Psyllid ID: psy10346

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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--
Protein Sequence
MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSETEFFFFFYDF
Secondary Structure (PSIPRED)
cccHHHHHHHHHHcccccccHHHHHHHccccHHHHHHHHHHHHHcccEEEEEEEEEEEEEccHHHHHHHHcccHHHHHHHHcccccccHHHHHHccccHHHHHHHHHHcccEEccccccEEEccccccHHHHHHHHHHHHccccccccHHHHHHHHHHccHHHHHHHHHHccccccHHHHHHHHHHHHHHHHHHcHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHHHHcccEEEEEEEEEEEEEEcHHHHHHHHcccHHHHHHHHcccccccHHHHHHHcccccHHHHHHHHcccEEEEccccEEEEccccccHHHHHHHHHHHHcccccccHHHHHHHHHHHHEEEEEEEEEEEEccccHHHHHHHHHccccHHHHHcccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccEcccccEEEEHHHHcccccccccccccccccccEEEccccccccEEEEEEcc
Coil and Loop (DISEMBL)
MASDLTEKILKYldtnppvdtldLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWEltgegnqvkdngshevlvfnnvpsegigqkellatfpnakvgfSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANneydkvpeankvdykkRKLLQEVTIKSFllkkgpefsttiqkpeteltpemiasgswktlnfkpynfdamgislpsghlhpLMKVRAEFRQIFLDmgftemptnnfvessfwnfdalfqpqqhpardahdtffvtdpktsetefFFFFYDF
Flexible Loop (DISEMBL)
MASDLTEKILkyldtnppvDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKlianneydkvpeankvdykkrkLLQEVTiksfllkkgpefsttiqkpeteltpeMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSETEFFFFFYDF
Low Complexity Region (SEG)
MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSETEfffffYDF
Disordered region (IsUnstruct)
********ILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEF*************EMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSETEFFFFFY**
Disordered Region (DISOPRED)
***DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNNVPS****************VGFSKAMAKGWISLDKATGKVLRKVDSVTDELQA********************************************TTIQKPETELT*******************DAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSETEFF***YDF
Disordered Region (DISEMBL)
MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSETEFFFFFYDF
Disordered Region (DISPRO)
*ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSETEFFFFFYDF
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSETEFFFFFYDF
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	292	2.2.26 [Sep-21-2011]
Q9W3J5	498	Probable phenylalanine--t	yes	N/A	0.962	0.564	0.602	2e-94
Q7SYV0	499	Phenylalanine--tRNA ligas	N/A	N/A	0.955	0.559	0.566	8e-87
Q6AZG6	498	Phenylalanine--tRNA ligas	N/A	N/A	0.962	0.564	0.548	1e-85
Q9Y285	508	Phenylalanine--tRNA ligas	yes	N/A	0.934	0.537	0.543	7e-85
Q5RFA2	508	Phenylalanine--tRNA ligas	yes	N/A	0.934	0.537	0.539	2e-84
Q1JPX3	497	Phenylalanine--tRNA ligas	yes	N/A	0.941	0.553	0.567	1e-83
Q8C0C7	508	Phenylalanine--tRNA ligas	yes	N/A	0.886	0.509	0.551	2e-83
Q505J8	508	Phenylalanine--tRNA ligas	yes	N/A	0.928	0.533	0.532	3e-83
Q5ZJQ2	443	Phenylalanine--tRNA ligas	yes	N/A	0.948	0.625	0.517	2e-81
Q9T034	485	Probable phenylalanine--t	yes	N/A	0.917	0.552	0.436	5e-52

>sp|Q9W3J5|SYFA_DROME Probable phenylalanine--tRNA ligase alpha subunit OS=Drosophila melanogaster GN=CG2263 PE=2 SV=1

 Score =  345 bits (885), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 171/284 (60%), Positives = 211/284 (74%), Gaps = 3/284 (1%)

Query: 1   MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWE 60
           M  DLTE+IL++L+T    DTLDLA LF EDHQK+VG +KSI+  GE +  E ++HK   
Sbjct: 1   MHPDLTERILQHLETTDKADTLDLAALFAEDHQKIVGSLKSIQAHGELVTAETVTHKSLG 60

Query: 61  LTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATF-PNAKVGFSKAMAKGWISLDKATG 119
           LT EG  V +NGSHE LV++ VP EGI Q  L+A    NAKVGFSKAM+ GWI +DK+  
Sbjct: 61  LTDEGRAVVENGSHEALVYDLVPPEGIAQAALMAAGGANAKVGFSKAMSHGWILVDKSVT 120

Query: 120 K--VLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEF 177
              V RKVD++TD ++  L+ +A  + D++P     D+KKRKLLQE T KSF+L +GPEF
Sbjct: 121 PPLVRRKVDTITDVVRNQLQQVALGKGDQLPAKEVADFKKRKLLQETTTKSFVLARGPEF 180

Query: 178 STTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDM 237
           +TT+ K ET+LT EM+A+G W  L FK YNFDA+G     GHLHPL+KVR EFRQIFL+M
Sbjct: 181 ATTLTKLETDLTVEMLANGLWDQLKFKAYNFDALGAPPTRGHLHPLLKVRTEFRQIFLEM 240

Query: 238 GFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS 281
           GF+EMPTNN+VESSFWNFDAL+QPQQHPARDAHDTFFV  P  S
Sbjct: 241 GFSEMPTNNYVESSFWNFDALYQPQQHPARDAHDTFFVNHPAKS 284

Drosophila melanogaster (taxid: 7227)
EC: 6EC: .EC: 1EC: .EC: 1EC: .EC: 2EC: 0

>sp|Q7SYV0|SYFAB_XENLA Phenylalanine--tRNA ligase alpha subunit B OS=Xenopus laevis GN=farsa-b PE=2 SV=1

 Score =  320 bits (820), Expect = 8e-87,   Method: Compositional matrix adjust.
 Identities = 162/286 (56%), Positives = 206/286 (72%), Gaps = 7/286 (2%)

Query: 5   LTEKILKYLDT--NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT 62
           L+E++L+ L    N  VDTL+LA + + DHQ+VVG +KS++ LGE +  E  S K WEL+
Sbjct: 6   LSEQLLQRLQDGDNKGVDTLELAAVLSVDHQQVVGAVKSLQCLGEIIEAEQRSSKKWELS 65

Query: 63  GEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATGK-- 120
            EG ++   GSHE  VF ++P EG+ Q EL+   P AKVGFSKAM+  WI LDKA     
Sbjct: 66  SEGEEIAQVGSHEARVFQSLPKEGLLQAELM-KLPFAKVGFSKAMSNKWIRLDKAAAGGP 124

Query: 121 -VLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFST 179
            V R V+++ D ++  L+LI     D V E +K + KKRKL+ EVT+KS+ + KG  FST
Sbjct: 125 CVYRVVETIEDTVKEKLQLILKGRADDVNEKDKNELKKRKLVNEVTVKSYWVTKGSGFST 184

Query: 180 TIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGF 239
           +I K ET+LTPEMIASGSW+   FK YNF+A+G+    GHLHPL+KVR +FRQIFL+MGF
Sbjct: 185 SITKQETDLTPEMIASGSWREKQFKGYNFNALGVMPECGHLHPLLKVRTQFRQIFLEMGF 244

Query: 240 TEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSETEF 285
           TEMPTNNF+ESSFWNFDALFQPQQHPARD HDTFF+ DP  + TEF
Sbjct: 245 TEMPTNNFIESSFWNFDALFQPQQHPARDQHDTFFLQDPALA-TEF 289

Xenopus laevis (taxid: 8355)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 0

>sp|Q6AZG6|SYFAA_XENLA Phenylalanine--tRNA ligase alpha subunit A OS=Xenopus laevis GN=farsa-a PE=2 SV=1

 Score =  316 bits (810), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 158/288 (54%), Positives = 206/288 (71%), Gaps = 7/288 (2%)

Query: 3   SDLTEKILKYLD--TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWE 60
           + ++E++L+ L    +  VD+L+LA L   +HQ+VVG +KS++ LGE +  E  S K WE
Sbjct: 4   NSVSEQLLQRLQDGGSKGVDSLELAALLGVEHQQVVGAVKSLQCLGEIIQAEQRSSKKWE 63

Query: 61  LTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATG- 119
           L+ EG ++   GSHE  VF  +P EG+ Q +L+   P +KVGFSKAM+  WI LDKA   
Sbjct: 64  LSSEGEEIGREGSHEARVFQTLPKEGLLQAQLMKQ-PFSKVGFSKAMSNKWIRLDKAAEG 122

Query: 120 --KVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEF 177
             ++ R VDS+ D ++  L+LI     D V E ++ + KKRKL+ EVT+KS+ + KG  F
Sbjct: 123 GPRIYRVVDSIEDTVKEKLQLILKGRADDVNEKDRNELKKRKLVNEVTVKSYWVTKGSGF 182

Query: 178 STTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDM 237
           ST+I K ET+LTPEMIASGSW+   FK YNFDA+G+    GHLHPL+KVR +FRQIFL+M
Sbjct: 183 STSITKQETDLTPEMIASGSWREKQFKGYNFDALGVMPECGHLHPLLKVRTQFRQIFLEM 242

Query: 238 GFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSETEF 285
           GFTEMPTNNF+ESSFWNFDALFQPQQHPARD HDTFF+ DP  + TEF
Sbjct: 243 GFTEMPTNNFIESSFWNFDALFQPQQHPARDQHDTFFLQDPALA-TEF 289

Xenopus laevis (taxid: 8355)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 0

>sp|Q9Y285|SYFA_HUMAN Phenylalanine--tRNA ligase alpha subunit OS=Homo sapiens GN=FARSA PE=1 SV=3

 Score =  313 bits (803), Expect = 7e-85,   Method: Compositional matrix adjust.
 Identities = 151/278 (54%), Positives = 202/278 (72%), Gaps = 5/278 (1%)

Query: 5   LTEKILKYLD-TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG 63
           + E +L+ L+ ++  +D+ +LA     +HQ VVG +KS++ LGE +  E  S K WELT 
Sbjct: 6   VAELLLRRLEASDGGLDSAELAAELGMEHQAVVGAVKSLQALGEVIEAELRSTKHWELTA 65

Query: 64  EGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATG---K 120
           EG ++   GSHE  VF ++P EG+ Q EL+   P+ KVGFSKAM+  WI +DK+     +
Sbjct: 66  EGEEIAREGSHEARVFRSIPPEGLAQSELM-RLPSGKVGFSKAMSNKWIRVDKSAADGPR 124

Query: 121 VLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTT 180
           V R VDS+ DE+Q  L+L+   + +K+ E  + + +KRKLL EVT+K++ + KG  FST+
Sbjct: 125 VFRVVDSMEDEVQRRLQLVRGGQAEKLGEKERSELRKRKLLAEVTLKTYWVSKGSAFSTS 184

Query: 181 IQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFT 240
           I K ETEL+PEMI+SGSW+   FKPYNF A G+   SGHLHPL+KVR++FRQIFL+MGFT
Sbjct: 185 ISKQETELSPEMISSGSWRDRPFKPYNFLAHGVLPDSGHLHPLLKVRSQFRQIFLEMGFT 244

Query: 241 EMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278
           EMPT+NF+ESSFWNFDALFQPQQHPARD HDTFF+ DP
Sbjct: 245 EMPTDNFIESSFWNFDALFQPQQHPARDQHDTFFLRDP 282

Homo sapiens (taxid: 9606)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 0

>sp|Q5RFA2|SYFA_PONAB Phenylalanine--tRNA ligase alpha subunit OS=Pongo abelii GN=FARSA PE=2 SV=1

 Score =  312 bits (799), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 150/278 (53%), Positives = 201/278 (72%), Gaps = 5/278 (1%)

Query: 5   LTEKILKYLD-TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG 63
           + E +L+ L+ ++  +D+ +LA     +HQ VVG +KS++ LGE +  E  S K WELT 
Sbjct: 6   VAELLLRRLEASDGGLDSAELAAELGMEHQAVVGAVKSLQALGEVIEAELRSTKRWELTA 65

Query: 64  EGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATG---K 120
           EG ++   GSHE  VF ++P EG+ Q EL+   P+ KVGFSKAM+  WI +DK+     +
Sbjct: 66  EGEEIAREGSHEARVFRSIPPEGLAQSELM-RLPSGKVGFSKAMSNKWIRVDKSAADGPR 124

Query: 121 VLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTT 180
           V R VDS+ DE+Q  L+L+   + +K+ E  + + +KRKLL EV +K++ + KG  FST+
Sbjct: 125 VFRVVDSMEDEVQRRLQLVRGGQAEKLGEKERSELRKRKLLAEVILKTYWVSKGSAFSTS 184

Query: 181 IQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFT 240
           I K ETEL+PEMI+SGSW+   FKPYNF A G+   SGHLHPL+KVR++FRQIFL+MGFT
Sbjct: 185 ISKQETELSPEMISSGSWRDRPFKPYNFLAHGVLPDSGHLHPLLKVRSQFRQIFLEMGFT 244

Query: 241 EMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278
           EMPT+NF+ESSFWNFDALFQPQQHPARD HDTFF+ DP
Sbjct: 245 EMPTDNFIESSFWNFDALFQPQQHPARDQHDTFFLRDP 282

Pongo abelii (taxid: 9601)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 0

>sp|Q1JPX3|SYFA_DANRE Phenylalanine--tRNA ligase alpha subunit OS=Danio rerio GN=farsa PE=2 SV=2

 Score =  309 bits (792), Expect = 1e-83,   Method: Compositional matrix adjust.
 Identities = 159/280 (56%), Positives = 205/280 (73%), Gaps = 5/280 (1%)

Query: 3   SDLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWEL 61
           + L E +L+ ++  +  VD+ D++     DHQ VVG +KS++ LGE +  E  S K WEL
Sbjct: 4   TGLLEALLQRVEQLDGGVDSQDVSAALGVDHQLVVGAVKSLQALGEVISAEQKSSKHWEL 63

Query: 62  TGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKA---T 118
           TGEG ++ + GSHE  VFN +P+EG+ Q +L+    + KVGFSKAM+  WI LDKA    
Sbjct: 64  TGEGREIAEQGSHEARVFNAIPAEGLPQNQLM-KMASGKVGFSKAMSNKWIRLDKAHEGG 122

Query: 119 GKVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFS 178
            +V R V+S+ D ++  L+L+ N +  K+ E  K + KKRKLL EVT+KS+ + KG  FS
Sbjct: 123 PRVFRTVESIEDTVRDKLQLVQNGQSAKLEEKEKNELKKRKLLAEVTVKSYWITKGNSFS 182

Query: 179 TTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMG 238
           TTI K ETELTPEMIASG+WK   FKPYNF+AMG++   GHLHPLMKVR +FRQIFL+MG
Sbjct: 183 TTITKQETELTPEMIASGNWKEKKFKPYNFEAMGVAPDCGHLHPLMKVRTQFRQIFLEMG 242

Query: 239 FTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278
           FTEMPTNNF+ESSFWNFD+LFQPQQHPARD HDTFF++DP
Sbjct: 243 FTEMPTNNFIESSFWNFDSLFQPQQHPARDQHDTFFISDP 282

Danio rerio (taxid: 7955)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 0

>sp|Q8C0C7|SYFA_MOUSE Phenylalanine--tRNA ligase alpha subunit OS=Mus musculus GN=Farsa PE=2 SV=1

 Score =  308 bits (790), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 145/263 (55%), Positives = 191/263 (72%), Gaps = 4/263 (1%)

Query: 19  VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLV 78
           +D+ +LA     +HQ VVG +KS++ LGE +  E  S K WELT EG ++   GSHE  V
Sbjct: 21  LDSAELATQLGVEHQAVVGAVKSLQALGEVIEAELRSTKCWELTTEGEEIAREGSHEARV 80

Query: 79  FNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATG---KVLRKVDSVTDELQAH 135
           F ++P EG+ Q EL+   P+ KVGFSKAM+  WI +DK+     +V R VDS+ DE+Q  
Sbjct: 81  FRSIPLEGLVQSELM-HLPSGKVGFSKAMSNKWIRVDKSAADGPRVFRVVDSIEDEVQKR 139

Query: 136 LKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTTIQKPETELTPEMIAS 195
           L+L+   + +K+ E  + + +KRKLL EV +K++ + KG  FST++ K E EL+PEMI+S
Sbjct: 140 LQLVQAGQAEKLAEKERNELRKRKLLTEVILKTYWVSKGKAFSTSVSKQEAELSPEMISS 199

Query: 196 GSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNF 255
           GSW+   FKPYNF A G+   SGHLHPL+KVR++FRQIFL+MGFTEMPT+NF+ESSFWNF
Sbjct: 200 GSWRDRPFKPYNFSARGVLPDSGHLHPLLKVRSQFRQIFLEMGFTEMPTDNFIESSFWNF 259

Query: 256 DALFQPQQHPARDAHDTFFVTDP 278
           DALFQPQQHPARD HDTFF+ DP
Sbjct: 260 DALFQPQQHPARDQHDTFFLRDP 282

Mus musculus (taxid: 10090)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 0

>sp|Q505J8|SYFA_RAT Phenylalanine--tRNA ligase alpha subunit OS=Rattus norvegicus GN=Farsa PE=1 SV=1

 Score =  308 bits (789), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 147/276 (53%), Positives = 198/276 (71%), Gaps = 5/276 (1%)

Query: 7   EKILKYLD-TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEG 65
           E++L+ L+  +  +D+ +LA     +HQ VVG +KS++ LGE +  E  S K WELT EG
Sbjct: 8   EQLLRRLEVADGGLDSAELATQLGVEHQAVVGAVKSLQALGEVIEAELRSTKCWELTTEG 67

Query: 66  NQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATG---KVL 122
            ++   GSHE  VF ++P EG+ Q EL+   P+ KVGFSKAM+  WI +DK+     +V 
Sbjct: 68  EEIAREGSHEARVFRSIPLEGLVQSELM-QLPSGKVGFSKAMSNKWIRVDKSAADGPRVF 126

Query: 123 RKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTTIQ 182
           R VDS+ DE+Q  L+ +   + +K+ E  + + +KRKLL EV +K++ + KG  FST++ 
Sbjct: 127 RVVDSIEDEVQRRLQQVQAGQAEKLAEKERNELRKRKLLTEVILKTYWVSKGKGFSTSVS 186

Query: 183 KPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEM 242
           K E EL+PEMI+SGSW+   FKPYNF A G+   SGHLHPL+KVR++FRQIFL+MGFTEM
Sbjct: 187 KQEAELSPEMISSGSWRDRPFKPYNFSARGVLPDSGHLHPLLKVRSQFRQIFLEMGFTEM 246

Query: 243 PTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278
           PT+NF+ESSFWNFDALFQPQQHPARD HDTFF+ DP
Sbjct: 247 PTDNFIESSFWNFDALFQPQQHPARDQHDTFFLRDP 282

Rattus norvegicus (taxid: 10116)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 0

>sp|Q5ZJQ2|SYFA_CHICK Phenylalanine--tRNA ligase alpha subunit OS=Gallus gallus GN=FARSA PE=1 SV=1

 Score =  302 bits (774), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 148/286 (51%), Positives = 199/286 (69%), Gaps = 9/286 (3%)

Query: 1   MASDLTEKILKYLDTNPP-----VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS 55
           M+  + E +L+ L+  PP     + +L+ A     DHQ +VG +KS++ LGE +  E  +
Sbjct: 1   MSPSVAELLLQRLERTPPGPEGGLCSLEAAAALGLDHQTLVGAVKSLQALGEVIEAETRA 60

Query: 56  HKIWELTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLD 115
              WEL+ EG +V  +GS EV +F +VPSEG+ Q + +   P A+VGFSKAMA  W+ LD
Sbjct: 61  TTRWELSAEGEEVLRDGSPEVRLFRSVPSEGLPQSDAM-KLPGAQVGFSKAMANKWLRLD 119

Query: 116 K-ATG--KVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLK 172
           K A G  ++ R VD+V D +Q+ L+ +       + E  + D K+RKLL EVT+KS+ ++
Sbjct: 120 KGAPGGPRIFRAVDAVQDVVQSSLRQVQEGNGGSLSERERTDLKRRKLLLEVTLKSYWIR 179

Query: 173 KGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQ 232
           KG  FST + + ET+LTPEMIA+GSW+ L FK YNF A+G+    GHLHPL+KVR++ RQ
Sbjct: 180 KGSAFSTAVVRQETDLTPEMIATGSWRKLPFKAYNFSALGLPPTCGHLHPLLKVRSQLRQ 239

Query: 233 IFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278
           IFL+MGFTEMPT+NFVESSFWNFDALFQPQQHPARD HDTFF+ DP
Sbjct: 240 IFLEMGFTEMPTDNFVESSFWNFDALFQPQQHPARDQHDTFFLQDP 285

Gallus gallus (taxid: 9031)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 0

>sp|Q9T034|SYFA_ARATH Probable phenylalanine--tRNA ligase alpha subunit OS=Arabidopsis thaliana GN=At4g39280 PE=2 SV=3

 Score =  204 bits (519), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 123/282 (43%), Positives = 169/282 (59%), Gaps = 14/282 (4%)

Query: 7   EKILKYLDTNPPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEG 65
           E IL +L  N  + D+   +  FN DH ++V  +KS+     Y+ V+ +  + W LT EG
Sbjct: 4   EAILGFLQNNEQITDSGQFSAEFNIDHNELVNVIKSLHGF-RYIDVQDIKKETWILTDEG 62

Query: 66  NQVKDNGSHEVLVFNNVPSEG-IGQKELLATFPNA--KVGFSKAMAKGWISLDKATGKVL 122
            +    GS EV +F  VP EG I + EL      A  K+G S+A    W+ + K   +V 
Sbjct: 63  KKYAAEGSPEVQLFLAVPEEGSISKDELQKKLAPAVFKIGCSQAGKNKWVEMGK---QVS 119

Query: 123 RKVDSVTDELQAHL-KLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTTI 181
           RKV  V D+++  L ++    E+DK    N +  K RKL+     K + +KKGP ++   
Sbjct: 120 RKVKDVEDKVKGQLLQIQQGKEFDK-ESINSL--KARKLIVPQIWKGYSVKKGPNYAPER 176

Query: 182 QKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTE 241
           +K  T+LT E + +  WK L FK YNF A G  + +GHLH L+KVR +F+ IF+ MGF E
Sbjct: 177 KKVATDLTRENLQN--WKELEFKEYNFKAKGAPVDAGHLHALLKVRKQFKDIFVQMGFEE 234

Query: 242 MPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSET 283
           MPTNN+VESSFWNFDALFQPQQHPARD+HDTFF+  P T+ T
Sbjct: 235 MPTNNYVESSFWNFDALFQPQQHPARDSHDTFFLKVPSTTRT 276

Arabidopsis thaliana (taxid: 3702)

EC: 6

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 0

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	292
242016298	496	phenylalanyl-tRNA synthetase alpha chain	0.962	0.566	0.609	2e-96
170035494	496	phenylalanyl-tRNA synthetase alpha chain	0.952	0.560	0.601	4e-94
91091732	492	PREDICTED: similar to Probable phenylala	0.952	0.565	0.6	5e-94
322803078	693	hypothetical protein SINV_05204 [Solenop	0.945	0.398	0.593	2e-93
306518662	491	phenylalanyl-tRNA synthetase alpha subun	0.955	0.568	0.609	3e-93
321478959	503	hypothetical protein DAPPUDRAFT_300019 [	0.958	0.556	0.585	7e-93
195565705	445	GD16126 [Drosophila simulans] gi|1942038	0.962	0.631	0.598	1e-92
18858079	498	CG2263 [Drosophila melanogaster] gi|1223	0.962	0.564	0.602	1e-92
195355817	498	GM11206 [Drosophila sechellia] gi|194130	0.962	0.564	0.598	2e-92
195480218	498	GE17477 [Drosophila yakuba] gi|194188707	0.962	0.564	0.598	4e-92

>gi|242016298|ref|XP_002428766.1| phenylalanyl-tRNA synthetase alpha chain, putative [Pediculus humanus corporis] gi|212513451|gb|EEB16028.1| phenylalanyl-tRNA synthetase alpha chain, putative [Pediculus humanus corporis]

 Score =  358 bits (919), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 173/284 (60%), Positives = 220/284 (77%), Gaps = 3/284 (1%)

Query: 1   MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWE 60
           MA+DLTEKILK +D+   +DT DLA   NEDHQK++G +KS++ LG  +  EP  H  WE
Sbjct: 1   MATDLTEKILKIIDSKNEIDTYDLAGELNEDHQKIIGTVKSLQALGNLVKGEPKVHSYWE 60

Query: 61  LTGEGNQVKDNGSHEVLVFNNVPSE-GIGQKELLATFPNAKVGFSKAMAKGWISLDKATG 119
           LT EG  V +NGSHE L+FN VP + GI Q +++AT PNAKVGFSKAM++GW+ +DK++G
Sbjct: 61  LTKEGQSVVENGSHEALIFNAVPPDTGIEQSKIMATVPNAKVGFSKAMSQGWVFIDKSSG 120

Query: 120 K--VLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEF 177
              V RKVD ++D ++ HLKLI N + + VP+  K DYKKRKL+QEV IKS LL KG EF
Sbjct: 121 VPVVKRKVDDISDVVRQHLKLILNKDGNSVPDNVKQDYKKRKLIQEVVIKSILLSKGSEF 180

Query: 178 STTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDM 237
             +++K ET+LT E++ + +WK   FK YNF+++G+   SGHLHPLMKVRAEFR+IF++M
Sbjct: 181 QLSVEKQETDLTAELLLNDAWKNKTFKDYNFNSLGVLPNSGHLHPLMKVRAEFRKIFIEM 240

Query: 238 GFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS 281
           GF EMPTNNFVESSFWNFDALFQPQQHPARDAHDTFF++ P TS
Sbjct: 241 GFQEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFLSFPATS 284

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170035494|ref|XP_001845604.1| phenylalanyl-tRNA synthetase alpha chain [Culex quinquefasciatus] gi|167877516|gb|EDS40899.1| phenylalanyl-tRNA synthetase alpha chain [Culex quinquefasciatus]

 Score =  350 bits (899), Expect = 4e-94,   Method: Compositional matrix adjust.
 Identities = 169/281 (60%), Positives = 214/281 (76%), Gaps = 3/281 (1%)

Query: 4   DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI-VEPLSHKIWELT 62
           DLTE+IL+Y+D +  VDTLDL  +F  DHQK+VGG+KSIE+  E +I  E  + K WELT
Sbjct: 3   DLTERILQYIDQHGTVDTLDLVPVFGLDHQKIVGGVKSIESTVEGVIRTEQATRKCWELT 62

Query: 63  GEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATGKVL 122
            EG  + + GSHE  +F  VP+EGI Q EL+ + PNAKVGFSKAM+ GWI +DK+ G  L
Sbjct: 63  EEGKVILEKGSHEAAIFRAVPAEGIAQAELMKSSPNAKVGFSKAMSNGWILMDKSGGAPL 122

Query: 123 --RKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTT 180
             RKV+++ D +Q ++K +A     +VP+A K +YKKRK+L EV  KSF+L KG EFST+
Sbjct: 123 IKRKVEAIEDAVQGYVKAVAEGRDGEVPDAVKAEYKKRKILTEVVTKSFVLSKGAEFSTS 182

Query: 181 IQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFT 240
           ++K ET+LT EM+ASG WK L FKPYNF+A+G+    GH+HPLMKVR EFRQIFL+MGF+
Sbjct: 183 LKKLETDLTVEMLASGIWKDLKFKPYNFEALGVPPERGHMHPLMKVRTEFRQIFLEMGFS 242

Query: 241 EMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS 281
           EMPTNNFVESSFWNFDAL+ PQQHPARD  DTFFV+ P+ S
Sbjct: 243 EMPTNNFVESSFWNFDALYVPQQHPARDQQDTFFVSHPRLS 283

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|91091732|ref|XP_967643.1| PREDICTED: similar to Probable phenylalanyl-tRNA synthetase alpha chain (Phenylalanine--tRNA ligase alpha chain) (PheRS) [Tribolium castaneum] gi|270000850|gb|EEZ97297.1| hypothetical protein TcasGA2_TC011106 [Tribolium castaneum]

 Score =  350 bits (897), Expect = 5e-94,   Method: Compositional matrix adjust.
 Identities = 168/280 (60%), Positives = 215/280 (76%), Gaps = 2/280 (0%)

Query: 3   SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT 62
           SDL+EKIL+++    P++TLDLA+L   DHQK+VG +KSI+  G+ +  EP + K  ELT
Sbjct: 2   SDLSEKILRHVSETSPLNTLDLAQLLATDHQKIVGALKSIQAHGDLIRAEPQTSKFIELT 61

Query: 63  GEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATGKVL 122
            EG QV ++GSHE  +F+ VPSEG+ Q EL+   PNAKVGFSKAM+ GW++LDK    V+
Sbjct: 62  EEGKQVAEHGSHEARIFHAVPSEGVAQAELM-RLPNAKVGFSKAMSAGWLTLDKGGPPVV 120

Query: 123 -RKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTTI 181
            RKVD + D +QA+L+LI      ++ ++ + +YKKRKL+QEV  KSF L KG +FS T+
Sbjct: 121 KRKVDKIVDTVQANLRLIQGGHLGQIEDSVRQEYKKRKLIQEVVQKSFNLTKGGDFSLTL 180

Query: 182 QKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTE 241
            K ET+LT EM+ +G W+ L FK YNFDA+G  L  G+LHPL+KVRAEFRQIFL+MGF+E
Sbjct: 181 AKLETDLTSEMLLTGGWQQLKFKDYNFDALGAPLDCGYLHPLLKVRAEFRQIFLEMGFSE 240

Query: 242 MPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS 281
           MPTNN+VESSFWNFDALFQPQQHPARDAHDTFFV+DPK S
Sbjct: 241 MPTNNYVESSFWNFDALFQPQQHPARDAHDTFFVSDPKIS 280

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322803078|gb|EFZ23166.1| hypothetical protein SINV_05204 [Solenopsis invicta]

 Score =  348 bits (893), Expect = 2e-93,   Method: Compositional matrix adjust.
 Identities = 168/283 (59%), Positives = 216/283 (76%), Gaps = 7/283 (2%)

Query: 1   MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWE 60
           MA  LT++IL+YLD +   ++LDLA  F EDHQKVVG +KS+ET+ + + V+P+S K WE
Sbjct: 1   MARQLTDRILEYLDAHGETNSLDLADEFQEDHQKVVGAIKSLETVDDLITVKPISKKKWE 60

Query: 61  LTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKA--T 118
           LT EG  + ++GSHE +++N VP  GI Q +L+ + P AKVGFSKAM  GWI LDK+   
Sbjct: 61  LTDEGKHIIEHGSHEAVIYNAVPDNGIPQSKLIKSSPYAKVGFSKAMVAGWIELDKSGDV 120

Query: 119 GKVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFS 178
             V ++V S+ D +QAHLK +AN     VPE  K +YKKRKLLQEV IK   L+KGP FS
Sbjct: 121 PIVRKRVPSIVDIIQAHLKNLAN-----VPENVKAEYKKRKLLQEVIIKIMQLEKGPNFS 175

Query: 179 TTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMG 238
           T ++K E +LT +++ +G+WK   FKPYNF+AMG SL  G+LHPL+KVR EFR+IFL+MG
Sbjct: 176 TKLEKLEADLTADLLVNGAWKNKKFKPYNFEAMGASLQIGYLHPLLKVRHEFRKIFLEMG 235

Query: 239 FTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS 281
           FTEMPTNN+VESSFWNFDALFQPQQHPARDAHDTFF+++P+ S
Sbjct: 236 FTEMPTNNYVESSFWNFDALFQPQQHPARDAHDTFFISEPRNS 278

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|306518662|ref|NP_001182394.1| phenylalanyl-tRNA synthetase alpha subunit [Bombyx mori] gi|303304919|dbj|BAJ14786.1| phenylalanyl-tRNA synthetase alpha subunit [Bombyx mori]

 Score =  347 bits (891), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 173/284 (60%), Positives = 216/284 (76%), Gaps = 5/284 (1%)

Query: 4   DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG 63
           +L E+ILKYL+ +   DTL L + FNE+HQK+VG +KS+E L E +I E +    WELT 
Sbjct: 2   ELNERILKYLENSDKADTLKLCEEFNEEHQKIVGAVKSLEAL-EMVISEAVKITKWELTE 60

Query: 64  EGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATGK--V 121
           EG  V +NGSHE +++ ++P  G+ Q E +   PNAKVGFSKAM+ GWI +DK++G   V
Sbjct: 61  EGELVANNGSHEAVLYRSIPDSGVPQSEAMKMVPNAKVGFSKAMSSGWIYIDKSSGPPLV 120

Query: 122 LRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTTI 181
            RKVDS+TD +Q +L  I     D + E  + DYKKRKLLQEVTIKSFLL KGP+F+ TI
Sbjct: 121 KRKVDSITDIVQENLSEIRKG-IDNLSENVRNDYKKRKLLQEVTIKSFLLSKGPQFAITI 179

Query: 182 QKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTE 241
           +K ET+LT +M+ SGSWKTL FKPYNFDA+G     GHLHPL+KVR+EFR+IFL+MGFTE
Sbjct: 180 KKLETDLTSDMLLSGSWKTLEFKPYNFDALGQPPECGHLHPLLKVRSEFREIFLEMGFTE 239

Query: 242 MPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSETEF 285
           MPTN +VESSFWNFDALFQPQQHPARDAHDTFF++ P  + TEF
Sbjct: 240 MPTNKYVESSFWNFDALFQPQQHPARDAHDTFFMSSPAAT-TEF 282

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|321478959|gb|EFX89915.1| hypothetical protein DAPPUDRAFT_300019 [Daphnia pulex]

 Score =  346 bits (887), Expect = 7e-93,   Method: Compositional matrix adjust.
 Identities = 171/292 (58%), Positives = 218/292 (74%), Gaps = 12/292 (4%)

Query: 1   MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWE 60
           MA+   EK+LKYL+ N    +L LA+L+NEDHQK+VG +KS+  LGE +  +  S  +W+
Sbjct: 1   MATAHGEKVLKYLEENGTASSLKLAELWNEDHQKIVGTVKSLLCLGEVIEADLQSSALWD 60

Query: 61  LTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLA---------TFPNAKVGFSKAMAKGW 111
           LT EG QV  +GSHE  VFN +P  G  Q E++A         T   AKVGFSKAM+ GW
Sbjct: 61  LTEEGKQVAKDGSHEAQVFNAIPPAGSTQAEIVAKVTEVNSKFTKDMAKVGFSKAMSLGW 120

Query: 112 ISLDKATG--KVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSF 169
           I +DK++G  K ++KV S+ D++Q HLK +A  + D +    + +YKKRKL+QE+ IKS+
Sbjct: 121 IVVDKSSGAPKFIKKVTSIEDKVQEHLKELATGK-DTLTNELRTEYKKRKLIQEIIIKSY 179

Query: 170 LLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAE 229
           ++K GP F+T++ K ET+LTPEMIASGSWKT  FK YN +A+G  +P GHLHPLMKVRAE
Sbjct: 180 VMKPGPSFTTSVTKQETDLTPEMIASGSWKTKEFKAYNLNALGTPIPRGHLHPLMKVRAE 239

Query: 230 FRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS 281
           FRQIFL+MGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFF++DP T+
Sbjct: 240 FRQIFLEMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFLSDPATA 291

Source: Daphnia pulex

Species: Daphnia pulex

Genus: Daphnia

Family: Daphniidae

Order: Diplostraca

Class: Branchiopoda

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195565705|ref|XP_002106439.1| GD16126 [Drosophila simulans] gi|194203815|gb|EDX17391.1| GD16126 [Drosophila simulans]

 Score =  345 bits (886), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 170/284 (59%), Positives = 212/284 (74%), Gaps = 3/284 (1%)

Query: 1   MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWE 60
           M  DLTE+IL++L+T    DTLDLA LF EDHQK+VG +KSI+  GE +  E ++HK   
Sbjct: 1   MHPDLTERILQHLETTDKADTLDLAALFAEDHQKIVGSLKSIQAHGELVTAETVTHKSLG 60

Query: 61  LTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELL-ATFPNAKVGFSKAMAKGWISLDKATG 119
           LT EG  V ++GSHE LV++ VP EGI Q  L+ A   NAKVGFSKAM+ GWI +DK+  
Sbjct: 61  LTDEGRSVVEHGSHEALVYDLVPPEGIAQAALMTAGGANAKVGFSKAMSHGWILVDKSVT 120

Query: 120 K--VLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEF 177
              V RKVD++TD +++ L+ +A  + D++P     D+KKRKLLQE T KSF+L +GPEF
Sbjct: 121 PPLVRRKVDTITDVVRSQLQQVALGKGDQLPAKEVADFKKRKLLQETTTKSFVLARGPEF 180

Query: 178 STTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDM 237
           +TT+ K ET+LT EM+A+G W  L FK YNFDA+G     GHLHPL+KVR EFRQIFL+M
Sbjct: 181 ATTLTKLETDLTVEMLANGLWDQLKFKAYNFDALGAPPTRGHLHPLLKVRTEFRQIFLEM 240

Query: 238 GFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS 281
           GF+EMPTNN+VESSFWNFDAL+QPQQHPARDAHDTFFV  P  S
Sbjct: 241 GFSEMPTNNYVESSFWNFDALYQPQQHPARDAHDTFFVNHPAKS 284

Source: Drosophila simulans

Species: Drosophila simulans

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|18858079|ref|NP_572448.1| CG2263 [Drosophila melanogaster] gi|12230004|sp|Q9W3J5.1|SYFA_DROME RecName: Full=Probable phenylalanine--tRNA ligase alpha subunit; AltName: Full=Phenylalanyl-tRNA synthetase alpha subunit; Short=PheRS gi|7290891|gb|AAF46332.1| CG2263 [Drosophila melanogaster] gi|15291699|gb|AAK93118.1| LD23968p [Drosophila melanogaster] gi|220944932|gb|ACL85009.1| CG2263-PA [synthetic construct] gi|220954698|gb|ACL89892.1| CG2263-PA [synthetic construct]

 Score =  345 bits (885), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 171/284 (60%), Positives = 211/284 (74%), Gaps = 3/284 (1%)

Query: 1   MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWE 60
           M  DLTE+IL++L+T    DTLDLA LF EDHQK+VG +KSI+  GE +  E ++HK   
Sbjct: 1   MHPDLTERILQHLETTDKADTLDLAALFAEDHQKIVGSLKSIQAHGELVTAETVTHKSLG 60

Query: 61  LTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATF-PNAKVGFSKAMAKGWISLDKATG 119
           LT EG  V +NGSHE LV++ VP EGI Q  L+A    NAKVGFSKAM+ GWI +DK+  
Sbjct: 61  LTDEGRAVVENGSHEALVYDLVPPEGIAQAALMAAGGANAKVGFSKAMSHGWILVDKSVT 120

Query: 120 K--VLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEF 177
              V RKVD++TD ++  L+ +A  + D++P     D+KKRKLLQE T KSF+L +GPEF
Sbjct: 121 PPLVRRKVDTITDVVRNQLQQVALGKGDQLPAKEVADFKKRKLLQETTTKSFVLARGPEF 180

Query: 178 STTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDM 237
           +TT+ K ET+LT EM+A+G W  L FK YNFDA+G     GHLHPL+KVR EFRQIFL+M
Sbjct: 181 ATTLTKLETDLTVEMLANGLWDQLKFKAYNFDALGAPPTRGHLHPLLKVRTEFRQIFLEM 240

Query: 238 GFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS 281
           GF+EMPTNN+VESSFWNFDAL+QPQQHPARDAHDTFFV  P  S
Sbjct: 241 GFSEMPTNNYVESSFWNFDALYQPQQHPARDAHDTFFVNHPAKS 284

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195355817|ref|XP_002044384.1| GM11206 [Drosophila sechellia] gi|194130702|gb|EDW52745.1| GM11206 [Drosophila sechellia]

 Score =  345 bits (884), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 170/284 (59%), Positives = 212/284 (74%), Gaps = 3/284 (1%)

Query: 1   MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWE 60
           M  DLTE+IL++L+T    DTLDLA LF EDHQK+VG +KSI+  GE +  E ++HK   
Sbjct: 1   MHPDLTERILQHLETTDKADTLDLAALFAEDHQKIVGSLKSIQAHGELVTAETVTHKSLG 60

Query: 61  LTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATF-PNAKVGFSKAMAKGWISLDKATG 119
           LT EG  V ++GSHE LV++ VP EGI Q  L+A    NAKVGFSKAM+ GWI +DK+  
Sbjct: 61  LTDEGRSVVEHGSHEALVYDLVPPEGIAQAALMAAGGANAKVGFSKAMSHGWILVDKSVT 120

Query: 120 K--VLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEF 177
              V RKVD++TD +++ L+ +A  + D++P     D+KKRKLLQE T KSF+L +GPEF
Sbjct: 121 PPLVRRKVDTITDVVRSQLQQVALGKGDQLPAKEVADFKKRKLLQETTTKSFVLARGPEF 180

Query: 178 STTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDM 237
           +TT+ K ET+LT EM+A+G W  L FK YNFDA+G     GHLHPL+KVR EFRQIFL+M
Sbjct: 181 ATTLTKLETDLTVEMLANGLWDQLKFKAYNFDALGAPPTRGHLHPLLKVRTEFRQIFLEM 240

Query: 238 GFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS 281
           GF+EMPTNN+VESSFWNFDAL+QPQQHPARDAHDTFFV  P  S
Sbjct: 241 GFSEMPTNNYVESSFWNFDALYQPQQHPARDAHDTFFVNHPAKS 284

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195480218|ref|XP_002101183.1| GE17477 [Drosophila yakuba] gi|194188707|gb|EDX02291.1| GE17477 [Drosophila yakuba]

 Score =  343 bits (881), Expect = 4e-92,   Method: Compositional matrix adjust.
 Identities = 170/284 (59%), Positives = 212/284 (74%), Gaps = 3/284 (1%)

Query: 1   MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWE 60
           M  DLTE+IL++L+T   VDTLDLA +F EDHQK+VG +KSI+  GE +  E ++HK   
Sbjct: 1   MHPDLTERILQHLETADKVDTLDLATIFAEDHQKIVGALKSIQAHGELVTAETVTHKSLG 60

Query: 61  LTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELL-ATFPNAKVGFSKAMAKGWISLDKATG 119
           LT EG  V ++GSHE LV+  VP EGI Q  L+ A   NAKVGFSKAM+ GWI +DK+  
Sbjct: 61  LTDEGRAVVEHGSHEALVYALVPPEGIAQAALMTAGGANAKVGFSKAMSHGWILVDKSVT 120

Query: 120 K--VLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEF 177
              V RKVD++TD +++ L+ +A  + D++P     D+KKRKLLQE T KSF+L +GPEF
Sbjct: 121 PPLVRRKVDTITDVVRSQLQQVALGKGDQLPAKEVADFKKRKLLQETTTKSFVLARGPEF 180

Query: 178 STTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDM 237
           +TT+ K ET+LT EM+A+G W  L FK YNFDA+G     GHLHPL+KVR EFRQIFL+M
Sbjct: 181 ATTLTKLETDLTVEMLANGLWDQLKFKAYNFDALGAPPTRGHLHPLLKVRTEFRQIFLEM 240

Query: 238 GFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS 281
           GF+EMPTNN+VESSFWNFDAL+QPQQHPARDAHDTFFV  P  S
Sbjct: 241 GFSEMPTNNYVESSFWNFDALYQPQQHPARDAHDTFFVNHPARS 284

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

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	292
FB|FBgn0030007	498	CG2263 [Drosophila melanogaste	0.962	0.564	0.602	2.9e-87
ZFIN|ZDB-GENE-050512-2	497	farsa "phenylalanyl-tRNA synth	0.934	0.549	0.575	1.3e-82
UNIPROTKB|E2QU31	508	FARSA "Uncharacterized protein	0.934	0.537	0.557	5.4e-79
UNIPROTKB|K7ER00	548	FARSA "Phenylalanine--tRNA lig	0.934	0.498	0.550	3e-78
UNIPROTKB|Q9Y285	508	FARSA "Phenylalanine--tRNA lig	0.934	0.537	0.550	3e-78
UNIPROTKB|A7MBD4	508	FARSA "Uncharacterized protein	0.948	0.545	0.535	6.2e-78
UNIPROTKB|F1SD97	509	FARSA "Uncharacterized protein	0.928	0.532	0.559	1.3e-77
MGI|MGI:1913840	508	Farsa "phenylalanyl-tRNA synth	0.948	0.545	0.537	5.5e-77
RGD|1310314	508	Farsa "phenylalanyl-tRNA synth	0.948	0.545	0.533	1.1e-76
UNIPROTKB|Q5ZJQ2	443	FARSA "Phenylalanine--tRNA lig	0.948	0.625	0.517	1.9e-74

FB|FBgn0030007 CG2263 [Drosophila melanogaster (taxid:7227)]

 Score = 872 (312.0 bits), Expect = 2.9e-87, P = 2.9e-87
 Identities = 171/284 (60%), Positives = 211/284 (74%)

Query:     1 MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWE 60
             M  DLTE+IL++L+T    DTLDLA LF EDHQK+VG +KSI+  GE +  E ++HK   
Sbjct:     1 MHPDLTERILQHLETTDKADTLDLAALFAEDHQKIVGSLKSIQAHGELVTAETVTHKSLG 60

Query:    61 LTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATF-PNAKVGFSKAMAKGWISLDKATG 119
             LT EG  V +NGSHE LV++ VP EGI Q  L+A    NAKVGFSKAM+ GWI +DK+  
Sbjct:    61 LTDEGRAVVENGSHEALVYDLVPPEGIAQAALMAAGGANAKVGFSKAMSHGWILVDKSVT 120

Query:   120 KVL--RKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEF 177
               L  RKVD++TD ++  L+ +A  + D++P     D+KKRKLLQE T KSF+L +GPEF
Sbjct:   121 PPLVRRKVDTITDVVRNQLQQVALGKGDQLPAKEVADFKKRKLLQETTTKSFVLARGPEF 180

Query:   178 STTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDM 237
             +TT+ K ET+LT EM+A+G W  L FK YNFDA+G     GHLHPL+KVR EFRQIFL+M
Sbjct:   181 ATTLTKLETDLTVEMLANGLWDQLKFKAYNFDALGAPPTRGHLHPLLKVRTEFRQIFLEM 240

Query:   238 GFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS 281
             GF+EMPTNN+VESSFWNFDAL+QPQQHPARDAHDTFFV  P  S
Sbjct:   241 GFSEMPTNNYVESSFWNFDALYQPQQHPARDAHDTFFVNHPAKS 284

GO:0009328 "phenylalanine-tRNA ligase complex" evidence=NAS

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=IEA;NAS

GO:0005737 "cytoplasm" evidence=IEA;NAS

GO:0000049 "tRNA binding" evidence=IEA

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

ZFIN|ZDB-GENE-050512-2 farsa "phenylalanyl-tRNA synthetase, alpha subunit" [Danio rerio (taxid:7955)]

 Score = 828 (296.5 bits), Expect = 1.3e-82, P = 1.3e-82
 Identities = 160/278 (57%), Positives = 205/278 (73%)

Query:     5 LTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG 63
             L E +L+ ++  +  VD+ D++     DHQ VVG +KS++ LGE +  E  S K WELTG
Sbjct:     6 LLEALLQRVEQLDGGVDSQDVSAALGVDHQLVVGAVKSLQALGEVISAEQKSSKHWELTG 65

Query:    64 EGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKA-TG--K 120
             EG ++ + GSHE  VFN +P+EG+ Q +L+    + KVGFSKAM+  WI LDKA  G  +
Sbjct:    66 EGREIAEQGSHEARVFNAIPAEGLPQNQLMK-MASGKVGFSKAMSNKWIRLDKAHEGGPR 124

Query:   121 VLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTT 180
             V R V+S+ D ++  L+L+ N +  K+ E  K + KKRKLL EVT+KS+ + KG  FSTT
Sbjct:   125 VFRTVESIEDTVRDKLQLVQNGQSAKLEEKEKNELKKRKLLAEVTVKSYWITKGNSFSTT 184

Query:   181 IQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFT 240
             I K ETELTPEMIASG+WK   FKPYNF+AMG++   GHLHPLMKVR +FRQIFL+MGFT
Sbjct:   185 ITKQETELTPEMIASGNWKEKKFKPYNFEAMGVAPDCGHLHPLMKVRTQFRQIFLEMGFT 244

Query:   241 EMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278
             EMPTNNF+ESSFWNFD+LFQPQQHPARD HDTFF++DP
Sbjct:   245 EMPTNNFIESSFWNFDSLFQPQQHPARDQHDTFFISDP 282

GO:0043039 "tRNA aminoacylation" evidence=IEA

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0004812 "aminoacyl-tRNA ligase activity" evidence=IEA

GO:0000049 "tRNA binding" evidence=IEA

GO:0006418 "tRNA aminoacylation for protein translation" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0016874 "ligase activity" evidence=IEA

UNIPROTKB|E2QU31 FARSA "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 794 (284.6 bits), Expect = 5.4e-79, P = 5.4e-79
 Identities = 155/278 (55%), Positives = 201/278 (72%)

Query:     5 LTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG 63
             + E +L+ L+  +  +D+ +LA     DHQ VVG +KS++ LGE +  E  S K WELT 
Sbjct:     6 VAEVLLRQLEAADGGLDSAELAAELGVDHQAVVGAVKSLQALGEIIEAELRSTKRWELTA 65

Query:    64 EGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDK--ATG-K 120
             EG ++   GSHE  VF+++P EG+ Q EL+   P+ KVGFSKAM+  WI +DK  A G +
Sbjct:    66 EGEEIAREGSHEARVFHSIPREGLAQSELMR-LPSGKVGFSKAMSNKWIRVDKSAADGPR 124

Query:   121 VLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTT 180
             V R VDSV DE+Q  L+L+   + +K+ E  + + +KRKLL EVT+K++ + KG  FST 
Sbjct:   125 VFRVVDSVEDEVQRRLQLVQGGQAEKLGEKERSELRKRKLLTEVTLKTYWVSKGSTFSTN 184

Query:   181 IQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFT 240
             I K ETEL+PEMI+SGSW+   FKPYNF A G+   SGHLHPL+KVR +FRQIFL+MGFT
Sbjct:   185 ISKQETELSPEMISSGSWRDRPFKPYNFLARGVLPDSGHLHPLLKVRTQFRQIFLEMGFT 244

Query:   241 EMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278
             EMPT+NF+ESSFWNFDALFQPQQHPARD HDTFF+ DP
Sbjct:   245 EMPTDNFIESSFWNFDALFQPQQHPARDQHDTFFLRDP 282

GO:0005737 "cytoplasm" evidence=IEA

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=IEA

GO:0000049 "tRNA binding" evidence=IEA

UNIPROTKB|K7ER00 FARSA "Phenylalanine--tRNA ligase alpha subunit" [Homo sapiens (taxid:9606)]

 Score = 787 (282.1 bits), Expect = 3.0e-78, P = 3.0e-78
 Identities = 153/278 (55%), Positives = 202/278 (72%)

Query:     5 LTEKILKYLDTNPP-VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG 63
             + E +L+ L+ +   +D+ +LA     +HQ VVG +KS++ LGE +  E  S K WELT 
Sbjct:    46 VAELLLRRLEASDGGLDSAELAAELGMEHQAVVGAVKSLQALGEVIEAELRSTKHWELTA 105

Query:    64 EGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDK--ATG-K 120
             EG ++   GSHE  VF ++P EG+ Q EL+   P+ KVGFSKAM+  WI +DK  A G +
Sbjct:   106 EGEEIAREGSHEARVFRSIPPEGLAQSELMR-LPSGKVGFSKAMSNKWIRVDKSAADGPR 164

Query:   121 VLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTT 180
             V R VDS+ DE+Q  L+L+   + +K+ E  + + +KRKLL EVT+K++ + KG  FST+
Sbjct:   165 VFRVVDSMEDEVQRRLQLVRGGQAEKLGEKERSELRKRKLLAEVTLKTYWVSKGSAFSTS 224

Query:   181 IQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFT 240
             I K ETEL+PEMI+SGSW+   FKPYNF A G+   SGHLHPL+KVR++FRQIFL+MGFT
Sbjct:   225 ISKQETELSPEMISSGSWRDRPFKPYNFLAHGVLPDSGHLHPLLKVRSQFRQIFLEMGFT 284

Query:   241 EMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278
             EMPT+NF+ESSFWNFDALFQPQQHPARD HDTFF+ DP
Sbjct:   285 EMPTDNFIESSFWNFDALFQPQQHPARDQHDTFFLRDP 322

GO:0000049 "tRNA binding" evidence=IEA

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=IEA

UNIPROTKB|Q9Y285 FARSA "Phenylalanine--tRNA ligase alpha subunit" [Homo sapiens (taxid:9606)]

 Score = 787 (282.1 bits), Expect = 3.0e-78, P = 3.0e-78
 Identities = 153/278 (55%), Positives = 202/278 (72%)

Query:     5 LTEKILKYLDTNPP-VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG 63
             + E +L+ L+ +   +D+ +LA     +HQ VVG +KS++ LGE +  E  S K WELT 
Sbjct:     6 VAELLLRRLEASDGGLDSAELAAELGMEHQAVVGAVKSLQALGEVIEAELRSTKHWELTA 65

Query:    64 EGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDK--ATG-K 120
             EG ++   GSHE  VF ++P EG+ Q EL+   P+ KVGFSKAM+  WI +DK  A G +
Sbjct:    66 EGEEIAREGSHEARVFRSIPPEGLAQSELMR-LPSGKVGFSKAMSNKWIRVDKSAADGPR 124

Query:   121 VLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTT 180
             V R VDS+ DE+Q  L+L+   + +K+ E  + + +KRKLL EVT+K++ + KG  FST+
Sbjct:   125 VFRVVDSMEDEVQRRLQLVRGGQAEKLGEKERSELRKRKLLAEVTLKTYWVSKGSAFSTS 184

Query:   181 IQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFT 240
             I K ETEL+PEMI+SGSW+   FKPYNF A G+   SGHLHPL+KVR++FRQIFL+MGFT
Sbjct:   185 ISKQETELSPEMISSGSWRDRPFKPYNFLAHGVLPDSGHLHPLLKVRSQFRQIFLEMGFT 244

Query:   241 EMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278
             EMPT+NF+ESSFWNFDALFQPQQHPARD HDTFF+ DP
Sbjct:   245 EMPTDNFIESSFWNFDALFQPQQHPARDQHDTFFLRDP 282

GO:0000049 "tRNA binding" evidence=IEA

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=IEA

GO:0005829 "cytosol" evidence=TAS

GO:0006418 "tRNA aminoacylation for protein translation" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|A7MBD4 FARSA "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 784 (281.0 bits), Expect = 6.2e-78, P = 6.2e-78
 Identities = 151/282 (53%), Positives = 203/282 (71%)

Query:     5 LTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG 63
             + E +L+ L+  +  +D+ +LA     +HQ VVG +KS++ LG+ +  E  S K WELT 
Sbjct:     6 VAEVLLRRLEAADGGLDSAELATELGVEHQTVVGAVKSLQALGQIIETELRSTKRWELTA 65

Query:    64 EGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDK--ATG-K 120
             EG ++   GSHE  VF ++P EG+ Q EL+   P+ KVGFSKAM+  WI +DK  A G +
Sbjct:    66 EGEEIAQEGSHEARVFRSIPPEGLPQSELMR-LPSGKVGFSKAMSNKWIRVDKSAADGPR 124

Query:   121 VLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTT 180
             V R VDSV DE+Q  L+L+   + +K+ E  + + +KRKLL E T+K++ + KG  FST+
Sbjct:   125 VFRVVDSVEDEVQRRLQLVRGGQAEKLGEKERSELRKRKLLTEATLKTYWVSKGSAFSTS 184

Query:   181 IQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFT 240
             I K ETEL+PEMI+SGSW+   FKPYNF A G+   SGHLHPL+KVR++FRQIFL+MGFT
Sbjct:   185 ISKQETELSPEMISSGSWRDRPFKPYNFSAHGVLPDSGHLHPLLKVRSQFRQIFLEMGFT 244

Query:   241 EMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSE 282
             EMPT+N++ESSFWNFDALFQPQQHPARD HDTFF+ DP  ++
Sbjct:   245 EMPTDNYIESSFWNFDALFQPQQHPARDQHDTFFLRDPAQAQ 286

GO:0005737 "cytoplasm" evidence=IEA

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=IEA

GO:0000049 "tRNA binding" evidence=IEA

UNIPROTKB|F1SD97 FARSA "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 781 (280.0 bits), Expect = 1.3e-77, P = 1.3e-77
 Identities = 155/277 (55%), Positives = 201/277 (72%)

Query:     7 EKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEG 65
             E +L+ L+  +  +D+ ++A     +HQ VVG +KS++TLGE +  E  S K WELT EG
Sbjct:     8 EVLLRRLEAADGGLDSAEVAAQLGLEHQAVVGAVKSLQTLGEIIEAELRSTKRWELTAEG 67

Query:    66 NQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDK--ATG-KVL 122
              ++   GSHE  VF +VP EG+ Q EL+   P+ KVGFSKAM+  WI +DK  A G +V 
Sbjct:    68 EEIAREGSHEARVFRSVPPEGLPQSELMR-LPSGKVGFSKAMSNKWIRVDKSAADGPRVF 126

Query:   123 RKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTTIQ 182
             R VDSV DE+Q  L+L+   + +K+ E  + + +KRKLL EVT+K++ + KG  FST+I 
Sbjct:   127 RVVDSVEDEVQRRLQLVQGGQAEKLGEKERSELRKRKLLTEVTLKTYWVSKGSAFSTSIS 186

Query:   183 KPETELTPEMIAS-GSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTE 241
             K ETEL+PEMI+S GSW+   FKPYNF A GI   SGHLHPL+KVR +FRQIFL+MGFTE
Sbjct:   187 KQETELSPEMISSSGSWRDRPFKPYNFSAHGILPESGHLHPLLKVRTQFRQIFLEMGFTE 246

Query:   242 MPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278
             MPT+N++ESSFWNFDALFQPQQHPARD HDTFF+ DP
Sbjct:   247 MPTDNYIESSFWNFDALFQPQQHPARDQHDTFFLRDP 283

GO:0005737 "cytoplasm" evidence=IEA

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=IEA

GO:0000049 "tRNA binding" evidence=IEA

MGI|MGI:1913840 Farsa "phenylalanyl-tRNA synthetase, alpha subunit" [Mus musculus (taxid:10090)]

 Score = 775 (277.9 bits), Expect = 5.5e-77, P = 5.5e-77
 Identities = 152/283 (53%), Positives = 203/283 (71%)

Query:     1 MASD-LTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKI 58
             MA + + E +L+ L+  +  +D+ +LA     +HQ VVG +KS++ LGE +  E  S K 
Sbjct:     1 MADNPVLELLLRRLEVADGGLDSAELATQLGVEHQAVVGAVKSLQALGEVIEAELRSTKC 60

Query:    59 WELTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDK-- 116
             WELT EG ++   GSHE  VF ++P EG+ Q EL+   P+ KVGFSKAM+  WI +DK  
Sbjct:    61 WELTTEGEEIAREGSHEARVFRSIPLEGLVQSELMH-LPSGKVGFSKAMSNKWIRVDKSA 119

Query:   117 ATG-KVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGP 175
             A G +V R VDS+ DE+Q  L+L+   + +K+ E  + + +KRKLL EV +K++ + KG 
Sbjct:   120 ADGPRVFRVVDSIEDEVQKRLQLVQAGQAEKLAEKERNELRKRKLLTEVILKTYWVSKGK 179

Query:   176 EFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFL 235
              FST++ K E EL+PEMI+SGSW+   FKPYNF A G+   SGHLHPL+KVR++FRQIFL
Sbjct:   180 AFSTSVSKQEAELSPEMISSGSWRDRPFKPYNFSARGVLPDSGHLHPLLKVRSQFRQIFL 239

Query:   236 DMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278
             +MGFTEMPT+NF+ESSFWNFDALFQPQQHPARD HDTFF+ DP
Sbjct:   240 EMGFTEMPTDNFIESSFWNFDALFQPQQHPARDQHDTFFLRDP 282

GO:0000049 "tRNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0004812 "aminoacyl-tRNA ligase activity" evidence=IEA

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0006418 "tRNA aminoacylation for protein translation" evidence=IEA

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=IEA

GO:0008150 "biological_process" evidence=ND

GO:0016874 "ligase activity" evidence=IEA

GO:0043039 "tRNA aminoacylation" evidence=IEA

RGD|1310314 Farsa "phenylalanyl-tRNA synthetase, alpha subunit" [Rattus norvegicus (taxid:10116)]

 Score = 772 (276.8 bits), Expect = 1.1e-76, P = 1.1e-76
 Identities = 151/283 (53%), Positives = 203/283 (71%)

Query:     1 MASD-LTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKI 58
             MA + + E++L+ L+  +  +D+ +LA     +HQ VVG +KS++ LGE +  E  S K 
Sbjct:     1 MADNPVLEQLLRRLEVADGGLDSAELATQLGVEHQAVVGAVKSLQALGEVIEAELRSTKC 60

Query:    59 WELTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDK-- 116
             WELT EG ++   GSHE  VF ++P EG+ Q EL+   P+ KVGFSKAM+  WI +DK  
Sbjct:    61 WELTTEGEEIAREGSHEARVFRSIPLEGLVQSELMQ-LPSGKVGFSKAMSNKWIRVDKSA 119

Query:   117 ATG-KVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGP 175
             A G +V R VDS+ DE+Q  L+ +   + +K+ E  + + +KRKLL EV +K++ + KG 
Sbjct:   120 ADGPRVFRVVDSIEDEVQRRLQQVQAGQAEKLAEKERNELRKRKLLTEVILKTYWVSKGK 179

Query:   176 EFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFL 235
              FST++ K E EL+PEMI+SGSW+   FKPYNF A G+   SGHLHPL+KVR++FRQIFL
Sbjct:   180 GFSTSVSKQEAELSPEMISSGSWRDRPFKPYNFSARGVLPDSGHLHPLLKVRSQFRQIFL 239

Query:   236 DMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278
             +MGFTEMPT+NF+ESSFWNFDALFQPQQHPARD HDTFF+ DP
Sbjct:   240 EMGFTEMPTDNFIESSFWNFDALFQPQQHPARDQHDTFFLRDP 282

GO:0000049 "tRNA binding" evidence=IEA

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=IEA

UNIPROTKB|Q5ZJQ2 FARSA "Phenylalanine--tRNA ligase alpha subunit" [Gallus gallus (taxid:9031)]

 Score = 751 (269.4 bits), Expect = 1.9e-74, P = 1.9e-74
 Identities = 148/286 (51%), Positives = 199/286 (69%)

Query:     1 MASDLTEKILKYLDTNPP-----VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS 55
             M+  + E +L+ L+  PP     + +L+ A     DHQ +VG +KS++ LGE +  E  +
Sbjct:     1 MSPSVAELLLQRLERTPPGPEGGLCSLEAAAALGLDHQTLVGAVKSLQALGEVIEAETRA 60

Query:    56 HKIWELTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLD 115
                WEL+ EG +V  +GS EV +F +VPSEG+ Q + +   P A+VGFSKAMA  W+ LD
Sbjct:    61 TTRWELSAEGEEVLRDGSPEVRLFRSVPSEGLPQSDAMK-LPGAQVGFSKAMANKWLRLD 119

Query:   116 K-ATG--KVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLK 172
             K A G  ++ R VD+V D +Q+ L+ +       + E  + D K+RKLL EVT+KS+ ++
Sbjct:   120 KGAPGGPRIFRAVDAVQDVVQSSLRQVQEGNGGSLSERERTDLKRRKLLLEVTLKSYWIR 179

