~~  102 (307)
                      -+...+...|.+..++|...|||++|++++.+.-             ..-|+.+.+..+++.+.+.
T Consensus        22 ~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~-------------~~~p~~~~l~ki~~~~~~~   74 (82)
T PHA00542         22 ELVCALIRAGWSQEQIADATDVSQPTICRIYSGR-------------HKDPRYSVVEKLRHLVLNL   74 (82)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCC-------------CCCCCHHHHHHHHHHHHHh
Confidence            3445567889999999999999999999976532             1235666667777777654

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

Probab=92.18  E-value=0.35  Score=38.03  Aligned_cols=47  Identities=17%  Similarity=0.335  Sum_probs=39.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ   76 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~   76 (307)
                      .++..++-++.+.++ .|.++.++|..+|+|.++|++...+....|-.
T Consensus       110 ~L~~~~~~ii~~~~~-~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~  156 (158)
T TIGR02937       110 KLPEREREVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKLRE  156 (158)
T ss_pred             hCCHHHHHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence            577888877777666 68999999999999999999999998776543

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.

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

Probab=92.12  E-value=0.4  Score=39.00  Aligned_cols=48  Identities=8%  Similarity=0.187  Sum_probs=41.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ   76 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~   76 (307)
                      ..+|+.++.++.|.|+. |.++.++|..+|+|.+||...+.+....|-.
T Consensus       121 ~~L~~~~r~vl~l~~~~-g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~  168 (170)
T TIGR02952       121 KILTPKQQHVIALRFGQ-NLPIAEVARILGKTEGAVKILQFRAIKKLAR  168 (170)
T ss_pred             HhCCHHHHHHHHHHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            46889999999998775 8999999999999999999999888776643

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.

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=91.97  E-value=0.36  Score=39.09  Aligned_cols=48  Identities=10%  Similarity=0.113  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .++++++-++.|.|+. |.++.++|..+|+|.+||...+.+...-|-..
T Consensus       109 ~L~~~~r~v~~l~~~~-~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~  156 (163)
T PRK07037        109 ELPARTRYAFEMYRLH-GETQKDIARELGVSPTLVNFMIRDALVHCRKC  156 (163)
T ss_pred             hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            5666777777777665 89999999999999999999888877776655

>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=91.90  E-value=0.73  Score=29.14  Aligned_cols=29  Identities=10%  Similarity=0.327  Sum_probs=23.8

Q ss_pred             hcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          44 ATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+.+..++|..+|+|.+|++++++++.+
T Consensus        15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~   43 (48)
T PF13412_consen   15 NPRITQKELAEKLGISRSTVNRYLKKLEE   43 (48)
T ss_dssp             CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            44589999999999999999999998764

...

>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=91.86  E-value=0.46  Score=30.08  Aligned_cols=38  Identities=13%  Similarity=0.219  Sum_probs=27.7

Q ss_pred             HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ++-+.........+..+++..+|+|++|+++.++...+
T Consensus         4 R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~   41 (47)
T PF01022_consen    4 RLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE   41 (47)
T ss_dssp             HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence            33443333345588999999999999999999987754

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 ....

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=91.80  E-value=0.44  Score=39.08  Aligned_cols=48  Identities=25%  Similarity=0.209  Sum_probs=40.9

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+++.++.++.|.|+ .|.++.++|..+|+|.+||...+.+...-|-..
T Consensus       128 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~  175 (182)
T PRK09652        128 SLPEELRTAITLREI-EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAK  175 (182)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            578888888888877 689999999999999999999888877766655

>PRK15320 transcriptional activator SprB; Provisional

Probab=91.77  E-value=0.49  Score=39.74  Aligned_cols=48  Identities=17%  Similarity=0.178  Sum_probs=41.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      +.+|..+.  -.|.+|+.|.+..+||..+++|.+||+.+..+...-+...
T Consensus       163 ~~LSdREI--EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLgAk  210 (251)
T PRK15320        163 PGVTQAKY--ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLGMD  210 (251)
T ss_pred             CCCCHHHH--HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcCCC
Confidence            44555554  6788999999999999999999999999999998887766

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=91.76  E-value=0.43  Score=35.35  Aligned_cols=47  Identities=19%  Similarity=0.427  Sum_probs=38.1

Q ss_pred             CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ++-.++--+-|+|+- ..|...+|..|+||+++|+..|+++...+..-
T Consensus        18 LT~KQ~~Y~~lyy~d-DlSl~EIAee~~VSRqAIyDnIKr~~~~L~~Y   64 (105)
T COG2739          18 LTKKQKNYLELYYLD-DLSLSEIAEEFNVSRQAIYDNIKRTEKILEDY   64 (105)
T ss_pred             HhHHHHHHHHHHHHh-hccHHHHHHHhCccHHHHHHHHHHHHHHHHHH
Confidence            344556666666654 68999999999999999999999999888764

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

Probab=91.69  E-value=0.49  Score=38.04  Aligned_cols=48  Identities=15%  Similarity=0.358  Sum_probs=42.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ   76 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~   76 (307)
                      ..+|+.++-.+.|.++ .|.++.++|..+|+|.+||...+.+....|-+
T Consensus       110 ~~L~~~~r~v~~l~~~-~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~  157 (159)
T TIGR02989       110 EKLPERQRELLQLRYQ-RGVSLTALAEQLGRTVNAVYKALSRLRVRLRD  157 (159)
T ss_pred             HHCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence            4688999999999776 68999999999999999999999988777654

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).

>PF13551 HTH_29: Winged helix-turn helix

Probab=91.52  E-value=0.35  Score=36.40  Aligned_cols=37  Identities=16%  Similarity=0.308  Sum_probs=31.4

Q ss_pred             HHHHHHhcCCc-HHHHHhhhCCChhhHHHHHHHHHHHc
Q psy4300          38 VALSYMATQLS-MRKIGDQFNLADSTVWSCIDSFLTAM   74 (307)
Q Consensus        38 i~L~~L~~g~~-~~~l~~~fgvs~stv~r~v~~~~~~l   74 (307)
                      .+|..+..|.+ ..++|..+|+|.+||+++++++...=
T Consensus         3 ~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G   40 (112)
T PF13551_consen    3 QILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGG   40 (112)
T ss_pred             HHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence            35667889995 99999999999999999999975433

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=91.39  E-value=0.53  Score=38.84  Aligned_cols=49  Identities=12%  Similarity=0.242  Sum_probs=41.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|++++-.+.|.++ .|.|+.++|..+|+|..||...+.+....|-+.
T Consensus       128 ~~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~  176 (179)
T PRK12514        128 EELEKDRAAAVRRAYL-EGLSYKELAERHDVPLNTMRTWLRRSLLKLREC  176 (179)
T ss_pred             HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence            3577888888888876 789999999999999999999998887776554

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=91.35  E-value=0.44  Score=42.44  Aligned_cols=50  Identities=2%  Similarity=0.260  Sum_probs=43.1

Q ss_pred             CCCCHHHHHHHHHHHHh-cCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMA-TQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~-~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..++..++..+.|+|+. .|.|+.++|..+|||+.+|+++..+.+.-|-..
T Consensus       217 ~~L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~  267 (270)
T TIGR02392       217 GSLDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA  267 (270)
T ss_pred             HcCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            36889999999999974 489999999999999999999988887766544

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.

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

Probab=91.30  E-value=0.37  Score=33.54  Aligned_cols=43  Identities=26%  Similarity=0.269  Sum_probs=34.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhC-CChhhHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFN-LADSTVWSCIDSF   70 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fg-vs~stv~r~v~~~   70 (307)
                      ..+...-++++.|..-..+.|+.++|..|| .+.|||...++++
T Consensus        27 ~~i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~ki   70 (70)
T PF08299_consen   27 RKIVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRKI   70 (70)
T ss_dssp             HHHHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred             hhhcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence            346667888998888888999999999999 9999998887764

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

>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=91.23  E-value=1.1  Score=38.27  Aligned_cols=187  Identities=14%  Similarity=0.120  Sum_probs=111.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhh-----hCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHHHHhh
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQ-----FNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALA  103 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~-----fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f~~~~  103 (307)
                      .++-......+=+||+.++|++++...     ..++.+|+++++.+.-+.+...+ ..     +.               
T Consensus         8 ~f~~~vi~~~V~~yl~~~Ls~r~v~e~l~~rgi~v~h~Ti~rwv~k~~~~~~~~~-~~-----r~---------------   66 (215)
T COG3316           8 QFPRNIIAVAVWLYLRYGLSLRDVEEMLAERGIEVDHETIHRWVQKYGPLLARRL-KR-----RK---------------   66 (215)
T ss_pred             hcchhhHHHHHHHHhhcchhhccHHHHHHHcCcchhHHHHHHHHHHHhHHHHHHh-hh-----hc---------------
Confidence            455556666666778889999988885     35778899999999988777773 11     10               


Q ss_pred             CCCCcceeecceeEEeecCCCCccccccccCCcceeEEeeeCCCcceEeeeeccccccCCCcccccchhhcchhhcCCCC
Q psy4300         104 KFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTS  183 (307)
Q Consensus       104 ~~p~~~g~iDgt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~S~l~~~l~~~~~~~  183 (307)
                      .-++-.-.||-|.|+|.     +.-.+.         =..||.+|-.+.+.....-+...+..|    +.+.+..     
T Consensus        67 ~~~~~~w~vDEt~ikv~-----gkw~yl---------yrAid~~g~~Ld~~L~~rRn~~aAk~F----l~kllk~-----  123 (215)
T COG3316          67 RKAGDSWRVDETYIKVN-----GKWHYL---------YRAIDADGLTLDVWLSKRRNALAAKAF----LKKLLKK-----  123 (215)
T ss_pred             cccccceeeeeeEEeec-----cEeeeh---------hhhhccCCCeEEEEEEcccCcHHHHHH----HHHHHHh-----
Confidence            01223447999999984     111111         136788899999988543334444333    3333443     


Q ss_pred             CCCCCCeEEEecCCCCCCccccccccCCCCCCHHHHHHhHHHHhh-hhHHHHHHHHHHhhcccccccccCChhhHHHHHH
Q psy4300         184 LLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKT-RVPIENVFGLIKGRWRRLKYIDVGDPKRMAYIIS  262 (307)
Q Consensus       184 ~~~~~~~~llgD~gY~~~~~l~~P~~~~~~lt~~q~~fN~~~s~~-R~~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~  262 (307)
                        ...+..++.|++=-....+    ..   +..   .+-++-++- ...+|+-+..+|.|=+-+.  .+.....+...+.
T Consensus       124 --~g~p~v~vtDka~s~~~A~----~~---l~~---~~ehr~~~ylnN~iE~dh~~iKrr~~~~~--~f~~~~sa~~~~~  189 (215)
T COG3316         124 --HGEPRVFVTDKAPSYTAAL----RK---LGS---EVEHRTSKYLNNRIEQDHRPIKRRTRPMK--RFKSLSSAASTIS  189 (215)
T ss_pred             --cCCCceEEecCccchHHHH----Hh---cCc---chheecccccccchhhcchhHHHHhcccc--cCCChHHHHHHHH
Confidence              2346677788764322111    10   010   122222233 3788999999998665442  2335666677777


Q ss_pred             HHHHhhhhhcc
Q psy4300         263 AACVLHNFCYL  273 (307)
Q Consensus       263 a~~~LhN~~~~  273 (307)
                      ..=.+|++--.
T Consensus       190 gie~i~~~~~~  200 (215)
T COG3316         190 GIESIHMLYKR  200 (215)
T ss_pred             hHHHHHHHHhh
Confidence            77777776443

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=91.17  E-value=0.53  Score=38.45  Aligned_cols=49  Identities=22%  Similarity=0.323  Sum_probs=41.3

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-++.|.++ .|.++.+||..+|+|.+||.+.+.+....|-..
T Consensus       124 ~~L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~  172 (179)
T PRK11924        124 DALPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRRARQLLREC  172 (179)
T ss_pred             HhCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            3577777887778777 589999999999999999999999987777655

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=91.10  E-value=0.53  Score=37.93  Aligned_cols=50  Identities=10%  Similarity=0.220  Sum_probs=42.7

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|..++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..+
T Consensus       105 ~~Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l  154 (161)
T PRK09047        105 QKLPARQREAFLLRYWE-DMDVAETAAAMGCSEGSVKTHCSRATHALAKAL  154 (161)
T ss_pred             HhCCHHHHHHHHHHHHh-cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            46777888888887765 899999999999999999999999888887764

>PF13610 DDE_Tnp_IS240: DDE domain

Probab=91.06  E-value=0.92  Score=36.08  Aligned_cols=132  Identities=16%  Similarity=0.086  Sum_probs=74.6

Q ss_pred             eeecceeEEeecCCCCccccccccCCcceeEEeeeCCCcceEeeeeccccccCCCcccccchhhcchhhcCCCCCCCCCC
Q psy4300         110 GAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRDE  189 (307)
Q Consensus       110 g~iDgt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~S~l~~~l~~~~~~~~~~~~~  189 (307)
                      -.||-|.|+|.     +.-         .=+=.++|++|+++++.+...-...++..|    +.+.+...      ...+
T Consensus         4 w~~DEt~iki~-----G~~---------~yl~~aiD~~~~~l~~~ls~~Rd~~aA~~F----l~~~l~~~------~~~p   59 (140)
T PF13610_consen    4 WHVDETYIKIK-----GKW---------HYLWRAIDAEGNILDFYLSKRRDTAAAKRF----LKRALKRH------RGEP   59 (140)
T ss_pred             EEEeeEEEEEC-----CEE---------EEEEEeecccccchhhhhhhhcccccceee----ccccceee------cccc
Confidence            36899999984     111         112468999999988888533333333222    22223221      1234


Q ss_pred             eEEEecCC--CCCCccccccc-cCCCCCCHHHHHHhHHHHhhhhHHHHHHHHHHhhcccccccccCChhhHHHHHHHHHH
Q psy4300         190 YHLLGDSA--YPLRTWCMVPY-KNFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACV  266 (307)
Q Consensus       190 ~~llgD~g--Y~~~~~l~~P~-~~~~~lt~~q~~fN~~~s~~R~~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~a~~~  266 (307)
                      ..++.|+.  |+.--.-+.+- ..+.....      ....-.++.||+-+..+|.|.+....+  .+.+.+...+.+-.+
T Consensus        60 ~~ivtDk~~aY~~A~~~l~~~~~~~~~v~~------~~~k~~nN~iE~~h~~~K~r~r~~~gF--ks~~~A~~~l~~~~~  131 (140)
T PF13610_consen   60 RVIVTDKLPAYPAAIKELNPEGRLHDKVEH------RQRKYLNNRIERDHRTIKRRTRPMNGF--KSFRSAQRTLSGFEA  131 (140)
T ss_pred             ceeecccCCccchhhhhcccccccccccce------eechhhhChhhHhhhhhhhhcccccCc--CCHHHHHHHHHHHHH
Confidence            56776764  32111111110 00000000      011123678999999999988776655  368888999999999


Q ss_pred             hhhhhcc
Q psy4300         267 LHNFCYL  273 (307)
Q Consensus       267 LhN~~~~  273 (307)
                      .||+...
T Consensus       132 ~~n~~r~  138 (140)
T PF13610_consen  132 YHNFRRP  138 (140)
T ss_pred             HHHHhCC
Confidence            9999764

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=91.04  E-value=0.97  Score=35.75  Aligned_cols=50  Identities=14%  Similarity=0.280  Sum_probs=42.5

Q ss_pred             CCCCHHHHHHHHHHHHhc-CCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMAT-QLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~-g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..++.+++-.+.++|+.. ..++..+|..+|+|++|+++.-+.++.-+...
T Consensus        81 ~~Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~  131 (134)
T TIGR01636        81 NEADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEE  131 (134)
T ss_pred             HhCCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            358899999999999843 35999999999999999999988888777654

This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=90.97  E-value=0.58  Score=39.16  Aligned_cols=49  Identities=10%  Similarity=0.164  Sum_probs=42.3

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|...+-++.|+|+. |.++.++|..+|+|.+||...+.+....|-..
T Consensus       133 ~~Lp~~~R~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~  181 (189)
T PRK12530        133 NHLPAQQARVFMMREYL-ELSSEQICQECDISTSNLHVLLYRARLQLQAC  181 (189)
T ss_pred             HhCCHHHHHHHhHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            35678888888888877 89999999999999999999888887777665

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=90.96  E-value=0.5  Score=41.00  Aligned_cols=50  Identities=14%  Similarity=0.218  Sum_probs=42.8

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++.++.|.|+   -.|.|+.++|..+|+|.+||.+..++....|...
T Consensus       174 ~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~  226 (233)
T PRK05803        174 DILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKE  226 (233)
T ss_pred             HhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            4688899999999886   4789999999999999999999888877666554

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=90.92  E-value=0.56  Score=38.17  Aligned_cols=50  Identities=10%  Similarity=0.078  Sum_probs=42.5

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus       111 ~~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l  160 (164)
T PRK12547        111 NLLSADQREAIILIGA-SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL  160 (164)
T ss_pred             HhCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence            4577788888888888 7899999999999999999999998887776653

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=90.91  E-value=0.54  Score=40.77  Aligned_cols=50  Identities=8%  Similarity=0.216  Sum_probs=42.7

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-++.|+|.   -.|.|+.++|..+|+|.+||...+.+....|-..
T Consensus       177 ~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~  229 (234)
T PRK08301        177 KKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE  229 (234)
T ss_pred             HhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            4578888888888874   6799999999999999999999988887777655

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=90.81  E-value=0.49  Score=41.83  Aligned_cols=49  Identities=18%  Similarity=0.315  Sum_probs=42.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+++.++..+.|+|+ .|.++.++|..+|+|.++|++...+...-|-..
T Consensus       204 ~~L~~~er~vi~l~y~-e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~  252 (257)
T PRK05911        204 LALEEKERKVMALYYY-EELVLKEIGKILGVSESRVSQIHSKALLKLRAT  252 (257)
T ss_pred             HcCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            3688889989999886 689999999999999999999999888777665

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=90.79  E-value=0.63  Score=38.76  Aligned_cols=49  Identities=18%  Similarity=0.193  Sum_probs=42.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+|...+-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus       111 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~  159 (182)
T PRK12511        111 DLPEEQRAALHLVAI-EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFE  159 (182)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence            678888888888888 5899999999999999999999888877776663

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=90.75  E-value=0.64  Score=39.08  Aligned_cols=49  Identities=18%  Similarity=0.166  Sum_probs=42.3

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|.+++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       135 ~~L~~~~r~i~~L~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~  183 (196)
T PRK12524        135 AALPERQRQAVVLRHI-EGLSNPEIAEVMEIGVEAVESLTARGKRALAAL  183 (196)
T ss_pred             HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            3577888888888877 789999999999999999999999887777665

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=90.66  E-value=0.55  Score=42.18  Aligned_cols=50  Identities=2%  Similarity=0.201  Sum_probs=43.7

Q ss_pred             CCCCHHHHHHHHHHHHh-cCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMA-TQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~-~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..++..++..+.++|+. .+.++.++|..+|||+++|+++..+.+.-|-..
T Consensus       229 ~~L~~rEr~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~  279 (284)
T PRK06596        229 EGLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA  279 (284)
T ss_pred             hcCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            46889999999999975 589999999999999999999999887766554

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=90.65  E-value=0.5  Score=40.65  Aligned_cols=50  Identities=20%  Similarity=0.245  Sum_probs=42.9

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|..++-++.|+|+ .|.++.+||..+|+|.+||...+.+....|...+
T Consensus       133 ~~Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l  182 (216)
T PRK12533        133 AKLPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAALL  182 (216)
T ss_pred             HcCCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            3567788888888888 5899999999999999999999998887777764

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

Probab=90.61  E-value=1.2  Score=29.95  Aligned_cols=41  Identities=15%  Similarity=0.256  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHHHh---cCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          32 VEKKTLVALSYMA---TQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        32 ~~~~l~i~L~~L~---~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+.-+-+++.|.   ...+-.+||..+|+|++||+..+++...
T Consensus         5 ~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~   48 (60)
T PF01325_consen    5 SEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAE   48 (60)
T ss_dssp             HHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence            3455556666665   5688899999999999999999998754

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

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

Probab=90.56  E-value=0.77  Score=29.91  Aligned_cols=29  Identities=7%  Similarity=0.205  Sum_probs=25.0

Q ss_pred             CCcHHHHHhhhCCChhhHHHHHHHHHHHc
Q psy4300          46 QLSMRKIGDQFNLADSTVWSCIDSFLTAM   74 (307)
Q Consensus        46 g~~~~~l~~~fgvs~stv~r~v~~~~~~l   74 (307)
                      +.+-.++|..++||+.||.+.++..-+..
T Consensus        15 ~it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen   15 PITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             SBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             CcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            47899999999999999999999887665

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 ....

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=90.55  E-value=0.31  Score=40.02  Aligned_cols=49  Identities=16%  Similarity=0.171  Sum_probs=41.9

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       125 ~~L~~~~r~v~~l~~~-~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~  173 (176)
T PRK09638        125 SKLDPEFRAPVILKHY-YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE  173 (176)
T ss_pred             HcCCHHHhheeeehhh-cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence            4578888888888887 599999999999999999998888887776554

>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=90.54  E-value=0.57  Score=31.04  Aligned_cols=45  Identities=16%  Similarity=0.282  Sum_probs=34.5

Q ss_pred             CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300          30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ   76 (307)
Q Consensus        30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~   76 (307)
                      ++..+.-  +|.+++.|.+..++|...|+|.+||......+..-+--
T Consensus         4 LT~~E~~--vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~   48 (58)
T PF00196_consen    4 LTERELE--VLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKLGV   48 (58)
T ss_dssp             S-HHHHH--HHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred             cCHHHHH--HHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence            4444443  67889999999999999999999999998887765543

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 ....

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

Probab=90.51  E-value=0.65  Score=38.37  Aligned_cols=47  Identities=17%  Similarity=0.186  Sum_probs=39.7

Q ss_pred             CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      +|+..+-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..
T Consensus       135 Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~  181 (183)
T TIGR02999       135 VDPRQAEVVELRFFA-GLTVEEIAELLGVSVRTVERDWRFARAWLADE  181 (183)
T ss_pred             CCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            778888877777665 79999999999999999999999887776554

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.

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=90.35  E-value=0.6  Score=40.35  Aligned_cols=50  Identities=12%  Similarity=0.194  Sum_probs=43.4

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-++.|+|+   ..|.|+.++|..+|+|.+||.+.+++....|-..
T Consensus       173 ~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~  225 (227)
T TIGR02846       173 SVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKE  225 (227)
T ss_pred             HhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            4678888889999886   4889999999999999999999999888777655

The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=90.26  E-value=0.78  Score=37.06  Aligned_cols=47  Identities=15%  Similarity=0.108  Sum_probs=38.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMS   75 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~   75 (307)
                      ..+|++++-++.|.++. |.++.++|..+|+|.+||...+.+....+.
T Consensus       112 ~~L~~~~r~v~~L~~~~-g~s~~EIA~~l~is~~tV~~~l~ra~~~~~  158 (161)
T PRK12528        112 DGLPPLVKRAFLLAQVD-GLGYGEIATELGISLATVKRYLNKAAMRCY  158 (161)
T ss_pred             HHCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            35777778777777665 799999999999999999998888766554

>PRK01381 Trp operon repressor; Provisional

Probab=90.22  E-value=0.52  Score=35.02  Aligned_cols=40  Identities=13%  Similarity=0.242  Sum_probs=30.8

Q ss_pred             CCCHHHHHHHHHHH-----H-hcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          29 FVPVEKKTLVALSY-----M-ATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        29 ~~~~~~~l~i~L~~-----L-~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      -+++.++=++..++     | ..+.||++|+...|||.+||+|.-+
T Consensus        32 llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn   77 (99)
T PRK01381         32 LLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSN   77 (99)
T ss_pred             hCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHH
Confidence            36777777777665     2 3459999999999999999887543

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=90.21  E-value=0.68  Score=38.32  Aligned_cols=49  Identities=24%  Similarity=0.382  Sum_probs=41.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..++.+++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       135 ~~L~~~~r~il~l~~~-~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~  183 (187)
T PRK09641        135 LQLPEKYRTVIVLKYI-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ  183 (187)
T ss_pred             HhCCHHHHHHhhhHHh-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            3577888888888887 699999999999999999999988887766554

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

Probab=90.15  E-value=1.3  Score=40.32  Aligned_cols=50  Identities=8%  Similarity=0.203  Sum_probs=43.3

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|+.++-++.|+|+ .|.++.+||..+|+|.+||...+.+....|-+.+
T Consensus       141 ~~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l  190 (324)
T TIGR02960       141 QYLPPRQRAVLLLRDV-LGWRAAETAELLGTSTASVNSALQRARATLDEVG  190 (324)
T ss_pred             HhCCHHHhhHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence            3567777777777776 6899999999999999999999999999998874

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.

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=90.11  E-value=0.71  Score=38.25  Aligned_cols=49  Identities=14%  Similarity=0.120  Sum_probs=39.5

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+..+.++.|. +-.|.++.++|..+|+|.+||...+.+....|-..
T Consensus       132 ~~L~~~~r~i~~l~-~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~  180 (182)
T PRK12537        132 EQLEPARRNCILHA-YVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALREC  180 (182)
T ss_pred             HhCCHHHHHHHHHH-HHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence            35666777666666 45689999999999999999999999888776554

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=90.08  E-value=0.8  Score=38.29  Aligned_cols=49  Identities=10%  Similarity=0.112  Sum_probs=42.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus       116 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l  164 (187)
T PRK12516        116 QLPDDQREAIILVGA-SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEIL  164 (187)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            567788888888877 7899999999999999999999998888877764

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=90.08  E-value=0.74  Score=40.62  Aligned_cols=48  Identities=8%  Similarity=0.241  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .++..++..+.|+|+ .|.++.++|..+|+|.++|++...+...-|-..
T Consensus       203 ~L~~~~r~vl~l~y~-~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~  250 (256)
T PRK07408        203 QLEERTREVLEFVFL-HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKL  250 (256)
T ss_pred             cCCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            578888998999886 589999999999999999999999988777665

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

Probab=90.07  E-value=0.34  Score=37.47  Aligned_cols=40  Identities=20%  Similarity=0.429  Sum_probs=31.7

Q ss_pred             CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ++..++++   -++..|.+.+.+|..|+||.+||.+|+.+.-.
T Consensus         5 ~DlR~rVl---~~~~~g~s~~eaa~~F~VS~~Tv~~W~k~~~~   44 (119)
T PF01710_consen    5 LDLRQRVL---AYIEKGKSIREAAKRFGVSRNTVYRWLKRKET   44 (119)
T ss_pred             HHHHHHHH---HHHHccchHHHHHHHhCcHHHHHHHHHHhccc
Confidence            44455544   47788999999999999999999999985433

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 [].

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

Probab=90.02  E-value=0.69  Score=40.31  Aligned_cols=49  Identities=12%  Similarity=0.355  Sum_probs=43.6

Q ss_pred             CCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .++..++..+.|+|.   ..+.++.++|..+|+|.++|+++..+.+.-|-..
T Consensus       176 ~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~  227 (238)
T TIGR02393       176 TLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHP  227 (238)
T ss_pred             hCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence            688999999999995   5789999999999999999999999888777665

This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=89.97  E-value=0.61  Score=38.99  Aligned_cols=48  Identities=19%  Similarity=0.270  Sum_probs=40.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+|++++-++.|+++. |.++.++|..+|+|.+||...+.+....|-..
T Consensus       141 ~L~~~~~~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~  188 (194)
T PRK12519        141 QLPESQRQVLELAYYE-GLSQSEIAKRLGIPLGTVKARARQGLLKLREL  188 (194)
T ss_pred             hCCHHHhhhhhhhhhc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            4677777777777766 89999999999999999999988887776655

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=89.97  E-value=0.89  Score=36.32  Aligned_cols=47  Identities=13%  Similarity=0.110  Sum_probs=39.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMS   75 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~   75 (307)
                      ..+|+.++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-
T Consensus       105 ~~L~~~~r~ii~l~~~~-~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr  151 (154)
T PRK06759        105 SVLDEKEKYIIFERFFV-GKTMGEIALETEMTYYQVRWIYRQALEKMR  151 (154)
T ss_pred             HhCCHHHHHHHHHHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            36778888888888765 799999999999999999999988776653

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=89.94  E-value=0.55  Score=39.36  Aligned_cols=49  Identities=12%  Similarity=0.138  Sum_probs=42.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+|..++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus       136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l  184 (195)
T PRK12532        136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCL  184 (195)
T ss_pred             hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            577888888888777 6899999999999999999999999888877764

>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=89.91  E-value=1  Score=30.12  Aligned_cols=42  Identities=17%  Similarity=0.201  Sum_probs=32.8

Q ss_pred             HHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          36 TLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        36 l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      +-+++....+| ++...|..+++|+|++++.++++-..+-..|
T Consensus         4 l~~f~~v~~~g-s~~~AA~~l~is~~~vs~~i~~LE~~lg~~L   45 (60)
T PF00126_consen    4 LRYFLAVAETG-SISAAAEELGISQSAVSRQIKQLEEELGVPL   45 (60)
T ss_dssp             HHHHHHHHHHS-SHHHHHHHCTSSHHHHHHHHHHHHHHHTS-S
T ss_pred             HHHHHHHHHhC-CHHHHHHHhhccchHHHHHHHHHHHHhCCeE
Confidence            34444444554 8999999999999999999999988877664

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 ....

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

Probab=89.80  E-value=0.77  Score=31.00  Aligned_cols=27  Identities=22%  Similarity=0.313  Sum_probs=24.4

Q ss_pred             CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          46 QLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        46 g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+..++|..+|+|++|+++.++.+..
T Consensus        25 ~~s~~ela~~~g~s~~tv~r~l~~L~~   51 (67)
T cd00092          25 PLTRQEIADYLGLTRETVSRTLKELEE   51 (67)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            378999999999999999999998866

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=89.76  E-value=0.85  Score=39.42  Aligned_cols=48  Identities=10%  Similarity=0.256  Sum_probs=41.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ   76 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~   76 (307)
                      ..++..++.++.++|+ .|.++.++|..+|+|+++|+++.++.+.-|-.
T Consensus       182 ~~L~~~e~~i~~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~  229 (231)
T TIGR02885       182 SKLDERERQIIMLRYF-KDKTQTEVANMLGISQVQVSRLEKKVLKKMKE  229 (231)
T ss_pred             HcCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence            4678888888888775 68899999999999999999999988876644

Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.

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

Probab=89.75  E-value=0.85  Score=37.75  Aligned_cols=49  Identities=14%  Similarity=0.213  Sum_probs=41.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+++.++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       139 ~~L~~~~r~vi~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~  187 (189)
T TIGR02984       139 AKLPEDYREVILLRHL-EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQI  187 (189)
T ss_pred             HcCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            3578888888888776 799999999999999999999998887766543

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

>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily

Probab=89.71  E-value=0.89  Score=39.16  Aligned_cols=49  Identities=10%  Similarity=0.301  Sum_probs=42.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|..++-++.|+|+ .|.++.++|..+|+|.+||++.+.+....|-..
T Consensus       177 ~~L~~~~r~vl~l~y~-~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~  225 (227)
T TIGR02980       177 AALPERERRILLLRFF-EDKTQSEIAERLGISQMHVSRLLRRALKKLREQ  225 (227)
T ss_pred             HcCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            3688888888888876 589999999999999999999999988776543

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.

>PRK05572 sporulation sigma factor SigF; Validated

Probab=89.66  E-value=0.86  Score=40.07  Aligned_cols=49  Identities=12%  Similarity=0.230  Sum_probs=43.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|..++.++.|+|+ .|.++.++|..+|+|.++|+++.++.+.-|-..
T Consensus       201 ~~L~~~~~~v~~l~~~-~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~  249 (252)
T PRK05572        201 RELDERERLIVYLRYF-KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK  249 (252)
T ss_pred             HcCCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            4688999999999886 579999999999999999999999988777654

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=89.57  E-value=0.95  Score=37.78  Aligned_cols=49  Identities=8%  Similarity=0.108  Sum_probs=42.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|++++-++.|+|+ .|.|+.++|..+|+|.+||...+.+....|-..
T Consensus       130 ~~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~  178 (189)
T PRK06811        130 NDLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN  178 (189)
T ss_pred             HhCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence            4688899999999887 589999999999999999999888887776554

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=89.42  E-value=0.93  Score=37.51  Aligned_cols=50  Identities=12%  Similarity=0.234  Sum_probs=42.7

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|.+++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..+
T Consensus       130 ~~L~~~~r~v~~l~~~~-g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l  179 (184)
T PRK12512        130 ETLPPRQRDVVQSISVE-GASIKETAAKLSMSEGAVRVALHRGLAALAAKF  179 (184)
T ss_pred             HhCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            35777888888887777 899999999999999999999999888877664

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

Probab=89.42  E-value=0.88  Score=36.74  Aligned_cols=48  Identities=21%  Similarity=0.357  Sum_probs=40.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+|++++.++.|.+ -.|.++.++|..+|+|.+||...+.+....|-..
T Consensus       110 ~L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~  157 (162)
T TIGR02983       110 RLPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRALARLREL  157 (162)
T ss_pred             hCCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            45778888877777 5589999999999999999999999988877665

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.