Query:   173 KGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQ 232
             KG  FST + + ET+LTPEMIA+GSW+ L FK YNF A+G+    GHLHPL+KVR++ RQ
Sbjct:   180 KGSAFSTAVVRQETDLTPEMIATGSWRKLPFKAYNFSALGLPPTCGHLHPLLKVRSQLRQ 239

Query:   233 IFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278
             IFL+MGFTEMPT+NFVESSFWNFDALFQPQQHPARD HDTFF+ DP
Sbjct:   240 IFLEMGFTEMPTDNFVESSFWNFDALFQPQQHPARDQHDTFFLQDP 285

GO:0000049 "tRNA binding" evidence=IEA

GO:0006432 "phenylalanyl-tRNA aminoacylation" evidence=IEA

GO:0004826 "phenylalanine-tRNA ligase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5RFA2	SYFA_PONAB	6, ., 1, ., 1, ., 2, 0	0.5395	0.9349	0.5374	yes	N/A
Q9W3J5	SYFA_DROME	6, ., 1, ., 1, ., 2, 0	0.6021	0.9623	0.5642	yes	N/A
Q505J8	SYFA_RAT	6, ., 1, ., 1, ., 2, 0	0.5326	0.9280	0.5334	yes	N/A
Q8C0C7	SYFA_MOUSE	6, ., 1, ., 1, ., 2, 0	0.5513	0.8869	0.5098	yes	N/A
Q5ZJQ2	SYFA_CHICK	6, ., 1, ., 1, ., 2, 0	0.5174	0.9486	0.6252	yes	N/A
Q9Y285	SYFA_HUMAN	6, ., 1, ., 1, ., 2, 0	0.5431	0.9349	0.5374	yes	N/A
Q1JPX3	SYFA_DANRE	6, ., 1, ., 1, ., 2, 0	0.5678	0.9417	0.5533	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
4th Layer	6.1.1.20	0.824
3rd Layer	6.1.1	0.766

---

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	292
PTZ00326	494	PTZ00326, PTZ00326, phenylalanyl-tRNA synthetase a	1e-115
PLN02853	492	PLN02853, PLN02853, Probable phenylalanyl-tRNA syn	1e-101
PRK04172	489	PRK04172, pheS, phenylalanyl-tRNA synthetase subun	2e-53
COG0016	335	COG0016, PheS, Phenylalanyl-tRNA synthetase alpha	3e-39
TIGR00468	293	TIGR00468, pheS, phenylalanyl-tRNA synthetase, alp	6e-32
pfam01409	245	pfam01409, tRNA-synt_2d, tRNA synthetases class II	8e-29
cd00496	218	cd00496, PheRS_alpha_core, Phenylalanyl-tRNA synth	1e-24
PRK00488	339	PRK00488, pheS, phenylalanyl-tRNA synthetase subun	1e-16

>gnl|CDD|240361 PTZ00326, PTZ00326, phenylalanyl-tRNA synthetase alpha chain; Provisional

 Score =  340 bits (873), Expect = e-115
 Identities = 131/293 (44%), Positives = 176/293 (60%), Gaps = 8/293 (2%)

Query: 1   MASDLTEKILKYLDTNPP-VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59
                   IL  L++    V++L LA+  N DHQKVVG +KS+E+   Y+  E      W
Sbjct: 3   QKELEENTILSKLESENEIVNSLALAESLNIDHQKVVGAIKSLESAN-YITTEMKKSNTW 61

Query: 60  ELTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATF--PNAKVGFSKAMAKGWISLDKA 117
            LT EG     NGS E  ++  +   GI + +         A +G   AM K WI L+K 
Sbjct: 62  TLTEEGEDYLKNGSPEYRLWQKLKEGGISKADDAKKLGGKVADIGLGNAMKKKWIKLNKG 121

Query: 118 TGKV---LRKVDSVTDELQAHLKLIANN-EYDKVPEANKVDYKKRKLLQEVTIKSFLLKK 173
             KV    + VDSV D ++  LK++A   + +K+      + KKRKL     IK F++ K
Sbjct: 122 DKKVFLSRKLVDSVVDTVRLLLKIVAKGSQAEKIDSKELKELKKRKLATLEKIKYFVVTK 181

Query: 174 GPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQI 233
           GP+F+  I+K  T+LT EM+ +GSWK   FK YNF+A+G  +  G+LHPL+KVR EFR+I
Sbjct: 182 GPKFAKEIKKQITDLTQEMLLNGSWKNAEFKEYNFNALGKKIGGGNLHPLLKVRREFREI 241

Query: 234 FLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSETEFF 286
            L+MGF EMPTN +VESSFWNFDALFQPQQHPARDA DTFF++ P+TS+    
Sbjct: 242 LLEMGFEEMPTNRYVESSFWNFDALFQPQQHPARDAQDTFFLSKPETSKVNDL 294

Length = 494

>gnl|CDD|215458 PLN02853, PLN02853, Probable phenylalanyl-tRNA synthetase alpha chain

 Score =  305 bits (782), Expect = e-101
 Identities = 128/287 (44%), Positives = 171/287 (59%), Gaps = 9/287 (3%)

Query: 2   ASDLTEKILKYLDTNPPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWE 60
           A+   E +L  L  N  + D+   A     DH +VVG +KS+     Y+  + +  + W 
Sbjct: 1   AAMAEEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGFR-YVDAQDIKRETWV 59

Query: 61  LTGEGNQVKDNGSHEVLVFNNVPSEG-IGQKELLATFPNA--KVGFSKAMAKGWISLDKA 117
           LT EG +    GS EV +F  VP+EG I + EL      A   +GF +AM   W+ +   
Sbjct: 60  LTEEGKKYAAEGSPEVQLFAAVPAEGSISKDELQKKLDPAVFDIGFKQAMKNKWLEMG-G 118

Query: 118 TGKVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRK-LLQEVTIKSFLLKKGPE 176
             +V RKV  V DE++  L  I   +  +V + +    KKR+ L+   T K + +KKGP 
Sbjct: 119 KPQVSRKVQHVEDEVKELLLAIQEGK--EVDDKDIDALKKRRKLITLETWKGYSIKKGPN 176

Query: 177 FSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLD 236
           ++   +K  T+LT EM+ SG WK L FK YNF+A+G     GHLHPL+KVR +FR+IFL 
Sbjct: 177 YAPERKKAATDLTREMLQSGDWKDLEFKEYNFNALGAPPEGGHLHPLLKVRQQFRKIFLQ 236

Query: 237 MGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSET 283
           MGF EMPTNNFVESSFWNFDALFQPQQHPARD+HDTFF+  P T+  
Sbjct: 237 MGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLKAPATTRQ 283

Length = 492

>gnl|CDD|235239 PRK04172, pheS, phenylalanyl-tRNA synthetase subunit alpha; Provisional

 Score =  181 bits (461), Expect = 2e-53
 Identities = 96/294 (32%), Positives = 141/294 (47%), Gaps = 29/294 (9%)

Query: 8   KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGE--YLIVEPLSHKIWELTGEG 65
           K+LK L         +LA+      + V   M++ E L E   + VE    +++ LT EG
Sbjct: 10  KVLKALKELKEATLEELAEKLGLPPEAV---MRAAEWLEEKGLVKVEERVEEVYVLTEEG 66

Query: 66  NQVKDNGSHEVLVFNNVPSEG---IGQ-KELLATFPNAKVGFSKAMAKGWISLDKATGKV 121
            +  + G  E  + N +   G   + + KE L       +       KGW  ++K  GKV
Sbjct: 67  KKYAEEGLPERRLLNALKDGGEVSLDELKEALLDKKEVGIALGNLARKGWAKIEK--GKV 124

Query: 122 LRKVDSVTDELQAHLKLIANNEYDKVPEANKV---DYKKRKLLQEVTIKSF--------- 169
           + K D+  D  +  LK +A  + +++ E +     + KKRKL++E               
Sbjct: 125 ILKPDAYEDPEEKALKALAEGDKEELSEEDLKVLKELKKRKLVEEKERTERSVELTDAGL 184

Query: 170 -LLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRA 228
            LLK+G E    I    T+LTPE++ SG WK   F+PYN  A    +  G  HP  +   
Sbjct: 185 ELLKEGIELKEEI----TQLTPELLKSGEWKEKEFRPYNVKAPPPKIYPGKKHPYREFID 240

Query: 229 EFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSE 282
           E R I ++MGF EM     VE+ FWNFDALFQPQ HPAR+  DTF++  P   +
Sbjct: 241 EVRDILVEMGFEEM-KGPLVETEFWNFDALFQPQDHPAREMQDTFYLKYPGIGD 293

Length = 489

>gnl|CDD|223095 COG0016, PheS, Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]

 Score =  139 bits (353), Expect = 3e-39
 Identities = 54/179 (30%), Positives = 82/179 (45%), Gaps = 14/179 (7%)

Query: 99  AKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKR 158
             +   +   KG  +++ A+            +L   L+ +      K      +  KK 
Sbjct: 2   VMIALGRLAKKGIAAIELAS------------DLLKALEELKVKYLGKKGVLTDL-LKKL 48

Query: 159 KLLQEVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSG 218
             L  +  +  +     E    ++   TELTPE+ A+G W+ L F+  +    G  +  G
Sbjct: 49  GKLSPLEERKEVGALINELKKEVEDAITELTPELEAAGLWERLAFEKIDVTLPGRRIYPG 108

Query: 219 HLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTD 277
            LHPL +   E   IFL MGFTE+     +E+ F+NFDAL  PQ HPARD  DTF++ D
Sbjct: 109 SLHPLTQTIEEIEDIFLGMGFTEVEGPE-IETDFYNFDALNIPQDHPARDMQDTFYLKD 166

Length = 335

>gnl|CDD|232988 TIGR00468, pheS, phenylalanyl-tRNA synthetase, alpha subunit

 Score =  119 bits (301), Expect = 6e-32
 Identities = 52/126 (41%), Positives = 67/126 (53%), Gaps = 1/126 (0%)

Query: 152 KVDYKKRKLLQEVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAM 211
           K   K+   L +   K  L     E    +Q   T+L PE+ ++G W  L F+ Y+    
Sbjct: 3   KDLLKQLGKLTKEETKPALGALINEVKIELQDELTKLKPELESAGLWSKLKFETYDVSLP 62

Query: 212 GISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHD 271
           G  +  G LHPL +V  E R IFL +GFTE      VE+ FWNFDAL  PQ HPARD  D
Sbjct: 63  GTKIYPGSLHPLTRVIDEIRDIFLGLGFTEET-GPEVETDFWNFDALNIPQDHPARDMQD 121

Query: 272 TFFVTD 277
           TF++ D
Sbjct: 122 TFYIKD 127

Most phenylalanyl-tRNA synthetases are heterodimeric, with 2 alpha (pheS) and 2 beta (pheT) subunits. This model describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this model. An interesting feature of the alignment of all sequences captured by this model is a deep split between non-spirochete bacterial examples and all other examples; supporting this split is a relative deletion of about 50 residues in the former set between two motifs well conserved throughout the alignment [Protein synthesis, tRNA aminoacylation]. Length = 293

>gnl|CDD|216483 pfam01409, tRNA-synt_2d, tRNA synthetases class II core domain (F)

 Score =  109 bits (276), Expect = 8e-29
 Identities = 39/80 (48%), Positives = 46/80 (57%), Gaps = 1/80 (1%)

Query: 205 PYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQH 264
           PY+    G  +  G LHPL +V  E R IFL MGF E+     VES F+NFDAL  PQ H
Sbjct: 1   PYDVTLPGRRIEPGGLHPLTRVLEEIRDIFLSMGFEEVE-GPEVESDFYNFDALNIPQDH 59

Query: 265 PARDAHDTFFVTDPKTSETE 284
           PARD  DTF++  P   E  
Sbjct: 60  PARDMQDTFYLKKPLKEEDR 79

Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only phenylalanyl-tRNA synthetases. This is the core catalytic domain. Length = 245

>gnl|CDD|238277 cd00496, PheRS_alpha_core, Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain

 Score = 98.0 bits (245), Expect = 1e-24
 Identities = 33/58 (56%), Positives = 39/58 (67%), Gaps = 1/58 (1%)

Query: 221 HPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278
           HPL KV  E   IF+ MGFTE+     VE+ F+NFDAL  PQ HPARD  DTF++ DP
Sbjct: 1   HPLNKVIEEIEDIFVSMGFTEV-EGPEVETDFYNFDALNIPQDHPARDMQDTFYINDP 57

PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer. Length = 218

>gnl|CDD|234780 PRK00488, pheS, phenylalanyl-tRNA synthetase subunit alpha; Validated

 Score = 78.2 bits (194), Expect = 1e-16
 Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 1/68 (1%)

Query: 212 GISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHD 271
           G  +  G LHP+ +   E   IF+ MGF        +E+ ++NF+AL  P+ HPARD  D
Sbjct: 99  GRRIELGSLHPITQTIEEIEDIFVGMGFEVA-EGPEIETDYYNFEALNIPKDHPARDMQD 157

Query: 272 TFFVTDPK 279
           TF++ D  
Sbjct: 158 TFYIDDGL 165

Length = 339

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	292
PLN02853	492	Probable phenylalanyl-tRNA synthetase alpha chain	100.0
PTZ00326	494	phenylalanyl-tRNA synthetase alpha chain; Provisio	100.0
KOG2784|consensus	483		100.0
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	100.0
COG0016	335	PheS Phenylalanyl-tRNA synthetase alpha subunit [T	100.0
PLN02788	402	phenylalanine-tRNA synthetase	99.88
PF01409	247	tRNA-synt_2d: tRNA synthetases class II core domai	99.86
PRK00488	339	pheS phenylalanyl-tRNA synthetase subunit alpha; V	99.86
TIGR00469	460	pheS_mito phenylalanyl-tRNA synthetase, mitochondr	99.77
TIGR00468	294	pheS phenylalanyl-tRNA synthetase, alpha subunit.	99.76
KOG2783|consensus	436		98.99
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	97.65
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	97.64
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	97.57
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	97.54
cd00496	218	PheRS_alpha_core Phenylalanyl-tRNA synthetase (Phe	97.42
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	97.38
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	97.37
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	97.04
COG1846	126	MarR Transcriptional regulators [Transcription]	97.02
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	96.96
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	96.94
PRK03573	144	transcriptional regulator SlyA; Provisional	96.91
PRK10870	176	transcriptional repressor MprA; Provisional	96.86
PRK13777	185	transcriptional regulator Hpr; Provisional	96.76
PF03551	75	PadR: Transcriptional regulator PadR-like family;	96.76
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	96.7
PRK03902	142	manganese transport transcriptional regulator; Pro	96.67
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	96.61
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	96.45
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	96.25
PRK14165	217	winged helix-turn-helix domain-containing protein/	96.24
COG1497	260	Predicted transcriptional regulator [Transcription	96.09
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	96.09
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	95.96
COG4754	157	Uncharacterized conserved protein [Function unknow	95.93
TIGR03433	100	padR_acidobact transcriptional regulator, Acidobac	95.92
PRK11050	152	manganese transport regulator MntR; Provisional	95.83
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	95.81
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	95.69
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	95.69
PF07381	90	DUF1495: Winged helix DNA-binding domain (DUF1495)	95.61
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	95.58
PF03501	95	S10_plectin: Plectin/S10 domain; InterPro: IPR0053	95.42
PRK09616	552	pheT phenylalanyl-tRNA synthetase subunit beta; Re	95.39
PTZ00034	124	40S ribosomal protein S10; Provisional	95.38
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	95.22
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	95.07
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	94.97
PHA00738	108	putative HTH transcription regulator	94.95
COG2345	218	Predicted transcriptional regulator [Transcription	94.94
COG1695	138	Predicted transcriptional regulators [Transcriptio	94.88
PRK09416	135	lstR lineage-specific thermal regulator protein; P	94.61
PRK09537	417	pylS pyrolysyl-tRNA synthetase; Reviewed	94.59
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	94.38
COG1733	120	Predicted transcriptional regulators [Transcriptio	94.35
COG4742	260	Predicted transcriptional regulator [Transcription	94.18
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	94.08
COG3432	95	Predicted transcriptional regulator [Transcription	93.97
PRK06253	529	O-phosphoseryl-tRNA synthetase; Reviewed	93.93
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	93.91
PRK05638	442	threonine synthase; Validated	93.88
COG5045	105	Ribosomal protein S10E [Translation, ribosomal str	93.87
TIGR00470	533	sepS O-phosphoseryl-tRNA(Cys) synthetase. This fam	93.82
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	93.75
TIGR02719	138	repress_PhaQ poly-beta-hydroxybutyrate-responsive	93.61
PHA02943	165	hypothetical protein; Provisional	93.58
TIGR02367	453	PylS pyrrolysyl-tRNA synthetase. PylS is the archa	93.58
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	93.5
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	93.45
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	93.34
TIGR02716	306	C20_methyl_CrtF C-20 methyltransferase BchU. Membe	93.34
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	93.22
COG2024	536	Phenylalanyl-tRNA synthetase alpha subunit (archae	93.06
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	93.03
PRK11169	164	leucine-responsive transcriptional regulator; Prov	92.7
PF09821	120	AAA_assoc_C: C-terminal AAA-associated domain; Int	92.63
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	92.61
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	92.53
COG1522	154	Lrp Transcriptional regulators [Transcription]	92.3
COG2512	258	Predicted membrane-associated trancriptional regul	92.28
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	92.2
COG3355	126	Predicted transcriptional regulator [Transcription	92.18
PRK00215	205	LexA repressor; Validated	92.09
PF02295	66	z-alpha: Adenosine deaminase z-alpha domain; Inter	92.05
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	91.93
PRK06266	178	transcription initiation factor E subunit alpha; V	91.91
PRK06474	178	hypothetical protein; Provisional	91.38
COG1339	214	Transcriptional regulator of a riboflavin/FAD bios	91.14
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	90.97
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	90.85
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	90.55
PF09202	82	Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This	90.16
COG2524	294	Predicted transcriptional regulator, contains C-te	90.13
KOG3344|consensus	150		90.09
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	89.68
TIGR02277	280	PaaX_trns_reg phenylacetic acid degradation operon	89.56
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	89.54
PF00126	60	HTH_1: Bacterial regulatory helix-turn-helix prote	89.46
PF03965	115	Penicillinase_R: Penicillinase repressor; InterPro	89.32
COG4189	308	Predicted transcriptional regulator [Transcription	89.22
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	88.57
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	88.38
COG1378	247	Predicted transcriptional regulators [Transcriptio	88.36
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	88.29
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	88.12
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	88.0
PRK13509	251	transcriptional repressor UlaR; Provisional	87.87
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	87.84
PF13814	191	Replic_Relax: Replication-relaxation	87.83
PF11313	85	DUF3116: Protein of unknown function (DUF3116); In	87.53
PF10771	65	DUF2582: Protein of unknown function (DUF2582); In	87.53
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	87.12
TIGR00637	99	ModE_repress ModE molybdate transport repressor do	87.11
PRK09954	362	putative kinase; Provisional	86.97
PRK03601	275	transcriptional regulator HdfR; Provisional	86.92
PF14338	92	Mrr_N: Mrr N-terminal domain	86.71
PHA02701	183	ORF020 dsRNA-binding PKR inhibitor; Provisional	86.58
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	86.56
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	86.29
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	86.29
PRK11242	296	DNA-binding transcriptional regulator CynR; Provis	86.17
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	85.9
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	85.73
PRK00082	339	hrcA heat-inducible transcription repressor; Provi	85.6
PF07848	70	PaaX: PaaX-like protein; InterPro: IPR012906 This	85.57
PRK09791	302	putative DNA-binding transcriptional regulator; Pr	85.52
PF04182	75	B-block_TFIIIC: B-block binding subunit of TFIIIC;	85.24
PF05158	327	RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; Inter	85.22
PF13730	55	HTH_36: Helix-turn-helix domain	85.09
PRK10094	308	DNA-binding transcriptional activator AllS; Provis	84.96
PRK15421	317	DNA-binding transcriptional regulator MetR; Provis	84.29
PRK10837	290	putative DNA-binding transcriptional regulator; Pr	84.08
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	83.66
PF14090	70	HTH_39: Helix-turn-helix domain	83.25
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	82.75
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	82.57
PRK10632	309	transcriptional regulator; Provisional	82.42
PF10771	65	DUF2582: Protein of unknown function (DUF2582); In	81.96
PRK11569	274	transcriptional repressor IclR; Provisional	81.91
PRK11074	300	putative DNA-binding transcriptional regulator; Pr	81.91
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	81.62
TIGR02036	302	dsdC D-serine deaminase transcriptional activator.	81.61
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	81.24
COG3373	108	Uncharacterized protein conserved in archaea [Func	81.01
TIGR02424	300	TF_pcaQ pca operon transcription factor PcaQ. Memb	80.97
TIGR03339	279	phn_lysR aminoethylphosphonate catabolism associat	80.95
PRK11062	296	nhaR transcriptional activator NhaR; Provisional	80.92
PF06969	66	HemN_C: HemN C-terminal domain; InterPro: IPR01072	80.81
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	80.68
COG1568	354	Predicted methyltransferases [General function pre	80.49
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	80.45

>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain

Probab=100.00  E-value=2e-73  Score=561.42  Aligned_cols=276  Identities=46%  Similarity=0.778  Sum_probs=254.6

Q ss_pred             CcHHHHHHHHHhccCCC-CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHHh
Q psy10346          2 ASDLTEKILKYLDTNPP-VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFN   80 (292)
Q Consensus         2 ~~~~e~~iL~~L~~~~~-~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~~   80 (292)
                      +.+.|++||.+|...+. ++++++|+.+|++|++|+++++||+++ |+|++++.+.+.|+||+||++|+++||||+||++
T Consensus         1 ~~~~e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-g~v~~~~~~~~~~~LT~eG~~~l~~G~PE~rl~~   79 (492)
T PLN02853          1 AAMAEEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGF-RYVDAQDIKRETWVLTEEGKKYAAEGSPEVQLFA   79 (492)
T ss_pred             CchHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhC-CCEEEEEEEEEEEEECHHHHHHHHcCCHHHHHHH
Confidence            35789999999988775 799999999999999999999999998 9999999999999999999999999999999999


Q ss_pred             hcCCCC-CChHHHhhcCC--chhhHHHHHHHcCCeecccCcceeeccCCCchHHHHHHHHHHhccCCCCCChhhHHhhhc
Q psy10346         81 NVPSEG-IGQKELLATFP--NAKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKK  157 (292)
Q Consensus        81 ~l~~~~-~~~~el~~~~~--~~~ig~~~a~k~gwi~i~~~~g~v~~~~~~~~d~~~~~L~~i~~~~~~~l~~~~~~~Lkk  157 (292)
                      +|++.| ++++||.+.++  .++||+|+|+|+|||+++++ |.+.+..+...|.++..|+.+..+.  .++++.+++|+|
T Consensus        80 ~l~~~~~~~~~eL~~~l~~~~~~i~~g~a~k~gwi~i~~~-~~v~~~~~~~~d~~~~~L~~l~~~~--~~~~~~l~~Lkk  156 (492)
T PLN02853         80 AVPAEGSISKDELQKKLDPAVFDIGFKQAMKNKWLEMGGK-PQVSRKVQHVEDEVKELLLAIQEGK--EVDDKDIDALKK  156 (492)
T ss_pred             HHhhcCCccHHHHHHhhCchhHHHHHHHHHHCCcEEECCC-CcEEeccCccchHHHHHHHHHhcCC--CCCHHHHHHHHh
Confidence            998744 89999988763  68999999999999999843 4666667777888999999998764  466678999999


Q ss_pred             cc-ceeeEEEEEEEEecCccccccccccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhhh
Q psy10346        158 RK-LLQEVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLD  236 (292)
Q Consensus       158 Rk-Lv~~~~~~~~~v~~g~~~~~~~~~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~  236 (292)
                      || ||+.++.+++.|++|+++..++++++|+||+|||+||+|+++.||+|||+++|+.++.|+.|||++++++|++||.+
T Consensus       157 Rk~Li~~~~~~~~~v~~~~~~~~~~~~~~t~LT~eml~sg~Wk~~~fk~Yn~~a~g~~~~~G~~HPl~~~~~ei~~if~~  236 (492)
T PLN02853        157 RRKLITLETWKGYSIKKGPNYAPERKKAATDLTREMLQSGDWKDLEFKEYNFNALGAPPEGGHLHPLLKVRQQFRKIFLQ  236 (492)
T ss_pred             hhcceEEEEEEEEEEEECCccccccccccccCCHHHhcCCCcccCCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHHHh
Confidence            98 99999999999999999888889999999999999999999999999999999999999999999999999999999


Q ss_pred             CCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCCCC
Q psy10346        237 MGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS  281 (292)
Q Consensus       237 mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~~  281 (292)
                      |||++|++||+|||+||||||||||||||||||||||||+.|..+
T Consensus       237 mGF~e~~~g~~ves~f~NFDaL~~PqdHPARd~qDTFyl~~~~~~  281 (492)
T PLN02853        237 MGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLKAPATT  281 (492)
T ss_pred             CCCEEecCCCCeechhhhhhhhcCCCCCCCCCccceEEEcCcccc
Confidence            999999779999999999999999999999999999999987654

>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional

Probab=100.00  E-value=7e-73  Score=559.40  Aligned_cols=279  Identities=47%  Similarity=0.779  Sum_probs=255.2

Q ss_pred             cHHHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHHhh
Q psy10346          3 SDLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNN   81 (292)
Q Consensus         3 ~~~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~~~   81 (292)
                      +..|++||..|.+ ++..+++++|+.+|++|++|+++++||+++ |+|++++++...|+||+||++|+++||||+||+++
T Consensus         5 ~~~e~~iL~~l~~~~~~~~~~~la~~~~~~~~~v~~~~~~L~~k-g~v~~~~~~~~~~~LT~eG~~~~~~G~PE~rl~~~   83 (494)
T PTZ00326          5 ELEENTILSKLESENEIVNSLALAESLNIDHQKVVGAIKSLESA-NYITTEMKKSNTWTLTEEGEDYLKNGSPEYRLWQK   83 (494)
T ss_pred             hHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhC-CCEEEEEEEEEEEEECHHHHHHHHcCCHHHHHHHH
Confidence            6889999999987 567899999999999999999999999997 99999999999999999999999999999999999


Q ss_pred             cCCCCCChHHHhhcC--CchhhHHHHHHHcCCeecccCcceeec---cCCCchHHHHHHHHHHhccC-CCCCChhhHHhh
Q psy10346         82 VPSEGIGQKELLATF--PNAKVGFSKAMAKGWISLDKATGKVLR---KVDSVTDELQAHLKLIANNE-YDKVPEANKVDY  155 (292)
Q Consensus        82 l~~~~~~~~el~~~~--~~~~ig~~~a~k~gwi~i~~~~g~v~~---~~~~~~d~~~~~L~~i~~~~-~~~l~~~~~~~L  155 (292)
                      |+++|.++.++.+.+  ++++||+|+|+|+|||+++++.+.+..   ..+.+.|.++.+|+.+..+. .+.++++.+++|
T Consensus        84 l~~~~~~~~~l~~~~~~~~~~i~~g~~~k~~wi~i~~~~~~i~~~~~~~~~~~d~~~~~L~~i~~~~~~~~~~~~~~~~L  163 (494)
T PTZ00326         84 LKEGGISKADDAKKLGGKVADIGLGNAMKKKWIKLNKGDKKVFLSRKLVDSVVDTVRLLLKIVAKGSQAEKIDSKELKEL  163 (494)
T ss_pred             hhhcCCCHHHHHhhhcchhHHHHHHHHHHCCcEEEcCCCceeecccccccccccHHHHHHHHHhccCccccCCHHHHHHH
Confidence            998888888877653  478999999999999999976444443   35566788999999998762 235777889999


Q ss_pred             hcccceeeEEEEEEEEecCccccccccccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhh
Q psy10346        156 KKRKLLQEVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFL  235 (292)
Q Consensus       156 kkRkLv~~~~~~~~~v~~g~~~~~~~~~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~  235 (292)
                      +|||||+.++.++|.|++|++++.++++++|+||+|||+||+|+++.||+|||+++|+.+++|+.|||++++++|++||.
T Consensus       164 kkRkLi~~~~~~~~~i~~~~~~~~~~~~~~t~LT~e~l~sg~Wk~~~fk~yn~~~~~~~~~~g~~HPl~~~~~~i~~if~  243 (494)
T PTZ00326        164 KKRKLATLEKIKYFVVTKGPKFAKEIKKQITDLTQEMLLNGSWKNAEFKEYNFNALGKKIGGGNLHPLLKVRREFREILL  243 (494)
T ss_pred             hcCCCeEEEEEEEEEEEECCccccccccccccCCHHHhhCCccccCCcccceecCCCCCCCCCCCChHHHHHHHHHHHHH
Confidence            99999999999999999999998889999999999999999999999999999999999999999999999999999999


Q ss_pred             hCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCCCCC
Q psy10346        236 DMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSE  282 (292)
Q Consensus       236 ~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~~~  282 (292)
                      +|||+||+++++|||+||||||||||||||||||||||||+.|..+.
T Consensus       244 ~mGF~e~~~~~~ves~f~NFDaL~~PqdHPARd~~DTFyl~~~~~~~  290 (494)
T PTZ00326        244 EMGFEEMPTNRYVESSFWNFDALFQPQQHPARDAQDTFFLSKPETSK  290 (494)
T ss_pred             hCCCEEecCCCCccccchhhhhhcCCCCCCCCCcCceEEEcCccccc
Confidence            99999998778999999999999999999999999999999876553

>KOG2784|consensus

Probab=100.00  E-value=7.7e-73  Score=533.86  Aligned_cols=272  Identities=57%  Similarity=0.931  Sum_probs=258.9

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHHhhc
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNNV   82 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~~~l   82 (292)
                      ++.+.+||..|+..++.++.+++...+.+|+.++++++||++. |+|+++..+...|.||.||++++.+||||++|+.++
T Consensus         2 ~~~~~~iL~~L~~~de~~s~~l~a~~~~~h~~~v~al~SL~a~-~~i~~~~~~~~~~~LT~EG~~i~~eGS~E~~v~~~i   80 (483)
T KOG2784|consen    2 EALAEKILEKLQESDEVDSSDLAAPFNEDHQQVVGALKSLQAG-GVIEVKDVETKTYELTAEGEEIAREGSHEALVFESI   80 (483)
T ss_pred             chHHHHHHHHHHhccCCChhhhcCchhhhhHHHHHHHHHHhhc-CceEEEeeeeEEEeeChhHHHHHhcCCcceeeeecc
Confidence            5788999999998888999999999999999999999999996 999999999999999999999999999999999999


Q ss_pred             CCCCCChHHHhhcCCchhhHHHHHHHcCCeecccCcceeeccCCCchHHHHHHHHHHhccCCCCCChhhHHhhhccccee
Q psy10346         83 PSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQ  162 (292)
Q Consensus        83 ~~~~~~~~el~~~~~~~~ig~~~a~k~gwi~i~~~~g~v~~~~~~~~d~~~~~L~~i~~~~~~~l~~~~~~~LkkRkLv~  162 (292)
                      ++.|+.++||.+.+ . .||+++|+|+|||+++++  .+.++++++.|++++.|.+|+.|..   .++++++|+|||||.
T Consensus        81 ~~~gl~~~el~~k~-~-giG~~~A~~nkWI~~d~~--~~~r~v~~itD~v~~~l~~ik~g~~---~ake~~dlkKrKLi~  153 (483)
T KOG2784|consen   81 PEEGLAIAELMKKL-V-GIGQSKAFKNKWIRVDKS--RVVRDVDSITDEVRNQLQQIKRGSA---DAKEVEDLKKRKLIS  153 (483)
T ss_pred             CccccCHHHHHhhh-h-ccchhhhhccceEEecCc--ccccchhhhhHHHHHHHHHHHcCcc---hHHHHHHHHhhhhhc
Confidence            99999999999854 3 399999999999999886  6778999999999999999998753   378899999999999


Q ss_pred             eEEEEEEEEecCccccccccccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhhhCCceec
Q psy10346        163 EVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEM  242 (292)
Q Consensus       163 ~~~~~~~~v~~g~~~~~~~~~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~  242 (292)
                      +.+.+.|.+++|++|+..+.+.+||||+|||.||+|++..||+|||++.|..+.+|++|||+++++++|+||.+|||+||
T Consensus       154 ~~~~~~f~v~KGp~Fst~l~k~eTdLT~emi~~gsw~dl~FK~YNF~a~G~~p~~G~lHPLmKvR~eFRqiF~emGFsEM  233 (483)
T KOG2784|consen  154 EVKIKVFSVTKGPNFSTSLTKLETDLTSEMIASGSWKDLKFKPYNFNAEGVPPSSGHLHPLMKVREEFRQIFFEMGFSEM  233 (483)
T ss_pred             cceeEEEEEecCCcccchHHHHhhhccHHHhccCchhhccCcccCcccCCCCCCCCccchHHHHHHHHHHHHHHcccccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCccccceeccccCCCCCCCCCCCCCCceeecCCCCCC
Q psy10346        243 PTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSE  282 (292)
Q Consensus       243 ~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~~~  282 (292)
                      +++++|||+|||||||||||+|||||.|||||+++|+.+.
T Consensus       234 ptn~yVEssFWNFDALfqPQqHpARDahDTFfl~~Pa~s~  273 (483)
T KOG2784|consen  234 PTNNYVESSFWNFDALFQPQQHPARDAHDTFFLKDPATST  273 (483)
T ss_pred             ccccchhhccccchhhcCcccCCccccccceEecChhhcc
Confidence            9999999999999999999999999999999999998764

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=100.00  E-value=2.8e-62  Score=486.98  Aligned_cols=273  Identities=31%  Similarity=0.507  Sum_probs=247.5

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHHhhc
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNNV   82 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~~~l   82 (292)
                      +..|..||..|...+.+++.++|+.+|+++++|++++++|+++ |||+.+......+.||++|++|+++|+||+|+++++
T Consensus         5 t~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~k-GlV~~~~~~~~~i~LTeeG~~~~~~g~pE~rl~~~l   83 (489)
T PRK04172          5 HPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEK-GLVKVEERVEEVYVLTEEGKKYAEEGLPERRLLNAL   83 (489)
T ss_pred             CHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhC-CCEEEEeeeEEEEEECHHHHHHHHhcCHHHHHHHhh
Confidence            5789999999988788899999999999999999999999997 999999988899999999999999999999999999


Q ss_pred             CC-CCCChHHHhhc-C--CchhhHHHHHHHcCCeecccCcceeeccCCCchHHHHHHHHHHhccCC---CCCChhhHHhh
Q psy10346         83 PS-EGIGQKELLAT-F--PNAKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANNEY---DKVPEANKVDY  155 (292)
Q Consensus        83 ~~-~~~~~~el~~~-~--~~~~ig~~~a~k~gwi~i~~~~g~v~~~~~~~~d~~~~~L~~i~~~~~---~~l~~~~~~~L  155 (292)
                      .+ .|++++||.+. +  +..++|+++|+|+||+++++|  .+.+..+...|.++..|+.+.+|..   ..++.+.+++|
T Consensus        84 ~~~~g~~~~el~~~aL~~~~~~i~~~~l~k~g~i~i~~G--~~i~~~~~~~d~~~~~L~~l~~g~~~~~~~~~~~~l~~L  161 (489)
T PRK04172         84 KDGGEVSLDELKEALLDKKEVGIALGNLARKGWAKIEKG--KVILKPDAYEDPEEKALKALAEGDKEELSEEDLKVLKEL  161 (489)
T ss_pred             HhcCCcCHHHHHHhhccchhHHHHHHHHHHCCCeecCCC--ceeecCcccCcHHHHHHHHHhccCccccccCCHHHHHHH
Confidence            85 46899999886 4  478999999999999999654  6666555667888999999987652   24567789999


Q ss_pred             hcccceeeEEEEEEEEe---cCcccc---ccccccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHH
Q psy10346        156 KKRKLLQEVTIKSFLLK---KGPEFS---TTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAE  229 (292)
Q Consensus       156 kkRkLv~~~~~~~~~v~---~g~~~~---~~~~~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~  229 (292)
                      +|||||+.++++.+.++   +|.+++   ..+++++|+||+|||+||+|+++.||+||++++++.+++|..||+.+++++
T Consensus       162 kkRkL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lt~e~l~~g~w~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~  241 (489)
T PRK04172        162 KKRKLVEEKERTERSVELTDAGLELLKEGIELKEEITQLTPELLKSGEWKEKEFRPYNVKAPPPKIYPGKKHPYREFIDE  241 (489)
T ss_pred             HhcCCeEEEEEEEEEEEEccchhhhhhcccccccccccCCHHHhcCCCccCCCCccceeCCCCCCCCCCCCChHHHHHHH
Confidence            99999999999999975   567776   347888999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCC
Q psy10346        230 FRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPK  279 (292)
Q Consensus       230 i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~  279 (292)
                      |+++|.+|||+||. +|.||++|||||+||||||||||++|||||++.|.
T Consensus       242 ~~~~f~~~Gf~e~~-~p~vE~~~~nfd~lf~p~~hpaR~~~dtf~~~~~~  290 (489)
T PRK04172        242 VRDILVEMGFEEMK-GPLVETEFWNFDALFQPQDHPAREMQDTFYLKYPG  290 (489)
T ss_pred             HHHHHHHCCCEEee-CCeeeecCcccccccCCCCCCCCCccceEEECCcc
Confidence            99999999999996 89999999999999999999999999999999876

>COG0016 PheS Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.1e-34  Score=275.43  Aligned_cols=163  Identities=34%  Similarity=0.517  Sum_probs=123.7

Q ss_pred             hhhHHHHHHHcCCeecccCcceeeccCCCchHHHHHHHHHHhccCCCCC-ChhhHHhh-hccc-ceeeEEEEEEEEecCc
Q psy10346         99 AKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANNEYDKV-PEANKVDY-KKRK-LLQEVTIKSFLLKKGP  175 (292)
Q Consensus        99 ~~ig~~~a~k~gwi~i~~~~g~v~~~~~~~~d~~~~~L~~i~~~~~~~l-~~~~~~~L-kkRk-Lv~~~~~~~~~v~~g~  175 (292)
                      ..+++++++++||..++..           .+. .+.|..+...   .+ +...+..+ ++.| +...++++.+.+... 
T Consensus         2 ~~~~l~~l~~~~~~~i~~~-----------~~~-~~~L~~~~~~---~lgk~g~l~~~~k~l~~~~~~eer~~~g~~in-   65 (335)
T COG0016           2 VMIALGRLAKKGIAAIELA-----------SDL-LKALEELKVK---YLGKKGVLTDLLKKLGKLSPLEERKEVGALIN-   65 (335)
T ss_pred             chHHHHHHHHHHHHHHHhh-----------ccH-HHHHHHHHHH---hcCcccchHHHHHHhccCChhhhhhhhhhhHH-
Confidence            3578999999999887642           222 3445544422   11 22235544 4443 443233333322110 


Q ss_pred             cccccccccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceecc
Q psy10346        176 EFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNF  255 (292)
Q Consensus       176 ~~~~~~~~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NF  255 (292)
                      ....++.+.++++|++++.+|.|++..+++||+++||+..++|+.|||++++++|+++|.+|||+++. ||+||++||||
T Consensus        66 ~~~~~~~~~~~~~~~~l~~~~~~~~l~~e~~dv~lp~~~~~~G~~Hpl~~~~e~i~~iF~~mGF~~~~-gp~IE~d~~NF  144 (335)
T COG0016          66 ELKKEVEDAITELTPELEAAGLWERLAFEKIDVTLPGRRIYPGSLHPLTQTIEEIEDIFLGMGFTEVE-GPEIETDFYNF  144 (335)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHhhhccCCCcCCCCccCCCCCcChHHHHHHHHHHHHHHcCceecc-CCcccccccch
Confidence            00123567789999999999999999999999999999999999999999999999999999999985 99999999999


Q ss_pred             ccCCCCCCCCCCCCCCceeecCC
Q psy10346        256 DALFQPQQHPARDAHDTFFVTDP  278 (292)
Q Consensus       256 D~L~~PqdHPAR~~~DTfyl~~~  278 (292)
                      ||||||||||||+||||||+++.
T Consensus       145 DaLn~P~dHPARdmqDTFy~~~~  167 (335)
T COG0016         145 DALNIPQDHPARDMQDTFYLKDD  167 (335)
T ss_pred             hhhcCCCCCCcccccceEEEcCC
Confidence            99999999999999999999974

>PLN02788 phenylalanine-tRNA synthetase

Probab=99.88  E-value=3.4e-23  Score=201.77  Aligned_cols=83  Identities=22%  Similarity=0.345  Sum_probs=76.3

Q ss_pred             cCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhhhC---CceecCCCCccccceeccccCCCCCCCCCCCCC
Q psy10346        194 ASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDM---GFTEMPTNNFVESSFWNFDALFQPQQHPARDAH  270 (292)
Q Consensus       194 ~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~m---GF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~  270 (292)
                      ....|.|.  .++++++.|+.++.|+.|||++++++|+++|.+|   ||++++..++||++|||||+||+|||||||++|
T Consensus        43 ~~~~~~n~--~~~i~~~~~~~l~~~~~HPl~~~~~~i~~~f~~~~~~gf~~~~~~~~iv~~~~NFD~L~~P~dHPaR~~~  120 (402)
T PLN02788         43 EDDPTNNV--PDHIFSKIGMQLHRRPDHPLGILKNAIYDYFDENYSNKFKKFDDLSPIVSTKQNFDDVLVPPDHVSRSYN  120 (402)
T ss_pred             cCCccCCC--ChhHhccCCccCCCCCCChHHHHHHHHHHHHhhcccCCcEEecCCCCccchhhhhhhhCCCCCCCccCcc
Confidence            34579987  4999999999999999999999999999999998   999986338999999999999999999999999


Q ss_pred             CceeecCC
Q psy10346        271 DTFFVTDP  278 (292)
Q Consensus       271 DTfyl~~~  278 (292)
                      |||||++.
T Consensus       121 DTfy~~~~  128 (402)
T PLN02788        121 DTYYVDAQ  128 (402)
T ss_pred             ceEEecCC
Confidence            99999864

>PF01409 tRNA-synt_2d: tRNA synthetases class II core domain (F); InterPro: IPR002319 The aminoacyl-tRNA synthetases (6

Probab=99.86  E-value=1.1e-22  Score=187.30  Aligned_cols=75  Identities=45%  Similarity=0.802  Sum_probs=69.7

Q ss_pred             CCcccCCCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCCC
Q psy10346        205 PYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKT  280 (292)
Q Consensus       205 ~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~  280 (292)
                      +||+++|++..+.|+.||+++++++|+++|.+|||+++. +++|||++||||+||+|+|||||++|||||+++|..
T Consensus         1 ~~d~~~p~~~~~~G~~hp~~~~~~~i~~~~~~~Gf~e~~-~~~v~s~~~nFD~Ln~p~dHpaR~~~Dtfyi~~p~~   75 (247)
T PF01409_consen    1 KIDVTLPGKRFTPGRLHPITKFIREIRDIFVGMGFQEVE-GPEVESEFYNFDALNIPQDHPARDMQDTFYISNPYS   75 (247)
T ss_dssp             ---TTSGCTTCCCSBTSHHHHHHHHHHHHHHCTTSEEES-TTSEEEHHHHTGGGTSTTTSCGGCGTTSEBSCSSSB
T ss_pred             CccccCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCeEee-CCeEEeeHHHHHhhCcCCCccccccccceeeecccc
Confidence            589999999999999999999999999999999999996 899999999999999999999999999999987765

1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases [].; GO: 0000049 tRNA binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0043039 tRNA aminoacylation, 0005737 cytoplasm; PDB: 3TUP_A 3HFV_A 3CMQ_A 3TEG_A 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B ....

>PRK00488 pheS phenylalanyl-tRNA synthetase subunit alpha; Validated

Probab=99.86  E-value=2.1e-22  Score=192.41  Aligned_cols=73  Identities=36%  Similarity=0.689  Sum_probs=69.4

Q ss_pred             CCcccCCCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCC
Q psy10346        205 PYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP  278 (292)
Q Consensus       205 ~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~  278 (292)
                      .||+++||+..+.|+.||+++++++|+++|.+|||+++. ||+||+++||||+||+|+|||||+|||||||++.
T Consensus        92 ~~d~t~p~~~~~~G~~HPl~~~~~~Ir~if~~mGF~ev~-gpeIes~~~NFdaLn~P~dHPaR~~~DTfyI~~~  164 (339)
T PRK00488         92 TIDVTLPGRRIELGSLHPITQTIEEIEDIFVGMGFEVAE-GPEIETDYYNFEALNIPKDHPARDMQDTFYIDDG  164 (339)
T ss_pred             cccccCCCCCCCCCCCCHHHHHHHHHHHHHHhCCCEEEe-CCccccHHHHHHHhCCCCCCcccccCceEEEcCC
Confidence            489999998899999999999999999999999999985 8999999999999999999999999999999754

>TIGR00469 pheS_mito phenylalanyl-tRNA synthetase, mitochondrial

Probab=99.77  E-value=1.8e-19  Score=177.51  Aligned_cols=82  Identities=20%  Similarity=0.259  Sum_probs=72.5

Q ss_pred             CCCee-ccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhhhC--------CceecCCCCccccceeccccCCCCCCCC
Q psy10346        195 SGSWK-TLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDM--------GFTEMPTNNFVESSFWNFDALFQPQQHP  265 (292)
Q Consensus       195 sg~w~-~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~m--------GF~e~~~~~~Ves~f~NFD~L~~PqdHP  265 (292)
                      +.+|. |.  -|.+++..|+.++.|..|||+.++++|+++|.+|        ||+.+...++|||+++|||+|++|+|||
T Consensus        17 ~d~~~~n~--~~~i~~~~~r~~~~~~~HPl~~~~~~I~~~F~~~~~~~~~~~gf~v~~~~~Pvvt~~~NFD~Ln~P~dHP   94 (460)
T TIGR00469        17 TDGQTTNV--TDKIIKLTDANKHLKEDHPLGIIRDLIEKKFNGADNNQRGNPLFKIFDNFKPVVTTMENFDNLGFPADHP   94 (460)
T ss_pred             CCcccCCC--ChHHHHhhccCccCCCCCcHHHHHHHHHHHHHhhhcccccCCCeEEeeCCCCccchhhhhhhcCCCCCCc
Confidence            34677 65  4788899999999999999999999999999999        9997652234999999999999999999


Q ss_pred             CCCCCCceeecCC
Q psy10346        266 ARDAHDTFFVTDP  278 (292)
Q Consensus       266 AR~~~DTfyl~~~  278 (292)
                      ||++|||||+++.
T Consensus        95 aR~~~DT~Yi~~~  107 (460)
T TIGR00469        95 GRQKSDCYYINEQ  107 (460)
T ss_pred             ccCcccceEecCC
Confidence            9999999999864

Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in Bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases. This alignment models the experimental example from Saccharomyces cerevisiae (designated MSF1) and its orthologs from other eukaryotic species.

>TIGR00468 pheS phenylalanyl-tRNA synthetase, alpha subunit

Probab=99.76  E-value=2.6e-20  Score=175.31  Aligned_cols=97  Identities=46%  Similarity=0.856  Sum_probs=90.8

Q ss_pred             cccccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCC
Q psy10346        180 TIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALF  259 (292)
Q Consensus       180 ~~~~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~  259 (292)
                      ++...++++|.+++.++.|++..+++||+.+|+.....|..||+.+++++|+++|.+|||.|+. ++.+++++||||+|+
T Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~d~tlp~~~~~~g~~~p~~~~~~~ir~~l~~~Gf~Ev~-~~~~~s~~~~fd~l~  109 (294)
T TIGR00468        31 ELEDELTKLKPELEKAGLWSKLKFETYDVTLPGTKIYPGSLHPLTRVIDEIRDIFLGLGFTEEK-GPEVETDFWNFDALN  109 (294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhccCcccCCCCCCCCCCcCHHHHHHHHHHHHHHHCCCEEee-CCceeccHHHHHHhC
Confidence            4567778999999999999999999999999987778899999999999999999999999985 788999999999999


Q ss_pred             CCCCCCCCCCCCceeecC
Q psy10346        260 QPQQHPARDAHDTFFVTD  277 (292)
Q Consensus       260 ~PqdHPAR~~~DTfyl~~  277 (292)
                      +|++||||++|||||+++
T Consensus       110 ~~~~hpar~~~d~~~l~d  127 (294)
T TIGR00468       110 IPQDHPARDMQDTFYIKD  127 (294)
T ss_pred             CCCCCcchhhccceeecC
Confidence            999999999999999974

Most phenylalanyl-tRNA synthetases are heterodimeric, with 2 alpha (pheS) and 2 beta (pheT) subunits. This model describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this model. An interesting feature of the alignment of all sequences captured by this model is a deep split between non-spirochete bacterial examples and all other examples; supporting this split is a relative deletion of about 50 residues in the former set between two motifs well conserved throughout the alignment.

>KOG2783|consensus

Probab=98.99  E-value=3e-10  Score=109.62  Aligned_cols=82  Identities=24%  Similarity=0.482  Sum_probs=73.2

Q ss_pred             CCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhhhCC---ceecCCCCccccceeccccCCCCCCCCCCCCCC
Q psy10346        195 SGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMG---FTEMPTNNFVESSFWNFDALFQPQQHPARDAHD  271 (292)
Q Consensus       195 sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mG---F~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~D  271 (292)
                      ...|.|.+++  .....|+.++.-..|||+.+++.|.+.|...|   |+..+.-++|++...|||+|++|.|||+|...|
T Consensus        48 ~d~~~Nv~~~--i~~~~gr~lh~~~~hplg~lr~~i~~~f~~~~~~~fs~~~~~spvvt~~qnfdsl~~p~dh~sr~ksd  125 (436)
T KOG2783|consen   48 TDAWSNVTPS--ILSLLGRNLHQKESHPLGILRQRIEDYFYKTYRNLFSIFENESPVVTTYQNFDSLLFPADHVSRSKSD  125 (436)
T ss_pred             CcccccCChh--hhhhcccchhhhccCchhHHHHHHHHHHHHhhcccchhccCCCceeehhhhcccccCcccccccCcCC
Confidence            5568887644  77788999999999999999999999998765   788777889999999999999999999999999


Q ss_pred             ceeecCC
Q psy10346        272 TFFVTDP  278 (292)
Q Consensus       272 Tfyl~~~  278 (292)
                      |||++..
T Consensus       126 tyy~n~~  132 (436)
T KOG2783|consen  126 TYYVNHT  132 (436)
T ss_pred             ceeecce
Confidence            9999974

>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A

Probab=97.65  E-value=0.00013  Score=55.74  Aligned_cols=62  Identities=16%  Similarity=0.197  Sum_probs=48.6

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD   70 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~   70 (292)
                      .+-.+||..+. .+.....+++...|+++..+...+..|.++ |+|   ......|.||+.|+++++
T Consensus         6 ~Ii~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~-gLI---~~~~~~Y~lTekG~~~l~   67 (77)
T PF14947_consen    6 EIIFDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEK-GLI---KKKDGKYRLTEKGKEFLE   67 (77)
T ss_dssp             HHHHHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHT-TSE---EEETTEEEE-HHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHC-cCe---eCCCCEEEECccHHHHHH
Confidence            45578999997 555677899999999999999999999987 999   347889999999999885

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=97.64  E-value=0.00021  Score=58.10  Aligned_cols=73  Identities=15%  Similarity=0.093  Sum_probs=62.9

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|..++.++..++|...|+++..|.+.+..|+.+ |+|.-..    .-...+.||++|+++++.-.|..+
T Consensus        28 ~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~-GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~~~~~~  104 (118)
T TIGR02337        28 EQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERD-GLVTRLKASNDQRRVYISLTPKGQALYASLSPQIE  104 (118)
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHC-CCEEeccCCCCCCeeEEEECHhHHHHHHHhhHHHH
Confidence            567889999988888888999999999999999999999987 9999753    345689999999999987776654

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.

>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=97.57  E-value=0.00032  Score=51.07  Aligned_cols=61  Identities=23%  Similarity=0.250  Sum_probs=48.0

Q ss_pred             HHHHHHHHHhc-cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhH
Q psy10346          4 DLTEKILKYLD-TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEG   65 (292)
Q Consensus         4 ~~e~~iL~~L~-~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG   65 (292)
                      ..|..||..|. .++.....+++..++++...+.+.++.|..+ |+|+-....    ...|.||++|
T Consensus         3 ~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~-glv~~~~~~~d~R~~~~~LT~~G   68 (68)
T PF13463_consen    3 RPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEK-GLVEKERDPHDKRSKRYRLTPAG   68 (68)
T ss_dssp             HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHT-TSEEEEEESSCTTSEEEEE-HHH
T ss_pred             HHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEecCCCCcCCeeEEEeCCCC
Confidence            45788999998 6777888999999999999999999999987 999665443    4789999998

>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A

Probab=97.54  E-value=0.00024  Score=54.85  Aligned_cols=64  Identities=20%  Similarity=0.234  Sum_probs=52.6

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee-----EEEEEeChhHHHHhh
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS-----HKIWELTGEGNQVKD   70 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~-----~~~~~LTeEG~~yl~   70 (292)
                      ...||..|...+..+..++.+.+|++...+..-++.|+.. |||+++...     .+.|.||+.|++.++
T Consensus         2 Rl~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~-GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~   70 (80)
T PF13601_consen    2 RLAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEA-GYVEVEKEFEGRRPRTWYSLTDKGREAFE   70 (80)
T ss_dssp             HHHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHT-TSEEEEEE-SSS--EEEEEE-HHHHHHHH
T ss_pred             HHHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHC-CCEEEEEeccCCCCeEEEEECHHHHHHHH
Confidence            4578999987777888999999999999999999999987 999996553     667999999999774

>cd00496 PheRS_alpha_core Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain

Probab=97.42  E-value=0.00023  Score=64.34  Aligned_cols=58  Identities=55%  Similarity=0.967  Sum_probs=51.4

Q ss_pred             ChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCC
Q psy10346        221 HPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPK  279 (292)
Q Consensus       221 Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~  279 (292)
                      ||+.++.+.||++|.++||.|+.+-+. .+...++|.+.++.+||.|.+.+++++.+|-
T Consensus         1 ~~~~~~~~~ir~~L~~~Gf~Ev~tys~-~~~~~~~~~~~~~~~~~~~~~~~~v~l~NP~   58 (218)
T cd00496           1 HPLNKVIEEIEDIFVSMGFTEVEGPEV-ETDFYNFDALNIPQDHPARDMQDTFYINDPA   58 (218)
T ss_pred             ChHHHHHHHHHHHHHHCCCEEEeCCcc-cccchhhhhcCCCCCCcccccCceEEECCCc
Confidence            899999999999999999999976544 4665789999999999999999999999884

PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer.

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=97.38  E-value=0.00094  Score=56.18  Aligned_cols=89  Identities=12%  Similarity=0.160  Sum_probs=68.7

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHH--H
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEV--L   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~--r   77 (292)
                      ..|..||..|...+.+...++|..+++++..|.+.++.|+.+ |||.-+.    .-...+.||++|+..++...++.  .
T Consensus        40 ~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~-GlI~R~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~~~  118 (144)
T PRK11512         40 AAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCK-GWVERLPNPNDKRGVLVKLTTSGAAICEQCHQLVGQD  118 (144)
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEeccCcccCCeeEeEEChhHHHHHHHHHHHHHHH
Confidence            567889999977777888999999999999999999999987 9998743    45677799999999988877664  2


Q ss_pred             HHhhcCCCCCChHHHhh
Q psy10346         78 VFNNVPSEGIGQKELLA   94 (292)
Q Consensus        78 l~~~l~~~~~~~~el~~   94 (292)
                      +...+- .+++-+|+..
T Consensus       119 ~~~~l~-~~ls~ee~~~  134 (144)
T PRK11512        119 LHQELT-KNLTADEVAT  134 (144)
T ss_pred             HHHHHH-ccCCHHHHHH
Confidence            333222 3555555443

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=97.37  E-value=0.00078  Score=51.68  Aligned_cols=67  Identities=19%  Similarity=0.231  Sum_probs=57.9

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhc
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDN   71 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~   71 (292)
                      ..+..||..|...+..+..+++...++++..|.+.++.|.+. |+|.....    ....|.||+.|..++..
T Consensus        10 ~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~-g~v~~~~~~~~~r~~~~~lT~~g~~~~~~   80 (101)
T smart00347       10 PTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKK-GLIRRLPSPEDRRSVLVSLTEEGRELIEE   80 (101)
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHC-CCeEecCCCCCCCeEEEEECHhHHHHHHH
Confidence            567889999987777888999999999999999999999987 99987644    45789999999998754

>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=97.04  E-value=0.0011  Score=48.89  Aligned_cols=58  Identities=19%  Similarity=0.199  Sum_probs=51.0

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT   62 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT   62 (292)
                      ..|.+|+..|-..+..+..++|..+|++...|-+++++|..+ |+|.........|..+
T Consensus         8 ~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~-GlV~~~~~~~~~Y~a~   65 (68)
T PF01978_consen    8 ENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEK-GLVEREEGRPKVYRAV   65 (68)
T ss_dssp             HHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT-TSEEEEEECCEEEEEE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEcCceEEEEEe
Confidence            567888888877777889999999999999999999999987 9999988877777665

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.

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=97.02  E-value=0.0045  Score=48.74  Aligned_cols=87  Identities=15%  Similarity=0.087  Sum_probs=65.3

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChHHHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHEVLVF   79 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE~rl~   79 (292)
                      ..|..+|..|...+.....++|..++++...|.+.++.|+.+ |+|.-...    -...+.||++|++.+..-.|...-+
T Consensus        22 ~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~-glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~~~~~~  100 (126)
T COG1846          22 PPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDK-GLIERLRDPEDRRAVLVRLTEKGRELLEQLLPAAQEL  100 (126)
T ss_pred             HHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHC-CCeeecCCccccceeeEEECccHHHHHHHhccHHHHH
Confidence            467888988876655432789999999999999999999987 99998554    3568899999999998888855533


Q ss_pred             hhcCCCCCChHH
Q psy10346         80 NNVPSEGIGQKE   91 (292)
Q Consensus        80 ~~l~~~~~~~~e   91 (292)
                      ...--.+.+-++
T Consensus       101 ~~~~~~~l~~~e  112 (126)
T COG1846         101 LAEILAGLSEEE  112 (126)
T ss_pred             HHHhccCCCHHH
Confidence            222223444444

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=96.96  E-value=0.0034  Score=50.65  Aligned_cols=73  Identities=18%  Similarity=0.110  Sum_probs=59.5

Q ss_pred             HHHHHHHHHhc----cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChH
Q psy10346          4 DLTEKILKYLD----TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHE   75 (292)
Q Consensus         4 ~~e~~iL~~L~----~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE   75 (292)
                      ..|..||..|.    .++.++..++|..++++...|.+.+..|+.+ |+|.-...    -...+.||++|++.++.-.+|
T Consensus        25 ~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~k-g~I~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~  103 (109)
T TIGR01889        25 LEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKK-GYLSKERSEDDERKVIISINKEQRSKIESLISE  103 (109)
T ss_pred             HHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHC-CCEeccCCcccCCeEEEEECHHHHHHHHHHHHH
Confidence            45778888887    4567889999999999999999999999987 99986333    367789999999988766655


Q ss_pred             HH
Q psy10346         76 VL   77 (292)
Q Consensus        76 ~r   77 (292)
                      ..
T Consensus       104 ~~  105 (109)
T TIGR01889       104 IE  105 (109)
T ss_pred             HH
Confidence            43

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.

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

Probab=96.94  E-value=0.0019  Score=48.25  Aligned_cols=60  Identities=27%  Similarity=0.366  Sum_probs=51.1

Q ss_pred             cHHHHHHHHHhccCCC--CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeCh
Q psy10346          3 SDLTEKILKYLDTNPP--VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG   63 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~--~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTe   63 (292)
                      ...+.+||..|...+.  +...+||+.+|++...|-+.+..|+.. |+|.........|.++.
T Consensus         5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~-G~V~~~~~~~~~W~i~~   66 (68)
T smart00550        5 DSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK-GKVCKQGGTPPLWKLTD   66 (68)
T ss_pred             hHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEecCCCCCceEeec
Confidence            4678899999987766  899999999999999999999999987 99987655446777764

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

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=96.91  E-value=0.0045  Score=51.81  Aligned_cols=89  Identities=15%  Similarity=0.161  Sum_probs=66.0

Q ss_pred             HHHHHHHHHhccC-CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH-
Q psy10346          4 DLTEKILKYLDTN-PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL-   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~-~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r-   77 (292)
                      ..+..+|..|... +..+..++|..+++++..|.+.+..|+.+ |+|.-..    .-...+.||+.|++.++...+-.. 
T Consensus        31 ~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~-GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~~  109 (144)
T PRK03573         31 QTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEK-GLISRQTCASDRRAKRIKLTEKAEPLISEVEAVINK  109 (144)
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHC-CCEeeecCCCCcCeeeeEEChHHHHHHHHHHHHHHH
Confidence            4567788888654 44677899999999999999999999987 9999753    345788999999999987666554 


Q ss_pred             HHhhcCCCCCChHHHhh
Q psy10346         78 VFNNVPSEGIGQKELLA   94 (292)
Q Consensus        78 l~~~l~~~~~~~~el~~   94 (292)
                      +...+ -.+++-+|+..
T Consensus       110 ~~~~~-~~~l~~ee~~~  125 (144)
T PRK03573        110 TRAEI-LHGISAEEIEQ  125 (144)
T ss_pred             HHHHH-HhCCCHHHHHH
Confidence            22222 13555555444

>PRK10870 transcriptional repressor MprA; Provisional

Probab=96.86  E-value=0.0048  Score=54.14  Aligned_cols=89  Identities=10%  Similarity=0.060  Sum_probs=67.2

Q ss_pred             HHHHHHHHHhcc--CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDT--NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~--~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|..  ++.+...++|..+++++..|.+.+..|+.+ |+|.-...    -...+.||++|+..++.-.|...
T Consensus        55 ~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~k-GlV~R~~~~~DrR~~~v~LT~~G~~~~~~i~~~~~  133 (176)
T PRK10870         55 ETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKR-GWIERRESDNDRRCLHLQLTEKGHEFLREVLPPQH  133 (176)
T ss_pred             HHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEecCCCCCCCeeEEEECHHHHHHHHHHHHHHH
Confidence            457788888864  345777899999999999999999999987 99997544    34688999999999988877766


Q ss_pred             -HHhhcCCCCCChHHHhh
Q psy10346         78 -VFNNVPSEGIGQKELLA   94 (292)
Q Consensus        78 -l~~~l~~~~~~~~el~~   94 (292)
                       ....+- .+++-+++..
T Consensus       134 ~~~~~~~-~~ls~~e~~~  150 (176)
T PRK10870        134 NCLHQLW-SALSTTEKDQ  150 (176)
T ss_pred             HHHHHHH-hcCCHHHHHH
Confidence             332221 3455555443

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=96.76  E-value=0.0054  Score=54.66  Aligned_cols=73  Identities=18%  Similarity=0.045  Sum_probs=62.1

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe----eeeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE----PLSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e----~~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..|..||..|..++.++..++|+..+++...|.+.+..|+.+ |+|.-.    .+-...+.||++|++.+++-.|...
T Consensus        45 ~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~k-GlI~R~~~~~DrR~~~I~LTekG~~l~~~l~~~~~  121 (185)
T PRK13777         45 INEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEER-GYLTFSKKEDDKRNTYIELTEKGEELLLETMEEYD  121 (185)
T ss_pred             HHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHC-CCEEecCCCCCCCeeEEEECHHHHHHHHHHHHHHH
Confidence            457789999987778889999999999999999999999987 999964    3556788999999999877666555

>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles

Probab=96.76  E-value=0.005  Score=46.31  Aligned_cols=42  Identities=12%  Similarity=0.122  Sum_probs=37.2

Q ss_pred             CCCHHHHHHHHHHhhccCCcEEEeeee------EEEEEeChhHHHHhhc
Q psy10346         29 NEDHQKVVGGMKSIETLGEYLIVEPLS------HKIWELTGEGNQVKDN   71 (292)
Q Consensus        29 ~~~~~~v~~~~~~L~s~~glv~~e~~~------~~~~~LTeEG~~yl~~   71 (292)
                      .+++..|-.+++.|+.. |+|+.....      ++.|.||+.|++++++
T Consensus        28 ~i~~g~lY~~L~~Le~~-gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~E   75 (75)
T PF03551_consen   28 KISPGSLYPALKRLEEE-GLIESRWEEEGNGRPRKYYRITEKGREELRE   75 (75)
T ss_dssp             ETTHHHHHHHHHHHHHT-TSEEEEEEEETTSSEEEEEEESHHHHHHHHH
T ss_pred             ccChhHHHHHHHHHHhC-CCEEEeeeccCCCCCCEEEEECHHHHHHhcC
Confidence            57899999999999987 999996665      8999999999998864

In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....

>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=96.70  E-value=0.0046  Score=42.47  Aligned_cols=46  Identities=26%  Similarity=0.377  Sum_probs=40.6

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI   50 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~   50 (292)
                      ..+.+||..|.+++.++..++|+.+|++...|-+.++.|..+ |+|+
T Consensus         3 ~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~-g~I~   48 (48)
T PF13412_consen    3 ETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEK-GLIE   48 (48)
T ss_dssp             HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHT-TSEE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHC-cCcC
Confidence            568899999998888999999999999999999999999987 9985

...

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=96.67  E-value=0.0077  Score=50.70  Aligned_cols=62  Identities=21%  Similarity=0.285  Sum_probs=50.4

Q ss_pred             HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN   71 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~   71 (292)
                      ..|+..+..++.....++|..+++++.+|.++++.|+.+ |+|....  ...+.||+.|+..+..
T Consensus        11 ~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~-Gli~~~~--~~~i~LT~~G~~~a~~   72 (142)
T PRK03902         11 EQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKD-EYLIYEK--YRGLVLTPKGKKIGKR   72 (142)
T ss_pred             HHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHC-CCEEEec--CceEEECHHHHHHHHH
Confidence            344555566777788999999999999999999999987 9998543  3569999999987755

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

Probab=96.61  E-value=0.015  Score=41.57  Aligned_cols=64  Identities=17%  Similarity=0.225  Sum_probs=52.6

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHHHh
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQVK   69 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~yl   69 (292)
                      ...+..||..+..++ +...+++..+|++...+-+++..|.+. |+|..... ....|.+|+ |+++.
T Consensus         6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~-g~i~~~~~~~~~~~~~~~-g~~~~   70 (78)
T cd00090           6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEA-GLVESRREGRRVYYSLTD-AERLL   70 (78)
T ss_pred             ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHC-CCeEEEEeccEEEEEeCC-chHHH
Confidence            356778898887666 788999999999999999999999987 99987543 467899998 77655

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.

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=96.45  E-value=0.0068  Score=54.10  Aligned_cols=61  Identities=16%  Similarity=0.182  Sum_probs=54.0

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEG   65 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG   65 (292)
                      ..+.+||..|..++..+..++|+.+|+++..+.+.+..|+.. |+|.........|.||+.|
T Consensus       143 ~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~-GlI~r~~~r~~~~~lT~~G  203 (203)
T TIGR01884       143 REELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKK-GLVEQKGRKGKRYSLTKLG  203 (203)
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEcCCccEEEeCCCC
Confidence            567899999987777888999999999999999999999987 9999876567789999987

Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=96.25  E-value=0.013  Score=52.23  Aligned_cols=66  Identities=23%  Similarity=0.248  Sum_probs=55.8

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee------eeEEEEEeChhHHHHhhc
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP------LSHKIWELTGEGNQVKDN   71 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~------~~~~~~~LTeEG~~yl~~   71 (292)
                      ...+||..|...+..+..++|..+|++...|.+.+..|+.. |+|....      .....|.||+.|+..+.+
T Consensus         2 tr~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~-GlV~r~~~~~~~gRp~~~y~LT~~G~~~~~~   73 (203)
T TIGR02702         2 TKEDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETE-GLIEYEAVVQGMGRPQYHYQLSRQGREQFPQ   73 (203)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeEEeecccCCCCCceEEEECcchhhhccc
Confidence            35789999977777889999999999999999999999987 9998652      345678999999987654

All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.

>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional

Probab=96.24  E-value=0.015  Score=53.22  Aligned_cols=66  Identities=12%  Similarity=0.125  Sum_probs=53.1

Q ss_pred             HHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHhhcCChHHH
Q psy10346         11 KYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus        11 ~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+.+...++..++|+.++++++++.+.++.|+.+ |+|+-+. .....+.||+.|++.++.-..++.
T Consensus        14 g~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~-GlI~R~~~~r~~~v~LTekG~~ll~~~~~d~~   80 (217)
T PRK14165         14 GAVNNTVKISSSEFANHTGTSSKTAARILKQLEDE-GYITRTIVPRGQLITITEKGLDVLYNEYADYS   80 (217)
T ss_pred             hccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEEcCCceEEEECHHHHHHHHHHHHHHH
Confidence            33344445788999999999999999999999987 9997643 345789999999999977666665

>COG1497 Predicted transcriptional regulator [Transcription]

Probab=96.09  E-value=0.018  Score=53.44  Aligned_cols=73  Identities=18%  Similarity=0.148  Sum_probs=63.6

Q ss_pred             HHHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHH
Q psy10346          4 DLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVF   79 (292)
Q Consensus         4 ~~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~   79 (292)
                      ....+||..|.- ++.+...++|.++|+..|+|...++.|-+. |+|+.  .-...|++|++|.+.+.+-+-|.|-|
T Consensus        10 ~t~fqIL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~e-G~i~~--~gR~~Y~iTkkG~e~l~~~~~dlr~f   83 (260)
T COG1497          10 LTRFQILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKE-GLIEK--EGRGEYEITKKGAEWLLEQLSDLRRF   83 (260)
T ss_pred             chHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhc-cceee--cCCeeEEEehhHHHHHHHHHHHHHHH
Confidence            566788888854 577899999999999999999999999976 99987  55668999999999999998888865

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=96.09  E-value=0.03  Score=38.92  Aligned_cols=59  Identities=17%  Similarity=0.188  Sum_probs=48.4

Q ss_pred             HHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeCh-hHHHHh
Q psy10346          9 ILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTG-EGNQVK   69 (292)
Q Consensus         9 iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTe-EG~~yl   69 (292)
                      ||..|. .+..+..+++..+|++...+.+.+..|.+. |+|.... .....|.+|+ .|.+.+
T Consensus         2 il~~l~-~~~~~~~~i~~~l~is~~~v~~~l~~L~~~-g~i~~~~~~~~~~~~~~~~~~~~~~   62 (66)
T smart00418        2 ILKLLA-EGELCVCELAEILGLSQSTVSHHLKKLREA-GLVESRREGKRVYYSLTDEKVADLL   62 (66)
T ss_pred             HHHHhh-cCCccHHHHHHHHCCCHHHHHHHHHHHHHC-CCeeeeecCCEEEEEEchHHHHHHH
Confidence            566666 566788999999999999999999999987 9999765 5567789998 776654

>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function

Probab=95.96  E-value=0.029  Score=44.81  Aligned_cols=67  Identities=22%  Similarity=0.257  Sum_probs=54.9

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee------------------eEEEEEeChh
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL------------------SHKIWELTGE   64 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~------------------~~~~~~LTeE   64 (292)
                      .+....||..|..-+.-.+-.+|..++++.+.|...+..|+.. |||+-..-                  -.+.|.||.+
T Consensus         6 ~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~-GLler~~g~~iK~~~~k~K~~~e~~~hHtYY~LTr~   84 (92)
T PF10007_consen    6 DPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEM-GLLERVEGKTIKRSEAKFKPKKEVHKHHTYYRLTRE   84 (92)
T ss_pred             ChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHC-CCeEEecCcccchhhhhcccchhhhcCCceeeecHh
Confidence            4678899999987666556779999999999999999999997 99864322                  2468999999


Q ss_pred             HHHHhh
Q psy10346         65 GNQVKD   70 (292)
Q Consensus        65 G~~yl~   70 (292)
                      |+.+++
T Consensus        85 G~~llR   90 (92)
T PF10007_consen   85 GELLLR   90 (92)
T ss_pred             HHHHHh
Confidence            998875

>COG4754 Uncharacterized conserved protein [Function unknown]

Probab=95.93  E-value=0.019  Score=49.42  Aligned_cols=67  Identities=21%  Similarity=0.142  Sum_probs=57.8

Q ss_pred             HHHHHhcc--CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHH
Q psy10346          8 KILKYLDT--NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLV   78 (292)
Q Consensus         8 ~iL~~L~~--~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl   78 (292)
                      -+|..+.+  +|..|..-++++.+++.+.+|.++.-++.. |+|+.+.-   -..||++|+.|++.+.||++-
T Consensus        16 GLL~~l~n~fnGraDl~~L~~e~~vdidDL~piv~ta~~L-glv~~e~G---DiilT~~Gk~~v~~~~~erK~   84 (157)
T COG4754          16 GLLYVLNNIFNGRADLPYLEKEMEVDIDDLMPIVETASLL-GLVTAESG---DIILTDEGKEYVESPIRERKE   84 (157)
T ss_pred             HHHHHHHHHhCCcccchhHHHHhCCChhhHHHHHHHHHhc-CceeccCC---CEEEehhhHHHHhCChHHHHH
Confidence            35566654  677899999999999999999999999998 99998764   478999999999999999983

>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family

Probab=95.92  E-value=0.025  Score=45.05  Aligned_cols=74  Identities=18%  Similarity=0.235  Sum_probs=55.5

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHh--------cCCCHHHHHHHHHHhhccCCcEEEee------eeEEEEEeChhHHHH
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKL--------FNEDHQKVVGGMKSIETLGEYLIVEP------LSHKIWELTGEGNQV   68 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~--------~~~~~~~v~~~~~~L~s~~glv~~e~------~~~~~~~LTeEG~~y   68 (292)
                      ..++.-||..|..+ +..-.++.+.        ..+++..|-.++..|+.+ |+|+...      ...+.|.||+.|+++
T Consensus         3 g~l~~~iL~~L~~~-~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~-GlI~~~~~~~~~~~~rk~y~iT~~Gr~~   80 (100)
T TIGR03433         3 GTLDLLILKTLSLG-PLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERR-GWIAAEWGESENNRRAKFYRLTAAGRKQ   80 (100)
T ss_pred             chHHHHHHHHHhcC-CCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHC-CCeEEEeeecCCCCCceEEEECHHHHHH
Confidence            35678899999744 3344555544        357889999999999987 9999842      225899999999999


Q ss_pred             hhcCChHHHH
Q psy10346         69 KDNGSHEVLV   78 (292)
Q Consensus        69 l~~GlPE~rl   78 (292)
                      +++-.++.+-
T Consensus        81 l~~~~~~~~~   90 (100)
T TIGR03433        81 LAAETESWAR   90 (100)
T ss_pred             HHHHHHHHHH
Confidence            9877666653

Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein

>PRK11050 manganese transport regulator MntR; Provisional

Probab=95.83  E-value=0.032  Score=47.81  Aligned_cols=71  Identities=15%  Similarity=0.175  Sum_probs=56.6

Q ss_pred             HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHHh
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFN   80 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~~   80 (292)
                      ..|+.++..++.....++|+.+++++..|.+++..|++. |+|....  ...+.||+.|+..+....+-.+.+.
T Consensus        40 ~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~-GlI~r~~--~~~v~LT~~G~~l~~~~~~~~~~le  110 (152)
T PRK11050         40 ELIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARD-GLVEMRP--YRGVFLTPEGEKLAQESRERHQIVE  110 (152)
T ss_pred             HHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEec--CCceEECchHHHHHHHHHHHHHHHH
Confidence            345556666677788999999999999999999999987 9987543  3468999999998877766666554

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=95.81  E-value=0.023  Score=49.22  Aligned_cols=59  Identities=24%  Similarity=0.247  Sum_probs=49.3

Q ss_pred             HHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346          9 ILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD   70 (292)
Q Consensus         9 iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~   70 (292)
                      |......++.+.+.++|..+++.+.+|..+++.|++. |||+.+.  ..-+.||+.|++.+.
T Consensus        15 Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~-GlV~~~~--y~gi~LT~~G~~~a~   73 (154)
T COG1321          15 IYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERL-GLVEYEP--YGGVTLTEKGREKAK   73 (154)
T ss_pred             HHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHC-CCeEEec--CCCeEEChhhHHHHH
Confidence            4444556778899999999999999999999999987 9998654  456899999998764

>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=95.69  E-value=0.027  Score=40.71  Aligned_cols=53  Identities=23%  Similarity=0.299  Sum_probs=45.8

Q ss_pred             CCcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346          1 MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL   54 (292)
Q Consensus         1 m~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~   54 (292)
                      |+++...+||..|...++.+..++|+.+|++.+.+..-++.|+.. |+|+.++.
T Consensus         7 L~~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a-Gli~~~~~   59 (61)
T PF12840_consen    7 LSDPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEA-GLIEVERE   59 (61)
T ss_dssp             HTSHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT-TSEEEEEE
T ss_pred             hCCHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCeEEecc
Confidence            456788999999966777889999999999999999999999986 99998764

...

>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=95.69  E-value=0.027  Score=40.04  Aligned_cols=49  Identities=18%  Similarity=0.165  Sum_probs=42.2

Q ss_pred             HHHHHHHHHhccCCC--CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346          4 DLTEKILKYLDTNPP--VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP   53 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~--~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~   53 (292)
                      ..+..||..|...+.  +...++|..++++++.|.+.++.|+++ |||..+.
T Consensus         5 ~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~-Glv~r~~   55 (62)
T PF12802_consen    5 PSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKK-GLVERER   55 (62)
T ss_dssp             HHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHT-TSEEEEE
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEeC
Confidence            568899999977666  788999999999999999999999987 9998764

...

>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length

Probab=95.61  E-value=0.053  Score=43.17  Aligned_cols=66  Identities=24%  Similarity=0.428  Sum_probs=52.8

Q ss_pred             HHHHHHHHHhccC--CCCChHHHHHhcCCCHHHHHHHHH----------HhhccCCcE--EEeeeeEEEEEeChhHHHHh
Q psy10346          4 DLTEKILKYLDTN--PPVDTLDLAKLFNEDHQKVVGGMK----------SIETLGEYL--IVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus         4 ~~e~~iL~~L~~~--~~~~~~ela~~~~~~~~~v~~~~~----------~L~s~~glv--~~e~~~~~~~~LTeEG~~yl   69 (292)
                      .+..+||..|.+.  ......++|...|.+.+.|.+++.          ||-.. |||  ..+..-.+.|.||++|+.++
T Consensus         9 ~~R~~vl~~L~~~yp~~~~~~eIar~v~~~~snV~GaL~G~g~rY~~e~SLv~l-GLV~~~~~~~g~k~Y~lT~~G~~~~   87 (90)
T PF07381_consen    9 KVRKKVLEYLCSIYPEPAYPSEIARSVGSDYSNVLGALRGDGKRYNKEDSLVGL-GLVEEEEEKGGFKYYRLTEKGKRIA   87 (90)
T ss_pred             HHHHHHHHHHHHcCCCcCCHHHHHHHHCCCHHHHHHHHhcCCCCcCcchhHHHc-CCeeEeeecCCeeEEEeChhhhhHH
Confidence            4567899999765  235678999999999999999985          67777 999  33445667999999999876


Q ss_pred             h
Q psy10346         70 D   70 (292)
Q Consensus        70 ~   70 (292)
                      +
T Consensus        88 ~   88 (90)
T PF07381_consen   88 E   88 (90)
T ss_pred             h
Confidence            4

The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.

>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure

Probab=95.58  E-value=0.06  Score=41.95  Aligned_cols=60  Identities=17%  Similarity=0.204  Sum_probs=47.4

Q ss_pred             HHHHHhccCCCCChHHHHHhc-CCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHh
Q psy10346          8 KILKYLDTNPPVDTLDLAKLF-NEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVK   69 (292)
Q Consensus         8 ~iL~~L~~~~~~~~~ela~~~-~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl   69 (292)
                      .||..|.. +.....++.+.+ |++...+...++.|++. |+|.-...    ....|.||+.|++.+
T Consensus         9 ~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~-GLv~r~~~~~~p~~v~Y~LT~~G~~l~   73 (90)
T PF01638_consen    9 LILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEA-GLVERRVYPEVPPRVEYSLTEKGKELL   73 (90)
T ss_dssp             HHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHT-TSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred             HHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHc-chhhcccccCCCCCCccCCCcCHHHHH
Confidence            57777765 566778898888 99999999999999997 99976543    357899999999865

The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.

>PF03501 S10_plectin: Plectin/S10 domain; InterPro: IPR005326 This presumed domain is found at the N terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein

Probab=95.42  E-value=0.019  Score=46.10  Aligned_cols=48  Identities=23%  Similarity=0.307  Sum_probs=36.0

Q ss_pred             cCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHhhc--CChHH
Q psy10346         28 FNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVKDN--GSHEV   76 (292)
Q Consensus        28 ~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl~~--GlPE~   76 (292)
                      ++++-=.|+.+++||.|+ |+|+-.- =....|.||+||.+||++  .+|+.
T Consensus        33 l~vpNL~V~k~mqSL~Sr-gyVke~faWrh~Yw~LT~eGIeyLR~yL~LP~e   83 (95)
T PF03501_consen   33 LNVPNLHVIKAMQSLKSR-GYVKEQFAWRHYYWYLTNEGIEYLREYLHLPAE   83 (95)
T ss_dssp             TSSBHHHHHHHHHHHHHC-TSEEEEECTTEEEEEE-HHHHHHHHHHC-SSTT
T ss_pred             cCCCcHHHHHHHhcccch-hhhcCeecceEEEEEEcchhHHHHHHHhCCChh
Confidence            366766799999999998 9998643 356678999999999975  34443

This domain may be involved in RNA binding.; PDB: 2XZM_7 2XZN_7 3U5C_K 3U5G_K.

>PRK09616 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed

Probab=95.39  E-value=0.037  Score=56.77  Aligned_cols=120  Identities=15%  Similarity=0.257  Sum_probs=74.1

Q ss_pred             CCChhh-HHhhhcccceeeEEEEEEEEecCccccccccccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHH
Q psy10346        146 KVPEAN-KVDYKKRKLLQEVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLM  224 (292)
Q Consensus       146 ~l~~~~-~~~LkkRkLv~~~~~~~~~v~~g~~~~~~~~~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~  224 (292)
                      .++.++ .+.|++-|+-.......+.|.. |.+-..+.- ..||-.|.+.---|.+..-     ..|. ....|..||..
T Consensus       291 ~i~~~~i~~iL~~Lgf~~~~~~~~~~v~v-P~~R~DI~~-~~DliEEiaR~yGyd~i~~-----~~p~-~~~~~~~~~~~  362 (552)
T PRK09616        291 DLSAEEIIELLERMRYDAEIGDDKVKVTV-PPYRVDILH-EVDVIEDVAIAYGYNNLEP-----ELPK-VFTIGRLHPIE  362 (552)
T ss_pred             CCCHHHHHHHHHHcCCCcEecCCeEEEEe-CCCcccccc-cchHHHHHHHHhCcccCCc-----cCCC-CccCCCCChHH
Confidence            444433 4557777764322222333432 122222222 2377777765444444321     1121 33458899999


Q ss_pred             HHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCCC
Q psy10346        225 KVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKT  280 (292)
Q Consensus       225 ~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~  280 (292)
                      ++.+.+|++|.++||.|+.+.+. .+..+||+.++++.+|+      +.-|.+|-+
T Consensus       363 ~~~~~ir~~L~~~Gf~Ev~tys~-~s~~~~~~~~~~~~~~~------~i~l~NPls  411 (552)
T PRK09616        363 KLERAIRDLMVGLGFQEVMNFTL-TSEEVLFEKMNLEPEED------YVEVLNPIS  411 (552)
T ss_pred             HHHHHHHHHHHhCCcceeccceE-echHHHHHHhCCCCCCC------eEEEcCCCc
Confidence            99999999999999999987665 47778899999998883      466777744

>PTZ00034 40S ribosomal protein S10; Provisional

Probab=95.38  E-value=0.024  Score=47.50  Aligned_cols=74  Identities=18%  Similarity=0.127  Sum_probs=47.4

Q ss_pred             HHHHHHHHHhccCCCC----ChH-HHHHhcCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHhhc--CChH
Q psy10346          4 DLTEKILKYLDTNPPV----DTL-DLAKLFNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVKDN--GSHE   75 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~----~~~-ela~~~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl~~--GlPE   75 (292)
                      .....|...|=+.|.+    |.. .--..++++-=.|+.+++||.|+ |+|+..- =....|.||+||.+||++  ++|+
T Consensus         7 ~~r~~Iye~LfkeGVlvakKd~~~~~h~el~vpNL~Vik~mqSL~Sr-g~Vke~f~WrhyYw~LT~eGieyLR~yL~LP~   85 (124)
T PTZ00034          7 ANRKAIYRYLFKEGVIVCKKDPKGPWHPELNVPNLHVMMLMRSLKSR-GLVKEQFAWQHYYYYLTDEGIEYLRTYLHLPP   85 (124)
T ss_pred             HHHHHHHHHHhhCceEEEecCCCCCCCCccCCccHHHHHHHHccccC-CceEEEEeeEEEEEEEchHHHHHHHHHhCCCc
Confidence            3455677777544431    110 00011245555799999999998 9998744 456677999999999975  4555


Q ss_pred             HHH
Q psy10346         76 VLV   78 (292)
Q Consensus        76 ~rl   78 (292)
                      ..+
T Consensus        86 eiv   88 (124)
T PTZ00034         86 DVF   88 (124)
T ss_pred             ccC
Confidence            543

>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress

Probab=95.22  E-value=0.039  Score=42.83  Aligned_cols=70  Identities=20%  Similarity=0.232  Sum_probs=60.1

Q ss_pred             CCcHHHHHHHHHhc-----cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346          1 MASDLTEKILKYLD-----TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN   71 (292)
Q Consensus         1 m~~~~e~~iL~~L~-----~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~   71 (292)
                      |=.+.|++||.+|.     .+.++.+.++|+.++++...|-..+..|++. |||+-.....--++.|+.|-+++..
T Consensus         1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~l-Glve~~p~~s~GriPT~~aYr~~~~   75 (78)
T PF03444_consen    1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEEL-GLVESQPHPSGGRIPTDKAYRALNR   75 (78)
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHC-CCccCCCCCCCCCCcCHHHHHHHcc
Confidence            44577899998884     3667899999999999999999999999998 9998777778889999999887754

Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent

>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element

Probab=95.07  E-value=0.037  Score=42.87  Aligned_cols=51  Identities=20%  Similarity=0.212  Sum_probs=42.5

Q ss_pred             HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChH
Q psy10346         22 LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHE   75 (292)
Q Consensus        22 ~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE   75 (292)
                      .++|..+|+++..|.+++..|+++ |+|.....  ..|.||+.|+.....=.+.
T Consensus         3 ~ela~~l~is~stvs~~l~~L~~~-glI~r~~~--~~~~lT~~g~~~~~~~~~~   53 (96)
T smart00529        3 SEIAERLNVSPPTVTQMLKKLEKD-GLVEYEPY--RGITLTEKGRRLARRLLRK   53 (96)
T ss_pred             HHHHHHhCCChHHHHHHHHHHHHC-CCEEEcCC--CceEechhHHHHHHHHHHH
Confidence            578999999999999999999987 99988664  3799999999986444333

iron dependent repressor

>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=94.97  E-value=0.047  Score=38.61  Aligned_cols=50  Identities=20%  Similarity=0.147  Sum_probs=43.3

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL   54 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~   54 (292)
                      ..|..+|..|...+.++..++|...++++..+.+.++.|+.+ |+|.-+..
T Consensus         3 ~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~-g~I~r~~~   52 (59)
T PF01047_consen    3 PSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKK-GLIERERD   52 (59)
T ss_dssp             HHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHT-TSEEEEEE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHC-CCEEeccC
Confidence            467889999988777888999999999999999999999987 99987654

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 ....

>PHA00738 putative HTH transcription regulator

Probab=94.95  E-value=0.1  Score=42.82  Aligned_cols=71  Identities=17%  Similarity=0.198  Sum_probs=57.9

Q ss_pred             CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEE-EEEeChhHHHHhhcCChHHHHHh
Q psy10346          2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHK-IWELTGEGNQVKDNGSHEVLVFN   80 (292)
Q Consensus         2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~-~~~LTeEG~~yl~~GlPE~rl~~   80 (292)
                      +++...+||..|..++.....+++..+++++.+|.+=++-|+.- |+|..+..-.. +|.|.        .+.|++++++
T Consensus        10 ~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreA-GLV~srK~Gr~vyY~Ln--------~~~~~~~l~~   80 (108)
T PHA00738         10 AKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQ-GYIELYKEGRTLYAKIR--------ENSKEIQILN   80 (108)
T ss_pred             CCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHC-CceEEEEECCEEEEEEC--------CCccHHHHHh
Confidence            35778899999987766778899999999999999999999986 99999766554 45655        6677887775


Q ss_pred             h
Q psy10346         81 N   81 (292)
Q Consensus        81 ~   81 (292)
                      .
T Consensus        81 ~   81 (108)
T PHA00738         81 S   81 (108)
T ss_pred             h
Confidence            4

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=94.94  E-value=0.07  Score=48.90  Aligned_cols=64  Identities=25%  Similarity=0.342  Sum_probs=56.5

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee------EEEEEeChhHHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS------HKIWELTGEGNQV   68 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~------~~~~~LTeEG~~y   68 (292)
                      +...+||.+|...+.....++|+.+|++..+|-+=+..|+++ |+|.++...      ...|.||+.|..-
T Consensus        11 ~tr~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~-Glv~~~~~~~g~GRP~~~y~Lt~~g~~~   80 (218)
T COG2345          11 STRERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAE-GLVEVERQQGGRGRPAKLYRLTEKGREQ   80 (218)
T ss_pred             cHHHHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhC-cceeeeeccCCCCCCceeeeecccchhh
Confidence            466789999998889999999999999999999999999987 999998544      3789999999873

>COG1695 Predicted transcriptional regulators [Transcription]

Probab=94.88  E-value=0.093  Score=43.69  Aligned_cols=68  Identities=18%  Similarity=0.157  Sum_probs=50.9

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHh----cC----CCHHHHHHHHHHhhccCCcEEEeeee------EEEEEeChhHHHHh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKL----FN----EDHQKVVGGMKSIETLGEYLIVEPLS------HKIWELTGEGNQVK   69 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~----~~----~~~~~v~~~~~~L~s~~glv~~e~~~------~~~~~LTeEG~~yl   69 (292)
                      .++..||..|... +..-.++.+.    .+    .++..|-.++..|+.. |+|+.....      ...|.||+.|++++
T Consensus         9 ~l~~~iL~~L~~~-~~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~-Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l   86 (138)
T COG1695           9 SLELLILSLLSEK-PSHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKE-GLIESRWEESGGGPPRKYYRLTEKGKEEL   86 (138)
T ss_pred             hHHHHHHHHHhcC-CchHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHC-CCeEEEecccCCCCCceEEEECHHHHHHH
Confidence            4678889988765 4333445443    22    6788999999999987 999986332      58999999999998


Q ss_pred             hcCC
Q psy10346         70 DNGS   73 (292)
Q Consensus        70 ~~Gl   73 (292)
                      ..-.
T Consensus        87 ~~~~   90 (138)
T COG1695          87 AELR   90 (138)
T ss_pred             HHHH
Confidence            6544

>PRK09416 lstR lineage-specific thermal regulator protein; Provisional

Probab=94.61  E-value=0.12  Score=44.09  Aligned_cols=67  Identities=19%  Similarity=0.299  Sum_probs=49.8

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHh--------cCCCHHHHHHHHHHhhccCCcEEEee--eeEEEEEeChhHHHHhhcC
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKL--------FNEDHQKVVGGMKSIETLGEYLIVEP--LSHKIWELTGEGNQVKDNG   72 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~--------~~~~~~~v~~~~~~L~s~~glv~~e~--~~~~~~~LTeEG~~yl~~G   72 (292)
                      +++...||..|...  ..-.++.+.        ..+++..|-.++..|+.. |+|+...  ..+..|.||+.|+++++.=
T Consensus        42 ~~~~l~IL~lL~~~--~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~-GlI~s~~~~~~RK~Y~ITe~Gre~L~e~  118 (135)
T PRK09416         42 EDILLAILQLLMNE--KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQN-RFIQSSWDHEGAKYYQLTDKGNKMLRKA  118 (135)
T ss_pred             ccHHHHHHHHHhCC--CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHC-CCeEEeecCCCceEEEECHHHHHHHHHH
Confidence            35667789988755  333445443        235689999999999987 9999843  4578999999999988643

>PRK09537 pylS pyrolysyl-tRNA synthetase; Reviewed

Probab=94.59  E-value=0.035  Score=55.36  Aligned_cols=58  Identities=16%  Similarity=0.221  Sum_probs=45.3

Q ss_pred             CCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeec
Q psy10346        215 LPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVT  276 (292)
Q Consensus       215 ~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~  276 (292)
                      ...|+.||+..+.+.|+++|.++||.|+.+ |.+++.. .|+.+..+.+++.++  +.|+++
T Consensus       198 ~~~g~~~~~s~Le~aIR~~f~~~GF~EV~T-PtLt~ee-~~e~~g~~~g~~i~~--~my~id  255 (417)
T PRK09537        198 YEEDREDYLGKLERDITKFFVDRGFLEIKS-PILIPAE-YIERMGIDNDTELSK--QIFRVD  255 (417)
T ss_pred             hccCCCCHHHHHHHHHHHHHHHCCCEEEEC-CeeecHH-HHHHhCCCCcccchh--hheeeC
Confidence            467999999999999999999999999974 7776544 389888877766543  345554

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

Probab=94.38  E-value=0.081  Score=38.05  Aligned_cols=45  Identities=18%  Similarity=0.275  Sum_probs=40.7

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      +..||..|..++.+...++|+.+|++...|-+.+..|+.. |+|.-
T Consensus         2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~-g~i~r   46 (57)
T PF08220_consen    2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQ-GLIKR   46 (57)
T ss_pred             HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEE
Confidence            4689999998999999999999999999999999999986 88653

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

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=94.35  E-value=0.19  Score=41.81  Aligned_cols=60  Identities=17%  Similarity=0.138  Sum_probs=49.1

Q ss_pred             HHHHHhccCCCCChHHHHHhcC-CCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHh
Q psy10346          8 KILKYLDTNPPVDTLDLAKLFN-EDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVK   69 (292)
Q Consensus         8 ~iL~~L~~~~~~~~~ela~~~~-~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl   69 (292)
                      .||..|.. +.....++-..++ +++..+.+-++.|+.. |+|.-+...    +..|.||+.|+...
T Consensus        27 lIl~~L~~-g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~-Glv~R~~~~~~PprveY~LT~~G~~L~   91 (120)
T COG1733          27 LILRDLFD-GPKRFNELRRSIGGISPKMLSRRLKELEED-GLVERVVYPEEPPRVEYRLTEKGRDLL   91 (120)
T ss_pred             HHHHHHhc-CCCcHHHHHHHccccCHHHHHHHHHHHHHC-CCEEeeecCCCCceeEEEEhhhHHHHH
Confidence            36666654 5667788888876 9999999999999987 999876664    89999999998744

>COG4742 Predicted transcriptional regulator [Transcription]

Probab=94.18  E-value=0.13  Score=48.43  Aligned_cols=78  Identities=12%  Similarity=0.190  Sum_probs=66.9

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHHhhc
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNNV   82 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~~~l   82 (292)
                      +...++||.+|.+ ++-+.+++-..++++..+++..++.|... |+|.-+   ...|.||+.|+-.+.+-.|=...++++
T Consensus        12 SekRk~lLllL~e-gPkti~EI~~~l~vs~~ai~pqiKkL~~~-~LV~~~---~~~Y~LS~~G~iiv~km~~ll~tl~v~   86 (260)
T COG4742          12 SEKRKDLLLLLKE-GPKTIEEIKNELNVSSSAILPQIKKLKDK-GLVVQE---GDRYSLSSLGKIIVEKMEPLLDTLEVF   86 (260)
T ss_pred             cHHHHHHHHHHHh-CCCCHHHHHHHhCCCcHHHHHHHHHHhhC-CCEEec---CCEEEecchHHHHHHHHHHHHHHHHHH
Confidence            3567789999986 56688999999999999999999999986 998744   789999999999999998888888888


Q ss_pred             CCC
Q psy10346         83 PSE   85 (292)
Q Consensus        83 ~~~   85 (292)
                      .++
T Consensus        87 e~n   89 (260)
T COG4742          87 EEN   89 (260)
T ss_pred             Hhh
Confidence            643

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=94.08  E-value=0.35  Score=40.12  Aligned_cols=65  Identities=11%  Similarity=0.137  Sum_probs=53.7

Q ss_pred             CCcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeE-EEEEeChhHH
Q psy10346          1 MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSH-KIWELTGEGN   66 (292)
Q Consensus         1 m~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~-~~~~LTeEG~   66 (292)
                      ++++...+||..|...++...-++++.+|+++..|..-++-|+.. |+|+.++.-. ..|.|.+...
T Consensus        13 LadptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~A-GLV~~~r~Gr~~~Y~l~~~~~   78 (117)
T PRK10141         13 LSDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRES-GLLLDRKQGKWVHYRLSPHIP   78 (117)
T ss_pred             hCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CceEEEEEcCEEEEEECchHH
Confidence            456788899999976667788999999999999999999999986 9999866644 5678876543

>COG3432 Predicted transcriptional regulator [Transcription]

Probab=93.97  E-value=0.11  Score=41.81  Aligned_cols=64  Identities=16%  Similarity=0.197  Sum_probs=47.8

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee-EEEEEeChhHHHHhh
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS-HKIWELTGEGNQVKD   70 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~-~~~~~LTeEG~~yl~   70 (292)
                      +-..||++. ..+.+....+.-..|++.......+..|.++ |++...... ...|.||+.|++.++
T Consensus        19 Ii~dIL~~~-~~~~~~~Tri~y~aNlny~~~~~yi~~L~~~-Gli~~~~~~~~~~y~lT~KG~~fle   83 (95)
T COG3432          19 IIFDILKAI-SEGGIGITRIIYGANLNYKRAQKYIEMLVEK-GLIIKQDNGRRKVYELTEKGKRFLE   83 (95)
T ss_pred             HHHHHHHHh-cCCCCCceeeeeecCcCHHHHHHHHHHHHhC-CCEEeccCCccceEEEChhHHHHHH
Confidence            344566663 4555555667777899999999999999987 966665444 559999999999763

>PRK06253 O-phosphoseryl-tRNA synthetase; Reviewed

Probab=93.93  E-value=0.051  Score=55.47  Aligned_cols=40  Identities=28%  Similarity=0.490  Sum_probs=34.1

Q ss_pred             CCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccc
Q psy10346        211 MGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESS  251 (292)
Q Consensus       211 ~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~  251 (292)
                      |-..+..|+.||+...++++|+...+|||+||- +|.|..+
T Consensus        37 p~~~~~~~~~hp~~~ti~~lr~ayl~~gf~e~~-np~iv~~   76 (529)
T PRK06253         37 PRLKPSYGKPHPVYDTIERLREAYLRMGFEEMI-NPVIVDE   76 (529)
T ss_pred             CcccccCCCCCcHHHHHHHHHHHHHhcChHhhc-CceeecH
Confidence            334567899999999999999999999999995 7877654

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=93.91  E-value=0.25  Score=37.59  Aligned_cols=63  Identities=11%  Similarity=0.128  Sum_probs=50.1

Q ss_pred             HHHHHHHHhccC-CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346          5 LTEKILKYLDTN-PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus         5 ~e~~iL~~L~~~-~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl   69 (292)
                      ....||..|... +.....++|..+|++...|.+.+..|.+. |+|.-.. ....|.|+.....+.
T Consensus         6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~-g~l~~~~-~~~~y~l~~~~~~~~   69 (91)
T smart00346        6 RGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQEL-GYVEQDG-QNGRYRLGPKVLELG   69 (91)
T ss_pred             HHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC-CCeeecC-CCCceeecHHHHHHH
Confidence            346788888765 67889999999999999999999999987 9997643 245688887665543

>PRK05638 threonine synthase; Validated

Probab=93.88  E-value=0.13  Score=51.19  Aligned_cols=65  Identities=20%  Similarity=0.224  Sum_probs=53.8

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcC--CCHHHHHHHHHHhhccCCcEEEe--eeeEEEEEeChhHHHHhh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFN--EDHQKVVGGMKSIETLGEYLIVE--PLSHKIWELTGEGNQVKD   70 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~--~~~~~v~~~~~~L~s~~glv~~e--~~~~~~~~LTeEG~~yl~   70 (292)
                      .....||..|..+ +....++++.++  ++...|.+.++.|+.. |||+..  +-....|.||+.|++++.
T Consensus       371 ~~r~~IL~~L~~~-~~~~~el~~~l~~~~s~~~v~~hL~~Le~~-GLV~~~~~~g~~~~Y~Lt~~g~~~l~  439 (442)
T PRK05638        371 GTKLEILKILSER-EMYGYEIWKALGKPLKYQAVYQHIKELEEL-GLIEEAYRKGRRVYYKLTEKGRRLLE  439 (442)
T ss_pred             chHHHHHHHHhhC-CccHHHHHHHHcccCCcchHHHHHHHHHHC-CCEEEeecCCCcEEEEECcHHHHHHH
Confidence            4577899999854 567799999998  8889999999999986 999864  334678999999999875

>COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]

Probab=93.87  E-value=0.13  Score=41.18  Aligned_cols=43  Identities=21%  Similarity=0.319  Sum_probs=34.7

Q ss_pred             cCCCHHHHHHHHHHhhccCCcEEE-eeeeEEEEEeChhHHHHhhc
Q psy10346         28 FNEDHQKVVGGMKSIETLGEYLIV-EPLSHKIWELTGEGNQVKDN   71 (292)
Q Consensus        28 ~~~~~~~v~~~~~~L~s~~glv~~-e~~~~~~~~LTeEG~~yl~~   71 (292)
                      ++++---|+.++++|-|+ |+|+. ..=....|.||+||.+||++
T Consensus        35 l~ipNL~vika~qsl~S~-GYvkt~~~W~~~YytLT~eGveyLRE   78 (105)
T COG5045          35 LEIPNLHVIKAMQSLISY-GYVKTIHVWRHSYYTLTPEGVEYLRE   78 (105)
T ss_pred             cCCCchHHHHHHHHHhhc-ceeEEEeeeeeeEEEecHHHHHHHHH
Confidence            355555689999999997 99987 45566778999999999964

>TIGR00470 sepS O-phosphoseryl-tRNA(Cys) synthetase

Probab=93.82  E-value=0.056  Score=54.80  Aligned_cols=40  Identities=33%  Similarity=0.605  Sum_probs=34.0

Q ss_pred             CCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccc
Q psy10346        211 MGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESS  251 (292)
Q Consensus       211 ~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~  251 (292)
                      |-..+..|+.||+...++++|+...+|||+||- +|.|..+
T Consensus        37 pr~~~~~gk~hpv~~ti~~lreayl~~gf~e~~-np~iv~e   76 (533)
T TIGR00470        37 PRLKFVYGKPHPLMETIERLREAYLRMGFSEMV-NPLIVDE   76 (533)
T ss_pred             CcccccCCCCCcHHHHHHHHHHHHHhcChHhhc-CceeecH
Confidence            334567899999999999999999999999995 7877654

This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains. Recently, it was shown to act in a proposed pathway of tRNA(Cys) indirect aminoacylation, resulting in Cys biosynthesis from O-phosphoserine, in certain archaea. It charges tRNA(Cys) with O-phosphoserine. The pscS gene product converts the phosphoserine to Cys.

>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=93.75  E-value=0.15  Score=34.94  Aligned_cols=45  Identities=20%  Similarity=0.254  Sum_probs=39.0

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI   50 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~   50 (292)
                      +...+||.+|.+ ++.+..++++.+|+++..|..-++.|+.. |+|+
T Consensus         2 ~~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~-glV~   46 (47)
T PF01022_consen    2 PTRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREA-GLVE   46 (47)
T ss_dssp             HHHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHT-TSEE
T ss_pred             HHHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHC-cCee
Confidence            456789999986 67788999999999999999999999987 9986

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 ....

>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor

Probab=93.61  E-value=0.36  Score=41.28  Aligned_cols=74  Identities=16%  Similarity=0.156  Sum_probs=52.4

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHh------cCCCHHHHHHHHHHhhccCCcEEEeee------eEEEEEeChhHHHHhhc
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKL------FNEDHQKVVGGMKSIETLGEYLIVEPL------SHKIWELTGEGNQVKDN   71 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~------~~~~~~~v~~~~~~L~s~~glv~~e~~------~~~~~~LTeEG~~yl~~   71 (292)
                      .++.-||..|..+.. --.++.+.      ..+++..|-.+++.|+.. |+|.....      ..+.|.||+.|++++..
T Consensus        24 ~l~~~IL~~L~~~p~-hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~-GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~  101 (138)
T TIGR02719        24 FLVPFLLLCLKDWNL-HGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKD-NLISSQWDTSAEGPAKRIYSLTDAGEQYLSM  101 (138)
T ss_pred             HHHHHHHHHHccCCC-CHHHHHHHHHHcCCCCCCcChHHHHHHHHHHC-CCEEEEeeecCCCCCcEEEEECHHHHHHHHH
Confidence            456678888876442 22333332      246788999999999986 99987432      25889999999999977


Q ss_pred             CChHHHHH
Q psy10346         72 GSHEVLVF   79 (292)
Q Consensus        72 GlPE~rl~   79 (292)
                      -..+.+.+
T Consensus       102 ~~~~w~~~  109 (138)
T TIGR02719       102 CANSFEHY  109 (138)
T ss_pred             HHHHHHHH
Confidence            66665543

Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).

>PHA02943 hypothetical protein; Provisional

Probab=93.58  E-value=0.38  Score=41.95  Aligned_cols=74  Identities=18%  Similarity=0.180  Sum_probs=54.6

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE-eeeeEEEEEeChhHHHHhhcCChHHH--HHhhc
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV-EPLSHKIWELTGEGNQVKDNGSHEVL--VFNNV   82 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~-e~~~~~~~~LTeEG~~yl~~GlPE~r--l~~~l   82 (292)
                      -.+||..| ..|..++.++|+.+|+++.++-..++-|+.. |+|.- +.-....|.|.+  ..|+ ++--+..  ++.+|
T Consensus        13 ~~eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErE-G~VkrV~~G~~tyw~l~~--day~-~~v~~~~Relwrlv   87 (165)
T PHA02943         13 MIKTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKE-GMVLKVEIGRAAIWCLDE--DAYT-NLVFEIKRELWRLV   87 (165)
T ss_pred             HHHHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHc-CceEEEeecceEEEEECh--HHHH-HHHHHHHHHHHHHH
Confidence            35688888 6777788999999999999999999999976 88766 445578889998  4444 3333332  55555


Q ss_pred             CC
Q psy10346         83 PS   84 (292)
Q Consensus        83 ~~   84 (292)
                      ..
T Consensus        88 ~s   89 (165)
T PHA02943         88 CN   89 (165)
T ss_pred             Hh
Confidence            43

>TIGR02367 PylS pyrrolysyl-tRNA synthetase

Probab=93.58  E-value=0.11  Score=52.37  Aligned_cols=57  Identities=16%  Similarity=0.216  Sum_probs=43.4

Q ss_pred             CCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeec
Q psy10346        216 PSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVT  276 (292)
Q Consensus       216 ~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~  276 (292)
                      ..|+.||+..+.+.||++|.++||.|+. .|.+++. -.||.+..+.+++  -.++.|.++
T Consensus       235 TiG~~~~~~~Led~IRevfvg~GFqEV~-TPtLt~e-E~~E~m~~~~g~e--I~n~Iyk~e  291 (453)
T TIGR02367       235 AEDREDYLGKLERDITKFFVDRGFLEIK-SPILIPA-EYIERMGIDNDTE--LSKQIFRVD  291 (453)
T ss_pred             ccCcccHHHHHHHHHHHHHHHCCCEEEE-CCeecch-HHHHhhcCccCCc--ccccceEec
Confidence            6799999999999999999999999996 4777533 3468888776644  234555543

PylS is the archaeal enzyme responsible for charging the pyrrolysine tRNA, PylT, by ligating a free molecule of pyrrolysine. Pyrrolysine is encoded at an in-frame UAG (amber) at least in several corrinoid-dependent methyltransferases of the archaeal genera Methanosarcina and Methanococcoides, such as trimethylamine methyltransferase.

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=93.50  E-value=0.17  Score=40.02  Aligned_cols=46  Identities=22%  Similarity=0.281  Sum_probs=42.3

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI   50 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~   50 (292)
                      ..+.+||..|..++.....++|+.+|++...|.+.+..|+.. |+|.
T Consensus         3 ~~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~-g~i~   48 (108)
T smart00344        3 EIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEE-GVIK   48 (108)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCee
Confidence            468899999988888888999999999999999999999987 9987

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

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=93.45  E-value=0.16  Score=37.73  Aligned_cols=46  Identities=20%  Similarity=0.247  Sum_probs=37.8

Q ss_pred             HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP   53 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~   53 (292)
                      .+|+..|...+.++..+||..++++++.|...+.-|..+ |+|.-..
T Consensus         3 ~~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~k-G~I~~~~   48 (69)
T PF09012_consen    3 QEIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRK-GYIRKVD   48 (69)
T ss_dssp             HHHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCC-TSCEEEE
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CcEEEec
Confidence            467888988999999999999999999999999999987 9887543

FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.

>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=93.34  E-value=0.19  Score=36.74  Aligned_cols=45  Identities=22%  Similarity=0.282  Sum_probs=36.5

Q ss_pred             HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346          8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP   53 (292)
Q Consensus         8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~   53 (292)
                      .|+..-..++.+.+.++|+.+|+++.+|..+++.|+.+ |||+.+.
T Consensus        12 ~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~-GlV~~~~   56 (60)
T PF01325_consen   12 AIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEK-GLVEYEP   56 (60)
T ss_dssp             HHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHT-TSEEEET
T ss_pred             HHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHC-CCEEecC
Confidence            34444455667889999999999999999999999986 9998764

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 ....

>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU

Probab=93.34  E-value=0.15  Score=47.78  Aligned_cols=68  Identities=13%  Similarity=0.163  Sum_probs=57.9

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      +.+..|...|.+ +..+.+++|+.+|++...+-+.+..|.+. |+++..   ...|.+|+.+..++..++|.+
T Consensus        10 a~~Lglfd~L~~-gp~t~~eLA~~~~~~~~~~~~lL~~L~~l-gll~~~---~~~y~~t~~~~~~l~~~~~~~   77 (306)
T TIGR02716        10 AIELDLFSHMAE-GPKDLATLAADTGSVPPRLEMLLETLRQM-RVINLE---DGKWSLTEFADYMFSPTPKEP   77 (306)
T ss_pred             HHHcCcHHHHhc-CCCCHHHHHHHcCCChHHHHHHHHHHHhC-CCeEec---CCcEecchhHHhhccCCccch
Confidence            456677888865 56788999999999999999999999998 999864   368999999999998888753

Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=93.22  E-value=0.32  Score=32.74  Aligned_cols=45  Identities=20%  Similarity=0.296  Sum_probs=39.3

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      +..||..|..++..+..+++..++++...|.+.+..|..+ |+|..
T Consensus         2 ~~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~-g~i~~   46 (53)
T smart00420        2 QQQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQ-GLLTR   46 (53)
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEE
Confidence            4678888877777889999999999999999999999987 89864

>COG2024 Phenylalanyl-tRNA synthetase alpha subunit (archaeal type) [Translation, ribosomal structure and biogenesis]

Probab=93.06  E-value=0.073  Score=52.58  Aligned_cols=40  Identities=30%  Similarity=0.605  Sum_probs=33.8

Q ss_pred             CCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccc
Q psy10346        211 MGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESS  251 (292)
Q Consensus       211 ~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~  251 (292)
                      |-.....|+.||+...++++|+...+|||+||. +|.|..+
T Consensus        37 PRl~f~~Gk~Hpl~~TIq~lReAYLr~GF~Emv-NPlivde   76 (536)
T COG2024          37 PRLKFETGKPHPLYETIQRLREAYLRMGFSEMV-NPLIVDE   76 (536)
T ss_pred             CccccccCCcCcHHHHHHHHHHHHHHhhHHHhc-CccccCH
Confidence            334556799999999999999999999999996 7877654

>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=93.03  E-value=0.22  Score=34.84  Aligned_cols=45  Identities=20%  Similarity=0.423  Sum_probs=36.1

Q ss_pred             HHHHHHHh-ccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe
Q psy10346          6 TEKILKYL-DTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE   52 (292)
Q Consensus         6 e~~iL~~L-~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e   52 (292)
                      +.+||..| ..++.++..++|+.+|++...|.+.++.|++. | +.++
T Consensus         2 ~~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~-~-~~I~   47 (55)
T PF08279_consen    2 QKQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREW-G-IPIE   47 (55)
T ss_dssp             HHHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHT-T--EEE
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC-C-CeEE
Confidence            56788888 55556899999999999999999999999976 6 4443

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 ....

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=92.70  E-value=0.27  Score=42.43  Aligned_cols=47  Identities=13%  Similarity=0.286  Sum_probs=43.5

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI   50 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~   50 (292)
                      .....+||..|..++.....++|+..|++...|.+-++.|+.. |+|+
T Consensus        13 D~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~-GvI~   59 (164)
T PRK11169         13 DRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQ-GFIQ   59 (164)
T ss_pred             HHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeE
Confidence            3578999999999999999999999999999999999999987 9986

>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation

Probab=92.63  E-value=0.24  Score=41.22  Aligned_cols=51  Identities=20%  Similarity=0.169  Sum_probs=46.0

Q ss_pred             HHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHH
Q psy10346         23 DLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus        23 ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      .+|..++++.+.++.++.-++-. |++++..   -.+.||+.|+++++.+..|++
T Consensus         2 ~La~~l~~eiDdL~p~~eAaelL-gf~~~~~---Gdi~LT~~G~~f~~a~~~~rK   52 (120)
T PF09821_consen    2 QLADELHLEIDDLLPIVEAAELL-GFAEVEE---GDIRLTPLGRRFAEADIDERK   52 (120)
T ss_pred             chHHHhCCcHHHHHHHHHHHHHc-CCeeecC---CcEEeccchHHHHHCChHHHH
Confidence            47888999999999999999988 9999865   578999999999999999988

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=92.61  E-value=0.26  Score=41.98  Aligned_cols=47  Identities=19%  Similarity=0.194  Sum_probs=43.7

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      ....+||..|..++.....++|+.+|++..+|.+-++.|++. |+|..
T Consensus         9 ~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~-GvI~~   55 (153)
T PRK11179          9 NLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQA-GIITG   55 (153)
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeee
Confidence            678999999998999999999999999999999999999997 99874

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=92.53  E-value=1.5  Score=36.77  Aligned_cols=91  Identities=10%  Similarity=0.086  Sum_probs=60.5

Q ss_pred             cHHHHHHHHHhccCCCCChHHH----HHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEE--eChhHH------HH-
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDL----AKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWE--LTGEGN------QV-   68 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~el----a~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~--LTeEG~------~y-   68 (292)
                      .+.|..|+..|=..+...+.++    ++..++++..|...+..|..| |+|..... ....|.  .|++--      +. 
T Consensus         3 t~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~K-G~v~~~k~gr~~~Y~p~vs~ee~~~~~~~~~~   81 (130)
T TIGR02698         3 SDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDK-GCLTTEKEGRKFIYTALVSEDEAVENAAQELF   81 (130)
T ss_pred             CHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHC-CceeeecCCCcEEEEecCCHHHHHHHHHHHHH
Confidence            3678889999965667777774    444588999999999999986 99986532 233555  343322      11 


Q ss_pred             --hhcCChHHHHHhhcCCCCCChHHHhh
Q psy10346         69 --KDNGSHEVLVFNNVPSEGIGQKELLA   94 (292)
Q Consensus        69 --l~~GlPE~rl~~~l~~~~~~~~el~~   94 (292)
                        +=.|++..-|..++.+..++.+|+.+
T Consensus        82 ~~~f~gs~~~ll~~l~~~~~ls~eele~  109 (130)
T TIGR02698        82 SRICSRKVGAVIADLIEESPLSQTDIEK  109 (130)
T ss_pred             HHHHCCCHHHHHHHHHhcCCCCHHHHHH
Confidence              22467776666666655566666554

This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=92.30  E-value=0.31  Score=40.70  Aligned_cols=50  Identities=18%  Similarity=0.280  Sum_probs=44.9

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP   53 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~   53 (292)
                      .+.+.+||..|+.++.....++|+..|++..+|..-++.|+.. |+|+-..
T Consensus         7 D~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~-GiI~~~~   56 (154)
T COG1522           7 DDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEE-GVIKGYT   56 (154)
T ss_pred             cHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CceeeEE
Confidence            5788999999998888888999999999999999999999987 9887533

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=92.28  E-value=0.32  Score=45.63  Aligned_cols=59  Identities=14%  Similarity=0.166  Sum_probs=48.8

Q ss_pred             HHHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE-EeCh
Q psy10346          4 DLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW-ELTG   63 (292)
Q Consensus         4 ~~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~-~LTe   63 (292)
                      +.++.||+++.. +|.+.-.|+.+++|++...|-++++.|+.+ |||+.++.-.+.+ +|.+
T Consensus       195 ~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~-GlIe~~K~G~~n~V~l~~  255 (258)
T COG2512         195 EDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKR-GLIEKEKKGRTNIVELRD  255 (258)
T ss_pred             HHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhC-CceEEEEeCCeeEEEEec
Confidence            578899999965 556888999999999999999999999976 9999977765544 4443

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=92.20  E-value=0.38  Score=35.81  Aligned_cols=50  Identities=18%  Similarity=0.404  Sum_probs=39.0

Q ss_pred             cHHHHHHHHHhcc----CC-CCChHHHHHhcCCC-HHHHHHHHHHhhccCCcEEEee
Q psy10346          3 SDLTEKILKYLDT----NP-PVDTLDLAKLFNED-HQKVVGGMKSIETLGEYLIVEP   53 (292)
Q Consensus         3 ~~~e~~iL~~L~~----~~-~~~~~ela~~~~~~-~~~v~~~~~~L~s~~glv~~e~   53 (292)
                      ...|.+||..+.+    ++ .-+..|+|+.+|+. +..|...++.|+.+ |+|+-..
T Consensus         5 T~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~k-G~I~r~~   60 (65)
T PF01726_consen    5 TERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERK-GYIRRDP   60 (65)
T ss_dssp             -HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHT-TSEEEGC
T ss_pred             CHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC-cCccCCC
Confidence            4778999998854    33 34669999999997 99999999999987 9998643

The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=92.18  E-value=0.44  Score=40.20  Aligned_cols=50  Identities=20%  Similarity=0.302  Sum_probs=41.7

Q ss_pred             HHHHHHHHHhc-cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346          4 DLTEKILKYLD-TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL   54 (292)
Q Consensus         4 ~~e~~iL~~L~-~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~   54 (292)
                      ..+..++.+|- .+++.+.+++|+.+|.+.+.|-++++.|... |+|.-+..
T Consensus        27 ~~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~-GlV~Rek~   77 (126)
T COG3355          27 ELDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEA-GLVEREKV   77 (126)
T ss_pred             HHHHHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHc-CCeeeeee
Confidence            45566776665 6888999999999999999999999999987 99875443

>PRK00215 LexA repressor; Validated

Probab=92.09  E-value=0.41  Score=42.39  Aligned_cols=66  Identities=15%  Similarity=0.271  Sum_probs=53.7

Q ss_pred             CCcHHHHHHHHHhcc-----CCCCChHHHHHhcCC-CHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHH
Q psy10346          1 MASDLTEKILKYLDT-----NPPVDTLDLAKLFNE-DHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQ   67 (292)
Q Consensus         1 m~~~~e~~iL~~L~~-----~~~~~~~ela~~~~~-~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~   67 (292)
                      |-...|..||..|..     +......++|..+|+ ++.+|.+.+..|+.+ |+|+-.......+.|+.+|.-
T Consensus         1 ~lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~-g~i~~~~~~~r~~~l~~~~~~   72 (205)
T PRK00215          1 MLTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERK-GFIRRDPGRSRAIEVAAPAQL   72 (205)
T ss_pred             CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC-CCEEeCCCCcceEEecccccc
Confidence            445778999998852     334577899999999 999999999999987 999888777778888777654

>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3

Probab=92.05  E-value=0.068  Score=39.97  Aligned_cols=63  Identities=24%  Similarity=0.253  Sum_probs=45.5

Q ss_pred             CCcHHHHHHHHHhccCCCCChHHHHHh--cCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChh
Q psy10346          1 MASDLTEKILKYLDTNPPVDTLDLAKL--FNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGE   64 (292)
Q Consensus         1 m~~~~e~~iL~~L~~~~~~~~~ela~~--~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeE   64 (292)
                      |..+.+.+||.+|.+.+......+|..  ++.+...|-+.+..|+.. |.|..+...--.|.||+.
T Consensus         1 ~~~~~ee~Il~~L~~~g~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~-g~v~k~~~~PP~W~l~~~   65 (66)
T PF02295_consen    1 DMQDLEEKILDFLKELGGSTATAIAKALGLSVPKKEVNRVLYRLEKQ-GKVCKEGGTPPKWSLTEK   65 (66)
T ss_dssp             HHHHHHHHHHHHHHHHTSSEEEHHHHHHHHTS-HHHHHHHHHHHHHT-TSEEEECSSSTEEEE-HC
T ss_pred             CchhHHHHHHHHHHhcCCccHHHHHHHhCcchhHHHHHHHHHHHHHC-CCEeeCCCCCCceEeccC
Confidence            345788999999977554444445544  555589999999999986 999877767777887753

5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=91.93  E-value=0.2  Score=35.00  Aligned_cols=45  Identities=13%  Similarity=0.152  Sum_probs=36.9

Q ss_pred             HHHHHHHhccCCC-CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          6 TEKILKYLDTNPP-VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         6 e~~iL~~L~~~~~-~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      -.+||.+|...+. ....++|+.+|++...+.+.+..|... |+|.-
T Consensus         5 al~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~-g~v~~   50 (52)
T PF09339_consen    5 ALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEE-GYVER   50 (52)
T ss_dssp             HHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT-TSEEE
T ss_pred             HHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-cCeec
Confidence            3468888865544 578999999999999999999999987 99874

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.

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=91.91  E-value=0.63  Score=41.24  Aligned_cols=60  Identities=13%  Similarity=0.001  Sum_probs=48.5

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeE-------EEEEeChhH
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSH-------KIWELTGEG   65 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~-------~~~~LTeEG   65 (292)
                      ....||.+|..++.++.+++|..+|+...+|-+.+..|... |||...+...       ..|.||.+-
T Consensus        23 ~~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~-gLv~~~r~r~~~~Gr~~y~w~l~~~~   89 (178)
T PRK06266         23 EGFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDA-RLADYKREKDEETNWYTYTWKPELEK   89 (178)
T ss_pred             cHhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCeEEeeeeccCCCcEEEEEEeCHHH
Confidence            34678898888788899999999999999999999999987 9999755333       356676543

>PRK06474 hypothetical protein; Provisional

Probab=91.38  E-value=0.78  Score=40.44  Aligned_cols=67  Identities=18%  Similarity=0.263  Sum_probs=54.8

Q ss_pred             CCcHHHHHHHHHhccCCC-CChHHHHHhc-CCCHHHHHHHHHHhhccCCcEEEeee------eEEEEEeChhHHHH
Q psy10346          1 MASDLTEKILKYLDTNPP-VDTLDLAKLF-NEDHQKVVGGMKSIETLGEYLIVEPL------SHKIWELTGEGNQV   68 (292)
Q Consensus         1 m~~~~e~~iL~~L~~~~~-~~~~ela~~~-~~~~~~v~~~~~~L~s~~glv~~e~~------~~~~~~LTeEG~~y   68 (292)
                      ++++...+||..|...+. .+..+++..+ +++...|-+-++.|+.. |+|.....      ....|.++.++-..
T Consensus         8 La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~-GLI~~~~~~~~~~~~ek~y~~~~~~~~~   82 (178)
T PRK06474          8 LMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDS-GILHVVKEKKVRSVSEKYYAINEEDAKI   82 (178)
T ss_pred             hCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHC-CCEEEeecccccCceeEEEEeccceeee
Confidence            357888999999976654 8889999988 78999999999999986 99997543      34789999887653

>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]

Probab=91.14  E-value=0.47  Score=43.03  Aligned_cols=67  Identities=19%  Similarity=0.237  Sum_probs=52.1

Q ss_pred             HHHHHhccCC-----CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHhhcCChH
Q psy10346          8 KILKYLDTNP-----PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVKDNGSHE   75 (292)
Q Consensus         8 ~iL~~L~~~~-----~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl~~GlPE   75 (292)
                      ++|+.|..-+     .+++.++|+.++.+.+...+.+++|+.. |+|.-+. ..-+...+||.|.+.|.+=.-+
T Consensus         4 ~~lk~l~~~~a~~~~~~t~~ela~~l~~S~qta~R~l~~le~~-~~I~R~~~~~Gq~i~iTekG~~~L~~~~~d   76 (214)
T COG1339           4 RLLKKLALRGAVRGVKVTSSELAKRLGVSSQTAARKLKELEDE-GYITRTISKRGQLITITEKGIDLLYKEYED   76 (214)
T ss_pred             HHHHHHHHhhhhcCccccHHHHHHHhCcCcHHHHHHHHhhccC-CcEEEEecCCCcEEEehHhHHHHHHHHHHH
Confidence            5666664322     2678999999999999999999999976 8888655 5667789999999988554333

>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=90.97  E-value=0.56  Score=31.90  Aligned_cols=40  Identities=23%  Similarity=0.335  Sum_probs=33.1

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIE   43 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~   43 (292)
                      .+..+||..|..++.....++|+..|++...|.+-+..|+
T Consensus         3 ~~D~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL~   42 (42)
T PF13404_consen    3 ELDRKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRLE   42 (42)
T ss_dssp             HHHHHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence            5678999999988888889999999999999999888774

...