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=89.42  E-value=0.7  Score=38.38  Aligned_cols=63  Identities=10%  Similarity=0.058  Sum_probs=48.2

Q ss_pred             CCCCHHHHHHHHHHHHhc--------------CCcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHH
Q psy4300          28 PFVPVEKKTLVALSYMAT--------------QLSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEES   92 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~--------------g~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~   92 (307)
                      ...+++++|+-+|.+|+.              ..+..++|...|+++.|++|+++++... +...  ....|..++.+.+
T Consensus       111 ~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~--~~~~i~I~d~~~L  188 (193)
T TIGR03697       111 AHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKKKLISI--HKKKITVHDPIAL  188 (193)
T ss_pred             HhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe--cCCEEEEeCHHHH
Confidence            356889999999987632              2589999999999999999999998776 4554  5556666655443

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

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=89.37  E-value=0.86  Score=37.83  Aligned_cols=50  Identities=14%  Similarity=0.169  Sum_probs=43.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|++++-++.|.|+. |.++.++|..+|+|..||...+.+....|...+
T Consensus       127 ~~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l  176 (186)
T PRK05602        127 AALPERQREAIVLQYYQ-GLSNIEAAAVMDISVDALESLLARGRRALRAQL  176 (186)
T ss_pred             HhCCHHHHHHhhHHHhc-CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence            35688888888888876 899999999999999999999998887777663

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=89.33  E-value=1  Score=37.81  Aligned_cols=49  Identities=14%  Similarity=0.322  Sum_probs=40.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+|.+.+-++.|.|+ .|.++.++|..+|+|.+||..-+.+....|-..+
T Consensus       141 ~Lp~~~r~v~~l~~~-eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l  189 (194)
T PRK12531        141 RLPKAQRDVLQAVYL-EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM  189 (194)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence            466677777777777 6899999999999999999988888877776653

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=89.31  E-value=0.3  Score=39.08  Aligned_cols=48  Identities=19%  Similarity=0.233  Sum_probs=38.8

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+|..++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-+.
T Consensus       105 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~  152 (154)
T TIGR02950       105 RLPENYRTVLILREF-KEFSYKEIAELLNLSLAKVKSNLFRARKELKKL  152 (154)
T ss_pred             hCCHhheeeeeehhh-ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            466666666777666 699999999999999999999988887766543

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

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=89.21  E-value=1.3  Score=38.41  Aligned_cols=71  Identities=11%  Similarity=0.141  Sum_probs=51.5

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCC-ChHHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWP-TEEESVIIERNFRA  101 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P-~~~~~~~~~~~f~~  101 (307)
                      ..++..++.++.|.++- |.++.++|...|+|.+||...+.+....|-..+  .....-+ ...+...+...|..
T Consensus       115 ~~Lp~~~R~v~lL~~~e-g~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l--~~~~~~~~~~~~~~~~~~~~~~  186 (228)
T PRK06704        115 SSLNVQQSAILLLKDVF-QYSIADIAKVCSVSEGAVKASLFRSRNRLKTVS--EEGIEIVEFTDDMEVVVTSIRE  186 (228)
T ss_pred             HhCCHHHhhHhhhHHhh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH--HhcCCCCCccccHHHHHHHHHh
Confidence            35777888877777755 799999999999999999999999888888774  3322222 22344555666653

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

Probab=89.19  E-value=0.98  Score=39.61  Aligned_cols=50  Identities=20%  Similarity=0.325  Sum_probs=42.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|..++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus       160 ~~Lp~~~R~v~~L~~~-eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l  209 (244)
T TIGR03001       160 AALSERERHLLRLHFV-DGLSMDRIGAMYQVHRSTVSRWVAQARERLLERT  209 (244)
T ss_pred             HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            3567777888888777 7899999999999999999999998888777765

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.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=89.05  E-value=1.2  Score=32.13  Aligned_cols=39  Identities=18%  Similarity=0.396  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHhc---CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          34 KKTLVALSYMAT---QLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        34 ~~l~i~L~~L~~---g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ++..-.|.+|..   +.+..+++..+|++++|+++.+.....
T Consensus         5 ~r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~   46 (91)
T smart00346        5 ERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE   46 (91)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            445555666643   489999999999999999999998865

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

Probab=89.02  E-value=0.97  Score=39.65  Aligned_cols=49  Identities=16%  Similarity=0.320  Sum_probs=43.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .++-.+++.+.|+|+- +.+...+|...|||+|.||++..+.+..|-..|
T Consensus       196 ~L~EREk~Vl~l~y~e-elt~kEI~~~LgISes~VSql~kkai~kLr~~l  244 (247)
T COG1191         196 PLPEREKLVLVLRYKE-ELTQKEIAEVLGISESRVSRLHKKAIKKLRKEL  244 (247)
T ss_pred             ccCHHHHHHHHHHHHh-ccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHh
Confidence            7889999999999954 689999999999999999999999988776653

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=89.01  E-value=0.92  Score=37.49  Aligned_cols=49  Identities=16%  Similarity=0.314  Sum_probs=42.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|..++-++.|.++. |.++.++|..+|+|.+||...+.+....|-..
T Consensus       126 ~~L~~~~r~v~~l~~~~-g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~  174 (179)
T PRK09415        126 MSLPIKYREVIYLFYYE-ELSIKEIAEVTGVNENTVKTRLKKAKELLKKG  174 (179)
T ss_pred             HhCCHHHhhHhHhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            35788888888888877 89999999999999999999888887776655

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

Probab=88.98  E-value=0.75  Score=26.71  Aligned_cols=25  Identities=20%  Similarity=0.307  Sum_probs=20.2

Q ss_pred             CcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300          47 LSMRKIGDQFNLADSTVWSCIDSFL   71 (307)
Q Consensus        47 ~~~~~l~~~fgvs~stv~r~v~~~~   71 (307)
                      .+..++|...|++..||+|++.++-
T Consensus         3 mtr~diA~~lG~t~ETVSR~l~~l~   27 (32)
T PF00325_consen    3 MTRQDIADYLGLTRETVSRILKKLE   27 (32)
T ss_dssp             --HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             cCHHHHHHHhCCcHHHHHHHHHHHH
Confidence            4678999999999999999998864

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

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=88.95  E-value=0.92  Score=40.84  Aligned_cols=51  Identities=6%  Similarity=0.156  Sum_probs=45.0

Q ss_pred             CCCCHHHHHHHHHHHH-hcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYM-ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L-~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..++..++..+.|+|+ ..|.++.++|..+|+|+++|+++.++.+.-|-..+
T Consensus       226 ~~L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l  277 (289)
T PRK07500        226 QTLNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRRAL  277 (289)
T ss_pred             hcCCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            3689999999999986 36899999999999999999999999888877664

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=88.94  E-value=1.1  Score=37.15  Aligned_cols=48  Identities=13%  Similarity=0.149  Sum_probs=38.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .++..++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       137 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~  184 (187)
T PRK12534        137 ELEPPRSELIRTAFF-EGITYEELAARTDTPIGTVKSWIRRGLAKLKAC  184 (187)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence            456666666666654 789999999999999999999999887776554

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=88.94  E-value=1  Score=39.71  Aligned_cols=48  Identities=10%  Similarity=0.182  Sum_probs=41.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .++..++..+.++|+ .|.++.++|..+|+|.++|+++.++.+.-|-..
T Consensus       209 ~L~~~er~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~  256 (258)
T PRK08215        209 KLNDREKLILNLRFF-QGKTQMEVAEEIGISQAQVSRLEKAALKHMRKY  256 (258)
T ss_pred             cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            688888888888875 689999999999999999999999887766543

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=88.94  E-value=1  Score=39.62  Aligned_cols=49  Identities=12%  Similarity=0.363  Sum_probs=41.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-++.|+|+ .|.++.++|..+|+|.+||.+...+....|-..
T Consensus       204 ~~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~  252 (257)
T PRK08583        204 PVLSDREKSIIQCTFI-ENLSQKETGERLGISQMHVSRLQRQAIKKLREA  252 (257)
T ss_pred             HhCCHHHHHHHHHHHh-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            3578888888888776 689999999999999999999999888877655

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=88.91  E-value=1.2  Score=36.42  Aligned_cols=49  Identities=12%  Similarity=0.130  Sum_probs=41.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+..+.++.|.| -.|.++.++|..+|+|.+||...+.+....+...
T Consensus       117 ~~L~~~~r~v~~L~~-~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~  165 (168)
T PRK12525        117 DGLSGKARAAFLMSQ-LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQG  165 (168)
T ss_pred             HhCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence            358888888888876 5589999999999999999999888887776654

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=88.81  E-value=1  Score=39.12  Aligned_cols=50  Identities=12%  Similarity=0.239  Sum_probs=43.0

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++..+.|+++   -.|.|+.++|...|+|.+||...+.+....|-..
T Consensus       177 ~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~  229 (234)
T TIGR02835       177 AKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKE  229 (234)
T ss_pred             HhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            4688999999999986   3789999999999999999999888877766554

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

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=88.62  E-value=0.95  Score=37.79  Aligned_cols=50  Identities=8%  Similarity=0.179  Sum_probs=42.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|+.++-++.|.|+. |.|+.++|..+|+|.+||...+.+....|...+
T Consensus       130 ~~Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l  179 (191)
T PRK12520        130 DRLPPRTGRVFMMREWL-ELETEEICQELQITATNAWVLLYRARMRLRECL  179 (191)
T ss_pred             HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            35778888888887765 799999999999999999999998888877764

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

Probab=88.62  E-value=1  Score=40.77  Aligned_cols=47  Identities=17%  Similarity=0.304  Sum_probs=41.0

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHc
Q psy4300          28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAM   74 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l   74 (307)
                      ..+|+.++..+.|+|.   ..+.++.++|..+|+|+.+|..+..+.+.-|
T Consensus       248 ~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kL  297 (298)
T TIGR02997       248 AELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKL  297 (298)
T ss_pred             HcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence            3589999999999995   6789999999999999999999988876543

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

>PF13751 DDE_Tnp_1_6: Transposase DDE domain

Probab=88.50  E-value=0.29  Score=37.99  Aligned_cols=49  Identities=24%  Similarity=0.274  Sum_probs=39.0

Q ss_pred             hHHHHhhhh-HHHHHHHHHHhhcccccccccCChhhHHHHHHHHHHhhhhh
Q psy4300         222 NTALSKTRV-PIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNFC  271 (307)
Q Consensus       222 N~~~s~~R~-~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~a~~~LhN~~  271 (307)
                      ...+.+.|. .||..||.||. +--|.+++......+..-+...|+-|||-
T Consensus        73 ~k~~y~~R~~~VE~~fg~~K~-~~g~~r~~~rG~~kv~~~~~l~a~a~Nl~  122 (125)
T PF13751_consen   73 GKELYKQRSIKVEGVFGTIKR-NHGLRRFRYRGLEKVRIEFLLAAIAYNLK  122 (125)
T ss_pred             hhhhhheeecccccccccchh-ccCCccccccchhhhHHHHHHHHHHHHHH
Confidence            456677787 99999999998 55666556557888888888888889984

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=88.49  E-value=1.1  Score=36.74  Aligned_cols=49  Identities=8%  Similarity=0.087  Sum_probs=41.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-++.|.++. |.++.++|..+|+|.+||...+.+...-+...
T Consensus       118 ~~Lp~~~r~v~~L~~~~-g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~  166 (172)
T PRK12523        118 GKLSSKARAAFLYNRLD-GMGHAEIAERLGVSVSRVRQYLAQGLRQCYIA  166 (172)
T ss_pred             HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            45778888888888775 89999999999999999999888877766554

>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=88.49  E-value=0.55  Score=30.40  Aligned_cols=37  Identities=24%  Similarity=0.395  Sum_probs=27.2

Q ss_pred             HHHHHHHHhc---CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          36 TLVALSYMAT---QLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        36 l~i~L~~L~~---g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      .+-.|.+++.   +.+..+|+...|+++||++|++.....
T Consensus         5 al~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~   44 (52)
T PF09339_consen    5 ALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE   44 (52)
T ss_dssp             HHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3344444433   357999999999999999999988764

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.

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=88.48  E-value=1.1  Score=39.42  Aligned_cols=48  Identities=8%  Similarity=0.203  Sum_probs=41.5

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ   76 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~   76 (307)
                      ..++..++.++.++|+ .|.++.++|..+|+|+++|+++.++.+.-|..
T Consensus       205 ~~L~~rer~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~  252 (254)
T TIGR02850       205 KRLNEREKMILNMRFF-EGKTQMEVAEEIGISQAQVSRLEKAALKHMRK  252 (254)
T ss_pred             HcCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence            4688889999999875 58899999999999999999999988776643

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

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=88.27  E-value=1  Score=40.38  Aligned_cols=51  Identities=8%  Similarity=0.139  Sum_probs=45.2

Q ss_pred             CCCCHHHHHHHHHHH-H--hcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSY-M--ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~-L--~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|..++..+.|+| |  -.|.|+.++|..+|+|.+||...+.+....|-..|
T Consensus       221 ~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l  274 (285)
T TIGR02394       221 AELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL  274 (285)
T ss_pred             HcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            468889999999998 4  56899999999999999999999999988887764

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).

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

Probab=88.19  E-value=1.3  Score=36.11  Aligned_cols=48  Identities=19%  Similarity=0.329  Sum_probs=40.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+|..++-++.|.++. |.++.++|..+|+|.+||...+.+....|...
T Consensus       119 ~L~~~~r~i~~l~~~~-g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~  166 (169)
T TIGR02954       119 TLNDKYQTAIILRYYH-DLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR  166 (169)
T ss_pred             hCCHHHhHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            5777777777777776 89999999999999999999999888777654

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.

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=88.19  E-value=1.4  Score=36.06  Aligned_cols=49  Identities=20%  Similarity=0.259  Sum_probs=40.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+|+..+-++.|.++. |.++.++|..+|+|.+||...+.+....|-..|
T Consensus       118 ~L~~~~r~vl~L~~~~-g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l  166 (173)
T PRK09645        118 QLSPEHRAVLVRSYYR-GWSTAQIAADLGIPEGTVKSRLHYALRALRLAL  166 (173)
T ss_pred             hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            4667777777777655 899999999999999999888888877776654

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=88.17  E-value=1.3  Score=36.81  Aligned_cols=50  Identities=14%  Similarity=0.098  Sum_probs=43.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|...+-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus       110 ~~Lp~~~R~v~~L~~~-~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l  159 (182)
T PRK12540        110 DKLPQDQREALILVGA-SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALL  159 (182)
T ss_pred             HhCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            3577788888888776 7899999999999999999999999888887775

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=88.07  E-value=1.2  Score=36.99  Aligned_cols=49  Identities=12%  Similarity=0.086  Sum_probs=40.3

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-+.
T Consensus       129 ~~Lp~~~r~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~  177 (185)
T PRK09649        129 ADLTTDQREALLLTQLL-GLSYADAAAVCGCPVGTIRSRVARARDALLAD  177 (185)
T ss_pred             HhCCHHHhHHhhhHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            35677777777777665 78999999999999999999998887777654

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=88.03  E-value=1.3  Score=37.17  Aligned_cols=50  Identities=16%  Similarity=0.133  Sum_probs=44.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|+.++-++.|+++ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus       112 ~~Lp~~~r~v~~L~~~-~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l  161 (188)
T PRK12546        112 AQLPDEQREALILVGA-SGFSYEEAAEMCGVAVGTVKSRANRARARLAELL  161 (188)
T ss_pred             HhCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            4678888888889888 7899999999999999999999999888887764

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=88.00  E-value=1.4  Score=37.51  Aligned_cols=50  Identities=10%  Similarity=0.062  Sum_probs=43.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|+.++-++.|+|+. |.++.++|..+|+|.+||...+.+....|-..+
T Consensus       147 ~~L~~~~r~v~~L~~~~-g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l  196 (206)
T PRK12544        147 DGLPAKYARVFMMREFI-ELETNEICHAVDLSVSNLNVLLYRARLRLRECL  196 (206)
T ss_pred             HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            46778888888888766 899999999999999999999999888877764

>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=87.86  E-value=0.64  Score=30.15  Aligned_cols=44  Identities=14%  Similarity=0.229  Sum_probs=30.9

Q ss_pred             HHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHH
Q psy4300          42 YMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNF   99 (307)
Q Consensus        42 ~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f   99 (307)
                      +...|.++.++|...|+|++|++++.+.              -..|+.+.+..++..|
T Consensus         5 r~~~gls~~~la~~~gis~~~i~~~~~g--------------~~~~~~~~~~~ia~~l   48 (55)
T PF01381_consen    5 RKEKGLSQKELAEKLGISRSTISRIENG--------------KRNPSLDTLKKIAKAL   48 (55)
T ss_dssp             HHHTTS-HHHHHHHHTS-HHHHHHHHTT--------------SSTSBHHHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHhCCCcchhHHHhcC--------------CCCCCHHHHHHHHHHH
Confidence            3467999999999999999999998765              2235555555655554

; 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 ....

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=87.85  E-value=1.4  Score=36.60  Aligned_cols=49  Identities=14%  Similarity=0.183  Sum_probs=42.9

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+..+-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..
T Consensus       130 ~~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~  178 (184)
T PRK12539        130 ARLPEKMRLAIQAVKLE-GLSVAEAATRSGMSESAVKVSVHRGLKALAAL  178 (184)
T ss_pred             HhCCHHHHHHHHHHHHc-CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            46788888888888885 89999999999999999999999888877665

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=87.84  E-value=1.4  Score=36.95  Aligned_cols=48  Identities=19%  Similarity=0.179  Sum_probs=39.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+|++++-++.|.|+ .|.++.++|..+|+|.+||..-+.+....|-..
T Consensus       134 ~Lp~~~r~i~~l~~~-~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~  181 (192)
T PRK09643        134 RLPVEQRAALVAVDM-QGYSVADAARMLGVAEGTVKSRCARGRARLAEL  181 (192)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            577888888877777 689999999999999999988887776666555

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=87.82  E-value=1.5  Score=35.27  Aligned_cols=49  Identities=16%  Similarity=0.085  Sum_probs=39.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+|+..+-++.|.++ .|.|+.++|..+|+|.+||...+.+....|-..+
T Consensus       106 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l  154 (160)
T PRK09642        106 ELPENYRDVVLAHYL-EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHW  154 (160)
T ss_pred             hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            466777777767665 5799999999999999999888888777766653

>PRK10402 DNA-binding transcriptional activator YeiL; Provisional

Probab=87.81  E-value=1.7  Score=37.39  Aligned_cols=67  Identities=4%  Similarity=0.024  Sum_probs=50.8

Q ss_pred             CCCHHHHHHHHHHHHhcC----CcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQ----LSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEESVIIER   97 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g----~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~~~~~~   97 (307)
                      ..+++++|+-+|..+..+    .+..++|..+|+++.|++|.++++.+. +.+.  ....|.-++.+.+.++..
T Consensus       148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~--~~~~i~I~d~~~L~~~~~  219 (226)
T PRK10402        148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKK--SKRGYLIKNRKQLSGLAL  219 (226)
T ss_pred             cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEe--eCCEEEEeCHHHHHHHHH
Confidence            458999999999876432    467899999999999999999999884 5555  555666666555554433

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=87.80  E-value=1.1  Score=37.03  Aligned_cols=49  Identities=24%  Similarity=0.390  Sum_probs=41.5

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|...
T Consensus       135 ~~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~  183 (187)
T TIGR02948       135 QALPPKYRMVIVLKYM-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ  183 (187)
T ss_pred             HhCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            4677888888888777 589999999999999999999999887777655

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

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=87.68  E-value=1.4  Score=36.38  Aligned_cols=48  Identities=19%  Similarity=0.187  Sum_probs=38.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       129 ~L~~~~r~v~~l~~~-~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~  176 (181)
T PRK12536        129 QLPDRQRLPIVHVKL-EGLSVAETAQLTGLSESAVKVGIHRGLKALAAK  176 (181)
T ss_pred             HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            466667766666654 589999999999999999999999887777655

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

Probab=87.67  E-value=1.4  Score=30.62  Aligned_cols=43  Identities=16%  Similarity=0.093  Sum_probs=30.2

Q ss_pred             CcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChH
Q psy4300          47 LSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEE   90 (307)
Q Consensus        47 ~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~   90 (307)
                      .+..++|...|+|+.|++++++++.+.=+-.. ....|.-.+.+
T Consensus        29 lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~-~~~~i~I~d~~   71 (76)
T PF13545_consen   29 LTQEEIADMLGVSRETVSRILKRLKDEGIIEV-KRGKIIILDPE   71 (76)
T ss_dssp             SSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE-ETTEEEESSHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE-cCCEEEECCHH
Confidence            67999999999999999999998865422221 34444444433

...

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=87.66  E-value=2  Score=34.20  Aligned_cols=46  Identities=4%  Similarity=0.018  Sum_probs=36.1

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ...+++.+-.++...+-..+.+..+||..++++++|+++.+++...
T Consensus        35 ~~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~   80 (144)
T PRK11512         35 PLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVC   80 (144)
T ss_pred             ccCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3467776665555445566789999999999999999999998754

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=87.64  E-value=1.4  Score=36.59  Aligned_cols=49  Identities=16%  Similarity=0.165  Sum_probs=40.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+|++++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus       106 ~L~~~~r~i~~l~~~-~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l  154 (181)
T PRK09637        106 ALPEKYAEALRLTEL-EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL  154 (181)
T ss_pred             hCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence            577777777777765 4799999999999999999999888877777663

>PRK06930 positive control sigma-like factor; Validated

Probab=87.63  E-value=1.6  Score=36.05  Aligned_cols=49  Identities=22%  Similarity=0.267  Sum_probs=40.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-++.|.+ ..|.++.++|..+|+|.+||...+.+....|-..
T Consensus       113 ~~L~~rer~V~~L~~-~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~  161 (170)
T PRK06930        113 SVLTEREKEVYLMHR-GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQ  161 (170)
T ss_pred             HhCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            367777777777664 6789999999999999999999999887777665

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=87.61  E-value=1.5  Score=36.26  Aligned_cols=49  Identities=12%  Similarity=0.195  Sum_probs=40.7

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|..++-.+.|+|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       134 ~~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~  182 (186)
T PRK13919        134 KALSPEERRVIEVLYY-QGYTHREAAQLLGLPLGTLKTRARRALSRLKEV  182 (186)
T ss_pred             HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            3477777878877775 479999999999999999999998887777655

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

Probab=87.60  E-value=0.93  Score=30.62  Aligned_cols=27  Identities=22%  Similarity=0.218  Sum_probs=21.4

Q ss_pred             HHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          42 YMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        42 ~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      +-+.|.|+.++|...|+|+|+++++-+
T Consensus        10 R~~~gls~~~lA~~~g~s~s~v~~iE~   36 (64)
T PF13560_consen   10 RERAGLSQAQLADRLGVSQSTVSRIER   36 (64)
T ss_dssp             HHCHTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            446689999999999999999998754

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=87.57  E-value=1.3  Score=30.00  Aligned_cols=36  Identities=17%  Similarity=0.268  Sum_probs=26.8

Q ss_pred             HHHHHHh---cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          38 VALSYMA---TQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        38 i~L~~L~---~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .+|+++.   ...+..+|+..++++++++++.+++.+..
T Consensus         7 ~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~   45 (68)
T PF13463_consen    7 QVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEK   45 (68)
T ss_dssp             HHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred             HHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            3455555   45888999999999999999999988654

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=87.28  E-value=1.4  Score=40.19  Aligned_cols=50  Identities=20%  Similarity=0.359  Sum_probs=43.5

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+++.++..+.|+|.   ..+.++.++|..+|+|+.+|..+..+.+.-|-..
T Consensus       255 ~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~  307 (317)
T PRK07405        255 EDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR  307 (317)
T ss_pred             HcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            3689999999999996   5679999999999999999999998887776553

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=87.09  E-value=1.5  Score=38.55  Aligned_cols=49  Identities=12%  Similarity=0.353  Sum_probs=41.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-.+.|+|+ .|.++.++|..+|+|.+||++.+.+....|-..
T Consensus       204 ~~L~~~~r~ii~l~~~-~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~  252 (255)
T TIGR02941       204 PILSEREKSIIHCTFE-ENLSQKETGERLGISQMHVSRLQRQAISKLKEA  252 (255)
T ss_pred             HcCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            4678888888888875 589999999999999999999998887776554

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

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

Probab=87.06  E-value=1.7  Score=36.29  Aligned_cols=49  Identities=6%  Similarity=0.100  Sum_probs=40.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+++.++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..+
T Consensus       131 ~L~~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l  179 (188)
T TIGR02943       131 HLPEQTARVFMMREVL-GFESDEICQELEISTSNCHVLLYRARLSLRACL  179 (188)
T ss_pred             hCCHHHHHHHHHHHHh-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence            4666677777777665 899999999999999999999988888777663

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.

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=86.92  E-value=1.3  Score=37.30  Aligned_cols=45  Identities=16%  Similarity=0.223  Sum_probs=37.3

Q ss_pred             CCCCHHHHHHHHHHHHhc-------------CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMAT-------------QLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~-------------g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ...++.++++-+|..|+.             ..+..+||...|+++.|++|+++++..
T Consensus       137 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~  194 (211)
T PRK11753        137 AFLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLED  194 (211)
T ss_pred             HhcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            567899999999887753             245689999999999999999988754

>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=86.83  E-value=1.5  Score=32.86  Aligned_cols=47  Identities=13%  Similarity=0.359  Sum_probs=33.4

Q ss_pred             CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ++..++=.+- .|+-.+.|...+|..+|||+.+|+..+++....|...
T Consensus        18 LT~kQ~~~l~-lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~y   64 (101)
T PF04297_consen   18 LTEKQREILE-LYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLEEY   64 (101)
T ss_dssp             S-HHHHHHHH-HHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHH-HHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            3444444444 5667789999999999999999999999998888664

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.

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=86.75  E-value=1.2  Score=36.81  Aligned_cols=49  Identities=22%  Similarity=0.188  Sum_probs=40.5

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..++.+.+-++.|.|+ .|.++.+||..+|+|.+||...+.+....|-+.
T Consensus       137 ~~L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~  185 (190)
T TIGR02939       137 EALPEDLRTAITLREL-EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR  185 (190)
T ss_pred             HcCCHHHhhhhhhhhh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            3466667776767665 789999999999999999999999888877766

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.

>PHA02591 hypothetical protein; Provisional

Probab=86.66  E-value=1.5  Score=30.88  Aligned_cols=38  Identities=13%  Similarity=0.176  Sum_probs=31.1

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          32 VEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        32 ~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      -.+-+.++=...+.|.+...+|...|+++.+|+++++.
T Consensus        45 ~dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~~   82 (83)
T PHA02591         45 EDDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLES   82 (83)
T ss_pred             cchHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence            34455566666788999999999999999999999864

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=86.65  E-value=3.4  Score=36.96  Aligned_cols=67  Identities=9%  Similarity=0.110  Sum_probs=48.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFR  100 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f~  100 (307)
                      .+|+.++-++.|+++- |.++.++|..+|+|.+||...+.+....|-+.  .+.+-  +..++...+.+.|-
T Consensus       108 ~L~~~~R~v~~L~~~~-g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~--~~~~~--~~~~~~~~~~~~f~  174 (281)
T TIGR02957       108 RLSPLERAVFVLREVF-DYPYEEIASIVGKSEANCRQLVSRARRHLDAR--RPRFE--VSREESRQLLERFV  174 (281)
T ss_pred             hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh--CCCCC--CChHHHHHHHHHHH
Confidence            5666767666666554 79999999999999999999999999999887  44332  22233345555553

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=86.58  E-value=1.9  Score=35.84  Aligned_cols=49  Identities=12%  Similarity=0.200  Sum_probs=40.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..
T Consensus       138 ~~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~  186 (189)
T PRK09648        138 DTLPEKQREILILRVVV-GLSAEETAEAVGSTPGAVRVAQHRALARLRAE  186 (189)
T ss_pred             HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            35777777777777776 89999999999999999999888877766544

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

Probab=86.52  E-value=1.6  Score=36.20  Aligned_cols=49  Identities=18%  Similarity=0.272  Sum_probs=41.9

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+|++++-++.|.++. |.|+.++|...|||.+||...+.+....+-..+
T Consensus       127 ~Lp~~~R~~~~l~~~~-gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l  175 (182)
T COG1595         127 RLPPRQREAFLLRYLE-GLSYEEIAEILGISVGTVKSRLHRARKKLREQL  175 (182)
T ss_pred             hCCHHHhHHhhhHhhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            5778888888887775 799999999999999999999999888777663

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=86.51  E-value=2  Score=35.10  Aligned_cols=49  Identities=18%  Similarity=0.194  Sum_probs=41.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++.++.|.++. |.++.++|..+|+|.+||...+.+....|-..
T Consensus        99 ~~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~  147 (170)
T TIGR02959        99 KELPDEYREAIRLTELE-GLSQQEIAEKLGLSLSGAKSRVQRGRKKLKEL  147 (170)
T ss_pred             HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            46788888888887764 79999999999999999999988887777666

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).

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=86.44  E-value=1.8  Score=34.94  Aligned_cols=48  Identities=15%  Similarity=0.144  Sum_probs=40.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+|+.++.++.|.++. |.++.++|..+|+|.+||...+.+....|-+.
T Consensus       112 ~L~~~~r~v~~l~~~~-~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~  159 (161)
T PRK12541        112 SLPLERRNVLLLRDYY-GFSYKEIAEMTGLSLAKVKIELHRGRKETKSI  159 (161)
T ss_pred             HCCHHHHHHhhhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            5788888888887765 78999999999999999999998887766543

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=86.42  E-value=1.8  Score=36.51  Aligned_cols=50  Identities=8%  Similarity=0.087  Sum_probs=41.3

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|+..+-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..+
T Consensus       138 ~~Lp~~~r~v~~L~~~e-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l  187 (201)
T PRK12545        138 DHLPEQIGRVFMMREFL-DFEIDDICTELTLTANHCSVLLYRARTRLRTCL  187 (201)
T ss_pred             HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            45777788888887654 789999999999999999988888877776663

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=86.38  E-value=2.1  Score=29.49  Aligned_cols=42  Identities=17%  Similarity=0.177  Sum_probs=32.6

Q ss_pred             CHHHHHHHHHHHHhc-CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          31 PVEKKTLVALSYMAT-QLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        31 ~~~~~l~i~L~~L~~-g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      +.+++++-+|.--+. +.+..+||..+|+++++|++.+..+..
T Consensus         6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~   48 (68)
T smart00550        6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEK   48 (68)
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            356666666665544 489999999999999999998887643

Helix-turn-helix-containing domain. Also known as Zab.

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=86.29  E-value=1.6  Score=32.19  Aligned_cols=30  Identities=17%  Similarity=0.211  Sum_probs=25.8

Q ss_pred             HhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          43 MATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        43 L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      .....+.++||...|+|++||+|.++++..
T Consensus        44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~   73 (95)
T TIGR01610        44 KQDRVTATVIAELTGLSRTHVSDAIKSLAR   73 (95)
T ss_pred             cCCccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            345689999999999999999999988754

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=86.27  E-value=1.7  Score=37.72  Aligned_cols=49  Identities=16%  Similarity=0.347  Sum_probs=41.5

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-.+.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       183 ~~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~  231 (236)
T PRK06986        183 ESLPEREQLVLSLYYQ-EELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR  231 (236)
T ss_pred             HhCCHHHHHHHHhHhc-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            3567888888888775 689999999999999999999999888777665

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=86.23  E-value=0.81  Score=41.83  Aligned_cols=68  Identities=16%  Similarity=0.173  Sum_probs=46.0

Q ss_pred             HHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHHHHHHHHHHHhhCCCCccee
Q psy4300          38 VALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGA  111 (307)
Q Consensus        38 i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~~~~~~~f~~~~~~p~~~g~  111 (307)
                      ++=.|+-.|.++.++|..+|+|+++|+|.+.+-.+. +.+.     -|.-|.. ....+...+++..++..|+-+
T Consensus        21 vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I-----~I~~~~~-~~~~Le~~L~~~fgLk~~iVv   89 (318)
T PRK15418         21 IAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRV-----QINSRFE-GCLELENALRQHFSLQHIRVL   89 (318)
T ss_pred             HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEE-----EEeCCCc-cHHHHHHHHHHHhCCCEEEEE
Confidence            556678889999999999999999999999976442 2222     2333432 223455556665577777543

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=86.21  E-value=1.9  Score=37.85  Aligned_cols=49  Identities=18%  Similarity=0.312  Sum_probs=41.5

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       200 ~~L~~~~r~vl~l~~~-~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~  248 (251)
T PRK07670        200 KQLSEKEQLVISLFYK-EELTLTEIGQVLNLSTSRISQIHSKALFKLKKL  248 (251)
T ss_pred             hcCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            4578888888888875 789999999999999999999998887766544

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=86.04  E-value=1.8  Score=36.04  Aligned_cols=49  Identities=22%  Similarity=0.196  Sum_probs=41.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..++.+++-.+.|.|+ .|.++.++|..+|+|..||...+.+....|-..
T Consensus       137 ~~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~  185 (193)
T PRK11923        137 QQLPEDLRTALTLREF-DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKA  185 (193)
T ss_pred             HhCCHHHhHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            3467777777888776 689999999999999999999998887777665

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=85.94  E-value=1.5  Score=35.93  Aligned_cols=48  Identities=21%  Similarity=0.267  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+|+..+-++.| ++-.|.++.++|..+|+|.+||...+.+....|...
T Consensus       119 ~L~~~~r~i~~l-~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~  166 (173)
T PRK12522        119 LLNEKYKTVLVL-YYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREH  166 (173)
T ss_pred             hCCHHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            344555544444 445689999999999999999999999888887766

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=85.93  E-value=2.1  Score=35.25  Aligned_cols=50  Identities=22%  Similarity=0.331  Sum_probs=40.3

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..|
T Consensus       116 ~~Lp~~~r~i~~l~~~-e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l  165 (179)
T PRK12543        116 HKLPYKLRQVIILRYL-HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKE  165 (179)
T ss_pred             HhCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            3577777777777655 4789999999999999999998888877776653

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=85.90  E-value=1.8  Score=38.48  Aligned_cols=49  Identities=12%  Similarity=0.339  Sum_probs=41.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..++..++-++.|+|+ .|.++.++|..+|+|.++|++++.+....|-..
T Consensus       214 ~~L~~rer~vl~l~y~-~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~  262 (264)
T PRK07122        214 AALPERERTVLVLRFF-ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQ  262 (264)
T ss_pred             HcCCHHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            3577888888888885 589999999999999999999999887766543

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=85.88  E-value=2.2  Score=34.27  Aligned_cols=48  Identities=17%  Similarity=0.135  Sum_probs=39.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+|++++-++.|.+ -.|.++.++|..+|+|.+||..-+.+....|-..
T Consensus       105 ~L~~~~r~v~~l~~-~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~  152 (159)
T PRK12527        105 ELPPACRDSFLLRK-LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVR  152 (159)
T ss_pred             hCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            46777777776765 5689999999999999999999988887777665

>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons

Probab=85.83  E-value=2  Score=29.26  Aligned_cols=43  Identities=19%  Similarity=0.229  Sum_probs=39.1

Q ss_pred             HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ++-.+..+|+...+..+.|...|+...++.+++..+...+.+.
T Consensus         2 ~~~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~L   44 (65)
T PF05344_consen    2 KARAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQL   44 (65)
T ss_pred             cHHHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHc
Confidence            4456788999999999999999999999999999999998887

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=85.71  E-value=3.8  Score=36.88  Aligned_cols=67  Identities=10%  Similarity=0.112  Sum_probs=47.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFR  100 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f~  100 (307)
                      .+|+.++-++.|+++ .|.++.++|...|+|.+||...+.+....|-..  .+.+-  +...+...+...|-
T Consensus       118 ~L~p~~R~vf~L~~~-~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~--~~~~~--~~~~~~~~~~~~f~  184 (290)
T PRK09635        118 RLGPAERVVFVLHEI-FGLPYQQIATTIGSQASTCRQLAHRARRKINES--RIAAS--VEPAQHRVVTRAFI  184 (290)
T ss_pred             hCCHHHHHHhhHHHH-hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh--CCCCC--CChHHHHHHHHHHH
Confidence            455555555555544 489999999999999999999999999988886  44332  22333445555554

>PF13309 HTH_22: HTH domain

Probab=85.66  E-value=3.1  Score=28.30  Aligned_cols=42  Identities=10%  Similarity=0.197  Sum_probs=35.0

Q ss_pred             CCCCCHHHHHHHHHHHHhcC-----CcHHHHHhhhCCChhhHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQ-----LSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g-----~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      ...++-++++-+.-.....|     .+-..+|..+|||+.||+++++
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            35688889988887777777     6678999999999999999863

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

Probab=85.60  E-value=1  Score=27.60  Aligned_cols=29  Identities=14%  Similarity=0.180  Sum_probs=21.9

Q ss_pred             HhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300          43 MATQLSMRKIGDQFNLADSTVWSCIDSFL   71 (307)
Q Consensus        43 L~~g~~~~~l~~~fgvs~stv~r~v~~~~   71 (307)
                      |.++.+..++|..+|+|.+.++|.+++..
T Consensus         5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk~~~   33 (42)
T PF00165_consen    5 LQQKLTLEDIAEQAGFSPSYFSRLFKKET   33 (42)
T ss_dssp             T-SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred             ccCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            45678899999999999999999998753

>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=85.59  E-value=2.2  Score=28.47  Aligned_cols=32  Identities=25%  Similarity=0.427  Sum_probs=26.2

Q ss_pred             HHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300          37 LVALSYMATQLSMRKIGDQFNLADSTVWSCIDSF   70 (307)
Q Consensus        37 ~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~   70 (307)
                      +..|++  .|.+..+||..+|++.+||+.+..+.
T Consensus         6 A~~LY~--~G~~~~eIA~~Lg~~~~TV~~W~~r~   37 (58)
T PF06056_consen    6 ARSLYL--QGWSIKEIAEELGVPRSTVYSWKDRY   37 (58)
T ss_pred             HHHHHH--cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence            444443  69999999999999999999988764

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

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=85.54  E-value=2.2  Score=34.62  Aligned_cols=50  Identities=14%  Similarity=0.074  Sum_probs=40.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus       107 ~~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l  156 (165)
T PRK09644        107 HTLPVIEAQAILLCDV-HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL  156 (165)
T ss_pred             HhCCHHHHHHHHhHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            4567777777766655 4799999999999999999999998887776653

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

Probab=85.51  E-value=2.2  Score=36.64  Aligned_cols=49  Identities=18%  Similarity=0.347  Sum_probs=41.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+++.++-++.|+|+ .|.++.++|..+|+|.+||.+.+.+....|-..
T Consensus       174 ~~L~~~~r~il~l~y~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~  222 (224)
T TIGR02479       174 ESLSEREQLVLSLYYY-EELNLKEIGEVLGLTESRVSQIHSQALKKLRAK  222 (224)
T ss_pred             HhCCHHHHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            3578888888888875 578999999999999999999988887766543

Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=85.48  E-value=2.4  Score=35.49  Aligned_cols=65  Identities=9%  Similarity=0.006  Sum_probs=49.0

Q ss_pred             CCCHHHHHHHHHHHHhc--------------CCcHHHHHhhhCCChhhHHHHHHHHHH-HccccccccccccCCChHHHH
Q psy4300          29 FVPVEKKTLVALSYMAT--------------QLSMRKIGDQFNLADSTVWSCIDSFLT-AMSQPQIQCQYIKWPTEEESV   93 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~--------------g~~~~~l~~~fgvs~stv~r~v~~~~~-~l~~~l~~~~~i~~P~~~~~~   93 (307)
                      ..+++++|+-+|..|+.              ..+..+||...|+++.|++|+++++.. -+...  ....|..++.+.+.
T Consensus       118 ~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~--~~~~i~I~d~~~L~  195 (202)
T PRK13918        118 GQRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSREGYIRS--GYGKIQLLDLKGLE  195 (202)
T ss_pred             hCchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEc--CCCEEEEECHHHHH
Confidence            45689999999987653              147899999999999999999999876 34443  55567666665554


Q ss_pred             HH
Q psy4300          94 II   95 (307)
Q Consensus        94 ~~   95 (307)
                      ++
T Consensus       196 ~~  197 (202)
T PRK13918        196 EL  197 (202)
T ss_pred             HH
Confidence            43

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=85.31  E-value=1.4  Score=27.46  Aligned_cols=27  Identities=19%  Similarity=0.287  Sum_probs=23.9

Q ss_pred             CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          46 QLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        46 g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+..++|..+|+|++|+++.++.+..
T Consensus         8 ~~s~~~la~~l~~s~~tv~~~l~~L~~   34 (48)
T smart00419        8 PLTRQEIAELLGLTRETVSRTLKRLEK   34 (48)
T ss_pred             ccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            467899999999999999999988765

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=85.22  E-value=1.9  Score=29.43  Aligned_cols=39  Identities=23%  Similarity=0.366  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          33 EKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        33 ~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      +.++...|. -..+.+..+|+...|+++++|+++++...+
T Consensus        10 E~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~   48 (68)
T PF01978_consen   10 EAKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEE   48 (68)
T ss_dssp             HHHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            445555554 244589999999999999999999998764

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.