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

Probab=90.85  E-value=0.78  Score=36.25  Aligned_cols=49  Identities=14%  Similarity=0.123  Sum_probs=38.7

Q ss_pred             HHHHHHHHHhc--------cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346          4 DLTEKILKYLD--------TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP   53 (292)
Q Consensus         4 ~~e~~iL~~L~--------~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~   53 (292)
                      ..+.++|..|.        ....++..++|+.+|++++.|.+++..|+.+ |+|..+.
T Consensus        25 ~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~-GlI~r~~   81 (95)
T TIGR01610        25 GREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARR-RIIFRQG   81 (95)
T ss_pred             HHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeeeec
Confidence            34556666664        2344677899999999999999999999987 9998654

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

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

Probab=90.55  E-value=0.3  Score=36.21  Aligned_cols=53  Identities=23%  Similarity=0.342  Sum_probs=40.1

Q ss_pred             HHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee---eeEEEEEe
Q psy10346          8 KILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP---LSHKIWEL   61 (292)
Q Consensus         8 ~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~---~~~~~~~L   61 (292)
                      +||..|.. +++..+.++|+.+|+++..+-..+..|+.. |.|+..+   -....|.|
T Consensus         4 ~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~e-G~V~~~~~~rG~~~~W~l   60 (62)
T PF04703_consen    4 KILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKE-GKVERSPVRRGKSTYWRL   60 (62)
T ss_dssp             CHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHC-TSEEEES-SSSSS-EEEE
T ss_pred             HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHC-CCEEEecCCCCcceeeee
Confidence            58888876 777899999999999999999999999976 9887533   22245555

>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain

Probab=90.16  E-value=1.1  Score=34.84  Aligned_cols=67  Identities=15%  Similarity=0.075  Sum_probs=50.3

Q ss_pred             cHHHHHHHHHhccCC---C-CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346          3 SDLTEKILKYLDTNP---P-VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD   70 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~---~-~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~   70 (292)
                      ++.+.+||.+++.+-   + +-.+.+++..|++++.+...+..|-.. ++|.-....-.-|.||-.|-+++.
T Consensus         5 ~~~d~rvL~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~-kLv~~~~~~Y~GYrLT~~GYD~LA   75 (82)
T PF09202_consen    5 SKEDFRVLRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKL-KLVSRRNKPYDGYRLTFLGYDYLA   75 (82)
T ss_dssp             -HHHHHHHHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHT-TSEEEE-SSS-EEEE-HHHHHHHH
T ss_pred             CHHHHHHHHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhc-CCccccCCCcceEEEeecchhHHH
Confidence            467889999997532   2 455788888999999999999999876 899986666678999999999873

It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.

>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]

Probab=90.13  E-value=0.41  Score=45.22  Aligned_cols=75  Identities=17%  Similarity=0.209  Sum_probs=67.0

Q ss_pred             cHHHHHHHHHhc-----cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHH
Q psy10346          3 SDLTEKILKYLD-----TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         3 ~~~e~~iL~~L~-----~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ++.|+.||.+|-     .++.+.++|+|..+|.++-.|-..+.||.+. |||+-..--+--|..|-.+-+.+..-.|+.-
T Consensus         5 T~~QkeIL~aLi~LY~~~~r~IKgeeIA~~l~rnpGTVRNqmq~LkaL-gLVegvpGPkGGY~PT~kAYe~L~iqt~~~~   83 (294)
T COG2524           5 TSSQKEILQALINLYRRKKRPIKGEEIAEVLNRNPGTVRNQMQSLKAL-GLVEGVPGPKGGYKPTSKAYEALSIQTLETE   83 (294)
T ss_pred             cHHHHHHHHHHHHHHHhcCCCcchHHHHHHHccCcchHHHHHHHHHhc-CccccccCCCCCccccHHHHHHhccCCCCcc
Confidence            689999999994     3667899999999999999999999999999 9999999999999999999999988887655


Q ss_pred             H
Q psy10346         78 V   78 (292)
Q Consensus        78 l   78 (292)
                      .
T Consensus        84 ~   84 (294)
T COG2524          84 F   84 (294)
T ss_pred             e
Confidence            4

>KOG3344|consensus

Probab=90.09  E-value=0.16  Score=43.44  Aligned_cols=41  Identities=24%  Similarity=0.355  Sum_probs=32.6

Q ss_pred             CCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHhhc
Q psy10346         30 EDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVKDN   71 (292)
Q Consensus        30 ~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl~~   71 (292)
                      ++--.||.+++||.|+ |||+..- =-..+|.||.||.+||++
T Consensus        37 vpNL~vikaMQSl~Sr-gYvkeqfaWrH~Yw~LTneGi~yLR~   78 (150)
T KOG3344|consen   37 VPNLHVIKAMQSLKSR-GYVKEQFAWRHFYWYLTNEGIEYLRE   78 (150)
T ss_pred             CccHHHHHHHHHHhhh-hhHHhhhhhheeeeeechhHHHHHHH
Confidence            4445689999999998 9998643 345677999999999965

>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=89.68  E-value=0.79  Score=32.67  Aligned_cols=42  Identities=12%  Similarity=0.234  Sum_probs=35.2

Q ss_pred             CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346         18 PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT   62 (292)
Q Consensus        18 ~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT   62 (292)
                      .+...++|+.+|+++..|.+.+..|+.. |+|....  ...|.||
T Consensus        25 ~~s~~ela~~~g~s~~tv~r~l~~L~~~-g~i~~~~--~~~~~l~   66 (67)
T cd00092          25 PLTRQEIADYLGLTRETVSRTLKELEEE-GLISRRG--RGKYRVN   66 (67)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEecC--CCeEEeC
Confidence            4677899999999999999999999987 9998765  3456665

>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX

Probab=89.56  E-value=0.49  Score=44.67  Aligned_cols=56  Identities=11%  Similarity=0.202  Sum_probs=46.1

Q ss_pred             HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHHHhhcCChHHHHHh
Q psy10346         22 LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQVKDNGSHEVLVFN   80 (292)
Q Consensus        22 ~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~yl~~GlPE~rl~~   80 (292)
                      ..+...+|++..+|..++..|.+. |+|+.+.. ....|.||+.|++.++.+  ..|++.
T Consensus        24 i~l~~~~gi~~~~vr~al~RL~~~-G~l~~~~~grr~~Y~LT~~g~~~l~~~--~~rIy~   80 (280)
T TIGR02277        24 IEFLAGLGINERLVRTAVSRLVAQ-GWLQSERKGRRSFYSLTDKGRRRFAAA--AQRIYD   80 (280)
T ss_pred             HHHHHhcCCCcchHHHHHHHHHHC-CCEEeeecCCCCEEEECHHHHHHHHHH--hhhhcC
Confidence            456777899999999999999986 99988643 358999999999999875  456665

This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=89.54  E-value=0.94  Score=41.84  Aligned_cols=62  Identities=16%  Similarity=0.112  Sum_probs=49.4

Q ss_pred             HHHHHHhccCC-CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346          7 EKILKYLDTNP-PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD   70 (292)
Q Consensus         7 ~~iL~~L~~~~-~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~   70 (292)
                      .+||..|...+ .+...+++..+|++...+.+.+..|+.. |||.-... ...|.||..+.++..
T Consensus        14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~-g~v~~~~~-~~~Y~Lg~~~~~l~~   76 (263)
T PRK09834         14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEE-GYVRRSAS-DDSFRLTLKVRQLSE   76 (263)
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEecC-CCcEEEcHHHHHHHH
Confidence            45788886544 4788999999999999999999999987 99985432 346999988766543

>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=89.46  E-value=0.55  Score=33.69  Aligned_cols=58  Identities=16%  Similarity=0.076  Sum_probs=40.7

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHH
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGN   66 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~   66 (292)
                      +.+++.++...+  +...-|+.+|+++..|.+.++.|+..-|.-=++ +....+.||+.|+
T Consensus         3 ~l~~f~~v~~~g--s~~~AA~~l~is~~~vs~~i~~LE~~lg~~Lf~-r~~~~~~lT~~G~   60 (60)
T PF00126_consen    3 QLRYFLAVAETG--SISAAAEELGISQSAVSRQIKQLEEELGVPLFE-RSGRGLRLTEAGE   60 (60)
T ss_dssp             HHHHHHHHHHHS--SHHHHHHHCTSSHHHHHHHHHHHHHHHTS-SEE-ECSSSEEE-HHHH
T ss_pred             HHHHHHHHHHhC--CHHHHHHHhhccchHHHHHHHHHHHHhCCeEEE-ECCCCeeEChhhC
Confidence            345566665544  467788899999999999999999865543233 3334599999996

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 ....

>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea

Probab=89.32  E-value=1.5  Score=35.54  Aligned_cols=91  Identities=19%  Similarity=0.152  Sum_probs=58.3

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhc----CCCHHHHHHHHHHhhccCCcEEEeeeeE-EEEEeChhHHHHh--------
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLF----NEDHQKVVGGMKSIETLGEYLIVEPLSH-KIWELTGEGNQVK--------   69 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~----~~~~~~v~~~~~~L~s~~glv~~e~~~~-~~~~LTeEG~~yl--------   69 (292)
                      .+.|..|+..|=+.+.+++.++.+.+    ++....|...+..|..| |+|+.+..-. ..|..+=.=++|+        
T Consensus         2 s~~E~~IM~~lW~~~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~K-g~l~~~~~gr~~~Y~p~is~~e~~~~~~~~~l   80 (115)
T PF03965_consen    2 SDLELEIMEILWESGEATVREIHEALPEERSWAYSTVQTLLNRLVEK-GFLTREKIGRAYVYSPLISREEYLAQELRQFL   80 (115)
T ss_dssp             -HHHHHHHHHHHHHSSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHT-TSEEEEEETTCEEEEESSSHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCCCCHHHHHHHHHhccccchhHHHHHHHHHHhC-CceeEeecCCceEEEeCCcHHHHHHHHHHHHH
Confidence            36788999999665667777776654    45699999999999987 9999976433 3354332222222        


Q ss_pred             ---hcCChHHHHHhhcCCCCCChHHHhh
Q psy10346         70 ---DNGSHEVLVFNNVPSEGIGQKELLA   94 (292)
Q Consensus        70 ---~~GlPE~rl~~~l~~~~~~~~el~~   94 (292)
                         -.|++..-+..++....++.+++..
T Consensus        81 ~~~~~gs~~~l~~~l~~~~~ls~~el~~  108 (115)
T PF03965_consen   81 DRLFDGSIPQLVAALVESEELSPEELEE  108 (115)
T ss_dssp             HHHSTTHHHHHHHHHHHCT-S-HHHHHH
T ss_pred             HHHhCCCHHHHHHHHHhcCCCCHHHHHH
Confidence               2567777777776655566665554

Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....

>COG4189 Predicted transcriptional regulator [Transcription]

Probab=89.22  E-value=0.66  Score=43.34  Aligned_cols=53  Identities=19%  Similarity=0.322  Sum_probs=46.5

Q ss_pred             CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee
Q psy10346          2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS   55 (292)
Q Consensus         2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~   55 (292)
                      |+.+.-+||..|...+..+..++|+..|++++.+..-++.|+.- |+|.++..+
T Consensus        21 aS~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~a-GlirT~t~k   73 (308)
T COG4189          21 ASKVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKA-GLIRTETVK   73 (308)
T ss_pred             HHHHHHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHHhc-Cceeeeeec
Confidence            45677789999988888999999999999999999999999975 999987653

>TIGR00498 lexA SOS regulatory protein LexA

Probab=88.57  E-value=0.63  Score=41.03  Aligned_cols=60  Identities=12%  Similarity=0.227  Sum_probs=48.2

Q ss_pred             cHHHHHHHHHhccC----C-CCChHHHHHhcCCC-HHHHHHHHHHhhccCCcEEEeeeeEEEEEeCh
Q psy10346          3 SDLTEKILKYLDTN----P-PVDTLDLAKLFNED-HQKVVGGMKSIETLGEYLIVEPLSHKIWELTG   63 (292)
Q Consensus         3 ~~~e~~iL~~L~~~----~-~~~~~ela~~~~~~-~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTe   63 (292)
                      .+.|.+||..|...    + ..+..++|+.+|++ ...|.+.+..|+.+ |+|+-+........+++
T Consensus         5 t~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~-g~i~~~~~~~~~~~~~~   70 (199)
T TIGR00498         5 TARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERK-GYIERDPGKPRAIRILD   70 (199)
T ss_pred             CHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHC-CCEecCCCCCCeEEeCC
Confidence            57899999999742    1 24568999999999 99999999999987 99998765555666664

LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.

>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea

Probab=88.38  E-value=0.82  Score=34.00  Aligned_cols=59  Identities=19%  Similarity=0.226  Sum_probs=43.3

Q ss_pred             HHHHHhcc-CCCCChHHHHHhc---CCC--HHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346          8 KILKYLDT-NPPVDTLDLAKLF---NED--HQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus         8 ~iL~~L~~-~~~~~~~ela~~~---~~~--~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl   69 (292)
                      -||..|.+ +.++....+++.+   |.+  .++|-+-++.|+.. |++.  ..-..-..||+.|.+.|
T Consensus         2 ~IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~-Glt~--~~g~~G~~iT~~G~~~L   66 (66)
T PF08461_consen    2 FILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERD-GLTR--KVGRQGRIITEKGLDEL   66 (66)
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHC-CCcc--ccCCcccccCHHHHhhC
Confidence            47888865 4557888887765   554  48999999999987 9766  34444568999998754

>COG1378 Predicted transcriptional regulators [Transcription]

Probab=88.36  E-value=0.85  Score=42.39  Aligned_cols=57  Identities=14%  Similarity=0.052  Sum_probs=47.8

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT   62 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT   62 (292)
                      -|-++..+|-..|..+..+++...|++...|-.++++|+.+ |+|.+..-.-..|+.-
T Consensus        17 yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~k-G~v~~~~g~P~~y~av   73 (247)
T COG1378          17 YEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKK-GLVEVIEGRPKKYRAV   73 (247)
T ss_pred             HHHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHHHC-CCEEeeCCCCceEEeC
Confidence            35566666666777889999999999999999999999987 9999987777777655

>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp

Probab=88.29  E-value=0.99  Score=34.47  Aligned_cols=61  Identities=16%  Similarity=0.219  Sum_probs=45.9

Q ss_pred             HHHHHHHHHhccCC---CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhH
Q psy10346          4 DLTEKILKYLDTNP---PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEG   65 (292)
Q Consensus         4 ~~e~~iL~~L~~~~---~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG   65 (292)
                      +...++|..|...+   .+++.++|+.+|+++..|.+.+..|... |+|+..+-..--|.|+...
T Consensus         8 ~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~-Gli~s~~G~~GGy~L~~~~   71 (83)
T PF02082_consen    8 DYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA-GLIESSRGRGGGYRLARPP   71 (83)
T ss_dssp             HHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT-TSEEEETSTTSEEEESS-C
T ss_pred             HHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC-CeeEecCCCCCceeecCCH
Confidence            34456677775433   2788999999999999999999999976 9999887767777776543

(strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=88.12  E-value=1.5  Score=30.10  Aligned_cols=37  Identities=14%  Similarity=0.191  Sum_probs=31.2

Q ss_pred             CCCC-ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346         16 NPPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP   53 (292)
Q Consensus        16 ~~~~-~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~   53 (292)
                      +..+ +..++|+.+|++...|.+++..|++. |+|....
T Consensus        17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~-g~i~~~~   54 (60)
T smart00345       17 GDKLPSERELAAQLGVSRTTVREALSRLEAE-GLVQRRP   54 (60)
T ss_pred             CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEec
Confidence            4445 67899999999999999999999986 9987543

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=88.00  E-value=1.1  Score=41.12  Aligned_cols=65  Identities=20%  Similarity=0.203  Sum_probs=50.4

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeCh----hHHHHhhcC
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG----EGNQVKDNG   72 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTe----EG~~yl~~G   72 (292)
                      -.+||..|...+.....++|+.+|++.+.+.+.+..|... |||.-. .....|.|+.    -|..|....
T Consensus        16 ~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~-G~l~~~-~~~~~Y~lG~~~~~lg~~~~~~~   84 (257)
T PRK15090         16 VFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTL-GYVAQE-GESEKYSLTLKLFELGAKALQNV   84 (257)
T ss_pred             HHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEc-CCCCcEEecHHHHHHHHHHHhhC
Confidence            3468888876666788999999999999999999999987 998754 3345688774    455555443

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=87.87  E-value=1.2  Score=41.24  Aligned_cols=48  Identities=8%  Similarity=0.028  Sum_probs=43.2

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      +..+.+||..|..++.+...++|+.+|++...|-+.++.|++. |++.-
T Consensus         4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~-g~i~r   51 (251)
T PRK13509          4 AQRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDES-GKLKK   51 (251)
T ss_pred             HHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEE
Confidence            4567889999999999999999999999999999999999987 88753

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=87.84  E-value=1.1  Score=41.86  Aligned_cols=47  Identities=15%  Similarity=0.210  Sum_probs=42.1

Q ss_pred             HHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346          6 TEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP   53 (292)
Q Consensus         6 e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~   53 (292)
                      -++||..|+. ++.+...++|...|++...+..+++.|++. |+|+...
T Consensus       185 v~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~a-GvIe~r~  232 (251)
T TIGR02787       185 VEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESA-GVIESRS  232 (251)
T ss_pred             HHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEecc
Confidence            3578999987 477888999999999999999999999997 9999887

This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.

>PF13814 Replic_Relax: Replication-relaxation

Probab=87.83  E-value=1.1  Score=38.76  Aligned_cols=61  Identities=16%  Similarity=0.183  Sum_probs=50.2

Q ss_pred             HHHhccCCCCChHHHHHhcCCCHH---HHHHHHHHhhccCCcEEEeee--------eEEEEEeChhHHHHhhc
Q psy10346         10 LKYLDTNPPVDTLDLAKLFNEDHQ---KVVGGMKSIETLGEYLIVEPL--------SHKIWELTGEGNQVKDN   71 (292)
Q Consensus        10 L~~L~~~~~~~~~ela~~~~~~~~---~v~~~~~~L~s~~glv~~e~~--------~~~~~~LTeEG~~yl~~   71 (292)
                      |..|...+.+++++++..++.+..   .+-+.++.|... |+|.....        ....|.||..|.+++..
T Consensus         1 L~~L~~~r~lt~~Qi~~l~~~~~~~~~~~~rrL~~L~~~-glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l~~   72 (191)
T PF13814_consen    1 LRLLARHRFLTTDQIARLLFPSSKSERTARRRLKRLREL-GLVDRFRRRVGARGGSQPYVYYLTPAGARLLAD   72 (191)
T ss_pred             ChhHHHhcCcCHHHHHHHHcCCCcchHHHHHHHHHHhhC-CcEEeecccccccCCCcceEEEECHHHHHHHHh
Confidence            455666777889999998887765   799999999876 99988665        55789999999999863

>PF11313 DUF3116: Protein of unknown function (DUF3116); InterPro: IPR021464 This family of proteins with unknown function appears to be restricted to Bacillales

Probab=87.53  E-value=1.9  Score=34.01  Aligned_cols=69  Identities=17%  Similarity=0.232  Sum_probs=44.6

Q ss_pred             CCcHHHHHHHHHhcc--CCCCChHHHHHh-------cCCCHHHHHHHHHHhhccCCcEEE-eeeeEEEEEeChhHHHHhh
Q psy10346          1 MASDLTEKILKYLDT--NPPVDTLDLAKL-------FNEDHQKVVGGMKSIETLGEYLIV-EPLSHKIWELTGEGNQVKD   70 (292)
Q Consensus         1 m~~~~e~~iL~~L~~--~~~~~~~ela~~-------~~~~~~~v~~~~~~L~s~~glv~~-e~~~~~~~~LTeEG~~yl~   70 (292)
                      |..+.+..|+..|..  +...+..++...       ......++.-.+.||+.. |+|.- .....+.|.+|+.|...++
T Consensus         1 M~~p~~~~I~~iL~~~~~~~~~i~~L~~e~~~~~~~~~~TKNelL~~vYWLE~n-gyI~R~~~~~~~rY~~T~kG~~ll~   79 (85)
T PF11313_consen    1 MEKPSEELIYQILNFVKDPNATINHLTFEFIDFPGAYDFTKNELLYTVYWLEEN-GYIFRDNNNNEKRYSLTEKGKELLA   79 (85)
T ss_pred             CCCccHHHHHHHHHHhcCccccHHHHHHHHHhccccccccHHHHHHHHHHHhhc-CeeEeecCCCcceeEEeccHHHHHH
Confidence            555555555555532  222333334332       234578999999999998 87765 5556677999999998664

>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea

Probab=87.53  E-value=1.4  Score=32.94  Aligned_cols=51  Identities=14%  Similarity=0.158  Sum_probs=42.7

Q ss_pred             HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346          8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW   59 (292)
Q Consensus         8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~   59 (292)
                      .|..+|..++..+..++++..|++...+..++-||.- +|=|.+++.....|
T Consensus        12 ~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLar-E~KI~~~~~~~~~~   62 (65)
T PF10771_consen   12 KVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLAR-ENKIEFEEKNGELY   62 (65)
T ss_dssp             HHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHC-TTSEEEEEETTEEE
T ss_pred             HHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhc-cCceeEEeeCCEEE
Confidence            5788898888889999999999999999999999975 58888877665554

The function is not known. ; PDB: 2L02_B 2L01_A.

>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]

Probab=87.12  E-value=0.94  Score=41.98  Aligned_cols=48  Identities=23%  Similarity=0.356  Sum_probs=43.6

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      +.-..+||..|..++.+...+||+.+|++...|-|.+..|++. |++.-
T Consensus         4 ~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~-g~l~R   51 (253)
T COG1349           4 EERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQ-GLLLR   51 (253)
T ss_pred             HHHHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHC-CcEEE
Confidence            4577889999999999999999999999999999999999987 87764

>TIGR00637 ModE_repress ModE molybdate transport repressor domain

Probab=87.11  E-value=1.9  Score=34.55  Aligned_cols=63  Identities=16%  Similarity=0.037  Sum_probs=46.8

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHh
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVK   69 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl   69 (292)
                      .+.++|.++.+.+.  ...-|+.+|+++.+|.+.++.|+..-|..=+++..    ..-++||+.|+.++
T Consensus         5 ~~l~~~~av~~~gS--is~AA~~L~iS~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~   71 (99)
T TIGR00637         5 RRVALLKAIARMGS--ISQAAKDAGISYKSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLI   71 (99)
T ss_pred             HHHHHHHHHHHhCC--HHHHHHHHCCCHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHH
Confidence            35567777766553  45678889999999999999999764544344432    35899999999877

ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.

>PRK09954 putative kinase; Provisional

Probab=86.97  E-value=1.3  Score=42.51  Aligned_cols=45  Identities=16%  Similarity=0.304  Sum_probs=41.3

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcE
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYL   49 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv   49 (292)
                      ..+++||..|.+++.+...++|+.+|++...|-..++.|+++ |+|
T Consensus         3 ~~~~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~-g~i   47 (362)
T PRK09954          3 NREKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRK-GRI   47 (362)
T ss_pred             hHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCc
Confidence            467789999998888899999999999999999999999986 887

>PRK03601 transcriptional regulator HdfR; Provisional

Probab=86.92  E-value=1.6  Score=39.79  Aligned_cols=64  Identities=11%  Similarity=-0.025  Sum_probs=49.2

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG   72 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G   72 (292)
                      +.+++..+.+.+  +...-|+.+++.+.+|.+.++.||+.=|. ..-.+....++||+.|+.+++.-
T Consensus         5 ~l~~f~~v~~~g--s~s~AA~~L~isqpavS~~I~~LE~~lG~-~LF~R~~r~~~lT~~G~~l~~~a   68 (275)
T PRK03601          5 LLKTFLEVSRTR--HFGRAAESLYLTQSAVSFRIRQLENQLGV-NLFTRHRNNIRLTAAGERLLPYA   68 (275)
T ss_pred             HHHHHHHHHHcC--CHHHHHHHhCCChHHHHHHHHHHHHHhCC-ceEEECCCceEECHhHHHHHHHH
Confidence            456666666555  34667888999999999999999986454 55666678899999999976443

>PF14338 Mrr_N: Mrr N-terminal domain

Probab=86.71  E-value=1.8  Score=33.73  Aligned_cols=32  Identities=13%  Similarity=0.285  Sum_probs=23.6

Q ss_pred             HHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346         38 GMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG   72 (292)
Q Consensus        38 ~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G   72 (292)
                      ++..|.. .|+|+  ....-.|.||++|++++.++
T Consensus        60 a~~~L~~-aGli~--~~~rG~~~iT~~G~~~l~~~   91 (92)
T PF14338_consen   60 ARSYLKK-AGLIE--RPKRGIWRITEKGRKALAEH   91 (92)
T ss_pred             HHHHHHH-CCCcc--CCCCCceEECHhHHHHHhhC
Confidence            3455665 48984  44477999999999998764

>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional

Probab=86.58  E-value=1.2  Score=39.89  Aligned_cols=63  Identities=16%  Similarity=0.210  Sum_probs=52.4

Q ss_pred             CCcHHHHHHHHHhccCC-CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChh
Q psy10346          1 MASDLTEKILKYLDTNP-PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGE   64 (292)
Q Consensus         1 m~~~~e~~iL~~L~~~~-~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeE   64 (292)
                      |+-+-+.+||..|...+ .+..-++|.++|++...|-+.+..|... |.|......--.|.++-+
T Consensus         1 ~~~~~~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~-~~v~~~~~~pP~W~~~~~   64 (183)
T PHA02701          1 MSCDCASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLES-DAVSCEDGCPPLWSVECE   64 (183)
T ss_pred             CcchHHHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhhc-CcEecCCCCCCccccccC
Confidence            77788999999998776 5788999999999999999999999976 899877666666655433

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=86.56  E-value=1.2  Score=41.28  Aligned_cols=48  Identities=19%  Similarity=0.280  Sum_probs=43.1

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      +.-+.+||..|...+.+...++|+.+|++...|-+.+..|+.. |+|.-
T Consensus         4 ~eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~-g~l~r   51 (256)
T PRK10434          4 RQRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHA-GTVIR   51 (256)
T ss_pred             HHHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEE
Confidence            5577889999999999999999999999999999999999986 87654

>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors

Probab=86.29  E-value=0.98  Score=36.00  Aligned_cols=51  Identities=16%  Similarity=0.034  Sum_probs=36.9

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeE
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSH   56 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~   56 (292)
                      ....||..|..++.+.-+++|..+|++...|-+.+..|... |+|.+.....
T Consensus        14 ~~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~-~lv~~~~~~d   64 (105)
T PF02002_consen   14 EAVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYED-GLVSYRRRKD   64 (105)
T ss_dssp             TTHHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHH-SS-EEEEE--
T ss_pred             hHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHC-CCeEEEEEEc
Confidence            34578888876777888999999999999999999999987 9998875433

Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=86.29  E-value=1.3  Score=41.02  Aligned_cols=48  Identities=13%  Similarity=0.239  Sum_probs=43.1

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      ...+.+||..|...+.+...++|+.++++...|.+.+..|++. |++.-
T Consensus         4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~-g~l~r   51 (252)
T PRK10906          4 TQRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQ-NKILR   51 (252)
T ss_pred             HHHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHC-CCEEE
Confidence            4567889999998998999999999999999999999999987 88753

>PRK11242 DNA-binding transcriptional regulator CynR; Provisional

Probab=86.17  E-value=1.7  Score=39.51  Aligned_cols=63  Identities=10%  Similarity=0.023  Sum_probs=48.6

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN   71 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~   71 (292)
                      +.+++.++.+.+  +...-|+.+|+++.+|.+.++.||+.-|. ..-.+....+.||++|+..++.
T Consensus         5 ~L~~f~~v~~~g--s~s~AA~~L~isqsavS~~i~~LE~~lg~-~Lf~R~~~~~~lT~~G~~l~~~   67 (296)
T PRK11242          5 HIRYFLAVAEHG--NFTRAAEALHVSQPTLSQQIRQLEESLGV-QLFDRSGRTVRLTDAGEVYLRY   67 (296)
T ss_pred             HHHHHHHHHHhC--CHHHHHHHcCCCchHHHHHHHHHHHHhCC-eeEeEcCCceeechhHHHHHHH
Confidence            345666665554  45677888999999999999999987444 5556678889999999987743

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=85.90  E-value=2.1  Score=37.09  Aligned_cols=48  Identities=6%  Similarity=-0.049  Sum_probs=41.5

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP   53 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~   53 (292)
                      ....||.+|-.++.++.+++|..+|++...|-+.+..|... |||...+
T Consensus        15 ~~v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~-~Lv~~~r   62 (158)
T TIGR00373        15 EVGLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDA-GLADYKR   62 (158)
T ss_pred             hHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCceeee
Confidence            44678888876778888999999999999999999999987 9997544

This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=85.73  E-value=2.3  Score=28.12  Aligned_cols=40  Identities=15%  Similarity=0.164  Sum_probs=32.5

Q ss_pred             CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346         19 VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT   62 (292)
Q Consensus        19 ~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT   62 (292)
                      ....++|..+|++...+.+.+..|++. |+|....   ..|.+|
T Consensus         9 ~s~~~la~~l~~s~~tv~~~l~~L~~~-g~l~~~~---~~~~i~   48 (48)
T smart00419        9 LTRQEIAELLGLTRETVSRTLKRLEKE-GLISREG---GRIVIL   48 (48)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEeC---CEEEEC
Confidence            456889999999999999999999987 9997653   345544

>PRK00082 hrcA heat-inducible transcription repressor; Provisional

Probab=85.60  E-value=1.4  Score=42.84  Aligned_cols=65  Identities=23%  Similarity=0.337  Sum_probs=56.5

Q ss_pred             CcHHHHHHHH-----HhccCCCCChHHHHHh--cCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHH
Q psy10346          2 ASDLTEKILK-----YLDTNPPVDTLDLAKL--FNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQV   68 (292)
Q Consensus         2 ~~~~e~~iL~-----~L~~~~~~~~~ela~~--~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~y   68 (292)
                      -+..+++||.     ++..++++.+.++|+.  +|++...|-+.+..|+.. |++. ......-...|+.|-+|
T Consensus         4 l~~R~~~Il~~IV~~yi~~~~pv~s~~l~~~~~l~~S~aTIR~dm~~Le~~-G~l~-~~h~sagrIPT~kGYR~   75 (339)
T PRK00082          4 LDERQREILRAIVEDYIATGEPVGSKTLSKRYGLGVSSATIRNDMADLEEL-GLLE-KPHTSSGRIPTDKGYRY   75 (339)
T ss_pred             cCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCCCChHHHHHHHHHHHhC-CCcC-CCcCCCCCCcCHHHHHH
Confidence            3567888998     6778888999999976  899999999999999987 9988 67777778999999887

>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT)

Probab=85.57  E-value=1.7  Score=32.86  Aligned_cols=43  Identities=19%  Similarity=0.262  Sum_probs=33.5

Q ss_pred             HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee-EEEEEeChhH
Q psy10346         22 LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS-HKIWELTGEG   65 (292)
Q Consensus        22 ~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~-~~~~~LTeEG   65 (292)
                      -++....|++..+|-.++..|.+. |+++.++.- ...|.||+.|
T Consensus        27 i~ll~~~Gv~e~avR~alsRl~~~-G~L~~~r~Gr~~~Y~Lt~~g   70 (70)
T PF07848_consen   27 IRLLAAFGVSESAVRTALSRLVRR-GWLESERRGRRSYYRLTERG   70 (70)
T ss_dssp             HHHHCCTT--HHHHHHHHHHHHHT-TSEEEECCCTEEEEEE-HHH
T ss_pred             HHHHHHcCCChHHHHHHHHHHHHc-CceeeeecCccceEeeCCCC
Confidence            455667899999999999999986 998886655 7889999987

PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.

>PRK09791 putative DNA-binding transcriptional regulator; Provisional

Probab=85.52  E-value=0.98  Score=41.53  Aligned_cols=65  Identities=9%  Similarity=0.052  Sum_probs=48.6

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG   72 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G   72 (292)
                      .+.+++..+.+.+  +...-|+.+|+.+.+|.+.++.||+.-|..=.+ +....+.||++|+.+++..
T Consensus         8 ~~L~~f~~v~~~g--s~s~AA~~L~isQ~avS~~i~~LE~~lG~~LF~-R~~r~~~lT~~G~~l~~~a   72 (302)
T PRK09791          8 HQIRAFVEVARQG--SIRGASRMLNMSQPALTKSIQELEEGLAAQLFF-RRSKGVTLTDAGESFYQHA   72 (302)
T ss_pred             HHHHHHHHHHHcC--CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEE-EcCCCceECccHHHHHHHH
Confidence            3444555555554  456778889999999999999999876664444 5667789999999987533

>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks

Probab=85.24  E-value=2.4  Score=32.03  Aligned_cols=50  Identities=18%  Similarity=0.320  Sum_probs=41.7

Q ss_pred             HHHHHHHHHhccCC--CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346          4 DLTEKILKYLDTNP--PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL   54 (292)
Q Consensus         4 ~~e~~iL~~L~~~~--~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~   54 (292)
                      +.++.+|..+...+  .+...+++..+|+|...+-..++.|+.. |||.-...
T Consensus         2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~-gLI~k~~~   53 (75)
T PF04182_consen    2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKK-GLIVKQSV   53 (75)
T ss_pred             chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHC-CCEEEEEe
Confidence            57899999996533  3566889999999999999999999987 99886555

This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.

>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase

Probab=85.22  E-value=3.6  Score=39.87  Aligned_cols=113  Identities=21%  Similarity=0.229  Sum_probs=72.4

Q ss_pred             cHHHHHHHHHhccC--C-CCChHHHHHh-cCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeC--hhHHHHhhcCChH
Q psy10346          3 SDLTEKILKYLDTN--P-PVDTLDLAKL-FNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELT--GEGNQVKDNGSHE   75 (292)
Q Consensus         3 ~~~e~~iL~~L~~~--~-~~~~~ela~~-~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LT--eEG~~yl~~GlPE   75 (292)
                      ..++.+||..+...  + .+..++|.+. .+++.+.++.++..|.+. |++++... ....|.+-  ++...+..--.-|
T Consensus         8 ~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~-~~~~~~~~~~~l~~~~~~~~~a~k~~~l~~~e   86 (327)
T PF05158_consen    8 SELEKKLLELCRENPSPKGFSQEDLQQLIPGLDLQELVKAINELLSS-GLLKLLKKGGGLSYKAVSEEEAKKLKGLSDEE   86 (327)
T ss_dssp             HHHHHHHHHHHHH---SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHH-TSEEEEE-SSSEEEEE--SSS-----SSSCCH
T ss_pred             HHHHHHHHHHHHHhcCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhC-CCEEEEEcCCEEEEEEeCHHHHhhhcCCCHHH
Confidence            36889999988654  2 3555778777 688999999999999987 88888553 44566665  5565555555566


Q ss_pred             HHHHhhcCC---CCCChHHHhhcC--C--chhhHHHHHHHcCCeeccc
Q psy10346         76 VLVFNNVPS---EGIGQKELLATF--P--NAKVGFSKAMAKGWISLDK  116 (292)
Q Consensus        76 ~rl~~~l~~---~~~~~~el~~~~--~--~~~ig~~~a~k~gwi~i~~  116 (292)
                      +.||.++.+   .|+-..+|+...  +  ...=.+..+-.++.|+--+
T Consensus        87 ~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vk  134 (327)
T PF05158_consen   87 RLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVK  134 (327)
T ss_dssp             HHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE-
T ss_pred             HHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEec
Confidence            668888874   468888998763  2  2333455566678887633

The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.

>PF13730 HTH_36: Helix-turn-helix domain

Probab=85.09  E-value=2.5  Score=29.30  Aligned_cols=45  Identities=18%  Similarity=0.206  Sum_probs=33.8

Q ss_pred             HHHHHHHHHhcc-----CCCC-ChHHHHHhcCCCHHHHHHHHHHhhccCCcE
Q psy10346          4 DLTEKILKYLDT-----NPPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYL   49 (292)
Q Consensus         4 ~~e~~iL~~L~~-----~~~~-~~~ela~~~~~~~~~v~~~~~~L~s~~glv   49 (292)
                      +.++.|+..|..     ++.. ..+.+|+.+|+....|.++++.|+.+ |+|
T Consensus         5 ~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~-G~I   55 (55)
T PF13730_consen    5 PTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEK-GLI   55 (55)
T ss_pred             HHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-cCC
Confidence            456666666632     2222 34899999999999999999999987 875

>PRK10094 DNA-binding transcriptional activator AllS; Provisional

Probab=84.96  E-value=2.9  Score=38.92  Aligned_cols=66  Identities=11%  Similarity=0.017  Sum_probs=50.5

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN   71 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~   71 (292)
                      .-.+.+++..+.+.+  +....|+++|+++.+|.+.++.||+.-|. ..-.+....+.||++|+.+++.
T Consensus         3 ~~~~L~~f~~v~e~g--s~s~AA~~L~iSQpavS~~I~~LE~~lg~-~Lf~R~~r~~~lT~~G~~l~~~   68 (308)
T PRK10094          3 DPETLRTFIAVAETG--SFSKAAERLCKTTATISYRIKLLEENTGV-ALFFRTTRSVTLTAAGEHLLSQ   68 (308)
T ss_pred             CHHHHHHHHHHHHhC--CHHHHHHHhcCCHHHHHHHHHHHHHHhCC-EEEeeCCCceeECHhHHHHHHH
Confidence            334556666676554  45678889999999999999999986443 5566677789999999998743

>PRK15421 DNA-binding transcriptional regulator MetR; Provisional

Probab=84.29  E-value=3  Score=39.12  Aligned_cols=67  Identities=12%  Similarity=0.057  Sum_probs=51.1

Q ss_pred             CCcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346          1 MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD   70 (292)
Q Consensus         1 m~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~   70 (292)
                      |-+-.+.+++.++.+.+  +...-|+++++.+.+|.+.++.||+.-|. ..-.+....+.||++|+..++
T Consensus         1 ~m~l~~L~~f~av~~~g--s~s~AA~~L~iSqpaVS~~Ik~LE~~lg~-~LF~R~~r~v~lT~~G~~l~~   67 (317)
T PRK15421          1 MIEVKHLKTLQALRNCG--SLAAAAATLHQTQSALSHQFSDLEQRLGF-RLFVRKSQPLRFTPQGEILLQ   67 (317)
T ss_pred             CccHHHHHHHHHHHHcC--CHHHHHHHhCCCHHHHHHHHHHHHHHhCC-EEEEecCCCceECHhHHHHHH
Confidence            44455667777776655  45678888999999999999999987555 444456677899999998874

>PRK10837 putative DNA-binding transcriptional regulator; Provisional

Probab=84.08  E-value=2.9  Score=37.79  Aligned_cols=66  Identities=8%  Similarity=-0.020  Sum_probs=50.3

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG   72 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G   72 (292)
                      -.+.+++.++.+.+  +...-|+.+|+.+.+|.+.++.||+.-|. ..-.+....++||+.|+.++...
T Consensus         5 l~~L~~f~~v~e~~--s~t~AA~~L~isqpavS~~I~~LE~~lg~-~Lf~R~~r~~~lT~~G~~l~~~a   70 (290)
T PRK10837          5 LRQLEVFAEVLKSG--STTQASVMLALSQSAVSAALTDLEGQLGV-QLFDRVGKRLVVNEHGRLLYPRA   70 (290)
T ss_pred             HHHHHHHHHHHHcC--CHHHHHHHhCCCccHHHHHHHHHHHHhCC-ccEeecCCeEEECHhHHHHHHHH
Confidence            34556666776555  45677888999999999999999986444 44555777799999999987643

>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family

Probab=83.66  E-value=2.5  Score=38.46  Aligned_cols=54  Identities=13%  Similarity=0.202  Sum_probs=44.3

Q ss_pred             HHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChh
Q psy10346          7 EKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGE   64 (292)
Q Consensus         7 ~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeE   64 (292)
                      ..||..+.. .+.....|+|..+|++.+.+.+.+..|.+. |||.-+   ...|.|+..
T Consensus        12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~-G~l~~~---~~~Y~lG~~   66 (248)
T TIGR02431        12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVEL-GYVTSD---GRLFWLTPR   66 (248)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEeC---CCEEEecHH
Confidence            467888864 456788999999999999999999999987 999742   357988754

Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.

>PF14090 HTH_39: Helix-turn-helix domain

Probab=83.25  E-value=5.6  Score=29.61  Aligned_cols=45  Identities=18%  Similarity=0.261  Sum_probs=34.5

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE   52 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e   52 (292)
                      +..+||.+|..++.+++.+....+|+-+  .-.-+..|+.+ |+--..
T Consensus         2 Q~~rIL~~L~~~~~it~~ea~~~~gi~~--~~aRI~eLR~~-G~~I~t   46 (70)
T PF14090_consen    2 QCKRILAALRRGGSITTLEARRELGIMR--LAARISELRKK-GYPIVT   46 (70)
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHcCCCC--HHHHHHHHHHc-CCeeeE
Confidence            5688999998899999988888888764  44667788876 874433

>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators

Probab=82.75  E-value=4.6  Score=28.20  Aligned_cols=39  Identities=13%  Similarity=0.122  Sum_probs=31.2

Q ss_pred             hHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346         21 TLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT   62 (292)
Q Consensus        21 ~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT   62 (292)
                      ..++|..+|++...|-.++..|+.. |+|+...  ...+.||
T Consensus        28 ~~~la~~~~is~~~v~~~l~~L~~~-G~i~~~~--~~~~~l~   66 (66)
T cd07377          28 ERELAEELGVSRTTVREALRELEAE-GLVERRP--GRGTFVA   66 (66)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHC-CCEEecC--CCeEEeC
Confidence            6789999999999999999999986 9987543  2344443

This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=82.57  E-value=2.6  Score=39.17  Aligned_cols=57  Identities=12%  Similarity=0.237  Sum_probs=45.6

Q ss_pred             HHHHHHHhccC-CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChh
Q psy10346          6 TEKILKYLDTN-PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGE   64 (292)
Q Consensus         6 e~~iL~~L~~~-~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeE   64 (292)
                      -..||..|... +.+...++|+.+|++.+.+.+.+..|.+. |||.-.. ....|.|+..
T Consensus        27 ~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~-G~l~~~~-~~~~Y~lG~~   84 (271)
T PRK10163         27 GIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAA-DFVYQDS-QLGWWHIGLG   84 (271)
T ss_pred             HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEcC-CCCeEEecHH
Confidence            34688888654 45788999999999999999999999987 9996543 4567888754

>PRK10632 transcriptional regulator; Provisional

Probab=82.42  E-value=3.3  Score=38.42  Aligned_cols=69  Identities=10%  Similarity=-0.029  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346          1 MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG   72 (292)
Q Consensus         1 m~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G   72 (292)
                      |-.-.+.+++..+.+.+  +...-|+.+++.+.+|.+.++.||..-|. ..-.+....+.||+.|+.+++.-
T Consensus         1 ~~~l~~L~~F~~v~e~g--S~t~AA~~L~isQpavS~~I~~LE~~lg~-~Lf~R~~r~i~lT~~G~~l~~~a   69 (309)
T PRK10632          1 MERLKRMSVFAKVVEFG--SFTAAARQLQMSVSSISQTVSKLEDELQV-KLLNRSTRSIGLTEAGRIYYQGC   69 (309)
T ss_pred             CcchHHHHHHHHHHhcC--CHHHHHHHhCCCHHHHHHHHHHHHHHhCC-eeecccCCCceechhHHHHHHHH
Confidence            43345566677776555  35667888999999999999999976444 55667778899999999987443

>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea

Probab=81.96  E-value=1.1  Score=33.55  Aligned_cols=43  Identities=12%  Similarity=0.129  Sum_probs=34.3

Q ss_pred             HHHhhcCCC-CCChHHHhhcC--C--chhhHHHHHHHcCCeecccCcc
Q psy10346         77 LVFNNVPSE-GIGQKELLATF--P--NAKVGFSKAMAKGWISLDKATG  119 (292)
Q Consensus        77 rl~~~l~~~-~~~~~el~~~~--~--~~~ig~~~a~k~gwi~i~~~~g  119 (292)
                      .|+++|.+. ..++++|.+..  +  ....|+||+.|.+.|.++..++
T Consensus        12 ~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~~~~   59 (65)
T PF10771_consen   12 KVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLARENKIEFEEKNG   59 (65)
T ss_dssp             HHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEETT
T ss_pred             HHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCceeEEeeCC
Confidence            578899875 48999998763  2  4678999999999999876655

The function is not known. ; PDB: 2L02_B 2L01_A.

>PRK11569 transcriptional repressor IclR; Provisional

Probab=81.91  E-value=2.7  Score=39.12  Aligned_cols=62  Identities=13%  Similarity=0.201  Sum_probs=48.0

Q ss_pred             HHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChh----HHHHhh
Q psy10346          7 EKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGE----GNQVKD   70 (292)
Q Consensus         7 ~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeE----G~~yl~   70 (292)
                      ..||..|.. ...+...++|+.+|++.+.|.+.+..|... ||+.-. .....|.|+..    |..++.
T Consensus        31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~-G~l~~~-~~~~~Y~lG~~l~~Lg~~~~~   97 (274)
T PRK11569         31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQ-GFVRQV-GELGHWAIGAHAFIVGSSFLQ   97 (274)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEc-CCCCeEecCHHHHHHHHHHHh
Confidence            457888865 445788999999999999999999999987 999743 33567887654    555543

>PRK11074 putative DNA-binding transcriptional regulator; Provisional

Probab=81.91  E-value=3.7  Score=37.77  Aligned_cols=66  Identities=15%  Similarity=0.065  Sum_probs=51.2

Q ss_pred             CCcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346          1 MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus         1 m~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl   69 (292)
                      |-+-.+.+++..+.+.+  +...-|+.+++.+.+|.+.++.||..-|. ..-.+....+.||+.|+.++
T Consensus         1 ~~~~~~L~~f~~v~e~~--s~s~AA~~L~isQpavS~~I~~LE~~lg~-~LF~R~~r~~~lT~~G~~l~   66 (300)
T PRK11074          1 MWSEYSLEVVDAVARTG--SFSAAAQELHRVPSAVSYTVRQLEEWLAV-PLFERRHRDVELTPAGEWFV   66 (300)
T ss_pred             CCCHHHHHHHHHHHHhC--CHHHHHHHhCCCHHHHHHHHHHHHHHhCC-eeEEeCCCCceECccHHHHH
Confidence            33445667777776655  35667888999999999999999976443 55566778899999999987

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

Probab=81.62  E-value=2.2  Score=27.62  Aligned_cols=29  Identities=17%  Similarity=0.234  Sum_probs=24.5

Q ss_pred             ChHHHHHhcCCCHHHHHHHHHHhhccCCcE
Q psy10346         20 DTLDLAKLFNEDHQKVVGGMKSIETLGEYL   49 (292)
Q Consensus        20 ~~~ela~~~~~~~~~v~~~~~~L~s~~glv   49 (292)
                      .-.++|.-+|+..+.|.+.++.|+.. |+|
T Consensus         4 tr~diA~~lG~t~ETVSR~l~~l~~~-glI   32 (32)
T PF00325_consen    4 TRQDIADYLGLTRETVSRILKKLERQ-GLI   32 (32)
T ss_dssp             -HHHHHHHHTS-HHHHHHHHHHHHHT-TSE
T ss_pred             CHHHHHHHhCCcHHHHHHHHHHHHHc-CCC
Confidence            34789999999999999999999986 886

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 ....

>TIGR02036 dsdC D-serine deaminase transcriptional activator

Probab=81.61  E-value=3.5  Score=38.15  Aligned_cols=64  Identities=14%  Similarity=0.010  Sum_probs=48.0

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG   72 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G   72 (292)
                      +.+++.++...+  +...-|+.+|+++.+|.+.++.||+.-|. ..-.+....+.||++|+.++..-
T Consensus        12 ~L~~F~~va~~g--s~s~AA~~L~isQpavS~~I~~LE~~lg~-~Lf~R~~r~~~lT~~G~~l~~~a   75 (302)
T TIGR02036        12 KMHTFEVAARHQ--SFSLAAEELSLTPSAISHRINQLEEELGI-QLFVRSHRKVELTHEGKRIYWAL   75 (302)
T ss_pred             HHHHHHHHHHhC--CHHHHHHHHCCCHHHHHHHHHHHHHHhCC-ceEEECCCceeECHhHHHHHHHH
Confidence            344455554444  34567888999999999999999987444 55677788999999999987443

This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=81.24  E-value=5.5  Score=29.10  Aligned_cols=52  Identities=15%  Similarity=0.218  Sum_probs=40.7

Q ss_pred             HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT   62 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT   62 (292)
                      .+||..|.+. .....++|+.+|++...|.+.+..|++. |+.....  ..-|.|.
T Consensus         3 ~~il~~L~~~-~~~~~eLa~~l~vS~~tv~~~l~~L~~~-g~~i~~~--~~g~~l~   54 (69)
T TIGR00122         3 LRLLALLADN-PFSGEKLGEALGMSRTAVNKHIQTLREW-GVDVLTV--GKGYRLP   54 (69)
T ss_pred             HHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCeEEec--CCceEec
Confidence            5788888754 4568999999999999999999999986 8865544  4455553

This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.

>COG3373 Uncharacterized protein conserved in archaea [Function unknown]

Probab=81.01  E-value=5.4  Score=32.07  Aligned_cols=65  Identities=26%  Similarity=0.355  Sum_probs=46.5

Q ss_pred             HHHHHHHHHhccCCC--CChHHHHHhcCCCHHHHHHHHHH----------hhccCCcEEEe-eeeEEEEEeChhHHHHh
Q psy10346          4 DLTEKILKYLDTNPP--VDTLDLAKLFNEDHQKVVGGMKS----------IETLGEYLIVE-PLSHKIWELTGEGNQVK   69 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~--~~~~ela~~~~~~~~~v~~~~~~----------L~s~~glv~~e-~~~~~~~~LTeEG~~yl   69 (292)
                      .+.++||-.|-+--+  .-..|++...+-|++.|.+.+.-          |-.. |+|.++ +.-.+.|.|||.|+...
T Consensus        17 eLRrkiL~yLy~iYP~~~YLSEIsR~V~SDPSNV~GcL~Glg~RYnGe~SLi~L-GLVe~~~~nGfKyykltdygkk~v   94 (108)
T COG3373          17 ELRRKILFYLYSIYPYRSYLSEISRAVKSDPSNVKGCLEGLGVRYNGEESLIGL-GLVEVEQKNGFKYYKLTEYGKKMV   94 (108)
T ss_pred             HHHHHHHHHHHHHccchhHHHHHHHHHcCCchHHHHHHHhcCCcccCchhhhhc-ceeEeeecCCEEEEehhHHHHHHH
Confidence            455677777743211  23478898899999999999864          4445 778774 45678899999999865

>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ

Probab=80.97  E-value=3.1  Score=37.99  Aligned_cols=61  Identities=10%  Similarity=0.007  Sum_probs=47.3

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl   69 (292)
                      +.+++..+.+.+  +...-|+++|+++.+|.+.++.||+.-|. ..-.+....++||+.|+.++
T Consensus         7 ~l~~f~~v~~~g--S~s~AA~~L~isq~avS~~I~~LE~~lg~-~LF~R~~~~~~lT~~G~~l~   67 (300)
T TIGR02424         7 HLQCFVEVARQG--SVKRAAEALHITQPAVSKTLRELEEILGT-PLFERDRRGIRLTRYGELFL   67 (300)
T ss_pred             HHHHHHHHHHhC--CHHHHHHHhCCChHHHHHHHHHHHHHhCC-eEEEEcCCCccccHhHHHHH
Confidence            445566665554  35677888999999999999999987554 45556677799999999987

Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.

>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator

Probab=80.95  E-value=2.7  Score=37.62  Aligned_cols=60  Identities=13%  Similarity=0.077  Sum_probs=45.5

Q ss_pred             HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346          8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD   70 (292)
Q Consensus         8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~   70 (292)
                      +.+.++.+.+  +...-|+.+++++.+|.+.++.||+.-|. ..-.+....++||++|+..++
T Consensus         3 ~~f~~v~~~g--s~~~AA~~L~isqsavS~~i~~LE~~lg~-~Lf~R~~~~~~lT~~G~~l~~   62 (279)
T TIGR03339         3 KAFHAVARCG--SFTRAAERLGLSQPTVTDQVRKLEERYGV-ELFHRNGRRLELTDAGHRLLP   62 (279)
T ss_pred             hhhHHHHhcC--CHHHHHHHhcCCchHHHHHHHHHHHHhCC-ccEEEcCCeEEEChhHHHHHH
Confidence            3455555444  34667888999999999999999986443 445557888999999998774

This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).

>PRK11062 nhaR transcriptional activator NhaR; Provisional

Probab=80.92  E-value=4.9  Score=36.98  Aligned_cols=64  Identities=14%  Similarity=-0.003  Sum_probs=48.0

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG   72 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G   72 (292)
                      +.+++..+.+.+  +...-|+.+|+++.+|.+.++.||+.-|. ..-.+....+.||++|+.+++..
T Consensus         8 ~L~~F~~v~e~g--s~s~AA~~L~isqpavS~~I~~LE~~lg~-~Lf~R~~r~~~lT~~G~~l~~~a   71 (296)
T PRK11062          8 HLYYFWMVCKEG--SVVGAAEALFLTPQTITGQIKALEERLQG-KLFKRKGRGLEPTELGELVFRYA   71 (296)
T ss_pred             HHHHHHHHHhcC--CHHHHHHHhCCChHHHHHHHHHHHHHcCc-cceeecCCceeECHhHHHHHHHH
Confidence            445555555544  35667888999999999999999986444 45556678899999999886433

>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN)

Probab=80.81  E-value=2  Score=31.01  Aligned_cols=55  Identities=18%  Similarity=0.222  Sum_probs=38.1

Q ss_pred             HHHHHhccCCCCChHHHHHhcCCCHHHH-HHHHHHhhccCCcEEEeeeeEEEEEeChhHH
Q psy10346          8 KILKYLDTNPPVDTLDLAKLFNEDHQKV-VGGMKSIETLGEYLIVEPLSHKIWELTGEGN   66 (292)
Q Consensus         8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v-~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~   66 (292)
                      .|...|.-...++..++.+.+|.+.... ...+..+.+. |+|+.+   ...++||++|.
T Consensus        10 ~i~~~LR~~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~-Gll~~~---~~~l~lT~~G~   65 (66)
T PF06969_consen   10 YIMLGLRCNEGIDLSEFEQRFGIDFAEEFQKELEELQED-GLLEID---GGRLRLTEKGR   65 (66)
T ss_dssp             HHHHHHHHHSEEEHHHHHHHTT--THHH-HHHHHHHHHT-TSEEE----SSEEEE-TTTG
T ss_pred             HHHHHHHhHCCcCHHHHHHHHCcCHHHHHHHHHHHHHHC-CCEEEe---CCEEEECcccC
Confidence            3444454455578899999999985444 7779999987 999654   47899999984

This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.

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

Probab=80.68  E-value=6.7  Score=32.08  Aligned_cols=98  Identities=20%  Similarity=0.204  Sum_probs=64.7

Q ss_pred             CC--cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHH
Q psy10346          1 MA--SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLV   78 (292)
Q Consensus         1 m~--~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl   78 (292)
                      ||  -++.++||.+.+.+.  +..+.|..++++...|.+|++ -... |-+........  .            .+...|
T Consensus         1 maYS~DlR~rVl~~~~~g~--s~~eaa~~F~VS~~Tv~~W~k-~~~~-G~~~~k~r~~~--K------------id~~~L   62 (119)
T PF01710_consen    1 MAYSLDLRQRVLAYIEKGK--SIREAAKRFGVSRNTVYRWLK-RKET-GDLEPKPRGRK--K------------IDRDEL   62 (119)
T ss_pred             CCCCHHHHHHHHHHHHccc--hHHHHHHHhCcHHHHHHHHHH-hccc-ccccccccccc--c------------ccHHHH
Confidence            66  478889999998654  568899999999999999999 3333 44433222211  1            123446


Q ss_pred             HhhcCCC-CCChHHHhhcCCchhhHHHHHHH-cCCeeccc
Q psy10346         79 FNNVPSE-GIGQKELLATFPNAKVGFSKAMA-KGWISLDK  116 (292)
Q Consensus        79 ~~~l~~~-~~~~~el~~~~~~~~ig~~~a~k-~gwi~i~~  116 (292)
                      -..|.+. +.++.|+.+.+....-++..+++ .|+....+
T Consensus        63 ~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t~KK~  102 (119)
T PF01710_consen   63 KALVEENPDATLRELAERLGVSPSTIWRALKRLGITRKKK  102 (119)
T ss_pred             HHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHcCchhccC
Confidence            6666665 48999998877654445565555 48865533

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 [].

>COG1568 Predicted methyltransferases [General function prediction only]

Probab=80.49  E-value=4.1  Score=39.24  Aligned_cols=58  Identities=17%  Similarity=0.189  Sum_probs=46.9

Q ss_pred             HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD   70 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~   70 (292)
                      ..||.+|-.++  +.-.++....++.-.|.+.+..|+.. |+|++++..   ..||+.|++.++
T Consensus        25 e~vl~ail~~~--d~wkIvd~s~~plp~v~~i~~~l~~e-giv~~~~g~---v~~TekG~E~~e   82 (354)
T COG1568          25 ENVLSAILATN--DFWKIVDYSDLPLPLVASILEILEDE-GIVKIEEGG---VELTEKGEELAE   82 (354)
T ss_pred             HHHHHHHHcCc--chHhhhhhccCCchHHHHHHHHHHhc-CcEEEecCc---EeehhhhHHHHH
Confidence            34666664443  66778888888888999999999986 999988776   899999999886

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=80.45  E-value=2  Score=38.00  Aligned_cols=47  Identities=15%  Similarity=0.169  Sum_probs=42.3

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI   50 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~   50 (292)
                      +.-+.+||..|..++.+...++|+.+|++.+.|-+.+..|+.. |++.
T Consensus         6 ~~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~-g~~~   52 (185)
T PRK04424          6 KERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIP-ELRE   52 (185)
T ss_pred             HHHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcc-hHHH
Confidence            4567889999999999999999999999999999999999986 8765

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	292
3l4g_A	508	Crystal Structure Of Homo Sapiens Cytoplasmic Pheny		4e-86
1pys_A	350	Phenylalanyl-Trna Synthetase From Thermus Thermophi		4e-09
2rhq_A	294	Phers From Staphylococcus Haemolyticus- Rational Pr		7e-09
2akw_A	266	Crystal Structure Of T.thermophilus Phenylalanyl-tr		1e-08
3pco_A	327	Crystal Structure Of E. Coli Phenylalanine-Trna Syn		4e-06

>pdb|3L4G|A Chain A, Crystal Structure Of Homo Sapiens Cytoplasmic Phenylalanyl-T Synthetase Length = 508

Iteration: 1
 Score =  314 bits (804), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 151/278 (54%), Positives = 202/278 (72%), Gaps = 5/278 (1%)
Query: 5   LTEKILKYLD-TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG 63
           + E +L+ L+ ++  +D+ +LA     +HQ VVG +KS++ LGE +  E  S K WELT 
Sbjct: 6   VAELLLRRLEASDGGLDSAELAAELGMEHQAVVGAVKSLQALGEVIEAELRSTKHWELTA 65
Query: 64  EGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATG---K 120
           EG ++   GSHE  VF ++P EG+ Q EL+   P+ KVGFSKAM+  WI +DK+     +
Sbjct: 66  EGEEIAREGSHEARVFRSIPPEGLAQSELM-RLPSGKVGFSKAMSNKWIRVDKSAADGPR 124
Query: 121 VLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTT 180
           V R VDS+ DE+Q  L+L+   + +K+ E  + + +KRKLL EVT+K++ + KG  FST+
Sbjct: 125 VFRVVDSMEDEVQRRLQLVRGGQAEKLGEKERSELRKRKLLAEVTLKTYWVSKGSAFSTS 184
Query: 181 IQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFT 240
           I K ETEL+PEMI+SGSW+   FKPYNF A G+   SGHLHPL+KVR++FRQIFL+MGFT
Sbjct: 185 ISKQETELSPEMISSGSWRDRPFKPYNFLAHGVLPDSGHLHPLLKVRSQFRQIFLEMGFT 244
Query: 241 EMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278
           EMPT+NF+ESSFWNFDALFQPQQHPARD HDTFF+ DP
Sbjct: 245 EMPTDNFIESSFWNFDALFQPQQHPARDQHDTFFLRDP 282

>pdb|1PYS|A Chain A, Phenylalanyl-Trna Synthetase From Thermus Thermophilus Length = 350

Iteration: 1
 Score = 58.5 bits (140), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 212 GISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHD 271
           G SL SG LHP+  +  E  +IF  +G+  +     VES F+NFDAL  P+ HPARD  D
Sbjct: 92  GASLFSGGLHPITLMERELVEIFRALGYQAVEGPE-VESEFFNFDALNIPEHHPARDMWD 150
Query: 272 TFFVT 276
           TF++T
Sbjct: 151 TFWLT 155

>pdb|2RHQ|A Chain A, Phers From Staphylococcus Haemolyticus- Rational Protein Engineering And Inhibitor Studies Length = 294

Iteration: 1
 Score = 57.8 bits (138), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 44/74 (59%), Gaps = 6/74 (8%)
Query: 209 DAMGISLPS-----GHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQ 263
           + + ++LPS     G  HPL +   E   +FL +G+ E+     VE  ++NF+AL  P+ 
Sbjct: 36  ETIDVTLPSRQISIGSKHPLTRTVEEIEDLFLGLGY-EIVDGYEVEQDYYNFEALNLPKS 94
Query: 264 HPARDAHDTFFVTD 277
           HPARD  D+F++TD
Sbjct: 95  HPARDMQDSFYITD 108

>pdb|2AKW|A Chain A, Crystal Structure Of T.thermophilus Phenylalanyl-trna Synthetase Complexed With P-cl-phenylalanine Length = 266

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 212 GISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHD 271
           G SL SG LHP+  +  E  +IF  +G+  +     VES F+NFDAL  P+ HPARD  D
Sbjct: 8   GASLFSGGLHPITLMERELVEIFRALGYQAVEGPE-VESEFFNFDALNIPEHHPARDMWD 66
Query: 272 TFFVT 276
           TF++T
Sbjct: 67  TFWLT 71

>pdb|3PCO|A Chain A, Crystal Structure Of E. Coli Phenylalanine-Trna Synthetase Complexed With Phenylalanine And Amp Length = 327

Iteration: 1
 Score = 48.9 bits (115), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 212 GISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHD 271
           G  + +G LHP+ +        F ++GFT + T   +E  + NFDAL  P  HPAR  HD
Sbjct: 98  GRRIENGGLHPVTRTIDRIESFFGELGFT-VATGPEIEDDYHNFDALNIPGHHPARADHD 156
Query: 272 TFFVTDPKTSETE 284
           TF+    +   T+
Sbjct: 157 TFWFDTTRLLRTQ 169

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	292
3l4g_A	508	Phenylalanyl-tRNA synthetase alpha chain; aminoacy	1e-104
2odr_C	701	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	1e-24
2odr_C	701	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	5e-08
2odr_D	685	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	2e-24
2odr_D	685	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	7e-07
2odr_A	665	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	2e-23
2odr_A	665	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	4e-07
2odr_B	648	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	5e-23
2odr_B	648	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	8e-07
3cmq_A	415	Phenylalanyl-tRNA synthetase, mitochondrial; class	6e-18
2du7_A	549	O-phosphoseryl-tRNA synthetase; alpha4 tetramer, l	1e-17
2du7_A	549	O-phosphoseryl-tRNA synthetase; alpha4 tetramer, l	3e-05
2du3_A	534	O-phosphoseryl-tRNA synthetase; alpha4 tetramer, l	2e-17
2du3_A	534	O-phosphoseryl-tRNA synthetase; alpha4 tetramer, l	6e-08
2rhq_A	294	Phenylalanyl-tRNA synthetase alpha chain; heterote	3e-17
1b7y_A	350	Phers, protein (phenylalanyl-tRNA synthetase); enz	4e-17
3pco_A	327	Phenylalanyl-tRNA synthetase, alpha subunit; amino	5e-17
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-07
3qtc_A	290	Pyrrolysyl-tRNA synthetase; aminoacyl-tRNA synthet	2e-04

>3l4g_A Phenylalanyl-tRNA synthetase alpha chain; aminoacylation, tRNA-binding, DNA-binding domain, four-helix acetylation, aminoacyl-tRNA synthetase; HET: PHE; 3.30A {Homo sapiens} Length = 508

 Score =  312 bits (800), Expect = e-104
 Identities = 153/287 (53%), Positives = 205/287 (71%), Gaps = 6/287 (2%)

Query: 1   MA-SDLTEKILKYLD-TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKI 58
           MA   + E +L+ L+ ++  +D+ +LA     +HQ VVG +KS++ LGE +  E  S K 
Sbjct: 1   MADGQVAELLLRRLEASDGGLDSAELAAELGMEHQAVVGAVKSLQALGEVIEAELRSTKH 60

Query: 59  WELTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKAT 118
           WELT EG ++   GSHE  VF ++P EG+ Q EL+   P+ KVGFSKAM+  WI +DK+ 
Sbjct: 61  WELTAEGEEIAREGSHEARVFRSIPPEGLAQSELMR-LPSGKVGFSKAMSNKWIRVDKSA 119

Query: 119 G---KVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQEVTIKSFLLKKGP 175
               +V R VDS+ DE+Q  L+L+   + +K+ E  + + +KRKLL EVT+K++ + KG 
Sbjct: 120 ADGPRVFRVVDSMEDEVQRRLQLVRGGQAEKLGEKERSELRKRKLLAEVTLKTYWVSKGS 179

Query: 176 EFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFL 235
            FST+I K ETEL+PEMI+SGSW+   FKPYNF A G+   SGHLHPL+KVR++FRQIFL
Sbjct: 180 AFSTSISKQETELSPEMISSGSWRDRPFKPYNFLAHGVLPDSGHLHPLLKVRSQFRQIFL 239

Query: 236 DMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSE 282
           +MGFTEMPT+NF+ESSFWNFDALFQPQQHPARD HDTFF+ DP  + 
Sbjct: 240 EMGFTEMPTDNFIESSFWNFDALFQPQQHPARDQHDTFFLRDPAEAL 286

>2odr_C Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis} Length = 701

 Score =  102 bits (255), Expect = 1e-24
 Identities = 22/107 (20%), Positives = 33/107 (30%), Gaps = 6/107 (5%)

Query: 167 KSFLLKKGPEFSTTIQKPE-TELTPEMIASGSWKT---LNFKPYNFDAMGISLPSGHLHP 222
                   P  S   ++ E  E+  +       +T   +  K  N     I    G  HP
Sbjct: 7   HHHSSGLVPRGSHMFKREEIIEMANKDFEKAWIETKDLIKAKKINESYPRIKPVFGKTHP 66

Query: 223 LMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDA 269
           +       RQ +L MGF E      V+    +    F P+     D 
Sbjct: 67  VNDTIENLRQAYLRMGFEEYINPVIVD--ERDIYKQFGPEAMAVLDR 111

>2odr_C Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis} Length = 701

 Score = 53.1 bits (127), Expect = 5e-08
 Identities = 19/185 (10%), Positives = 48/185 (25%), Gaps = 22/185 (11%)

Query: 119 GKVLRKVDSVTDELQAHL--------KLIANNEYDKVPEANKVDYKKRKLLQEVT--IKS 168
           G  + K + + +               LI   + ++     K  + K   + +    ++ 
Sbjct: 17  GSHMFKREEIIEMANKDFEKAWIETKDLIKAKKINESYPRIKPVFGKTHPVNDTIENLRQ 76

Query: 169 FLL------KKGP---EFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGH 219
             L         P   +     ++   E    +        L           IS     
Sbjct: 77  AYLRMGFEEYINPVIVDERDIYKQFGPEAMAVLDRCFYLAGLPRPDVGLSDEKISQIEKL 136

Query: 220 LHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPK 279
              + + +   ++I        +  ++ +     N  AL    +   +   D F      
Sbjct: 137 GIKVSEHKESLQKILHGYKKGTLDGDD-LVLEISN--ALEISSEMGLKILEDVFPEFKDL 193

Query: 280 TSETE 284
           T+ + 
Sbjct: 194 TAVSS 198

>2odr_D Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis} Length = 685

 Score =  101 bits (254), Expect = 2e-24
 Identities = 22/99 (22%), Positives = 33/99 (33%), Gaps = 6/99 (6%)

Query: 175 PEFSTTIQKPE-TELTPEMIASGSWKT---LNFKPYNFDAMGISLPSGHLHPLMKVRAEF 230
           P  S   ++ E  E+  +       +T   +  K  N     I    G  HP+       
Sbjct: 15  PRGSHMFKREEIIEMANKDFEKAWIETKDLIKAKKINESYPRIKPVFGKTHPVNDTIENL 74

Query: 231 RQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDA 269
           RQ +L MGF E      V+    +    F P+     D 
Sbjct: 75  RQAYLRMGFEEYINPVIVD--ERDIYKQFGPEAMAVLDR 111

>2odr_D Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis} Length = 685

 Score = 49.2 bits (117), Expect = 7e-07
 Identities = 17/159 (10%), Positives = 43/159 (27%), Gaps = 14/159 (8%)

Query: 137 KLIANNEYDKVPEANKVDYKKRKLLQEVT--IKSFLLKKGP---------EFSTTIQKPE 185
            LI   + ++     K  + K   + +    ++   L+ G          +     ++  
Sbjct: 43  DLIKAKKINESYPRIKPVFGKTHPVNDTIENLRQAYLRMGFEEYINPVIVDERDIYKQFG 102

Query: 186 TELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTN 245
            E    +        L           IS        + + +   ++I        +  +
Sbjct: 103 PEAMAVLDRCFYLAGLPRPDVGLSDEKISQIEKLGIKVSEHKESLQKILHGYKKGTLDGD 162

Query: 246 NFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSETE 284
           + +     N  AL    +   +   D F      T+ + 
Sbjct: 163 D-LVLEISN--ALEISSEMGLKILEDVFPEFKDLTAVSS 198

>2odr_A Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis} Length = 665

 Score = 98.9 bits (246), Expect = 2e-23
 Identities = 22/107 (20%), Positives = 33/107 (30%), Gaps = 6/107 (5%)

Query: 167 KSFLLKKGPEFSTTIQKPE-TELTPEMIASGSWKT---LNFKPYNFDAMGISLPSGHLHP 222
                   P  S   ++ E  E+  +       +T   +  K  N     I    G  HP
Sbjct: 7   HHHSSGLVPRGSHMFKREEIIEMANKDFEKAWIETKDLIKAKKINESYPRIKPVFGKTHP 66

Query: 223 LMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDA 269
           +       RQ +L MGF E      V+    +    F P+     D 
Sbjct: 67  VNDTIENLRQAYLRMGFEEYINPVIVD--ERDIYKQFGPEAMAVLDR 111

>2odr_A Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis} Length = 665

 Score = 50.0 bits (119), Expect = 4e-07
 Identities = 19/185 (10%), Positives = 48/185 (25%), Gaps = 22/185 (11%)

Query: 119 GKVLRKVDSVTDELQAHL--------KLIANNEYDKVPEANKVDYKKRKLLQEVT--IKS 168
           G  + K + + +               LI   + ++     K  + K   + +    ++ 
Sbjct: 17  GSHMFKREEIIEMANKDFEKAWIETKDLIKAKKINESYPRIKPVFGKTHPVNDTIENLRQ 76

Query: 169 FLL------KKGP---EFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGH 219
             L         P   +     ++   E    +        L           IS     
Sbjct: 77  AYLRMGFEEYINPVIVDERDIYKQFGPEAMAVLDRCFYLAGLPRPDVGLSDEKISQIEKL 136

Query: 220 LHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPK 279
              + + +   ++I        +  ++ +     N  AL    +   +   D F      
Sbjct: 137 GIKVSEHKESLQKILHGYKKGTLDGDD-LVLEISN--ALEISSEMGLKILEDVFPEFKDL 193

Query: 280 TSETE 284
           T+ + 
Sbjct: 194 TAVSS 198

>2odr_B Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis} Length = 648

 Score = 97.7 bits (243), Expect = 5e-23
 Identities = 22/107 (20%), Positives = 33/107 (30%), Gaps = 6/107 (5%)

Query: 167 KSFLLKKGPEFSTTIQKPE-TELTPEMIASGSWKT---LNFKPYNFDAMGISLPSGHLHP 222
                   P  S   ++ E  E+  +       +T   +  K  N     I    G  HP
Sbjct: 7   HHHSSGLVPRGSHMFKREEIIEMANKDFEKAWIETKDLIKAKKINESYPRIKPVFGKTHP 66

Query: 223 LMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDA 269
           +       RQ +L MGF E      V+    +    F P+     D 
Sbjct: 67  VNDTIENLRQAYLRMGFEEYINPVIVD--ERDIYKQFGPEAMAVLDR 111

>2odr_B Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis} Length = 648

 Score = 49.2 bits (117), Expect = 8e-07
 Identities = 19/185 (10%), Positives = 48/185 (25%), Gaps = 22/185 (11%)

Query: 119 GKVLRKVDSVTDELQAHL--------KLIANNEYDKVPEANKVDYKKRKLLQEVT--IKS 168
           G  + K + + +               LI   + ++     K  + K   + +    ++ 
Sbjct: 17  GSHMFKREEIIEMANKDFEKAWIETKDLIKAKKINESYPRIKPVFGKTHPVNDTIENLRQ 76

Query: 169 FLL------KKGP---EFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGH 219
             L         P   +     ++   E    +        L           IS     
Sbjct: 77  AYLRMGFEEYINPVIVDERDIYKQFGPEAMAVLDRCFYLAGLPRPDVGLSDEKISQIEKL 136

Query: 220 LHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPK 279
              + + +   ++I        +  ++ +     N  AL    +   +   D F      
Sbjct: 137 GIKVSEHKESLQKILHGYKKGTLDGDD-LVLEISN--ALEISSEMGLKILEDVFPEFKDL 193

Query: 280 TSETE 284
           T+ + 
Sbjct: 194 TAVSS 198

>3cmq_A Phenylalanyl-tRNA synthetase, mitochondrial; classii aarss fold, RRM domain, RNA recogntion, aminoacyl-tRNA synthetase, ATP-binding, ligase; HET: FA5; 2.20A {Homo sapiens} PDB: 3hfv_A* 3teg_A* 3tup_A Length = 415

 Score = 82.2 bits (203), Expect = 6e-18
 Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 8/75 (10%)

Query: 212 GISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNF--------VESSFWNFDALFQPQQ 263
           G +L +   HPL  ++   ++ F         T  F        V +++ NFD+L  P  
Sbjct: 39  GRNLHNQQHHPLWLIKERVKEHFYKQYVGRFGTPLFSVYDNLSPVVTTWQNFDSLLIPAD 98

Query: 264 HPARDAHDTFFVTDP 278
           HP+R   D +++   
Sbjct: 99  HPSRKKGDNYYLNRT 113

>2du7_A O-phosphoseryl-tRNA synthetase; alpha4 tetramer, ligase, structural genomics, NPPSFA; 3.60A {Methanocaldococcus jannaschii} Length = 549

 Score = 81.9 bits (202), Expect = 1e-17
 Identities = 23/104 (22%), Positives = 34/104 (32%), Gaps = 7/104 (6%)

Query: 170 LLKKGPEFSTTIQKPETELTPEMIASGSWKTLNF----KPYNFDAMGISLPSGHLHPLMK 225
           L  K  +      K   EL  +     +W+        K  +     +    G  HP+M+
Sbjct: 3   LKHKRDDKMRFDIKKVLELAEKDF-ETAWRETRALIKDKHIDNKYPRLKPVYGKPHPVME 61

Query: 226 VRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDA 269
                RQ +L MGF EM     V+         F P+     D 
Sbjct: 62  TIERLRQAYLRMGFEEMINPVIVDE--MEIYKQFGPEAMAVLDR 103

>2du7_A O-phosphoseryl-tRNA synthetase; alpha4 tetramer, ligase, structural genomics, NPPSFA; 3.60A {Methanocaldococcus jannaschii} Length = 549

 Score = 44.6 bits (105), Expect = 3e-05
 Identities = 6/64 (9%), Positives = 16/64 (25%), Gaps = 3/64 (4%)

Query: 221 HPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKT 280
               + +   R++        +  +   +  F    AL    +   +     F       
Sbjct: 131 DIDEEKKERLREVLHLYKKGAIDGD---DLVFEIAKALNVSNEMGLKVLETAFPEFKDLK 187

Query: 281 SETE 284
            E+ 
Sbjct: 188 PEST 191

>2du3_A O-phosphoseryl-tRNA synthetase; alpha4 tetramer, ligase/RNA complex; HET: SEP; 2.60A {Archaeoglobus fulgidus} PDB: 2du4_A 2du5_A* 2du6_A* Length = 534

 Score = 80.7 bits (199), Expect = 2e-17
 Identities = 17/109 (15%), Positives = 28/109 (25%), Gaps = 15/109 (13%)

Query: 186 TELTPEMIASGSWKTLNFKPYNFDAMGI----SLPSGHLHPLMKVRAEFRQIFLDMGFTE 241
            EL  +     +WK             +        G  HPL       R+ +L +GF+E
Sbjct: 9   RELAEKDF-EAAWKAGKEILAERSPNELYPRVGFSFGKEHPLFATIQRLREAYLSIGFSE 67

Query: 242 MPTNN----------FVESSFWNFDALFQPQQHPARDAHDTFFVTDPKT 280
           +              F   +    D  F     P  +   +        
Sbjct: 68  VVNPLIVEDVHVKKQFGREALAVLDRCFYLATLPKPNVGISAEKIRQIE 116

>2du3_A O-phosphoseryl-tRNA synthetase; alpha4 tetramer, ligase/RNA complex; HET: SEP; 2.60A {Archaeoglobus fulgidus} PDB: 2du4_A 2du5_A* 2du6_A* Length = 534

 Score = 52.6 bits (126), Expect = 6e-08
 Identities = 6/69 (8%), Positives = 17/69 (24%), Gaps = 3/69 (4%)

Query: 216 PSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFV 275
               +          ++IF      E+  +   + S+   + L        +   + F  
Sbjct: 114 QIEAITKREVDSKPLQEIFHRYKKGEIDGD---DLSYLIAEVLDVDDITAVKILDEVFPE 170

Query: 276 TDPKTSETE 284
                  + 
Sbjct: 171 FKELKPISS 179

>2rhq_A Phenylalanyl-tRNA synthetase alpha chain; heterotetramer, phenylalanine, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase; HET: GAX; 2.20A {Staphylococcus haemolyticus} PDB: 2rhs_A* Length = 294

 Score = 78.8 bits (195), Expect = 3e-17
 Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 5/68 (7%)

Query: 212 GISLPSGHLHPLMKVRAEFRQIFLDMGFT--EMPTNNFVESSFWNFDALFQPQQHPARDA 269
              +  G  HPL +   E   +FL +G+   +      VE  ++NF+AL  P+ HPARD 
Sbjct: 44  SRQISIGSKHPLTRTVEEIEDLFLGLGYEIVDGYE---VEQDYYNFEALNLPKSHPARDM 100

Query: 270 HDTFFVTD 277
            D+F++TD
Sbjct: 101 QDSFYITD 108

>1b7y_A Phers, protein (phenylalanyl-tRNA synthetase); enzyme, alpha/beta homodimer, ligase; HET: FYA; 2.50A {Thermus thermophilus} SCOP: d.104.1.1 PDB: 1b70_A* 1eiy_A 1jjc_A* 1pys_A 2iy5_A* 3hfz_A* 3teh_A* 2aly_A* 2akw_A* 2amc_A* Length = 350

 Score = 79.2 bits (196), Expect = 4e-17
 Identities = 33/75 (44%), Positives = 42/75 (56%), Gaps = 5/75 (6%)

Query: 212 GISLPSGHLHPLMKVRAEFRQIFLDMGFT--EMPTNNFVESSFWNFDALFQPQQHPARDA 269
           G SL SG LHP+  +  E  +IF  +G+   E P    VES F+NFDAL  P+ HPARD 
Sbjct: 92  GASLFSGGLHPITLMERELVEIFRALGYQAVEGPE---VESEFFNFDALNIPEHHPARDM 148

Query: 270 HDTFFVTDPKTSETE 284
            DTF++T        
Sbjct: 149 WDTFWLTGEGFRLEG 163

>3pco_A Phenylalanyl-tRNA synthetase, alpha subunit; aminoacylation, tRNA-binding, DNA-binding domain, four-helix aminoacyl-tRNA synthetase, ATP-binding; HET: PHE AMP; 3.02A {Escherichia coli} Length = 327

 Score = 78.7 bits (195), Expect = 5e-17
 Identities = 25/70 (35%), Positives = 35/70 (50%), Gaps = 5/70 (7%)

Query: 212 GISLPSGHLHPLMKVRAEFRQIFLDMGFT--EMPTNNFVESSFWNFDALFQPQQHPARDA 269
           G  + +G LHP+ +        F ++GFT    P    +E  + NFDAL  P  HPAR  
Sbjct: 98  GRRIENGGLHPVTRTIDRIESFFGELGFTVATGPE---IEDDYHNFDALNIPGHHPARAD 154

Query: 270 HDTFFVTDPK 279
           HDTF+    +
Sbjct: 155 HDTFWFDTTR 164

>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 = 50.2 bits (119), Expect = 4e-07
 Identities = 48/279 (17%), Positives = 85/279 (30%), Gaps = 78/279 (27%)

Query: 4   DLTEKILKYLDT-NPPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWEL 61
           +L+ KIL  L T    V D L  A   +         +   E     L+++ L  +  +L
Sbjct: 263 NLSCKIL--LTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS--LLLKYLDCRPQDL 318

Query: 62  TGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGW--ISLDKATG 119
                        EVL  N      I   E +                 W  ++ DK T 
Sbjct: 319 -----------PREVLTTNPRRLSIIA--ESIRDGLA--------TWDNWKHVNCDKLTT 357

Query: 120 KVLRKVDSVT-DELQAHLKLIANNEYD-KVPEA-------NKVDYKKRKLLQEVTIKSFL 170
            +   ++ +   E +     ++       +P         + +      ++ ++   S +
Sbjct: 358 IIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLV 417

Query: 171 LKKGPEFSTTI----------QKPETELTPEMIASGSWKTLNFKPYN----FDAMGISLP 216
            K+  E + +I           + E  L   ++            YN    FD+  +  P
Sbjct: 418 EKQPKESTISIPSIYLELKVKLENEYALHRSIVDH----------YNIPKTFDSDDLIPP 467

Query: 217 S---------GHLHPLMKVR-----AEFRQIFLDMGFTE 241
                     GH H L  +        FR +FLD  F E
Sbjct: 468 YLDQYFYSHIGH-H-LKNIEHPERMTLFRMVFLDFRFLE 504

>3qtc_A Pyrrolysyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP B O-methyl tyrosine binding, magnesium binding, aminoacylatio esterification; HET: 0A1 ANP; 1.75A {Methanosarcina mazei} PDB: 2q7e_A* 2q7g_A* 2q7h_A* 2zim_A* 2zin_A* 2e3c_A* 2zcd_A* 2zce_A* 2zio_A* Length = 290

 Score = 41.4 bits (97), Expect = 2e-04
 Identities = 19/114 (16%), Positives = 32/114 (28%), Gaps = 21/114 (18%)

Query: 132 LQAHLKLIANNEYD-KVPEANKVDYKKRKLLQEVTIKSFLLKKGPEFSTTIQKPETELTP 190
              H  L+    +    P   K    + ++L         L  G  F         EL  
Sbjct: 7   HHHHGGLVPRGSHGASAPALTKSQTDRLEVLLN-PKDEISLNSGKPFR--------ELES 57

Query: 191 EMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPT 244
           E+                  +         + L K+  E  + F+D GF E+ +
Sbjct: 58  EL-----------LSRRKKDLQQIYAEERENYLGKLEREITRFFVDRGFLEIKS 100

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	292
3l4g_A	508	Phenylalanyl-tRNA synthetase alpha chain; aminoacy	100.0
3cmq_A	415	Phenylalanyl-tRNA synthetase, mitochondrial; class	99.83
2du7_A	549	O-phosphoseryl-tRNA synthetase; alpha4 tetramer, l	99.79
2odr_B	648	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	99.79
2odr_D	685	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	99.77
2odr_A	665	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	99.77
2odr_C	701	Phosphoseryl-tRNA synthetase; phosphoserine tRNA s	99.77
3pco_A	327	Phenylalanyl-tRNA synthetase, alpha subunit; amino	99.71
1b7y_A	350	Phers, protein (phenylalanyl-tRNA synthetase); enz	99.68
2rhq_A	294	Phenylalanyl-tRNA synthetase alpha chain; heterote	99.37
2du3_A	534	O-phosphoseryl-tRNA synthetase; alpha4 tetramer, l	99.14
2nnn_A	140	Probable transcriptional regulator; structural gen	97.74
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	97.72
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	97.71
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	97.68
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	97.68
2gxg_A	146	146AA long hypothetical transcriptional regulator;	97.61
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	97.59
2pex_A	153	Transcriptional regulator OHRR; transcription regu	97.59
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	97.59
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	97.58
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	97.58
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	97.57
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	97.57
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	97.57
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	97.56
3l4g_B	589	Phenylalanyl-tRNA synthetase beta chain; aminoacyl	97.55
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	97.54
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	97.53
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	97.53
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	97.51
2eth_A	154	Transcriptional regulator, putative, MAR family; M	97.5
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	97.5
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	97.49
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	97.49
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	97.48
1bja_A	95	Transcription regulatory protein MOTA; activation	97.48
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	97.47
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	97.47
3s2w_A	159	Transcriptional regulator, MARR family; structural	97.47
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	97.45
3f3x_A	144	Transcriptional regulator, MARR family, putative;	97.44
3bja_A	139	Transcriptional regulator, MARR family, putative;	97.43
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	97.41
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	97.41
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	97.41
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	97.41
1z91_A	147	Organic hydroperoxide resistance transcriptional;	97.4
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	97.4
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	97.39
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	97.39
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	97.36
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	97.35
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	97.34
2pg4_A	95	Uncharacterized protein; structural genomics, join	97.33
3nqo_A	189	MARR-family transcriptional regulator; structural	97.33
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	97.32
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	97.31
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	97.31
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	97.29
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	97.28
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	97.24
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	97.22
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	97.19
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	97.19
3df8_A	111	Possible HXLR family transcriptional factor; APC89	97.18
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	97.18
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	97.16
1sfx_A	109	Conserved hypothetical protein AF2008; structural	97.16
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	97.15
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	97.11
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	97.1
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	97.09
1y0u_A	96	Arsenical resistance operon repressor, putative; s	97.03
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	97.03
1okr_A	123	MECI, methicillin resistance regulatory protein ME	97.01
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	97.0
1yyv_A	131	Putative transcriptional regulator; reductive meth	96.93
4esf_A	117	PADR-like transcriptional regulator; PADR family,	96.92
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	96.88
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	96.85
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	96.82
2fxa_A	207	Protease production regulatory protein HPR; protea	96.81
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	96.81
4fx0_A	148	Probable transcriptional repressor protein; helix-	96.8
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	96.74
1xma_A	145	Predicted transcriptional regulator; southea colla	96.73
3qtc_A	290	Pyrrolysyl-tRNA synthetase; aminoacyl-tRNA synthet	96.72
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	96.71
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	96.71
2rhq_B	795	Phenylalanyl-tRNA synthetase beta chain; heterotet	96.68
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	96.66
3ri2_A	123	Transcriptional regulator, PADR-like family; PSI-b	96.64
3jth_A	98	Transcription activator HLYU; transcription factor	96.61
3elk_A	117	Putative transcriptional regulator TA0346; structu	96.61
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	96.6
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	96.59
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	96.58
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	96.54
2obp_A	96	Putative DNA-binding protein; structural genomics,	96.53
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	96.48
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	96.45
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	96.4
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	96.36
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	96.31
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	96.3
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	96.3
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	96.29
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	96.29
2dql_A	115	PEX protein; circadian clock associated protein, c	96.28
2h09_A	155	Transcriptional regulator MNTR; transcription regu	96.27
2kko_A	108	Possible transcriptional regulatory protein (possi	96.2
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	96.13
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	96.04
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	95.98
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	95.94
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	95.83
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	95.76
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	95.72
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	95.71
3dsq_A	288	Pyrrolysyl-tRNA synthetase; homodimer, aminoacyl-t	95.54
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	95.51
1hsj_A	487	Fusion protein consisting of staphylococcus access	95.44
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	95.39
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	95.38
3cta_A	230	Riboflavin kinase; structural genomics, transferas	95.18
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	95.17
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	95.16
2co5_A	99	Viral protein F93; viral protein-winged helix comp	95.03
3l9f_A	204	Putative uncharacterized protein SMU.1604C; PADR,	94.97
1ku9_A	152	Hypothetical protein MJ223; putative transcription	94.92
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	94.9
2xzm_7	162	Plectin/S10 domain containing protein; ribosome, t	94.87
2e1n_A	138	PEX, period extender; circadian clock, DNA binding	94.86
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	94.8
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	94.66
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	94.66
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	94.55
3u5c_K	105	40S ribosomal protein S10-A; translation, ribosome	94.53
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	94.47
1b7y_B	785	Phers, protein (phenylalanyl-tRNA synthetase); enz	94.27
1p6r_A	82	Penicillinase repressor; transcription regulation,	94.19
4a6d_A	353	Hydroxyindole O-methyltransferase; melatonin, circ	94.18
2o0m_A	345	Transcriptional regulator, SORC family; structural	93.99
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	93.99
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	93.97
2zfw_A	148	PEX; five alpha-helices + one beta-sheet, circadia	93.93
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	93.88
3r0a_A	123	Putative transcriptional regulator; structural gen	93.81
2w25_A	150	Probable transcriptional regulatory protein; trans	93.79
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	93.67
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	93.66
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	93.45
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	93.42
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	93.37
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	93.33
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	93.18
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	93.12
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	93.11
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	92.94
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	92.92
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	92.48
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	92.46
1nnh_A	294	Asparaginyl-tRNA synthetase-related peptide; struc	92.35
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	92.18
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	91.95
1x54_A	434	Asparaginyl-tRNA synthetase; aminoacyl-tRNA synthe	91.94
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	91.83
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	91.61
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	91.38
4g6q_A	182	Putative uncharacterized protein; structural genom	90.49
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	89.94
2vn2_A	128	DNAD, chromosome replication initiation protein; D	89.69
3eyi_A	72	Z-DNA-binding protein 1; alternative splicing, DNA	89.53
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	89.3
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	89.07
1bm9_A	122	RTP, TER, replication terminator protein; DNA-bind	88.94
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	88.89
1mkm_A	249	ICLR transcriptional regulator; structural genomic	88.79
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	88.19
1wyd_A	429	Hypothetical aspartyl-tRNA synthetase; archaea, LI	88.06
2g7u_A	257	Transcriptional regulator; ICLR family, structural	87.7
1n9w_A	422	Aspartyl-tRNA synthetase 2; biosynthetic protein;	87.5
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	87.33
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	86.8
2rkh_A	180	Putative APHA-like transcription factor; ZP_002083	86.42
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	85.79
2ijl_A	135	AGR_C_4647P, molybdenum-binding transcriptional re	85.68
2hgc_A	102	YJCQ protein; SR346, structure, autostructure, NES	85.1
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	85.09
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	85.06
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	85.01
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	84.99
1bia_A	321	BIRA bifunctional protein; transcription regulatio	84.98
3ig2_A	213	Phenylalanyl-tRNA synthetase beta chain; phers, MC	84.95
3l09_A	266	Putative transcriptional regulator; structural gen	84.27
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	84.23
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	84.23
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	84.0
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	83.63
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	83.11
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	82.9
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	81.44
2gqq_A	163	Leucine-responsive regulatory protein; helix-turn-	81.39
1ylf_A	149	RRF2 family protein; structural genomics, transcri	81.2
2l02_A	82	Uncharacterized protein; structural genomics, nort	81.18
3b02_A	195	Transcriptional regulator, CRP family; structural	81.12
3ica_A	213	Phenylalanyl-tRNA synthetase beta chain; APC61692.	80.49
3szp_A	291	Transcriptional regulator, LYSR family; winged hel	80.36

>3l4g_A Phenylalanyl-tRNA synthetase alpha chain; aminoacylation, tRNA-binding, DNA-binding domain, four-helix acetylation, aminoacyl-tRNA synthetase; HET: PHE; 3.30A {Homo sapiens}

Probab=100.00  E-value=5.5e-69  Score=533.99  Aligned_cols=279  Identities=54%  Similarity=0.928  Sum_probs=99.9

Q ss_pred             CC-cHHHHHHHHHhccCC-CCChHHHHHhcCCCHHHHHHHHHHhhccCC-cEEEeeeeEEEEEeChhHHHHhhcCChHHH
Q psy10346          1 MA-SDLTEKILKYLDTNP-PVDTLDLAKLFNEDHQKVVGGMKSIETLGE-YLIVEPLSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         1 m~-~~~e~~iL~~L~~~~-~~~~~ela~~~~~~~~~v~~~~~~L~s~~g-lv~~e~~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      |+ .+++++||.+|.+++ .++++++|+..|++|++|++++++|+++ | ||++++++...|+||+||++|+++||||+|
T Consensus         1 ~~~~~~~~~iL~~l~~~~~~~~~~~~a~~~~~~~~~v~~~~~~L~~~-~~~v~~~~~~~~~~~Lt~eg~~~~~~G~pE~~   79 (508)
T 3l4g_A            1 MADGQVAELLLRRLEASDGGLDSAELAAELGMEHQAVVGAVKSLQAL-GEVIEAELRSTKHWELTAEGEEIAREGSHEAR   79 (508)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCchHHHHHHHHHHHhcCCCcCHHHHHHHcCCCHHHHHHHHHHHHhC-CCeEEEEEEEEEEEEECHHHHHHHHcCCHHHH
Confidence            66 479999999998777 7899999999999999999999999997 7 999999999999999999999999999999


Q ss_pred             HHhhcCCCCCChHHHhhcCCchhhHHHHHHHcCCeecccCc-c--eeeccCCCchHHHHHHHHHHhccCCCCCChhhHHh
Q psy10346         78 VFNNVPSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKAT-G--KVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVD  154 (292)
Q Consensus        78 l~~~l~~~~~~~~el~~~~~~~~ig~~~a~k~gwi~i~~~~-g--~v~~~~~~~~d~~~~~L~~i~~~~~~~l~~~~~~~  154 (292)
                      |+++|+++|+++++|.+ ++.++||+|||+|+|||+++++. |  .+.++++.+.|.++..|+.+.++....++++.+++
T Consensus        80 ~~~~~~~~~~~~~~l~~-~~~~~i~~~~~~k~~wi~~~~~~~~~~~~~~~~~~~~d~~~~~l~~~~~~~~~~~~~~~~~~  158 (508)
T 3l4g_A           80 VFRSIPPEGLAQSELMR-LPSGKVGFSKAMSNKWIRVDKSAADGPRVFRVVDSMEDEVQRRLQLVRGGQAEKLGEKERSE  158 (508)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHhhhcCccHHHHhc-CcchhHHHHHHHHCCCEEecCCCcCcceEeeccCccchHHHHHHHHHHcCCCCCCCHHHHHH
Confidence            99999987899999987 57789999999999999998863 2  46677777888889999999876533456778999


Q ss_pred             hhcccceeeEEEEEEEEecCccccccccccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHh
Q psy10346        155 YKKRKLLQEVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIF  234 (292)
Q Consensus       155 LkkRkLv~~~~~~~~~v~~g~~~~~~~~~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if  234 (292)
                      |||||||...+.++|.|++|++|+.++++++|+||+|||+||+|+++.||+||++++|+....|+.||+++++++|+++|
T Consensus       159 lkkRklv~~~~~~~~~v~~g~~~~~~~~~~~t~lT~e~l~sg~Wk~~~f~~y~~~~~g~~~~~G~lHPl~~v~~~Ir~if  238 (508)
T 3l4g_A          159 LRKRKLLAEVTLKTYWVSKGSAFSTSISKQETELSPEMISSGSWRDRPFKPYNFLAHGVLPDSGHLHPLLKVRSQFRQIF  238 (508)
T ss_dssp             ------------------------CCSCCCCCSCCTTTTTSSTTTTSCCCCCCSSSCCCCCCCCBCCHHHHHHHHHHHHH
T ss_pred             HHhcCCeEEEEEEEEEEecchhhhhhhhhhhccCCHHHhcCCCcCCCCceecccCCCCCCCCCCCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCCCC
Q psy10346        235 LDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS  281 (292)
Q Consensus       235 ~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~~  281 (292)
                      .+|||+||.+||+|+++|||||+||+|||||||+|||||||++|.++
T Consensus       239 ~~mGF~Ev~t~~~ves~~~NFDaLn~P~dHPaR~~~Dtfyi~~P~~~  285 (508)
T 3l4g_A          239 LEMGFTEMPTDNFIESSFWNFDALFQPQQHPARDQHDTFFLRDPAEA  285 (508)
T ss_dssp             HHTTCEECCCCCSEEEHHHHTGGGTCCSSSTTSSTTTSCBBSTTCBC
T ss_pred             HHCcCeEeccCCccccHHHHHHhcCCCCCCcccccCceEEEcCcccc
Confidence            99999998789999999999999999999999999999999998643

>3cmq_A Phenylalanyl-tRNA synthetase, mitochondrial; classii aarss fold, RRM domain, RNA recogntion, aminoacyl-tRNA synthetase, ATP-binding, ligase; HET: FA5; 2.20A {Homo sapiens} PDB: 3hfv_A* 3teg_A* 3tup_A

Probab=99.83  E-value=9e-22  Score=191.79  Aligned_cols=101  Identities=23%  Similarity=0.377  Sum_probs=86.2

Q ss_pred             ccccccc-ccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhhhC--------CceecCCCC
Q psy10346        176 EFSTTIQ-KPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDM--------GFTEMPTNN  246 (292)
Q Consensus       176 ~~~~~~~-~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~m--------GF~e~~~~~  246 (292)
                      +|+.++. +...+++..++.+++|.|.+.+  +++++|+..+.|+.||+++++++|+++|.+|        ||+++.+++
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~ni~~~--~~~~~~~~~~~g~~hPl~~~~~~i~~~f~~~~~~~~g~~Gf~e~~~~~   81 (415)
T 3cmq_A            4 ECATQRAPGSVVELLGKSYPQDDHSNLTRK--VLTRVGRNLHNQQHHPLWLIKERVKEHFYKQYVGRFGTPLFSVYDNLS   81 (415)
T ss_dssp             -------CCSEEEETTEEEECCSSCCCCHH--HHTTTTCCGGGSTTCHHHHHHHHHHHHHHHHHHHCSSSCCCEEECCCC
T ss_pred             hhhhhccCCCcEEECCeeeccCccccCChh--hhcCCCCCCCCCCCCHHHHHHHHHHHHHHhhhccccCCCCcEEEcCCC
Confidence            3444443 4557899999999999998644  8889999999999999999999999999999        999997559


Q ss_pred             ccccceeccccCCCCCCCCCCCCCCceeecCC
Q psy10346        247 FVESSFWNFDALFQPQQHPARDAHDTFFVTDP  278 (292)
Q Consensus       247 ~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~  278 (292)
                      +|+|++||||+||+|+|||||++||||||++.
T Consensus        82 ~v~s~~~NFd~L~~p~dHpaR~~~Dtfyi~~~  113 (415)
T 3cmq_A           82 PVVTTWQNFDSLLIPADHPSRKKGDNYYLNRT  113 (415)
T ss_dssp             SEEEHHHHTGGGTCCTTCGGGCGGGSCBSSSS
T ss_pred             ccccHHHHHHHhCCCCCCCcccccceEEecCC
Confidence            99999999999999999999999999999864

>2du7_A O-phosphoseryl-tRNA synthetase; alpha4 tetramer, ligase, structural genomics, NPPSFA; 3.60A {Methanocaldococcus jannaschii}

Probab=99.79  E-value=8.8e-21  Score=189.61  Aligned_cols=91  Identities=26%  Similarity=0.336  Sum_probs=84.2

Q ss_pred             cccccccCcccccCCCeecc--ccCCCcccCCCCCC--CCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceecccc
Q psy10346        182 QKPETELTPEMIASGSWKTL--NFKPYNFDAMGISL--PSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDA  257 (292)
Q Consensus       182 ~~~~t~LT~eml~sg~w~~~--~fk~y~~~~~~~~~--~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~  257 (292)
                      .+++++||+|||. |+|++.  .|++|+++...+..  ..|+.||+++++++||++|.+|||+||. +|.|+++|||   
T Consensus        15 ~~~~~~lt~~~~~-~~w~~~~~~~~~~~~d~~~P~~~~~~G~~HPl~~~~~~ir~~f~~mGF~e~~-~p~ies~~~n---   89 (549)
T 2du7_A           15 IKKVLELAEKDFE-TAWRETRALIKDKHIDNKYPRLKPVYGKPHPVMETIERLRQAYLRMGFEEMI-NPVIVDEMEI---   89 (549)
T ss_dssp             HHHHHTTSTTCCS-STTTSCCCSSCCCTTTTSSSSSCCCCCCCCHHHHHHHHHHHHHHTTTCEECC-CCSCEEHHHH---
T ss_pred             hHHHHHhhHHHHH-HHHHhhhhhhhccCcCCCCCCCCCCCCCcCHHHHHHHHHHHHHHHCCCEEee-CCeEeehHHh---
Confidence            4568999999999 999999  99999998877655  7899999999999999999999999986 8999999999   


Q ss_pred             CCCCCC-CCCCCCCC-ceeecCCC
Q psy10346        258 LFQPQQ-HPARDAHD-TFFVTDPK  279 (292)
Q Consensus       258 L~~Pqd-HPAR~~~D-Tfyl~~~~  279 (292)
                        +||+ ||||++|| ||||++|.
T Consensus        90 --~pq~ghpAr~~~D~tfyl~~p~  111 (549)
T 2du7_A           90 --YKQFGPEAMAVLDRCFYLAGLP  111 (549)
T ss_dssp             --HHHTCTTHHHHGGGCCEEECCC
T ss_pred             --CCCcCCCcccccCceEEECCCC
Confidence              6999 99999999 99999874

>2odr_B Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis}

Probab=99.79  E-value=3.8e-21  Score=194.05  Aligned_cols=91  Identities=20%  Similarity=0.247  Sum_probs=61.4

Q ss_pred             cccccccCcccccCCCeecc--ccCCCcccCCCCCC--CCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceecccc
Q psy10346        182 QKPETELTPEMIASGSWKTL--NFKPYNFDAMGISL--PSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDA  257 (292)
Q Consensus       182 ~~~~t~LT~eml~sg~w~~~--~fk~y~~~~~~~~~--~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~  257 (292)
                      .+++++||+||| +|+|++.  .|++|+++...+..  ..|+.||+++++++||++|.+|||+||. +|.|+++|||   
T Consensus        23 ~~~~~~lt~e~~-~~~W~~~~~~~~~~~id~~~P~~~~~~G~~HPl~~~~~~IR~if~~mGF~E~~-~p~vese~~n---   97 (648)
T 2odr_B           23 REEIIEMANKDF-EKAWIETKDLIKAKKINESYPRIKPVFGKTHPVNDTIENLRQAYLRMGFEEYI-NPVIVDERDI---   97 (648)
T ss_dssp             ----------------------------CTTSGGGCCCCCCBCCHHHHHHHHHHHHHHHTTCEECC-CCSEEEHHHH---
T ss_pred             hHHHHHhCHHHh-hHHHHhhhhhccccccCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEee-CCEEeehhhh---
Confidence            456899999999 9999999  89999998877655  7899999999999999999999999996 8999999999   


Q ss_pred             CCCCCC-CCCCCCCC-ceeecCCC
Q psy10346        258 LFQPQQ-HPARDAHD-TFFVTDPK  279 (292)
Q Consensus       258 L~~Pqd-HPAR~~~D-Tfyl~~~~  279 (292)
                        +||+ ||||++|| ||||++|.
T Consensus        98 --~pq~gHpAR~~~D~tFyl~~P~  119 (648)
T 2odr_B           98 --YKQFGPEAMAVLDRCFYLAGLP  119 (648)
T ss_dssp             --HHHHGGGHHHHHHTCEEEEBCC
T ss_pred             --CCCcCCCccccCCceEEECCCC
Confidence              6999 99999999 99999875

>2odr_D Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis}

Probab=99.77  E-value=4.6e-21  Score=194.01  Aligned_cols=91  Identities=20%  Similarity=0.247  Sum_probs=84.6

Q ss_pred             cccccccCcccccCCCeecc--ccCCCcccCCCCCC--CCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceecccc
Q psy10346        182 QKPETELTPEMIASGSWKTL--NFKPYNFDAMGISL--PSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDA  257 (292)
Q Consensus       182 ~~~~t~LT~eml~sg~w~~~--~fk~y~~~~~~~~~--~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~  257 (292)
                      .+++++||+||| +|+|++.  .|++|+++...+..  ..|+.||+++++++||++|.+|||+||. +|.|+++|||   
T Consensus        23 ~~~~~~lt~e~~-~~~W~~~~~~~~~~~id~~~P~~~~~~G~~HPl~~~~~~IReif~~mGF~E~~-~p~vese~~n---   97 (685)
T 2odr_D           23 REEIIEMANKDF-EKAWIETKDLIKAKKINESYPRIKPVFGKTHPVNDTIENLRQAYLRMGFEEYI-NPVIVDERDI---   97 (685)
T ss_dssp             CHHHHHHHHHCH-HHHHHHHGGGSCCCCGGGSTTTCCCCCCBCCHHHHHHHHHHHHHHHTTCEECC-CCSEEEHHHH---
T ss_pred             hHHHhhhCHHHh-hHHHHhhhhhccccccCCCCCCCCCCCCCcCHHHHHHHHHHHHHHHCCCEEee-CCEEeehHHh---
Confidence            456899999999 9999999  99999998877755  7899999999999999999999999996 8999999999   


Q ss_pred             CCCCCC-CCCCCCCC-ceeecCCC
Q psy10346        258 LFQPQQ-HPARDAHD-TFFVTDPK  279 (292)
Q Consensus       258 L~~Pqd-HPAR~~~D-Tfyl~~~~  279 (292)
                        +||+ ||||++|| ||||++|.
T Consensus        98 --~pq~gHPAR~~~D~tFyL~~P~  119 (685)
T 2odr_D           98 --YKQFGPEAMAVLDRCFYLAGLP  119 (685)
T ss_dssp             --HHHHGGGHHHHHHTCEEEEBCC
T ss_pred             --CCCcCCCccccCCcEEEECCCC
Confidence              6999 99999999 99999875

>2odr_A Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis}

Probab=99.77  E-value=4.2e-21  Score=194.03  Aligned_cols=91  Identities=20%  Similarity=0.247  Sum_probs=84.4

Q ss_pred             cccccccCcccccCCCeecc--ccCCCcccCCCCCC--CCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceecccc
Q psy10346        182 QKPETELTPEMIASGSWKTL--NFKPYNFDAMGISL--PSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDA  257 (292)
Q Consensus       182 ~~~~t~LT~eml~sg~w~~~--~fk~y~~~~~~~~~--~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~  257 (292)
                      .+++++||+||| +|+|++.  .|++|+++...+..  ..|+.||+++++++||++|.+|||+||. +|.|+++|||   
T Consensus        23 ~~~~~~lt~e~~-~~~W~~~~~~~~~~~id~~~P~~~~~~G~~HPl~~~~~~IR~if~~mGF~E~~-~p~vese~~n---   97 (665)
T 2odr_A           23 REEIIEMANKDF-EKAWIETKDLIKAKKINESYPRIKPVFGKTHPVNDTIENLRQAYLRMGFEEYI-NPVIVDERDI---   97 (665)
T ss_dssp             CHHHHHHHHHCH-HHHHHHHGGGSCCCCTTTSGGGSCCCCCBCCHHHHHHHHHHHHHHHTTCEECC-CCSEEEHHHH---
T ss_pred             hHHHHHhCHHHh-hHHHHhhhhhccccccCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEee-CCEEeeehhh---
Confidence            456899999999 9999999  99999998877654  7899999999999999999999999996 8999999999   


Q ss_pred             CCCCCC-CCCCCCCC-ceeecCCC
Q psy10346        258 LFQPQQ-HPARDAHD-TFFVTDPK  279 (292)
Q Consensus       258 L~~Pqd-HPAR~~~D-Tfyl~~~~  279 (292)
                        +||+ ||||++|| ||||++|.
T Consensus        98 --~pq~gHpAR~~~D~tFyL~~P~  119 (665)
T 2odr_A           98 --YKQFGPEAMAVLDRCFYLAGLP  119 (665)
T ss_dssp             --HHHHGGGHHHHHHTCEEEEBCC
T ss_pred             --CCCcCCCccccCCcEEEECCCC
Confidence              6999 99999999 99999875

>2odr_C Phosphoseryl-tRNA synthetase; phosphoserine tRNA synthetase class II, ligase; 3.23A {Methanococcus maripaludis}

Probab=99.77  E-value=5.1e-21  Score=194.05  Aligned_cols=91  Identities=20%  Similarity=0.247  Sum_probs=84.6

Q ss_pred             cccccccCcccccCCCeecc--ccCCCcccCCCCCC--CCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceecccc
Q psy10346        182 QKPETELTPEMIASGSWKTL--NFKPYNFDAMGISL--PSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDA  257 (292)
Q Consensus       182 ~~~~t~LT~eml~sg~w~~~--~fk~y~~~~~~~~~--~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~  257 (292)
                      .+++++||+||| +|+|++.  .|++|+++...+..  ..|+.||+++++++||++|.+|||+||. +|.|+++|||   
T Consensus        23 ~~~~~~lt~e~~-~~~W~~~~~~~~~~~id~~~P~~~~~~G~~HPl~~~~~~IReif~~mGF~Ev~-~p~Vese~~n---   97 (701)
T 2odr_C           23 REEIIEMANKDF-EKAWIETKDLIKAKKINESYPRIKPVFGKTHPVNDTIENLRQAYLRMGFEEYI-NPVIVDERDI---   97 (701)
T ss_dssp             CHHHHHHHHHCH-HHHHHHHGGGSCCCCTTTSSTTCCCCCCBCCHHHHHHHHHHHHHHHTTCEECC-CCSEEEHHHH---
T ss_pred             hHHHHHhCHHHh-hHHHHhhhhhccccccCCCCCCCCCCCCCcCHHHHHHHHHHHHHHHCCCEEee-CCEEeeehhh---
Confidence            456899999999 9999999  99999998877755  7899999999999999999999999996 8999999999   


Q ss_pred             CCCCCC-CCCCCCCC-ceeecCCC
Q psy10346        258 LFQPQQ-HPARDAHD-TFFVTDPK  279 (292)
Q Consensus       258 L~~Pqd-HPAR~~~D-Tfyl~~~~  279 (292)
                        +||+ ||||++|| ||||++|.
T Consensus        98 --~pq~gHPAR~~~D~tFYL~~P~  119 (701)
T 2odr_C           98 --YKQFGPEAMAVLDRCFYLAGLP  119 (701)
T ss_dssp             --HHHHGGGHHHHHHTCEEEEECC
T ss_pred             --CCCcCCCccccCCcEEEECCCC
Confidence              6999 99999999 99999875

>3pco_A Phenylalanyl-tRNA synthetase, alpha subunit; aminoacylation, tRNA-binding, DNA-binding domain, four-helix aminoacyl-tRNA synthetase, ATP-binding; HET: PHE AMP; 3.02A {Escherichia coli}

Probab=99.71  E-value=2.3e-18  Score=163.11  Aligned_cols=72  Identities=35%  Similarity=0.617  Sum_probs=68.2

Q ss_pred             CCcccCCCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecC
Q psy10346        205 PYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTD  277 (292)
Q Consensus       205 ~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~  277 (292)
                      .+++++|++....|+.||+++++++|+++|.+|||+|+ .+|.|++++||||+||+|+|||||++|||||+++
T Consensus        91 ~id~TLP~~~~~~G~~hp~~~~~~~Ir~if~~~Gf~ev-~~~~ve~~~~nFd~Ln~p~dhpaR~~~dt~~i~e  162 (327)
T 3pco_A           91 TIDVSLPGRRIENGGLHPVTRTIDRIESFFGELGFTVA-TGPEIEDDYHNFDALNIPGHHPARADHDTFWFDT  162 (327)
T ss_dssp             CCCTTSCCCCCCCCCCCHHHHHHHHHHHHHHTTTCBCC-CCCSEECTCCCCCTTTCCSSSHHHHHTTCCBSSS
T ss_pred             CCCCcCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCeEE-ECCCccCCHHHHHhhCCCCCChhhcccccEEeCC
Confidence            36888999999999999999999999999999999997 5899999999999999999999999999999974

>1b7y_A Phers, protein (phenylalanyl-tRNA synthetase); enzyme, alpha/beta homodimer, ligase; HET: FYA; 2.50A {Thermus thermophilus} SCOP: d.104.1.1 PDB: 1b70_A* 1eiy_A 1jjc_A* 1pys_A 2iy5_A* 3hfz_A* 3teh_A* 2aly_A* 2akw_A* 2amc_A*

Probab=99.68  E-value=2.3e-17  Score=157.65  Aligned_cols=74  Identities=42%  Similarity=0.665  Sum_probs=69.6

Q ss_pred             CcccCCCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCCC
Q psy10346        206 YNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKT  280 (292)
Q Consensus       206 y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~  280 (292)
                      +++..|+.....|+.||+++++++|+++|.+|||.|+. +|+|++++||||+|++|++||||+++|||||++|..
T Consensus        86 i~~tlP~~~~~~g~~hp~~~~~~~Ir~~f~~~Gf~Ev~-~p~v~~~~~nfd~L~~p~~hpar~~~dt~~l~nP~s  159 (350)
T 1b7y_A           86 VDVSLPGASLFSGGLHPITLMERELVEIFRALGYQAVE-GPEVESEFFNFDALNIPEHHPARDMWDTFWLTGEGF  159 (350)
T ss_dssp             CCTTSCCCCCCCCBCCHHHHHHHHHHHHHHTTTCEECC-CCSEEEHHHHTTTTTCCSSSTTTTSSCCCBEECSSC
T ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEE-CcchhcchhHHHhhCCCCCCccccccccEEEcCccc
Confidence            57788888889999999999999999999999999986 899999999999999999999999999999998754

>2rhq_A Phenylalanyl-tRNA synthetase alpha chain; heterotetramer, phenylalanine, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase; HET: GAX; 2.20A {Staphylococcus haemolyticus} PDB: 2rhs_A*

Probab=99.37  E-value=3.5e-13  Score=125.41  Aligned_cols=72  Identities=32%  Similarity=0.650  Sum_probs=66.0

Q ss_pred             CCCcccCCCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeec
Q psy10346        204 KPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVT  276 (292)
Q Consensus       204 k~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~  276 (292)
                      -.++...|+.....|..||+.++++.||++|.++||.|+ +.|.|+++.||||+|++|++||||+++|||||+
T Consensus        36 d~i~~tlp~~~~~~g~~~~~~~~~~~iR~~l~~~Gf~Ev-~~s~l~~~~~nf~~l~~~~~~par~~~d~~~l~  107 (294)
T 2rhq_A           36 ETIDVTLPSRQISIGSKHPLTRTVEEIEDLFLGLGYEIV-DGYEVEQDYYNFEALNLPKSHPARDMQDSFYIT  107 (294)
T ss_dssp             TCCCTTSCCCCCCCCCCCHHHHHHHHHHHHHHTTTCEEC-CCCSEEEHHHHTGGGTCCTTCGGGCTTTSCBSS
T ss_pred             ccCCccCCCcccCCCCCCHHHHHHHHHHHHHHHCCCEEE-cCcceeeehhhHHhhCCCCCccccccCCcEEEc
Confidence            345666777777889999999999999999999999999 789999999999999999999999999999995

>2du3_A O-phosphoseryl-tRNA synthetase; alpha4 tetramer, ligase/RNA complex; HET: SEP; 2.60A {Archaeoglobus fulgidus} PDB: 2du4_A 2du5_A* 2du6_A*

Probab=99.14  E-value=1.2e-12  Score=130.94  Aligned_cols=88  Identities=20%  Similarity=0.352  Sum_probs=76.8

Q ss_pred             ccccccCcccccCCCeecc--ccCCCcccCCCCCC--CCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccC
Q psy10346        183 KPETELTPEMIASGSWKTL--NFKPYNFDAMGISL--PSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDAL  258 (292)
Q Consensus       183 ~~~t~LT~eml~sg~w~~~--~fk~y~~~~~~~~~--~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L  258 (292)
                      ++++.+|+..| +++|+-.  .+|.|.++..++.+  ..|+.||+.+++++|+++|.+|||+|+. ++.+++++||    
T Consensus         6 ~~~~~~tR~Di-~~~~DliEEvaR~yGyd~i~~~~~~~~g~~hp~~~~~~~Ir~~l~~lGF~Ev~-~~s~~s~~~n----   79 (534)
T 2du3_A            6 QKYRELAEKDF-EAAWKAGKEILAERSPNELYPRVGFSFGKEHPLFATIQRLREAYLSIGFSEVV-NPLIVEDVHV----   79 (534)
T ss_dssp             HHHHHHHHHCH-HHHHHHGGGGSCCCCGGGSTTSSCCCCCCCCHHHHHHHHHHHHHHHTTCEECC-CCCEEETHHH----
T ss_pred             HHhccCChhhc-chhhHHHhhhhhccCCCCCCCccCCCCCCCCHHHHHHHHHHHHHHHCCCEEEe-CceEeChhhc----
Confidence            34567777766 5678766  78999999888766  7899999999999999999999999986 7899999999    


Q ss_pred             CCCCC-CCCCCCCC-ceeecC
Q psy10346        259 FQPQQ-HPARDAHD-TFFVTD  277 (292)
Q Consensus       259 ~~Pqd-HPAR~~~D-Tfyl~~  277 (292)
                       +||+ ||||++|| |||++.
T Consensus        80 -~p~~~Hpar~~~Dr~fyl~~   99 (534)
T 2du3_A           80 -KKQFGREALAVLDRCFYLAT   99 (534)
T ss_dssp             -HHHHGGGHHHHHTTSCEEEE
T ss_pred             -ccccccchhhhccceeeccC
Confidence             9998 99999999 999975

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=97.74  E-value=9.8e-05  Score=58.57  Aligned_cols=73  Identities=14%  Similarity=0.114  Sum_probs=61.9

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe----eeeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE----PLSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e----~~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|...+.++..++|..+|+++..|.+.+..|+++ |+|...    ..-...+.||++|+.++....+...
T Consensus        38 ~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~L~~~-glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~~  114 (140)
T 2nnn_A           38 PTQWAALVRLGETGPCPQNQLGRLTAMDAATIKGVVERLDKR-GLIQRSADPDDGRRLLVSLSPAGRAELEAGLAAAR  114 (140)
T ss_dssp             HHHHHHHHHHHHHSSBCHHHHHHHTTCCHHHHHHHHHHHHHT-TCEEEEEETTEEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEeeCCCCCCCeeeeEECHhHHHHHHHHHHHHH
Confidence            467889999977677889999999999999999999999987 999875    3445678999999999987766654

>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=97.72  E-value=0.00012  Score=55.99  Aligned_cols=71  Identities=18%  Similarity=0.112  Sum_probs=58.8

Q ss_pred             HHHHHHHHHhccCCCCChHHH----HHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHHHhhcCChH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDL----AKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQVKDNGSHE   75 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~el----a~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~yl~~GlPE   75 (292)
                      ..|..||..|...+.....++    |+.++++...|.+.++.|+.+ |||.-... ....+.||++|+++++.-.+.
T Consensus         8 ~~q~~iL~~l~~~~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~-gli~r~~~~r~~~~~LT~~G~~~~~~~~~~   83 (99)
T 1tbx_A            8 YPEAIVLAYLYDNEGIATYDLYKKVNAEFPMSTATFYDAKKFLIQE-GFVKERQERGEKRLYLTEKGKLFAISLKTA   83 (99)
T ss_dssp             CHHHHHHHHHTTCTTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEECHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHC-CCEEEEecCCceEEEECHHHHHHHHHHHHH
Confidence            567889999987777888899    888999999999999999987 99986433 456789999999988654443

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=97.71  E-value=0.00013  Score=58.04  Aligned_cols=88  Identities=18%  Similarity=0.147  Sum_probs=68.7

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHh-hcCChHHH-
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVK-DNGSHEVL-   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl-~~GlPE~r-   77 (292)
                      ..+..||..|...+.++..++|..+|+++..|.+.+..|+.+ |+|....    .....+.||++|++++ ..-.+... 
T Consensus        31 ~~~~~iL~~l~~~~~~~~~ela~~l~is~~~vs~~l~~L~~~-gli~~~~~~~d~r~~~~~lT~~G~~~~~~~~~~~~~~  109 (142)
T 3bdd_A           31 LTRYSILQTLLKDAPLHQLALQERLQIDRAAVTRHLKLLEES-GYIIRKRNPDNQREVLVWPTEQAREALITNPSAHHQA  109 (142)
T ss_dssp             HHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECSSSTTCEEEEECHHHHHHHTTSCCHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEecCCCCCCCeeEEEECHHHHHHHHHHHHHHHHH
Confidence            467889999977677889999999999999999999999987 9998765    3366789999999999 88887765 


Q ss_pred             HHhhcCCCCCChHHHh
Q psy10346         78 VFNNVPSEGIGQKELL   93 (292)
Q Consensus        78 l~~~l~~~~~~~~el~   93 (292)
                      +...+- .+++-+++.
T Consensus       110 ~~~~~~-~~l~~~e~~  124 (142)
T 3bdd_A          110 IKTSMN-QILTVEESE  124 (142)
T ss_dssp             HHHHHH-TSSCHHHHH
T ss_pred             HHHHHH-hcCCHHHHH
Confidence            332222 245544443

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=97.68  E-value=0.00016  Score=57.24  Aligned_cols=88  Identities=16%  Similarity=0.158  Sum_probs=67.7

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH-H
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL-V   78 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r-l   78 (292)
                      ..+..||..|..++.+...++|+.+|+++..|.+.+..|+.+ |+|....    .-...+.||+.|+.++....+... +
T Consensus        29 ~~~~~iL~~l~~~~~~~~~ela~~l~~s~~tvs~~l~~L~~~-glv~~~~~~~d~R~~~~~lT~~G~~~~~~~~~~~~~~  107 (138)
T 3bpv_A           29 DAQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEES-GFIEREQDPENRRRYILEVTRRGEEIIPLILKVEERW  107 (138)
T ss_dssp             HHHHHHHHHHHHSTTCBHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEEEEECHHHHHTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEeecCCCCceeEEeeECHhHHHHHHHHHHHHHHH
Confidence            567889999987778889999999999999999999999987 9998743    445678999999999887666544 2


Q ss_pred             HhhcCCCCCChHHHh
Q psy10346         79 FNNVPSEGIGQKELL   93 (292)
Q Consensus        79 ~~~l~~~~~~~~el~   93 (292)
                      ...+- .+++-+++.
T Consensus       108 ~~~~~-~~l~~~e~~  121 (138)
T 3bpv_A          108 EDLLF-RDFTEDERK  121 (138)
T ss_dssp             HHHHT-TTSCHHHHH
T ss_pred             HHHHH-hcCCHHHHH
Confidence            22222 345544443

>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=97.68  E-value=9.9e-05  Score=59.37  Aligned_cols=88  Identities=15%  Similarity=0.128  Sum_probs=67.5

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVLVF   79 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~rl~   79 (292)
                      ..|..||..|...+.+...++|..+++++..|.+.+..|+.+ |+|+...    .-...+.||++|+++++.-.+...-+
T Consensus        36 ~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~-Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~~~~~~~  114 (140)
T 3hsr_A           36 YTGYIVLMAIENDEKLNIKKLGERVFLDSGTLTPLLKKLEKK-DYVVRTREEKDERNLQISLTEQGKAIKSPLAEISVKV  114 (140)
T ss_dssp             HHHHHHHHHSCTTCEEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEC-------CEEEECHHHHHTHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHC-CCeEecCCCCCcceeeeeEChHHHHHHHHHHHHHHHH
Confidence            567889999987777888999999999999999999999987 9999763    34567899999999998766665532


Q ss_pred             hhcCCCCCChHHHhh
Q psy10346         80 NNVPSEGIGQKELLA   94 (292)
Q Consensus        80 ~~l~~~~~~~~el~~   94 (292)
                      ..--  +++-+|+..
T Consensus       115 ~~~~--~l~~~e~~~  127 (140)
T 3hsr_A          115 FNEF--NISEREASD  127 (140)
T ss_dssp             HHTS--CCCHHHHHH
T ss_pred             HHhc--CCCHHHHHH
Confidence            2211  555555444

>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=97.61  E-value=0.00022  Score=56.96  Aligned_cols=88  Identities=15%  Similarity=0.202  Sum_probs=67.4

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChHHH-H
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHEVL-V   78 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE~r-l   78 (292)
                      ..+..||..|. .+.+...++|..+|+++..|.+.+..|+.+ |+|.....    -...+.||+.|+.++....+... +
T Consensus        37 ~~~~~iL~~l~-~~~~~~~ela~~l~~s~~tvs~~l~~Le~~-glv~r~~~~~d~r~~~~~lT~~G~~~~~~~~~~~~~~  114 (146)
T 2gxg_A           37 YLDFLVLRATS-DGPKTMAYLANRYFVTQSAITASVDKLEEM-GLVVRVRDREDRRKILIEITEKGLETFNKGIEIYKKL  114 (146)
T ss_dssp             HHHHHHHHHHT-TSCBCHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEEECSSCTTCEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHh-cCCcCHHHHHHHhCCCchhHHHHHHHHHHC-CCEEeecCCCCCceEEEEECHHHHHHHHHHHHHHHHH
Confidence            56888999998 778899999999999999999999999987 99987542    35678999999999987666544 2


Q ss_pred             HhhcCCCCCChHHHhh
Q psy10346         79 FNNVPSEGIGQKELLA   94 (292)
Q Consensus        79 ~~~l~~~~~~~~el~~   94 (292)
                      ...+- .+++-+++..
T Consensus       115 ~~~~~-~~l~~~e~~~  129 (146)
T 2gxg_A          115 ANEVT-GDLSEDEVIL  129 (146)
T ss_dssp             HHHHT-TTSCHHHHHH
T ss_pred             HHHHH-hcCCHHHHHH
Confidence            22222 3455444433

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=97.59  E-value=0.00017  Score=57.61  Aligned_cols=89  Identities=16%  Similarity=0.068  Sum_probs=67.2

Q ss_pred             HHHHHHHHHh-ccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH-
Q psy10346          4 DLTEKILKYL-DTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL-   77 (292)
Q Consensus         4 ~~e~~iL~~L-~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r-   77 (292)
                      ..+..||..| ..++.++..++|+.+|+++..|.+.+..|+.+ |+|....    .-...+.||++|+.++..-.+... 
T Consensus        37 ~~~~~iL~~l~~~~~~~t~~~la~~l~~s~~~vs~~l~~L~~~-glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~~~  115 (146)
T 2fbh_A           37 QARWLVLLHLARHRDSPTQRELAQSVGVEGPTLARLLDGLESQ-GLVRRLAVAEDRRAKHIVLTPKADVLIADIEAIAAS  115 (146)
T ss_dssp             TTHHHHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEECCBTTBCSCEEEECTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHC-CCeeecCCCcccCeeeeEECHhHHHHHHHHHHHHHH
Confidence            4577899999 66777889999999999999999999999987 9998864    345678999999999877655543 