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=85.06  E-value=2.3  Score=35.99  Aligned_cols=48  Identities=25%  Similarity=0.310  Sum_probs=38.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+|.+++.++.|.|+ .|.++.++|..+|+|.+||...+.+....|...
T Consensus       153 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~  200 (206)
T PRK12526        153 KLPEAQQTVVKGVYF-QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ  200 (206)
T ss_pred             hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            466677777666665 479999999999999999999888887777655

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=84.99  E-value=1.8  Score=35.76  Aligned_cols=48  Identities=13%  Similarity=0.182  Sum_probs=40.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.|.  =+|.+++.|.+..++|...++|.+||...+.++..-+--.
T Consensus       132 ~~LSpREr--EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKLgV~  179 (198)
T PRK15201        132 RHFSVTER--HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLHVK  179 (198)
T ss_pred             CCCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence            45777665  5677899999999999999999999999998887766554

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=84.93  E-value=2.3  Score=35.51  Aligned_cols=47  Identities=15%  Similarity=0.324  Sum_probs=36.7

Q ss_pred             CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      +++++.=.+.|+++ .|.++.++|...|+|.+||.+-+...-..+...
T Consensus       136 l~~~~~~~v~l~~~-~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~~  182 (185)
T PF07638_consen  136 LDPRQRRVVELRFF-EGLSVEEIAERLGISERTVRRRLRRARAWLRRE  182 (185)
T ss_pred             cCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            55555556666555 789999999999999999999988876665544

>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=84.86  E-value=2  Score=28.73  Aligned_cols=31  Identities=13%  Similarity=0.274  Sum_probs=26.5

Q ss_pred             HhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          43 MATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        43 L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      -..+.+..+|+..+|++++|+++.++...++
T Consensus        21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a   51 (61)
T PF12840_consen   21 SNGPMTVSELAEELGISQSTVSYHLKKLEEA   51 (61)
T ss_dssp             HCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred             cCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            5778999999999999999999999887654

...

>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors

Probab=84.84  E-value=2.8  Score=28.39  Aligned_cols=29  Identities=17%  Similarity=0.329  Sum_probs=25.0

Q ss_pred             hcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          44 ATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+.+..+++..+|++.+|+++.++.+..
T Consensus        18 ~~~~~~~ei~~~~~i~~~~i~~~l~~L~~   46 (78)
T cd00090          18 EGPLTVSELAERLGLSQSTVSRHLKKLEE   46 (78)
T ss_pred             HCCcCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence            34489999999999999999999988754

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.

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=84.75  E-value=2.5  Score=36.65  Aligned_cols=47  Identities=11%  Similarity=0.261  Sum_probs=39.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMS   75 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~   75 (307)
                      ..++..++-.+.|+|+ .|.++.++|..+|+|+++|+++.++...-|-
T Consensus       182 ~~L~~~er~vi~l~~~-~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr  228 (231)
T PRK12427        182 SQLDEREQLILHLYYQ-HEMSLKEIALVLDLTEARICQLNKKIAQKIK  228 (231)
T ss_pred             HcCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            3578888888888885 6899999999999999999999888776553

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=84.73  E-value=2  Score=37.38  Aligned_cols=49  Identities=18%  Similarity=0.205  Sum_probs=40.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+|..++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus       171 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l  219 (233)
T PRK12538        171 RLPEQQRIAVILSYH-ENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL  219 (233)
T ss_pred             hCCHHHHHHhhhHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            466777777777665 4799999999999999999999999888877763

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

Probab=84.65  E-value=2  Score=30.63  Aligned_cols=37  Identities=8%  Similarity=0.234  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHHH--hcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          32 VEKKTLVALSYM--ATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        32 ~~~~l~i~L~~L--~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      ....|+..|..+  ..|.++.++|...|+++|+++++.+
T Consensus        15 ~k~~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~   53 (80)
T PF13744_consen   15 AKAQLMAAIRELREERGLTQAELAERLGISQPRVSRLEN   53 (80)
T ss_dssp             HHHHHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence            445566666655  5689999999999999999999875

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=84.48  E-value=2.4  Score=39.70  Aligned_cols=50  Identities=16%  Similarity=0.333  Sum_probs=43.5

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..++..++..+.|+|+   ..+.++.+||..+|||+.+|+++..+.+.-|-..
T Consensus       310 ~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~  362 (373)
T PRK07406        310 ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHP  362 (373)
T ss_pred             HcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhch
Confidence            3689999999999986   3468999999999999999999999988777654

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=84.44  E-value=2.7  Score=35.20  Aligned_cols=49  Identities=16%  Similarity=0.234  Sum_probs=39.9

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|..++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       141 ~~L~~~~r~vl~l~~~-~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~  189 (194)
T PRK09646        141 DALTDTQRESVTLAYY-GGLTYREVAERLAVPLGTVKTRMRDGLIRLRDC  189 (194)
T ss_pred             HhCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence            3577777777776665 579999999999999999999998887777665

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=84.41  E-value=1.9  Score=28.30  Aligned_cols=29  Identities=17%  Similarity=0.280  Sum_probs=25.6

Q ss_pred             hcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          44 ATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ....+..+++..+|+|.+|+++.++++..
T Consensus         8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~   36 (66)
T smart00418        8 EGELCVCELAEILGLSQSTVSHHLKKLRE   36 (66)
T ss_pred             cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            45688999999999999999999998765

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

Probab=84.31  E-value=4.9  Score=30.96  Aligned_cols=65  Identities=17%  Similarity=0.285  Sum_probs=38.2

Q ss_pred             CHHHHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300           2 RKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSF   70 (307)
Q Consensus         2 s~~~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~   70 (307)
                      ++.|..+.+...+ . +.......++..++.+ . +..+.--....+..++|..||||.+|+++.++++
T Consensus        31 S~~Tv~~W~k~~~-~-G~~~~k~r~~~Kid~~-~-L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl   95 (119)
T PF01710_consen   31 SRNTVYRWLKRKE-T-GDLEPKPRGRKKIDRD-E-LKALVEENPDATLRELAERLGVSPSTIWRALKRL   95 (119)
T ss_pred             HHHHHHHHHHhcc-c-ccccccccccccccHH-H-HHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence            4566666666222 2 1112212222256532 2 3333333456888999999999999999888775

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 [].

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=84.21  E-value=2.7  Score=35.44  Aligned_cols=48  Identities=13%  Similarity=0.245  Sum_probs=39.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..++..++-++.| |+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus       154 ~~L~~~~r~vl~l-~~-e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~  201 (208)
T PRK08295        154 ELLSELEKEVLEL-YL-DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKY  201 (208)
T ss_pred             HhCCHHHHHHHHH-HH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            3567777777777 65 689999999999999999998888877776665

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=84.21  E-value=2.7  Score=34.77  Aligned_cols=50  Identities=6%  Similarity=0.112  Sum_probs=39.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|+..+-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus       121 ~~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l  170 (185)
T PRK12542        121 KELNESNRQVFKYKVF-YNLTYQEISSVMGITEANVRKQFERARKRVQNMI  170 (185)
T ss_pred             HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            3466666666666655 4799999999999999999999888887776663

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=84.19  E-value=6.4  Score=30.01  Aligned_cols=46  Identities=2%  Similarity=0.034  Sum_probs=34.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+++.+-.++....-..+.+..+|+..++++++|+++.+++....
T Consensus        24 ~~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~   69 (118)
T TIGR02337        24 HGLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERD   69 (118)
T ss_pred             cCCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHC
Confidence            3566666444433344567889999999999999999999987654

This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=84.15  E-value=5.6  Score=35.71  Aligned_cols=49  Identities=4%  Similarity=0.005  Sum_probs=41.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-++.|+++- |.++.++|..+|+|.+||...+.+....|-+.
T Consensus       114 ~~L~~~~R~v~~L~~~~-g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~  162 (293)
T PRK09636        114 ERLSPLERAAFLLHDVF-GVPFDEIASTLGRSPAACRQLASRARKHVRAA  162 (293)
T ss_pred             HhCCHHHHHHHHHHHHh-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            35677777777776655 79999999999999999999999999999887

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=83.96  E-value=3.5  Score=37.79  Aligned_cols=48  Identities=10%  Similarity=0.225  Sum_probs=40.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+|..++-++.|+|+ .|.++.+||..+|+|.+||...+.+....|-..
T Consensus       153 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~  200 (339)
T PRK08241        153 HLPPRQRAVLILRDV-LGWSAAEVAELLDTSVAAVNSALQRARATLAER  200 (339)
T ss_pred             hCCHHHhhhhhhHHh-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhc
Confidence            466666776666654 579999999999999999999999999999885

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=83.91  E-value=1.6  Score=28.53  Aligned_cols=25  Identities=20%  Similarity=0.351  Sum_probs=22.6

Q ss_pred             cHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          48 SMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        48 ~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      +..+++..||+|++|+.+.+.....
T Consensus        22 s~~~la~~~~vs~~tv~~~l~~L~~   46 (60)
T smart00345       22 SERELAAQLGVSRTTVREALSRLEA   46 (60)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            7889999999999999999988765

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

Probab=83.80  E-value=2.8  Score=31.65  Aligned_cols=49  Identities=12%  Similarity=0.191  Sum_probs=38.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+++++-=++-|..+- |.++.+.|...|||++|+.++++..-.-+.+.|
T Consensus        41 ~L~~dElEAiRL~D~e-gl~QeeaA~~MgVSR~T~~ril~~ARkKiA~AL   89 (106)
T PF02001_consen   41 VLTVDELEAIRLVDYE-GLSQEEAAERMGVSRPTFQRILESARKKIADAL   89 (106)
T ss_pred             EeeHHHHHHHHHHHHc-CCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHH
Confidence            4677777777777765 699999999999999999999987655554443

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

Probab=83.55  E-value=1.4  Score=36.84  Aligned_cols=49  Identities=16%  Similarity=0.142  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+|...+-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus       131 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l  179 (193)
T TIGR02947       131 GLPEEFRQAVYLADV-EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL  179 (193)
T ss_pred             hCCHHHhhheeehhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            456666666666554 5799999999999999999999998887777663

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.

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=83.55  E-value=4  Score=40.63  Aligned_cols=51  Identities=24%  Similarity=0.266  Sum_probs=46.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ...+...-+++|.|.+=-++.|+..|+..||.+.|||...++++-..|.+.
T Consensus       550 ~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~d  600 (617)
T PRK14086        550 SRVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMAER  600 (617)
T ss_pred             CcccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHhC
Confidence            557889999999999999999999999999999999999999998877654

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=83.51  E-value=2.3  Score=33.79  Aligned_cols=45  Identities=9%  Similarity=0.119  Sum_probs=33.3

Q ss_pred             CCCCHHHH-HHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          28 PFVPVEKK-TLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        28 ~~~~~~~~-l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+++.+- ++..|.....+.+..+|+..++++++|+++.+++...
T Consensus        27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~   72 (144)
T PRK03573         27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE   72 (144)
T ss_pred             cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHH
Confidence            45666664 3344443444678999999999999999999998754

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

Probab=83.38  E-value=3.8  Score=27.27  Aligned_cols=42  Identities=17%  Similarity=0.024  Sum_probs=29.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCC---cHHHHHhhhCCChhhHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQL---SMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~---~~~~l~~~fgvs~stv~r~v~   68 (307)
                      +...++.-+|-+.-++..++.   .++..|..|||++..|.+|..
T Consensus         3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~k   47 (58)
T PF09607_consen    3 RRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRK   47 (58)
T ss_dssp             -----HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHT
T ss_pred             ccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHH
Confidence            567889999988888888875   679999999999999888764

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.

>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A

Probab=83.37  E-value=2.7  Score=28.50  Aligned_cols=38  Identities=18%  Similarity=0.198  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300          34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFL   71 (307)
Q Consensus        34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~   71 (307)
                      ++++-+|.-..++++-+++|..+|+|..++.+++....
T Consensus         3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le   40 (62)
T PF04703_consen    3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLE   40 (62)
T ss_dssp             HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            45566666677889999999999999999999887764

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=83.29  E-value=4.1  Score=39.12  Aligned_cols=72  Identities=14%  Similarity=0.170  Sum_probs=54.7

Q ss_pred             HHHHHHHHhhhcCcccc---cCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhh-CCChhhHHHHHHHHHHHcccc
Q psy4300           6 FGFLVEALAAINGYETL---YERGVPFVPVEKKTLVALSYMATQLSMRKIGDQF-NLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus         6 F~~L~~~l~~~~~~~~~---~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~f-gvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+.|.+.+...++.-..   +.++...+...-+++|.|.+--++.|+.++|..| |.++|||...++++-..+..-
T Consensus       359 ~~~i~~~v~~~~~i~~~~l~~~~R~~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~~d  434 (450)
T PRK00149        359 IENIQKVVAEYYNIKVSDLKSKSRTRNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLLEED  434 (450)
T ss_pred             HHHHHHHHHHHcCCCHHHHhCCCCCcccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHHHhC
Confidence            45555665555432111   1233568889999999999999999999999999 599999999999998876543

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=83.29  E-value=1.5  Score=37.91  Aligned_cols=49  Identities=14%  Similarity=0.231  Sum_probs=40.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+|.+++-++.|+++. |.++.++|..+|+|.+||...+.+....|-..+
T Consensus       149 ~L~~~~r~i~~l~~~~-g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l  197 (231)
T PRK11922        149 ALPDAFRAVFVLRVVE-ELSVEETAQALGLPEETVKTRLHRARRLLRESL  197 (231)
T ss_pred             hCCHHHhhhheeehhc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            4667777777676655 899999999999999999999888877777764

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=83.12  E-value=1.5  Score=34.67  Aligned_cols=36  Identities=11%  Similarity=0.467  Sum_probs=30.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVW   64 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~   64 (307)
                      ..+|+..+-++.|.|+. |.|+.++|..+|+|.+||.
T Consensus       106 ~~Lp~~~r~v~~l~~~~-~~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209       106 SILPNKQKKIIYMKFFE-DMKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHhhc
Confidence            46778888888886654 7999999999999999985

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

>COG2522 Predicted transcriptional regulator [General function prediction only]

Probab=83.07  E-value=2.6  Score=32.50  Aligned_cols=27  Identities=19%  Similarity=0.298  Sum_probs=23.8

Q ss_pred             HhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          43 MATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        43 L~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      -.-|.|+..+|...|+|++.||+++..
T Consensus        19 ~eeG~Sq~~iA~LLGltqaAVS~Yls~   45 (119)
T COG2522          19 IEEGLSQYRIAKLLGLTQAAVSQYLSG   45 (119)
T ss_pred             HHcCCcHHHHHHHhCCCHHHHHHHHcc
Confidence            344999999999999999999999863

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=83.05  E-value=2.9  Score=39.61  Aligned_cols=50  Identities=16%  Similarity=0.317  Sum_probs=42.9

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+++.++-.+.|+|.   ..+.++.+||..+|+|+++|..+.++....|-..
T Consensus       349 ~~L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR~~  401 (415)
T PRK07598        349 ADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQP  401 (415)
T ss_pred             HhCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhch
Confidence            3688999999999986   3568999999999999999999999887776643

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=83.05  E-value=5.1  Score=36.66  Aligned_cols=65  Identities=15%  Similarity=0.227  Sum_probs=42.6

Q ss_pred             HHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH-HccccccccccccCCChHHHHHHHHHHHHhhCCCCccee
Q psy4300          41 SYMATQLSMRKIGDQFNLADSTVWSCIDSFLT-AMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGA  111 (307)
Q Consensus        41 ~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~-~l~~~l~~~~~i~~P~~~~~~~~~~~f~~~~~~p~~~g~  111 (307)
                      .|+-.|.++.+||..+|+|+.+|+|.+.+-.+ -|.+.     .|.-|. ...-++.+..++..+++.|+-+
T Consensus        21 lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I-----~i~~~~-~~~~~Le~~L~~~fgL~~a~VV   86 (321)
T COG2390          21 LYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKI-----SINSPV-EGCLELEQQLKERFGLKEAIVV   86 (321)
T ss_pred             HHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEE-----EeCCCC-cchHHHHHHHHHhcCCCeEEEE
Confidence            46688999999999999999999999987543 23333     233222 2223345555555577776543

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=83.02  E-value=1.7  Score=36.79  Aligned_cols=30  Identities=10%  Similarity=0.189  Sum_probs=26.5

Q ss_pred             HHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          40 LSYMATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        40 L~~L~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      ..++..|.|+..+|..+|||++|++|+++.
T Consensus       166 ~~~~~~g~s~~~iak~lgis~~Tv~r~~k~  195 (200)
T PRK13413        166 KKLLDKGTSKSEIARKLGVSRTTLARFLKT  195 (200)
T ss_pred             HHHHHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            445788999999999999999999999874

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=83.02  E-value=8  Score=29.13  Aligned_cols=45  Identities=13%  Similarity=0.228  Sum_probs=32.6

Q ss_pred             CCCHHHHHHH-HHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLV-ALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i-~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .+++.+-..+ .|.++   ..+.+..+|+..++++++|+++.+++....
T Consensus        22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~k   70 (109)
T TIGR01889        22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKK   70 (109)
T ss_pred             CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            4566554444 33322   245999999999999999999999987653

This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=82.67  E-value=2.7  Score=34.39  Aligned_cols=48  Identities=13%  Similarity=0.062  Sum_probs=37.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+|++++-++.|.++ .|.++.++|..+|+|.+||...+.+....+...
T Consensus       119 ~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~  166 (172)
T PRK09651        119 GLNGKTREAFLLSQL-DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLF  166 (172)
T ss_pred             hCCHHHhHHhhhhhc-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            566777766555555 478999999999999999998888877665543

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=82.66  E-value=4.9  Score=27.78  Aligned_cols=40  Identities=13%  Similarity=0.173  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHHHhcC-CcHHHHHhhhCC-ChhhHHHHHHHHH
Q psy4300          32 VEKKTLVALSYMATQ-LSMRKIGDQFNL-ADSTVWSCIDSFL   71 (307)
Q Consensus        32 ~~~~l~i~L~~L~~g-~~~~~l~~~fgv-s~stv~r~v~~~~   71 (307)
                      ...++.-++.+|..+ .+..++|..+|. |.+++++.+++..
T Consensus        35 ~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~   76 (84)
T smart00342       35 RDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLF   76 (84)
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence            355677788888776 899999999999 9999999998764

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=82.60  E-value=3.1  Score=35.00  Aligned_cols=50  Identities=10%  Similarity=0.134  Sum_probs=41.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|+..+-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..+
T Consensus       132 ~~Lp~~~r~v~~l~~~~-g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l  181 (196)
T PRK12535        132 DALPPERREALILTQVL-GYTYEEAAKIADVRVGTIRSRVARARADLIAAT  181 (196)
T ss_pred             HcCCHHHHHHhhhHHHh-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence            34677777777777665 688999999999999999999998888888774

>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=82.54  E-value=6.1  Score=24.37  Aligned_cols=25  Identities=24%  Similarity=0.393  Sum_probs=19.7

Q ss_pred             CCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300          46 QLSMRKIGDQFNLADSTVWSCIDSF   70 (307)
Q Consensus        46 g~~~~~l~~~fgvs~stv~r~v~~~   70 (307)
                      -.||.++|...|+|.+||.+=+.+.
T Consensus        17 r~s~~~la~~lglS~~~v~~Ri~rL   41 (42)
T PF13404_consen   17 RRSYAELAEELGLSESTVRRRIRRL   41 (42)
T ss_dssp             TS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             CccHHHHHHHHCcCHHHHHHHHHHh
Confidence            3789999999999999998877653

...

>PHA00738 putative HTH transcription regulator

Probab=82.46  E-value=2.2  Score=32.21  Aligned_cols=27  Identities=22%  Similarity=0.183  Sum_probs=24.1

Q ss_pred             CcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          47 LSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        47 ~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ++-.+|+..|++|+++||+.++-.-++
T Consensus        27 ~~V~eLae~l~lSQptVS~HLKvLreA   53 (108)
T PHA00738         27 LSASLISHTLLLSYTTVLRHLKILNEQ   53 (108)
T ss_pred             ccHHHHHHhhCCCHHHHHHHHHHHHHC
Confidence            788899999999999999999877655

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=82.42  E-value=3.7  Score=39.32  Aligned_cols=71  Identities=14%  Similarity=0.164  Sum_probs=54.1

Q ss_pred             HHHHHHHHhhhcCcccc---cCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300           6 FGFLVEALAAINGYETL---YERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ   76 (307)
Q Consensus         6 F~~L~~~l~~~~~~~~~---~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~   76 (307)
                      .+.|.+.+...++....   +.++...+...-+++|.|.+=-++.|+.++|..||.+.|||...++++-..+.+
T Consensus       344 ~~~I~~~V~~~~~i~~~~l~s~~R~~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~~~  417 (440)
T PRK14088        344 IDELIEIVAKVTGVSREEILSNSRNVKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSLLK  417 (440)
T ss_pred             HHHHHHHHHHHcCCcHHHHhCCCCCccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence            45555555555432111   122356788999999999999999999999999999999999999999887644

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=82.28  E-value=4.7  Score=30.13  Aligned_cols=37  Identities=22%  Similarity=0.323  Sum_probs=28.6

Q ss_pred             HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      +++..|.. ....++.+++..+|+|++|+.+.++++..
T Consensus         7 ~il~~L~~-~~~~~~~~la~~l~~s~~tv~~~l~~L~~   43 (108)
T smart00344        7 KILEELQK-DARISLAELAKKVGLSPSTVHNRVKRLEE   43 (108)
T ss_pred             HHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            33333333 33589999999999999999999998866

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

>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=81.86  E-value=4.6  Score=31.50  Aligned_cols=46  Identities=11%  Similarity=0.083  Sum_probs=33.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .+++|.+.+.-+.=.. ..|.+-.+++..+.||+++|++++.++-+.
T Consensus        15 GrPLp~~~R~rIvela-~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eT   60 (125)
T PF00292_consen   15 GRPLPNELRQRIVELA-KEGVRPCDISRQLRVSHGCVSKILSRYRET   60 (125)
T ss_dssp             TSSS-HHHHHHHHHHH-HTT--HHHHHHHHT--HHHHHHHHHHHHHH
T ss_pred             CccCcHHHHHHHHHHh-hhcCCHHHHHHHHccchhHHHHHHHHHHHh
Confidence            5788888888776333 469999999999999999999999998543

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.

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=81.83  E-value=3  Score=38.89  Aligned_cols=50  Identities=10%  Similarity=0.264  Sum_probs=42.4

Q ss_pred             CCCCHHHHHHHHHHHH-h--cCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYM-A--TQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L-~--~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..++..++..+.|+|. .  .+.++.+||..||||+..|+++-.+.+.-|-..
T Consensus       304 ~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~  356 (367)
T PRK09210        304 DTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP  356 (367)
T ss_pred             HhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhCh
Confidence            3689999999999985 3  458999999999999999999988877766554

>PRK05949 RNA polymerase sigma factor; Validated

Probab=81.74  E-value=3.3  Score=38.05  Aligned_cols=50  Identities=18%  Similarity=0.357  Sum_probs=42.5

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+++.++-.+.|+|.   ..+.++.++|..+|+|+++|..+..+.+.-|-..
T Consensus       265 ~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~  317 (327)
T PRK05949        265 AELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR  317 (327)
T ss_pred             HhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            3588999999999984   3569999999999999999999999887776553

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=81.70  E-value=2.6  Score=35.90  Aligned_cols=47  Identities=17%  Similarity=0.125  Sum_probs=40.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+++.|+  =+|.+++.|.+..++|...++|.+||...+.++..-+--.
T Consensus       137 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v~  183 (207)
T PRK15411        137 SLSRTES--SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTH  183 (207)
T ss_pred             cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCCC
Confidence            4777666  5678899999999999999999999999999887777655

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=81.55  E-value=4.5  Score=34.75  Aligned_cols=64  Identities=14%  Similarity=0.215  Sum_probs=46.0

Q ss_pred             CCCCHHHHHHHHHHHHhc--------------CCcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHH
Q psy4300          28 PFVPVEKKTLVALSYMAT--------------QLSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEES   92 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~--------------g~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~   92 (307)
                      ...+++++++-+|..|..              ..+..+||...|+++.|++|+++++-.. +.+.  ....|...+...+
T Consensus       152 ~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~--~~~~i~i~d~~~L  229 (235)
T PRK11161        152 SKKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQKSGMLAV--KGKYITIENNDAL  229 (235)
T ss_pred             hCCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe--cCCEEEEcCHHHH
Confidence            346899999999998752              2578899999999999999999877543 3333  4445555544443


Q ss_pred             H
Q psy4300          93 V   93 (307)
Q Consensus        93 ~   93 (307)
                      .
T Consensus       230 ~  230 (235)
T PRK11161        230 A  230 (235)
T ss_pred             H
Confidence            3

>smart00352 POU Found in Pit-Oct-Unc transcription factors

Probab=81.54  E-value=2  Score=30.21  Aligned_cols=28  Identities=7%  Similarity=0.171  Sum_probs=24.1

Q ss_pred             HHHhcCCcHHHHHhhhC------CChhhHHHHHH
Q psy4300          41 SYMATQLSMRKIGDQFN------LADSTVWSCID   68 (307)
Q Consensus        41 ~~L~~g~~~~~l~~~fg------vs~stv~r~v~   68 (307)
                      .+...|.++.++|...|      +|++||+|+-.
T Consensus        19 ~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es   52 (75)
T smart00352       19 RRIKLGFTQADVGLALGALYGPDFSQTTICRFEA   52 (75)
T ss_pred             HHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence            35677999999999999      59999999765

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=81.53  E-value=3.1  Score=35.86  Aligned_cols=46  Identities=20%  Similarity=0.152  Sum_probs=38.7

Q ss_pred             CCCCHHHHHHHHHHHHhc----------CCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMAT----------QLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~----------g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ...+++++|+-+|..+..          ..+..+||...|+++.|++|+++++.+.
T Consensus       151 ~~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~~  206 (230)
T PRK09391        151 GRKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQDR  206 (230)
T ss_pred             cCCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            346899999999998743          2567899999999999999999988654

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=81.52  E-value=5.2  Score=28.94  Aligned_cols=45  Identities=16%  Similarity=0.218  Sum_probs=34.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .++..+...+.+..-..+.+..+++..+++|++++++.++.+...
T Consensus         7 ~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~   51 (101)
T smart00347        7 GLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKK   51 (101)
T ss_pred             CCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence            455554444444444556899999999999999999999998775

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=81.39  E-value=5.7  Score=38.69  Aligned_cols=50  Identities=8%  Similarity=0.257  Sum_probs=43.8

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..++..++..+.++|.   ..+.++.+||..||||++.|+++-.+.+.-|-..
T Consensus       446 ~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~  498 (509)
T PRK05901        446 ETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHP  498 (509)
T ss_pred             hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            3699999999999995   4679999999999999999999998887776654

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=81.32  E-value=3.3  Score=34.51  Aligned_cols=43  Identities=12%  Similarity=0.110  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300          32 VEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ   76 (307)
Q Consensus        32 ~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~   76 (307)
                      ...+.+ .+.++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus       153 ~~~~~i-~~~~~-~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~  195 (198)
T TIGR02859       153 DLEWKV-LQSYL-DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK  195 (198)
T ss_pred             HHHHHH-HHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence            333443 34554 79999999999999999999888887766544

Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=81.30  E-value=3.8  Score=36.35  Aligned_cols=49  Identities=16%  Similarity=0.344  Sum_probs=40.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-++.|+|+ .|.++.++|..+|+|.+||.+.+.+....|-..
T Consensus       211 ~~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~  259 (268)
T PRK06288        211 KTLPEREKKVLILYYY-EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAK  259 (268)
T ss_pred             HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            3588888888888875 589999999999999999998888777666554

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=81.18  E-value=3.5  Score=37.84  Aligned_cols=51  Identities=8%  Similarity=0.111  Sum_probs=44.4

Q ss_pred             CCCCHHHHHHHHHHH-H--hcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSY-M--ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~-L--~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..++..++.++.++| |  -.|.++.++|..+|+|.+||..++.+....|-..|
T Consensus       261 ~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l  314 (325)
T PRK05657        261 FELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL  314 (325)
T ss_pred             HcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            468899999999887 4  46899999999999999999999999888887764

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=80.53  E-value=4.6  Score=33.63  Aligned_cols=49  Identities=14%  Similarity=0.139  Sum_probs=39.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+|...+-++.|.++ .|.++.++|..+|+|.+||...+.+....|...+
T Consensus       128 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l  176 (188)
T PRK12517        128 KLDPEYREPLLLQVI-GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL  176 (188)
T ss_pred             hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            456666665555544 5899999999999999999999998888777763

>PRK13870 transcriptional regulator TraR; Provisional

Probab=80.37  E-value=3  Score=36.32  Aligned_cols=48  Identities=13%  Similarity=0.180  Sum_probs=41.3

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|++|+  =+|.|.+.|.+..++|...|||++||...++....-|-..
T Consensus       172 ~~LT~RE~--E~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga~  219 (234)
T PRK13870        172 AWLDPKEA--TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVR  219 (234)
T ss_pred             CCCCHHHH--HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            45777665  4689999999999999999999999999999988777665

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

Probab=80.29  E-value=5.6  Score=30.40  Aligned_cols=47  Identities=9%  Similarity=0.201  Sum_probs=37.9

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ   76 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~   76 (307)
                      .++.+++ .....++.+..+..+++..+|||=+||..-+++++..|--
T Consensus        33 ~L~~E~~-~Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~   79 (113)
T PF09862_consen   33 RLSPEQL-EFIKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY   79 (113)
T ss_pred             cCCHHHH-HHHHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence            4555554 4555566667789999999999999999999999998876

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=80.19  E-value=5.2  Score=31.43  Aligned_cols=47  Identities=17%  Similarity=0.277  Sum_probs=39.4

Q ss_pred             CCCHHHHHHHHHHHHhc-CCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300          29 FVPVEKKTLVALSYMAT-QLSMRKIGDQFNLADSTVWSCIDSFLTAMS   75 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~-g~~~~~l~~~fgvs~stv~r~v~~~~~~l~   75 (307)
                      .+..+++-.+-|+|-+. +.+|..+|..+++|.+|+.++..+|-+.+.
T Consensus        81 ~l~de~k~Ii~lry~~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i~  128 (130)
T PF05263_consen   81 TLIDEEKRIIKLRYDRRSRRTWYQIAQKLHISERTARRWRDRFKNDIY  128 (130)
T ss_pred             hhCHHHHHHHHHHHcccccchHHHHHHHhCccHHHHHHHHHHHHHHhc
Confidence            45666777778888866 899999999999999999999998876554

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=80.16  E-value=6.5  Score=24.64  Aligned_cols=29  Identities=7%  Similarity=0.268  Sum_probs=25.0

Q ss_pred             cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          45 TQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        45 ~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .+.+..+++..|++|++|+++.+..+...
T Consensus        13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~   41 (53)
T smart00420       13 GKVSVEELAELLGVSEMTIRRDLNKLEEQ   41 (53)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            35789999999999999999999887553

---

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	307
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-06

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

 Score = 47.2 bits (111), Expect = 5e-06
 Identities = 53/348 (15%), Positives = 100/348 (28%), Gaps = 106/348 (30%)

Query: 4   TTFGFLVEALAAINGYE-TLYERGVPFVPVEKKTLVA---------LSYMATQ-----LS 48
           T F  + + L+A      +L    +   P E K+L+          L           LS
Sbjct: 272 TRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLS 331

Query: 49  MRKIG----------DQF-NLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIER 97
           +  I           D + ++    + + I+S L  +            P E       +
Sbjct: 332 I--IAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLE-----------PAE-----YRK 373

Query: 98  NFRALAKFPGVIGAIDGCHIE--------GKFSKDIRNDYNNRKCTQSMILQGVCTSNKL 149
            F  L+ FP         HI             K       N+    S++ +      + 
Sbjct: 374 MFDRLSVFP------PSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ---PKES 424

Query: 150 LTNIH-----VGCTGRN----HDAKVLSTSQIGRRIDAYGPTSLLYRDEY-------HL- 192
             +I      +     N    H   ++    I +  D+       Y D+Y       HL 
Sbjct: 425 TISIPSIYLELKVKLENEYALH-RSIVDHYNIPKTFDSDDL-IPPYLDQYFYSHIGHHLK 482

Query: 193 ---LGDSAYPLRTWCMVPYKNFGHMTEEEK-KYNTALSKTRVPIENVFGLIKGRWRRLKY 248
                +     R      + +F  +  E+K ++++        I N    +K  ++   Y
Sbjct: 483 NIEHPERMTLFRMV----FLDFRFL--EQKIRHDSTAWNASGSILNTLQQLK-FYK--PY 533

Query: 249 IDVGDPKRMAYI---------ISAACVLHNFCYLQDDVVEEIITHPIE 287
           I   DPK    +         I    +   +     D++   +    E
Sbjct: 534 ICDNDPKYERLVNAILDFLPKIEENLICSKYT----DLLRIALMAEDE 577