Q ss_pred             HHhhcCCCCCChHHHhh
Q psy10346         78 VFNNVPSEGIGQKELLA   94 (292)
Q Consensus        78 l~~~l~~~~~~~~el~~   94 (292)
                      +...+- .+++-+|+..
T Consensus       116 ~~~~~~-~~l~~~e~~~  131 (146)
T 2fbh_A          116 VRNDVL-TGIDESEQAL  131 (146)
T ss_dssp             HHHHHT-TTCCHHHHHH
T ss_pred             HHHHHH-cCCCHHHHHH
Confidence            222222 3455555443

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=97.59  E-value=0.00024  Score=57.58  Aligned_cols=88  Identities=10%  Similarity=0.024  Sum_probs=67.8

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVLVF   79 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~rl~   79 (292)
                      ..+..||..|...+.+...++|..++++...|.+.+..|+.+ |+|....    .-...+.||++|+.+++.-.+...-+
T Consensus        47 ~~~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~Le~~-glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~~~~  125 (153)
T 2pex_A           47 YPQYLVMLVLWETDERSVSEIGERLYLDSATLTPLLKRLQAA-GLVTRTRAASDERQVIIALTETGRALRSKAGAVPEQV  125 (153)
T ss_dssp             HHHHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEC-------CEEEECHHHHHGGGGSTTHHHHH
T ss_pred             HHHHHHHHHHHhCCCcCHHHHHHHhCCCcccHHHHHHHHHHC-CCEeecCCcccCCeeEeeECHHHHHHHHHHHHHHHHH
Confidence            567889999987777888999999999999999999999987 9998753    23456899999999998888766633


Q ss_pred             hhcCCCCCChHHHhh
Q psy10346         80 NNVPSEGIGQKELLA   94 (292)
Q Consensus        80 ~~l~~~~~~~~el~~   94 (292)
                      ...  .+++-+++..
T Consensus       126 ~~~--~~l~~~e~~~  138 (153)
T 2pex_A          126 FCA--SACSLDELRQ  138 (153)
T ss_dssp             HHH--HTCCHHHHHH
T ss_pred             Hhc--cCCCHHHHHH
Confidence            322  3455555443

>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=97.59  E-value=7.8e-05  Score=56.33  Aligned_cols=70  Identities=10%  Similarity=0.064  Sum_probs=57.6

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCC
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGS   73 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~Gl   73 (292)
                      .+.+.+||..|...+.....++|+.+|+++..|.+.++.|+.. |+|....    .....|.||++|.+.+..-.
T Consensus        15 ~~~~~~iL~~L~~~~~~~~~ela~~l~is~~tvs~~l~~L~~~-gli~~~~~~~~~r~~~~~lt~~g~~~~~~~~   88 (100)
T 1ub9_A           15 NPVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERN-GLVKTYKVIADRPRTVVEITDFGMEEAKRFL   88 (100)
T ss_dssp             SHHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEEEECSSSCEEEEEECHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHhcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEecCCCcceEEEEECHHHHHHHHHHH
Confidence            4567889998865566788999999999999999999999987 9998644    45678999999987665433

>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=97.58  E-value=0.0002  Score=59.02  Aligned_cols=89  Identities=12%  Similarity=0.057  Sum_probs=69.2

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChHHH-H
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHEVL-V   78 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE~r-l   78 (292)
                      ..+..||..|...+.+...++|..+|+++..|.+.+..|+.+ |||.....    -...+.||++|+++++.-.+... +
T Consensus        46 ~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~-Glv~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~~~  124 (162)
T 3k0l_A           46 LPQFTALSVLAAKPNLSNAKLAERSFIKPQSANKILQDLLAN-GWIEKAPDPTHGRRILVTVTPSGLDKLNQCNQVVQQL  124 (162)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHTSCGGGHHHHHHHHHHT-TSEEEEECCSSSCCEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-cCeEecCCCCcCCeeEeEECHhHHHHHHHHHHHHHHH
Confidence            567889999988788899999999999999999999999987 99987543    35678999999999987766554 2


Q ss_pred             HhhcCCCCCChHHHhh
Q psy10346         79 FNNVPSEGIGQKELLA   94 (292)
Q Consensus        79 ~~~l~~~~~~~~el~~   94 (292)
                      ...+- .+++-+++..
T Consensus       125 ~~~~~-~~l~~~e~~~  139 (162)
T 3k0l_A          125 EAQML-QGVDINLAFL  139 (162)
T ss_dssp             HHHHT-TTSCHHHHHH
T ss_pred             HHHHH-hCCCHHHHHH
Confidence            22221 3455555444

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=97.58  E-value=0.00011  Score=59.00  Aligned_cols=89  Identities=16%  Similarity=0.173  Sum_probs=68.4

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH-H
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL-V   78 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r-l   78 (292)
                      ..+..||..|...+.++..++|..+|+++..|.+.+..|+.+ |+|+...    .-...+.||++|+++++.-.+... +
T Consensus        37 ~~~~~iL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~-Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~~~~~~~  115 (143)
T 3oop_A           37 PEQWSVLEGIEANEPISQKEIALWTKKDTPTVNRIVDVLLRK-ELIVREISTEDRRISLLSLTDKGRKETTELRDIVEAS  115 (143)
T ss_dssp             HHHHHHHHHHHHHSSEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEC----CCSCEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHHCCCHhhHHHHHHHHHHC-CCeeccCCCccCceeeeeECHHHHHHHHHHHHHHHHH
Confidence            568889999977777888999999999999999999999987 9998753    335678999999999987666655 2


Q ss_pred             HhhcCCCCCChHHHhh
Q psy10346         79 FNNVPSEGIGQKELLA   94 (292)
Q Consensus        79 ~~~l~~~~~~~~el~~   94 (292)
                      ...+- .+++-+|+..
T Consensus       116 ~~~~~-~~l~~~e~~~  130 (143)
T 3oop_A          116 CEKMF-AGVTRTDLEQ  130 (143)
T ss_dssp             HHHHT-TTCCHHHHHH
T ss_pred             HHHHH-cCCCHHHHHH
Confidence            22222 3455555443

>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=97.57  E-value=0.00014  Score=58.23  Aligned_cols=87  Identities=16%  Similarity=0.133  Sum_probs=69.1

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHHH-
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVLV-   78 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~rl-   78 (292)
                      ..+..||..|...+.++..++|+.+|++...|.+.+..|+.+ |+|....    .-...+.||++|+.++..-.+...- 
T Consensus        37 ~~~~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~-gli~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~~~~  115 (142)
T 2bv6_A           37 YPQFLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQV-DLIKRERSEVDQREVFIHLTDKSETIRPELSNASDKV  115 (142)
T ss_dssp             HHHHHHHHHHHHSSEEEHHHHHHHTTCCTTTHHHHHHHHHHT-TSEEEEECSSSTTCEEEEECHHHHHHHHHHTTHHHHH
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHC-CCEEeecCCCCcceEEEEEChHHHHHHHHHHHHHHHH
Confidence            567889999987777788999999999999999999999987 9998765    3456889999999999888776653 


Q ss_pred             HhhcCCCCCChHHHhh
Q psy10346         79 FNNVPSEGIGQKELLA   94 (292)
Q Consensus        79 ~~~l~~~~~~~~el~~   94 (292)
                      ...+   +++-+++..
T Consensus       116 ~~~~---~l~~~e~~~  128 (142)
T 2bv6_A          116 ASAS---SLSQDEVKE  128 (142)
T ss_dssp             HHHT---TCCHHHHHH
T ss_pred             HHHh---CCCHHHHHH
Confidence            3333   555555443

>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=97.57  E-value=0.00018  Score=57.26  Aligned_cols=89  Identities=18%  Similarity=0.179  Sum_probs=66.9

Q ss_pred             HHHHHHHHHhccCC--CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNP--PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~--~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|...+  .+...++|..+|+++..|.+.++.|+.+ |+|....    .-...+.||++|+.++..-.+...
T Consensus        34 ~~~~~iL~~l~~~~~~~~~~~ela~~l~~~~~tvs~~l~~Le~~-Gli~r~~~~~d~R~~~i~lT~~G~~~~~~~~~~~~  112 (141)
T 3bro_A           34 GTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIK-KLLYRKVSGKDSRQKCLKLTKKANKLETIILSYMD  112 (141)
T ss_dssp             HHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECSSCTTSEEEEECHHHHTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCcchHHHHHHHHHHC-CCEEeeCCCcCCCeeeeEECHHHHHHHHHHHHHHH
Confidence            46788999997665  6888999999999999999999999987 9998764    234578999999998877666544


Q ss_pred             -HHhhcCCCCCChHHHhh
Q psy10346         78 -VFNNVPSEGIGQKELLA   94 (292)
Q Consensus        78 -l~~~l~~~~~~~~el~~   94 (292)
                       +...+- .+++-+++..
T Consensus       113 ~~~~~~~-~~l~~~e~~~  129 (141)
T 3bro_A          113 SDQSQMT-SGLNKEEVVF  129 (141)
T ss_dssp             HHHHHHT-TTCCHHHHHH
T ss_pred             HHHHHHH-hcCCHHHHHH
Confidence             222222 3455555433

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=97.57  E-value=8.1e-05  Score=59.90  Aligned_cols=65  Identities=14%  Similarity=0.167  Sum_probs=57.1

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhc--CCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLF--NEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD   70 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~--~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~   70 (292)
                      .....+||..|..++.....++|...  |++...|.+-++.|+.. |+|+....-  .|.||++|++++.
T Consensus        12 d~~d~~IL~~L~~~g~~s~~eLA~~l~~giS~~aVs~rL~~Le~~-GLV~~~~rg--~Y~LT~~G~~~l~   78 (111)
T 3b73_A           12 TIWDDRILEIIHEEGNGSPKELEDRDEIRISKSSVSRRLKKLADH-DLLQPLANG--VYVITEEGEAYLN   78 (111)
T ss_dssp             CHHHHHHHHHHHHHSCBCHHHHHTSTTCCSCHHHHHHHHHHHHHT-TSEEECSTT--CEEECHHHHHHHT
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHhcCCCHHHHHHHHHHHHHC-CCEEecCCc--eEEECchHHHHHH
Confidence            35688999999877788999999999  99999999999999987 999976433  8999999998874

>1xmk_A Double-stranded RNA-specific adenosine deaminase; winged helix-turn-helix, RNA editing, interferon, ADAR1, hydrolase; 0.97A {Homo sapiens} SCOP: a.4.5.19

Probab=97.56  E-value=7.2e-05  Score=56.88  Aligned_cols=65  Identities=22%  Similarity=0.282  Sum_probs=56.9

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHH-HHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQ-KVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~-~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl   69 (292)
                      +.+.+||.+|...+.....++|+.+|++.. +|-+.+..|+.. |+|.....-.-.|.||+.|++.+
T Consensus        11 ~~~~~IL~~Lk~~g~~ta~eiA~~Lgit~~~aVr~hL~~Le~e-GlV~~~~~gRP~w~LT~~g~~~~   76 (79)
T 1xmk_A           11 EIKEKICDYLFNVSDSSALNLAKNIGLTKARDINAVLIDMERQ-GDVYRQGTTPPIWHLTDKKRERM   76 (79)
T ss_dssp             HHHHHHHHHHHHTCCEEHHHHHHHHCGGGHHHHHHHHHHHHHT-TSEEEECSSSCEEEECHHHHTTT
T ss_pred             hHHHHHHHHHHHcCCcCHHHHHHHcCCCcHHHHHHHHHHHHHC-CCEEecCCCCCCeEeCHhHHhHh
Confidence            568899999999999899999999999999 999999999986 99986544445999999998754

>3l4g_B Phenylalanyl-tRNA synthetase beta chain; aminoacylation, tRNA-binding, DNA-binding domain, four-helix acetylation, aminoacyl-tRNA synthetase; HET: PHE; 3.30A {Homo sapiens}

Probab=97.55  E-value=7.8e-05  Score=75.30  Aligned_cols=61  Identities=25%  Similarity=0.201  Sum_probs=52.8

Q ss_pred             CCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCCCC
Q psy10346        215 LPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS  281 (292)
Q Consensus       215 ~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~~  281 (292)
                      ...|..||..++++.+|++|.++||.|+-+.+ .++..||||+|++|.+|     +|+++|.+|-+.
T Consensus       385 ~~~g~~~~~~~~~~~ir~~l~~~Gf~Evitys-f~s~~~~~~~l~~~~~~-----~~~v~L~NPis~  445 (589)
T 3l4g_B          385 YTIANQFPLNKLTELLRHDMAAAGFTEALTFA-LCSQEDIADKLGVDISA-----TKAVHISNPKTA  445 (589)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHHHTTCEECCCCS-EECHHHHTGGGTSCTTS-----SCCCBBSSCSSG
T ss_pred             cccCCCCHHHHHHHHHHHHHHHCCCEEEecCc-ccCHHHHHHHhCCCCCC-----CCeEEEcCCCch
Confidence            45688999999999999999999999987554 56888999999999988     489999988543

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=97.54  E-value=0.00018  Score=57.14  Aligned_cols=72  Identities=14%  Similarity=0.094  Sum_probs=60.2

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      ..+..||..|...+.++..++|+.+|+++..|.+.+..|+.+ |+|....    .-...+.||+.|++++..-.+..
T Consensus        36 ~~~~~iL~~l~~~~~~t~~ela~~l~~s~~~vs~~l~~Le~~-glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~  111 (142)
T 2fbi_A           36 EQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLERD-GIVRRWKAPKDQRRVYVNLTEKGQQCFVSMSGDM  111 (142)
T ss_dssp             HHHHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCCHhHHHHHHHHHHHC-CCEEeecCCCCCCeeEEEECHHHHHHHHHHHHHH
Confidence            567889999977667888999999999999999999999987 9998753    34567899999999987655543

>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=97.53  E-value=0.00023  Score=56.80  Aligned_cols=72  Identities=21%  Similarity=0.220  Sum_probs=60.4

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      ..+..||..|...+.++..++|..+|+++..|.+.+..|+.+ |+|+...    .-...+.||++|+.++..-.+..
T Consensus        33 ~~~~~iL~~l~~~~~~~~~~la~~l~~s~~tvs~~l~~L~~~-glv~r~~~~~d~r~~~~~lT~~G~~~~~~~~~~~  108 (145)
T 2a61_A           33 PAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEAD-GYLTRTPDPADRRAYFLVITRKGEEVIEKVIERR  108 (145)
T ss_dssp             HHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHHHC-CCeeecCCCCCCceEEEEECHHHHHHHHHHHHHH
Confidence            567889999977677889999999999999999999999987 9998853    44567899999999986655443

>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=97.53  E-value=0.00015  Score=57.64  Aligned_cols=73  Identities=14%  Similarity=0.127  Sum_probs=61.6

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|...+.+...++|..+|+++..|.+.++.|+.+ |+|....    .-...+.||++|++++..-.+...
T Consensus        34 ~~~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~~L~~~-gli~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~~  110 (138)
T 1jgs_A           34 AAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCK-GWVERLPNPNDKRGVLVKLTTGGAAICEQCHQLVG  110 (138)
T ss_dssp             HHHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECTTCSSCEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHCCChHHHHHHHHHHHHC-CCEEecCCcccCceeEeEEChhHHHHHHHHHHHHH
Confidence            567889999977677888999999999999999999999987 9998753    235678999999999987777653

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=97.51  E-value=0.00018  Score=57.86  Aligned_cols=73  Identities=8%  Similarity=-0.023  Sum_probs=60.7

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|...+.+...++|+.+|+++..|.+.+..|+.+ |+|....    .-...+.||++|++++..-.+...
T Consensus        42 ~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~-Glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~~  118 (150)
T 2rdp_A           42 PPQFVALQWLLEEGDLTVGELSNKMYLACSTTTDLVDRMERN-GLVARVRDEHDRRVVRIRLLEKGERIIEEVIEKRQ  118 (150)
T ss_dssp             HHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECCC---CEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHHHC-CCeeecCCCCCcceeEeEECHhHHHHHHHHHHHHH
Confidence            567889999977677888999999999999999999999987 9998753    345678999999999877666544

>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=97.50  E-value=0.00022  Score=58.14  Aligned_cols=73  Identities=14%  Similarity=0.113  Sum_probs=61.4

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|...+.+...++|+.+|++...|.+.+..|+.+ |+|+...    .-...+.||++|+.++..-.+...
T Consensus        44 ~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~-Gli~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~~  120 (154)
T 2eth_A           44 TTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEKR-GLVVREMDPVDRRTYRVVLTEKGKEIFGEILSNFE  120 (154)
T ss_dssp             HHHHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHHHHHHT-TSEEEEECTTTSSCEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEeeCCCCCcceeEEEECHHHHHHHHHHHHHHH
Confidence            567889999977667888999999999999999999999987 9998764    235678999999999877655544

>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=97.50  E-value=0.00022  Score=56.80  Aligned_cols=73  Identities=16%  Similarity=0.131  Sum_probs=60.7

Q ss_pred             HHHHHHHHHhccCC--CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNP--PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~--~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|...+  .++..++|..+|+++..|.+.+..|+.+ |+|....    .-...+.||++|+++++.-.+...
T Consensus        31 ~~~~~vL~~l~~~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~-Gli~r~~~~~D~R~~~~~LT~~G~~~~~~~~~~~~  109 (139)
T 3eco_A           31 NEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNLERK-KLIYRYVDAQDTRRKNIGLTTSGIKLVEAFTSIFD  109 (139)
T ss_dssp             HHHHHHHHHHHHSTTTCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECCC--CCEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCcCHHHHHHHhCCCcccHHHHHHHHHHC-CCEeecCCCCCCCeeeeEECHHHHHHHHHHHHHHH
Confidence            56888999997654  6788999999999999999999999987 9998764    335778999999999976665544

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=97.49  E-value=0.00023  Score=58.26  Aligned_cols=89  Identities=15%  Similarity=0.078  Sum_probs=67.7

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH-H
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL-V   78 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r-l   78 (292)
                      ..+..||..|...+.+...++|+.+|++...|.+.+..|+.+ |+|....    .-...+.||++|+.++..-.+... +
T Consensus        52 ~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~-Gli~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~~~~  130 (162)
T 3cjn_A           52 TAKMRALAILSAKDGLPIGTLGIFAVVEQSTLSRALDGLQAD-GLVRREVDSDDQRSSRVYLTPAGRAVYDRLWPHMRAS  130 (162)
T ss_dssp             HHHHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEC--CCSSEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCChhHHHHHHHHHHHC-CCEEecCCCCCCCeeEEEECHHHHHHHHHHHHHHHHH
Confidence            467889999987777888999999999999999999999987 9998753    334678999999999877666554 2


Q ss_pred             HhhcCCCCCChHHHhh
Q psy10346         79 FNNVPSEGIGQKELLA   94 (292)
Q Consensus        79 ~~~l~~~~~~~~el~~   94 (292)
                      ...+- .+++-+++..
T Consensus       131 ~~~~~-~~l~~~e~~~  145 (162)
T 3cjn_A          131 HDRMF-QGITPQERQA  145 (162)
T ss_dssp             HHHHT-TTCCHHHHHH
T ss_pred             HHHHH-hcCCHHHHHH
Confidence            22222 3455555443

>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=97.49  E-value=0.00022  Score=57.02  Aligned_cols=89  Identities=17%  Similarity=0.112  Sum_probs=67.5

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH-H
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL-V   78 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r-l   78 (292)
                      ..+..||..|...+.++..++|..+|+++..|.+.+..|+.+ |+|....    .-...+.||++|+.++..-.+... +
T Consensus        29 ~~~~~iL~~l~~~~~~t~~~la~~l~~s~~~vs~~l~~Le~~-gli~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~~~~  107 (144)
T 1lj9_A           29 RGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQ-GFIYRQEDASNKKIKRIYATEKGKNVYPIIVRENQHS  107 (144)
T ss_dssp             TTHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECSSCTTCEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCcCcCHHHHHHHHCCCHhHHHHHHHHHHHC-CCEEeecCCCCCceeeeEEChhHHHHHHHHHHHHHHH
Confidence            457789999977777788999999999999999999999987 9998864    335678999999999977666554 2


Q ss_pred             HhhcCCCCCChHHHhh
Q psy10346         79 FNNVPSEGIGQKELLA   94 (292)
Q Consensus        79 ~~~l~~~~~~~~el~~   94 (292)
                      ...+- .+++-+++..
T Consensus       108 ~~~~~-~~l~~~e~~~  122 (144)
T 1lj9_A          108 NQVAL-QGLSEVEISQ  122 (144)
T ss_dssp             HHHHT-TTCCHHHHHH
T ss_pred             HHHHH-hcCCHHHHHH
Confidence            22221 3455554443

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=97.48  E-value=0.00014  Score=58.48  Aligned_cols=73  Identities=16%  Similarity=0.212  Sum_probs=59.4

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|...+.++..++|..+|+++..|.+.+..|+.+ |+|..+.    .-...+.||++|+.+++.-.+...
T Consensus        40 ~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~-Glv~r~~~~~D~R~~~~~lT~~G~~~~~~~~~~~~  116 (148)
T 3nrv_A           40 MTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEK-KYIEVNGHSEDKRTYAINLTEMGQELYEVASDFAI  116 (148)
T ss_dssp             HHHHHHHHHHHHSSSBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEC---------CCBEECHHHHHHHHHHHHHTH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEeecCCCCcceeEeEECHhHHHHHHHHHHHHH
Confidence            567889999987778889999999999999999999999987 9998653    235678999999999877655543

>1bja_A Transcription regulatory protein MOTA; activation domain, middle mode transcription, alpha helical structure, transcription regulation; 2.19A {Enterobacteria phage T4} SCOP: a.4.5.9 PDB: 1i1s_A

Probab=97.48  E-value=0.00017  Score=56.77  Aligned_cols=69  Identities=12%  Similarity=0.093  Sum_probs=59.8

Q ss_pred             HHHHHHHHHhccCCCCChHHHHH-hcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAK-LFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~-~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      ..|..||..|...+.....++|. ..+++.+.|.+.++.|+.+ |||. .....  +.||++|+..++.|.|-.
T Consensus        16 ~~QfsiL~~L~~~~~~t~~~Lae~~l~~drstvsrnl~~L~r~-GlVe-~~~~D--l~LT~~G~~~l~~a~~~W   85 (95)
T 1bja_A           16 EKTATILITIAKKDFITAAEVREVHPDLGNAVVNSNIGVLIKK-GLVE-KSGDG--LIITGEAQDIISNAATLY   85 (95)
T ss_dssp             HHHHHHHHHHHHSTTBCHHHHHHTCTTSCHHHHHHHHHHHHTT-TSEE-EETTE--EEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHhcccHHHHHHHHHHHHHC-CCee-cCCCC--eeeCHhHHHHHHHHHHHH
Confidence            56889999998888888899999 9999999999999999986 9999 33332  999999999999888754

>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=97.47  E-value=0.00013  Score=59.28  Aligned_cols=88  Identities=14%  Similarity=0.174  Sum_probs=65.6

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee------eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP------LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~------~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..| ..+.++..++|+.+|+++.+|.+.+..|+.+ |+|..+.      .-...+.||++|+.++..-.+...
T Consensus        38 ~~q~~iL~~l-~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~-Glv~r~~~~~~~D~R~~~~~lT~~G~~~~~~~~~~~~  115 (151)
T 3kp7_A           38 AEQSHVLNML-SIEALTVGQITEKQGVNKAAVSRRVKKLLNA-ELVKLEKPDSNTDQRLKIIKLSNKGKKYIKERKAIMS  115 (151)
T ss_dssp             HHHHHHHHHH-HHSCBCHHHHHHHHCSCSSHHHHHHHHHHHT-TSEEC-----------CCBEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHH-HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEeeCCCCCCCCCeeEEEECHhHHHHHHHHHHHHH
Confidence            5678899999 7788899999999999999999999999987 9999643      445567999999999877666654


Q ss_pred             -HHhhcCCCCCChHHHhh
Q psy10346         78 -VFNNVPSEGIGQKELLA   94 (292)
Q Consensus        78 -l~~~l~~~~~~~~el~~   94 (292)
                       +...+- .+++-+|+..
T Consensus       116 ~~~~~~~-~~l~~~e~~~  132 (151)
T 3kp7_A          116 HIASDMT-SDFDSKEIEK  132 (151)
T ss_dssp             HHHHHTT-TTSCHHHHHH
T ss_pred             HHHHHHH-hcCCHHHHHH
Confidence             223322 3455555443

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=97.47  E-value=0.00018  Score=57.67  Aligned_cols=69  Identities=19%  Similarity=0.257  Sum_probs=57.2

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCC
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGS   73 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~Gl   73 (292)
                      ...+..||..|..++ ++..++|..+|+++..|.+.+..|+.+ |||....    .-...+.||+.|+.++....
T Consensus        37 t~~~~~iL~~l~~~~-~t~~eLa~~l~~s~~tvs~~l~~L~~~-Glv~r~~~~~d~R~~~~~lT~~g~~~~~~~~  109 (146)
T 3tgn_A           37 TNTQEHILMLLSEES-LTNSELARRLNVSQAAVTKAIKSLVKE-GMLETSKDSKDARVIFYQLTDLARPIAEEHH  109 (146)
T ss_dssp             CHHHHHHHHHHTTCC-CCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEC----------CCEECGGGHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHHHHC-CCeEeccCCCCCceeEEEECHhHHHHHHHHH
Confidence            367889999998877 899999999999999999999999987 9998754    44567899999999987775

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=97.47  E-value=0.00016  Score=59.20  Aligned_cols=73  Identities=11%  Similarity=0.074  Sum_probs=60.7

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..|..||..|...+.+...++|..+|+++..|.+.+..|+.+ |||....    .-...+.||++|++++..-.+...
T Consensus        50 ~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~-Glv~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~  126 (159)
T 3s2w_A           50 SGQFPFLMRLYREDGINQESLSDYLKIDKGTTARAIQKLVDE-GYVFRQRDEKDRRSYRVFLTEKGKKLEPDMKKIAS  126 (159)
T ss_dssp             TTTHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECC---CCEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEecCCCCCCeeEEEECHHHHHHHHHHHHHHH
Confidence            346788999977777888999999999999999999999987 9998764    235678999999999977666554

>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=97.45  E-value=0.00032  Score=56.21  Aligned_cols=73  Identities=12%  Similarity=0.046  Sum_probs=60.0

Q ss_pred             HHHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|.. .+.+...++|..+|+++..|.+.+..|+.+ |+|....    .-...+.||++|+.++..-.+...
T Consensus        35 ~~~~~iL~~l~~~~~~~~~~~la~~l~i~~~~vs~~l~~Le~~-glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~~  112 (147)
T 2hr3_A           35 FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERG-GLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKRE  112 (147)
T ss_dssp             HHHHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEEC------CCEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHC-CCEeeCCCCCCCCceeeEECHHHHHHHHHHHHHHH
Confidence            467889999987 777889999999999999999999999987 9998753    234568999999998876655443

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=97.44  E-value=0.00032  Score=56.27  Aligned_cols=72  Identities=19%  Similarity=0.156  Sum_probs=60.2

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|..++. ...++|..+|+++..|.+.+..|+.+ |+|....    .-...+.||++|+.++....+...
T Consensus        37 ~~~~~iL~~l~~~~~-~~~~la~~l~~~~~tvs~~l~~Le~~-Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~~~~~  112 (144)
T 3f3x_A           37 YLDFSILKATSEEPR-SMVYLANRYFVTQSAITAAVDKLEAK-GLVRRIRDSKDRRIVIVEITPKGRQVLLEANEVLR  112 (144)
T ss_dssp             HHHHHHHHHHHHSCE-EHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCC-CHHHHHHHHCCChhHHHHHHHHHHHC-CCEEeccCCCCCceEEEEECHHHHHHHHHHHHHHH
Confidence            567889999987766 78999999999999999999999987 9998764    334578999999999877665544

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}

Probab=97.43  E-value=0.00019  Score=56.85  Aligned_cols=73  Identities=12%  Similarity=0.124  Sum_probs=61.4

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|...+.+...++|+.+|+++..|.+.+..|+.+ |+|....    .-...+.||+.|++++..-.+...
T Consensus        33 ~~~~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~-gli~r~~~~~d~r~~~~~lT~~G~~~~~~~~~~~~  109 (139)
T 3bja_A           33 YVQFGVIQVLAKSGKVSMSKLIENMGCVPSNMTTMIQRMKRD-GYVMTEKNPNDQRETLVYLTKKGEETKKQVDVQYS  109 (139)
T ss_dssp             HHHHHHHHHHHHSCSEEHHHHHHHCSSCCTTHHHHHHHHHHT-TSEEEEECSSCTTCEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHHCCChhHHHHHHHHHHHC-CCeeeccCCCCCceeEEEECHHHHHHHHHHHHHHH
Confidence            567889999987777888999999999999999999999987 9998753    335678999999999877665543

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=97.41  E-value=0.00024  Score=57.14  Aligned_cols=73  Identities=11%  Similarity=-0.001  Sum_probs=57.6

Q ss_pred             HHHHHHHHHhc----cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHH
Q psy10346          4 DLTEKILKYLD----TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVF   79 (292)
Q Consensus         4 ~~e~~iL~~L~----~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~   79 (292)
                      ..+..+|..|.    .++.....++|+.+|++...|.+.++.|+.+ |+|....   ..|.||+.|++++..-.+..+++
T Consensus        13 ~~~~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~~~l~~Le~~-Gli~r~~---~~~~Lt~~g~~~~~~~~~~~~~~   88 (139)
T 2x4h_A           13 RREFSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVFEEVSHLEEK-GLVKKKE---DGVWITNNGTRSINYLIKAHRVI   88 (139)
T ss_dssp             HHHHHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEET---TEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHHHHHHHHHHC-CCEEecC---CeEEEChhHHHHHHHHHHHHHHH
Confidence            45566666553    3556788999999999999999999999987 9998765   57999999999887666655444


Q ss_pred             h
Q psy10346         80 N   80 (292)
Q Consensus        80 ~   80 (292)
                      .
T Consensus        89 ~   89 (139)
T 2x4h_A           89 E   89 (139)
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=97.41  E-value=0.0002  Score=58.57  Aligned_cols=73  Identities=14%  Similarity=0.115  Sum_probs=59.3

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|...+.+...++|..+|+++..|.+.+..|+.+ |||....    .-...+.||++|+.++....+...
T Consensus        49 ~~~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~-glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~~  125 (162)
T 2fa5_A           49 IPEWRVITILALYPGSSASEVSDRTAMDKVAVSRAVARLLER-GFIRRETHGDDRRRSMLALSPAGRQVYETVAPLVN  125 (162)
T ss_dssp             HHHHHHHHHHHHSTTCCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEC---------CCCEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEeeecCCCCCCeeEEEECHHHHHHHHHHHHHHH
Confidence            467889999987778889999999999999999999999987 9998643    223568999999999977666554

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=97.41  E-value=0.00012  Score=58.98  Aligned_cols=73  Identities=14%  Similarity=0.073  Sum_probs=61.2

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|...+.+...++|..+|+++..|.+.+..|+.+ |+|.....    -...+.||++|+++++.-.+...
T Consensus        31 ~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~-Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~~~~~  107 (145)
T 3g3z_A           31 YNLFAVLYTLATEGSRTQKHIGEKWSLPKQTVSGVCKTLAGQ-GLIEWQEGEQDRRKRLLSLTETGKAYAAPLTESAQ  107 (145)
T ss_dssp             HHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEECCCSSCGGGSCEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEeeccCCCCCceeeeeEChhHHHHHHHHHHHHH
Confidence            567889999977677889999999999999999999999987 99987433    35679999999998876665554

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=97.41  E-value=0.00015  Score=58.69  Aligned_cols=71  Identities=10%  Similarity=0.180  Sum_probs=59.9

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE--e----eeeEEEEEeChhHHHHhhcCChH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV--E----PLSHKIWELTGEGNQVKDNGSHE   75 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~--e----~~~~~~~~LTeEG~~yl~~GlPE   75 (292)
                      ..+..||..|...+.++..++|+.+|+++..|.+.+..|+.+ |+|..  .    ..-...+.||++|+.+++.-.+.
T Consensus        41 ~~~~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~-Glv~r~~~~~~~d~R~~~~~LT~~G~~~~~~~~~~  117 (154)
T 2qww_A           41 IQQLAMINVIYSTPGISVADLTKRLIITGSSAAANVDGLISL-GLVVKLNKTIPNDSMDLTLKLSKKGEDLSKRSTAN  117 (154)
T ss_dssp             HHHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEESCC--CTTCTTCEEEECHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEecCcCCCCCCceeEeEECHHHHHHHHHHHhh
Confidence            567889999987777888999999999999999999999987 99987  2    23345789999999998766555

>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=97.40  E-value=0.00023  Score=57.03  Aligned_cols=87  Identities=11%  Similarity=0.060  Sum_probs=68.6

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChHHH-H
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHEVL-V   78 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE~r-l   78 (292)
                      ..+..||..|...+.+...++|+.+|+++..|.+.+..|+.+ |+|.....    -...+.||++|+.++..-.+... +
T Consensus        40 ~~~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l~~L~~~-glv~r~~~~~d~R~~~~~LT~~G~~~~~~~~~~~~~~  118 (147)
T 1z91_A           40 YPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQ-GLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTI  118 (147)
T ss_dssp             HHHHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHHHHHHH-TSEECCBCSSCTTSBEEEECHHHHSGGGGTTTHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCcCcHHHHHHHHHHC-CCEEeccCCCCCCeeEEEECHhHHHHHHHHHHHHHHH
Confidence            567889999976667788999999999999999999999987 99987542    35678999999999988887765 4


Q ss_pred             HhhcCCCCCChHHHhh
Q psy10346         79 FNNVPSEGIGQKELLA   94 (292)
Q Consensus        79 ~~~l~~~~~~~~el~~   94 (292)
                      ...+   +++-+++..
T Consensus       119 ~~~~---~l~~~e~~~  131 (147)
T 1z91_A          119 LGLS---KQSGEDLKQ  131 (147)
T ss_dssp             HHHT---CCCTHHHHH
T ss_pred             HHHc---CCCHHHHHH
Confidence            4444   555555443

>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=97.40  E-value=0.00021  Score=57.70  Aligned_cols=73  Identities=12%  Similarity=0.104  Sum_probs=61.3

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|...+.+...++|+.+|+++..|.+.+..|+.+ |+|....    .-...+.||+.|++++..-.+...
T Consensus        40 ~~~~~iL~~l~~~~~~t~~ela~~l~~~~~~vs~~l~~Le~~-Glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~~  116 (152)
T 3bj6_A           40 VGQRAILEGLSLTPGATAPQLGAALQMKRQYISRILQEVQRA-GLIERRTNPEHARSHRYWLTPRGEAIITAIRADEM  116 (152)
T ss_dssp             HHHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEECCSSSTTSCEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCeeecCCcccccceeeEEChhhHHHHHHHHHHHH
Confidence            567889999987777888999999999999999999999987 9998754    334578999999999877655544

>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi}

Probab=97.39  E-value=0.00018  Score=59.18  Aligned_cols=89  Identities=11%  Similarity=0.033  Sum_probs=67.3

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChHHH-H
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHEVL-V   78 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE~r-l   78 (292)
                      ..+..||..|...+.+...++|..+|+++..|.+.+..|+.+ |||..+..    -...+.||++|+++++.-.+... +
T Consensus        53 ~~q~~vL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~-Glv~r~~~~~DrR~~~~~LT~~G~~~~~~~~~~~~~~  131 (161)
T 3e6m_A           53 TPKLRLLSSLSAYGELTVGQLATLGVMEQSTTSRTVDQLVDE-GLAARSISDADQRKRTVVLTRKGKKKLAEISPLINDF  131 (161)
T ss_dssp             HHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEECC---CCCSCEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEeeCCcccCCeeEeeECHHHHHHHHHHHHHHHHH
Confidence            457889999977667788999999999999999999999987 99987543    34678999999999987766554 2


Q ss_pred             HhhcCCCCCChHHHhh
Q psy10346         79 FNNVPSEGIGQKELLA   94 (292)
Q Consensus        79 ~~~l~~~~~~~~el~~   94 (292)
                      ...+- .+++-+|+..
T Consensus       132 ~~~~~-~~l~~~e~~~  146 (161)
T 3e6m_A          132 HAELV-GNVDPDKLQT  146 (161)
T ss_dssp             HHHHH-TTCCHHHHHH
T ss_pred             HHHHH-hcCCHHHHHH
Confidence            22221 3455555443

>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=97.39  E-value=0.00019  Score=57.61  Aligned_cols=73  Identities=16%  Similarity=0.155  Sum_probs=56.0

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|...+.++..++|..+|+++..|.+.+..|+.+ |+|+....    -...+.||++|++++..-.+...
T Consensus        37 ~~~~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~-Glv~r~~~~~DrR~~~~~LT~~G~~~~~~~~~~~~  113 (142)
T 3ech_A           37 PPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGR-NLVRRERNPSDQRSFQLFLTDEGLAIHLHAELIMS  113 (142)
T ss_dssp             HHHHHHHHHHHHTTTCCHHHHHHHHC---CHHHHHHHHHHHT-TSEEC----------CCEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC-CCEeeccCCCCCCeeeeEECHHHHHHHHHHHHHHH
Confidence            568899999988788899999999999999999999999987 99986533    34557899999999977666444

>1r7j_A Conserved hypothetical protein SSO10A; winged helix-turn-helix, two-stranded antiparallel coiled CO structural genomics, PSI; 1.47A {Sulfolobus solfataricus} SCOP: a.4.5.49 PDB: 1xsx_A

Probab=97.36  E-value=0.00047  Score=53.54  Aligned_cols=60  Identities=17%  Similarity=0.099  Sum_probs=52.2

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl   69 (292)
                      .+-+.||..+.. + +...++|..+|+++..+...+..|+.+ |+|.....   .|.||++|++++
T Consensus         8 eIi~~IL~~i~~-~-~~~t~La~~~~ls~~~~~~~l~~L~~~-GLI~~~~~---~~~LT~kG~~~l   67 (95)
T 1r7j_A            8 EIIQAILEACKS-G-SPKTRIMYGANLSYALTGRYIKMLMDL-EIIRQEGK---QYMLTKKGEELL   67 (95)
T ss_dssp             HHHHHHHHHHTT-C-BCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEETT---EEEECHHHHHHH
T ss_pred             HHHHHHHHHHHc-C-CCHHHHHHHhCcCHHHHHHHHHHHHHC-CCeEEECC---eeEEChhHHHHH
Confidence            456789999974 4 788999999999999999999999987 99998643   499999999876

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=97.35  E-value=0.00035  Score=56.72  Aligned_cols=72  Identities=14%  Similarity=0.080  Sum_probs=59.6

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      ..+..||..|...+.+...++|..+|++...|.+.+..|+.+ |+|.....    -...+.||+.|+.++..-.+..
T Consensus        43 ~~~~~iL~~l~~~~~~t~~ela~~l~i~~~tvs~~l~~Le~~-Glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~  118 (155)
T 3cdh_A           43 VPEWRVLACLVDNDAMMITRLAKLSLMEQSRMTRIVDQMDAR-GLVTRVADAKDKRRVRVRLTDDGRALAESLVASA  118 (155)
T ss_dssp             HHHHHHHHHHSSCSCBCHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEECC------CCCEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEeccCCCcCCeeEeEECHHHHHHHHHHHHHH
Confidence            567889999987778889999999999999999999999987 99986432    2356899999999987655553

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=97.34  E-value=0.00019  Score=58.26  Aligned_cols=72  Identities=14%  Similarity=0.125  Sum_probs=58.2

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      ..+..||..|...+.++..++|..+++++..|.+.+..|+.+ |||+...    .-...+.||++|+++++.-.+..
T Consensus        41 ~~q~~iL~~l~~~~~~~~~eLa~~l~~~~~~vs~~l~~L~~~-Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~~~~  116 (149)
T 4hbl_A           41 YSQYLVMLTLWEENPQTLNSIGRHLDLSSNTLTPMLKRLEQS-GWVKRERQQSDKRQLIITLTDNGQQQQEAVFEAI  116 (149)
T ss_dssp             HHHHHHHHHHHHSSSEEHHHHHHHHTCCHHHHHHHHHHHHHH-TSEEC---------CEEEECSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEeeCCCCCCcceeeeeECHHHHHHHHHHHHHH
Confidence            567899999987788888999999999999999999999987 9998653    34567899999999986544433

>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=97.33  E-value=0.00035  Score=53.17  Aligned_cols=70  Identities=13%  Similarity=0.063  Sum_probs=54.8

Q ss_pred             HHHHHHhccCC-CCChHHHHHhcCCCHHH-HHHHHHHhhccCCcEEEeee--eEEEEEeChhHHHHhhcCChHHH
Q psy10346          7 EKILKYLDTNP-PVDTLDLAKLFNEDHQK-VVGGMKSIETLGEYLIVEPL--SHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         7 ~~iL~~L~~~~-~~~~~ela~~~~~~~~~-v~~~~~~L~s~~glv~~e~~--~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+|..|...+ .....++|+.+|+++.. |.+.++.|+.+ |+|.....  -...+.||++|++.++.=.|..+
T Consensus        18 l~~L~~l~~~~~~~t~~eLa~~l~is~~t~vs~~l~~Le~~-Glv~~~~~drR~~~~~LT~~G~~~~~~~~~~~~   91 (95)
T 2pg4_A           18 LPTLLEFEKKGYEPSLAEIVKASGVSEKTFFMGLKDRLIRA-GLVKEETLSYRVKTLKLTEKGRRLAECLEKCRD   91 (95)
T ss_dssp             HHHHHHHHHTTCCCCHHHHHHHHCCCHHHHHTTHHHHHHHT-TSEEEEEEETTEEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHCCCchHHHHHHHHHHHHC-CCeecCCCCCCeEEEEECHhHHHHHHHHHHHHH
Confidence            44666666665 68899999999999999 99999999987 99983221  35678999999998866555443

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=97.33  E-value=0.0005  Score=58.54  Aligned_cols=89  Identities=15%  Similarity=0.103  Sum_probs=69.6

Q ss_pred             HHHHHHHHHhcc--CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDT--NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~--~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|..  .+.+...++|..+|+++..|.+.+..|+.+ |||......    ...+.||++|++++..-.+...
T Consensus        41 ~~q~~vL~~L~~~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~-GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~  119 (189)
T 3nqo_A           41 SRQYMTILSILHLPEEETTLNNIARKMGTSKQNINRLVANLEKN-GYVDVIPSPHDKRAINVKVTDLGKKVMVTCSRTGI  119 (189)
T ss_dssp             HHHHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEEECSSCSSCEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEeccCCCCCCeeEEEECHHHHHHHHHHHHHHH
Confidence            567889999975  456889999999999999999999999987 999875443    3788999999999987777655


Q ss_pred             -HHhhcCCCCCChHHHhh
Q psy10346         78 -VFNNVPSEGIGQKELLA   94 (292)
Q Consensus        78 -l~~~l~~~~~~~~el~~   94 (292)
                       ++..+- .+++-+++..
T Consensus       120 ~~~~~~~-~~l~~ee~~~  136 (189)
T 3nqo_A          120 NFMADVF-HEFTKDELET  136 (189)
T ss_dssp             HHHHHHT-TTCCHHHHHH
T ss_pred             HHHHHHH-HhCCHHHHHH
Confidence             333332 4566666554

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=97.32  E-value=0.00025  Score=50.70  Aligned_cols=47  Identities=19%  Similarity=0.357  Sum_probs=42.1

Q ss_pred             HHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe
Q psy10346          5 LTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE   52 (292)
Q Consensus         5 ~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e   52 (292)
                      .|.+||..+.+ +|.++.+.+++.+|++.+.|+.++++|++| |+|+++
T Consensus        11 ~e~~lL~yIr~sGGildI~~~a~kygV~kdeV~~~LrrLe~K-GLI~le   58 (59)
T 2xvc_A           11 TERELLDYIVNNGGFLDIEHFSKVYGVEKQEVVKLLEALKNK-GLIAVE   58 (59)
T ss_dssp             CHHHHHHHHHHTTSEEEHHHHHHHHCCCHHHHHHHHHHHHHT-TSEEEE
T ss_pred             cHHHHHHHHHHcCCEEeHHHHHHHhCCCHHHHHHHHHHHHHC-CCeecc
Confidence            47889999965 555899999999999999999999999997 999986

>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=97.31  E-value=0.00035  Score=58.24  Aligned_cols=73  Identities=14%  Similarity=0.146  Sum_probs=59.2

Q ss_pred             HHHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..|..||..|.. ++.+...++|..++++...|.+.+..|+.+ |||..+.    .-...+.||++|+++++.-.+...
T Consensus        53 ~~q~~vL~~L~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~-GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~  130 (166)
T 3deu_A           53 QTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDK-GLISRQTCASDRRAKRIKLTEKAEPLIAEMEEVIH  130 (166)
T ss_dssp             HHHHHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEC--------CEEEECGGGHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHCCCHhhHHHHHHHHHHC-CCEEeeCCCCCCCeeEEEECHHHHHHHHHHHHHHH
Confidence            567889999976 566788999999999999999999999987 9998753    334678999999999876665544

>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=97.31  E-value=0.00037  Score=56.42  Aligned_cols=89  Identities=18%  Similarity=0.177  Sum_probs=62.9

Q ss_pred             HHHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHhhcCChHHHH
Q psy10346          4 DLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVKDNGSHEVLV   78 (292)
Q Consensus         4 ~~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl~~GlPE~rl   78 (292)
                      ..+..||..|.. .+.+...++|..+++++..|.+.+..|+.+ |||......    ...+.||++|+++++.-.+...-
T Consensus        39 ~~q~~vL~~l~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~-Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~~~~~~  117 (150)
T 3fm5_A           39 VRSYSVLVLACEQAEGVNQRGVAATMGLDPSQIVGLVDELEER-GLVVRTLDPSDRRNKLIAATEEGRRLRDDAKARVDA  117 (150)
T ss_dssp             HHHHHHHHHHHHSTTCCCSHHHHHHHTCCHHHHHHHHHHHHTT-TSEEC-----------CEECHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHHCCCHhHHHHHHHHHHHC-CCEEeeCCccccchheeeECHHHHHHHHHHHHHHHH
Confidence            567889999964 445788999999999999999999999987 999864432    34589999999999877666552


Q ss_pred             H-hhcCCCCCChHHHhh
Q psy10346         79 F-NNVPSEGIGQKELLA   94 (292)
Q Consensus        79 ~-~~l~~~~~~~~el~~   94 (292)
                      + ..+- .+++-+|+..
T Consensus       118 ~~~~~~-~~l~~~e~~~  133 (150)
T 3fm5_A          118 AHGRYF-EGIPDTVVNQ  133 (150)
T ss_dssp             HHHHHH-TTSCHHHHHH
T ss_pred             HHHHHH-hcCCHHHHHH
Confidence            2 2221 3455555443

>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=97.29  E-value=0.00013  Score=58.99  Aligned_cols=89  Identities=15%  Similarity=0.224  Sum_probs=59.6

Q ss_pred             HHHHHHHHHhccC--CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTN--PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~--~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..|..||..|...  +.+...++|..+|+++..|.+.+..|+.+ |||....    .-...+.||++|+++++.-.+...
T Consensus        41 ~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~-Glv~r~~~~~DrR~~~~~LT~~G~~~~~~~~~~~~  119 (148)
T 3jw4_A           41 SQQGRMIGYIYENQESGIIQKDLAQFFGRRGASITSMLQGLEKK-GYIERRIPENNARQKNIYVLPKGAALVEEFNNIFL  119 (148)
T ss_dssp             HHHHHHHHHHHHHTTTCCCHHHHHHC------CHHHHHHHHHHT-TSBCCC--------CCCCBCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHCCChhHHHHHHHHHHHC-CCEEeeCCCCCchhheeeECHHHHHHHHHHHHHHH
Confidence            5678899999765  67889999999999999999999999987 9998653    334567899999999977666555


Q ss_pred             H-HhhcCCCCCChHHHhh
Q psy10346         78 V-FNNVPSEGIGQKELLA   94 (292)
Q Consensus        78 l-~~~l~~~~~~~~el~~   94 (292)
                      - ...+- .+++-+|+..
T Consensus       120 ~~~~~~~-~~l~~~e~~~  136 (148)
T 3jw4_A          120 EVEESIT-KGLTKDEQKQ  136 (148)
T ss_dssp             HHHHHTT-TTCCHHHHHH
T ss_pred             HHHHHHH-hcCCHHHHHH
Confidence            2 22221 3555555443

>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=97.28  E-value=0.00032  Score=56.76  Aligned_cols=73  Identities=12%  Similarity=0.012  Sum_probs=60.7

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..||..|...+.+...++|..+|+++..|.+.+..|+.+ |+|......    ...+.||+.|+.++..-.+...
T Consensus        37 ~~~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~Le~~-glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~~  113 (155)
T 1s3j_A           37 PAQLFVLASLKKHGSLKVSEIAERMEVKPSAVTLMADRLEQK-NLIARTHNTKDRRVIDLSLTDEGDIKFEEVLAGRK  113 (155)
T ss_dssp             HHHHHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEEECSSCTTSEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEeecCCCCCCceEEEEECHHHHHHHHHHHHHHH
Confidence            457889999977666788999999999999999999999987 999876432    4578999999999877665544

>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=97.24  E-value=0.00057  Score=52.13  Aligned_cols=69  Identities=22%  Similarity=0.120  Sum_probs=51.4

Q ss_pred             HHHHHHHHh-ccCCC---CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHhhcCCh
Q psy10346          5 LTEKILKYL-DTNPP---VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVKDNGSH   74 (292)
Q Consensus         5 ~e~~iL~~L-~~~~~---~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl~~GlP   74 (292)
                      .+..||..| ...+.   +...++|+.+|+++..|.+.+..|+.+ |||.... .-...+.||++|+++++.-.+
T Consensus        13 ~~~~iL~~l~~~~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~-Glv~~~~d~R~~~v~LT~~G~~~~~~~~~   86 (95)
T 2qvo_A           13 KALEILMTIYYESLGGNDVYIQYIASKVNSPHSYVWLIIKKFEEA-KMVECELEGRTKIIRLTDKGQKIAQQIKS   86 (95)
T ss_dssp             HHHHHHHHHHHHHHTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEECHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-cCccCCCCCCeEEEEEChhHHHHHHHHHH
Confidence            445566555 32223   678999999999999999999999987 9994322 224578999999998865443

>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=97.22  E-value=0.00079  Score=52.58  Aligned_cols=62  Identities=18%  Similarity=0.211  Sum_probs=52.5

Q ss_pred             HHHHHHHhccCCCCChHHHHHhc-CCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHh
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLF-NEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVK   69 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~-~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl   69 (292)
                      ...||..|. .+.....++++.+ |++...+.+.++.|++. |+|+-...    ....|.||+.|++++
T Consensus        16 ~~~IL~~L~-~~~~~~~eLa~~l~~is~~tls~~L~~Le~~-GlI~r~~~~~d~r~~~y~LT~~G~~l~   82 (107)
T 2hzt_A           16 KXVILXHLT-HGKKRTSELKRLMPNITQKMLTQQLRELEAD-GVINRIVYNQVPPKVEYELSEYGRSLE   82 (107)
T ss_dssp             HHHHHHHHT-TCCBCHHHHHHHCTTSCHHHHHHHHHHHHHT-TSEEEEEECSSSCEEEEEECTTGGGGH
T ss_pred             HHHHHHHHH-hCCCCHHHHHHHhcCCCHHHHHHHHHHHHHC-CCEEEeecCCCCCeEEEEECccHHHHH
Confidence            346888887 5677889999999 99999999999999987 99987553    367899999998765

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=97.19  E-value=0.00075  Score=50.78  Aligned_cols=67  Identities=9%  Similarity=0.068  Sum_probs=56.2

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHhh
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVKD   70 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl~   70 (292)
                      .+.+.+||..|..++.....++|+.+|++...|.+.++.|+.. |+|.... .....|.||++|...+.
T Consensus        23 ~~~~~~il~~l~~~~~~s~~ela~~l~is~~tvs~~l~~L~~~-glv~~~~~~r~~~y~l~~~~~~~l~   90 (99)
T 3cuo_A           23 HPKRLLILCMLSGSPGTSAGELTRITGLSASATSQHLARMRDE-GLIDSQRDAQRILYSIKNEAVNAII   90 (99)
T ss_dssp             SHHHHHHHHHHTTCCSEEHHHHHHHHCCCHHHHHHHHHHHHHT-TSEEEEECSSCEEEEECCHHHHHHH
T ss_pred             ChHHHHHHHHHHhCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEecCCEEEEEEChHHHHHHH
Confidence            4677889999987767888999999999999999999999987 9998754 34568999999976553

>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69

Probab=97.19  E-value=0.0012  Score=51.88  Aligned_cols=63  Identities=13%  Similarity=0.139  Sum_probs=53.1

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhc-CCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHh
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLF-NEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVK   69 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~-~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl   69 (292)
                      ....||..|.. +.....++++.+ |+++..|.+.++.|+.. |+|.-...    -...|.||+.|++.+
T Consensus        23 ~~~~IL~~L~~-~~~~~~eLa~~l~~is~~tvs~~L~~Le~~-GlI~r~~~~~d~r~~~~~LT~~G~~~~   90 (112)
T 1z7u_A           23 WKLSLMDELFQ-GTKRNGELMRALDGITQRVLTDRLREMEKD-GLVHRESFNELPPRVEYTLTPEGYALY   90 (112)
T ss_dssp             THHHHHHHHHH-SCBCHHHHHHHSTTCCHHHHHHHHHHHHHH-TSEEEEEECCSSCEEEEEECHHHHHHH
T ss_pred             cHHHHHHHHHh-CCCCHHHHHHHhccCCHHHHHHHHHHHHHC-CCEEEeecCCCCCeEEEEECHhHHHHH
Confidence            34568888874 567889999999 99999999999999987 99987653    457899999999865

>3df8_A Possible HXLR family transcriptional factor; APC89000, structural genomics, midwest center for structural genomics, MCSG; 1.65A {Thermoplasma volcanium} SCOP: a.4.5.0

Probab=97.18  E-value=0.0011  Score=52.50  Aligned_cols=62  Identities=16%  Similarity=0.124  Sum_probs=52.3

Q ss_pred             HHHHHHHhccCCCCC--hHHHHHhc-CCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346          6 TEKILKYLDTNPPVD--TLDLAKLF-NEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus         6 e~~iL~~L~~~~~~~--~~ela~~~-~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl   69 (292)
                      ...||..|. .+...  ..+++..+ |+++..+.+.++.|+.. |+|+-.......|.||+.|+..+
T Consensus        29 rl~IL~~L~-~g~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~-GlV~r~~~r~~~y~LT~~G~~l~   93 (111)
T 3df8_A           29 TMLIISVLG-NGSTRQNFNDIRSSIPGISSTILSRRIKDLIDS-GLVERRSGQITTYALTEKGMNVR   93 (111)
T ss_dssp             HHHHHHHHT-SSSSCBCHHHHHHTSTTCCHHHHHHHHHHHHHT-TSEEEEESSSEEEEECHHHHHHH
T ss_pred             HHHHHHHHh-cCCCCCCHHHHHHHccCCCHHHHHHHHHHHHHC-CCEEEeecCcEEEEECccHHHHH
Confidence            356888887 45556  89999999 99999999999999987 99987555678999999999855

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=97.18  E-value=0.00045  Score=57.34  Aligned_cols=72  Identities=17%  Similarity=0.119  Sum_probs=60.2

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      ..+..||..|...+.+...++|..+|++...|.+.+..|+.+ |||....    .-...+.||++|+.+++...+..
T Consensus        45 ~~~~~iL~~L~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~-GlV~r~~~~~DrR~~~~~LT~~G~~~~~~~~~~~  120 (168)
T 2nyx_A           45 IPQFRTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGA-ELIDRLPHPTSRRELLAALTKRGRDVVRQVTEHR  120 (168)
T ss_dssp             HHHHHHHHHHHHHCSEEHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEEECSSCSSCEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHC-CCEEeccCCCCCCeeEEEECHHHHHHHHHHHHHH
Confidence            567889999977667888999999999999999999999987 9998753    33567899999999987655544

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=97.16  E-value=0.0011  Score=54.29  Aligned_cols=73  Identities=10%  Similarity=0.137  Sum_probs=58.3

Q ss_pred             HHHHHHHHHhc--cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLD--TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~--~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..|..||..|.  .++.+...++|..+++++..|.+.+..|+.+ |||.-....    ...+.||++|++.++.-.+...
T Consensus        35 ~~q~~vL~~L~~~~~~~~t~~eLa~~l~~~~~tvs~~v~~Le~~-Glv~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~  113 (147)
T 4b8x_A           35 FARYEALVLLTFSKSGELPMSKIGERLMVHPTSVTNTVDRLVRS-GLVAKRPNPNDGRGTLATITDKGREVVEAATRDLM  113 (147)
T ss_dssp             HHHHHHHHHHHTSGGGEEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECC----CEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHhC-CCEEEeecCCcCceeEEEECHHHHHHHHHHHHHHH
Confidence            45778888884  3455778999999999999999999999987 999875543    4678999999999876555433

>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=97.16  E-value=0.0013  Score=49.64  Aligned_cols=72  Identities=10%  Similarity=-0.002  Sum_probs=59.2

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee---eEEEEEeChhHHHHhhcCChH
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL---SHKIWELTGEGNQVKDNGSHE   75 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~---~~~~~~LTeEG~~yl~~GlPE   75 (292)
                      ...+..||..|...+..+..++|..+|++...|.+.++.|+.+ |+|.....   ....+.+|+.|+.++..-.+.
T Consensus        19 ~~~~~~il~~l~~~~~~s~~ela~~l~is~~tv~~~l~~L~~~-glv~~~~~~~~r~~~~~~t~~g~~~~~~~~~~   93 (109)
T 1sfx_A           19 KPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKR-GFVRREIVEKGWVGYIYSAEKPEKVLKEFKSS   93 (109)
T ss_dssp             CHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEEESSSEEEEEEECCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEEeecCCceEEEEecCcHHHHHHHHHHH
Confidence            3567889999976677889999999999999999999999987 99987553   256778999999887654443

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=97.15  E-value=0.00052  Score=55.85  Aligned_cols=89  Identities=9%  Similarity=0.051  Sum_probs=64.9

Q ss_pred             HHHHHHHHHh-ccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH-
Q psy10346          4 DLTEKILKYL-DTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL-   77 (292)
Q Consensus         4 ~~e~~iL~~L-~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r-   77 (292)
                      ..+..||..| ...+.+...++|..+|+++..|.+.+..|+.+ |||....    .-...+.||++|++++..-.+... 
T Consensus        47 ~~~~~iL~~L~~~~~~~~~~ela~~l~i~~~tvs~~l~~Le~~-Gli~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~~~~  125 (160)
T 3boq_A           47 LAKFDAMAQLARNPDGLSMGKLSGALKVTNGNVSGLVNRLIKD-GMVVKAMSADDRRSFSAKLTDAGLTTFKQASEAHNR  125 (160)
T ss_dssp             HHHHHHHHHHHHCTTCEEHHHHHHHCSSCCSCHHHHHHHHHHH-TSEEEC--------CEEEECHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHCCChhhHHHHHHHHHHC-CCEEeecCCCCCCeEEEEEChhHHHHHHHHHHHHHH
Confidence            4678899999 46667888999999999999999999999987 9998753    334568999999999977655544 


Q ss_pred             HHhhcCCCCCChHHHhh
Q psy10346         78 VFNNVPSEGIGQKELLA   94 (292)
Q Consensus        78 l~~~l~~~~~~~~el~~   94 (292)
                      ....+- .+++-+++..
T Consensus       126 ~~~~~~-~~l~~~e~~~  141 (160)
T 3boq_A          126 ILAELL-RAVSDQDMVE  141 (160)
T ss_dssp             HHHHHT-TTCCHHHHHH
T ss_pred             HHHHHH-hcCCHHHHHH
Confidence            222222 2455555443

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=97.11  E-value=0.0014  Score=54.05  Aligned_cols=89  Identities=15%  Similarity=0.181  Sum_probs=65.6

Q ss_pred             HHHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChHHHH
Q psy10346          4 DLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHEVLV   78 (292)
Q Consensus         4 ~~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE~rl   78 (292)
                      ..+..||..|.. ++.....++|..+++++..|.+.+..|+.+ |||.-...    -...+.||++|++.++.-.|...-
T Consensus        31 ~~q~~vL~~L~~~~~~~~~~eLa~~l~~~~~tvs~~v~~Le~~-GlV~R~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~~  109 (151)
T 4aik_A           31 QTHWVTLYNINRLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEK-GLITRHTSANDRRAKRIKLTEQSSPIIEQVDGVISS  109 (151)
T ss_dssp             HHHHHHHHHHHHSCTTSCHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEEECSSCTTCEEEEECGGGHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHHCcCHHHHHHHHHHHHhC-CCeEeecCCCCCcchhhhcCHHHHHHHHHHHHHHHH
Confidence            567889999965 444566899999999999999999999987 99986543    346789999999998776665542


Q ss_pred             -HhhcCCCCCChHHHhh
Q psy10346         79 -FNNVPSEGIGQKELLA   94 (292)
Q Consensus        79 -~~~l~~~~~~~~el~~   94 (292)
                       ...+- .+++-+|+..
T Consensus       110 ~~~~~~-~~l~~ee~~~  125 (151)
T 4aik_A          110 TRKEIL-GGISSDEIAV  125 (151)
T ss_dssp             HHHHHT-TTSCHHHHHH
T ss_pred             HHHHHH-hCCCHHHHHH
Confidence             22221 3556555443

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=97.10  E-value=0.001  Score=54.96  Aligned_cols=72  Identities=13%  Similarity=0.103  Sum_probs=56.5

Q ss_pred             HHHHHHHHHhcc--CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHH
Q psy10346          4 DLTEKILKYLDT--NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         4 ~~e~~iL~~L~~--~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      ..|..||..|..  ++.+...+||..+++++..|.+.+..|+.+ |||.-..    .-...+.||++|+++++.-.+..
T Consensus        46 ~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~-Glv~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~  123 (168)
T 3u2r_A           46 AQQYNTLRLLRSVHPEGMATLQIADRLISRAPDITRLIDRLDDR-GLVLRTRKPENRRVVEVALTDAGLKLLKDLEEPV  123 (168)
T ss_dssp             HHHHHHHHHHHHHTTSCEEHHHHHHHC---CTHHHHHHHHHHHT-TSEEEEEETTEEEEEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCcCHHHHHHHHCCChhhHHHHHHHHHHC-CCEeecCCCCCCCeeEeEECHHHHHHHHHHHHHH
Confidence            567889999976  346788999999999999999999999987 9998754    34567899999999887655543

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=97.09  E-value=0.0019  Score=50.00  Aligned_cols=68  Identities=10%  Similarity=0.060  Sum_probs=56.1

Q ss_pred             CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHhhc
Q psy10346          2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVKDN   71 (292)
Q Consensus         2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl~~   71 (292)
                      +.+...+||..| ..+.....++|..+|++...|.+.++.|+.. |+|.... .....|.||+.|...+..
T Consensus        19 ~~~~r~~IL~~L-~~~~~~~~ela~~l~is~~tv~~~l~~L~~~-gli~~~~~gr~~~y~l~~~~~~~~~~   87 (114)
T 2oqg_A           19 SDETRWEILTEL-GRADQSASSLATRLPVSRQAIAKHLNALQAC-GLVESVKVGREIRYRALGAELNKTAR   87 (114)
T ss_dssp             TCHHHHHHHHHH-HHSCBCHHHHHHHSSSCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEECSHHHHHHHH
T ss_pred             CChHHHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeeEEecCCEEEEEechHHHHHHHH
Confidence            346778899999 4566788999999999999999999999987 9998754 346779999999876543