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	307
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	97.07
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	96.94
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	96.64
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	96.43
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	96.4
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	96.21
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	95.87
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	95.85
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	95.78
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	95.77
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	95.68
2jrt_A	95	Uncharacterized protein; solution, structure, NESG	95.25
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	95.22
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	95.06
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	95.0
1u78_A	141	TC3 transposase, transposable element TC3 transpos	94.96
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	94.92
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	94.89
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	94.88
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	94.76
2rn7_A	108	IS629 ORFA; helix, all alpha, unknown function, st	94.63
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	94.46
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	94.38
1j1v_A	94	Chromosomal replication initiator protein DNAA, 5'	94.15
3c57_A	95	Two component transcriptional regulatory protein;	93.96
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	93.85
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	93.66
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	93.54
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	92.89
2k27_A	159	Paired box protein PAX-8; paired domain, solution	92.86
3frw_A	107	Putative Trp repressor protein; structural genomic	92.79
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	92.7
3pvv_A	101	Chromosomal replication initiator protein DNAA; he	92.7
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	92.62
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	92.26
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	92.25
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	91.88
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	91.84
2l1p_A	83	DNA-binding protein SATB1; PSI-biology, NESG, stru	91.44
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	91.09
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	90.99
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	90.68
3hot_A	345	Transposable element mariner, complete CDS; protei	90.55
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	90.52
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	90.35
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	90.32
2cob_A	70	LCOR protein; MLR2, KIAA1795, helix-turn-helix, st	90.22
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	89.99
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	89.84
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	89.67
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	89.61
4dyq_A	140	Gene 1 protein; GP1, octamer, DNA-binding, viral p	89.53
1u78_A	141	TC3 transposase, transposable element TC3 transpos	89.28
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	88.97
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	88.93
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	88.91
3bja_A	139	Transcriptional regulator, MARR family, putative;	88.66
2pij_A	67	Prophage PFL 6 CRO; transcription factor, helix-tu	88.61
3mky_B	189	Protein SOPB; partition, F plasmid, centromere, DN	88.56
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	88.21
1y0u_A	96	Arsenical resistance operon repressor, putative; s	88.2
1sfx_A	109	Conserved hypothetical protein AF2008; structural	88.12
2oa4_A	101	SIR5; structure, structural genomics, PSI-2, prote	88.08
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	88.05
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	87.98
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	87.84
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	87.75
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	87.65
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	87.48
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	87.48
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	87.45
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	87.31
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	87.27
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	87.27
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	87.12
3r0a_A	123	Putative transcriptional regulator; structural gen	86.95
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	86.89
2nnn_A	140	Probable transcriptional regulator; structural gen	86.6
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	86.51
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	86.46
2gxg_A	146	146AA long hypothetical transcriptional regulator;	86.31
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	86.21
2eth_A	154	Transcriptional regulator, putative, MAR family; M	86.17
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	86.01
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	85.97
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	85.79
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	85.77
2pex_A	153	Transcriptional regulator OHRR; transcription regu	85.76
1ku9_A	152	Hypothetical protein MJ223; putative transcription	85.75
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	85.7
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	85.65
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	85.6
1z91_A	147	Organic hydroperoxide resistance transcriptional;	85.58
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	85.38
1r71_A	178	Transcriptional repressor protein KORB; INCP, plas	85.21
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	85.16
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	85.04
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	84.95
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	84.84
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	84.81
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	84.61
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	84.5
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	84.42
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	84.4
2pg4_A	95	Uncharacterized protein; structural genomics, join	84.29
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	84.22
3b02_A	195	Transcriptional regulator, CRP family; structural	84.12
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	84.11
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	84.11
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	84.05
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	83.99
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	83.91
2ao9_A	155	Phage protein; structural genomics, nine-fold NCS.	83.87
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	83.83
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	83.77
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	83.73
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	83.71
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	83.62
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	83.62
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	83.49
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	83.32
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	83.28
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	83.25
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	83.24
1rzs_A	61	Antirepressor, regulatory protein CRO; helix-turn-	83.2
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	83.17
2q0o_A	236	Probable transcriptional activator protein TRAR; h	83.1
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	83.05
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	83.02
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	82.88
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	82.87
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	82.86
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	82.85
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	82.81
2w25_A	150	Probable transcriptional regulatory protein; trans	82.62
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	82.61
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	82.61
3s2w_A	159	Transcriptional regulator, MARR family; structural	82.59
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	82.44
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	82.44
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	82.34
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	82.18
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	82.1
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	82.09
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	81.91
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	81.88
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	81.83
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	81.75
1p6r_A	82	Penicillinase repressor; transcription regulation,	81.67
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	81.67
4ghj_A	101	Probable transcriptional regulator; structural gen	81.66
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	81.58
2hin_A	71	GP39, repressor protein; transcription factor, dim	81.58
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	81.55
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	81.26
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	81.21
2kko_A	108	Possible transcriptional regulatory protein (possi	81.2
2ovg_A	66	Phage lambda CRO; transcription factor, helix-turn	81.18
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	81.04
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	80.98
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	80.82
3f3x_A	144	Transcriptional regulator, MARR family, putative;	80.81
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	80.8
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	80.73
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	80.69
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	80.68
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	80.68
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	80.61
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	80.56
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	80.5
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	80.43
1okr_A	123	MECI, methicillin resistance regulatory protein ME	80.38
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	80.36
3jth_A	98	Transcription activator HLYU; transcription factor	80.3
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	80.3
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	80.23
1gdt_A	183	GD resolvase, protein (gamma delta resolvase); pro	80.16
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	80.04

>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=97.07  E-value=0.0015  Score=40.66  Aligned_cols=42  Identities=2%  Similarity=0.097  Sum_probs=34.4

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      ...++.+++..+... +..|.++.++|..+|||.+||++++.+
T Consensus         3 ~~~l~~~~~~~i~~~-~~~g~s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            3 GSALSDTERAQLDVM-KLLNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             SCCCCHHHHHHHHHH-HHTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            356888877666554 468999999999999999999998864

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

Probab=96.94  E-value=0.0017  Score=42.67  Aligned_cols=43  Identities=12%  Similarity=0.094  Sum_probs=38.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCc----HHHHHhhhCCChhhHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLS----MRKIGDQFNLADSTVWSCIDSF   70 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~----~~~l~~~fgvs~stv~r~v~~~   70 (307)
                      +...|++.++-+ +.++..|.+    ..++|..||||.+|+++|+...
T Consensus         3 r~~ys~efK~~~-~~~~~~g~s~~~~~~~vA~~~gIs~~tl~~W~~~~   49 (59)
T 2glo_A            3 RRIFTPHFKLQV-LESYRNDNDCKGNQRATARKYNIHRRQIQKWLQCE   49 (59)
T ss_dssp             CCCCCHHHHHHH-HHHHHHCTTTTTCHHHHHHHTTSCHHHHHHHHTTH
T ss_pred             CCcCCHHHHHHH-HHHHHcCCCcchHHHHHHHHHCcCHHHHHHHHHHH
Confidence            567899999998 788888989    9999999999999999998754

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=96.64  E-value=0.0037  Score=45.84  Aligned_cols=59  Identities=12%  Similarity=0.184  Sum_probs=47.3

Q ss_pred             CCHHHHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300           1 MRKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMS   75 (307)
Q Consensus         1 ms~~~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~   75 (307)
                      ||.++|+.+...+               .++ +..+-++=.||-.|.++.++|..+|+|+++|+|.+.+..+...
T Consensus         5 mT~~eFe~~~~~l---------------~~~-~~~~~~A~lyYv~g~tQ~eIA~~lGiSR~~VsrlL~~Ar~~~~   63 (101)
T 2w7n_A            5 LTESQFQEAIQGL---------------EVG-QQTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVHRVWAAFE   63 (101)
T ss_dssp             CCHHHHHHHHTTC---------------CCC-HHHHHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHccC---------------ChH-HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            7889999887554               121 2346667778899999999999999999999999999877753

>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=96.43  E-value=0.0036  Score=45.84  Aligned_cols=48  Identities=10%  Similarity=0.171  Sum_probs=39.0

Q ss_pred             CCCHHHHHHHHHHH-----HhcC-CcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSY-----MATQ-LSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~-----L~~g-~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      -+++.++-.+.++|     |..| .+|++||...|+|.|||+|+ .+.+.-+...
T Consensus        35 lLT~~Er~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L~~l~~~   88 (101)
T 1jhg_A           35 MLTPDEREALGTRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSLKAAPVE   88 (101)
T ss_dssp             HSCHHHHHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHHHHSCHH
T ss_pred             hCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHHHHccHH
Confidence            57888887777775     3467 99999999999999999999 7776665554

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

Probab=96.40  E-value=0.0057  Score=44.33  Aligned_cols=45  Identities=16%  Similarity=0.124  Sum_probs=39.7

Q ss_pred             CCCCCHHHHHHHHHHHHhc-CCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMAT-QLSMRKIGDQFNLADSTVWSCIDSFL   71 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~-g~~~~~l~~~fgvs~stv~r~v~~~~   71 (307)
                      ++.+|.+.++.++-.++.. |.+..++|..||||.+|+++|+.+.-
T Consensus         3 r~~ys~e~k~~~v~~~~~~~g~s~~~ia~~~gIs~~tl~rW~~~~~   48 (97)
T 2jn6_A            3 TKTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKYG   48 (97)
T ss_dssp             CCCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHHC
T ss_pred             CCCCCHHHHHHHHHHHHHcCCChHHHHHHHHCcCHHHHHHHHHHHh
Confidence            3578899999888888877 99999999999999999999998764

>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=96.21  E-value=0.015  Score=39.07  Aligned_cols=51  Identities=12%  Similarity=0.362  Sum_probs=45.5

Q ss_pred             CCCCHHHHHHHHHHH-H--hcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSY-M--ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~-L--~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|+.++-.+.|+| |  ..|.++.++|..+|+|.+||...+.+....|-..+
T Consensus         4 ~~L~~~er~il~l~~~l~~~~g~s~~eIA~~lgis~~tV~~~~~ra~~kLr~~~   57 (68)
T 2p7v_B            4 AGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPS   57 (68)
T ss_dssp             CCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSCC
T ss_pred             HcCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            368999999999988 3  57999999999999999999999999998888774

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=95.87  E-value=0.018  Score=40.87  Aligned_cols=45  Identities=9%  Similarity=-0.001  Sum_probs=36.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      +..++.+.+..+.-.+ ..|.+..++|..||||++|+++|+.+.-.
T Consensus        20 ~~~ys~e~k~~~v~~~-~~g~s~~~iA~~~gIs~sTl~rW~k~~~~   64 (87)
T 2elh_A           20 LRSLTPRDKIHAIQRI-HDGESKASVARDIGVPESTLRGWCKNEDK   64 (87)
T ss_dssp             CSSCCHHHHHHHHHHH-HHTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHH-HCCCCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            4578888877666555 67899999999999999999999876543

>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=95.85  E-value=0.0072  Score=37.79  Aligned_cols=40  Identities=8%  Similarity=0.105  Sum_probs=29.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      .++.++. ..++..+..|.+..++|..+|||++|+++++.+
T Consensus         5 ~~~~~~~-~~i~~l~~~g~s~~~ia~~lgvs~~Tv~r~l~~   44 (52)
T 1jko_C            5 AINKHEQ-EQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPA   44 (52)
T ss_dssp             SSCTTHH-HHHHHHHHTTCCHHHHHHTTSCCHHHHHHHSCT
T ss_pred             CCCHHHH-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4444433 333444678899999999999999999998753

>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=95.78  E-value=0.025  Score=38.51  Aligned_cols=50  Identities=6%  Similarity=0.169  Sum_probs=44.4

Q ss_pred             CCCCHHHHHHHHHHHH-h--cCCcHHHHHhhhCCChhhHHHHHHHHHHHcc-cc
Q psy4300          28 PFVPVEKKTLVALSYM-A--TQLSMRKIGDQFNLADSTVWSCIDSFLTAMS-QP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L-~--~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~-~~   77 (307)
                      ..+|+.++-.+.|+|+ .  .|.++.++|..+|+|.+||.....+....|- ..
T Consensus         9 ~~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~~   62 (73)
T 1ku3_A            9 SKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHE   62 (73)
T ss_dssp             TTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHTT
T ss_pred             HhCCHHHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhH
Confidence            4689999999999885 3  7899999999999999999999999988887 55

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

Probab=95.77  E-value=0.023  Score=40.23  Aligned_cols=51  Identities=12%  Similarity=0.264  Sum_probs=45.6

Q ss_pred             CCCCHHHHHHHHHHHH-h--cCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYM-A--TQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L-~--~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|+.++-.+.|+|+ .  .|.|+.++|..+|+|.+||...+.+....|-..+
T Consensus        17 ~~L~~~er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~kLr~~l   70 (87)
T 1tty_A           17 KTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHPS   70 (87)
T ss_dssp             TTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTTB
T ss_pred             HhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence            4689999999999984 4  7899999999999999999999999998888774

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

Probab=95.68  E-value=0.031  Score=37.35  Aligned_cols=50  Identities=12%  Similarity=0.082  Sum_probs=41.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|+.++-.+.|+|+ .|.++.++|..+|+|.+||.+.+.+....|-..+
T Consensus        14 ~~L~~~~r~il~l~~~-~g~s~~eIA~~lgis~~tv~~~~~ra~~~l~~~l   63 (70)
T 2o8x_A           14 ADLTTDQREALLLTQL-LGLSYADAAAVCGCPVGTIRSRVARARDALLADA   63 (70)
T ss_dssp             TSSCHHHHHHHHHHHT-SCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHC--
T ss_pred             HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence            3588888888877764 6899999999999999999999999988887764

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

Probab=95.25  E-value=0.047  Score=39.50  Aligned_cols=51  Identities=10%  Similarity=0.070  Sum_probs=44.8

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ....+.+.++.+++.++..+.+..++|..|+||.+++.+|...+...-...
T Consensus        30 ~rrWs~~~Kl~VV~~~~~g~~s~~e~arry~Is~s~i~~W~r~~~~~G~~~   80 (95)
T 2jrt_A           30 TRRWVASRKAAVVKAVIHGLITEREALDRYSLSEEEFALWRSAVAAHGEKA   80 (95)
T ss_dssp             CCCCCHHHHHHHHHHHHTTSSCHHHHHHHTTCCHHHHHHHHHHTTTCCTTS
T ss_pred             hhccCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhHHH
Confidence            567999999999999999999999999999999999999988875444444

>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=95.22  E-value=0.079  Score=38.58  Aligned_cols=51  Identities=12%  Similarity=0.323  Sum_probs=45.0

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|+.++-.+.|+|.   ..|.++.++|..+|+|.+||.....+.+..|-..+
T Consensus        18 ~~Lp~reR~Vi~Lry~l~~~e~~s~~EIA~~lgiS~~tVr~~~~rAlkkLR~~~   71 (99)
T 3t72_q           18 AGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPS   71 (99)
T ss_pred             HcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            3689999999999986   37899999999999999999999999888887763

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

Probab=95.06  E-value=0.051  Score=38.79  Aligned_cols=49  Identities=20%  Similarity=0.294  Sum_probs=41.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..++..++-++.|+|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus        36 ~~L~~~~r~vl~l~~~-~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~   84 (92)
T 3hug_A           36 AQLSAEHRAVIQRSYY-RGWSTAQIATDLGIAEGTVKSRLHYAVRALRLT   84 (92)
T ss_dssp             HTSCHHHHHHHHHHHT-SCCCHHHHHHHHTSCHHHHHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            3578888888888775 689999999999999999999999887777655

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

Probab=95.00  E-value=0.088  Score=38.31  Aligned_cols=64  Identities=17%  Similarity=0.171  Sum_probs=49.3

Q ss_pred             HHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300           5 TFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus         5 ~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ....+++.|.+.    +   .....++..++-.+.|  +..|.++.++|..+|+|.+||...+.+...-|-..
T Consensus        17 ~~~~~l~~l~~~----~---~~~~~Lt~re~~Vl~l--~~~G~s~~EIA~~L~iS~~TV~~~l~ri~~KLgv~   80 (99)
T 1p4w_A           17 SVAKLLEKISAG----G---YGDKRLSPKESEVLRL--FAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVD   80 (99)
T ss_dssp             HHHHHHHHHHCC----C---CSSSSCCHHHHHHHHH--HHHTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCS
T ss_pred             hhHHHHHHHccC----C---cccCCCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            445666666554    1   1146799988877666  45899999999999999999999999887777655

>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=94.96  E-value=0.034  Score=42.68  Aligned_cols=44  Identities=2%  Similarity=0.072  Sum_probs=37.0

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFL   71 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~   71 (307)
                      ...++.+++..+...+ ..|.+..++|..+|+|.+||++++.+..
T Consensus         4 ~~~~s~~~r~~i~~~~-~~G~s~~~ia~~lgis~~Tv~r~~~~~~   47 (141)
T 1u78_A            4 GSALSDTERAQLDVMK-LLNVSLHEMSRKISRSRHCIRVYLKDPV   47 (141)
T ss_dssp             SCCCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHSGG
T ss_pred             cccCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHccc
Confidence            4678888887766654 7899999999999999999999998753

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

Probab=94.92  E-value=0.072  Score=35.92  Aligned_cols=49  Identities=12%  Similarity=0.325  Sum_probs=42.0

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ...++..++-.+.+  +..|.++.++|..+|+|.+||+..+.+....+...
T Consensus         9 ~~~L~~~e~~il~~--~~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~   57 (74)
T 1fse_A            9 KPLLTKREREVFEL--LVQDKTTKEIASELFISEKTVRNHISNAMQKLGVK   57 (74)
T ss_dssp             CCCCCHHHHHHHHH--HTTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCS
T ss_pred             CCCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence            46788888877777  38899999999999999999999999988777655

>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=94.89  E-value=0.052  Score=40.62  Aligned_cols=45  Identities=11%  Similarity=0.087  Sum_probs=38.4

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ...++.+.+..+...+ ..|.+..++|..||+|.+||++++.+...
T Consensus        15 ~~~~s~~~r~~i~~~~-~~g~s~~~ia~~lgis~~Tv~~w~~~~~~   59 (128)
T 1pdn_C           15 GRPLPNNIRLKIVEMA-ADGIRPCVISRQLRVSHGCVSKILNRYQE   59 (128)
T ss_dssp             TSCCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            3478898888776655 58999999999999999999999998754

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

Probab=94.88  E-value=0.044  Score=34.88  Aligned_cols=36  Identities=6%  Similarity=0.170  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          32 VEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        32 ~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      ++..-.+... +..|.++.++|..+|+|++||++++.
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            4444333333 57899999999999999999999875

>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=94.76  E-value=0.056  Score=42.15  Aligned_cols=46  Identities=9%  Similarity=0.052  Sum_probs=39.6

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ...++.+.+..+...+ ..|.+..++|..||+|.+||++++.++...
T Consensus        30 ~~~~s~e~r~~iv~~~-~~G~s~~~iA~~lgis~~TV~rw~~~~~~~   75 (149)
T 1k78_A           30 GRPLPDVVRQRIVELA-HQGVRPCDISRQLRVSHGCVSKILGRYYET   75 (149)
T ss_dssp             TSCCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence            3578999988887766 579999999999999999999999987653

>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri}

Probab=94.63  E-value=0.035  Score=40.89  Aligned_cols=44  Identities=9%  Similarity=0.062  Sum_probs=38.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcC-------CcHHHHHhhhCCChhhHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQ-------LSMRKIGDQFNLADSTVWSCIDSF   70 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g-------~~~~~l~~~fgvs~stv~r~v~~~   70 (307)
                      +..+|.+.++.++..++..|       .+..++|..||||.+|+++|+...
T Consensus         4 ~~~ys~e~K~~~v~~~~~~~~~~~s~g~s~~~va~~~gIs~~tl~~W~~~~   54 (108)
T 2rn7_A            4 NTRFSPEVRQRAVRMVLESQGEYDSQWATICSIAPKIGCTPETLRVWVRQH   54 (108)
T ss_dssp             SCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhcccccccccccHHHHHHHHCcCHHHHHHHHHHH
Confidence            45789999999888888765       799999999999999999998875

>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=94.46  E-value=0.086  Score=36.76  Aligned_cols=48  Identities=19%  Similarity=0.297  Sum_probs=42.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..++..++-.+.| + ..|.++.++|..+|+|.+||...+.+....|-..
T Consensus        20 ~~Lt~~e~~vl~l-~-~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~   67 (82)
T 1je8_A           20 NQLTPRERDILKL-I-AQGLPNKMIARRLDITESTVKVHVKHMLKKMKLK   67 (82)
T ss_dssp             GGSCHHHHHHHHH-H-TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCS
T ss_pred             ccCCHHHHHHHHH-H-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCC
Confidence            5688988888877 3 7899999999999999999999999988877665

>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=94.38  E-value=0.065  Score=40.75  Aligned_cols=47  Identities=13%  Similarity=0.114  Sum_probs=39.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHH-HHHhhhCCChhhHHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMR-KIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~-~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      +..++.+.++-+.-.+..+|.+.. ++|..||||++|++++++.--..
T Consensus         5 r~~~t~e~K~~iv~~~~~~g~~~~~~~A~~~gvs~stl~~~~~~~~~~   52 (131)
T 1hlv_A            5 RRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAI   52 (131)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTHHHH
T ss_pred             ceeCCHHHHHHHHHHHHHCCCCcHHHHHHHhCCCHHHHHHHHhchhhh
Confidence            568999999998887767776665 99999999999999999975543

>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=94.15  E-value=0.071  Score=38.46  Aligned_cols=70  Identities=19%  Similarity=0.173  Sum_probs=52.5

Q ss_pred             HHHHHHHhhhcCcccc---cCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhh-CCChhhHHHHHHHHHHHccc
Q psy4300           7 GFLVEALAAINGYETL---YERGVPFVPVEKKTLVALSYMATQLSMRKIGDQF-NLADSTVWSCIDSFLTAMSQ   76 (307)
Q Consensus         7 ~~L~~~l~~~~~~~~~---~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~f-gvs~stv~r~v~~~~~~l~~   76 (307)
                      +.|.+.+...++.-..   +..+...+...-+++|.|.+--++.|+.++|..| |.+.|||...++++-..+..
T Consensus         4 ~~I~~~Va~~f~i~~~dl~s~~R~~~i~~aRqiamyL~r~~t~~Sl~~IG~~fggrdHsTV~ha~~ki~~~~~~   77 (94)
T 1j1v_A            4 DNIQKTVAEYYKIKVADLLSKRRSRSVARPRQMAMALAKELTNHSLPEIGDAFGGRDHTTVLHACRKIEQLREE   77 (94)
T ss_dssp             HHHHHHHHHHTTCCHHHHHSCCCCHHHHHHHHHHHHHHHHHSCCCHHHHHHHTTSCCHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHhCCCCCchhHHHHHHHHHHHHHHHCcCHHHHHHHhCCCCHHHHHHHHHHHHHHHHh
Confidence            4455555555432111   1223457888899999999999999999999999 89999999999998887654

>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=93.96  E-value=0.13  Score=36.93  Aligned_cols=48  Identities=23%  Similarity=0.352  Sum_probs=42.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..++..++-++.|.  ..|.++.++|..+|+|.+||...+.+...-|-..
T Consensus        26 ~~Lt~~e~~vl~l~--~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~   73 (95)
T 3c57_A           26 SGLTDQERTLLGLL--SEGLTNKQIADRMFLAEKTVKNYVSRLLAKLGME   73 (95)
T ss_dssp             -CCCHHHHHHHHHH--HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCC
T ss_pred             hcCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCC
Confidence            56899998888884  8899999999999999999999999998888766

>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=93.85  E-value=0.14  Score=38.21  Aligned_cols=49  Identities=16%  Similarity=0.339  Sum_probs=41.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+|+.++-++.|+|+ .|.++.++|..+|+|.+||.+.+.+....|-..+
T Consensus        22 ~L~~~~r~vl~l~y~-~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l   70 (113)
T 1s7o_A           22 LLTDKQMNYIELYYA-DDYSLAEIADEFGVSRQAVYDNIKRTEKILETYE   70 (113)
T ss_dssp             GSCHHHHHHHHHHHH-TCCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            477888877776665 6899999999999999999999999988887764

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

Probab=93.66  E-value=0.093  Score=33.98  Aligned_cols=35  Identities=9%  Similarity=0.130  Sum_probs=31.2

Q ss_pred             HhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          43 MATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        43 L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      +..|.++.++|..+|+|.+||...+.+...-+-..
T Consensus        10 ~~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~   44 (61)
T 2jpc_A           10 IDEGYTNHGISEKLHISIKTVETHRMNMMRKLQVH   44 (61)
T ss_dssp             HHTSCCSHHHHHHTCSCHHHHHHHHHHHHHHHTCS
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHCCC
Confidence            68899999999999999999999999887766554

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

Probab=93.54  E-value=0.14  Score=35.03  Aligned_cols=46  Identities=11%  Similarity=0.188  Sum_probs=38.6

Q ss_pred             CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      +++.++-.+.| + ..|.++.++|..+|+|.+||...+.+...-+-..
T Consensus        17 L~~~e~~vl~l-~-~~g~s~~eIA~~l~is~~tV~~~~~r~~~kl~~~   62 (79)
T 1x3u_A           17 LSERERQVLSA-V-VAGLPNKSIAYDLDISPRTVEVHRANVMAKMKAK   62 (79)
T ss_dssp             HCHHHHHHHHH-H-TTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTTCC
T ss_pred             CCHHHHHHHHH-H-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCC
Confidence            56667766666 3 7899999999999999999999999988777654

>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=92.89  E-value=0.28  Score=34.81  Aligned_cols=49  Identities=8%  Similarity=0.165  Sum_probs=39.8

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ...++..++-.+.|.  ..|.++.++|..+|+|.+||...+.+...-+--.
T Consensus        27 ~~~Lt~rE~~Vl~l~--~~G~s~~eIA~~L~iS~~TV~~~~~~i~~Klgv~   75 (90)
T 3ulq_B           27 QDVLTPRECLILQEV--EKGFTNQEIADALHLSKRSIEYSLTSIFNKLNVG   75 (90)
T ss_dssp             --CCCHHHHHHHHHH--HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCS
T ss_pred             ccCCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            567888888766664  4999999999999999999999999987776554

>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=92.86  E-value=0.14  Score=40.28  Aligned_cols=43  Identities=9%  Similarity=0.050  Sum_probs=36.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSF   70 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~   70 (307)
                      ...++.+.+..+...+ ..|.+..++|..||+|++||++++++.
T Consensus        23 ~~~~s~e~r~~ii~l~-~~G~s~~~IA~~lgis~~TV~rwl~r~   65 (159)
T 2k27_A           23 GRPLPEVVRQRIVDLA-HQGVRPCDISRQLRVSHGCVSKILGRY   65 (159)
T ss_dssp             SCSSCHHHHHHHHHHH-HHTCCHHHHHHHHTCCSHHHHHHHCCS
T ss_pred             CCCCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            3578898888776655 689999999999999999999999865

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

Probab=92.79  E-value=0.13  Score=37.74  Aligned_cols=30  Identities=10%  Similarity=0.149  Sum_probs=25.9

Q ss_pred             HHHhcCCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300          41 SYMATQLSMRKIGDQFNLADSTVWSCIDSF   70 (307)
Q Consensus        41 ~~L~~g~~~~~l~~~fgvs~stv~r~v~~~   70 (307)
                      .+|..|.+|++++...|+|.+||+|+-+..
T Consensus        53 ~lL~~G~SyreIa~~tG~StaTIsRv~r~L   82 (107)
T 3frw_A           53 KMLTDKRTYLDISEKTGASTATISRVNRSL   82 (107)
T ss_dssp             HHHHTTCCHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             HHHHcCCCHHHHHHHHCccHHHHHHHHHHH
Confidence            358999999999999999999999965543

>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=92.70  E-value=0.23  Score=36.97  Aligned_cols=49  Identities=18%  Similarity=0.346  Sum_probs=41.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      .+|+.++-++.|+| ..|.++.++|..+|+|.+||...+.+....|-..+
T Consensus        25 ~L~~~~r~vl~l~~-~~g~s~~EIA~~lgiS~~tV~~~l~ra~~kLr~~l   73 (113)
T 1xsv_A           25 LLTNKQRNYLELFY-LEDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDYE   73 (113)
T ss_dssp             GSCHHHHHHHHHHH-TSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            47788887777765 46899999999999999999999999988887764

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

Probab=92.70  E-value=0.17  Score=36.99  Aligned_cols=72  Identities=19%  Similarity=0.166  Sum_probs=54.6

Q ss_pred             HHHHHHHHhhhcCccccc---CCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300           6 FGFLVEALAAINGYETLY---ERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus         6 F~~L~~~l~~~~~~~~~~---~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+.|.+.+...++.-...   ..+...+...-|++|.|.+=-++.|+.++|..||...|||...++++-..+.+-
T Consensus         7 ~~~I~~~Va~~f~v~~~dl~s~~R~~~i~~aRqiAmYL~r~~t~~Sl~~IG~~fgRDHsTV~ha~~ki~~~~~~d   81 (101)
T 3pvv_A            7 AATIMAATAEYFDTTVEELRGPGKTRALAQSRQIAMYLCRELTDLSLPKIGQAFGRDHTTVMYAQRKILSEMAER   81 (101)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHSSCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHCCCHHHHhCCCCCchhhHHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhC
Confidence            456666666654332111   122456778889999999988999999999999999999999999998877664

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

Probab=92.62  E-value=0.14  Score=36.32  Aligned_cols=48  Identities=15%  Similarity=0.229  Sum_probs=41.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..++..++-.+.|  +..|.++.++|..+|+|.+||...+.+....|-..
T Consensus        28 ~~Lt~~e~~vl~l--~~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~   75 (91)
T 2rnj_A           28 EMLTEREMEILLL--IAKGYSNQEIASASHITIKTVKTHVSNILSKLEVQ   75 (91)
T ss_dssp             GGCCSHHHHHHHH--HHTTCCTTHHHHHHTCCHHHHHHHHHHHHHHTTCC
T ss_pred             hcCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence            4578888877777  37899999999999999999999999988777665

>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=92.26  E-value=0.096  Score=40.83  Aligned_cols=51  Identities=8%  Similarity=0.184  Sum_probs=42.7

Q ss_pred             CCCCCCHHHHHHHHHHH--HhcCCcHHHHHh----hh--CCChhhHHHHHHHHHHHccc
Q psy4300          26 GVPFVPVEKKTLVALSY--MATQLSMRKIGD----QF--NLADSTVWSCIDSFLTAMSQ   76 (307)
Q Consensus        26 ~~~~~~~~~~l~i~L~~--L~~g~~~~~l~~----~f--gvs~stv~r~v~~~~~~l~~   76 (307)
                      .+..++.++++.+..++  -..+.+..+||.    .|  +||+|||+++++.=-..+..
T Consensus         8 ~R~~lT~~qK~~i~~~~~~~~~~~~q~~la~wa~~~f~~~is~stis~ilk~k~~~l~~   66 (144)
T 1iuf_A            8 KRRAITEHEKRALRHYFFQLQNRSGQQDLIEWFREKFGKDISQPSVSQILSSKYSYLDN   66 (144)
T ss_dssp             SSSCCCSHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHSSCCSSSSTTHHHHHHHHHTTT
T ss_pred             cCccCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCCCCcHHHHHHHHhhHHHHhhh
Confidence            36889999999999998  345689999999    99  99999999999986555433

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=92.25  E-value=0.32  Score=39.82  Aligned_cols=42  Identities=12%  Similarity=0.138  Sum_probs=35.3

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      ...+..+.=.-..+++..|.++.++|..+|||+++|+|.+..
T Consensus         6 ke~sl~eiG~ria~~y~~g~tQ~eIA~~lGiSr~~VSR~L~~   47 (192)
T 1zx4_A            6 LQHSIREIGLRLMRMKNDGMSQKDIAAKEGLSQAKVTRALQA   47 (192)
T ss_dssp             CSSCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             ccccHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHH
Confidence            456676666666677889999999999999999999998875

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

Probab=91.88  E-value=0.25  Score=36.98  Aligned_cols=37  Identities=11%  Similarity=0.143  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          32 VEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        32 ~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      ..++ .-++..|..|.+|++|+...|+|.+||+|+-+.
T Consensus        62 Ls~R-~eV~klL~~G~syreIA~~~g~S~aTIsRv~r~   98 (119)
T 3kor_A           62 LSQR-LQVAKMIKQGYTYATIEQESGASTATISRVKRS   98 (119)
T ss_dssp             HHHH-HHHHHHHHHTCCHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHH-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            3344 455677899999999999999999999995543

>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=91.84  E-value=0.3  Score=40.62  Aligned_cols=49  Identities=14%  Similarity=0.223  Sum_probs=43.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-++.|+|+ .|.++.++|..+|+|.+||.+.+.+....|-..
T Consensus       186 ~~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~~V~~~~~ra~~~Lr~~  234 (239)
T 1rp3_A          186 SKLPEREKLVIQLIFY-EELPAKEVAKILETSVSRVSQLKAKALERLREM  234 (239)
T ss_dssp             TTSCHHHHHHHHHHHT-SCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence            5689999999999886 589999999999999999999999888777655

>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=91.44  E-value=0.27  Score=34.06  Aligned_cols=35  Identities=17%  Similarity=0.234  Sum_probs=27.8

Q ss_pred             HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      .+-.-|..+..|.++.+||...|||++|++.+++.
T Consensus        21 ~~~~kLK~il~GikQ~eLAK~iGIsqsTLSaIenG   55 (83)
T 2l1p_A           21 TVRNALKDLLKDMNQSSLAKECPLSQSMISSIVNS   55 (83)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHSSSCHHHHHHHHTC
T ss_pred             HHHHHHHHHHHhcCHHHHHHHcCCCHHHHHHHHcC
Confidence            34445555555999999999999999999988763

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=91.09  E-value=0.89  Score=34.53  Aligned_cols=45  Identities=13%  Similarity=0.233  Sum_probs=33.8

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ...+++.+...+...+ .++.+..+||..+|++++|+++.+++...
T Consensus        33 ~~~lt~~~~~iL~~l~-~~~~t~~eLa~~l~~s~~tvs~~l~~L~~   77 (146)
T 3tgn_A           33 EVALTNTQEHILMLLS-EESLTNSELARRLNVSQAAVTKAIKSLVK   77 (146)
T ss_dssp             SSCCCHHHHHHHHHHT-TCCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             ccCCCHHHHHHHHHHH-hCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3467776654444333 34499999999999999999999998764

>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A

Probab=90.99  E-value=0.33  Score=39.03  Aligned_cols=48  Identities=21%  Similarity=0.191  Sum_probs=40.8

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+|+.++-++.|+|+ .|.|+.++|..+|+|.+||...+.+....|-..
T Consensus       140 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~  187 (194)
T 1or7_A          140 SLPEDLRMAITLREL-DGLSYEEIAAIMDCPVGTVRSRIFRAREAIDNK  187 (194)
T ss_dssp             HSCHHHHHHHHHHHT-TCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHhHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            467777777777776 589999999999999999999999988877666

>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=90.68  E-value=0.51  Score=33.88  Aligned_cols=30  Identities=17%  Similarity=0.389  Sum_probs=26.7

Q ss_pred             hcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          44 ATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+.+..+|+..+|+|++|+++.++.....
T Consensus        34 ~~~~t~~ela~~l~is~~tv~~~l~~L~~~   63 (109)
T 2d1h_A           34 EKPITSEELADIFKLSKTTVENSLKKLIEL   63 (109)
T ss_dssp             CSCEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            567899999999999999999999988654

>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=90.55  E-value=8.4  Score=33.73  Aligned_cols=149  Identities=9%  Similarity=-0.041  Sum_probs=77.8

Q ss_pred             CCHHHHHHHHHHHhhhc-Cc-ccccCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300           1 MRKTTFGFLVEALAAIN-GY-ETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus         1 ms~~~F~~L~~~l~~~~-~~-~~~~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ++++|+.+.+...+.-. .. ...+.++...++. +++.- +.--....+.+.++..++||.+||.+++++.  .+... 
T Consensus        41 vs~~tv~~w~~r~~~g~~~l~~~~r~grp~~~~~-~~i~~-~v~~~~~~t~~~ia~~l~vs~~tV~r~L~~~--g~~~k-  115 (345)
T 3hot_A           41 PTVKTCERWFQRFKSGDFDVDDKEHGKPPKRYED-AELQA-LLDEDDAQTQKQLAEQLEVSQQAVSNRLREM--GKIQK-  115 (345)
T ss_dssp             CCHHHHHHHHHHHTTCCCCCSCCCCCCCCCSSCH-HHHHH-HHHHCSCCCHHHHHHHTTSCHHHHHHHHHHT--TCEEE-
T ss_pred             CcHHHHHHHHHHHhCCCccccCCCCCCCCCcccH-HHHHH-HHHhCccchHHHHHHHHCCCHHHHHHHHHHh--CCeee-
Confidence            46788888887765421 01 1111222344554 33332 2233445789999999999999999999982  22222 


Q ss_pred             ccccccc-CCChHHHH---HHHHHHHH---hhCCCCcceeecceeEEeecCCCCccccc-----------cccCCcceeE
Q psy4300          79 IQCQYIK-WPTEEESV---IIERNFRA---LAKFPGVIGAIDGCHIEGKFSKDIRNDYN-----------NRKCTQSMIL  140 (307)
Q Consensus        79 ~~~~~i~-~P~~~~~~---~~~~~f~~---~~~~p~~~g~iDgt~i~i~~P~~~~~~y~-----------~~k~~~s~~~  140 (307)
                       ...... .-+.....   ........   ...+++-+-..|-+.+....+... ..|.           ...+...+.+
T Consensus       116 -~~~~~~~~l~~~~~~~r~~~~~~~l~~~~~~~~~~~Iv~~DE~~~~~~~~~~~-~~w~~~g~~~~~~~~~~~~~~~~~v  193 (345)
T 3hot_A          116 -VGRWVPHELNERQMERRKNTCEILLSRYKRKSFLHRIVTGDEKWIFFVNPKRK-KSYVDPGQPATSTARPNRFGKKTML  193 (345)
T ss_dssp             -ECCEESSCCCHHHHHHHHHHHHHHHHHHHHSCCGGGEEEEEEEEEESCCCCCC-EEEECSSSCCCCEECCCTTCCEEEE
T ss_pred             -ccccccccCChhhhhhhHHHHHHHHHhhCCcchHHhhhcccceeEEecCccce-eeeccCCCCCCCCcCccCcCCcEEE
Confidence             222221 11222111   11111111   124667778899998876422111 1111           1112335667


Q ss_pred             EeeeCCCcceEeeeec
Q psy4300         141 QGVCTSNKLLTNIHVG  156 (307)
Q Consensus       141 q~v~d~~g~i~~v~~~  156 (307)
                      .++.+.+|.+.+....
T Consensus       194 ~~~~~~~g~~~~~~~~  209 (345)
T 3hot_A          194 CVWWDQSGVIYYELLK  209 (345)
T ss_dssp             EEEEESSSEEEEEEEC
T ss_pred             EEEEcccCceeeEecC
Confidence            7778888866555553

>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=90.52  E-value=0.48  Score=36.67  Aligned_cols=47  Identities=11%  Similarity=0.037  Sum_probs=39.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+|+.++-++. + +-.|.++.++|..+|+|.+||...+.+....|-..
T Consensus       109 ~L~~~~r~v~~-~-~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~  155 (164)
T 3mzy_A          109 NFSKFEKEVLT-Y-LIRGYSYREIATILSKNLKSIDNTIQRIRKKSEEW  155 (164)
T ss_dssp             HSCHHHHHHHH-H-HTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHH-H-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            57777777766 3 55799999999999999999999999887777665

>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=90.35  E-value=0.2  Score=33.34  Aligned_cols=22  Identities=14%  Similarity=0.193  Sum_probs=19.7

Q ss_pred             cHHHHHhhhCCChhhHHHHHHH
Q psy4300          48 SMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        48 ~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      +..+||...|||++||+++++.
T Consensus         2 T~~diA~~aGVS~sTVSrvLng   23 (65)
T 1uxc_A            2 KLDEIARLAGVSRTTASYVING   23 (65)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHT
T ss_pred             CHHHHHHHHCcCHHHHHHHHcC
Confidence            5789999999999999998863

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=90.32  E-value=0.6  Score=31.02  Aligned_cols=40  Identities=15%  Similarity=0.155  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          33 EKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        33 ~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      +++++-.|.--....+..+||..+|+|++||++.+.....
T Consensus        12 ~~~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L~~   51 (67)
T 2heo_A           12 EQKILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLKK   51 (67)
T ss_dssp             HHHHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4555555543223579999999999999999999988765

>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=90.22  E-value=0.73  Score=30.91  Aligned_cols=46  Identities=15%  Similarity=0.019  Sum_probs=38.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcC-CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQ-LSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g-~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      +..--.++.|..++.-+++| +|....|..|||..||+..-++.-..
T Consensus        10 ryr~Yte~~L~~Ai~aVr~g~mS~~~Aak~yGVP~sTL~~RVk~~~~   56 (70)
T 2cob_A           10 RYRQYNSEILEEAISVVMSGKMSVSKAQSIYGIPHSTLEYKVKERLG   56 (70)
T ss_dssp             CSCCCCHHHHHHHHHHHHTTSSCHHHHHHHHTCCHHHHHHHHHHHTT
T ss_pred             cccccCHHHHHHHHHHHHcCCccHHHHHHHhCCChHHHHHHHHhhcc
Confidence            44456788999999999999 89999999999999998877765433

>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=89.99  E-value=1.2  Score=32.30  Aligned_cols=30  Identities=23%  Similarity=0.309  Sum_probs=26.5

Q ss_pred             hcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          44 ATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+.+..+++..+|+|++|+++.++.....
T Consensus        37 ~~~~~~~ela~~l~is~stvs~~L~~L~~~   66 (106)
T 1r1u_A           37 VSEASVGHISHQLNLSQSNVSHQLKLLKSV   66 (106)
T ss_dssp             HCCBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            456799999999999999999999998763

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=89.84  E-value=0.33  Score=33.91  Aligned_cols=41  Identities=7%  Similarity=0.143  Sum_probs=32.7

Q ss_pred             CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      -+..++++..|.  ..|.+..+||..+|+|+++|.+.+.....
T Consensus        16 ~~~~~~IL~lL~--~~g~sa~eLAk~LgiSk~aVr~~L~~Le~   56 (82)
T 1oyi_A           16 AEIVCEAIKTIG--IEGATAAQLTRQLNMEKREVNKALYDLQR   56 (82)
T ss_dssp             HHHHHHHHHHHS--SSTEEHHHHHHHSSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            345666665555  56799999999999999999999888744

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=89.67  E-value=0.5  Score=33.60  Aligned_cols=38  Identities=26%  Similarity=0.420  Sum_probs=29.8

Q ss_pred             HHHHHHHHhcC---CcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          36 TLVALSYMATQ---LSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        36 l~i~L~~L~~g---~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ++..|..-..+   .+..+|+..++++++|+++++++....
T Consensus        17 iL~~l~~~~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~   57 (95)
T 2qvo_A           17 ILMTIYYESLGGNDVYIQYIASKVNSPHSYVWLIIKKFEEA   57 (95)
T ss_dssp             HHHHHHHHHHTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            33444444445   899999999999999999999988764

>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=89.61  E-value=0.7  Score=31.72  Aligned_cols=40  Identities=10%  Similarity=0.180  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHhc--CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          33 EKKTLVALSYMAT--QLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        33 ~~~l~i~L~~L~~--g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      +.+++-+|.-.+.  +.+..+||..+|+|++||.+.+.+...
T Consensus        16 ~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~   57 (77)
T 1qgp_A           16 EQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAK   57 (77)
T ss_dssp             HHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4566666665552  579999999999999999999988754

>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=89.53  E-value=0.31  Score=37.71  Aligned_cols=42  Identities=14%  Similarity=0.044  Sum_probs=34.0

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCC-ChhhHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNL-ADSTVWSCIDS   69 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgv-s~stv~r~v~~   69 (307)
                      .+.++. +..--.+.+++.|.+.+.++..+|| |++|+++++++
T Consensus        10 Ptk~t~-e~~e~I~~~i~~G~sl~~i~~~~~~ps~~T~~~W~~~   52 (140)
T 4dyq_A           10 PSDYMP-EVADDICSLLSSGESLLKVCKRPGMPDKSTVFRWLAK   52 (140)
T ss_dssp             CCSCCT-THHHHHHHHHHTTCCHHHHHTSTTCCCHHHHHHHHHH
T ss_pred             CCCCCH-HHHHHHHHHHHCCCcHHHHHhcCCCCCHHHHHHHHHc
Confidence            344444 3444577788999999999999999 99999999987

>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=89.28  E-value=2.1  Score=32.26  Aligned_cols=68  Identities=10%  Similarity=0.096  Sum_probs=42.8

Q ss_pred             CCHHHHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhC--CChhhHHHHHHHH
Q psy4300           1 MRKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFN--LADSTVWSCIDSF   70 (307)
Q Consensus         1 ms~~~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fg--vs~stv~r~v~~~   70 (307)
                      ++++|+.+.+...... +.... .+..+.++.++...+.-.......+...|+..+|  +|.+||++++++.
T Consensus        34 is~~Tv~r~~~~~~~~-g~~~~-~gr~~~l~~~~~~~i~~~~~~~~~s~~~i~~~lg~~~s~~tV~r~l~~~  103 (141)
T 1u78_A           34 RSRHCIRVYLKDPVSY-GTSKR-APRRKALSVRDERNVIRAASNSCKTARDIRNELQLSASKRTILNVIKRS  103 (141)
T ss_dssp             CCHHHHHHHHHSGGGT-TCCCC-CCCCCSSCHHHHHHHHHHHHHCCCCHHHHHHHTTCCSCHHHHHHHHHHT
T ss_pred             cCHHHHHHHHHccccc-CCcCC-CCCCCcCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCccHHHHHHHHHHC
Confidence            3566766666655433 11111 2334567776654443333344589999999999  8999999999863

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

Probab=88.97  E-value=0.5  Score=33.82  Aligned_cols=36  Identities=25%  Similarity=0.422  Sum_probs=27.2

Q ss_pred             HHHHHHHHHH-hcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          34 KKTLVALSYM-ATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        34 ~~l~i~L~~L-~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      ++.-..+.+| ..+.+..++|..+|||.+||+|.++.
T Consensus         7 ~R~~~I~~~l~~~~~ti~dlA~~~gVS~~TVsR~L~~   43 (93)
T 2l0k_A            7 ERTIKIGKYIVETKKTVRVIAKEFGVSKSTVHKDLTE   43 (93)
T ss_dssp             HHHHHHHHHHHHHCCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence            3333344444 44689999999999999999999875

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

Probab=88.93  E-value=0.98  Score=36.75  Aligned_cols=65  Identities=8%  Similarity=0.106  Sum_probs=49.7

Q ss_pred             CCCHHHHHHHHHHHHhc-------CCcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMAT-------QLSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEESVII   95 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~-------g~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~~~~   95 (307)
                      ..+++++++-+|..+..       ..+..++|...|+|+.|++|+++++... +...  ....|.-.+.+.++.+
T Consensus       145 ~~~~~~Rl~~~L~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~--~~~~i~i~d~~~L~~~  217 (220)
T 3dv8_A          145 WKSLDKRVASFLLEETSIEGTNELKITHETIANHLGSHREVITRMLRYFQVEGLVKL--SRGKITILDSKRLETL  217 (220)
T ss_dssp             HSCHHHHHHHHHHHHHHHHTSSEECCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE--ETTEEEESCHHHHHHH
T ss_pred             cCCHHHHHHHHHHHhhhhcCCceecCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe--CCCEEEEeCHHHHHHH
Confidence            46799999999998865       6789999999999999999999998654 3333  4555555565555443

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=88.91  E-value=0.87  Score=34.55  Aligned_cols=47  Identities=17%  Similarity=0.039  Sum_probs=36.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ...+++.+...+...+-..+.+..+|+..++++++|+++.+++....
T Consensus        32 ~~~lt~~~~~iL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~   78 (143)
T 3oop_A           32 SYDVTPEQWSVLEGIEANEPISQKEIALWTKKDTPTVNRIVDVLLRK   78 (143)
T ss_dssp             TSSSCHHHHHHHHHHHHHSSEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             hCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCHhhHHHHHHHHHHC
Confidence            34677766655554444578899999999999999999999987653

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}

Probab=88.66  E-value=0.35  Score=36.46  Aligned_cols=46  Identities=11%  Similarity=0.077  Sum_probs=34.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..++..+...+...+-..+.+..+++..++++++|+++.+++....
T Consensus        29 ~~l~~~~~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~   74 (139)
T 3bja_A           29 YDISYVQFGVIQVLAKSGKVSMSKLIENMGCVPSNMTTMIQRMKRD   74 (139)
T ss_dssp             GTCCHHHHHHHHHHHHSCSEEHHHHHHHCSSCCTTHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence            3577655544444344556899999999999999999999988764

>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens}

Probab=88.61  E-value=0.54  Score=30.79  Aligned_cols=27  Identities=4%  Similarity=0.089  Sum_probs=23.2

Q ss_pred             HHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          41 SYMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        41 ~~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      .....| ++..+|...|+|+++++++++
T Consensus         9 ~~~~~g-s~~~~A~~lgis~~~vs~~~~   35 (67)
T 2pij_A            9 YLEEHG-TQSALAAALGVNQSAISQMVR   35 (67)
T ss_dssp             HHHHTC-CHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHcC-CHHHHHHHHCcCHHHHHHHHc
Confidence            344567 999999999999999999984

>3mky_B Protein SOPB; partition, F plasmid, centromere, DNA binding protein- complex; HET: DNA; 2.86A {Escherichia coli} PDB: 3mkw_B* 3mkz_A*

Probab=88.56  E-value=0.78  Score=37.23  Aligned_cols=43  Identities=12%  Similarity=0.163  Sum_probs=38.8

Q ss_pred             CCCCCHHHHHHHHHHHHhcC--CcHHHHHhhhCCChhhHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQ--LSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g--~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      .+++|..++=.-.+..|.+|  .++.++|..+|+|++.|+|+++-
T Consensus        21 ~rplS~yErg~~y~r~L~~g~~~~Q~~lA~~~giS~a~VSR~L~~   65 (189)
T 3mky_B           21 YRPTSAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINT   65 (189)
T ss_dssp             --CCCHHHHHHHHHHHHHTTTTTCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHhcCcccCHHHHHHHHCCCHHHHHHHHHH
Confidence            57899999999999999887  89999999999999999999984

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=88.21  E-value=0.56  Score=31.15  Aligned_cols=29  Identities=7%  Similarity=0.109  Sum_probs=23.0

Q ss_pred             HHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          40 LSYMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        40 L~~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      |..+....++..+|..+|||+++||++++
T Consensus         7 Lk~l~~~~sq~~~A~~Lgvsq~aVS~~~~   35 (65)
T 2cw1_A            7 LKKFVEDKNQEYAARALGLSQKLIEEVLK   35 (65)
T ss_dssp             HHHHHTTSCHHHHHHHSSSCHHHHHHHHH
T ss_pred             HHHHHHHcCHHHHHHHhCCCHHHHHHHHH
Confidence            33333344999999999999999999874

>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=88.20  E-value=0.66  Score=32.98  Aligned_cols=30  Identities=10%  Similarity=0.051  Sum_probs=26.5

Q ss_pred             hcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          44 ATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+.+..+|+..+|+|++|+++.++.....
T Consensus        41 ~~~~~~~eLa~~l~is~~tv~~~L~~L~~~   70 (96)
T 1y0u_A           41 DKGRSEEEIMQTLSLSKKQLDYHLKVLEAG   70 (96)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            567899999999999999999999887654

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=88.12  E-value=1.3  Score=31.60  Aligned_cols=43  Identities=12%  Similarity=0.182  Sum_probs=32.1

Q ss_pred             CCHHH-HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          30 VPVEK-KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        30 ~~~~~-~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ++..+ +++..| .-..+.+..+|+..+|++++|+++.++.....
T Consensus        18 l~~~~~~il~~l-~~~~~~s~~ela~~l~is~~tv~~~l~~L~~~   61 (109)
T 1sfx_A           18 FKPSDVRIYSLL-LERGGMRVSEIARELDLSARFVRDRLKVLLKR   61 (109)
T ss_dssp             CCHHHHHHHHHH-HHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHH-HHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            34433 344444 33467899999999999999999999998765

>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=88.08  E-value=1.3  Score=32.15  Aligned_cols=51  Identities=10%  Similarity=0.098  Sum_probs=44.5

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      +......++.++.....++.|+.+.+..|+||.+++.+|...+-..-.+.|
T Consensus        32 rRWva~rK~~VV~~v~~g~lS~~EAa~ry~Is~~ei~~W~r~y~~~G~~aL   82 (101)
T 2oa4_A           32 RRWVASRKIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVSALAEHGKDAL   82 (101)
T ss_dssp             SCCCHHHHHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHHHHHCCCSSSS
T ss_pred             HHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhHHHh
Confidence            456666899999999999999999999999999999999998876666664

>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=88.05  E-value=1.2  Score=30.85  Aligned_cols=40  Identities=10%  Similarity=0.182  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHh--cCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          33 EKKTLVALSYMA--TQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        33 ~~~l~i~L~~L~--~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      +++++-.|.-.+  ...+..+||..+|+|++||.+.+.+...
T Consensus        12 ~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~   53 (81)
T 1qbj_A           12 EQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAK   53 (81)
T ss_dssp             HHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            455555555443  2478999999999999999998888754

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=87.98  E-value=1.4  Score=33.37  Aligned_cols=45  Identities=11%  Similarity=0.113  Sum_probs=36.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+++.+-..+...+-..+.+..+|+..++++++|+++.+++...
T Consensus        27 ~~lt~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~   71 (145)
T 3g3z_A           27 QDLNYNLFAVLYTLATEGSRTQKHIGEKWSLPKQTVSGVCKTLAG   71 (145)
T ss_dssp             TTCCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            467777655555555566799999999999999999999998765

>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription regulator, activator, DNA-binding, repressor; HET: SAL; 2.30A {Salmonella typhimurium} SCOP: a.4.5.28

Probab=87.84  E-value=0.58  Score=36.90  Aligned_cols=46  Identities=4%  Similarity=-0.018  Sum_probs=34.0

Q ss_pred             CCCCCHHHHHHHHHHHH-hcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYM-ATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L-~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ...++..+-.++...+- ..+.+..+|+..++++++|+++.+++...
T Consensus        48 ~~glt~~q~~vL~~L~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~   94 (166)
T 3deu_A           48 PLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLED   94 (166)
T ss_dssp             TTTCCHHHHHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             hcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHhhHHHHHHHHHH
Confidence            34677766443333332 45689999999999999999999998765

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85

Probab=87.75  E-value=1.2  Score=31.73  Aligned_cols=46  Identities=11%  Similarity=0.033  Sum_probs=37.3

Q ss_pred             CCCCCHHHHHHHHHHHHh--cCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMA--TQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~--~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ...++..+.+.+.+.+-+  .|.+.++|+...+++++|+.+++++...
T Consensus        15 ~~~Lt~~q~~Vl~~I~~~g~~gi~qkeLa~~~~l~~~tvt~iLk~LE~   62 (91)
T 2dk5_A           15 MKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLES   62 (91)
T ss_dssp             CCCSCSSHHHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             hcCCCHHHHHHHHHHHHcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            456777777766666653  3899999999999999999999988754

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=87.65  E-value=0.86  Score=34.20  Aligned_cols=46  Identities=4%  Similarity=0.018  Sum_probs=34.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+++.+...+...+-..+.+..+++..+|++++|+++.+++....
T Consensus        25 ~~l~~~~~~iL~~l~~~~~~~~~ela~~l~~s~~tvs~~l~~L~~~   70 (138)
T 3bpv_A           25 LNLTDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEES   70 (138)
T ss_dssp             GTCCHHHHHHHHHHHHSTTCBHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            3566655544444444567899999999999999999999987653

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=87.48  E-value=1.1  Score=33.91  Aligned_cols=41  Identities=15%  Similarity=0.268  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          33 EKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        33 ~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ...++..|+.+   ..+.+..++|..+|++++|+++.+++....
T Consensus        15 ~~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~~~l~~Le~~   58 (139)
T 2x4h_A           15 EFSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVFEEVSHLEEK   58 (139)
T ss_dssp             HHHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHHHHHHHHHHC
Confidence            34555566665   345799999999999999999999988664

>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=87.48  E-value=0.98  Score=33.92  Aligned_cols=46  Identities=4%  Similarity=0.028  Sum_probs=35.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..++..+...+...+-..+.+..+++..+|++++|+++.+++....
T Consensus        30 ~~lt~~~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~~L~~~   75 (138)
T 1jgs_A           30 LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCK   75 (138)
T ss_dssp             TTSCHHHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHhcCCCCHHHHHHHHCCChHHHHHHHHHHHHC
Confidence            4577766544444444567899999999999999999999998765

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

Probab=87.45  E-value=1.1  Score=36.96  Aligned_cols=46  Identities=7%  Similarity=0.135  Sum_probs=39.2

Q ss_pred             CCCCCHHHHHHHHHHHHhc--------CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMAT--------QLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~--------g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ....+++++++-+|..++.        ..+..+||...|+++.|++|+++++..
T Consensus       159 l~~~~~~~Rl~~~L~~l~~~~~~~~~~~~t~~~lA~~lG~sr~tvsR~l~~l~~  212 (232)
T 1zyb_A          159 EPTLDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQD  212 (232)
T ss_dssp             CCCCSHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HhhcCHHHHHHHHHHHHHhhcCCeEEecCCHHHHHHHhCCChhHHHHHHHHHHH
Confidence            4567899999999988753        258999999999999999999998753

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=87.31  E-value=1.4  Score=30.31  Aligned_cols=50  Identities=12%  Similarity=0.196  Sum_probs=35.1

Q ss_pred             CCHHHHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300           1 MRKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus         1 ms~~~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      |+++....|++.|+..+.   ...                   +...+.++||..||+|.+||.+.+.....
T Consensus         1 ~~~~r~~~IL~~I~~~i~---~~~-------------------g~~psv~EIa~~lgvS~~TVrr~L~~Le~   50 (77)
T 2jt1_A            1 MSESIVTKIISIVQERQN---MDD-------------------GAPVKTRDIADAAGLSIYQVRLYLEQLHD   50 (77)
T ss_dssp             CCCTHHHHHHHHHHHHHH---HHT-------------------TSCEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHh---hcc-------------------CCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            667777777777766521   000                   12357899999999999999888877654

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=87.27  E-value=1.1  Score=34.18  Aligned_cols=46  Identities=13%  Similarity=0.084  Sum_probs=35.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..++..+...+...+-..+.+..+|+..++++++|+++.+++....
T Consensus        38 ~~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~   83 (150)
T 2rdp_A           38 YPITPPQFVALQWLLEEGDLTVGELSNKMYLACSTTTDLVDRMERN   83 (150)
T ss_dssp             SSSCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence            4577755444433333557899999999999999999999988764

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=87.27  E-value=0.63  Score=32.92  Aligned_cols=27  Identities=11%  Similarity=0.027  Sum_probs=24.8

Q ss_pred             CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          46 QLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        46 g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      +.+..+|+..+|+|++|+++.++....
T Consensus        38 ~~s~~ela~~l~is~~tvs~~l~~L~~   64 (99)
T 3cuo_A           38 GTSAGELTRITGLSASATSQHLARMRD   64 (99)
T ss_dssp             SEEHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            589999999999999999999998865

>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=87.12  E-value=1.3  Score=33.55  Aligned_cols=46  Identities=11%  Similarity=0.057  Sum_probs=33.9

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+++.+-..+...+-..+.+..+||..+|++++|+++.+++....
T Consensus        33 ~~lt~~~~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~   78 (142)
T 3ech_A           33 LDLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGR   78 (142)
T ss_dssp             CCCCHHHHHHHHHHHHTTTCCHHHHHHHHC---CHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            5677777655555555568999999999999999999999987663

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=86.95  E-value=1.3  Score=33.25  Aligned_cols=41  Identities=10%  Similarity=0.165  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHhcC-CcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          33 EKKTLVALSYMATQ-LSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        33 ~~~l~i~L~~L~~g-~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      +.+++..|..-... .+..+|+..+++|+|||+|.+..+...
T Consensus        28 e~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L~~L~~~   69 (123)
T 3r0a_A           28 DLNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSVKKLHEK   69 (123)
T ss_dssp             HHHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            33444444433323 699999999999999999999998764

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=86.89  E-value=0.44  Score=37.26  Aligned_cols=50  Identities=12%  Similarity=0.104  Sum_probs=43.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      ..+|+.++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..+
T Consensus        92 ~~Lp~~~r~vl~L~~~~-g~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l  141 (157)
T 2lfw_A           92 ARMTPLSRQALLLTAME-GFSPEDAAYLIEVDTSEVETLVTEALAEIEKQT  141 (157)
T ss_dssp             TTSCTTHHHHHTTTSSS-CCCHHHHHHTTTSCHHHHHHHHHHHHHHHHTTS
T ss_pred             HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence            56888888888776654 799999999999999999999999988888875

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=86.60  E-value=1.6  Score=32.71  Aligned_cols=45  Identities=4%  Similarity=-0.022  Sum_probs=35.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .++..+...+...+-..+.+..+++..+|++++|+++.+++....
T Consensus        35 ~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~L~~~   79 (140)
T 2nnn_A           35 GLTPTQWAALVRLGETGPCPQNQLGRLTAMDAATIKGVVERLDKR   79 (140)
T ss_dssp             CCCHHHHHHHHHHHHHSSBCHHHHHHHTTCCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            677766544444444457899999999999999999999998764

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=86.46  E-value=0.7  Score=34.85  Aligned_cols=46  Identities=13%  Similarity=0.120  Sum_probs=33.7

Q ss_pred             CCCCHHHHHHHHHHHHh--cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMA--TQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~--~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+++.+-..+...+-.  .+.+..+||..++++++|+++.+++....
T Consensus        27 ~~lt~~~~~vL~~l~~~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~   74 (139)
T 3eco_A           27 FDITNEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNLERK   74 (139)
T ss_dssp             GTCCHHHHHHHHHHHHSTTTCEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHhcCCCCcCHHHHHHHhCCCcccHHHHHHHHHHC
Confidence            34666554433333333  37899999999999999999999988663

>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=86.31  E-value=1.4  Score=33.32  Aligned_cols=45  Identities=7%  Similarity=0.090  Sum_probs=35.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..++..+...+...+ ..+.+..+|+..+|++++|+++.+++....
T Consensus        33 ~~l~~~~~~iL~~l~-~~~~~~~ela~~l~~s~~tvs~~l~~Le~~   77 (146)
T 2gxg_A           33 LNLSYLDFLVLRATS-DGPKTMAYLANRYFVTQSAITASVDKLEEM   77 (146)
T ss_dssp             TTCCHHHHHHHHHHT-TSCBCHHHHHHHTTCCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHh-cCCcCHHHHHHHhCCCchhHHHHHHHHHHC
Confidence            457775554444444 778999999999999999999999987654

>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=86.21  E-value=0.27  Score=32.93  Aligned_cols=22  Identities=14%  Similarity=0.215  Sum_probs=19.7

Q ss_pred             CcHHHHHhhhCCChhhHHHHHH
Q psy4300          47 LSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        47 ~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      .+..+||...|||++||+++++
T Consensus        10 ~t~~diA~~aGVS~sTVSr~ln   31 (67)
T 2l8n_A           10 ATMKDVALKAKVSTATVSRALM   31 (67)
T ss_dssp             CCHHHHHHHTTCCHHHHHHTTT
T ss_pred             CCHHHHHHHHCCCHHHHHHHHc
Confidence            5789999999999999999764

>2eth_A Transcriptional regulator, putative, MAR family; MARR family, structural genomics, joint center for structura genomics, JCSG; 2.30A {Thermotoga maritima} SCOP: a.4.5.28

Probab=86.17  E-value=1.2  Score=34.31  Aligned_cols=46  Identities=13%  Similarity=0.099  Sum_probs=34.3

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..++..+...+...+-..+.+..+|+..++++++|+++.+++....
T Consensus        40 ~~lt~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~   85 (154)
T 2eth_A           40 SDMKTTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEKR   85 (154)
T ss_dssp             HHSBHHHHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            3466655444433333457899999999999999999999988764

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=86.01  E-value=1.6  Score=33.12  Aligned_cols=45  Identities=16%  Similarity=0.208  Sum_probs=36.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .+++.+-..+...+-..+.+..+||..++++++|+++.+++....
T Consensus        37 ~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~   81 (148)
T 3nrv_A           37 GIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEK   81 (148)
T ss_dssp             TCCHHHHHHHHHHHHSSSBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            677766655555455558999999999999999999999988765

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=85.97  E-value=1.5  Score=32.98  Aligned_cols=45  Identities=2%  Similarity=0.040  Sum_probs=34.8

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .++..+...+...+-..+.+..+++..++++++|+++.+++....
T Consensus        33 ~lt~~~~~iL~~l~~~~~~t~~ela~~l~~s~~~vs~~l~~Le~~   77 (142)
T 2fbi_A           33 GLTEQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLERD   77 (142)
T ss_dssp             TCCHHHHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHhHHHHHHHHHHHC
Confidence            466665544444444557899999999999999999999998764

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

Probab=85.79  E-value=1.7  Score=31.97  Aligned_cols=28  Identities=11%  Similarity=0.216  Sum_probs=26.2

Q ss_pred             cCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          45 TQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        45 ~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      .+.+..+++..+|+|++|+++.++....
T Consensus        44 ~~~s~~ela~~l~is~stvsr~l~~Le~   71 (119)
T 2lkp_A           44 GPLPVTDLAEAIGMEQSAVSHQLRVLRN   71 (119)
T ss_dssp             CCCCHHHHHHHHSSCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4789999999999999999999999877

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=85.77  E-value=1.8  Score=29.56  Aligned_cols=29  Identities=10%  Similarity=0.044  Sum_probs=24.9

Q ss_pred             cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          45 TQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        45 ~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ...+..+||..+|+|++|+++.++.....
T Consensus        13 ~~~s~~eLa~~lgvs~~tv~r~L~~L~~~   41 (81)
T 2htj_A           13 NGGKTAEIAEALAVTDYQARYYLLLLEKA   41 (81)
T ss_dssp             CCCCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            35789999999999999999998887543

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=85.76  E-value=1.4  Score=33.79  Aligned_cols=47  Identities=13%  Similarity=0.197  Sum_probs=35.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ...++..+...+...+-..+.+..+|+..++++++|+++.+++....
T Consensus        42 ~~~l~~~~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~Le~~   88 (153)
T 2pex_A           42 ALDLTYPQYLVMLVLWETDERSVSEIGERLYLDSATLTPLLKRLQAA   88 (153)
T ss_dssp             TTTCCHHHHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HCCCCHHHHHHHHHHHhCCCcCHHHHHHHhCCCcccHHHHHHHHHHC
Confidence            34677766554444444567899999999999999999999887553

>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=85.75  E-value=1.5  Score=33.27  Aligned_cols=42  Identities=12%  Similarity=0.271  Sum_probs=32.4

Q ss_pred             CCHH-HHHHHHHHHH-hcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          30 VPVE-KKTLVALSYM-ATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        30 ~~~~-~~l~i~L~~L-~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ++.. .+++..| ++ ..+.+..+|+..+|+++||+++.++....
T Consensus        24 l~~~~~~il~~L-~~~~~~~t~~ela~~l~~~~stvs~~l~~L~~   67 (152)
T 1ku9_A           24 LNKSVGAVYAIL-YLSDKPLTISDIMEELKISKGNVSMSLKKLEE   67 (152)
T ss_dssp             CCHHHHHHHHHH-HHCSSCEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CChhHHHHHHHH-HHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            5554 4455555 54 46789999999999999999999988754

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28

Probab=85.70  E-value=2.1  Score=32.06  Aligned_cols=46  Identities=11%  Similarity=0.103  Sum_probs=33.8

Q ss_pred             CCCCHHHHHHHHHHHHhc--CCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMAT--QLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~--g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..++..+...+...+-..  +.+..+|+..++++++|+++.+++....
T Consensus        30 ~~lt~~~~~iL~~l~~~~~~~~~~~ela~~l~~~~~tvs~~l~~Le~~   77 (141)
T 3bro_A           30 YDLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIK   77 (141)
T ss_dssp             TTCCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCcchHHHHHHHHHHC
Confidence            356765544333333333  6899999999999999999999988764

>3jw4_A Transcriptional regulator, MARR/EMRR family; DNA-binding protein, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Clostridium acetobutylicum} SCOP: a.4.5.0

Probab=85.65  E-value=0.73  Score=35.25  Aligned_cols=46  Identities=7%  Similarity=0.153  Sum_probs=29.0

Q ss_pred             CCCCHHHHHHHHHHHHh--cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMA--TQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~--~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+++.+-..+...+-.  .+.+..+||..++++++|+++.+++....
T Consensus        37 ~glt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~   84 (148)
T 3jw4_A           37 LGLNSQQGRMIGYIYENQESGIIQKDLAQFFGRRGASITSMLQGLEKK   84 (148)
T ss_dssp             TTCCHHHHHHHHHHHHHTTTCCCHHHHHHC------CHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHhCCCCCCCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence            45777654444433334  68999999999999999999999987664

>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=85.60  E-value=1.9  Score=32.58  Aligned_cols=45  Identities=11%  Similarity=0.082  Sum_probs=34.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .++..+...+...+-..+.+..+++..++++++|+++.+++....
T Consensus        30 ~l~~~~~~iL~~l~~~~~~~~~~la~~l~~s~~tvs~~l~~L~~~   74 (145)
T 2a61_A           30 GITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEAD   74 (145)
T ss_dssp             TCCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence            466655444443334567899999999999999999999987764

>1z91_A Organic hydroperoxide resistance transcriptional; OHRR, MARR family, bacterial transcription factor, DNA bindi protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB: 1z9c_A*

Probab=85.58  E-value=1.4  Score=33.37  Aligned_cols=47  Identities=15%  Similarity=0.213  Sum_probs=35.0

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ...++..+...+...+-..+.+..+|+..++++++|+++.+++....
T Consensus        35 ~~~l~~~~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~~L~~~   81 (147)
T 1z91_A           35 KLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQ   81 (147)
T ss_dssp             TTCCCHHHHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCcCcHHHHHHHHHHC
Confidence            34577765544433333457899999999999999999999887654

>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=85.38  E-value=1.9  Score=33.52  Aligned_cols=45  Identities=11%  Similarity=0.121  Sum_probs=35.7

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+++.+-.++...+-..+.+..+||..+|++++|+++.+++...
T Consensus        42 ~glt~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~   86 (162)
T 3k0l_A           42 LEISLPQFTALSVLAAKPNLSNAKLAERSFIKPQSANKILQDLLA   86 (162)
T ss_dssp             TTCCHHHHHHHHHHHHCTTCCHHHHHHHHTSCGGGHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            457776655555444456799999999999999999999998765

>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=85.21  E-value=1.4  Score=35.53  Aligned_cols=42  Identities=5%  Similarity=-0.087  Sum_probs=38.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      +..+++-++...+...+..|.+...+|..+|+|+++|++++.
T Consensus        33 RedL~piE~A~a~~~L~~~G~t~eeiA~~lG~s~s~V~~~Lr   74 (178)
T 1r71_A           33 RNELTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVT   74 (178)
T ss_dssp             TTCCCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHG
T ss_pred             cCCCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            578999999999899999999999999999999999998765

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=85.16  E-value=1.9  Score=32.31  Aligned_cols=45  Identities=4%  Similarity=0.109  Sum_probs=33.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .++..+...+...+-..+.+..+++..+++|++|+++.+++....
T Consensus        28 ~l~~~~~~iL~~l~~~~~~~~~ela~~l~is~~~vs~~l~~L~~~   72 (142)
T 3bdd_A           28 GISLTRYSILQTLLKDAPLHQLALQERLQIDRAAVTRHLKLLEES   72 (142)
T ss_dssp             SSCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            466655443333333457899999999999999999999887653

>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=85.04  E-value=1.8  Score=32.90  Aligned_cols=30  Identities=10%  Similarity=0.124  Sum_probs=26.3

Q ss_pred             hcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          44 ATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+.+..+||..+|+|++|+++.+++....
T Consensus        20 ~~~~~~~ela~~l~vs~~tvs~~l~~Le~~   49 (142)
T 1on2_A           20 KGYARVSDIAEALAVHPSSVTKMVQKLDKD   49 (142)
T ss_dssp             HSSCCHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             cCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            356899999999999999999999987653

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

Probab=84.95  E-value=1.3  Score=40.94  Aligned_cols=48  Identities=8%  Similarity=0.179  Sum_probs=42.1

Q ss_pred             CCCCHHHHHHHHHHHH-h--cCCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300          28 PFVPVEKKTLVALSYM-A--TQLSMRKIGDQFNLADSTVWSCIDSFLTAMS   75 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L-~--~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~   75 (307)
                      ..++..++-.+.|+|. .  .+.++.+||..+|||+.+|..+..+.+.-|-
T Consensus       374 ~~L~ereR~VI~LRygL~~~e~~TleEIAe~LgIS~erVRqi~~RAlkKLR  424 (438)
T 1l9z_H          374 SKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK  424 (438)
T ss_pred             HhCCHHHHHHHHHHHhccCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            3588888899999884 3  6799999999999999999999999888776