>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=97.03  E-value=0.00072  Score=51.58  Aligned_cols=59  Identities=15%  Similarity=0.211  Sum_probs=50.5

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHH
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQ   67 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~   67 (292)
                      .....+||..|  .+.....++|+.+|++...|.+.++.|+.. |+|....   ..|.||++|+.
T Consensus        30 ~~~r~~Il~~L--~~~~~~~eLa~~l~is~~tv~~~L~~L~~~-Glv~~~~---g~y~l~~~g~~   88 (96)
T 1y0u_A           30 NPVRRKILRML--DKGRSEEEIMQTLSLSKKQLDYHLKVLEAG-FCIERVG---ERWVVTDAGKI   88 (96)
T ss_dssp             CHHHHHHHHHH--HTTCCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEET---TEEEECTTTCC
T ss_pred             CHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEC---CEEEECCCchH
Confidence            45667899999  456788999999999999999999999987 9998766   39999999854

>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=97.03  E-value=0.00029  Score=56.34  Aligned_cols=71  Identities=13%  Similarity=0.107  Sum_probs=58.1

Q ss_pred             HHHHHHHHHhccC--CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChH
Q psy10346          4 DLTEKILKYLDTN--PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHE   75 (292)
Q Consensus         4 ~~e~~iL~~L~~~--~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE   75 (292)
                      ..|..||..|...  +.+...++|..+++++..|.+.+..|+.+ |||.-..    .-...+.||++|+++++.-.+.
T Consensus        37 ~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~-Glv~r~~~~~D~R~~~i~LT~~G~~~~~~~~~~  113 (127)
T 2frh_A           37 FEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQE-DYFDKKRNEHDERTVLILVNAQQRKKIESLLSR  113 (127)
T ss_dssp             HHHHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHT-TSSCCBCCSSSSCCCEEECCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEecCCCCCCCeeEEEECHHHHHHHHHHHHH
Confidence            5678899999765  66788999999999999999999999987 9998632    3356778999999988654443

>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=97.01  E-value=0.00083  Score=52.76  Aligned_cols=68  Identities=3%  Similarity=-0.009  Sum_probs=55.6

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcC----CCHHHHHHHHHHhhccCCcEEEeee--eEEEEEeChhHHHHhhcC
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFN----EDHQKVVGGMKSIETLGEYLIVEPL--SHKIWELTGEGNQVKDNG   72 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~----~~~~~v~~~~~~L~s~~glv~~e~~--~~~~~~LTeEG~~yl~~G   72 (292)
                      ..|..||..|...+..+..++|..++    +++..|.+.+..|+.+ |+|.....  ....+.||+.|+.+++.-
T Consensus        10 ~~~~~vL~~l~~~~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~-Glv~r~~~~rr~~~~~lT~~g~~~~~~~   83 (123)
T 1okr_A           10 SAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKK-GFIDRKKDNKIFQYYSLVEESDIKYKTS   83 (123)
T ss_dssp             HHHHHHHHHHHHHSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHH-TSEEEEEETTEEEEEESSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHC-CCeEEEecCCeEEEEEecCHHHHHHHHH
Confidence            57888999997667788899999988    7799999999999987 99987653  233468999999876543

>2fsw_A PG_0823 protein; alpha-beta structure, helix-turn-helix, winged-helix-turn-HE structural genomics, PSI, protein structure initiative; HET: MSE; 2.16A {Porphyromonas gingivalis} SCOP: a.4.5.69

Probab=97.00  E-value=0.0015  Score=50.86  Aligned_cols=61  Identities=11%  Similarity=0.107  Sum_probs=50.5

Q ss_pred             HHHHHHhccCCCCChHHHHHhc-CCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHh
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLF-NEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVK   69 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~-~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl   69 (292)
                      ..||..|. .+.....++++.+ |+++..|.+.++.|+.. |+|+-...    ....|.||+.|+..+
T Consensus        28 ~~IL~~L~-~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~-GlV~r~~~~~d~r~~~y~LT~~G~~l~   93 (107)
T 2fsw_A           28 LLIIFQIN-RRIIRYGELKRAIPGISEKMLIDELKFLCGK-GLIKKKQYPEVPPRVEYSLTPLGEKVL   93 (107)
T ss_dssp             HHHHHHHT-TSCEEHHHHHHHSTTCCHHHHHHHHHHHHHT-TSEEEEEECSSSCEEEEEECHHHHTTH
T ss_pred             HHHHHHHH-hCCcCHHHHHHHcccCCHHHHHHHHHHHHHC-CCEEEeecCCCCCeeEEEECccHHHHH
Confidence            45788886 5667789999999 59999999999999987 99986553    357899999998754

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=96.93  E-value=0.0022  Score=52.32  Aligned_cols=61  Identities=21%  Similarity=0.226  Sum_probs=51.6

Q ss_pred             HHHHHHhccCCCCChHHHHHhc-CCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHh
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLF-NEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVK   69 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~-~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl   69 (292)
                      ..||..|. .+.....++++.+ |+++..+.+.++.|+.. |||+-...    ....|.||+.|++.+
T Consensus        38 l~IL~~L~-~g~~~~~eLa~~l~gis~~tls~~L~~Le~~-GlV~r~~~~~d~r~~~y~LT~~G~~l~  103 (131)
T 1yyv_A           38 VLILVALR-DGTHRFSDLRRXMGGVSEXMLAQSLQALEQD-GFLNRVSYPVVPPHVEYSLTPLGEQVS  103 (131)
T ss_dssp             HHHHHHGG-GCCEEHHHHHHHSTTCCHHHHHHHHHHHHHH-TCEEEEEECSSSCEEEEEECHHHHHHH
T ss_pred             HHHHHHHH-cCCCCHHHHHHHhccCCHHHHHHHHHHHHHC-CcEEEEecCCCCCeEEEEECccHHHHH
Confidence            45788887 5667789999999 79999999999999987 99987554    467899999998865

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=96.92  E-value=0.0032  Score=50.52  Aligned_cols=68  Identities=13%  Similarity=0.133  Sum_probs=54.3

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhc------CCCHHHHHHHHHHhhccCCcEEEee------eeEEEEEeChhHHHHhhc
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLF------NEDHQKVVGGMKSIETLGEYLIVEP------LSHKIWELTGEGNQVKDN   71 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~------~~~~~~v~~~~~~L~s~~glv~~e~------~~~~~~~LTeEG~~yl~~   71 (292)
                      .++..||..|.. ++..-.++++.+      ++++..|-..++.|+.. |+|+...      ..++.|.||+.|++++..
T Consensus        11 ~l~~~IL~lL~~-~p~~Gyei~~~l~~~g~~~is~gtlY~~L~rLe~~-GlI~~~~~~~~~g~~rk~Y~LT~~G~~~l~~   88 (117)
T 4esf_A           11 SLEGCVLEIISR-RETYGYEITRHLNDLGFTEVVEGTVYTILVRLEKK-KLVNIEKKPSDMGPPRKFYSLNEAGRQELEL   88 (117)
T ss_dssp             HHHHHHHHHHHH-SCBCHHHHHHHHHHHTCTTCCHHHHHHHHHHHHHT-TCEEEEEEC-----CEEEEEECHHHHHHHHH
T ss_pred             hHHHHHHHHHHc-CCCCHHHHHHHHHHcCCCCCCccHHHHHHHHHHHC-CCEEEEeecCCCCCCceEEEECHHHHHHHHH
Confidence            456778999975 445567888776      78999999999999987 9999864      347889999999999865


Q ss_pred             CC
Q psy10346         72 GS   73 (292)
Q Consensus        72 Gl   73 (292)
                      =.
T Consensus        89 ~~   90 (117)
T 4esf_A           89 FW   90 (117)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=96.88  E-value=0.0013  Score=57.71  Aligned_cols=84  Identities=15%  Similarity=0.127  Sum_probs=63.5

Q ss_pred             HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHHhhcCC--
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNNVPS--   84 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~~~l~~--   84 (292)
                      +.|+.....++.+...++|+.+|+++.+|.++++.|+.+ |||+.+..  ..+.||++|++.+..=.+-.+++...-.  
T Consensus         9 ~~I~~l~~~~~~~~~~~lA~~l~vs~~tvs~~l~~Le~~-GlV~r~~~--~~i~LT~~G~~~~~~~~~~h~~~e~~l~~~   85 (214)
T 3hrs_A            9 KCLYELGTRHNKITNKEIAQLMQVSPPAVTEMMKKLLAE-ELLIKDKK--AGYLLTDLGLKLVSDLYRKHRLIEVFLVHH   85 (214)
T ss_dssp             HHHHHTTSSCSCCCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEETT--TEEEECHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHhcCCCcCHHHHHHHHCCChhHHHHHHHHHHHC-CCEEEecC--CCeEECHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345554455667889999999999999999999999987 99987654  5789999999998877776665544321  


Q ss_pred             CCCChHHHh
Q psy10346         85 EGIGQKELL   93 (292)
Q Consensus        85 ~~~~~~el~   93 (292)
                      -|++.+++.
T Consensus        86 lg~~~~e~~   94 (214)
T 3hrs_A           86 LGYTTEEIH   94 (214)
T ss_dssp             TCCCHHHHH
T ss_pred             hCCCHHHHH
Confidence            256655443

>3l7w_A Putative uncharacterized protein SMU.1704; PADR, transcriptional factor, transcription; HET: MSE; 2.20A {Streptococcus mutans} SCOP: a.4.5.0

Probab=96.85  E-value=0.0037  Score=49.09  Aligned_cols=72  Identities=17%  Similarity=0.128  Sum_probs=55.6

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHh----cCCCHHHHHHHHHHhhccCCcEEEeee-----eEEEEEeChhHHHHhhcCCh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKL----FNEDHQKVVGGMKSIETLGEYLIVEPL-----SHKIWELTGEGNQVKDNGSH   74 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~----~~~~~~~v~~~~~~L~s~~glv~~e~~-----~~~~~~LTeEG~~yl~~GlP   74 (292)
                      ..+..||..|..+ +..-.++.+.    .++++..|.+.++.|+.. |+|+....     ....|.||+.|++.+..=.+
T Consensus         9 ~l~~~IL~~L~~~-~~~gyel~~~l~~~~~i~~~tly~~L~~Le~~-GlI~~~~~~~~~r~r~~y~LT~~G~~~l~~~~~   86 (108)
T 3l7w_A            9 LIEYLILAIVSKH-DSYGYDISQTIKLIASIKESTLYPILKKLEKA-GYLSTYTQEHQGRRRKYYHLTDSGEKHLVYLTK   86 (108)
T ss_dssp             HHHHHHHHHHHHS-CEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHT-TSEEEEEEEETTEEEEEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcC-CCcHHHHHHHHHHHhCCCcChHHHHHHHHHHC-CCeEEEeecCCCCcceEEEECHHHHHHHHHHHH
Confidence            5678899999753 3344556555    589999999999999987 99988643     36789999999999866555


Q ss_pred             HHH
Q psy10346         75 EVL   77 (292)
Q Consensus        75 E~r   77 (292)
                      +.+
T Consensus        87 ~~~   89 (108)
T 3l7w_A           87 EWS   89 (108)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

>3f8b_A Transcriptional regulator, PADR-like family; winged helix turn helix, transcription regulator; 2.00A {Lactococcus lactis subsp} SCOP: a.4.5.0 PDB: 3f8c_A* 3f8f_A*

Probab=96.82  E-value=0.0042  Score=49.54  Aligned_cols=72  Identities=13%  Similarity=-0.000  Sum_probs=56.4

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhc--------CCCHHHHHHHHHHhhccCCcEEEee------eeEEEEEeChhHHHHh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLF--------NEDHQKVVGGMKSIETLGEYLIVEP------LSHKIWELTGEGNQVK   69 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~--------~~~~~~v~~~~~~L~s~~glv~~e~------~~~~~~~LTeEG~~yl   69 (292)
                      .++..||..|.. ++..-.++.+.+        ++++..|-..++.|+.. |+|+...      .....|.||+.|++++
T Consensus        12 ~l~~~IL~~L~~-~~~~Gyei~~~l~~~~~~~~~i~~gtly~~L~rLe~~-GlI~~~~~~~~~~~~rk~Y~LT~~G~~~l   89 (116)
T 3f8b_A           12 QTNVILLNVLKQ-GDNYVYGIIKQVKEASNGEMELNEATLYTIFKRLEKD-GIISSYWGDESQGGRRKYYRLTEIGHENM   89 (116)
T ss_dssp             HHHHHHHHHHHH-CCBCHHHHHHHHHHHTTTCCCCCHHHHHHHHHHHHHT-TSEEEEEEC----CCEEEEEECHHHHHHH
T ss_pred             hHHHHHHHHHHh-CCCCHHHHHHHHHHHhCCCCCCCcchHHHHHHHHHHC-CCEEEEeeccCCCCCceEEEECHHHHHHH
Confidence            466778999975 344556676654        78999999999999987 9999864      3477899999999999


Q ss_pred             hcCChHHH
Q psy10346         70 DNGSHEVL   77 (292)
Q Consensus        70 ~~GlPE~r   77 (292)
                      ..-.++..
T Consensus        90 ~~~~~~~~   97 (116)
T 3f8b_A           90 RLAFESWS   97 (116)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            77666654

>2fxa_A Protease production regulatory protein HPR; protease porduction, regulation, STR genomics, PSI, protein structure initiative; HET: PGE P6G 1PE; 2.40A {Bacillus subtilis} SCOP: a.4.5.28

Probab=96.81  E-value=0.0016  Score=56.67  Aligned_cols=68  Identities=19%  Similarity=0.028  Sum_probs=56.1

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcC
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNG   72 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~G   72 (292)
                      ..+..||..|...+.+...++|..+++++..|.+.+..|+.+ |||.-..    .-...+.||++|+.+++.-
T Consensus        48 ~~q~~iL~~L~~~~~~t~~eLa~~l~i~~stvs~~l~~Le~~-GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~  119 (207)
T 2fxa_A           48 INEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEER-GYLRFSKRLNDKRNTYVQLTEEGTEVFWSL  119 (207)
T ss_dssp             HHHHHHHHHHHHHTSEEHHHHHHHTTCCHHHHHHHHHHHHHH-TSEEEECC------CEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEecCCCCCceEEEEECHHHHHHHHHH
Confidence            567889999976677888999999999999999999999987 9998754    2345789999999988543

>3hhh_A Transcriptional regulator, PADR family; PF03551, structural PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.70A {Enterococcus faecalis} SCOP: a.4.5.0

Probab=96.81  E-value=0.0041  Score=49.85  Aligned_cols=70  Identities=16%  Similarity=0.178  Sum_probs=55.4

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhc------CCCHHHHHHHHHHhhccCCcEEEee------eeEEEEEeChhHHHHhhc
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLF------NEDHQKVVGGMKSIETLGEYLIVEP------LSHKIWELTGEGNQVKDN   71 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~------~~~~~~v~~~~~~L~s~~glv~~e~------~~~~~~~LTeEG~~yl~~   71 (292)
                      .++.-||..|.. ++..-.++++.+      ++++..|-..++.|+.. |+|+...      ..++.|.||+.|++++..
T Consensus        13 ~l~~~IL~lL~~-~p~~Gyei~~~l~~~g~~~is~gtlY~~L~rLe~~-GlI~~~~~~~~~g~~rk~Y~lT~~G~~~l~~   90 (116)
T 3hhh_A           13 ILEGLVLAIIQR-KETYGYEITKILNDQGFTEIVEGTVYTILLRLEKN-QWVIAEKKPSEKGPMRKFYRLTSSGEAELAD   90 (116)
T ss_dssp             HHHHHHHHHHHH-SCBCHHHHHHHHHTTSCSSCCHHHHHHHHHHHHHT-TSEEEEEEECC--CEEEEEEECHHHHHHHHH
T ss_pred             hHHHHHHHHHhc-CCCCHHHHHHHHHHcCCCCCCccHHHHHHHHHHHC-CCEEEEeeecCCCCCceEEEECHHHHHHHHH
Confidence            456779999975 344557888776      68999999999999987 9999864      347789999999999866


Q ss_pred             CChH
Q psy10346         72 GSHE   75 (292)
Q Consensus        72 GlPE   75 (292)
                      =..+
T Consensus        91 ~~~~   94 (116)
T 3hhh_A           91 FWQR   94 (116)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            4444

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=96.80  E-value=0.001  Score=54.63  Aligned_cols=73  Identities=12%  Similarity=0.059  Sum_probs=52.8

Q ss_pred             HHHHHHHHHhccC-----CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee---eEEEEEeChhHHHHhhcCChH
Q psy10346          4 DLTEKILKYLDTN-----PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL---SHKIWELTGEGNQVKDNGSHE   75 (292)
Q Consensus         4 ~~e~~iL~~L~~~-----~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~---~~~~~~LTeEG~~yl~~GlPE   75 (292)
                      ..|..||..|...     +.++..++|..+++++..|.+.+..|+.+ |+|.....   -...+.||++|++.++.-.|.
T Consensus        33 ~~q~~vL~~l~~~~~~~~~~~t~~eLa~~l~~~~~tvsr~v~~Le~~-glVr~~~~~DrR~~~v~LT~~G~~~~~~~~~~  111 (148)
T 4fx0_A           33 NTQFSTLAVISLSEGSAGIDLTMSELAARIGVERTTLTRNLEVMRRD-GLVRVMAGADARCKRIELTAKGRAALQKAVPL  111 (148)
T ss_dssp             HHHHHHHHHHHC---------CHHHHHHHHTCCHHHHHHHHHHHHHT-TSBC-----------CCBCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCCCCCCcCHHHHHHHHCCChhhHHHHHHHHHHC-CCEEeeCCCCCCeeEEEECHHHHHHHHHHHHH
Confidence            4578899988543     34678999999999999999999999987 99965322   234679999999998877665


Q ss_pred             HH
Q psy10346         76 VL   77 (292)
Q Consensus        76 ~r   77 (292)
                      .+
T Consensus       112 ~~  113 (148)
T 4fx0_A          112 WR  113 (148)
T ss_dssp             HH
T ss_pred             HH
Confidence            33

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=96.74  E-value=0.0039  Score=51.21  Aligned_cols=61  Identities=8%  Similarity=0.072  Sum_probs=51.0

Q ss_pred             HHHHHHhccCCCCChHHHHHhc-CCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHh
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLF-NEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVK   69 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~-~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl   69 (292)
                      ..||..|. .+.....+++..+ |++...+.+.++.|+.. |||+-....    ...|.||+.|+..+
T Consensus        29 l~IL~~L~-~g~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~-GLV~R~~~~~d~r~v~y~LT~~G~~l~   94 (131)
T 4a5n_A           29 GILFYHMI-DGKKRFNEFRRICPSITQRMLTLQLRELEAD-GIVHREVYHQVPPKVEYSLTEFGRTLE   94 (131)
T ss_dssp             HHHHHHHT-TSCBCHHHHHHHCTTSCHHHHHHHHHHHHHT-TSEEEEEECSSSCEEEEEECTTGGGGH
T ss_pred             HHHHHHHh-cCCcCHHHHHHHhcccCHHHHHHHHHHHHHC-CCEEEEecCCCCCeEEEEECHhHHHHH
Confidence            34777776 5677889999999 99999999999999987 999865443    68999999998754

>1xma_A Predicted transcriptional regulator; southea collaboratory for structural genomics, secsg, protein struc initiative, PSI; 2.30A {Clostridium thermocellum} SCOP: a.4.5.61

Probab=96.73  E-value=0.0043  Score=51.62  Aligned_cols=71  Identities=14%  Similarity=0.094  Sum_probs=55.4

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhc--------CCCHHHHHHHHHHhhccCCcEEEeee------eEEEEEeChhHHHHh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLF--------NEDHQKVVGGMKSIETLGEYLIVEPL------SHKIWELTGEGNQVK   69 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~--------~~~~~~v~~~~~~L~s~~glv~~e~~------~~~~~~LTeEG~~yl   69 (292)
                      ..+..||..|.. ++....++++.+        ++++..|...++.|+.. |+|+....      ..+.|.||+.|++.+
T Consensus        41 ~~~~~IL~~L~~-~~~~gyeI~~~l~~~~~~~~~is~gtLy~~L~rLE~~-GlI~~~~~~~~~~~~rk~Y~LT~~G~~~l  118 (145)
T 1xma_A           41 YVDTIILSLLIE-GDSYGYEISKNIRIKTDELYVIKETTLYSAFARLEKN-GYIKSYYGEETQGKRRTYYRITPEGIKYY  118 (145)
T ss_dssp             THHHHHHHHHHH-CCEEHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHT-TSEEEEEEEEC--CEEEEEEECHHHHHHH
T ss_pred             cHHHHHHHHHHh-CCCCHHHHHHHHHHhhCCccCcChhHHHHHHHHHHHC-CCEEEEEeccCCCCCeEEEEECHHHHHHH
Confidence            567889999975 444556776665        68999999999999987 99988643      468899999999998


Q ss_pred             hcCChHH
Q psy10346         70 DNGSHEV   76 (292)
Q Consensus        70 ~~GlPE~   76 (292)
                      ..-..+.
T Consensus       119 ~~~~~~~  125 (145)
T 1xma_A          119 KQKCEEW  125 (145)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            7654443

>3qtc_A Pyrrolysyl-tRNA synthetase; aminoacyl-tRNA synthetase, ATP B O-methyl tyrosine binding, magnesium binding, aminoacylatio esterification; HET: 0A1 ANP; 1.75A {Methanosarcina mazei} PDB: 2q7e_A* 2q7g_A* 2q7h_A* 2zim_A* 2zin_A* 2e3c_A* 2zcd_A* 2zce_A* 2zio_A* 3vqv_A* 3vqw_A* 3vqx_A* 3vqy_A*

Probab=96.72  E-value=0.001  Score=61.13  Aligned_cols=58  Identities=17%  Similarity=0.210  Sum_probs=49.1

Q ss_pred             CCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecC
Q psy10346        216 PSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTD  277 (292)
Q Consensus       216 ~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~  277 (292)
                      ..|..||..++++.|+++|.++||.|+. .|.+++. .+|+.++.|.+||.+  .|+||+++
T Consensus        72 ~~g~~~~~~~i~~~ir~~l~~~Gf~EV~-Tp~l~~~-~~~~~~~~~~~~p~~--~~~~~~~~  129 (290)
T 3qtc_A           72 AEERENYLGKLEREITRFFVDRGFLEIK-SPILIPL-EYIERMGIDNDTELS--KQIFRVDK  129 (290)
T ss_dssp             HTTCCCHHHHHHHHHHHHHHHTTCEEEC-CCSEEET-HHHHHTTCCTTSSGG--GGCCEETT
T ss_pred             ccccccHHHHHHHHHHHHHHHCCCEEEE-CCceeeH-HHHHhcCCCcCCchh--hhheeeCC
Confidence            4689999999999999999999999996 5777776 489999999999986  35666653

>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=96.71  E-value=0.0022  Score=51.63  Aligned_cols=63  Identities=19%  Similarity=0.233  Sum_probs=50.3

Q ss_pred             HHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCCh
Q psy10346          9 ILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSH   74 (292)
Q Consensus         9 iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlP   74 (292)
                      |+..+..++..+..++|..+|++...|.+.+..|+.+ |+|.....  ..+.||+.|+..+..-.+
T Consensus        13 i~~l~~~~~~~~~~ela~~l~vs~~tvs~~l~~Le~~-Glv~r~~~--~~~~LT~~g~~~~~~~~~   75 (142)
T 1on2_A           13 IYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKD-EYLIYEKY--RGLVLTSKGKKIGKRLVY   75 (142)
T ss_dssp             HHHHHHHHSSCCHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEETT--TEEEECHHHHHHHHHHHH
T ss_pred             HHHHHhhcCCCCHHHHHHHhCCCHHHHHHHHHHHHHC-CCEEEeeC--ceEEEchhHHHHHHHHHH
Confidence            3333444566888999999999999999999999987 99987543  579999999998765333

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=96.71  E-value=0.0018  Score=58.38  Aligned_cols=64  Identities=17%  Similarity=0.243  Sum_probs=55.7

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl   69 (292)
                      ..+.+||..|..++.+...++|+.+|++..+|.+.++.|+.. |+|.... ....|.||+.|+..+
T Consensus       152 ~~~~~IL~~L~~~~~~s~~eLA~~lglsksTv~r~L~~Le~~-GlV~r~~-r~~~~~LT~~G~~l~  215 (244)
T 2wte_A          152 REEMKLLNVLYETKGTGITELAKMLDKSEKTLINKIAELKKF-GILTQKG-KDRKVELNELGLNVI  215 (244)
T ss_dssp             HHHHHHHHHHHHHTCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEET-TTTEEEECHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEeC-CccEEEECHHHHHHH
Confidence            568889999876677888999999999999999999999987 9998763 356799999999875

>2rhq_B Phenylalanyl-tRNA synthetase beta chain; heterotetramer, phenylalanine, aminoacyl-tRNA synthetase, ATP-binding, cytoplasm, ligase; HET: GAX; 2.20A {Staphylococcus haemolyticus} PDB: 2rhs_B*

Probab=96.68  E-value=0.0031  Score=65.82  Aligned_cols=59  Identities=17%  Similarity=0.238  Sum_probs=48.1

Q ss_pred             CCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCCCC
Q psy10346        214 SLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS  281 (292)
Q Consensus       214 ~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~~  281 (292)
                      ....|..||..++++++|++|.++||.|+-+.++|..++|  +.|+ |+++|      +++|.+|-..
T Consensus       486 ~~~~g~~~~~~~~~~~ir~~L~~~Gf~Evitysfvs~~~~--~~l~-~~~~~------~v~L~NPis~  544 (795)
T 2rhq_B          486 EVTSGELTDRQHKTRTLKETLEGAGLNQAITYSLVSKDHA--KDFA-LQERP------TISLLMPMSE  544 (795)
T ss_dssp             SCCCCCCCHHHHHHHHHHHHHHHTTCEECCCCSEECTTTT--TTTC-SSCCC------CEECSSCSCT
T ss_pred             ccCCCCCCHHHHHHHHHHHHHHHCCCEEEecCCccCHHHH--HhhC-CCCCc------eEEEcCCCch
Confidence            4567899999999999999999999999988999877755  6665 64332      7999988554

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=96.66  E-value=0.003  Score=50.30  Aligned_cols=70  Identities=20%  Similarity=0.212  Sum_probs=55.2

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhc------C--CCH-HHHHHHHHHhhccCCcEEEeee-----eEEEEEeChhHHHHh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLF------N--EDH-QKVVGGMKSIETLGEYLIVEPL-----SHKIWELTGEGNQVK   69 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~------~--~~~-~~v~~~~~~L~s~~glv~~e~~-----~~~~~~LTeEG~~yl   69 (292)
                      ..+..||..|.. ++....++++.+      +  +++ ..|...++.|+.. |+|+....     ..+.|.||+.|++.+
T Consensus        13 ~~~~~IL~~L~~-~~~~gyel~~~l~~~g~~~~~is~~~tly~~L~~Le~~-GlI~~~~~~~~~~~r~~Y~LT~~G~~~l   90 (118)
T 2esh_A           13 WLASTILLLVAE-KPSHGYELAERLAEFGIEIPGIGHMGNIYRVLADLEES-GFLSTEWDTTVSPPRKIYRITPQGKLYL   90 (118)
T ss_dssp             HHHHHHHHHHHH-SCBCHHHHHHHHHTTCCSSTTCCCCCCHHHHHHHHHHT-TSEEEEEECSSSSCEEEEEECHHHHHHH
T ss_pred             hHHHHHHHHHHc-CCCCHHHHHHHHHHhCCcccCCCCcchHHHHHHHHHHC-CCeEEEeecCCCCCceEEEEChHHHHHH
Confidence            567889999965 455667787776      3  788 9999999999987 99988653     467899999999988


Q ss_pred             hcCChH
Q psy10346         70 DNGSHE   75 (292)
Q Consensus        70 ~~GlPE   75 (292)
                      ..-..+
T Consensus        91 ~~~~~~   96 (118)
T 2esh_A           91 REILRS   96 (118)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            664333

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=96.61  E-value=0.0033  Score=47.75  Aligned_cols=66  Identities=11%  Similarity=0.084  Sum_probs=55.0

Q ss_pred             CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHHHh
Q psy10346          2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQVK   69 (292)
Q Consensus         2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~yl   69 (292)
                      +.+...+||..|.. +.....++|+.+|+++..|.+.++.|+.. |+|..+.. ....|.||+++...+
T Consensus        21 ~~~~r~~Il~~L~~-~~~~~~ela~~l~is~~tvs~~L~~L~~~-Glv~~~~~g~~~~y~l~~~~~~~l   87 (98)
T 3jth_A           21 ANERRLQILCMLHN-QELSVGELCAKLQLSQSALSQHLAWLRRD-GLVTTRKEAQTVYYTLKSEEVKAM   87 (98)
T ss_dssp             CSHHHHHHHHHTTT-SCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEECCTTCCEEEECCHHHHHH
T ss_pred             CCHHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeEEEEeCCEEEEEECHHHHHHH
Confidence            35667789999976 67788999999999999999999999987 99987544 357899999987654

>3elk_A Putative transcriptional regulator TA0346; structural genomics, PSI-2, prote structure initiative; 1.70A {Thermoplasma acidophilum}

Probab=96.61  E-value=0.0037  Score=50.10  Aligned_cols=72  Identities=19%  Similarity=0.229  Sum_probs=55.3

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcC------CCHHHHHHHHHHhhccCCcEEEeee------eEEEEEeChhHHHHhhc
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFN------EDHQKVVGGMKSIETLGEYLIVEPL------SHKIWELTGEGNQVKDN   71 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~------~~~~~v~~~~~~L~s~~glv~~e~~------~~~~~~LTeEG~~yl~~   71 (292)
                      ..+..||..|.. ++..-.++++.+.      +++..|-..++.|+.. |+|+....      ..+.|.||+.|++++..
T Consensus        14 ~l~~~IL~lL~~-~p~~gyel~~~l~~~~~~~i~~gtly~~L~~Le~~-GlI~~~~~~~~~~~~rk~Y~lT~~G~~~l~~   91 (117)
T 3elk_A           14 LITLYILKELVK-RPMHGYELQKSMFETTGQALPQGSIYILLKTMKER-GFVISESSVNEKGQQLTVYHITDAGKKFLCD   91 (117)
T ss_dssp             HHHHHHHHHHHH-SCEEHHHHHHHHHHHHSCCCCTTHHHHHHHHHHHH-TSEEEEEEEC-CCCEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHHHHhCCCCCcchHHHHHHHHHHC-CCEEEEeeecCCCCCceEEEECHHHHHHHHH
Confidence            456778999975 3444566766654      7889999999999987 99998653      57889999999999876


Q ss_pred             CChHHH
Q psy10346         72 GSHEVL   77 (292)
Q Consensus        72 GlPE~r   77 (292)
                      -..+..
T Consensus        92 ~~~~~~   97 (117)
T 3elk_A           92 HSQALQ   97 (117)
T ss_dssp             TSTTHH
T ss_pred             HHHHHH
Confidence            554433

>2f2e_A PA1607; transcription factor, helix-TRUN-helix, APC5613, structural genomics, PSI, protein structure initiative; HET: GLC; 1.85A {Pseudomonas aeruginosa} SCOP: a.4.5.69

Probab=96.60  E-value=0.0045  Score=51.16  Aligned_cols=61  Identities=11%  Similarity=0.154  Sum_probs=50.8

Q ss_pred             HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee---EEEEEeChhHHHHh
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS---HKIWELTGEGNQVK   69 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~---~~~~~LTeEG~~yl   69 (292)
                      ..||..|. .+.....++++.+|++...|.+.++.|+.. |+|+-....   ...|.||+.|+..+
T Consensus        27 l~IL~~L~-~g~~~~~eLa~~lgis~~tls~~L~~Le~~-GlI~r~~~~~d~~~~y~LT~~G~~l~   90 (146)
T 2f2e_A           27 MLIVRDAF-EGLTRFGEFQKSLGLAKNILAARLRNLVEH-GVMVAVPAESGSHQEYRLTDKGRALF   90 (146)
T ss_dssp             HHHHHHHH-TTCCSHHHHHHHHCCCHHHHHHHHHHHHHT-TSEEEEECSSSSCEEEEECHHHHTTH
T ss_pred             HHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHHHHHHC-CCEEEEecCCCCeEEEEECchHHHHH
Confidence            45778785 566788999999999999999999999987 999875422   57999999998754

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}

Probab=96.59  E-value=0.0044  Score=49.46  Aligned_cols=72  Identities=11%  Similarity=0.037  Sum_probs=56.4

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhc------CCCHHHHHHHHHHhhccCCcEEEee------eeEEEEEeChhHHHHhhc
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLF------NEDHQKVVGGMKSIETLGEYLIVEP------LSHKIWELTGEGNQVKDN   71 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~------~~~~~~v~~~~~~L~s~~glv~~e~------~~~~~~~LTeEG~~yl~~   71 (292)
                      .++..||..|.. ++..-.++++.+      ++++..|-..++.|+.. |+|+...      ..++.|.||+.|++++..
T Consensus         9 ~l~~~IL~~L~~-~~~~Gyei~~~l~~~~~~~is~gtlY~~L~rLe~~-GlI~~~~~~~~~g~~rk~Y~LT~~G~~~l~~   86 (115)
T 4esb_A            9 VLEGCILYIISQ-EEVYGYELSTKLNKHGFTFVSEGSIYPLLLRMQKE-KLIEGTLKASSLGPKRKYYHITDKGLEQLEE   86 (115)
T ss_dssp             THHHHHHHHHHH-SCEEHHHHHHHHHHTTCTTCCHHHHHHHHHHHHHT-TSEEEEEEECTTSCEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHC-CCeEEEeeecCCCCCcEEEEECHHHHHHHHH
Confidence            467789999975 344557777765      48999999999999987 9999864      257889999999999876


Q ss_pred             CChHHH
Q psy10346         72 GSHEVL   77 (292)
Q Consensus        72 GlPE~r   77 (292)
                      -..+..
T Consensus        87 ~~~~~~   92 (115)
T 4esb_A           87 FKQSWG   92 (115)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            655543

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=96.58  E-value=0.00061  Score=57.23  Aligned_cols=73  Identities=12%  Similarity=0.041  Sum_probs=58.5

Q ss_pred             HHHHHHHHHhccCCC---CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHH
Q psy10346          4 DLTEKILKYLDTNPP---VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~---~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      ..+..||..|...+.   +...++|..+|+++..|.+.+..|+.+ |||+...    .-...+.||+.|+.++..-.+..
T Consensus        69 ~~~~~iL~~L~~~~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~-GlV~r~~~~~DrR~~~~~LT~~G~~~~~~~~~~~  147 (181)
T 2fbk_A           69 AAGWDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRIVRLLEK-GLIERREDERDRRSASIRLTPQGRALVTHLLPAH  147 (181)
T ss_dssp             HHHHHHHHHHHHHCCSSCBCHHHHHHHCSCCSGGGSSHHHHHHHH-TSEECCC-------CCBEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-cCEEecCCCCCCCeeEEEECHHHHHHHHHHHHHH
Confidence            567889999976443   788999999999999999999999987 9998753    33456899999999997766554


Q ss_pred             H
Q psy10346         77 L   77 (292)
Q Consensus        77 r   77 (292)
                      .
T Consensus       148 ~  148 (181)
T 2fbk_A          148 L  148 (181)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=96.54  E-value=0.0044  Score=49.00  Aligned_cols=74  Identities=15%  Similarity=0.129  Sum_probs=60.0

Q ss_pred             CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHHHhhcCChHHH
Q psy10346          2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      +.+...+||..|. .++....++|..+|++...|.+.++.|+.. |+|..+.. ....|.||++|..-+..-+.++.
T Consensus        16 ~~~~R~~Il~~L~-~~~~~~~eLa~~l~is~~tvs~hL~~L~~~-GlV~~~~~gr~~~y~l~~~~~~~l~~~~~~~~   90 (118)
T 3f6o_A           16 ADPTRRAVLGRLS-RGPATVSELAKPFDMALPSFMKHIHFLEDS-GWIRTHKQGRVRTCAIEKEPFTAVEAWLAEQQ   90 (118)
T ss_dssp             TSHHHHHHHHHHH-TCCEEHHHHHTTCCSCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEECSHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-hCCCCHHHHHHHhCcCHHHHHHHHHHHHHC-CCeEEEecCCEEEEEECHHHHHHHHHHHHHHH
Confidence            3467788999887 466788999999999999999999999986 99988654 46789999999887755544443

>2obp_A Putative DNA-binding protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE; 1.70A {Ralstonia eutropha} SCOP: a.4.5.71

Probab=96.53  E-value=0.0035  Score=49.20  Aligned_cols=70  Identities=14%  Similarity=0.019  Sum_probs=55.8

Q ss_pred             HHHHHHHHHhcc------CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee--eEEEEEeChhHHHHhhcCCh
Q psy10346          4 DLTEKILKYLDT------NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL--SHKIWELTGEGNQVKDNGSH   74 (292)
Q Consensus         4 ~~e~~iL~~L~~------~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~--~~~~~~LTeEG~~yl~~GlP   74 (292)
                      +.+..+|..|..      ++.+...+||+..+++...+.+.+..|+.. |||.+...  ......||++|+..++.-.|
T Consensus        16 ~~q~~vL~~L~~~~~~~~g~~~s~~eLa~~l~l~~stLsR~l~rLe~~-GLV~r~~~~D~R~~v~LT~~G~~~l~~~~p   93 (96)
T 2obp_A           16 PAIVEVLLVLREAGIENGATPWSLPKIAKRAQLPMSVLRRVLTQLQAA-GLADVSVEADGRGHASLTQEGAALAAQLFP   93 (96)
T ss_dssp             HHHHHHHHHHHHHTSSTTCCCCBHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECTTSCEEEEECHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHhhCCCCCcCHHHHHHHhCCchhhHHHHHHHHHHC-CCEEeecCCCCceeEEECHHHHHHHHHhcC
Confidence            567888887743      256788999999999999999999999986 99998433  12247999999998876655

>1yg2_A Gene activator APHA; virulence factor, winged helix, transcripti factor, transcription; 2.20A {Vibrio cholerae} SCOP: a.4.5.61

Probab=96.48  E-value=0.0041  Score=52.91  Aligned_cols=65  Identities=22%  Similarity=0.314  Sum_probs=51.6

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhc--------CCCHHHHHHHHHHhhccCCcEEEeee------eEEEEEeChhHHHHhh
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLF--------NEDHQKVVGGMKSIETLGEYLIVEPL------SHKIWELTGEGNQVKD   70 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~--------~~~~~~v~~~~~~L~s~~glv~~e~~------~~~~~~LTeEG~~yl~   70 (292)
                      ++..||..|.. ++....++++.+        ++++..|...++.|+.. |+|+....      .++.|.||+.|++.+.
T Consensus         3 l~~~iL~lL~~-~~~~gyel~~~l~~~~~~~~~~s~~~ly~~L~~Le~~-GlI~~~~~~~~~~~~r~~Y~lT~~G~~~l~   80 (179)
T 1yg2_A            3 LPHVILTVLST-RDATGYDITKEFSASIGYFWKASHQQVYRELNKMGEQ-GLVTCVLEPQEGKPDRKVYSITQAGRSALG   80 (179)
T ss_dssp             HHHHHHHHHHH-CCBCHHHHHHHHTTGGGGTCCCCHHHHHHHHHHHHHT-TSEEECCC---------CEEECHHHHHHHH
T ss_pred             hHHHHHHHHhc-CCCCHHHHHHHHHHHhCCccCCCcCcHHHHHHHHHHC-CCeEEEeecCCCCCCceEEEeChHHHHHHH
Confidence            57789999975 556778888877        68999999999999986 99997543      4678999999999775


Q ss_pred             c
Q psy10346         71 N   71 (292)
Q Consensus        71 ~   71 (292)
                      +
T Consensus        81 ~   81 (179)
T 1yg2_A           81 E   81 (179)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=96.45  E-value=0.012  Score=45.60  Aligned_cols=64  Identities=11%  Similarity=0.132  Sum_probs=53.4

Q ss_pred             CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHH
Q psy10346          2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQ   67 (292)
Q Consensus         2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~   67 (292)
                      +.....+||..|. .+.....++|+.+|+++..|.+.++.|+.. |+|..... ....|.||+++..
T Consensus        24 ~~~~r~~IL~~L~-~~~~~~~ela~~l~is~stvs~~L~~L~~~-Glv~~~~~gr~~~y~l~~~~~~   88 (106)
T 1r1u_A           24 GDYNRIRIMELLS-VSEASVGHISHQLNLSQSNVSHQLKLLKSV-HLVKAKRQGQSMIYSLDDIHVA   88 (106)
T ss_dssp             CSHHHHHHHHHHH-HCCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEESSHHHH
T ss_pred             CCHHHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeEEEEeCCEEEEEEChHHHH
Confidence            4567788999997 456788999999999999999999999986 99987553 4568899998864

>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=96.40  E-value=0.0045  Score=46.88  Aligned_cols=62  Identities=18%  Similarity=0.275  Sum_probs=50.2

Q ss_pred             cHHHHHHHHHhccCC---CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhH
Q psy10346          3 SDLTEKILKYLDTNP---PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEG   65 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~---~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG   65 (292)
                      .+.+.+||..|..++   .+...++|+.+|++...|-+.+..|+.. |+|.......-.|.++.-.
T Consensus         9 ~~~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~-G~I~~~g~~~~~W~i~~~~   73 (81)
T 1qbj_A            9 QDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKK-GKLQKEAGTPPLWKIAVST   73 (81)
T ss_dssp             HHHHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEESSSSCEEEEC---
T ss_pred             hHHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEecCCCCCeeEEeCcH
Confidence            467889999998766   6888999999999999999999999986 9998765555677776543

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=96.36  E-value=0.0061  Score=50.93  Aligned_cols=68  Identities=10%  Similarity=0.152  Sum_probs=56.8

Q ss_pred             CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHHHhhc
Q psy10346          2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQVKDN   71 (292)
Q Consensus         2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~yl~~   71 (292)
                      +.+...+||..|. .+.....+||..+|++...|..-++.|+.. |+|..++. ....|.||++|...+.+
T Consensus        56 ~~p~R~~IL~~L~-~~~~t~~eLa~~lgls~stvs~hL~~L~~a-GlV~~~~~Gr~~~y~lt~~~~~~l~~  124 (151)
T 3f6v_A           56 AEPTRRRLVQLLT-SGEQTVNNLAAHFPASRSAISQHLRVLTEA-GLVTPRKDGRFRYYRLDPQGLAQLRA  124 (151)
T ss_dssp             TSHHHHHHHHHGG-GCCEEHHHHHTTSSSCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEecCCEEEEEEChHHHHHHHH
Confidence            4567889999998 456788999999999999999999999987 99987543 45789999999876643

>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=96.31  E-value=0.0051  Score=49.06  Aligned_cols=66  Identities=11%  Similarity=0.075  Sum_probs=52.9

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHHHh
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQVK   69 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~yl   69 (292)
                      .+...+||..|...+.....++|..+|+++..|.+.++.|+.. |+|..... ....|.||++|..-+
T Consensus        41 ~~~rl~IL~~L~~~~~~s~~eLa~~l~is~stvs~~L~~L~~~-Glv~~~~~gr~~~y~l~~~~~~~~  107 (122)
T 1u2w_A           41 DENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQ-GVVNFRKEGKLALYSLGDEHIRQI  107 (122)
T ss_dssp             SHHHHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEC----CCEEEESCHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeEEEEECCEEEEEECHHHHHHH
Confidence            3556789999976667788999999999999999999999986 99987543 346899999986543

>2p8t_A Hypothetical protein PH0730; pyrococcus horikoshii OT3, STR genomics, PSI, protein structure initiative; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.72 d.74.4.2

Probab=96.30  E-value=0.007  Score=53.41  Aligned_cols=50  Identities=12%  Similarity=0.224  Sum_probs=44.2

Q ss_pred             CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346         16 NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus        16 ~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl   69 (292)
                      ++.+...++|+.+|+...+|..+++.|+++ |||+.+.   .-..||++|++++
T Consensus        28 ~~~V~~~~LA~~LgvS~~SV~~~lkkL~e~-GLV~~~~---~Gv~LTe~G~~~A   77 (200)
T 2p8t_A           28 KEPLGRKQISERLELGEGSVRTLLRKLSHL-DIIRSKQ---RGHFLTLKGKEIR   77 (200)
T ss_dssp             TSCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEC-----CEEECHHHHHHH
T ss_pred             cCCccHHHHHHHhCCCHHHHHHHHHHHHHC-CCEEEeC---CCeEECHHHHHHH
Confidence            356788999999999999999999999987 9999887   6899999999987

>1sd4_A Penicillinase repressor; BLAI, MECI, methicillin, B-lactam, DNA binding PR; 2.00A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1xsd_A

Probab=96.29  E-value=0.016  Score=45.47  Aligned_cols=91  Identities=12%  Similarity=0.094  Sum_probs=61.2

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcC----CCHHHHHHHHHHhhccCCcEEEeeeeEE-EEE-eChhHHH-------Hh
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFN----EDHQKVVGGMKSIETLGEYLIVEPLSHK-IWE-LTGEGNQ-------VK   69 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~----~~~~~v~~~~~~L~s~~glv~~e~~~~~-~~~-LTeEG~~-------yl   69 (292)
                      ...|..||..|-..+.++..+++..++    +++..|.+.+..|+.+ |+|.-+..... .|. ++.+|..       .+
T Consensus         9 t~~q~~vL~~L~~~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~k-Glv~R~~~~r~~~~~~~~~~~~~~~~~~~~~~   87 (126)
T 1sd4_A            9 SMAEWDVMNIIWDKKSVSANEIVVEIQKYKEVSDKTIRTLITRLYKK-EIIKRYKSENIYFYSSNIKEDDIKMKTAKTFL   87 (126)
T ss_dssp             CHHHHHHHHHHHHSSSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEECSCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhcCCCCHHHHHHHHhhcCCCChhhHHHHHHHHHHC-CceEEEeCCCeEEEEEecCHHHHHHHHHHHHH
Confidence            367899999998777888899999886    5899999999999987 99987653322 332 4444432       21


Q ss_pred             ---hcCChHHHHHhhcCCCCCChHHHhh
Q psy10346         70 ---DNGSHEVLVFNNVPSEGIGQKELLA   94 (292)
Q Consensus        70 ---~~GlPE~rl~~~l~~~~~~~~el~~   94 (292)
                         -+|+....+-.++...+++-+|+..
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~ls~ee~~~  115 (126)
T 1sd4_A           88 NKLYGGDMKSLVLNFAKNEELNNKEIEE  115 (126)
T ss_dssp             HHHHTTCHHHHHHHHHHTTCSCHHHHHH
T ss_pred             HHHHCCCHHHHHHHHHhcCCCCHHHHHH
Confidence               1344444444444334566666554

>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=96.29  E-value=0.0039  Score=46.57  Aligned_cols=58  Identities=19%  Similarity=0.317  Sum_probs=48.1

Q ss_pred             HHHHHHHHHhccCC---CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346          4 DLTEKILKYLDTNP---PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT   62 (292)
Q Consensus         4 ~~e~~iL~~L~~~~---~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT   62 (292)
                      +.+.+||.+|..++   .+...++|+.+|++...|-+.+..|+.. |+|.......-.|.++
T Consensus        14 ~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~~-G~I~~~g~~~~~W~i~   74 (77)
T 1qgp_A           14 DQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKK-GKLQKEAGTPPLWKIA   74 (77)
T ss_dssp             HHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHHHH-TSEEEECSSSCEEEEC
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEecCCCCCceEec
Confidence            56789999997766   6788999999999999999999999987 9998765444566655

>2dql_A PEX protein; circadian clock associated protein, circadian clock protein; 1.70A {Anabaena SP}

Probab=96.28  E-value=0.017  Score=45.97  Aligned_cols=67  Identities=10%  Similarity=0.052  Sum_probs=49.6

Q ss_pred             HHHH-HHHHhccCCCCChHHHHHhc-------CCCHHHHHHHHHHhhccCCcEEEeee-------eEEEEEeChhHHHHh
Q psy10346          5 LTEK-ILKYLDTNPPVDTLDLAKLF-------NEDHQKVVGGMKSIETLGEYLIVEPL-------SHKIWELTGEGNQVK   69 (292)
Q Consensus         5 ~e~~-iL~~L~~~~~~~~~ela~~~-------~~~~~~v~~~~~~L~s~~glv~~e~~-------~~~~~~LTeEG~~yl   69 (292)
                      ++.. ||..|..+ +..-.++.+.+       ++++..|-..++.|+.. |+|+....       ..+.|.||+.|++.+
T Consensus        22 l~~~~IL~lL~~~-~~~Gyei~~~l~~~~~~~~is~gtLY~~L~rLe~~-GlI~~~~~~~~~~~~~rk~Y~LT~~G~~~l   99 (115)
T 2dql_A           22 VAICYILYVLLQG-ESYGTELIQQLETEHPTYRLSDTVLYSAIKFLEDN-RAITGYWKKLEGRGRPRRMYQVSPEWQHQA   99 (115)
T ss_dssp             HHHHHHHHHHTTS-CBCHHHHHHHHHHHCTTEECCHHHHHHHHHHHHHT-TSEEEEEECCTTCSSCEEEEEECGGGHHHH
T ss_pred             HHHHHHHHHHHhC-CCCHHHHHHHHHHHcCCCCCCcchHHHHHHHHHHC-CCEEEEeeecCCCCCCcEEEEECHHHHHHH
Confidence            4444 88888753 33345554433       58999999999999986 99998643       368999999999988


Q ss_pred             hcCC
Q psy10346         70 DNGS   73 (292)
Q Consensus        70 ~~Gl   73 (292)
                      .+-.
T Consensus       100 ~~~~  103 (115)
T 2dql_A          100 EDLA  103 (115)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6543

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=96.27  E-value=0.0065  Score=49.64  Aligned_cols=63  Identities=19%  Similarity=0.241  Sum_probs=50.5

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN   71 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~   71 (292)
                      -..|+..+..++.....++|+.+|++...|.+++..|+.+ |+|....  ...+.||+.|+..+..
T Consensus        42 ~~~i~~~l~~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~-Glv~r~~--~~~~~lT~~g~~~~~~  104 (155)
T 2h09_A           42 VELISDLIREVGEARQVDMAARLGVSQPTVAKMLKRLATM-GLIEMIP--WRGVFLTAEGEKLAQE  104 (155)
T ss_dssp             HHHHHHHHHHHSCCCHHHHHHHHTSCHHHHHHHHHHHHHT-TCEEEET--TTEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCcCHHHHHHHhCcCHHHHHHHHHHHHHC-CCEEEec--CCceEEChhHHHHHHH
Confidence            3445556665566788999999999999999999999987 9987653  3568999999987654

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=96.20  E-value=0.0055  Score=47.83  Aligned_cols=64  Identities=9%  Similarity=0.096  Sum_probs=51.9

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHHHh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQVK   69 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~yl   69 (292)
                      +...+||..|.. +.....++|+.+|++...|.+.++.|+.. |+|..+.. ....|.||++|..-+
T Consensus        25 ~~r~~IL~~L~~-~~~s~~eLa~~lgis~stvs~~L~~L~~~-GlV~~~~~gr~~~y~l~~~~~~~l   89 (108)
T 2kko_A           25 GRRLQILDLLAQ-GERAVEAIATATGMNLTTASANLQALKSG-GLVEARREGTRQYYRIAGEDVARL   89 (108)
T ss_dssp             STTHHHHHHHTT-CCEEHHHHHHHHTCCHHHHHHHHHHHHHH-TSEEEEEETTEEEEEESCHHHHHH
T ss_pred             HHHHHHHHHHHc-CCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeEEEEeCCEEEEEEChHHHHHH
Confidence            445678888874 66778999999999999999999999987 99987543 356899999986543

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=96.13  E-value=0.0066  Score=43.87  Aligned_cols=55  Identities=22%  Similarity=0.331  Sum_probs=44.7

Q ss_pred             HHHHHHHHhccC-CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346          5 LTEKILKYLDTN-PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT   62 (292)
Q Consensus         5 ~e~~iL~~L~~~-~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT   62 (292)
                      ...+||..|... ..+...++|+.+|++.+.|.+.++.|+.. |+|..  ...-.|.|+
T Consensus        11 ~~~~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L~~~-G~I~~--~~~G~y~lg   66 (67)
T 2heo_A           11 LEQKILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLKKE-DRVSS--PSPKYWSIG   66 (67)
T ss_dssp             HHHHHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHHHT-TSEEE--EETTEEEEC
T ss_pred             HHHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CcEec--CCCceEeeC
Confidence            567899999754 45788999999999999999999999987 99754  333567775

>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=96.04  E-value=0.0087  Score=45.76  Aligned_cols=66  Identities=6%  Similarity=0.026  Sum_probs=53.7

Q ss_pred             CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHh
Q psy10346          2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVK   69 (292)
Q Consensus         2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl   69 (292)
                      +.+...+||..|.. ++....++|+.+|+++..|.+.++.|+.. |+|..+. -....|.||+++..-+
T Consensus        21 ~~~~r~~Il~~L~~-~~~~~~ela~~l~is~~tvs~~L~~L~~~-Glv~~~~~g~~~~y~l~~~~~~~~   87 (102)
T 3pqk_A           21 SHPVRLMLVCTLVE-GEFSVGELEQQIGIGQPTLSQQLGVLRES-GIVETRRNIKQIFYRLTEAKAAQL   87 (102)
T ss_dssp             CSHHHHHHHHHHHT-CCBCHHHHHHHHTCCTTHHHHHHHHHHHT-TSEEEECSSSCCEEEECSSTHHHH
T ss_pred             CCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeEEEEeCCEEEEEECcHHHHHH
Confidence            34667788999864 56788999999999999999999999987 9998754 3457899999866543

>2qq9_A Diphtheria toxin repressor; regulator, DTXR, helix-turn-helix, metal ION, ACT DNA-binding, ferrous iron, transcription; 1.71A {Corynebacterium diphtheriae} PDB: 2tdx_A 1ddn_A 1g3t_A 1g3s_A 1g3w_A 2qqa_A 2qqb_A 2dtr_A 1bi0_A 1bi2_A 1bi3_A 1dpr_A 1bi1_A 1fwz_A 1g3y_A 1c0w_A* 3glx_A 1p92_A 1xcv_A 1f5t_A ...