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

Probab=84.84  E-value=2.5  Score=33.92  Aligned_cols=64  Identities=9%  Similarity=0.026  Sum_probs=48.8

Q ss_pred             CCCHHHHHHHHHHHHhc-------------CCcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHHHH
Q psy4300          29 FVPVEKKTLVALSYMAT-------------QLSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEESVI   94 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~-------------g~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~~~   94 (307)
                      ..+++++|+-+|..|+.             ..+..+||...|+|+.|++|+++++... +...  ....|...+.+.+..
T Consensus       116 ~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~--~~~~i~i~d~~~L~~  193 (202)
T 2zcw_A          116 TQRLKNRMAAALLELSETPLAHEEEGKVVLKATHDELAAAVGSVRETVTKVIGELAREGYIRS--GYGKIQLLDLKGLKE  193 (202)
T ss_dssp             HCCHHHHHHHHHHHHTTSTTEEEETTEEEEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE--ETTEEEESCHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHhcCCCCCCcEEccCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe--CCCEEEEeCHHHHHH
Confidence            46799999999998853             2688999999999999999999998754 4443  555666666555443

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

Probab=84.81  E-value=1.4  Score=35.44  Aligned_cols=44  Identities=18%  Similarity=0.261  Sum_probs=37.8

Q ss_pred             CCCHHHHHHHHHHHHhc-------------CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMAT-------------QLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~-------------g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+++++++-+|..++.             ..+..++|...|+|+.|++|+++++..
T Consensus       137 ~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~iA~~lg~sr~tvsR~l~~L~~  193 (210)
T 3ryp_A          137 FLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLED  193 (210)
T ss_dssp             HSCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHHHHhcCcCCCCCceEeccCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            46799999999998854             257899999999999999999998754

>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein, divalent metal binding, transcription; 2.50A {Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A 1fzp_D

Probab=84.61  E-value=1.4  Score=33.04  Aligned_cols=46  Identities=9%  Similarity=0.117  Sum_probs=34.8

Q ss_pred             CCCCHHHHHHHHHHHHh--cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMA--TQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~--~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+++.+-..+...+-.  .+.+..+|+..++++++|+++.+++....
T Consensus        33 ~~lt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~   80 (127)
T 2frh_A           33 FSISFEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQE   80 (127)
T ss_dssp             TCCCHHHHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            45777655444433334  56899999999999999999999987653

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=84.50  E-value=1.7  Score=33.60  Aligned_cols=46  Identities=15%  Similarity=0.113  Sum_probs=34.9

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..++..+...+...+-..+.+..+|+..+|++++|+++.+++....
T Consensus        48 ~~lt~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~   93 (162)
T 3cjn_A           48 LGLSTAKMRALAILSAKDGLPIGTLGIFAVVEQSTLSRALDGLQAD   93 (162)
T ss_dssp             HTCCHHHHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence            3467665544444444557899999999999999999999987654

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=84.42  E-value=1.6  Score=33.83  Aligned_cols=44  Identities=9%  Similarity=0.167  Sum_probs=32.7

Q ss_pred             CCCHHH-HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          29 FVPVEK-KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        29 ~~~~~~-~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      .+++.+ .++..|.....+.+..+||..++++++|+++++++...
T Consensus        28 gLt~~q~~vL~~L~~~~~~~~~~eLa~~l~~~~~tvs~~v~~Le~   72 (151)
T 4aik_A           28 ELTQTHWVTLYNINRLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE   72 (151)
T ss_dssp             CCCHHHHHHHHHHHHSCTTSCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCCcHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            466655 33444444455678899999999999999999988754

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=84.40  E-value=1.8  Score=33.07  Aligned_cols=45  Identities=9%  Similarity=0.154  Sum_probs=35.1

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+++.+-..+...+-..+.+..+|+..++++++|+++.+++...
T Consensus        37 ~~lt~~q~~iL~~l~~~~~~~~~eLa~~l~~~~~~vs~~l~~L~~   81 (149)
T 4hbl_A           37 FGITYSQYLVMLTLWEENPQTLNSIGRHLDLSSNTLTPMLKRLEQ   81 (149)
T ss_dssp             TTCCHHHHHHHHHHHHSSSEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            457776655544444457789999999999999999999988754

>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=84.29  E-value=1.1  Score=31.65  Aligned_cols=42  Identities=17%  Similarity=0.146  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHHh-c--CCcHHHHHhhhCCChhh-HHHHHHHHHHH
Q psy4300          32 VEKKTLVALSYMA-T--QLSMRKIGDQFNLADST-VWSCIDSFLTA   73 (307)
Q Consensus        32 ~~~~l~i~L~~L~-~--g~~~~~l~~~fgvs~st-v~r~v~~~~~~   73 (307)
                      ...+.+.+|..+. +  +.+..+|+..++++++| +++.+++....
T Consensus        13 ~~~~~l~~L~~l~~~~~~~t~~eLa~~l~is~~t~vs~~l~~Le~~   58 (95)
T 2pg4_A           13 HLIRILPTLLEFEKKGYEPSLAEIVKASGVSEKTFFMGLKDRLIRA   58 (95)
T ss_dssp             HHHHHHHHHHHHHHTTCCCCHHHHHHHHCCCHHHHHTTHHHHHHHT
T ss_pred             hHHHHHHHHHHHHhcCCCCCHHHHHHHHCCCchHHHHHHHHHHHHC
Confidence            4444555555553 2  58999999999999999 99999998765

>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=84.22  E-value=4.2  Score=33.80  Aligned_cols=49  Identities=12%  Similarity=0.159  Sum_probs=41.4

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ...++..++-.+.|  +..|.++.++|...|+|.+||...+.+...-|-..
T Consensus       171 ~~~Lt~~e~~vl~~--~~~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~  219 (234)
T 1l3l_A          171 AAWLDPKEATYLRW--IAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVR  219 (234)
T ss_dssp             CCCCCHHHHHHHHH--HTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCS
T ss_pred             CCCCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence            45799988877655  57999999999999999999999999887776554

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

Probab=84.12  E-value=3.5  Score=32.80  Aligned_cols=65  Identities=9%  Similarity=0.030  Sum_probs=48.9

Q ss_pred             CCCCHHHHHHHHHHHHhc-------------CCcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHHH
Q psy4300          28 PFVPVEKKTLVALSYMAT-------------QLSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEESV   93 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~-------------g~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~~   93 (307)
                      ...+++++|+-+|..|..             ..+..++|...|+|+.|++|+++++... +...  ....|...+.+.+.
T Consensus       108 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~--~~~~i~i~d~~~L~  185 (195)
T 3b02_A          108 QTGELRARIARYLLFLADTPLSARDRQGIYVTVSHEEIADATASIRESVSKVLADLRREGLIAT--AYRRVYLLDLAALE  185 (195)
T ss_dssp             TSSCHHHHHHHHHHHHTTSTTEEEETTEEEEECCHHHHHHTTTSCHHHHHHHHHHHHHHTSEEE--ETTEEEECCHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHcCCCCCCCeeeccCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe--cCCEEEEeCHHHHH
Confidence            457899999999998753             2578999999999999999999998743 4444  44556666655444


Q ss_pred             H
Q psy4300          94 I   94 (307)
Q Consensus        94 ~   94 (307)
                      .
T Consensus       186 ~  186 (195)
T 3b02_A          186 R  186 (195)
T ss_dssp             H
T ss_pred             H
Confidence            3

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=84.11  E-value=1.4  Score=33.25  Aligned_cols=45  Identities=11%  Similarity=0.160  Sum_probs=33.0

Q ss_pred             CCCHHH-HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEK-KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~-~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .+++.+ .++..|..-..+.+..+|+..+|++++|+++.+++....
T Consensus        34 ~l~~~~~~iL~~l~~~~~~~t~~~la~~l~~s~~~vs~~l~~L~~~   79 (146)
T 2fbh_A           34 GLSQARWLVLLHLARHRDSPTQRELAQSVGVEGPTLARLLDGLESQ   79 (146)
T ss_dssp             CCTTTHHHHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHC
Confidence            355443 344444244557899999999999999999999988764

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=84.11  E-value=2  Score=36.52  Aligned_cols=48  Identities=17%  Similarity=0.185  Sum_probs=43.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|..++-++.|.  ..|.++.++|...|+|.+||...+.+....|-..
T Consensus       196 ~~L~~~erevl~L~--~~G~s~~EIA~~L~iS~~TVk~~l~ra~~kL~~~  243 (258)
T 3clo_A          196 NILSEREKEILRCI--RKGLSSKEIAATLYISVNTVNRHRQNILEKLSVG  243 (258)
T ss_dssp             TSSCHHHHHHHHHH--HTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCS
T ss_pred             ccCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCC
Confidence            57999999999996  4999999999999999999999999988877665

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

Probab=84.05  E-value=1.3  Score=36.20  Aligned_cols=63  Identities=13%  Similarity=0.055  Sum_probs=46.4

Q ss_pred             CCCHHHHHHHHHHHHhc--------------CCcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccc-cccccCCChHHH
Q psy4300          29 FVPVEKKTLVALSYMAT--------------QLSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQ-CQYIKWPTEEES   92 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~--------------g~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~-~~~i~~P~~~~~   92 (307)
                      ..+++++++-+|..+..              ..+..++|...|+|+.|++|+++++... +...  . ...|...+.+.+
T Consensus       136 ~~~~~~Rl~~~L~~l~~~~g~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~--~~~~~i~i~d~~~L  213 (220)
T 2fmy_A          136 FKDARLRLAEFLVQAAMDTGLKVPQGIKLELGLNTEEIALMLGTTRQTVSVLLNDFKKMGILER--VNQRTLLLKDLQKL  213 (220)
T ss_dssp             THHHHHHHHHHHHHHHHHHCEEETTEEEEECSSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE--SSSSEEEESCHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhCCCCCCcEEEeccCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEE--cCCCEEEEcCHHHH
Confidence            45789999999988753              4789999999999999999999998643 3333  3 445555555444


Q ss_pred             H
Q psy4300          93 V   93 (307)
Q Consensus        93 ~   93 (307)
                      .
T Consensus       214 ~  214 (220)
T 2fmy_A          214 K  214 (220)
T ss_dssp             H
T ss_pred             H
Confidence            3

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=83.99  E-value=2.3  Score=32.80  Aligned_cols=45  Identities=9%  Similarity=0.143  Sum_probs=33.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .++..+...+...+-..+.+..+|+..+|++++|+++.+++....
T Consensus        46 ~lt~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~   90 (162)
T 2fa5_A           46 GMAIPEWRVITILALYPGSSASEVSDRTAMDKVAVSRAVARLLER   90 (162)
T ss_dssp             CCCHHHHHHHHHHHHSTTCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            466655443333333567999999999999999999999987654

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=83.91  E-value=1.5  Score=31.90  Aligned_cols=39  Identities=8%  Similarity=0.155  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          33 EKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        33 ~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+++..|  -..+.+..+|+..+|+|++|+++.++.....
T Consensus        23 r~~IL~~L--~~~~~~~~ela~~l~is~~tv~~~l~~L~~~   61 (114)
T 2oqg_A           23 RWEILTEL--GRADQSASSLATRLPVSRQAIAKHLNALQAC   61 (114)
T ss_dssp             HHHHHHHH--HHSCBCHHHHHHHSSSCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            34444444  3456899999999999999999999998654

>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=83.87  E-value=1.9  Score=33.86  Aligned_cols=42  Identities=7%  Similarity=0.187  Sum_probs=33.7

Q ss_pred             CCCCHHHHHHHHHHHHhc--------CCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMAT--------QLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~--------g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      +.++.+.+..+.+.-...        |.+..++|...|||++|+++|.+.
T Consensus        22 r~yt~EfK~aAv~l~~~~~~~p~~~~~lTv~eIA~~LGIS~~TLyrW~k~   71 (155)
T 2ao9_A           22 QKLTAKQIQAAYLLVENELMESNNEEKRTQDEMANELGINRTTLWEWRTK   71 (155)
T ss_dssp             TTSCHHHHHHHHHHHHHHHCC---CCCCCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             hhcCHHHHHHHHHHHHccccccccccCCCHHHHHHHhCCCHHHHHHHHHc
Confidence            457888888876543322        789999999999999999999983

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=83.83  E-value=2  Score=32.90  Aligned_cols=44  Identities=9%  Similarity=0.305  Sum_probs=33.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      .+++.+...+...+-..+.+..+|+..++++++|+++.+++...
T Consensus        38 ~lt~~~~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~   81 (154)
T 2qww_A           38 GLTIQQLAMINVIYSTPGISVADLTKRLIITGSSAAANVDGLIS   81 (154)
T ss_dssp             TCCHHHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            46775544443333345689999999999999999999988765

>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=83.77  E-value=1.1  Score=29.99  Aligned_cols=28  Identities=7%  Similarity=-0.008  Sum_probs=24.2

Q ss_pred             HHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          41 SYMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        41 ~~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      .+-..|.++.++|...|||++|+++|-+
T Consensus        19 ~R~~~gltq~elA~~~gvs~~tis~~E~   46 (73)
T 3fmy_A           19 VRKKLSLTQKEASEIFGGGVNAFSRYEK   46 (73)
T ss_dssp             HHHHTTCCHHHHHHHHCSCTTHHHHHHT
T ss_pred             HHHHcCCCHHHHHHHhCcCHHHHHHHHc
Confidence            3456799999999999999999998754

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

Probab=83.73  E-value=1.8  Score=34.70  Aligned_cols=44  Identities=16%  Similarity=0.238  Sum_probs=37.6

Q ss_pred             CCCHHHHHHHHHHHHhc-------------CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMAT-------------QLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~-------------g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+++++++-+|..|..             ..+..+||...|+|+.|++|+++++..
T Consensus       134 ~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~~  190 (207)
T 2oz6_A          134 FLDVTGRVARTLLDLCQQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKSLEE  190 (207)
T ss_dssp             HCCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHhcCCCCCCCceecccCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            46799999999988754             258899999999999999999998764

>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=83.71  E-value=2.4  Score=27.16  Aligned_cols=36  Identities=11%  Similarity=0.145  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHh--cCCcHHHHHhhh-----CCChhhHHHHHHH
Q psy4300          34 KKTLVALSYMA--TQLSMRKIGDQF-----NLADSTVWSCIDS   69 (307)
Q Consensus        34 ~~l~i~L~~L~--~g~~~~~l~~~f-----gvs~stv~r~v~~   69 (307)
                      ++..+.+..+.  ...+..+|+..+     +||.+||+|.+++
T Consensus         5 ~R~~~i~~ll~~~~~~t~~el~~~l~~~~~~vs~~Tv~R~L~~   47 (64)
T 2p5k_A            5 QRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIKE   47 (64)
T ss_dssp             HHHHHHHHHHHHSCCCSHHHHHHHHHHTTCCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCcCHHHHHHHHHH
Confidence            44444444443  347889999999     9999999999983

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28

Probab=83.62  E-value=1.7  Score=33.20  Aligned_cols=46  Identities=15%  Similarity=0.081  Sum_probs=35.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..++..+...+...+-..+.+..+|+..++++++|+++.+++....
T Consensus        33 ~~l~~~~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~Le~~   78 (155)
T 1s3j_A           33 QGVTPAQLFVLASLKKHGSLKVSEIAERMEVKPSAVTLMADRLEQK   78 (155)
T ss_dssp             TTCCHHHHHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            4577766544444444557899999999999999999999987654

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}

Probab=83.62  E-value=2  Score=32.67  Aligned_cols=46  Identities=9%  Similarity=0.141  Sum_probs=34.9

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+++.+...+...+-..+.+..+|+..+|++++|+++.+++....
T Consensus        36 ~~lt~~~~~iL~~l~~~~~~t~~ela~~l~~~~~~vs~~l~~Le~~   81 (152)
T 3bj6_A           36 EGVTVGQRAILEGLSLTPGATAPQLGAALQMKRQYISRILQEVQRA   81 (152)
T ss_dssp             TTCCHHHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            3567665544444444557899999999999999999999987654

>2hr3_A Probable transcriptional regulator; MCSG, structural genomics, PSI-2, protein structure initiati midwest center for structural genomics; 2.40A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=83.49  E-value=2.2  Score=32.32  Aligned_cols=45  Identities=4%  Similarity=0.021  Sum_probs=32.5

Q ss_pred             CCCHHHHHHHHHHHH-hcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYM-ATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L-~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .++..+-..+...+- ..+.+..+|+..+|++++|+++.+++....
T Consensus        32 ~l~~~~~~iL~~l~~~~~~~~~~~la~~l~i~~~~vs~~l~~Le~~   77 (147)
T 2hr3_A           32 PVQFSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERG   77 (147)
T ss_dssp             HHHHHHHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHC
Confidence            455544333322233 457899999999999999999999988764

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

Probab=83.32  E-value=1.8  Score=34.96  Aligned_cols=65  Identities=9%  Similarity=0.019  Sum_probs=48.2

Q ss_pred             CCHHHHHHHHHHHHhc-------CCcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHHHHHH
Q psy4300          30 VPVEKKTLVALSYMAT-------QLSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEESVIIE   96 (307)
Q Consensus        30 ~~~~~~l~i~L~~L~~-------g~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~~~~~   96 (307)
                      .+++++++-+|..+..       ..+..++|...|+++.|++|+++++... +...  ....|...+.+.++.++
T Consensus       140 ~~~~~Rl~~~L~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~--~~~~i~i~d~~~L~~~a  212 (216)
T 4ev0_A          140 EEARNRVAYALLKLLRQGLGPLFQIRHHELAALAGTSRETVSRVLHALAEEGVVRL--GPGTVEVREAALLEEIA  212 (216)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCSEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE--ETTEEEESCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhhcCCccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe--cCCEEEEeCHHHHHHHh
Confidence            4688999999987742       2589999999999999999999998654 3333  55556666665554443

>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28

Probab=83.28  E-value=1.4  Score=33.21  Aligned_cols=45  Identities=9%  Similarity=0.044  Sum_probs=32.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .++..+...+...+-..+.+..+++..++++++|+++.+++....
T Consensus        26 ~lt~~~~~iL~~l~~~~~~t~~~la~~l~~s~~~vs~~l~~Le~~   70 (144)
T 1lj9_A           26 SLTRGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQ   70 (144)
T ss_dssp             TCTTTHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHCcCcCHHHHHHHHCCCHhHHHHHHHHHHHC
Confidence            455544433333333456899999999999999999999887653

>1tbx_A ORF F-93, hypothetical 11.0 kDa protein; sulfolobus spindle virus, winged helix, fusellovirus; 2.70A {Sulfolobus virus 1} SCOP: a.4.5.48

Probab=83.25  E-value=1.4  Score=31.29  Aligned_cols=33  Identities=6%  Similarity=0.272  Sum_probs=27.9

Q ss_pred             cCCcHHHH----HhhhCCChhhHHHHHHHHHH-Hcccc
Q psy4300          45 TQLSMRKI----GDQFNLADSTVWSCIDSFLT-AMSQP   77 (307)
Q Consensus        45 ~g~~~~~l----~~~fgvs~stv~r~v~~~~~-~l~~~   77 (307)
                      .+.+..+|    +..++++++|+++.+++... -+...
T Consensus        21 ~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r   58 (99)
T 1tbx_A           21 EGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKE   58 (99)
T ss_dssp             TTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEE
Confidence            46889999    89999999999999999888 44443

>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=83.24  E-value=0.96  Score=29.04  Aligned_cols=27  Identities=7%  Similarity=0.108  Sum_probs=23.4

Q ss_pred             HHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          42 YMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        42 ~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      +-..|.++.++|...|+|++|++++.+
T Consensus        10 r~~~g~s~~~lA~~~gis~~~i~~~e~   36 (66)
T 2xi8_A           10 REKKKISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             HHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            345789999999999999999998765

>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=83.20  E-value=0.43  Score=31.09  Aligned_cols=24  Identities=13%  Similarity=0.155  Sum_probs=20.6

Q ss_pred             hcCCcHHHHHhhhCCChhhHHHHH
Q psy4300          44 ATQLSMRKIGDQFNLADSTVWSCI   67 (307)
Q Consensus        44 ~~g~~~~~l~~~fgvs~stv~r~v   67 (307)
                      ..+.++.++|..+|||++||+++.
T Consensus         8 ~~~~tq~~lA~~lGvs~~~Vs~we   31 (61)
T 1rzs_A            8 DHFGTQRAVAKALGISDAAVSQWK   31 (61)
T ss_dssp             HHHSSHHHHHHHHTCCHHHHHHCC
T ss_pred             HHcCCHHHHHHHhCCCHHHHHHHH
Confidence            344589999999999999999974

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

Probab=83.17  E-value=2.1  Score=34.93  Aligned_cols=45  Identities=9%  Similarity=0.206  Sum_probs=38.3

Q ss_pred             CCCCHHHHHHHHHHHHhcC-------------CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQ-------------LSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g-------------~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ...+++++++-+|..+...             .+..++|...|+++.|++|+++++..
T Consensus       156 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~lt~~~lA~~lg~sr~tvsR~l~~L~~  213 (230)
T 3iwz_A          156 AFLDVTDRIVRTLHDLSKEPEAMSHPQGTQLRVSRQELARLVGCSREMAGRVLKKLQA  213 (230)
T ss_dssp             HHCCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHhhCCCCCCCceecCCCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence            3468999999999988542             47899999999999999999998754

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=83.10  E-value=2.9  Score=34.88  Aligned_cols=49  Identities=6%  Similarity=0.030  Sum_probs=41.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ...++..++-.+.|  +..|.++.++|...|+|.+||...+.+...-|-..
T Consensus       173 ~~~Lt~~e~~vl~~--~~~g~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~  221 (236)
T 2q0o_A          173 KQMLSPREMLCLVW--ASKGKTASVTANLTGINARTVQHYLDKARAKLDAE  221 (236)
T ss_dssp             GGSCCHHHHHHHHH--HHTTCCHHHHHHHHCCCHHHHHHHHHHHHHHHTCS
T ss_pred             cCCCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence            35699988877655  57999999999999999999999999887766554

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

Probab=83.05  E-value=2.2  Score=35.09  Aligned_cols=67  Identities=4%  Similarity=-0.092  Sum_probs=50.1

Q ss_pred             CCCCCHHHHHHHHHHHHhc----------CCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMAT----------QLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVII   95 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~----------g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~   95 (307)
                      ....+++++++-+|..+..          ..+..++|...|+++.|++|+++++...=...  ....|.-.+.+.+..+
T Consensus       149 l~~~~~~~Rl~~~L~~~~~~~~~~~~~~l~~t~~~iA~~lg~sr~tvsR~l~~L~~~gi~~--~~~~i~I~d~~~L~~~  225 (237)
T 3fx3_A          149 LKAQTGAQRVAEFLLELCDCDTGACEVTLPYDKMLIAGRLGMKPESLSRAFSRLKAAGVTV--KRNHAEIEDIALLRDY  225 (237)
T ss_dssp             CCCCCHHHHHHHHHHHHCCC-----EEECCSCTHHHHHHTTCCHHHHHHHHHHHGGGTEEC--CTTEEEESCHHHHHHH
T ss_pred             HhcCCHHHHHHHHHHHHhhhcCCCeEEEecCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEe--eCCEEEEcCHHHHHHH
Confidence            3568899999999999853          24588999999999999999999876554433  5555665555544433

>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=83.02  E-value=2.8  Score=32.03  Aligned_cols=29  Identities=24%  Similarity=0.431  Sum_probs=25.4

Q ss_pred             cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          45 TQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        45 ~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ...++.+||..+|+|++|+++.+++..+.
T Consensus        18 ~~~s~~ela~~lg~s~~tv~~~l~~L~~~   46 (144)
T 2cfx_A           18 SRLSMRELGRKIKLSPPSVTERVRQLESF   46 (144)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            45899999999999999999999887653

>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=82.88  E-value=1.8  Score=31.41  Aligned_cols=30  Identities=3%  Similarity=0.058  Sum_probs=25.8

Q ss_pred             hcCCcHHHHHhhh-CCChhhHHHHHHHHHHH
Q psy4300          44 ATQLSMRKIGDQF-NLADSTVWSCIDSFLTA   73 (307)
Q Consensus        44 ~~g~~~~~l~~~f-gvs~stv~r~v~~~~~~   73 (307)
                      ..+.++.+|+..+ |+|++|+++.+++....
T Consensus        25 ~~~~~~~eLa~~l~~is~~tls~~L~~Le~~   55 (107)
T 2hzt_A           25 HGKKRTSELKRLMPNITQKMLTQQLRELEAD   55 (107)
T ss_dssp             TCCBCHHHHHHHCTTSCHHHHHHHHHHHHHT
T ss_pred             hCCCCHHHHHHHhcCCCHHHHHHHHHHHHHC
Confidence            3458999999999 99999999999987654

>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28

Probab=82.87  E-value=1.8  Score=32.67  Aligned_cols=45  Identities=9%  Similarity=0.168  Sum_probs=33.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .++..+...+...+-..+.+..+|+..++++++|+++.+++....
T Consensus        34 ~l~~~~~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~   78 (142)
T 2bv6_A           34 NLTYPQFLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQV   78 (142)
T ss_dssp             TCCHHHHHHHHHHHHSSEEEHHHHHHHTTCCTTTHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHC
Confidence            466655444333333456899999999999999999999987664

>3kp7_A Transcriptional regulator TCAR; multiple drug resistance, biofilm, transcription regulation, binding, transcription regulator; 2.30A {Staphylococcus epidermidis RP62A} PDB: 3kp3_A* 3kp4_A* 3kp5_A* 3kp2_A* 3kp6_A

Probab=82.86  E-value=2.3  Score=32.44  Aligned_cols=44  Identities=14%  Similarity=0.239  Sum_probs=34.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .+++.+-..+... -..+.+..+||..++++++|+++.+++....
T Consensus        35 ~lt~~q~~iL~~l-~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~   78 (151)
T 3kp7_A           35 GISAEQSHVLNML-SIEALTVGQITEKQGVNKAAVSRRVKKLLNA   78 (151)
T ss_dssp             TCCHHHHHHHHHH-HHSCBCHHHHHHHHCSCSSHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHH-HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            4666555444444 6678999999999999999999999987643

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

Probab=82.85  E-value=0.24  Score=41.17  Aligned_cols=45  Identities=9%  Similarity=0.184  Sum_probs=0.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+|+.++-++.|+|+ .|.++.++|..+|+|.+||.+.+.+....
T Consensus       197 ~~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~~~ra~~~  241 (243)
T 1l0o_C          197 EELDERERLIVYLRYY-KDQTQSEVASRLGISQVQMSRLEKKILQH  241 (243)
T ss_dssp             ----------------------------------------------
T ss_pred             HhCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            5688888888888886 57999999999999999999888776543

>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=82.81  E-value=3.4  Score=31.82  Aligned_cols=44  Identities=18%  Similarity=0.233  Sum_probs=31.5

Q ss_pred             CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ++..+.-.+.+..-....++.+||..+|+|++|+++.+++....
T Consensus         5 ld~~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~   48 (151)
T 2cyy_A            5 LDEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRES   48 (151)
T ss_dssp             CCHHHHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            44544433332222345899999999999999999999988654

>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=82.62  E-value=2.9  Score=32.14  Aligned_cols=28  Identities=14%  Similarity=0.197  Sum_probs=24.9

Q ss_pred             cCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          45 TQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        45 ~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ...++.+||..+|+|++|+++.+++...
T Consensus        20 ~~~s~~ela~~lg~s~~tv~~~l~~L~~   47 (150)
T 2w25_A           20 GRATLSELATRAGLSVSAVQSRVRRLES   47 (150)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4589999999999999999999888754

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=82.61  E-value=2.3  Score=33.27  Aligned_cols=46  Identities=7%  Similarity=0.123  Sum_probs=35.2

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..++..+...+...+-..+.+..+|+..+|++++|+++.+++....
T Consensus        41 ~~lt~~~~~iL~~L~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~   86 (168)
T 2nyx_A           41 ENITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGA   86 (168)
T ss_dssp             SSCCHHHHHHHHHHHHHCSEEHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence            3577765544444444557999999999999999999999987654

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

Probab=82.61  E-value=2  Score=35.81  Aligned_cols=44  Identities=14%  Similarity=0.147  Sum_probs=37.9

Q ss_pred             CCCHHHHHHHHHHHHhc--------------CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMAT--------------QLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~--------------g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+++++|+-+|..++.              ..+..+||...|+|+.|++|+++++..
T Consensus       162 ~~~~~~Rla~~L~~l~~~~g~~~~~~~~i~~~lt~~~lA~~lG~sr~tvsR~l~~L~~  219 (243)
T 3la7_A          162 HRDMGSRLVSFLLILCRDFGVPCADGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLRE  219 (243)
T ss_dssp             CSSHHHHHHHHHHHHHHHHEEECSSSEEECSCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhCCCCCCCeEEeccCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence            46799999999988742              368899999999999999999998765

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=82.59  E-value=0.74  Score=35.75  Aligned_cols=44  Identities=9%  Similarity=0.156  Sum_probs=32.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      .++..+-..+...+-..+.+..+||..++++++|+++.+++...
T Consensus        47 ~lt~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~   90 (159)
T 3s2w_A           47 GIGSGQFPFLMRLYREDGINQESLSDYLKIDKGTTARAIQKLVD   90 (159)
T ss_dssp             TCCTTTHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            45554433333333346789999999999999999999998765

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=82.44  E-value=2.2  Score=29.33  Aligned_cols=28  Identities=7%  Similarity=0.224  Sum_probs=23.4

Q ss_pred             cCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          45 TQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        45 ~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ...+..+|+..|+||.+||.+-++.+..
T Consensus        15 g~vsv~eLa~~l~VS~~TIRrdL~~Le~   42 (78)
T 1xn7_A           15 GRMEAAQISQTLNTPQPMINAMLQQLES   42 (78)
T ss_dssp             CSBCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3478999999999999998887776644

>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=82.44  E-value=1.3  Score=32.97  Aligned_cols=34  Identities=6%  Similarity=0.121  Sum_probs=27.9

Q ss_pred             HHHHh--cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          40 LSYMA--TQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        40 L~~L~--~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      |..|.  .+.+..+|+..+|+|++|+++.++.....
T Consensus        48 L~~L~~~~~~s~~eLa~~l~is~stvs~~L~~L~~~   83 (122)
T 1u2w_A           48 TYALCQDEELCVCDIANILGVTIANASHHLRTLYKQ   83 (122)
T ss_dssp             HHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            33444  45799999999999999999999988653

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=82.34  E-value=1.4  Score=29.93  Aligned_cols=23  Identities=26%  Similarity=0.401  Sum_probs=21.4

Q ss_pred             hcCCcHHHHHhhhCCChhhHHHH
Q psy4300          44 ATQLSMRKIGDQFNLADSTVWSC   66 (307)
Q Consensus        44 ~~g~~~~~l~~~fgvs~stv~r~   66 (307)
                      ..|.+..+||...|+|++|++++
T Consensus        20 ~~glT~~~LA~~~Gvs~stls~~   42 (74)
T 1neq_A           20 KRKLSLSALSRQFGYAPTTLANA   42 (74)
T ss_dssp             TTSCCHHHHHHHHSSCHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHH
Confidence            77999999999999999999975

>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=82.18  E-value=1.4  Score=28.78  Aligned_cols=27  Identities=4%  Similarity=0.110  Sum_probs=23.4

Q ss_pred             HHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          42 YMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        42 ~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      +...|.++.++|...|+|+++++++.+
T Consensus        12 r~~~glsq~~lA~~~gis~~~i~~~e~   38 (71)
T 1zug_A           12 RIALKMTQTELATKAGVKQQSIQLIEA   38 (71)
T ss_dssp             HHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            345689999999999999999998765

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=82.10  E-value=2.1  Score=37.64  Aligned_cols=37  Identities=11%  Similarity=0.170  Sum_probs=31.0

Q ss_pred             HHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          36 TLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        36 l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      .-+...|+..+.+..+||..||||++||+|-+....+
T Consensus        11 ~~ia~l~~~~~~~~~ela~~l~vS~~tIrRdL~~l~~   47 (315)
T 2w48_A           11 VKIAQLYYEQDMTQAQIARELGIYRTTISRLLKRGRE   47 (315)
T ss_dssp             HHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3455556778899999999999999999999997654

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

Probab=82.09  E-value=3.5  Score=33.61  Aligned_cols=63  Identities=16%  Similarity=0.172  Sum_probs=46.6

Q ss_pred             CCCHHHHHHHHHHHHh--------------cCCcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHHH
Q psy4300          29 FVPVEKKTLVALSYMA--------------TQLSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEESV   93 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~--------------~g~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~~   93 (307)
                      ..+++++++-+|..++              ...+..++|...|+|+.|++|+++++... +...  ....|...+.+.+.
T Consensus       146 ~~~~~~Rl~~~L~~l~~~~~~~~~~~~~i~~~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~--~~~~i~i~d~~~L~  223 (227)
T 3d0s_A          146 FTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRL--EGKSVLISDSERLA  223 (227)
T ss_dssp             HSCHHHHHHHHHHHHHHHHEEEETTEEEEECCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE--ETTEEEESCHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhCCcCCCceEEcCCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe--cCCEEEEcCHHHHH
Confidence            4679999999998874              13689999999999999999999998753 3333  44555555554444

>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=81.91  E-value=1.4  Score=28.49  Aligned_cols=27  Identities=4%  Similarity=0.099  Sum_probs=23.4

Q ss_pred             HHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          42 YMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        42 ~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      +...|.++.++|...|+|+++++++.+
T Consensus        10 r~~~glsq~~lA~~~gis~~~i~~~e~   36 (69)
T 1r69_A           10 RIQLGLNQAELAQKVGTTQQSIEQLEN   36 (69)
T ss_dssp             HHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            345789999999999999999999765

>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi}

Probab=81.88  E-value=2.2  Score=33.03  Aligned_cols=45  Identities=16%  Similarity=0.173  Sum_probs=34.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .+++.+-..+...+-..+.+..+|+..+|++++|+++.+++....
T Consensus        50 glt~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~   94 (161)
T 3e6m_A           50 KLPTPKLRLLSSLSAYGELTVGQLATLGVMEQSTTSRTVDQLVDE   94 (161)
T ss_dssp             TCCHHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            466655544444444558999999999999999999999987653

>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=81.83  E-value=1.4  Score=30.24  Aligned_cols=26  Identities=12%  Similarity=0.143  Sum_probs=23.2

Q ss_pred             HhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          43 MATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        43 L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      -..|.++.++|...|+|+++++++.+
T Consensus        28 ~~~glsq~elA~~~gis~~~is~~e~   53 (83)
T 2a6c_A           28 RNSGLTQFKAAELLGVTQPRVSDLMR   53 (83)
T ss_dssp             HTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            46689999999999999999999775

>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=81.75  E-value=3.5  Score=31.75  Aligned_cols=44  Identities=9%  Similarity=0.190  Sum_probs=31.5

Q ss_pred             CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ++..+.-.+.+..-....++.+||..+|+|++|+++.+++..+.
T Consensus         6 ld~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~   49 (152)
T 2cg4_A            6 IDNLDRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQA   49 (152)
T ss_dssp             CCHHHHHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence            44444333332222345899999999999999999999988664

>1p6r_A Penicillinase repressor; transcription regulation, DNA-binding, winged helix protein, bacterial resistance to antibiotics; NMR {Bacillus licheniformis} SCOP: a.4.5.39 PDB: 2p7c_B

Probab=81.67  E-value=2.7  Score=28.66  Aligned_cols=43  Identities=2%  Similarity=0.118  Sum_probs=31.8

Q ss_pred             CCCHHH-HHHHHHHHHhcCCcHHHHHhhhC----CChhhHHHHHHHHHH
Q psy4300          29 FVPVEK-KTLVALSYMATQLSMRKIGDQFN----LADSTVWSCIDSFLT   72 (307)
Q Consensus        29 ~~~~~~-~l~i~L~~L~~g~~~~~l~~~fg----vs~stv~r~v~~~~~   72 (307)
                      .++..+ .++.+|+. ..+.+..+|+..++    ++.+||++.+++...
T Consensus         6 ~lt~~e~~vL~~L~~-~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~   53 (82)
T 1p6r_A            6 QISDAELEVMKVIWK-HSSINTNEVIKELSKTSTWSPKTIQTMLLRLIK   53 (82)
T ss_dssp             CCCHHHHHHHHHHHT-SSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHc-CCCCCHHHHHHHHhhcCCccHHHHHHHHHHHHH
Confidence            456644 44444544 55789999999996    799999999988754

>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=81.67  E-value=2.6  Score=31.92  Aligned_cols=29  Identities=7%  Similarity=0.283  Sum_probs=25.4

Q ss_pred             cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          45 TQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        45 ~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ...++.+||..+|+|++|+++.+++....
T Consensus        17 ~~~~~~ela~~lg~s~~tv~~~l~~L~~~   45 (141)
T 1i1g_A           17 ARTPFTEIAKKLGISETAVRKRVKALEEK   45 (141)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            34799999999999999999999987654

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus}

Probab=81.66  E-value=1.2  Score=32.33  Aligned_cols=37  Identities=14%  Similarity=0.139  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHH--hcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          32 VEKKTLVALSYM--ATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        32 ~~~~l~i~L~~L--~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      ..+.+.-.|..+  ..|.++.++|...|||++|++++=+
T Consensus        33 l~~~lG~~ir~~R~~~glTQ~eLA~~~gvs~~~is~~E~   71 (101)
T 4ghj_A           33 LAEEIGDRLKQARLNRDLTQSEVAEIAGIARKTVLNAEK   71 (101)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHC
Confidence            456677666655  6799999999999999999998743

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=81.58  E-value=1.4  Score=29.81  Aligned_cols=28  Identities=14%  Similarity=0.088  Sum_probs=24.3

Q ss_pred             HHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          41 SYMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        41 ~~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      .+...|.++.++|...|||+++++++.+
T Consensus        18 ~R~~~gltq~elA~~~gis~~~is~~E~   45 (78)
T 3qq6_A           18 YRKEKGYSLSELAEKAGVAKSYLSSIER   45 (78)
T ss_dssp             HHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4567799999999999999999998754

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=81.58  E-value=1.2  Score=30.07  Aligned_cols=22  Identities=9%  Similarity=0.247  Sum_probs=20.0

Q ss_pred             cHHHHHhhhCCChhhHHHHHHH
Q psy4300          48 SMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        48 ~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      +...||..+|||++||++|++.
T Consensus        12 ~~~~lA~~lGVs~~aVs~W~~g   33 (71)
T 2hin_A           12 DVEKAAVGVGVTPGAVYQWLQA   33 (71)
T ss_dssp             SHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHhC
Confidence            4889999999999999999864

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=81.55  E-value=3.4  Score=31.73  Aligned_cols=44  Identities=18%  Similarity=0.226  Sum_probs=31.4

Q ss_pred             CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ++..++-.+.+..-....++.+||..+|+|++|+++.+++....
T Consensus         7 ld~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~   50 (151)
T 2dbb_A            7 LDRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKL   50 (151)
T ss_dssp             CCHHHHHHHHHHHHCTTCCHHHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            44544433333233345899999999999999999999987654

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=81.26  E-value=1.6  Score=29.50  Aligned_cols=25  Identities=8%  Similarity=0.106  Sum_probs=22.2

Q ss_pred             hcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          44 ATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        44 ~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      ..| ++.++|...|||++|++++.+.
T Consensus        10 ~~g-sq~~lA~~lgvs~~~is~~e~g   34 (79)
T 3bd1_A           10 KLG-SVSALAASLGVRQSAISNWRAR   34 (79)
T ss_dssp             HHS-SHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HhC-CHHHHHHHHCCCHHHHHHHHHC
Confidence            447 9999999999999999998774

>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=81.21  E-value=1.9  Score=30.75  Aligned_cols=30  Identities=10%  Similarity=0.221  Sum_probs=26.1

Q ss_pred             hcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          44 ATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ....+..+|+..+|+|++|+++.++....+
T Consensus        34 ~~~~~~~ela~~l~is~~tvs~~L~~L~~~   63 (102)
T 3pqk_A           34 EGEFSVGELEQQIGIGQPTLSQQLGVLRES   63 (102)
T ss_dssp             TCCBCHHHHHHHHTCCTTHHHHHHHHHHHT
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            345799999999999999999999988664

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=81.20  E-value=1.8  Score=31.52  Aligned_cols=30  Identities=7%  Similarity=0.099  Sum_probs=26.3

Q ss_pred             hcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          44 ATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+.+..+|+..+|+|++|+++.++....+
T Consensus        36 ~~~~s~~eLa~~lgis~stvs~~L~~L~~~   65 (108)
T 2kko_A           36 QGERAVEAIATATGMNLTTASANLQALKSG   65 (108)
T ss_dssp             TCCEEHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             cCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            345799999999999999999999988764

>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=81.18  E-value=0.84  Score=30.35  Aligned_cols=21  Identities=14%  Similarity=0.213  Sum_probs=20.1

Q ss_pred             cHHHHHhhhCCChhhHHHHHH
Q psy4300          48 SMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        48 ~~~~l~~~fgvs~stv~r~v~   68 (307)
                      ++..+|..+||++++||++++
T Consensus        15 s~t~aA~~L~vtQ~AVS~~ir   35 (66)
T 2ovg_A           15 GQTKTAKDLGVYPSSINQAIH   35 (66)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHH
T ss_pred             CHHHHHHHhCCCHHHHHHHHH
Confidence            999999999999999999985

>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=81.04  E-value=3.5  Score=28.12  Aligned_cols=34  Identities=12%  Similarity=0.003  Sum_probs=28.7

Q ss_pred             HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      .+.-.|..++...++.++|...|||+++++++-+
T Consensus        16 ~~g~~l~~~R~~~sq~~lA~~~gis~~~is~~E~   49 (86)
T 2ofy_A           16 RLGELLRSARGDMSMVTVAFDAGISVETLRKIET   49 (86)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHCCHHHHHHHhCCCHHHHHHHHc
Confidence            4666777787777999999999999999998765

>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structu genomics, protein structure initiative, midwest center for structural genomics; HET: GOL; 2.00A {Rhodococcus jostii}

Probab=80.98  E-value=2.1  Score=32.61  Aligned_cols=45  Identities=13%  Similarity=0.162  Sum_probs=31.9

Q ss_pred             CCCCHHHHHHHH-HHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVA-LSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        28 ~~~~~~~~l~i~-L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..++..+-..+. |..-..+.+..+|+..++++++|+++.+++...
T Consensus        35 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~   80 (150)
T 3fm5_A           35 TGLRVRSYSVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVDELEE   80 (150)
T ss_dssp             GTCCHHHHHHHHHHHHSTTCCCSHHHHHHHTCCHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHhCCCCcCHHHHHHHHCCCHhHHHHHHHHHHH
Confidence            346665543333 222233569999999999999999999998764

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=80.82  E-value=1.4  Score=29.19  Aligned_cols=43  Identities=12%  Similarity=0.019  Sum_probs=31.8

Q ss_pred             HhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHH
Q psy4300          43 MATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNF   99 (307)
Q Consensus        43 L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f   99 (307)
                      -..|.++.++|...|+|++|++++.+.           .   .-|+.+.+..+++.|
T Consensus        18 ~~~glsq~~lA~~~gis~~~is~~e~g-----------~---~~~~~~~l~~ia~~l   60 (73)
T 3omt_A           18 AEKGKTNLWLTETLDKNKTTVSKWCTN-----------D---VQPSLETLFDIAEAL   60 (73)
T ss_dssp             HHHTCCHHHHHHHTTCCHHHHHHHHTT-----------S---SCCCHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHcC-----------C---CCCCHHHHHHHHHHH
Confidence            356899999999999999999997652           1   225655566666655

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=80.81  E-value=2.8  Score=31.64  Aligned_cols=44  Identities=9%  Similarity=0.154  Sum_probs=31.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .+++.+-..+...+ .++.+..+|+..+|++++|+++.+++....
T Consensus        34 ~lt~~~~~iL~~l~-~~~~~~~~la~~l~~~~~tvs~~l~~Le~~   77 (144)
T 3f3x_A           34 NLSYLDFSILKATS-EEPRSMVYLANRYFVTQSAITAAVDKLEAK   77 (144)
T ss_dssp             SCCHHHHHHHHHHH-HSCEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHH-HCCCCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence            46665533332222 233399999999999999999999998764

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=80.80  E-value=1.6  Score=29.04  Aligned_cols=34  Identities=15%  Similarity=0.073  Sum_probs=26.4

Q ss_pred             HHHHHHHHH--hcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          35 KTLVALSYM--ATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        35 ~l~i~L~~L--~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      .+.-.|..+  ..|.++.++|...|+|+++++++.+
T Consensus        10 ~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   45 (77)
T 2b5a_A           10 KFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVER   45 (77)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHC
Confidence            344444443  5689999999999999999999765

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=80.73  E-value=0.85  Score=34.58  Aligned_cols=46  Identities=11%  Similarity=0.117  Sum_probs=33.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+++.+-..+...+-..+.+..+|+..++++++|+++.+++....
T Consensus        32 ~glt~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~   77 (140)
T 3hsr_A           32 YDLTYTGYIVLMAIENDEKLNIKKLGERVFLDSGTLTPLLKKLEKK   77 (140)
T ss_dssp             GTCCHHHHHHHHHSCTTCEEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHC
Confidence            3567666433333222456899999999999999999999987653

>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=80.69  E-value=2.7  Score=29.47  Aligned_cols=29  Identities=14%  Similarity=0.155  Sum_probs=26.2

Q ss_pred             cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          45 TQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        45 ~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .+.+..+++..+|+|++|+++.++.....
T Consensus        29 ~~~~~~ela~~l~is~~tvs~~l~~L~~~   57 (100)
T 1ub9_A           29 RKAPFSQIQKVLDLTPGNLDSHIRVLERN   57 (100)
T ss_dssp             SEEEHHHHHHHTTCCHHHHHHHHHHHHHT
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            46899999999999999999999998764

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi}

Probab=80.68  E-value=1.7  Score=30.01  Aligned_cols=35  Identities=11%  Similarity=0.044  Sum_probs=27.6

Q ss_pred             HHHHHHHHHH--hcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          34 KKTLVALSYM--ATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        34 ~~l~i~L~~L--~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      ..+.-.|..+  ..|.++.++|...|+|+++++++-+
T Consensus        13 ~~~g~~l~~~R~~~gltq~elA~~~gis~~~is~~E~   49 (86)
T 3eus_A           13 VYLCQRLRQARLDAGLTQADLAERLDKPQSFVAKVET   49 (86)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHC
Confidence            3455555544  5799999999999999999998754

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

Probab=80.68  E-value=1.5  Score=36.68  Aligned_cols=66  Identities=15%  Similarity=0.063  Sum_probs=48.9

Q ss_pred             CCCCHHHHHHHHHHHHhc--------------CCcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHH
Q psy4300          28 PFVPVEKKTLVALSYMAT--------------QLSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEES   92 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~--------------g~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~   92 (307)
                      ...+++++|+-+|..++.              ..+..++|...|+|+.|++|+++++... +...  ....|...+.+.+
T Consensus       145 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~i~~~~t~~~iA~~lG~sr~tvsR~l~~L~~~g~I~~--~~~~i~i~d~~~L  222 (250)
T 3e6c_C          145 NTYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLASLKRENILDK--KKNKIIVYNLGEL  222 (250)
T ss_dssp             TTSCHHHHHHHHHHHHHHHHCEEETTEEEEECCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE--CSSEEEESCHHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHhCCCCCCCcEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCeEe--CCCEEEEecHHHH
Confidence            457899999999988742              3589999999999999999999998764 4444  4445555555444


Q ss_pred             HHH
Q psy4300          93 VII   95 (307)
Q Consensus        93 ~~~   95 (307)
                      ..+
T Consensus       223 ~~~  225 (250)
T 3e6c_C          223 KHL  225 (250)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=80.61  E-value=3.7  Score=32.03  Aligned_cols=45  Identities=9%  Similarity=0.110  Sum_probs=32.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .++..+.-.+.+..-....++.+||..+|+|++|+++.+++....
T Consensus         7 ~ld~~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~   51 (162)
T 2p5v_A            7 TLDKTDIKILQVLQENGRLTNVELSERVALSPSPCLRRLKQLEDA   51 (162)
T ss_dssp             CCCHHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            355555433333222345899999999999999999999988654

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

Probab=80.56  E-value=1.6  Score=40.24  Aligned_cols=47  Identities=9%  Similarity=0.174  Sum_probs=36.7

Q ss_pred             CCCHHHHHHHHHHHH-h--cCCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300          29 FVPVEKKTLVALSYM-A--TQLSMRKIGDQFNLADSTVWSCIDSFLTAMS   75 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L-~--~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~   75 (307)
                      .++..++-.+.|+|. .  .+.++.+||..+|||+.+|..+..+...-|-
T Consensus       360 ~L~~rer~Vl~lr~~L~~~e~~Tl~EIA~~lgiS~erVrqi~~rAl~kLR  409 (423)
T 2a6h_F          360 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK  409 (423)
T ss_dssp             SSCHHHHHHHHHHHHTTCC-----CHHHHSSSSCHHHHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence            578888888999884 3  5789999999999999999999998887776

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=80.50  E-value=2.4  Score=32.48  Aligned_cols=46  Identities=9%  Similarity=0.036  Sum_probs=34.0

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..++..+...+...+-..+.+..+|+..+|++++|+++.+++....
T Consensus        39 ~~lt~~~~~iL~~l~~~~~~t~~ela~~l~i~~~tvs~~l~~Le~~   84 (155)
T 3cdh_A           39 QGLRVPEWRVLACLVDNDAMMITRLAKLSLMEQSRMTRIVDQMDAR   84 (155)
T ss_dssp             TTCCHHHHHHHHHHSSCSCBCHHHHHHHTTCCHHHHHHHHHHHHHT
T ss_pred             cCCCHHHHHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            3567665544333333446899999999999999999999987654

>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=80.43  E-value=2.8  Score=31.28  Aligned_cols=34  Identities=21%  Similarity=0.327  Sum_probs=28.3

Q ss_pred             HHHHhc-CCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          40 LSYMAT-QLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        40 L~~L~~-g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      |..|.. +.+..+++..+|+|++|+++.++....+
T Consensus        52 L~~L~~~~~s~~ela~~lgis~stvs~~L~~Le~~   86 (122)
T 1r1t_A           52 LSLLARSELCVGDLAQAIGVSESAVSHQLRSLRNL   86 (122)
T ss_dssp             HHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            334444 5799999999999999999999998774

>1okr_A MECI, methicillin resistance regulatory protein MECI; bacterial antibiotic resistance, MECI protein, transcriptional regulatory element; 2.4A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1sax_A 1sd7_A 2d45_A 1sd6_A

Probab=80.38  E-value=3.1  Score=30.52  Aligned_cols=44  Identities=9%  Similarity=0.076  Sum_probs=33.8

Q ss_pred             CCCHHHH-HHHHHHHHhcCCcHHHHHhhhC----CChhhHHHHHHHHHHH
Q psy4300          29 FVPVEKK-TLVALSYMATQLSMRKIGDQFN----LADSTVWSCIDSFLTA   73 (307)
Q Consensus        29 ~~~~~~~-l~i~L~~L~~g~~~~~l~~~fg----vs~stv~r~v~~~~~~   73 (307)
                      .++..+. ++.+|+. ..+.+..+|+..++    ++++|+++++++....
T Consensus         7 ~lt~~~~~vL~~l~~-~~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~   55 (123)
T 1okr_A            7 EISSAEWEVMNIIWM-KKYASANNIIEEIQMQKDWSPKTIRTLITRLYKK   55 (123)
T ss_dssp             CCCHHHHHHHHHHHH-HSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHh-CCCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHC
Confidence            4666544 4444544 66899999999999    8899999999987763

>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=80.36  E-value=2  Score=29.41  Aligned_cols=27  Identities=4%  Similarity=0.162  Sum_probs=23.8

Q ss_pred             HhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          43 MATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        43 L~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      ...|.++.++|...|+|+++++++.+.
T Consensus        22 ~~~glsq~~lA~~~gis~~~i~~~e~g   48 (88)
T 2wiu_B           22 QQNGWTQSELAKKIGIKQATISNFENN   48 (88)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence            356899999999999999999998763

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=80.30  E-value=1.4  Score=31.28  Aligned_cols=33  Identities=12%  Similarity=0.219  Sum_probs=27.4

Q ss_pred             HHHhc-CCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          41 SYMAT-QLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        41 ~~L~~-g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..|.. +.+..+|+..+|+|++|+++.++...++
T Consensus        30 ~~L~~~~~~~~ela~~l~is~~tvs~~L~~L~~~   63 (98)
T 3jth_A           30 CMLHNQELSVGELCAKLQLSQSALSQHLAWLRRD   63 (98)
T ss_dssp             HHTTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            44444 5699999999999999999999988664

>3szt_A QCSR, quorum-sensing control repressor; quorum sensing acyl-homoserine lactone, helix-turn-helix, transcription factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas aeruginosa}

Probab=80.30  E-value=3.4  Score=34.53  Aligned_cols=49  Identities=12%  Similarity=0.107  Sum_probs=41.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ...+++.++-.+.|  ++.|.+..++|...|+|..||...+.+...-+-..
T Consensus       173 ~~~Lt~re~~vl~~--~~~G~s~~eIa~~l~is~~tV~~~~~~~~~kl~~~  221 (237)
T 3szt_A          173 NVRLTARETEMLKW--TAVGKTYGEIGLILSIDQRTVKFHIVNAMRKLNSS  221 (237)
T ss_dssp             GCCCCHHHHHHHHH--HHTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCS
T ss_pred             CCCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence            46799988866655  68999999999999999999999999887766544

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=80.23  E-value=3.1  Score=30.09  Aligned_cols=28  Identities=14%  Similarity=0.253  Sum_probs=24.9

Q ss_pred             CCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          46 QLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        46 g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+..+||..+|+|++||++.+......
T Consensus        33 ~~s~~eLa~~lgvs~~tV~~~L~~L~~~   60 (110)
T 1q1h_A           33 EMTDEEIANQLNIKVNDVRKKLNLLEEQ   60 (110)
T ss_dssp             CBCHHHHHHTTTSCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            5799999999999999999999987654

>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=80.16  E-value=2.7  Score=33.58  Aligned_cols=38  Identities=26%  Similarity=0.357  Sum_probs=29.2

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      .++.+++.   + ..++..|.+...+|..+|+|.+|+++++.
T Consensus       143 ~~~~~~~~---i-~~~~~~G~s~~~Ia~~l~is~~tv~r~l~  180 (183)
T 1gdt_A          143 KRKIDRDA---V-LNMWQQGLGASHISKTMNIARSTVYKVIN  180 (183)
T ss_dssp             CCCSCHHH---H-HHHHHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCCHHH---H-HHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence            44555542   2 34557899999999999999999999875

>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=80.04  E-value=1.6  Score=28.17  Aligned_cols=26  Identities=4%  Similarity=0.119  Sum_probs=22.6

Q ss_pred             HhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          43 MATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        43 L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      -..|.++.++|...|+|+++++++.+
T Consensus        15 ~~~g~s~~~lA~~~gis~~~i~~~e~   40 (68)
T 2r1j_L           15 KKLKIRQAALGKMVGVSNVAISQWER   40 (68)
T ss_dssp             HHHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            34688999999999999999998764

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	307
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	97.53
d1hlva1	66	DNA-binding domain of centromere binding protein B	96.93
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	95.94
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	95.91
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	95.57
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	95.5
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	95.2
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	95.17
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	94.78
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	94.57
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	94.4
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	94.09
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	94.06
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	93.93
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	93.55
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	93.35
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	93.11
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	92.92
d2ofya1	82	Putative transcriptional regulator RHA1_ro04071 {R	92.88
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	92.82
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	92.67
d1l8qa1	110	Chromosomal replication initiation factor DnaA C-t	92.62
d1zyba1	73	Probable transcription regulator BT4300, C-termina	92.39
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	92.26
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	92.14
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	91.91
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	91.76
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	91.64
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	91.23
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	90.99
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	90.73
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	90.33
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	90.31
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	90.27
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	89.96
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	89.42
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	89.34
d1j1va_	94	Chromosomal replication initiation factor DnaA C-t	89.32
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	88.91
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	88.29
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	88.24
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	88.05
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	87.93
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	87.86
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	87.56
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	86.4
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	86.35
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	85.69
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	85.29
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	85.25
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	85.24
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	85.07
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	85.0
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	84.47
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	84.05
d1ixca1	89	LysR-type regulatory protein CbnR {Ralstonia eutro	83.23
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	82.8
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	82.72
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	82.7
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	82.58
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	82.34
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	81.96
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	81.85
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	81.68
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	81.6
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	81.27
d1y7ya1	69	Restriction-modification controller protein C.AhdI	81.27
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	80.75
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	80.68
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	80.68
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	80.08
d2esna1	89	Probable LysR-type transcriptional regulator PA047	80.01

>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=97.53  E-value=5e-05  Score=46.09  Aligned_cols=40  Identities=8%  Similarity=0.068  Sum_probs=34.7

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCI   67 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v   67 (307)
                      .+.++. +|+..+...++.|.+..+||..||||++|++|++
T Consensus         3 ~~~lt~-~q~~~a~~l~~~G~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           3 PRAINK-HEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             CCSSCH-HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             CCcCCH-HHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHhhC
Confidence            344554 7888889999999999999999999999999985

>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=96.93  E-value=0.001  Score=43.07  Aligned_cols=43  Identities=16%  Similarity=0.219  Sum_probs=37.3

Q ss_pred             CCCCCHHHHHHHHHHHHhcC-CcHHHHHhhhCCChhhHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQ-LSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g-~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      +..++.++++-+.-.+=.+. .+..+||..|||++|||+.|++.
T Consensus         5 Rk~LT~~eK~~ii~~~e~g~k~sq~eIA~~fGv~~STvs~IlKn   48 (66)
T d1hlva1           5 RRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKN   48 (66)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHT
T ss_pred             cccCCHHHHHHHHHHHHcCCcchHHHHHHHhCCChhHHHHHHHH
Confidence            56899999999877766654 58999999999999999999875

>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=95.94  E-value=0.013  Score=37.34  Aligned_cols=44  Identities=9%  Similarity=0.125  Sum_probs=32.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      +++|.+.+--+. -....|.|-+++|..|+||.+|+++|+.+.-+
T Consensus        13 rPls~DLR~Riv-~~~~~G~s~r~aA~rf~VS~s~v~k~l~r~re   56 (63)
T d1k78a1          13 RPLPDVVRQRIV-ELAHQGVRPCDISRQLRVSHGCVSKILGRYYE   56 (63)
T ss_dssp             SCCCHHHHHHHH-HHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            455554443333 23458999999999999999999999988643

>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=95.91  E-value=0.0099  Score=38.70  Aligned_cols=49  Identities=14%  Similarity=0.223  Sum_probs=42.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+|+.++-++.|+|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus        20 ~~L~~~~r~v~~l~~~-~~~s~~eIA~~lgis~~tv~~~~~ra~~~Lr~~   68 (71)
T d1rp3a2          20 SKLPEREKLVIQLIFY-EELPAKEVAKILETSVSRVSQLKAKALERLREM   68 (71)
T ss_dssp             TTSCHHHHHHHHHHHT-SCCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCHHHHHHHHHHHh-HhCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence            4688999999999887 479999999999999999999999887776554

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=95.57  E-value=0.011  Score=40.44  Aligned_cols=44  Identities=16%  Similarity=0.160  Sum_probs=38.5

Q ss_pred             CCCCCHHHHHHHHHHHHhc-CCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMAT-QLSMRKIGDQFNLADSTVWSCIDSF   70 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~-g~~~~~l~~~fgvs~stv~r~v~~~   70 (307)
                      +...|.+-+.-++-.++.+ |.|+.++|..+|||.+|+++|+++.
T Consensus         3 rk~Ys~EfK~~aV~l~~~~~g~s~~~vA~~lGIs~~tl~~W~k~~   47 (89)
T d2jn6a1           3 TKTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKY   47 (89)
T ss_dssp             CCCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHcCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence            3568999888888777764 8999999999999999999999986

>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=95.50  E-value=0.016  Score=42.36  Aligned_cols=46  Identities=11%  Similarity=0.089  Sum_probs=40.0

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..++|.+.+.-+.-.+ ..|.+.+++|..|+||++||++++.+.-..
T Consensus        14 GrpLs~dlR~rIv~~~-~~G~s~r~iA~~~~VS~~tV~k~l~r~~~~   59 (123)
T d1pdnc_          14 GRPLPNNIRLKIVEMA-ADGIRPCVISRQLRVSHGCVSKILNRYQET   59 (123)
T ss_dssp             TSCCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CcCCCHHHHHHHHHHH-HhcCCHHHHHHHHCcCHHHHHHHHHHHHcc
Confidence            5788888888777754 679999999999999999999999998763

>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=95.20  E-value=0.021  Score=40.42  Aligned_cols=47  Identities=17%  Similarity=0.325  Sum_probs=42.1

Q ss_pred             CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      +|+.++-++.|+|+. |.|+.++|..+|||++||+..+++....|-+.
T Consensus        17 Lp~~qR~v~~L~y~~-~ls~~EIA~~lgiS~~aV~~~l~RA~~~L~~~   63 (106)
T d1s7oa_          17 LTDKQMNYIELYYAD-DYSLAEIADEFGVSRQAVYDNIKRTEKILETY   63 (106)
T ss_dssp             SCHHHHHHHHHHHHT-CCCHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            788899999888875 79999999999999999999999998888663

>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=95.17  E-value=0.019  Score=37.01  Aligned_cols=48  Identities=21%  Similarity=0.189  Sum_probs=41.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+|+.++-++.|+|+. |.++.++|..+|+|.+||...+.+....|-+.
T Consensus        18 ~Lp~~~r~v~~l~~~~-~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~   65 (68)
T d1or7a1          18 SLPEDLRMAITLRELD-GLSYEEIAAIMDCPVGTVRSRIFRAREAIDNK   65 (68)
T ss_dssp             HSCHHHHHHHHHHHTT-CCCHHHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            4778889888888876 68899999999999999999999887776654

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

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

Probab=94.78  E-value=0.034  Score=35.87  Aligned_cols=42  Identities=17%  Similarity=0.203  Sum_probs=33.7

Q ss_pred             CHHHHHHHHHHHHhc-------------CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          31 PVEKKTLVALSYMAT-------------QLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        31 ~~~~~l~i~L~~L~~-------------g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ++..+|+-+|..|+.             ..+..++|...|+|+.||+|+++++..
T Consensus         1 Dv~~Rla~~Ll~l~~~~g~~~~~~~i~l~lt~~~lA~~~G~sRetvsr~L~~l~~   55 (69)
T d1i5za1           1 DVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLED   55 (69)
T ss_dssp             CHHHHHHHHHHHGGGSTTCCCCSSSCEEECCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHcCCCCCCCeeecCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            356677777777652             278999999999999999999998864

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

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

Probab=94.57  E-value=0.027  Score=37.56  Aligned_cols=60  Identities=17%  Similarity=0.094  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHhc--------------CCcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHHH
Q psy4300          32 VEKKTLVALSYMAT--------------QLSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEESV   93 (307)
Q Consensus        32 ~~~~l~i~L~~L~~--------------g~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~~   93 (307)
                      +..+|+-+|..|+.              ..+..++|...|+|+.||+|+++++... +.+.  ....|..++.+.++
T Consensus         2 ~~~Rla~~L~~L~~~~g~~~~~~~~i~~~lt~~elA~~~g~sretvsr~l~~l~~~glI~~--~~~~i~I~d~~~L~   76 (80)
T d3e5ua1           2 PTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLASLKRENILDK--KKNKIIVYNLGELK   76 (80)
T ss_dssp             HHHHHHHHHHHHHHHHCEEETTEEECCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC------CEESCHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCCeEEeeCCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEe--cCCEEEEcCHHHHH
Confidence            45666666666521              2678999999999999999999999877 4444  56666655554443

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

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

Probab=94.40  E-value=0.064  Score=35.55  Aligned_cols=48  Identities=17%  Similarity=0.138  Sum_probs=37.2

Q ss_pred             CcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHHHHHH
Q psy4300          47 LSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEESVIIE   96 (307)
Q Consensus        47 ~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~~~~~   96 (307)
                      .+..++|...|+|+.||+|+++++... +...  ....|...+.+.+.+++
T Consensus        30 lt~~eLA~~~G~sretvsr~L~~l~~~glI~~--~~~~i~I~d~~~L~~~a   78 (81)
T d2gaua1          30 LSREELATLSNMTVSNAIRTLSTFVSERMLAL--DGKRIKIIDCDRLQKTA   78 (81)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEE--ETTEEEESCHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe--cCCEEEEcCHHHHHHHH
Confidence            689999999999999999999998876 4554  56666666665555444

>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=94.09  E-value=0.056  Score=31.16  Aligned_cols=39  Identities=23%  Similarity=0.321  Sum_probs=30.8

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      .+.++.++    +......|..-..+|...||++++|+|++++
T Consensus         3 k~~Id~~~----V~~L~~~G~gat~IAk~lgI~R~SVYR~L~~   41 (43)
T d1gdta1           3 KRKIDRDA----VLNMWQQGLGASHISKTMNIARSTVYKVINE   41 (43)
T ss_dssp             CCCSCHHH----HHHHHHTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             CCccCHHH----HHHHHHcCCCHHHHHHHHCCCHHHHHHHHhh
Confidence            45677764    2333478999999999999999999999864

>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=94.06  E-value=0.05  Score=38.36  Aligned_cols=47  Identities=19%  Similarity=0.362  Sum_probs=41.0

Q ss_pred             CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      +|..++-++.|+|+ .|.|+.++|...|+|++||+..+++....|-+.
T Consensus        19 Lpe~QR~vl~L~~~-e~ls~~EIA~~lgiS~~aV~~~l~Ra~~~L~~y   65 (106)
T d1xsva_          19 LTNKQRNYLELFYL-EDYSLSEIADTFNVSRQAVYDNIRRTGDLVEDY   65 (106)
T ss_dssp             SCHHHHHHHHHHHT-SCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH-hCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence            67888888887775 479999999999999999999999998888663

>d2a61a1 a.4.5.28 (A:5-143) Transcriptional regulator TM0710 {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: Transcriptional regulator TM0710
species: Thermotoga maritima [TaxId: 2336]

Probab=93.93  E-value=0.025  Score=41.80  Aligned_cols=69  Identities=10%  Similarity=0.025  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300           4 TTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus         4 ~~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      +.|+.|+..+...+......-.....+++.+-.++...+-..+.+..+||...|++++|++++++++..
T Consensus         2 ~~~~~llr~l~~~~~~~~~~~l~~~glt~~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~~L~~   70 (139)
T d2a61a1           2 QPFERILREICFMVKVEGRKVLRDFGITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEA   70 (139)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTHHHHTCCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHh
Confidence            456666555544431111111112357777666666556666899999999999999999999998754

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

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

Probab=93.55  E-value=0.053  Score=35.98  Aligned_cols=60  Identities=8%  Similarity=0.081  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHHHhc--------------CCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHH
Q psy4300          32 VEKKTLVALSYMAT--------------QLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEE   91 (307)
Q Consensus        32 ~~~~l~i~L~~L~~--------------g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~   91 (307)
                      ++++|+-+|.+|+.              ..+..++|...|+|+.|++|.+..+...=+-.+.....|...+.+.
T Consensus         2 v~~Rla~~Ll~l~~~~g~~~~~~~~i~~~~t~~eiA~~lG~sretvsr~l~~l~~~g~I~~~~~~~i~I~d~~~   75 (80)
T d1ft9a1           2 IKQRIAGFFIDHANTTGRQTQGGVIVSVDFTVEEIANLIGSSRQTTSTALNSLIKEGYISRQGRGHYTIPNLVR   75 (80)
T ss_dssp             HHHHHHHHHHHTCBCCCSCC--CCCCEECCCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEECSTTCEECSSHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCCCCCeEEecCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCeEEECCHHH
Confidence            45667766666633              3678999999999999999999998876333210234455555443

>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=93.35  E-value=0.16  Score=34.24  Aligned_cols=67  Identities=16%  Similarity=0.136  Sum_probs=47.9

Q ss_pred             CHHHHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300           2 RKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus         2 s~~~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      +++....+++.+...       ......+++.+.  -+|.+|+.|.+..++|..+++|.+||...+..+..-+--.
T Consensus         2 ~Pe~v~~ll~~~~~~-------~~~~~~LT~rE~--~vl~ll~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~~~   68 (87)
T d1p4wa_           2 TPESVAKLLEKISAG-------GYGDKRLSPKES--EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVD   68 (87)
T ss_dssp             CCSHHHHHHHHHHCC-------CCSSSSCCHHHH--HHHHHHHHTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCS
T ss_pred             ChHHHHHHHHHhccC-------CCCCCCCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCC
Confidence            344555565555433       112457888774  4566788999999999999999999999988887665433

>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=93.11  E-value=0.069  Score=34.17  Aligned_cols=47  Identities=19%  Similarity=0.277  Sum_probs=38.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+++.+.  -+|.+++.|.+..++|...|+|..||...+..+..-+--.
T Consensus         6 ~LT~rE~--~vl~ll~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv~   52 (67)
T d1a04a1           6 QLTPRER--DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLK   52 (67)
T ss_dssp             GSCHHHH--HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCC
T ss_pred             cCCHHHH--HHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence            4666553  3467889999999999999999999999999887766544

>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=92.92  E-value=0.16  Score=32.29  Aligned_cols=48  Identities=10%  Similarity=0.330  Sum_probs=39.4

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      +.+++.+.=.  |.+++.|.+..++|..+|+|.+||...+.++..-+.-.
T Consensus         3 p~LT~rE~~v--l~l~~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v~   50 (67)
T d1fsea_           3 PLLTKREREV--FELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVK   50 (67)
T ss_dssp             CCCCHHHHHH--HHHHTTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCS
T ss_pred             CCCCHHHHHH--HHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            4577766654  56689999999999999999999999999887766554

>d2ofya1 a.35.1.3 (A:3-84) Putative transcriptional regulator RHA1_ro04071 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcriptional regulator RHA1 ro04071
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=92.88  E-value=0.11  Score=34.78  Aligned_cols=53  Identities=13%  Similarity=0.029  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHH
Q psy4300          34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNF   99 (307)
Q Consensus        34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f   99 (307)
                      +.|.-.|..++.+.++.++|...|+|+++++++-+             .-+.-|+...+.++++.+
T Consensus        13 ~~lG~~ir~~R~~~t~~eLA~~~Gvs~~~ls~iE~-------------G~~~~ps~~tl~kia~~L   65 (82)
T d2ofya1          13 QRLGELLRSARGDMSMVTVAFDAGISVETLRKIET-------------GRIATPAFFTIAAVARVL   65 (82)
T ss_dssp             HHHHHHHHHHHTTSCHHHHHHHHTCCHHHHHHHHT-------------TCCSSCBHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHHcCCHHHHHHHHc-------------CCcCCCCHHHHHHHHHHH
Confidence            57888899999999999999999999999998643             123345655566666655

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

Probab=92.82  E-value=0.16  Score=31.74  Aligned_cols=48  Identities=6%  Similarity=0.180  Sum_probs=41.3

Q ss_pred             CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300          28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMS   75 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~   75 (307)
                      ..++..++-.+.++|-   ....++.++|..+|||++.|+++..+.+.-|-
T Consensus         7 ~~L~~rer~Ii~~ryGl~~~~~~tl~eIa~~lgiS~erVrqi~~~al~kLR   57 (61)
T d1ku3a_           7 SKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK   57 (61)
T ss_dssp             TTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHHHHhCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence            4689999999999993   45689999999999999999999998876553

>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=92.67  E-value=0.088  Score=33.40  Aligned_cols=47  Identities=15%  Similarity=0.200  Sum_probs=38.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+++.+.=  +|.+++.|.+..++|..+++|.+||...+.++..-+--.
T Consensus         4 ~Lt~rE~~--vl~l~~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv~   50 (65)
T d1l3la1           4 WLDPKEAT--YLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVR   50 (65)
T ss_dssp             CCCHHHHH--HHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCS
T ss_pred             ccCHHHHH--HHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            45665543  457899999999999999999999999999887666543

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

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

Probab=92.62  E-value=0.22  Score=35.14  Aligned_cols=73  Identities=16%  Similarity=0.111  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHhhhcCcccc---cCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhC-CChhhHHHHHHHHHHHccc
Q psy4300           4 TTFGFLVEALAAINGYETL---YERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFN-LADSTVWSCIDSFLTAMSQ   76 (307)
Q Consensus         4 ~~F~~L~~~l~~~~~~~~~---~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fg-vs~stv~r~v~~~~~~l~~   76 (307)
                      .+.+.|++.+...++.-..   +..+...+...-+++|.|.+--++.|+.++|..|| -+.|||...++.+-..+..
T Consensus        14 ~~l~~Ii~~Va~~f~i~~~di~sk~R~~~vv~aR~ia~yL~r~~t~~sl~~IG~~fg~rdHsTV~~a~kki~~~~~~   90 (110)
T d1l8qa1          14 DKLMQIVEFVANYYAVKVEDILSDKRNKRTSEARKIAMYLCRKVCSASLIEIARAFKRKDHTTVIHAIRSVEEEKKK   90 (110)
T ss_dssp             HHHHHHHHHHHHHHSCCHHHHSSCCCCSSSHHHHHHHHHHHHHHHCCCHHHHHHHSSCCCSTHHHHHHHHHHHTTC-
T ss_pred             CCHHHHHHHHHHHhCCCHHHHhCCCCcHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCCccHHHHHHHHHHHHHHh
Confidence            4567777777776543111   11234567778889999999899999999999996 8999999999998776654

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

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

Probab=92.39  E-value=0.14  Score=33.33  Aligned_cols=44  Identities=5%  Similarity=0.112  Sum_probs=34.4

Q ss_pred             CCHHHHHHHHHHHHhc--------CCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          30 VPVEKKTLVALSYMAT--------QLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        30 ~~~~~~l~i~L~~L~~--------g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .+++++|+-+|..+..        ..+..++|...|+|+.|++|.++++...
T Consensus         3 ~dv~~Rla~~Ll~~~~~~~~~~~i~lt~~elA~~lg~sr~tvsr~l~~l~~~   54 (73)
T d1zyba1           3 LDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQDN   54 (73)
T ss_dssp             CSHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHhhhhhCCCeEeecCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            4567777776655433        2589999999999999999999988654

>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=92.26  E-value=0.049  Score=33.79  Aligned_cols=22  Identities=18%  Similarity=0.416  Sum_probs=20.0

Q ss_pred             cHHHHHhhhCCChhhHHHHHHH
Q psy4300          48 SMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        48 ~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      +..++|...|||.+|||++++.
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~   23 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINK   23 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHT
T ss_pred             CHHHHHHHHCcCHHHHHHHHCC
Confidence            5789999999999999999874

>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=92.14  E-value=0.12  Score=33.38  Aligned_cols=47  Identities=13%  Similarity=0.188  Sum_probs=37.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      .+++.+.-.  |.+++.|.+..++|...|+|.+||...+..+..-|--.
T Consensus        12 ~LT~rE~~v--l~~l~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv~   58 (70)
T d1yioa1          12 SLTGREQQV--LQLTIRGLMNKQIAGELGIAEVTVKVHRHNIMQKLNVR   58 (70)
T ss_dssp             TSCHHHHHH--HHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHTTCS
T ss_pred             cCCHHHHHH--HHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence            356655544  45589999999999999999999999999887766443

>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=91.76  E-value=0.051  Score=33.68  Aligned_cols=23  Identities=9%  Similarity=0.251  Sum_probs=20.5

Q ss_pred             CcHHHHHhhhCCChhhHHHHHHH
Q psy4300          47 LSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        47 ~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      .+..++|...|+|.+|||++++.
T Consensus         2 vTi~dvA~~agvS~~TVSr~Ln~   24 (57)
T d2hsga1           2 VTIYDVAREASVSMATVSRVVNG   24 (57)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             cCHHHHHHHHCcCHHHHHHHhCC
Confidence            46789999999999999998874

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

Probab=91.64  E-value=0.22  Score=31.84  Aligned_cols=50  Identities=12%  Similarity=0.328  Sum_probs=42.4

Q ss_pred             CCCCHHHHHHHHHHHH-h--cCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSYM-A--TQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L-~--~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+++.++..+.++|- .  ...++.++|..+|||+..|.++-.+.+.-|-..
T Consensus         4 ~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrerVrqie~~al~kLr~~   56 (68)
T d2p7vb1           4 AGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHP   56 (68)
T ss_dssp             CCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHHGGGSC
T ss_pred             hcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence            3689999999999984 2  347999999999999999999999888877654

>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=91.23  E-value=0.068  Score=33.35  Aligned_cols=22  Identities=14%  Similarity=0.193  Sum_probs=19.8

Q ss_pred             cHHHHHhhhCCChhhHHHHHHH
Q psy4300          48 SMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        48 ~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      +..++|...|+|.+|||++++.
T Consensus         2 Tl~diA~~agvS~sTVSrvLn~   23 (59)
T d1uxda_           2 KLDEIARLAGVSRTTASYVING   23 (59)
T ss_dssp             CHHHHHHHHTSCTTHHHHHHHT
T ss_pred             CHHHHHHHHCcCHHHHHHHHcC
Confidence            5689999999999999999874

>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=90.99  E-value=0.21  Score=32.04  Aligned_cols=32  Identities=13%  Similarity=0.136  Sum_probs=27.5

Q ss_pred             HHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          42 YMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        42 ~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      +-..+.+-.+||...|+|.+||++++.+.++.
T Consensus        16 ~~~g~~sr~eLa~~~glS~~Tv~~~l~~L~~~   47 (71)
T d1z05a1          16 DQKGPISRIDLSKESELAPASITKITRELIDA   47 (71)
T ss_dssp             HHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            44557899999999999999999999988654

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

Probab=90.73  E-value=0.32  Score=32.68  Aligned_cols=50  Identities=12%  Similarity=0.321  Sum_probs=43.4

Q ss_pred             CCCCHHHHHHHHHHH-H--hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300          28 PFVPVEKKTLVALSY-M--ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~-L--~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~   77 (307)
                      ..+++.++..+.++| |  ....++.++|..||||+..|.++-.+.+.-|-..
T Consensus        17 ~~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrERVRQie~~al~kLr~~   69 (87)
T d1ttya_          17 KTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLRHP   69 (87)
T ss_dssp             TTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHBTT
T ss_pred             hcCCHHHHHHHHHHcCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHHHhCc
Confidence            468999999999999 4  3458999999999999999999999988887654

>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=90.33  E-value=0.069  Score=33.30  Aligned_cols=23  Identities=9%  Similarity=0.229  Sum_probs=20.5

Q ss_pred             CcHHHHHhhhCCChhhHHHHHHH
Q psy4300          47 LSMRKIGDQFNLADSTVWSCIDS   69 (307)
Q Consensus        47 ~~~~~l~~~fgvs~stv~r~v~~   69 (307)
                      .+..++|...|+|.+|||++++.
T Consensus         3 ~Ti~diA~~agvS~sTVSr~l~~   25 (59)
T d1efaa1           3 VTLYDVAEYAGVSYQTVSRVVNQ   25 (59)
T ss_dssp             CCHHHHHHTTTSCHHHHHHHHTT
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCC
Confidence            46789999999999999998864

>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=90.31  E-value=0.11  Score=32.51  Aligned_cols=27  Identities=11%  Similarity=0.175  Sum_probs=23.7

Q ss_pred             HHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          42 YMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        42 ~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      +-+.|.++.++|..+|||++|+++|=+
T Consensus         8 R~~~gltQ~elA~~lGvs~~tvs~~E~   34 (62)
T d2ppxa1           8 RRALKLTQEEFSARYHIPLGTLRDWEQ   34 (62)
T ss_dssp             HHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence            457799999999999999999998654

>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=90.27  E-value=0.31  Score=30.49  Aligned_cols=26  Identities=12%  Similarity=0.296  Sum_probs=23.0

Q ss_pred             CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          47 LSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        47 ~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      .|..+||..||||++||.+.+.....
T Consensus        20 ~s~~eLa~~l~vS~~ti~r~i~~L~~   45 (63)
T d1biaa1          20 HSGEQLGETLGMSRAAINKHIQTLRD   45 (63)
T ss_dssp             BCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            67889999999999999999887654

>d1lnwa_ a.4.5.28 (A:) MexR repressor {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: MexR repressor
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=89.96  E-value=0.48  Score=34.50  Aligned_cols=45  Identities=11%  Similarity=0.063  Sum_probs=36.8

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+++.+--.+....-..|.+..+|+...+++++++++++++...
T Consensus        32 ~~lt~~q~~vL~~l~~~~~~t~~~la~~l~~~~~~vsr~l~~L~~   76 (141)
T d1lnwa_          32 LDLTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEG   76 (141)
T ss_dssp             CCCCHHHHHHHHHHHSSTTCBHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHCCCCCHHHHHHHHCccHhHHHHHHHHHHH
Confidence            457877666665555666799999999999999999999998765

>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=89.42  E-value=0.29  Score=34.11  Aligned_cols=41  Identities=15%  Similarity=0.347  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          33 EKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        33 ~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      +-.++..|+.-..+.+..+||..+|++++|+++.+++....
T Consensus        23 ~~~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~l~~L~~~   63 (109)
T d2d1ha1          23 DVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIEL   63 (109)
T ss_dssp             HHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCccHhHHHHHHHHHHHC
Confidence            34444455444444799999999999999999999987753

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

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

Probab=89.34  E-value=0.43  Score=32.89  Aligned_cols=51  Identities=14%  Similarity=0.081  Sum_probs=39.4

Q ss_pred             CcHHHHHhhhCCC-hhhHHHHHHHHHHH-ccccccccccccCCChHHHHHHHHHH
Q psy4300          47 LSMRKIGDQFNLA-DSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEESVIIERNF   99 (307)
Q Consensus        47 ~~~~~l~~~fgvs-~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~~~~~~~f   99 (307)
                      .+..+||...|+| +.||+|+++++-.. +.+.  ....|..++.+.+++++...
T Consensus        32 lTqeeLA~~lG~s~ReTVsR~L~~L~~~GlI~~--~~~~i~I~D~~~L~~~A~~~   84 (100)
T d2bgca1          32 LTMQELGYSSGIAHSSAVSRIISKLKQEKVIVY--KNSCFYVQNLDYLKRYAPKL   84 (100)
T ss_dssp             CCHHHHHHHTTCCCHHHHHHHHHHHHHTTSEEE--ETTEEEESCHHHHHHHCHHH
T ss_pred             cCHHHHHHHhCCchHHHHHHHHHHHHHCCCEEE--cCCEEEEeCHHHHHHHhccc
Confidence            6899999999997 89999999998764 4444  66677778877776665443

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

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

Probab=89.32  E-value=0.27  Score=33.56  Aligned_cols=72  Identities=18%  Similarity=0.171  Sum_probs=52.0

Q ss_pred             HHHHHHHHhhhcCccccc---CCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhC-CChhhHHHHHHHHHHHcccc
Q psy4300           6 FGFLVEALAAINGYETLY---ERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFN-LADSTVWSCIDSFLTAMSQP   77 (307)
Q Consensus         6 F~~L~~~l~~~~~~~~~~---~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fg-vs~stv~r~v~~~~~~l~~~   77 (307)
                      .+.|++.+...++.-+..   ..+...+...-++++.|.+=-++.|+.++|..|| -+.|||..-++.+-..+..-
T Consensus         3 i~~I~~~Va~~f~v~~~~i~~~~R~~~iv~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHsTV~~a~kki~~~~~~d   78 (94)
T d1j1va_           3 IDNIQKTVAEYYKIKVADLLSKRRSRSVARPRQMAMALAKELTNHSLPEIGDAFGGRDHTTVLHACRKIEQLREES   78 (94)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHSCCCCHHHHHHHHHHHHHHHHHSCCCHHHHHHHTTSCCHHHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHhCCCHHHHhCCCCchhHHHHHHHHHHHHHHHhCCCHHHHHHHhCCCCchHHHHHHHHHHHHHHhC
Confidence            345555555554321111   1224566778999999999999999999999995 79999999999887766543

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=88.91  E-value=0.17  Score=32.28  Aligned_cols=26  Identities=12%  Similarity=0.127  Sum_probs=23.8

Q ss_pred             HHHhcCCcHHHHHhhhCCChhhHHHH
Q psy4300          41 SYMATQLSMRKIGDQFNLADSTVWSC   66 (307)
Q Consensus        41 ~~L~~g~~~~~l~~~fgvs~stv~r~   66 (307)
                      ++.+.|.|+.++|..+|||+.|+++|
T Consensus         9 ~R~~~gltQ~elA~~LGvs~~ti~~y   34 (67)
T d2auwa1           9 WMHRNNLSLTTAAEALGISRRMVSYY   34 (67)
T ss_dssp             HHHHTTCCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHH
Confidence            56788999999999999999999986

>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=88.29  E-value=0.51  Score=30.50  Aligned_cols=40  Identities=20%  Similarity=0.411  Sum_probs=30.9

Q ss_pred             HHHHHHHHHHh---cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          34 KKTLVALSYMA---TQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        34 ~~l~i~L~~L~---~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ++.+-.|..++   .+.+..+||...|+++||++|++...++.
T Consensus         5 ~r~l~IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~tL~~~   47 (75)
T d1mkma1           5 KKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEK   47 (75)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            34444555553   45799999999999999999999987654

>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=88.24  E-value=0.45  Score=33.48  Aligned_cols=42  Identities=5%  Similarity=-0.087  Sum_probs=36.5

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      |..+++-+.-..+-..+..|.+..+||..+|.|+++|++++.
T Consensus        11 R~~L~p~e~A~a~~~l~~~g~s~~eiA~~~G~s~~~V~~~l~   52 (114)
T d1r71a_          11 RNELTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVT   52 (114)
T ss_dssp             TTCCCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHG
T ss_pred             ccCCCHHHHHHHHHHHHHhCCCHHHHHHHHCCcHHHHHHHHH
Confidence            457888887777777788899999999999999999999876

>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=88.05  E-value=0.34  Score=32.59  Aligned_cols=36  Identities=14%  Similarity=0.162  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHH--hcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          33 EKKTLVALSYM--ATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        33 ~~~l~i~L~~L--~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      ...|+..|..+  ..|.++.++|...|+|++|++++.+
T Consensus         9 k~~l~~~i~~~r~~~gltq~~lA~~~gis~~~is~ie~   46 (89)
T d2o38a1           9 KLRLAYALNAVIDRARLSQAAAAARLGINQPKVSALRN   46 (89)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHhhHhHHHHHHc
Confidence            34556666655  5699999999999999999999765

>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=87.93  E-value=0.94  Score=30.87  Aligned_cols=58  Identities=16%  Similarity=0.219  Sum_probs=39.9

Q ss_pred             CCHHHHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHHH-hcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300           1 MRKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYM-ATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus         1 ms~~~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~L-~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      |++++++.+.+.++..-              -..++-| |..| ....+..+|+..+|+|+||+|..++...++
T Consensus         5 ~~pe~~~~la~~~kaL~--------------~p~Rl~I-l~~L~~~~~~v~ela~~l~is~stvS~HL~~L~~a   63 (98)
T d1r1ta_           5 IAPEVAQSLAEFFAVLA--------------DPNRLRL-LSLLARSELCVGDLAQAIGVSESAVSHQLRSLRNL   63 (98)
T ss_dssp             CCHHHHHHHHHHHHHHC--------------CHHHHHH-HHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHHhC--------------CHHHHHH-HHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            46777777777776441              1122333 3344 445889999999999999999999877643

>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=87.86  E-value=0.41  Score=34.77  Aligned_cols=45  Identities=13%  Similarity=0.106  Sum_probs=36.7

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..++..+-..+...+-..+.+..+||..++++++|+++++++...
T Consensus        28 ~~lt~~q~~iL~~l~~~~~~t~~~La~~l~i~~~~vs~~v~~L~~   72 (140)
T d2etha1          28 SDMKTTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEK   72 (140)
T ss_dssp             HHSBHHHHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            357777766665556666799999999999999999999998764

>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=87.56  E-value=0.62  Score=29.17  Aligned_cols=39  Identities=5%  Similarity=0.152  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHhc---CCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300          33 EKKTLVALSYMAT---QLSMRKIGDQFNLADSTVWSCIDSFL   71 (307)
Q Consensus        33 ~~~l~i~L~~L~~---g~~~~~l~~~fgvs~stv~r~v~~~~   71 (307)
                      .+++.-.|..|.+   ..+-.+||..|+||..||.|-+...-
T Consensus         6 ~eR~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L~   47 (65)
T d1j5ya1           6 QERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLR   47 (65)
T ss_dssp             HHHHHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4555556666643   36889999999999999999888753

>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=86.40  E-value=1.7  Score=29.98  Aligned_cols=41  Identities=12%  Similarity=0.187  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          32 VEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        32 ~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .+-++..+|. -..+.+..+||...|++++||++++++....
T Consensus        21 ~e~~v~~~L~-~~g~~t~~eia~~~~i~~~~v~~~l~~L~~~   61 (109)
T d1sfxa_          21 SDVRIYSLLL-ERGGMRVSEIARELDLSARFVRDRLKVLLKR   61 (109)
T ss_dssp             HHHHHHHHHH-HHCCBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHH-hcCCCCHHHHHHHhCCCcchHHHHHHHHHhC
Confidence            3556666664 3457999999999999999999999987653

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=86.35  E-value=0.34  Score=30.44  Aligned_cols=45  Identities=9%  Similarity=0.067  Sum_probs=33.9

Q ss_pred             HHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHH
Q psy4300          41 SYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNF   99 (307)
Q Consensus        41 ~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f   99 (307)
                      .+...|.++.++|...|||+++++++.+.              ...|+.+.+..++..|
T Consensus         9 lR~~~g~tq~elA~~~gis~~~is~~e~g--------------~~~p~~~~l~~ia~~l   53 (66)
T d1utxa_           9 IREKKKISQSELAALLEVSRQTINGIEKN--------------KYNPSLQLALKIAYYL   53 (66)
T ss_dssp             HHHHTTCCHHHHHHHHTSCHHHHHHHHTT--------------SCCCCHHHHHHHHHHT
T ss_pred             HHHHcCCCHHHHHHhcccCHHHHHHHHcC--------------CCCCCHHHHHHHHHHH
Confidence            34578999999999999999999987532              2346666666666665

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=85.69  E-value=0.32  Score=35.21  Aligned_cols=43  Identities=12%  Similarity=0.210  Sum_probs=31.4

Q ss_pred             CCHHH-HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          30 VPVEK-KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        30 ~~~~~-~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ++..+ .++..|.....+.+..+|+..++++++|+++++++...
T Consensus        26 lt~~q~~iL~~l~~~~~~~t~~~la~~~~~~~~~vs~~v~~L~~   69 (137)
T d2fbha1          26 LSQARWLVLLHLARHRDSPTQRELAQSVGVEGPTLARLLDGLES   69 (137)
T ss_dssp             CTTTHHHHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            44433 33334444444689999999999999999999998765

>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=85.29  E-value=1.1  Score=28.63  Aligned_cols=27  Identities=4%  Similarity=0.136  Sum_probs=23.1

Q ss_pred             CCcHHHHHhhhCC-ChhhHHHHHHHHHH
Q psy4300          46 QLSMRKIGDQFNL-ADSTVWSCIDSFLT   72 (307)
Q Consensus        46 g~~~~~l~~~fgv-s~stv~r~v~~~~~   72 (307)
                      ..++++++..||+ |.+||++.+.....
T Consensus        24 ~Ps~rei~~~~g~~S~stv~~~l~~Le~   51 (71)
T d1jhfa1          24 PPTRAEIAQRLGFRSPNAAEEHLKALAR   51 (71)
T ss_dssp             CCCHHHHHHHTTCSSHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            3899999999998 89999998877653

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=85.25  E-value=0.82  Score=29.02  Aligned_cols=29  Identities=17%  Similarity=0.201  Sum_probs=25.4

Q ss_pred             cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          45 TQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        45 ~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ...+-.+||...|+|.+||+++++++++.
T Consensus        18 g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~   46 (70)
T d1z6ra1          18 GPVSRIDLSRLAQLAPASITKIVHEMLEA   46 (70)
T ss_dssp             CSCCHHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            34778899999999999999999998764

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=85.24  E-value=0.58  Score=35.16  Aligned_cols=45  Identities=11%  Similarity=0.104  Sum_probs=37.5

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..++..+-..+.+.+-..+.+..+||...+++++|+++++++...
T Consensus        37 ~~Lt~~q~~vL~~l~~~~~~t~~~la~~~~l~~~tvs~~i~rL~~   81 (162)
T d2fxaa1          37 YDLNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEE   81 (162)
T ss_dssp             GTCCHHHHHHHHHHHHHTSEEHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHhhhccCCCcCHHHHHHHHcCCchhhHHHHHHHHH
Confidence            468888876666666666899999999999999999999998764

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=85.07  E-value=0.6  Score=33.75  Aligned_cols=46  Identities=15%  Similarity=0.219  Sum_probs=37.8

Q ss_pred             CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      .-.+++.+-.++...+-..|.+..+|+...+++++|++++++....
T Consensus        28 ~~gLt~~q~~vL~~l~~~~~~t~~~La~~~~i~~~~vsr~i~~L~~   73 (137)
T d1z91a1          28 KLNITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQ   73 (137)
T ss_dssp             TTCCCHHHHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHHHHHH
T ss_pred             HcCcCHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence            3567887766666666678999999999999999999999988754

>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=85.00  E-value=1.1  Score=30.23  Aligned_cols=56  Identities=18%  Similarity=0.258  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHHHh-cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300           3 KTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMA-TQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus         3 ~~~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~L~-~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .++++.+.+.++..              +-..++-| |..|. ...+..+++..+|+|++|+|+-++....+
T Consensus         2 ~d~~e~~a~~fkaL--------------~d~~Rl~I-l~~L~~~~~~v~el~~~l~~s~~~vS~HL~~L~~~   58 (94)
T d1r1ua_           2 TDTLERVTEIFKAL--------------GDYNRIRI-MELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSV   58 (94)
T ss_dssp             HHHHHHHHHHHHHT--------------CSHHHHHH-HHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHh--------------CCHHHHHH-HHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence            45677777666543              22334444 33444 45788899999999999999999877664

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Multiple antibiotic resistance repressor, MarR
species: Escherichia coli [TaxId: 562]

Probab=84.47  E-value=0.8  Score=33.08  Aligned_cols=45  Identities=4%  Similarity=0.031  Sum_probs=36.6

Q ss_pred             CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..++..+-.++...+-..+.+..+|+...+++++++++.+++...
T Consensus        30 ~~Lt~~q~~vL~~l~~~~~~t~~ela~~~~i~~~~vs~~v~~L~~   74 (138)
T d1jgsa_          30 LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVC   74 (138)
T ss_dssp             TTSCHHHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHhHHhCcCCCHHHHHHHHCCCHhHHHHHHHHHhh
Confidence            467777765555555566899999999999999999999998754

>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=84.05  E-value=0.8  Score=28.90  Aligned_cols=35  Identities=14%  Similarity=0.196  Sum_probs=27.4

Q ss_pred             HHHHHHHHHH--hcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          34 KKTLVALSYM--ATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        34 ~~l~i~L~~L--~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      ..+...|..+  ..|.++.++|...|+++++++++.+
T Consensus         5 ~~l~~~i~~~r~~~gltq~elA~~~gv~~~~is~ie~   41 (69)
T d2a6ca1           5 SQLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMR   41 (69)
T ss_dssp             HHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHcCHhHHHHHHc
Confidence            3455555544  5689999999999999999998764

>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=83.23  E-value=0.98  Score=30.12  Aligned_cols=43  Identities=2%  Similarity=0.073  Sum_probs=35.4

Q ss_pred             HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      +|-+++....+| ++...|...|+|+|+|++.++.+-..+-..|
T Consensus         5 ~L~~f~~v~e~g-s~~~AA~~L~isq~avs~~i~~LE~~lg~~L   47 (89)
T d1ixca1           5 QLKYFIAVAEAG-NMAAAAKRLHVSQPPITRQMQALEADLGVVL   47 (89)
T ss_dssp             HHHHHHHHHHHS-SHHHHHHHHTCCHHHHHHHHHHHHHHHTSCC
T ss_pred             HHHHHHHHHHhC-CHHHHHHHhCCChHHHHHHHHHHHhcCCcee
Confidence            455555555554 8999999999999999999999999888776

>d2hr3a1 a.4.5.28 (A:2-146) Probable transcriptional regulator PA3067 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA3067
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=82.80  E-value=1  Score=32.68  Aligned_cols=45  Identities=7%  Similarity=0.076  Sum_probs=31.2

Q ss_pred             CCCCHHHHHH-HHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          28 PFVPVEKKTL-VALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        28 ~~~~~~~~l~-i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..+++.+-.+ .+|.....+.+..+|+..+|++++|++++++++..
T Consensus        30 ~glt~~q~~vL~~L~~~~g~~t~~~La~~~~~~~~~vs~~i~~L~~   75 (145)
T d2hr3a1          30 DPVQFSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELER   75 (145)
T ss_dssp             CHHHHHHHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            3444433333 33333333479999999999999999999998764

>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=82.72  E-value=0.53  Score=29.34  Aligned_cols=26  Identities=4%  Similarity=0.137  Sum_probs=22.9

Q ss_pred             HhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          43 MATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        43 L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      -..|.++.++|...|||++|++++.+
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            35689999999999999999999854

>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=82.70  E-value=2.2  Score=26.31  Aligned_cols=27  Identities=26%  Similarity=0.473  Sum_probs=23.6

Q ss_pred             CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          46 QLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        46 g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      -.+++++|...|+|.+||++-++++.+
T Consensus        19 r~s~~~iA~~lgis~~tv~~Ri~~L~~   45 (63)
T d2cfxa1          19 RLSMRELGRKIKLSPPSVTERVRQLES   45 (63)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            378999999999999999998887654

>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=82.58  E-value=2  Score=26.40  Aligned_cols=29  Identities=14%  Similarity=0.323  Sum_probs=25.6

Q ss_pred             cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          45 TQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        45 ~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ...|+.+||...|+|.+||.+-++++.+.
T Consensus        18 ~r~s~~eiA~~l~ls~~~v~~Ri~rL~~~   46 (63)
T d2cg4a1          18 ARTAYAELAKQFGVSPETIHVRVEKMKQA   46 (63)
T ss_dssp             TTSCHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            34799999999999999999999888765

>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=82.34  E-value=0.44  Score=28.57  Aligned_cols=26  Identities=8%  Similarity=0.117  Sum_probs=23.2

Q ss_pred             CCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300          46 QLSMRKIGDQFNLADSTVWSCIDSFL   71 (307)
Q Consensus        46 g~~~~~l~~~fgvs~stv~r~v~~~~   71 (307)
                      ..+..++|..+|+|+++++|.|++..
T Consensus        19 ~itl~~lA~~~~~S~~~l~r~Fk~~~   44 (54)
T d1d5ya1          19 PLSLDNVAAKAGYSKWHLQRMFKDVT   44 (54)
T ss_dssp             SCCCHHHHTTTSSCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            36788999999999999999999875

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=81.96  E-value=1  Score=32.23  Aligned_cols=45  Identities=16%  Similarity=0.107  Sum_probs=33.1

Q ss_pred             CCCCHHHHHH-HHHHHHh-cCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          28 PFVPVEKKTL-VALSYMA-TQLSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        28 ~~~~~~~~l~-i~L~~L~-~g~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..++..+-.. .+|.... .+.+..+|+...+++++|++++++....
T Consensus        25 ~glt~~q~~vL~~l~~~~~~~it~~ela~~~~~~~~~vs~~l~~L~~   71 (135)
T d3broa1          25 YDLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEI   71 (135)
T ss_dssp             TTCCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHcCCCCCCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence            4577766444 4444432 2379999999999999999999988754

>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=81.85  E-value=1.4  Score=27.31  Aligned_cols=28  Identities=11%  Similarity=0.156  Sum_probs=24.5

Q ss_pred             CCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          46 QLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        46 g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ..+-.+||..+|||++||++.+++..+.
T Consensus        23 ~v~~~~iA~~L~vs~~SVt~mvkrL~~~   50 (63)
T d2isya1          23 TPLRARIAERLDQSGPTVSQTVSRMERD   50 (63)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCcHHHHHHHhCCCchhHHHHHHHHHHC
Confidence            4778899999999999999999987653

>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=81.68  E-value=1.6  Score=29.38  Aligned_cols=28  Identities=18%  Similarity=0.265  Sum_probs=24.1

Q ss_pred             HHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300          41 SYMATQLSMRKIGDQFNLADSTVWSCID   68 (307)
Q Consensus        41 ~~L~~g~~~~~l~~~fgvs~stv~r~v~   68 (307)
                      ..+..|.+..++|..+|.|+++|+..+.
T Consensus        14 ~L~e~g~t~~~iA~~~Gks~~~V~~~Lr   41 (93)
T d1vz0a1          14 ALLEMGLTQEEVARRVGKARSTVANALR   41 (93)
T ss_dssp             HHHHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHcCCCHHHHHHHHccchHHHHHHHH
Confidence            4446789999999999999999988765

>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=81.60  E-value=0.92  Score=26.97  Aligned_cols=26  Identities=12%  Similarity=0.131  Sum_probs=23.2

Q ss_pred             CCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300          46 QLSMRKIGDQFNLADSTVWSCIDSFL   71 (307)
Q Consensus        46 g~~~~~l~~~fgvs~stv~r~v~~~~   71 (307)
                      ..+..++|..+|+|+++++|.|++..
T Consensus        19 ~~tl~~lA~~~~~s~~~l~r~Fk~~~   44 (54)
T d1bl0a1          19 PLSLEKVSERSGYSKWHLQRMFKKET   44 (54)
T ss_dssp             CCCCHHHHHHSSSCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            36788999999999999999999865

>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=81.27  E-value=1.1  Score=29.09  Aligned_cols=46  Identities=13%  Similarity=0.127  Sum_probs=33.7

Q ss_pred             HHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHH
Q psy4300          40 LSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNF   99 (307)
Q Consensus        40 L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f   99 (307)
                      =.+...|.++.++|...|+|++++++|-+.              ..-|+.+.+..++..|
T Consensus        13 ~~R~~~gltq~~lA~~~gis~~~is~~E~G--------------~~~p~~~~l~~la~~l   58 (78)
T d1x57a1          13 QGRQSKGLTQKDLATKINEKPQVIADYESG--------------RAIPNNQVLGKIERAI   58 (78)
T ss_dssp             HHHHTTTCCHHHHHHHHTSCHHHHHHHHHT--------------CSCCCHHHHHHHHHHH
T ss_pred             HHHHHcCCChhHHHHcCCCCHHHHHHHHcc--------------CCCCCHHHHHHHHHHh
Confidence            345577999999999999999999986542              2336665566666655

>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=81.27  E-value=0.63  Score=29.36  Aligned_cols=44  Identities=14%  Similarity=-0.029  Sum_probs=32.3

Q ss_pred             HHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHH
Q psy4300          42 YMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNF   99 (307)
Q Consensus        42 ~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f   99 (307)
                      +...|.++.++|...|+|+++++++-+.              -.-|+.+.+..++..|
T Consensus        18 R~~~gltq~~lA~~~gis~~~i~~~E~g--------------~~~p~~~~l~~ia~~l   61 (69)
T d1y7ya1          18 RTAKGLSQETLAFLSGLDRSYVGGVERG--------------QRNVSLVNILKLATAL   61 (69)
T ss_dssp             HHHTTCCHHHHHHHHTCCHHHHHHHHTT--------------CSCCBHHHHHHHHHHT
T ss_pred             HHHcCCCHHHHHhHhCCCHHHHHHHHCC--------------CCCCCHHHHHHHHHHh
Confidence            4467999999999999999999987431              1236666566666555

>d2frha1 a.4.5.28 (A:102-216) Pleiotropic regulator of virulence genes, SarA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Pleiotropic regulator of virulence genes, SarA
species: Staphylococcus aureus [TaxId: 1280]

Probab=80.75  E-value=1.4  Score=30.72  Aligned_cols=45  Identities=9%  Similarity=0.120  Sum_probs=35.2

Q ss_pred             CCCCHHHHHHHHHHHHhcC--CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300          28 PFVPVEKKTLVALSYMATQ--LSMRKIGDQFNLADSTVWSCIDSFLT   72 (307)
Q Consensus        28 ~~~~~~~~l~i~L~~L~~g--~~~~~l~~~fgvs~stv~r~v~~~~~   72 (307)
                      ..++..+-..+...+...+  .+..+|+..++++++|+++.+++...
T Consensus        29 ~~Ls~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~tvs~~i~~Le~   75 (115)
T d2frha1          29 FSISFEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQ   75 (115)
T ss_dssp             TCCCHHHHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHcCCCCCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence            4688877666655554433  68999999999999999999998764

>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=80.68  E-value=2.7  Score=25.50  Aligned_cols=27  Identities=26%  Similarity=0.345  Sum_probs=24.4

Q ss_pred             CcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          47 LSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        47 ~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      .|+.++|...|+|.+||.+-++++.+.
T Consensus        18 ~s~~eiA~~l~ls~~~v~~Ri~~L~~~   44 (60)
T d2cyya1          18 APLREISKITGLAESTIHERIRKLRES   44 (60)
T ss_dssp             CCHHHHHHHHCSCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence            689999999999999999999887654

>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=80.68  E-value=1.9  Score=26.49  Aligned_cols=29  Identities=10%  Similarity=0.133  Sum_probs=25.0

Q ss_pred             cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300          45 TQLSMRKIGDQFNLADSTVWSCIDSFLTA   73 (307)
Q Consensus        45 ~g~~~~~l~~~fgvs~stv~r~v~~~~~~   73 (307)
                      ...+-.+||..+|||++||+..+++..+.
T Consensus        20 ~~v~~~~iA~~L~vs~~SVs~mikrL~~~   48 (61)
T d2ev0a1          20 GYARVSDIAEALAVHPSSVTKMVQKLDKD   48 (61)
T ss_dssp             SSCCHHHHHHHHTCCHHHHHHHHHHHHHT
T ss_pred             CCccHHHHHHHhCCCchhHHHHHHHHHHC
Confidence            34778899999999999999999987653

>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=80.08  E-value=0.73  Score=28.90  Aligned_cols=45  Identities=11%  Similarity=0.056  Sum_probs=32.6

Q ss_pred             HHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHH
Q psy4300          42 YMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNF   99 (307)
Q Consensus        42 ~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f   99 (307)
                      +-..|.++.++|...|+|+++++++-+..             -..|+.+.+..+++.|
T Consensus        10 R~~~gltq~~la~~~gis~~~i~~~E~g~-------------~~~ps~~~l~~ia~~l   54 (68)
T d1b0na2          10 RKEKGYSLSELAEKAGVAKSYLSSIERNL-------------QTNPSIQFLEKVSAVL   54 (68)
T ss_dssp             HHHTTCCHHHHHHHHTCCHHHHHHHHTTC-------------CSCCCHHHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHHcCC-------------CCCCCHHHHHHHHHHH
Confidence            45679999999999999999999875421             1235555566666655

>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=80.01  E-value=0.89  Score=30.32  Aligned_cols=42  Identities=7%  Similarity=0.093  Sum_probs=33.7

Q ss_pred             HHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300          36 TLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ   78 (307)
Q Consensus        36 l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l   78 (307)
                      |-++.....+ .++...|...++|++++++.+.++-..+-..|
T Consensus        11 L~~f~~v~~~-gs~t~AA~~l~isq~avs~~l~~lE~~~g~~L   52 (89)
T d2esna1          11 LLVFDALYRH-RNVGTAASELAISASAFSHALGRLRQGLDDEL   52 (89)
T ss_dssp             HHHHHHHHHH-SSHHHHHHHHTCCHHHHHHHHHHHHHHHTSCC
T ss_pred             HHHHHHHHHh-CCHHHHHHHHCCCCcHhhHHHHHHHhcCCcee
Confidence            3333333444 58999999999999999999999999987776