Probab=95.98  E-value=0.0075  Score=53.13  Aligned_cols=87  Identities=11%  Similarity=0.101  Sum_probs=60.6

Q ss_pred             HHHHHHHHHhc---cCCC-CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHH
Q psy10346          4 DLTEKILKYLD---TNPP-VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVF   79 (292)
Q Consensus         4 ~~e~~iL~~L~---~~~~-~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~   79 (292)
                      ..+..+|..|-   ..+. ....++|+.+|+++.+|.++++.|+.+ |||..+..  ..+.||++|++.+..=.+-.+++
T Consensus         6 ~~~e~yL~~i~~l~~~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~-GlV~r~~~--~~v~LT~~G~~~~~~~~~~~~~~   82 (226)
T 2qq9_A            6 ATTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERD-GLVVVASD--RSLQMTPTGRTLATAVMRKHRLA   82 (226)
T ss_dssp             HHHHHHHHHHHHHHHHTCCCBHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEECTT--SBEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhcCCCccHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEeCC--CCeEECHHHHHHHHHHHHHHHHH
Confidence            45566666652   2222 233899999999999999999999987 99987653  67899999999887666555544


Q ss_pred             hhcC-C-CCCChHHHh
Q psy10346         80 NNVP-S-EGIGQKELL   93 (292)
Q Consensus        80 ~~l~-~-~~~~~~el~   93 (292)
                      ...- + -|++-+++.
T Consensus        83 e~~l~~~lgl~~ee~~   98 (226)
T 2qq9_A           83 ERLLTDIIGLDINKVH   98 (226)
T ss_dssp             HHHHHHTTCCCHHHHH
T ss_pred             HHHHHHHcCCCHHHHH
Confidence            3221 1 256655543

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=95.94  E-value=0.0065  Score=45.65  Aligned_cols=51  Identities=20%  Similarity=0.223  Sum_probs=45.7

Q ss_pred             CCcHHHHHHHHHhccC------CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe
Q psy10346          1 MASDLTEKILKYLDTN------PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE   52 (292)
Q Consensus         1 m~~~~e~~iL~~L~~~------~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e   52 (292)
                      |.+....+||..|...      +..+..|+|+.+|++...|-+.+..|+.+ |+|.-.
T Consensus         1 ~~~~r~~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~Le~k-G~I~R~   57 (77)
T 2jt1_A            1 MSESIVTKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQLHDV-GVLEKV   57 (77)
T ss_dssp             CCCTHHHHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEE
T ss_pred             CCHHHHHHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CcEEec
Confidence            8888999999999765      67788999999999999999999999987 998764

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=95.83  E-value=0.016  Score=51.99  Aligned_cols=62  Identities=13%  Similarity=0.055  Sum_probs=50.8

Q ss_pred             CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee--e-----EEEEEeChhH
Q psy10346          2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL--S-----HKIWELTGEG   65 (292)
Q Consensus         2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~--~-----~~~~~LTeEG   65 (292)
                      +.....+||..|.. ++....++|..+|+++..|...++.|+.. |+|.....  .     ...|.||+.|
T Consensus        10 ~~~~R~~IL~~L~~-g~~s~~ELa~~lglS~stVs~hL~~Le~a-GLV~~~~~~gr~~GRp~~~Y~Lt~~~   78 (232)
T 2qlz_A           10 GNKVRRDLLSHLTC-MECYFSLLSSKVSVSSTAVAKHLKIMERE-GVLQSYEKEERFIGPTKKYYKISIAK   78 (232)
T ss_dssp             TSHHHHHHHHHHTT-TTTCSSSSCTTCCCCHHHHHHHHHHHHHT-TSEEEEEECC-----CEEEEEECCCE
T ss_pred             CCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEeeecCCCCCCccEEEEEccch
Confidence            34667889999974 66777899999999999999999999987 99998332  3     6789998866

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=95.76  E-value=0.012  Score=53.11  Aligned_cols=72  Identities=15%  Similarity=0.154  Sum_probs=59.0

Q ss_pred             HHHHHHHHHhccCC--CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHH
Q psy10346          4 DLTEKILKYLDTNP--PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         4 ~~e~~iL~~L~~~~--~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      ..|..||..|...+  .+...++|..+++++..|.+.+..|+.+ |+|.-+.    .-...+.||++|++.++.-.|..
T Consensus       158 ~~q~~vL~~L~~~~~~~~t~~eLa~~l~i~~~tvt~~v~rLe~~-GlV~R~~~~~DrR~~~i~LT~~G~~~~~~~~~~~  235 (250)
T 1p4x_A          158 FVEFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQ-GYLIKERSTEDERKILIHMDDAQQDHAEQLLAQV  235 (250)
T ss_dssp             HHHHHHHHHHHTTTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHH-TSSEEEECSSSTTCEEEECCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCcCHHHHHHHHCCChhhHHHHHHHHHHC-CCEEeeCCCCCCCeEEEEECHHHHHHHHHHHHHH
Confidence            56788999997544  4788999999999999999999999987 9998754    34568899999999886554443

>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=95.72  E-value=0.026  Score=45.17  Aligned_cols=63  Identities=16%  Similarity=0.179  Sum_probs=51.9

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHH
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQ   67 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~   67 (292)
                      .....+||..|.. +.....++|+.+|+++..|.+.++.|+.. |+|..++. ....|.||+++-.
T Consensus        45 ~~~rl~IL~~L~~-~~~s~~ela~~lgis~stvs~~L~~Le~~-Glv~~~~~gr~~~y~l~~~~l~  108 (122)
T 1r1t_A           45 DPNRLRLLSLLAR-SELCVGDLAQAIGVSESAVSHQLRSLRNL-RLVSYRKQGRHVYYQLQDHHIV  108 (122)
T ss_dssp             CHHHHHHHHHHTT-CCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEESSHHHH
T ss_pred             CHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeEEEEeCCEEEEEEChHHHH
Confidence            4566789999874 56788999999999999999999999986 99987653 3467999998743

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=95.71  E-value=0.0098  Score=45.40  Aligned_cols=60  Identities=12%  Similarity=0.205  Sum_probs=51.7

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEG   65 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG   65 (292)
                      +.-.+||..|..++ ....+||+.+|++..+|-+-+..|+.. |+|......--.|.||.+-
T Consensus        17 ~~~~~IL~lL~~~g-~sa~eLAk~LgiSk~aVr~~L~~Le~e-G~I~~~~~~PP~W~~~~~~   76 (82)
T 1oyi_A           17 EIVCEAIKTIGIEG-ATAAQLTRQLNMEKREVNKALYDLQRS-AMVYSSDDIPPRWFMTTEA   76 (82)
T ss_dssp             HHHHHHHHHHSSST-EEHHHHHHHSSSCHHHHHHHHHHHHHH-TSSEECSSSSCEEESCC--
T ss_pred             HHHHHHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEeCCCCCCcceeccCc
Confidence            56778999998766 788999999999999999999999987 9999988888888888653

>3dsq_A Pyrrolysyl-tRNA synthetase; homodimer, aminoacyl-tRNA synthetase, ligase; 2.10A {Desulfitobacterium hafniense} PDB: 2znj_A 2zni_A

Probab=95.54  E-value=0.012  Score=54.30  Aligned_cols=56  Identities=11%  Similarity=0.209  Sum_probs=40.3

Q ss_pred             CCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCC-Cceeec
Q psy10346        216 PSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAH-DTFFVT  276 (292)
Q Consensus       216 ~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~-DTfyl~  276 (292)
                      ..|+.||+..+.+.|+++|.++||.|+. +|.+++...++. ...+.+|   ++. ++|+++
T Consensus        66 ~~g~~h~~~~l~~~ir~~~~~~Gf~EV~-tP~Le~~~l~~~-~g~~~~~---~m~~~~npl~  122 (288)
T 3dsq_A           66 TVKHRPALLELEEKLAKALHQQGFVQVV-TPTIITKSALAK-MTIGEDH---PLFSQVFWLD  122 (288)
T ss_dssp             HTTSSCHHHHHHHHHHHHHHTTTCEECC-CCSEEEHHHHHT-TSSCC-----CCTTTSCEEE
T ss_pred             cCCCcCHHHHHHHHHHHHHHHCCCEEEE-CCeeecHHHHhh-cCCCccc---ccEEeecccc
Confidence            5699999999999999999999999985 688888655443 3334444   344 344554

>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=95.51  E-value=0.017  Score=44.57  Aligned_cols=58  Identities=12%  Similarity=0.157  Sum_probs=45.8

Q ss_pred             HHHHHHHHHhcc--CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE-ee---eeEEEEEeC
Q psy10346          4 DLTEKILKYLDT--NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV-EP---LSHKIWELT   62 (292)
Q Consensus         4 ~~e~~iL~~L~~--~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~-e~---~~~~~~~LT   62 (292)
                      +.|..||..|..  +..+...+|+..++++...|.+.++.|+++ |||+- ..   .....|.|+
T Consensus        20 ~~q~~Vl~~I~~~g~~gi~qkeLa~~~~l~~~tvt~iLk~LE~k-glIkr~~~~~~~~rKvy~Ly   83 (91)
T 2dk5_A           20 NQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESK-KLIKAVKSVAASKKKVYMLY   83 (91)
T ss_dssp             SSHHHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEECCSSCSSCCEEEES
T ss_pred             HHHHHHHHHHHHcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEecCCCCCCcEEEEEe
Confidence            467889999976  446888999999999999999999999987 99983 22   224555554

>1hsj_A Fusion protein consisting of staphylococcus accessary regulator protein R and maltose...; novel fold for DNA binding; HET: GLC; 2.30A {Escherichia coli} SCOP: a.4.5.28 c.94.1.1

Probab=95.44  E-value=0.0087  Score=57.34  Aligned_cols=67  Identities=12%  Similarity=0.038  Sum_probs=56.8

Q ss_pred             HHHHHHHHHhccC--CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhc
Q psy10346          4 DLTEKILKYLDTN--PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDN   71 (292)
Q Consensus         4 ~~e~~iL~~L~~~--~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~   71 (292)
                      ..|..||..|...  +.++..+||+.++++...|.+.+..|+.+ |||+-++    +-...+.||++|++.++.
T Consensus       404 ~~q~~vl~~l~~~~~~~~~~~~l~~~~~~~~~~~t~~~~~le~~-g~v~r~~~~~D~R~~~i~lT~~g~~~~~~  476 (487)
T 1hsj_A          404 YEEIYILNHILRSESNEISSKEIAKCSEFKPYYLTKALQKLKDL-KLLSKKRSLQDERTVIVYVTDTQKANIQK  476 (487)
T ss_dssp             HHHHHHHHHHHTCSCSEEEHHHHHHSSCCCHHHHHHHHHHHHTT-TTSCCEECCSSSSCCEEECCSSHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEeecCCCCCCCeEEEEECHHHHHHHHH
Confidence            5688999999776  67888999999999999999999999987 9997643    445688999999987643

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=95.39  E-value=0.023  Score=41.80  Aligned_cols=58  Identities=21%  Similarity=0.301  Sum_probs=47.1

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee---eEEEEEeChh
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL---SHKIWELTGE   64 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~---~~~~~~LTeE   64 (292)
                      ..+||..|...+.+...++|+.+|++...|.+.+..|++. |+|.....   ....|.++++
T Consensus         2 r~~Il~~L~~~~~~s~~eLa~~lgvs~~tv~r~L~~L~~~-GlI~~~~~~~gr~~~y~l~~~   62 (81)
T 2htj_A            2 KNEILEFLNRHNGGKTAEIAEALAVTDYQARYYLLLLEKA-GMVQRSPLRRGMATYWFLKGE   62 (81)
T ss_dssp             HHHHHHHHHHSCCCCHHHHHHHHTSCHHHHHHHHHHHHHH-TSEEEECCSSSSSCEEEESSC
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEeccCCCCcEEEEEChh
Confidence            4678999977777889999999999999999999999987 99985422   3456777654

>1fx7_A Iron-dependent repressor IDER; DTXR, iron-dependent regulator, signaling protein; 2.00A {Mycobacterium tuberculosis} SCOP: a.4.5.24 a.76.1.1 b.34.1.2 PDB: 1u8r_A

Probab=95.38  E-value=0.012  Score=51.85  Aligned_cols=72  Identities=19%  Similarity=0.173  Sum_probs=54.4

Q ss_pred             HHHHHHHHHh---ccCCCCCh--HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHH
Q psy10346          4 DLTEKILKYL---DTNPPVDT--LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLV   78 (292)
Q Consensus         4 ~~e~~iL~~L---~~~~~~~~--~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl   78 (292)
                      ..+..+|..|   ...+ ...  .++|+.+|+++..|.++++.|+.+ |||+....  ..+.||+.|++.+..-.+-.++
T Consensus         6 ~~~e~~L~~L~~l~~~~-~~~~~~~La~~l~vs~~tvs~~l~~Le~~-GlV~r~~~--~~v~LT~~G~~~~~~~~~~~~~   81 (230)
T 1fx7_A            6 DTTEMYLRTIYDLEEEG-VTPLRARIAERLDQSGPTVSQTVSRMERD-GLLRVAGD--RHLELTEKGRALAIAVMRKHRL   81 (230)
T ss_dssp             SHHHHHHHHHHHHHHHT-SCCCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEECTT--SCEEECHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhcC-CCCcHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEeCC--ccEEECHHHHHHHHHHHHHHHH
Confidence            4455555554   2222 444  899999999999999999999987 99997654  4789999999988766555554


Q ss_pred             H
Q psy10346         79 F   79 (292)
Q Consensus        79 ~   79 (292)
                      +
T Consensus        82 ~   82 (230)
T 1fx7_A           82 A   82 (230)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein structure initiative; 2.20A {Thermoplasma acidophilum dsm 1728} SCOP: a.4.5.28 b.43.5.2

Probab=95.18  E-value=0.047  Score=47.78  Aligned_cols=72  Identities=15%  Similarity=0.178  Sum_probs=55.0

Q ss_pred             HHHHHHHHHhccCCC------CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHHHhhcCChHH
Q psy10346          4 DLTEKILKYLDTNPP------VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~------~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      ..+.++|..|...+.      .+..++|+.+++++.+|.+.++.|+.. ||+.-... -...+.||++|+.+++.-.+-.
T Consensus         7 ~~~l~~l~~l~~~~~l~~~~~~s~s~aA~~L~isq~avSr~I~~LE~~-~L~~R~~~~R~~~v~LT~~G~~l~~~~~~~~   85 (230)
T 3cta_A            7 DQYYRAIKKIKEAAEASNRAYLTSSKLADMLGISQQSASRIIIDLEKN-GYITRTVTKRGQILNITEKGLDVLYTEFADL   85 (230)
T ss_dssp             CHHHHHHHHHHHHTTTSSEEECCHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcccccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEEEcCCeEEEEECHHHHHHHHHHHHHH
Confidence            456777877754332      557899999999999999999999986 99864321 1678899999999985554433

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

Probab=95.17  E-value=0.03  Score=43.68  Aligned_cols=59  Identities=17%  Similarity=0.259  Sum_probs=47.7

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeCh
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTG   63 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTe   63 (292)
                      ...+.+||..|.. +..+..++|+.+|+++..|.+.++.|+.. |+|..+.. ....|.+|.
T Consensus        31 ~~~~~~il~~L~~-~~~s~~ela~~l~is~stvsr~l~~Le~~-Glv~~~~~~r~~~~~~~~   90 (119)
T 2lkp_A           31 TPSRLMILTQLRN-GPLPVTDLAEAIGMEQSAVSHQLRVLRNL-GLVVGDRAGRSIVYSLYD   90 (119)
T ss_dssp             CHHHHHHHHHHHH-CCCCHHHHHHHHSSCHHHHHHHHHHHHHH-CSEEEEEETTEEEEEESC
T ss_pred             CHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEecCCEEEEEEch
Confidence            4567889998876 56788999999999999999999999986 99987643 335566763

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=95.16  E-value=0.061  Score=45.38  Aligned_cols=68  Identities=12%  Similarity=0.096  Sum_probs=54.8

Q ss_pred             cHHHHHHHHHhccC--CCCChHHHHHhcC-CCHHHHHHHHHHhhccCCcEEEee---------eeEEEEEeChhHHHHhh
Q psy10346          3 SDLTEKILKYLDTN--PPVDTLDLAKLFN-EDHQKVVGGMKSIETLGEYLIVEP---------LSHKIWELTGEGNQVKD   70 (292)
Q Consensus         3 ~~~e~~iL~~L~~~--~~~~~~ela~~~~-~~~~~v~~~~~~L~s~~glv~~e~---------~~~~~~~LTeEG~~yl~   70 (292)
                      ......||..|..+  +..+..+++...+ ++...|-+-++.|... |+|....         .....|.||++|+..+.
T Consensus        28 ~~tR~~IL~~Ll~~p~~~~ta~eL~~~l~~lS~aTVyrhL~~L~ea-GLV~~~~~~~~~~~rGrP~k~Y~LT~~Gr~~l~  106 (151)
T 3u1d_A           28 HETRLDVLHQILAQPDGVLSVEELLYRNPDETEANLRYHVDELVDR-GIVEKIPVPRAKSVDDPPTTFYAVTGEGIALLR  106 (151)
T ss_dssp             CHHHHHHHHHHHHSTTSCBCHHHHHHHCTTSCHHHHHHHHHHHHHT-TSEEEEECCCCTTSSSCCCEEEEECHHHHHHHH
T ss_pred             chHHHHHHHHHHcCCCCCCCHHHHHHhcCCCCHHHHHHHHHHHHHC-CCeEEeecCcCcccCCCCceEEEECHHHHHHHH
Confidence            35667788888554  3367789999888 9999999999999987 9999653         34569999999999885


Q ss_pred             c
Q psy10346         71 N   71 (292)
Q Consensus        71 ~   71 (292)
                      .
T Consensus       107 ~  107 (151)
T 3u1d_A          107 A  107 (151)
T ss_dssp             H
T ss_pred             H
Confidence            4

>2co5_A Viral protein F93; viral protein-winged helix complex, winged helix, DNA-bindin WHTH, disulfide bond, STIV; 2.2A {Sulfolobus turreted icosahedral virus} SCOP: a.4.5.48

Probab=95.03  E-value=0.026  Score=44.12  Aligned_cols=66  Identities=21%  Similarity=0.115  Sum_probs=48.6

Q ss_pred             HHHHHHHhccCC-CCCh----HHHHHhc--CCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHhhcC
Q psy10346          6 TEKILKYLDTNP-PVDT----LDLAKLF--NEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVKDNG   72 (292)
Q Consensus         6 e~~iL~~L~~~~-~~~~----~ela~~~--~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl~~G   72 (292)
                      .+-||..|..++ ...-    .++++..  .+++..+-.+++.|+.. |+|+... ...+.|.||++|++.+++-
T Consensus        11 ~~~IL~lL~~~~~~~~g~~i~~ei~~~~~~~is~GtlYp~L~rLe~~-GlI~~~~~~~rk~Y~iT~~Gr~~l~~~   84 (99)
T 2co5_A           11 YYIILKVLVINGSRLEKKRLRSEILKRFDIDISDGVLYPLIDSLIDD-KILREEEAPDGKVLFLTEKGMKEFEEL   84 (99)
T ss_dssp             HHHHHHHHHHTTTEEEGGGHHHHHHHHHCCBCCHHHHHHHHHHHHHT-TSEEEECCTTSCEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCcHHHHHHHHHHHhCCCCCCCcHHHHHHHHHHC-CCEEEeeCCCcEEEEECHHHHHHHHHH
Confidence            456888885322 2222    4555555  47899999999999987 9999864 3467899999999988653

>3l9f_A Putative uncharacterized protein SMU.1604C; PADR, transcription regulator; 1.80A {Streptococcus mutans}

Probab=94.97  E-value=0.03  Score=49.22  Aligned_cols=63  Identities=13%  Similarity=0.231  Sum_probs=50.0

Q ss_pred             HHHHHHHhccCCCCChHHHHHhc--------CCCHHHHHHHHHHhhccCCcEEEeee------eEEEEEeChhHHHHhh
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLF--------NEDHQKVVGGMKSIETLGEYLIVEPL------SHKIWELTGEGNQVKD   70 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~--------~~~~~~v~~~~~~L~s~~glv~~e~~------~~~~~~LTeEG~~yl~   70 (292)
                      ...||..|.. ++..-.++++.+        ++++..|-..++.|+.. |+|+.+..      .++.|.||+.|++.+.
T Consensus        38 r~~IL~lL~~-~p~~GYeL~~~l~~~~~~~~~~s~g~lY~~L~rLe~~-GlI~~~~~~~~~~p~rk~Y~iT~~Gr~~l~  114 (204)
T 3l9f_A           38 KDIILGILSK-KERSGYEINDILQNQLSYFYDGTYGMIYPTLRKLEKD-GKITKEVVIQDGRPNKNIYAITESGKKELA  114 (204)
T ss_dssp             HHHHHHHTSS-CCEEHHHHHHHHHHTSTTTEECCTTCHHHHHHHHHHT-TSEEEEEECCTTSCCEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHc-CCCCHHHHHHHHHHHhCCccCCCcchHHHHHHHHHHC-CCeEEEeeccCCCCCceEEEEChHHHHHHH
Confidence            4578998874 444557777665        57899999999999986 99998653      4789999999999873

>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=94.92  E-value=0.02  Score=45.18  Aligned_cols=66  Identities=14%  Similarity=0.122  Sum_probs=48.9

Q ss_pred             HHHHHHHHHhc-cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee--eeEEEEEeChhHHHHhh
Q psy10346          4 DLTEKILKYLD-TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP--LSHKIWELTGEGNQVKD   70 (292)
Q Consensus         4 ~~e~~iL~~L~-~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~--~~~~~~~LTeEG~~yl~   70 (292)
                      ..+.++|..|. ..+.....++|..+|++++.|.+.+..|+.+ |+|....  .....+.++..|...+.
T Consensus        26 ~~~~~il~~L~~~~~~~t~~ela~~l~~~~stvs~~l~~L~~~-G~v~r~~~~~d~r~~~~~~~~~~~~~   94 (152)
T 1ku9_A           26 KSVGAVYAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEEL-GFVRKVWIKGERKNYYEAVDGFSSIK   94 (152)
T ss_dssp             HHHHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEECCTTCSSCEEEECCHHHHHH
T ss_pred             hhHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEecCCCceEEEeecchHHHHH
Confidence            45677888774 3566788999999999999999999999987 9998763  33344445545554443

>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=94.90  E-value=0.092  Score=39.25  Aligned_cols=64  Identities=13%  Similarity=0.202  Sum_probs=48.2

Q ss_pred             HHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-------eEEEEEeChhHHHHh
Q psy10346          5 LTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-------SHKIWELTGEGNQVK   69 (292)
Q Consensus         5 ~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-------~~~~~~LTeEG~~yl   69 (292)
                      .+..+|..|.. ++.....++|+.+|++...|.+.+..|+.. |+|.....       ....|.+|++..+.+
T Consensus        22 ~~~~~l~~l~~~~~~~t~~ela~~l~is~~tv~~~l~~L~~~-g~v~~~~~~~~~~gr~~~~~~l~~~~~~~~   93 (109)
T 2d1h_A           22 TDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIEL-GLVVRTKTEGKKIGRPKYYYSISSNILEKI   93 (109)
T ss_dssp             HHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEC-------CCEEEEECTTHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeEeeccccCCCCCCCeeeecCHHHHHHH
Confidence            34555555533 667788999999999999999999999987 99987653       245688888554433

>2xzm_7 Plectin/S10 domain containing protein; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_7

Probab=94.87  E-value=0.021  Score=48.49  Aligned_cols=47  Identities=13%  Similarity=0.035  Sum_probs=36.5

Q ss_pred             CCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHHHhhc--CChHH
Q psy10346         29 NEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQVKDN--GSHEV   76 (292)
Q Consensus        29 ~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~yl~~--GlPE~   76 (292)
                      +++-=.||.+++||.|+ |+|+..-. ...+|.||+||.+||++  .+|+.
T Consensus        36 ~vpNL~ViKamqSLkSR-GyVkEqFaWrhyYw~LTnEGIeYLR~yLhLP~e   85 (162)
T 2xzm_7           36 GVPNLHCYILVRSLKDR-GFLEEIFNWGFTYYYLNKEGCEYLKTKLGISAD   85 (162)
T ss_dssp             CCBHHHHHHHHHHHHHH-TSEEEEEETTEEEEEECHHHHHHHHHHHCSSTT
T ss_pred             CcCcHHHHHHHhccccc-ccccceeeeEEEEEEEchHHHHHHHHHhCCCcc
Confidence            35556799999999998 99987444 45778999999999965  34444

>2e1n_A PEX, period extender; circadian clock, DNA binding protein, circadian clock protei; 1.80A {Synechococcus elongatus pcc 7942}

Probab=94.86  E-value=0.04  Score=45.46  Aligned_cols=65  Identities=9%  Similarity=0.067  Sum_probs=48.2

Q ss_pred             HHHHHHHhccCCCCChHHHHHhc-------CCCHHHHHHHHHHhhccCCcEEEeee-------eEEEEEeChhHHHHhhc
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLF-------NEDHQKVVGGMKSIETLGEYLIVEPL-------SHKIWELTGEGNQVKDN   71 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~-------~~~~~~v~~~~~~L~s~~glv~~e~~-------~~~~~~LTeEG~~yl~~   71 (292)
                      +.-||..|..+ ...-.++.+.+       ++++..|-..++.|+.. |+|+....       .++.|.||+.|++++..
T Consensus        36 ~~~IL~lL~~~-~~~Gyei~k~l~~~~~~~~is~gtLYp~L~rLe~~-GlI~~~~~~~~~~g~~rk~Y~LT~~Gr~~l~~  113 (138)
T 2e1n_A           36 VCYVLAVLRHE-DSYGTELIQHLETHWPNYRLSDTVLYTALKFLEDE-QIISGYWKKVEGRGRPRRMYQLAQANDDRSRD  113 (138)
T ss_dssp             HHHHHHHHTTS-CEEHHHHHHHHHHHSTTEECCHHHHHHHHHHHHHT-TSEEEEEECCTTCSSCEEEEEESCSCCHHHHH
T ss_pred             HHHHHHHHHhC-CCcHHHHHHHHHHHcCCCCCCccHHHHHHHHHHHC-CCEEEEeecccCCCCCcEEEEECHHHHHHHHH
Confidence            34488888653 33334444433       58999999999999986 99988642       46889999999998865


Q ss_pred             C
Q psy10346         72 G   72 (292)
Q Consensus        72 G   72 (292)
                      -
T Consensus       114 ~  114 (138)
T 2e1n_A          114 L  114 (138)
T ss_dssp             H
T ss_pred             H
Confidence            3

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=94.80  E-value=0.048  Score=41.25  Aligned_cols=56  Identities=20%  Similarity=0.278  Sum_probs=46.5

Q ss_pred             HHHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346          4 DLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT   62 (292)
Q Consensus         4 ~~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT   62 (292)
                      +.+.+||.+|.+ +.++.+-++|+.+|+|...|-.+++.|... |.|...  ..-+|.++
T Consensus        19 d~eekVLe~LkeaG~PlkageIae~~GvdKKeVdKaik~LKkE-gkI~SP--kRCyw~~~   75 (80)
T 2lnb_A           19 HLEQRILQVLTEAGSPVKLAQLVKECQAPKRELNQVLYRMKKE-LKVSLT--SPATWCLG   75 (80)
T ss_dssp             HHHHHHHHHHHHHTSCEEHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEE--ETTEEEES
T ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHc-CCccCC--CCceeeCC
Confidence            578999999965 556889999999999999999999999975 886654  55566766

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=94.66  E-value=0.044  Score=41.11  Aligned_cols=44  Identities=7%  Similarity=0.182  Sum_probs=40.1

Q ss_pred             HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      .+||..|...+.++..++|+.++++...|-+.+..|+.+ |+|.-
T Consensus         5 ~~Il~~L~~~g~vsv~eLa~~l~VS~~TIRrdL~~Le~~-G~l~R   48 (78)
T 1xn7_A            5 IQVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESM-GKAVR   48 (78)
T ss_dssp             HHHHHHHHHSCSBCHHHHHHHTTCCHHHHHHHHHHHHHH-TSEEE
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEE
Confidence            568999998999999999999999999999999999987 88753

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=94.66  E-value=0.048  Score=44.01  Aligned_cols=63  Identities=8%  Similarity=0.092  Sum_probs=49.3

Q ss_pred             cHHHHHHHHHhcc-CCCCChHHHHHhcC----CCHHHHHHHHHHhhccCCcEEEeeeeE-EEE--EeChhHH
Q psy10346          3 SDLTEKILKYLDT-NPPVDTLDLAKLFN----EDHQKVVGGMKSIETLGEYLIVEPLSH-KIW--ELTGEGN   66 (292)
Q Consensus         3 ~~~e~~iL~~L~~-~~~~~~~ela~~~~----~~~~~v~~~~~~L~s~~glv~~e~~~~-~~~--~LTeEG~   66 (292)
                      ...|..||..|.. ++.++..++++.++    ++...|.+.+..|+.+ |+|.-+.... ..|  .||++|.
T Consensus         8 t~~e~~vL~~L~~~~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~k-Glv~r~~~~r~~~~~~~lt~~~~   78 (138)
T 2g9w_A            8 GDLERAVMDHLWSRTEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKK-NLVLQIRDDRAHRYAPVHGRDEL   78 (138)
T ss_dssp             CHHHHHHHHHHHTCSSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHT-TSEEEEC---CCEEEESSCHHHH
T ss_pred             CHHHHHHHHHHHhcCCCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHC-CCEEEEecCCeEEEEeCCCHHHH
Confidence            3678999999976 57788899999987    7999999999999987 9998754322 233  4787774

>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=94.55  E-value=0.062  Score=43.58  Aligned_cols=48  Identities=10%  Similarity=0.232  Sum_probs=43.6

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      .+.+.+||..|..++.....++|+.+|++...|.+.++.|+.. |+|.-
T Consensus         4 d~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~-G~i~~   51 (144)
T 2cfx_A            4 DQIDLNIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQLESF-GIIKQ   51 (144)
T ss_dssp             CHHHHHHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEE
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeEE
Confidence            5678899999988888889999999999999999999999987 99974

>3u5c_K 40S ribosomal protein S10-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_K

Probab=94.53  E-value=0.018  Score=45.85  Aligned_cols=42  Identities=17%  Similarity=0.233  Sum_probs=33.7

Q ss_pred             CCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHHHhhc
Q psy10346         29 NEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQVKDN   71 (292)
Q Consensus        29 ~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~yl~~   71 (292)
                      +++-=-|+.++.||.|+ |+|+..-. ....|.||+||.+||++
T Consensus        36 ~vpNL~Vik~mqSLkSr-GyVkeqFaWrh~Yw~LTnEGieyLR~   78 (105)
T 3u5c_K           36 DTKNLYVIKALQSLTSK-GYVKTQFSWQYYYYTLTEEGVEYLRE   78 (105)
T ss_dssp             SSCHHHHHHHHHHHHHT-SSEEEECTTTCCEEEECHHHHHHHHH
T ss_pred             CccchhHHHHHhccccc-ceeccEecceEEEEEEchhhHHHHHH
Confidence            35556799999999997 99886433 45678999999999974

>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR, heat shock, transcriptional regulation, winged DNA binding; 2.60A {Pyrococcus furiosus} SCOP: a.4.5.64

Probab=94.47  E-value=0.031  Score=48.85  Aligned_cols=64  Identities=13%  Similarity=0.154  Sum_probs=53.3

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee------eEEEEEeChhHHHH
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL------SHKIWELTGEGNQV   68 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~------~~~~~~LTeEG~~y   68 (292)
                      .+....||..|. .+.....++++.+|+++..|...++.|+.. |+|+....      ....|.||++|...
T Consensus        14 ~~~rl~IL~~L~-~~~~s~~eLa~~l~is~stvs~hLk~Le~~-GLV~~~~~~~~~g~~~~~Y~Lt~~~~~~   83 (202)
T 2p4w_A           14 NETRRRILFLLT-KRPYFVSELSRELGVGQKAVLEHLRILEEA-GLIESRVEKIPRGRPRKYYMIKKGLRLE   83 (202)
T ss_dssp             SHHHHHHHHHHH-HSCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECCBTTBCCCEEEEECTTEEEE
T ss_pred             CHHHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CceEEEeeccCCCCceEEEEEChHHHHH
Confidence            466788999995 456778999999999999999999999987 99998653      56788898888653

>1b7y_B Phers, protein (phenylalanyl-tRNA synthetase); enzyme, alpha/beta homodimer, ligase; HET: FYA; 2.50A {Thermus thermophilus} SCOP: a.6.1.1 a.6.1.1 b.40.4.4 b.153.1.1 d.58.13.1 d.104.1.1 PDB: 1b70_B* 1eiy_B 1jjc_B* 1pys_B 2akw_B* 2aly_B* 2amc_B* 3hfz_B* 3teh_B* 2iy5_B*

Probab=94.27  E-value=0.043  Score=57.27  Aligned_cols=54  Identities=15%  Similarity=0.312  Sum_probs=45.1

Q ss_pred             CCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCCCCC
Q psy10346        219 HLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSE  282 (292)
Q Consensus       219 ~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~~~  282 (292)
                      ..||..++.+++|++|.++||.|+-+.+++..++|  +.|  |++      +|+++|.+|-+.+
T Consensus       487 ~~~~~~~~~~~ir~~L~~~Gf~Evitysfvs~~~~--~~l--~~~------~~~v~L~NPis~d  540 (785)
T 1b7y_B          487 GVEAPYRKEQRLREVLSGLGFQEVYTYSFMDPEDA--RRF--RLD------PPRLLLLNPLAPE  540 (785)
T ss_dssp             STTHHHHHHHHHHHHHHHHTCEECCCCSEECTTHH--HHT--TCC------CCSCEESSCSSTT
T ss_pred             cCCHHHHHHHHHHHHHHHCCCEEEecCcccCHHHH--Hhc--CCC------CCeEEEcCCCchh
Confidence            78999999999999999999999888999987766  543  552      7789999886554

>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=94.19  E-value=0.088  Score=38.49  Aligned_cols=50  Identities=12%  Similarity=0.081  Sum_probs=43.1

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcC----CCHHHHHHHHHHhhccCCcEEEee
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFN----EDHQKVVGGMKSIETLGEYLIVEP   53 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~----~~~~~v~~~~~~L~s~~glv~~e~   53 (292)
                      ...|..||..|...+.++..+++..++    ++...|.+.+..|+.+ |+|....
T Consensus         8 t~~e~~vL~~L~~~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~k-Glv~r~~   61 (82)
T 1p6r_A            8 SDAELEVMKVIWKHSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKK-GALNHHK   61 (82)
T ss_dssp             CHHHHHHHHHHHTSSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHT-TSEEEEE
T ss_pred             CHHHHHHHHHHHcCCCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHC-CCeEEEe
Confidence            467899999997777788899998875    7899999999999987 9998765

>4a6d_A Hydroxyindole O-methyltransferase; melatonin, circadian clock; HET: SAM; 2.40A {Homo sapiens} PDB: 4a6e_A*

Probab=94.18  E-value=0.13  Score=47.77  Aligned_cols=72  Identities=14%  Similarity=0.063  Sum_probs=60.2

Q ss_pred             HHHHHHHHHhccC-CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHHHhhcCChHH
Q psy10346          4 DLTEKILKYLDTN-PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         4 ~~e~~iL~~L~~~-~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      +++..|...|.+. +.++.+++|..+|++...+-+.+..|.+. |+++.+.. ....|.+|+.+..++..++|..
T Consensus        28 a~eLglfd~L~~~~~p~t~~eLA~~~g~~~~~l~rlLr~L~~~-gll~~~~~~~~~~y~~t~~s~~~l~~~~~~~  101 (353)
T 4a6d_A           28 ACELGVFDLLAEAPGPLDVAAVAAGVRASAHGTELLLDICVSL-KLLKVETRGGKAFYRNTELSSDYLTTVSPTS  101 (353)
T ss_dssp             HHHHTHHHHHHHSSSCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEECHHHHHHHSTTSTTC
T ss_pred             HHHcCHHHHHhcCCCCCCHHHHHHhhCcCHHHHHHHHHHHHHC-CCEEEeccCccceeeCCHHHHHHhhcCCchH
Confidence            4566778888653 56888999999999999999999999997 99987544 3568999999999999988854

>2o0m_A Transcriptional regulator, SORC family; structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 1.60A {Enterococcus faecalis} SCOP: c.124.1.8

Probab=93.99  E-value=0.0097  Score=55.69  Aligned_cols=62  Identities=15%  Similarity=0.126  Sum_probs=0.0

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl   69 (292)
                      ..++.||..|...+.+...++|+.+|++...|.+.+..|+.+ |+|+...   .-..||++|++.+
T Consensus        20 ~r~~~iL~~l~~~~~~t~~eLa~~l~vs~~Tv~r~l~~Le~~-Glv~~~~---~gi~LT~~G~~~~   81 (345)
T 2o0m_A           20 QERFQILRNIYWMQPIGRRSLSETMGITERVLRTETDVLKQL-NLIEPSK---SGMTLTERGLEVY   81 (345)
T ss_dssp             ------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEe---cceEEcHHHHHHH
Confidence            456778999987777888999999999999999999999987 9997433   3589999999766

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=93.99  E-value=0.084  Score=42.92  Aligned_cols=47  Identities=17%  Similarity=0.352  Sum_probs=43.3

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI   50 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~   50 (292)
                      ...+.+||..|..++.....++|+.+|++...|.+.++.|+.. |+|.
T Consensus         8 d~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~-G~i~   54 (151)
T 2dbb_A            8 DRVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKL-GIIR   54 (151)
T ss_dssp             CHHHHHHHHHHHHCTTCCHHHHHHHTTSCHHHHHHHHHHHHHH-TSEE
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEE
Confidence            4678899999988888899999999999999999999999987 9987

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=93.97  E-value=0.048  Score=41.87  Aligned_cols=46  Identities=7%  Similarity=0.120  Sum_probs=40.9

Q ss_pred             HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP   53 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~   53 (292)
                      .+||..|...+.++..+||+.+|++...|-+.+..|+.+ |+|.-.+
T Consensus         5 ~~Il~~L~~~g~vsv~eLA~~l~VS~~TIRrDL~~Le~~-G~l~R~~   50 (87)
T 2k02_A            5 MEVRDMLALQGRMEAKQLSARLQTPQPLIDAMLERMEAM-GKVVRIS   50 (87)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHTTCCHHHHHHHHHHHHTT-CCSEEEE
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEe
Confidence            468999998999999999999999999999999999987 8776443

>2zfw_A PEX; five alpha-helices + one beta-sheet, circadian clock protein; 2.90A {Synechococcus SP}

Probab=93.93  E-value=0.023  Score=47.63  Aligned_cols=65  Identities=9%  Similarity=0.072  Sum_probs=48.1

Q ss_pred             HHHHHHhccCCCCChHHHHHhc-------CCCHHHHHHHHHHhhccCCcEEEee-------eeEEEEEeChhHHHHhhcC
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLF-------NEDHQKVVGGMKSIETLGEYLIVEP-------LSHKIWELTGEGNQVKDNG   72 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~-------~~~~~~v~~~~~~L~s~~glv~~e~-------~~~~~~~LTeEG~~yl~~G   72 (292)
                      .-||..|..+ ...-.++.+.+       ++++..|-..++.|+.. |+|+...       ..++.|.||+.|++++..-
T Consensus        47 ~~IL~lL~~~-p~~GYeI~k~l~~~~~~~~is~gtLYp~L~rLE~~-GlI~~~~~~~~~~g~~rk~Y~LT~~Gr~~l~~~  124 (148)
T 2zfw_A           47 CYVLAVLRHE-DSYGTELIQHLETHWPNYRLSDTVLYTALKFLEDE-QIISGYWKKVEGRGRPRRMYQLAQANDDRSRDL  124 (148)
T ss_dssp             HHHHHHHTTC-CEEHHHHHHHHHHHCTTEECCSHHHHHHHHHHHHT-SSEEEECCCCTTSSCCCCEEEESSSSCSTTHHH
T ss_pred             HHHHHHHHhC-CCcHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHC-CCEEEEeeccCCCCCCcEEEEECHHHHHHHHHH
Confidence            3478888653 33335555443       58899999999999986 9999863       3468899999999887554


Q ss_pred             C
Q psy10346         73 S   73 (292)
Q Consensus        73 l   73 (292)
                      .
T Consensus       125 ~  125 (148)
T 2zfw_A          125 A  125 (148)
T ss_dssp             H
T ss_pred             H
Confidence            3

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=93.88  E-value=0.032  Score=50.27  Aligned_cols=73  Identities=10%  Similarity=0.007  Sum_probs=59.2

Q ss_pred             HHHHHHHHHhccC--CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTN--PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~--~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..|..||..|...  +.++..++|..++++...+.+.++.|+.+ |+|.-.+    +-...+.||++|++.+..=.|+..
T Consensus        34 ~~q~~vL~~L~~~~~~~~~~~el~~~l~~~~~t~t~~l~rLe~~-G~i~R~~~~~DrR~~~i~LT~~G~~~~~~~~~~~~  112 (250)
T 1p4x_A           34 IKEFILLTYLFHQQENTLPFKKIVSDLCYKQSDLVQHIKVLVKH-SYISKVRSKIDERNTYISISEEQREKIAERVTLFD  112 (250)
T ss_dssp             HHHHHHHHHHHSCSCSEEEHHHHHHHSSSCGGGTHHHHHHHHHT-TSCEEEECSSSTTSEEEECCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHhhHHHHHHHHHHC-CCEEecCCCCCCCeEEEEECHHHHHHHHHHHHHHH
Confidence            5688899999653  45788999999999999999999999987 9997643    334578999999997766666554

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=93.81  E-value=0.1  Score=41.59  Aligned_cols=49  Identities=22%  Similarity=0.248  Sum_probs=42.6

Q ss_pred             HHHHHHHHHhccCCC--CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346          4 DLTEKILKYLDTNPP--VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP   53 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~--~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~   53 (292)
                      ..+..||..|...+.  ++..++|+.+|++...|.+.+..|+.+ |+|.-..
T Consensus        26 ~~e~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L~~L~~~-GlV~r~~   76 (123)
T 3r0a_A           26 KADLNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSVKKLHEK-EILQRSQ   76 (123)
T ss_dssp             HHHHHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEEE
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEeeC
Confidence            567889999976554  788999999999999999999999987 9998754

>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=93.79  E-value=0.097  Score=42.55  Aligned_cols=48  Identities=13%  Similarity=0.127  Sum_probs=43.4

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      .+.+.+||..|..++.....++|+.+|++...|.+.++.|+.. |+|.-
T Consensus         6 d~~~~~iL~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~-G~i~~   53 (150)
T 2w25_A            6 DDIDRILVRELAADGRATLSELATRAGLSVSAVQSRVRRLESR-GVVQG   53 (150)
T ss_dssp             CHHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEE
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEE
Confidence            4678899999988888889999999999999999999999987 99963

>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=93.67  E-value=0.1  Score=42.48  Aligned_cols=48  Identities=19%  Similarity=0.208  Sum_probs=43.7

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      .+.+.+||..|..++.....++|+.+|++...|.+.++.|+.. |+|.-
T Consensus         7 d~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~-G~i~~   54 (152)
T 2cg4_A            7 DNLDRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQA-GIITG   54 (152)
T ss_dssp             CHHHHHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHHHHH-TSEEE
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHc-CCcce
Confidence            4678899999988888899999999999999999999999987 99874

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=93.66  E-value=0.11  Score=38.85  Aligned_cols=57  Identities=14%  Similarity=0.223  Sum_probs=44.3

Q ss_pred             HHHHHHH---HhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346          5 LTEKILK---YLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT   62 (292)
Q Consensus         5 ~e~~iL~---~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT   62 (292)
                      +...|+.   .|..++.....++|.++|++.+.|-+.+.+|+.+ |+|......--.|.++
T Consensus        13 ~~~~v~~~i~~L~~~~~~Ta~~IAkkLg~sK~~vNr~LY~L~kk-G~V~~~~~~PP~W~~~   72 (75)
T 1sfu_A           13 IFSLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKE-DTVKMVPSNPPKWFKN   72 (75)
T ss_dssp             HHHHHHHHHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEECCSSCEEEEC
T ss_pred             HHHHHHHHHHhCCCCcchHHHHHHHHHCCCHHHHHHHHHHHHHC-CCEecCCCCCCCccCC
Confidence            3444544   4444444678999999999999999999999986 9999888777777665

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=93.45  E-value=0.13  Score=39.30  Aligned_cols=66  Identities=9%  Similarity=0.065  Sum_probs=51.4

Q ss_pred             CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHh
Q psy10346          2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVK   69 (292)
Q Consensus         2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl   69 (292)
                      +++...+||..|...++....++|+.+|+++..|.+-++.|+. . +|..++ -....|.||++|..-+
T Consensus        25 ~~~~Rl~IL~~l~~~~~~~~~ela~~l~is~stvs~hL~~L~~-~-lv~~~~~gr~~~y~l~~~~~~~~   91 (99)
T 2zkz_A           25 AHPMRLKIVNELYKHKALNVTQIIQILKLPQSTVSQHLCKMRG-K-VLKRNRQGLEIYYSINNPKVEGI   91 (99)
T ss_dssp             CSHHHHHHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHHHHBT-T-TBEEEEETTEEEEECCCHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCcCHHHHHHHHCcCHHHHHHHHHHHHH-H-hhhheEeCcEEEEEEChHHHHHH
Confidence            4567788896665456678899999999999999999999986 4 877643 3456899999986543

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=93.42  E-value=0.11  Score=52.42  Aligned_cols=107  Identities=11%  Similarity=0.138  Sum_probs=52.6

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhc-----cCCcEEEeeeeEEEEEeChhHHHHhhcC-------
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIET-----LGEYLIVEPLSHKIWELTGEGNQVKDNG-------   72 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s-----~~glv~~e~~~~~~~~LTeEG~~yl~~G-------   72 (292)
                      .+..||..|..++.++..++++.+|++...+.+.++.|..     . |+|+-..   ..|.|++.-...+.+.       
T Consensus       431 ~~~~iL~~l~~~~~it~~~la~~l~~s~~~~~~~L~~L~~~~~~~~-glie~~g---~~y~L~~~~~~~~~~~~~~~~~~  506 (583)
T 3lmm_A          431 RIAIVLYLLFQRPFITIDVVARGLQSGKEAARNALEAARQTTVAGA-PLIIAHD---GVWLLGNACREILRKVEPSPFSP  506 (583)
T ss_dssp             HHHHHHHHHHHSSSBCHHHHHHHHTSCHHHHHHHHHHHHTCEETTE-ESEEEET---TEEEECHHHHHHHTSCC------
T ss_pred             hHHHHHHHHHHCCCcCHHHHHHHhCcCHHHHHHHHHHHHhhhcccc-ceEEEeC---CEEEECHHHHHHhcccccccccc
Confidence            4568999998888999999999999999999999999987     4 7887754   5799999865545332       


Q ss_pred             ------Ch---HHHHHhhcCCCC-CChHHHhhcC----CchhhHHHHHHHcCCeecc
Q psy10346         73 ------SH---EVLVFNNVPSEG-IGQKELLATF----PNAKVGFSKAMAKGWISLD  115 (292)
Q Consensus        73 ------lP---E~rl~~~l~~~~-~~~~el~~~~----~~~~ig~~~a~k~gwi~i~  115 (292)
                            .|   +..++++|.+.| ++..++.+.+    ..+.-.+..+.+.|.|+..
T Consensus       507 ~~~~~~~~~~~~~~I~~~l~~~g~it~~di~~l~~ls~~qa~~~L~~Lv~~G~l~~~  563 (583)
T 3lmm_A          507 VRYLSTDQAELTNAAMLWLSEVGDLATSDLMAMCGVSRGTAKACVDGLVDEERVVAV  563 (583)
T ss_dssp             ---------------------------------------------------------
T ss_pred             cccccCChhHHHHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEe
Confidence                  01   234667777654 6667776642    2334445555556655443

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=93.37  E-value=0.093  Score=42.53  Aligned_cols=47  Identities=17%  Similarity=0.160  Sum_probs=42.6

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      +.+.+||..|..++.....++|+.+|++...|.+.++.|+.. |+|.-
T Consensus         3 ~~~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~-G~i~~   49 (150)
T 2pn6_A            3 EIDLRILKILQYNAKYSLDEIAREIRIPKATLSYRIKKLEKD-GVIKG   49 (150)
T ss_dssp             HHHHHHHHHHTTCTTSCHHHHHHHHTSCHHHHHHHHHHHHHT-TSSCC
T ss_pred             hHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CcEEE
Confidence            567899999988888889999999999999999999999987 99863

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=93.33  E-value=0.13  Score=42.50  Aligned_cols=48  Identities=17%  Similarity=0.205  Sum_probs=43.5

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      ...+.+||..|..++.....++|+.+|++...|.+.++.|+.. |+|.-
T Consensus         9 d~~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~-G~i~~   56 (162)
T 2p5v_A            9 DKTDIKILQVLQENGRLTNVELSERVALSPSPCLRRLKQLEDA-GIVRQ   56 (162)
T ss_dssp             CHHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEE
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEee
Confidence            4678899999988888889999999999999999999999987 99873

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=93.18  E-value=0.26  Score=35.87  Aligned_cols=57  Identities=19%  Similarity=0.178  Sum_probs=45.5

Q ss_pred             HHHHHHHHHhccC--CCCChHHHHHhc-----CCCHHHHHHHHHHhhccCCcEEEeee--eEEEEEe
Q psy10346          4 DLTEKILKYLDTN--PPVDTLDLAKLF-----NEDHQKVVGGMKSIETLGEYLIVEPL--SHKIWEL   61 (292)
Q Consensus         4 ~~e~~iL~~L~~~--~~~~~~ela~~~-----~~~~~~v~~~~~~L~s~~glv~~e~~--~~~~~~L   61 (292)
                      .....||..|...  +..+..++++.+     +++...|-+.+..|+.. |+|.-...  ....|.+
T Consensus        17 ~~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~-Glv~~~~~~~~~~~y~~   82 (83)
T 2fu4_A           17 LPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDA-GIVTRHNFEGGKSVFEL   82 (83)
T ss_dssp             HHHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHH-TSEEEEECGGGCEEEEE
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHC-CCeEEEeeCCCceEeec
Confidence            5667899999754  578889999998     99999999999999987 99986443  3445554

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=93.12  E-value=0.1  Score=43.26  Aligned_cols=46  Identities=22%  Similarity=0.252  Sum_probs=42.5

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI   50 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~   50 (292)
                      ....+||..|..++.+...++|+.+|++...|.+-++.|+.. |+|.
T Consensus         3 ~~d~~il~~L~~~~~~s~~~la~~lg~s~~tv~~rl~~L~~~-g~i~   48 (162)
T 3i4p_A            3 RLDRKILRILQEDSTLAVADLAKKVGLSTTPCWRRIQKMEED-GVIR   48 (162)
T ss_dssp             HHHHHHHHHHTTCSCSCHHHHHHHHTCCHHHHHHHHHHHHHT-TSSC
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCee
Confidence            567899999998889999999999999999999999999987 9876

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=93.11  E-value=0.14  Score=43.15  Aligned_cols=47  Identities=15%  Similarity=0.277  Sum_probs=43.1

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI   50 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~   50 (292)
                      .+.+.+||..|..++.....++|+.+|++...|.+.++.|++. |+|.
T Consensus        16 d~~d~~IL~~L~~~~~~s~~eLA~~lglS~~tv~~~l~~L~~~-G~I~   62 (171)
T 2ia0_A           16 DDLDRNILRLLKKDARLTISELSEQLKKPESTIHFRIKKLQER-GVIE   62 (171)
T ss_dssp             CHHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHT-TSEE
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEE
Confidence            4678899999988888899999999999999999999999987 9986

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=92.94  E-value=0.18  Score=42.76  Aligned_cols=62  Identities=13%  Similarity=0.014  Sum_probs=50.8

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE-eeeeEEEEEeChhHHHHhh
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV-EPLSHKIWELTGEGNQVKD   70 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~-e~~~~~~~~LTeEG~~yl~   70 (292)
                      .-.+||+.|. .|+..+..+|+.+|++|+++--.++.|+-. |+|.. ..-....|+|.+.  +|+.
T Consensus        12 rk~~ILE~Lk-~G~~~t~~Iak~LGlShg~aq~~Ly~LeRE-G~V~~Vk~GK~ayw~L~~s--~y~~   74 (165)
T 2vxz_A           12 RLRDILALLA-DGCKTTSLIQQRLGLSHGRAKALIYVLEKE-GRVTRVAFGNVALVCLSMD--QYRQ   74 (165)
T ss_dssp             HHHHHHHHHT-TCCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSCEEEEETTEEEEESCHH--HHHH
T ss_pred             HHHHHHHHHH-hCCccHHHHHHHhCCcHHHHHHHHHHHHhc-CceEEEEEccEEEEEecHH--HHHH
Confidence            4567999999 888899999999999999999999999965 88776 5555666788755  6664

>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=92.92  E-value=0.098  Score=41.77  Aligned_cols=47  Identities=17%  Similarity=0.215  Sum_probs=42.3

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI   50 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~   50 (292)
                      ...+.+||..|..++.....++|+.+|++...|.+.++.|+.. |+|.
T Consensus         3 d~~~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~-G~i~   49 (141)
T 1i1g_A            3 DERDKIILEILEKDARTPFTEIAKKLGISETAVRKRVKALEEK-GIIE   49 (141)
T ss_dssp             CSHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHH-TSSC
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEe
Confidence            4578899999987778888999999999999999999999987 9985

>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=92.48  E-value=0.12  Score=42.11  Aligned_cols=48  Identities=10%  Similarity=0.225  Sum_probs=43.3

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      ...+.+||..|..++.....++|+.+|++...|.+.++.|++. |+|.-
T Consensus         6 d~~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~-G~i~~   53 (151)
T 2cyy_A            6 DEIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRES-GVIKK   53 (151)
T ss_dssp             CHHHHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHH-TSSCC
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeEE
Confidence            4678899999988888889999999999999999999999987 99863

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=92.46  E-value=0.2  Score=41.00  Aligned_cols=48  Identities=8%  Similarity=0.029  Sum_probs=39.3

Q ss_pred             CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee------EEEEEeChhH
Q psy10346         17 PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS------HKIWELTGEG   65 (292)
Q Consensus        17 ~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~------~~~~~LTeEG   65 (292)
                      ...+++++|+.+|++...|.+.+..|..+ |+|.++...      ...|-||+-=
T Consensus        50 ~~ps~~~LA~~~~~s~~~v~~~L~~L~~K-GlI~i~~~~d~~g~~~~~ydL~pL~  103 (135)
T 2v79_A           50 YFPTPNQLQEGMSISVEECTNRLRMFIQK-GFLFIEECEDQNGIKFEKYSLQPLW  103 (135)
T ss_dssp             CSCCHHHHHTTSSSCHHHHHHHHHHHHHH-TSCEEEEEECTTCCEEEEEECHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEeEecCCCceEEEeeHHHHH
Confidence            33688999999999999999999999987 999996443      2577777543

>1nnh_A Asparaginyl-tRNA synthetase-related peptide; structural genomics, PSI, protein structure initiative, southeast COLL for structural genomics; 1.65A {Pyrococcus furiosus} SCOP: d.104.1.1 PDB: 3p8t_A 3p8v_A 3p8y_A 3reu_A* 3rex_A* 3rl6_A*

Probab=92.35  E-value=0.095  Score=48.20  Aligned_cols=42  Identities=17%  Similarity=0.179  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCC-----CCCCCCc
Q psy10346        223 LMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHP-----ARDAHDT  272 (292)
Q Consensus       223 l~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHP-----AR~~~DT  272 (292)
                      -+.+++.||++|.++||.|+. .|.+++++   |    |.+||     ||..++.
T Consensus        18 rs~i~~~ir~~f~~~GF~EVe-TP~l~~~~---~----~~~~~~~~e~a~~f~~~   64 (294)
T 1nnh_A           18 QTKILEYMTDFFVKEGFKWLL-PVIISPIT---D----PLWPDPAGEGMEPAEVE   64 (294)
T ss_dssp             HHHHHHHHHHHHHHTTCEEEC-CCCEESCC---C----CCCSCTTCCCCCCCEEE
T ss_pred             HHHHHHHHHHHHHHCCCEEEE-CCEEEEcc---c----hhccCCCCCcceeEEEE
Confidence            567889999999999999996 69998882   3    88999     7766543

>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=92.18  E-value=0.13  Score=39.54  Aligned_cols=47  Identities=13%  Similarity=0.149  Sum_probs=39.7

Q ss_pred             HHHHHHHHhc-cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe
Q psy10346          5 LTEKILKYLD-TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE   52 (292)
Q Consensus         5 ~e~~iL~~L~-~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e   52 (292)
                      ...+||..|. .+...+..++|+.+|++...|.+++..|++. |+|...
T Consensus        19 ~~l~Il~~l~~~g~~~s~~eLa~~lgvs~~tV~~~L~~L~~~-GlV~~~   66 (110)
T 1q1h_A           19 DVIDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQ-GFVSYR   66 (110)
T ss_dssp             TTHHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHH-TSCEEE
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEE
Confidence            4457887774 4446788999999999999999999999987 999876

>1x54_A Asparaginyl-tRNA synthetase; aminoacyl-tRNA synthetase, riken structural genomics/proteom initiative, RSGI, structural genomics, ligase; HET: 4AD; 1.45A {Pyrococcus horikoshii} PDB: 1x55_A* 1x56_A

Probab=91.94  E-value=0.084  Score=51.32  Aligned_cols=49  Identities=8%  Similarity=0.070  Sum_probs=41.2

Q ss_pred             CCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecC
Q psy10346        218 GHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTD  277 (292)
Q Consensus       218 g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~  277 (292)
                      ...|+-+.+++.||++|.++||.|+. .|.++++          ..||||++.+|.|.+.
T Consensus       133 ~~~~~rs~i~~~ir~~f~~~gF~eVe-TP~l~~~----------~~e~~~~~f~~~~~~~  181 (434)
T 1x54_A          133 AIMKVKETLIMAAREWLLKDGWHEVF-PPILVTG----------AVEGGATLFKLKYFDK  181 (434)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCEECC-CCSEESC----------CSSCGGGCCEEEETTE
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEEe-CcEEEee----------cCCCCceeEEEeecCC
Confidence            34566788999999999999999986 6888866          6899999999987653

>1x19_A CRTF-related protein; methyltransferase, bacteriochllochlorophyll, BCHU, SAM, SAH, adenosylmethyonine, S-adenosylhomocysteine, ADO-Met; 2.27A {Chlorobium tepidum} PDB: 1x1a_A* 1x1b_A* 1x1c_A* 1x1d_A*

Probab=91.83  E-value=0.32  Score=44.69  Aligned_cols=66  Identities=12%  Similarity=0.153  Sum_probs=56.1

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCCh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSH   74 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlP   74 (292)
                      ..+..|+..|.+ +..+..+||+.+|+++..+-++++.|.+. |+++...   ..|.+|+.+..++..++|
T Consensus        51 a~~lgif~~L~~-~~~t~~eLA~~~g~~~~~l~rlLr~L~~~-gll~~~~---~~y~~t~~~~~~l~~~~~  116 (359)
T 1x19_A           51 AIELDLFSHMAE-GPKDLATLAADTGSVPPRLEMLLETLRQM-RVINLED---GKWSLTEFADYMFSPTPK  116 (359)
T ss_dssp             HHHHTHHHHHTT-CCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEET---TEEEECHHHHHHSSSSCS
T ss_pred             HHHcCcHHHHcC-CCCCHHHHHHHhCcChHHHHHHHHHHHhC-CCeEeeC---CeEecCHHHHHHhcCCCC
Confidence            456677888864 66788999999999999999999999997 9998653   389999998889988877

>3mcz_A O-methyltransferase; adomet_mtases, S-adenosylmethionine-dependent methyltransfer structural genomics, PSI-2; HET: MSE; 1.90A {Burkholderia thailandensis}

Probab=91.61  E-value=0.29  Score=44.65  Aligned_cols=66  Identities=15%  Similarity=0.143  Sum_probs=55.4

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHH
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      .+..|...|..  ..+.+++|+.+|++...+-+++..|.+. |+++...   ..|.+|+.+..++..+.|.+
T Consensus        45 ~~lgif~~l~~--~~t~~elA~~~~~~~~~l~rlLr~L~~~-gll~~~~---~~y~~t~~s~~~l~~~~~~~  110 (352)
T 3mcz_A           45 VADKLFDLTQT--GRTPAEVAASFGMVEGKAAILLHALAAL-GLLTKEG---DAFRNTALTERYLTTTSADY  110 (352)
T ss_dssp             HHTTHHHHTTS--CBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEET---TEEEECHHHHHHHSTTCTTC
T ss_pred             HHCChHHHhCC--CCCHHHHHHHhCcChHHHHHHHHHHHHC-CCeEecC---CeeecCHHHHhhccCCChhh
Confidence            45556777753  6788999999999999999999999997 9998643   46999999999998888864

>2r3s_A Uncharacterized protein; methyltransferase domain, structural genomics, joint center structural genomics, JCSG, protein structure initiative; HET: MSE; 2.15A {Nostoc punctiforme}

Probab=91.38  E-value=0.25  Score=44.53  Aligned_cols=67  Identities=9%  Similarity=0.076  Sum_probs=55.7

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHE   75 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE   75 (292)
                      ..+..|+..|.+ +..+.+++|+.+|+++..+-+++..|.+. |+++.   ....|.+|..+..++..+.|.
T Consensus        26 ~~~l~i~~~l~~-~~~t~~ela~~~~~~~~~l~r~L~~L~~~-g~l~~---~~~~y~~t~~~~~~l~~~~~~   92 (335)
T 2r3s_A           26 AVELNVFTAISQ-GIESSQSLAQKCQTSERGMRMLCDYLVII-GFMTK---QAEGYRLTSDSAMFLDRQSKF   92 (335)
T ss_dssp             HHHTTHHHHHTT-SEECHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEE---ETTEEEECHHHHHHTCTTSTT
T ss_pred             HHHcChHHHHhc-CCCCHHHHHHHhCCCchHHHHHHHHHHhc-CCeEe---cCCEEecCHHHHHHhccCCcH
Confidence            355667888874 56788999999999999999999999997 99974   346899999998888877663

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=90.49  E-value=0.69  Score=39.26  Aligned_cols=65  Identities=15%  Similarity=0.192  Sum_probs=53.5

Q ss_pred             CCcHHHHHHHHHhccCCCCChHHHHHhcC-CCHHHHHHHHHHhhccCCcEEEeeee------EEEEEeChhHHH
Q psy10346          1 MASDLTEKILKYLDTNPPVDTLDLAKLFN-EDHQKVVGGMKSIETLGEYLIVEPLS------HKIWELTGEGNQ   67 (292)
Q Consensus         1 m~~~~e~~iL~~L~~~~~~~~~ela~~~~-~~~~~v~~~~~~L~s~~glv~~e~~~------~~~~~LTeEG~~   67 (292)
                      ++++.-.+||..|.. ++....+++..+| ++...|..-++.|+.. |+|++.+..      ...|.++.++-.
T Consensus        20 La~P~Rl~il~~L~~-~~~~~~~l~~~l~~~~~~~~s~Hl~~L~~a-glv~~~~e~~~~g~~er~y~~~~~~~~   91 (182)
T 4g6q_A           20 LHHPLRWRITQLLIG-RSLTTRELAELLPDVATTTLYRQVGILVKA-GVLMVTAEHQVRGAVERTYTLNTQAGD   91 (182)
T ss_dssp             TTSHHHHHHHHHTTT-SCEEHHHHHHHCTTBCHHHHHHHHHHHHHH-TSEEEEEEEEETTEEEEEEEECTTTTT
T ss_pred             hCCHHHHHHHHHHHh-CCCCHHHHHHHhcCCCHHHHHHHHHHHHHC-CCeEEEEeecccCcceeEEEecccccc
Confidence            467888999999964 5667789999986 8999999999999987 999986654      578999988743

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=89.94  E-value=0.34  Score=38.35  Aligned_cols=60  Identities=12%  Similarity=0.000  Sum_probs=44.6

Q ss_pred             HHHHHHHHhcc---CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhH
Q psy10346          5 LTEKILKYLDT---NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEG   65 (292)
Q Consensus         5 ~e~~iL~~L~~---~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG   65 (292)
                      ...+||..|..   ++.+.+.++|+.+|++...|.+.+..|+.. |+|...+-..--|.|+...
T Consensus        10 ~al~iL~~la~~~~~~~~s~~ela~~~~i~~~~v~~il~~L~~~-Glv~~~~g~~ggy~L~~~~   72 (129)
T 2y75_A           10 YGLTIMIELAKKHGEGPTSLKSIAQTNNLSEHYLEQLVSPLRNA-GLVKSIRGAYGGYVLGSEP   72 (129)
T ss_dssp             HHHHHHHHHHHTTTSCCBCHHHHHHHTTSCHHHHHHHHHHHHHT-TSEEEC----CCEEESSCG
T ss_pred             HHHHHHHHHHhCCCCCcCCHHHHHHHHCcCHHHHHHHHHHHHHC-CceEecCCCCCceEeCCCH
Confidence            34567777754   345788999999999999999999999986 9998765544567776544

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=89.69  E-value=0.44  Score=38.18  Aligned_cols=51  Identities=8%  Similarity=0.054  Sum_probs=38.7

Q ss_pred             HHHHHHHHHhcc----C-CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee
Q psy10346          4 DLTEKILKYLDT----N-PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS   55 (292)
Q Consensus         4 ~~e~~iL~~L~~----~-~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~   55 (292)
                      +.|..||..|..    + ...+..++|..+|++..+|.+++..|+.+ |+|+.+...
T Consensus        32 ~~e~~vll~L~~~~~~~~~~ps~~~LA~~l~~s~~~V~~~l~~Le~k-GlI~~~~~~   87 (128)
T 2vn2_A           32 EGELVLLLHMQSFFEEGVLFPTPAELAERMTVSAAECMEMVRRLLQK-GMIAIEEHT   87 (128)
T ss_dssp             HHHHHHHHHHHHHHTTTCSSCCHHHHHHTSSSCHHHHHHHHHHHHHT-TSSEECC--
T ss_pred             HHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEeEE
Confidence            345556666632    2 22678999999999999999999999987 999986553

>3eyi_A Z-DNA-binding protein 1; alternative splicing, DNA-binding, polymorphism, DNA binding protein/Z-DNA complex, DNA binding protein/DNA complex; 1.45A {Homo sapiens} PDB: 2l4m_A

Probab=89.53  E-value=0.18  Score=37.33  Aligned_cols=49  Identities=20%  Similarity=0.292  Sum_probs=42.5

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhcCCCHHH-HHHHHHHhhccCCcEEEeee
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQK-VVGGMKSIETLGEYLIVEPL   54 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~-v~~~~~~L~s~~glv~~e~~   54 (292)
                      .+.+|+..|..+|+.....+|+.+|+.... |-+.+.+|+.+ +++...+.
T Consensus        11 ~ee~I~~fL~~~Gp~~AL~IAK~LGlktAK~VNp~LY~m~~~-~lL~~Dek   60 (72)
T 3eyi_A           11 REEDIYRFLKDNGPQRALVIAQALGMRTAKDVNRDLYRMKSR-HLLDMDEQ   60 (72)
T ss_dssp             HHHHHHHHHHHHCSEEHHHHHHHTTCCSGGGTHHHHHHHHHT-TSEEECTT
T ss_pred             hHHHHHHHHHHcCCchHHHHHHHhCcchhhhcCHHHHHHHHc-cCcCCCCC
Confidence            478899999998888889999999998655 99999999987 99987543

>1uly_A Hypothetical protein PH1932; helix-turn-helix, structural genomics, DNA binding protein; 2.50A {Pyrococcus horikoshii} SCOP: a.4.5.58 PDB: 2cwe_A

Probab=89.30  E-value=0.47  Score=40.83  Aligned_cols=48  Identities=21%  Similarity=0.331  Sum_probs=42.9

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE   52 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e   52 (292)
                      ...+.+||..|. ++.....++|+.+|++...|.+.++.|+.. |+|...
T Consensus        19 d~~~~~IL~~L~-~~~~s~~eLA~~lglS~stv~~~l~~Le~~-GlI~~~   66 (192)
T 1uly_A           19 EDTRRKILKLLR-NKEMTISQLSEILGKTPQTIYHHIEKLKEA-GLVEVK   66 (192)
T ss_dssp             SHHHHHHHHHHT-TCCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEE
T ss_pred             CHHHHHHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEE
Confidence            466788999998 567888999999999999999999999987 999876

>3dp7_A SAM-dependent methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research; 2.33A {Bacteroides vulgatus}

Probab=89.07  E-value=0.44  Score=44.15  Aligned_cols=67  Identities=12%  Similarity=0.044  Sum_probs=53.7

Q ss_pred             HHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHH
Q psy10346          5 LTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         5 ~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      .+..|...|.. ++..+.++||..+|++...+-+.+..|.+. |+++.+   ...|.+|+.++ ++..+.|-.
T Consensus        36 ~~lgifd~L~~~~~~~t~~eLA~~~g~~~~~l~rlLr~l~~~-g~l~~~---~~~y~~t~~s~-~L~~~~~~~  103 (363)
T 3dp7_A           36 LKFGIFQLLSGKREGYTLQEISGRTGLTRYAAQVLLEASLTI-GTILLE---EDRYVLAKAGW-FLLNDKMAR  103 (363)
T ss_dssp             HHTTHHHHHHTCTTCBCHHHHHHHHTCCHHHHHHHHHHHHHH-TSEEEE---TTEEEECHHHH-HHHHCHHHH
T ss_pred             HHhCHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHhhC-CCeEec---CCEEecccchH-HhhCCCccc
Confidence            45567778865 467889999999999999999999999998 999653   56899999995 565555543

>1bm9_A RTP, TER, replication terminator protein; DNA-binding protein, contrahelicase; 2.00A {Bacillus subtilis} SCOP: a.4.5.7 PDB: 1f4k_A 1j0r_A 2dpd_A 2dpu_A 2efw_A* 2dqr_A

Probab=88.94  E-value=0.53  Score=38.30  Aligned_cols=66  Identities=11%  Similarity=0.108  Sum_probs=46.7

Q ss_pred             HHHHHHHHhccCCC--CCh-HHHHH-----hcCCCHHHHHHHHHHhhccCCcEEEeeee---E-----EEEEeChhHHH-
Q psy10346          5 LTEKILKYLDTNPP--VDT-LDLAK-----LFNEDHQKVVGGMKSIETLGEYLIVEPLS---H-----KIWELTGEGNQ-   67 (292)
Q Consensus         5 ~e~~iL~~L~~~~~--~~~-~ela~-----~~~~~~~~v~~~~~~L~s~~glv~~e~~~---~-----~~~~LTeEG~~-   67 (292)
                      +..-||..|.....  ... .++.+     -..+++.+|-.++..|+.. |+|+.+...   .     +.|.||+.|+. 
T Consensus        19 l~l~IL~ll~~~p~YGYeI~~~L~e~~~~~~~~is~gtlYp~L~rLe~~-Gll~~~~~~~~g~~r~~rkyY~lT~~G~~~   97 (122)
T 1bm9_A           19 LKLYMITMTEQERLYGLKLLEVLRSEFKEIGFKPNHTEVYRSLHELLDD-GILKQIKVKKEGAKLQEVVLYQFKDYEAAK   97 (122)
T ss_dssp             HHHHHHHHHHTTCCBSTTHHHHHHHHHTTTTCCCCHHHHHHHHHHHHHT-TSEEEEEEECTTSTTCEEEEEEESCHHHHH
T ss_pred             HHHHHHHHHccCCchHHHHHHHHHHhhccCcccCCcccHHHHHHHHHHC-CCeEEEEeecCCCCCCceeEEEEChhhhhH
Confidence            34557888865433  222 34432     2356799999999999987 999987762   2     88999999999 


Q ss_pred             -Hhhc
Q psy10346         68 -VKDN   71 (292)
Q Consensus        68 -yl~~   71 (292)
                       |+++
T Consensus        98 ~~~~~  102 (122)
T 1bm9_A           98 LYKKQ  102 (122)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence             7743

>2yu3_A DNA-directed RNA polymerase III 39 kDa polypeptide F variant; winged helix domain, RNA polymerase III C39 subunit, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=88.89  E-value=0.48  Score=36.88  Aligned_cols=50  Identities=10%  Similarity=0.098  Sum_probs=42.2

Q ss_pred             cHHHHHHHHHhcc--CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346          3 SDLTEKILKYLDT--NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP   53 (292)
Q Consensus         3 ~~~e~~iL~~L~~--~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~   53 (292)
                      .+.|..|+..++.  +..+-+.+|....|+++..|.+.++.|+++ |||+-..
T Consensus        36 t~~E~lVy~~I~~aGn~GIw~kdL~~~tnL~~~~vtkiLK~LE~k-~lIK~Vk   87 (95)
T 2yu3_A           36 DNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESK-KLIKAVK   87 (95)
T ss_dssp             SHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHH-TSEEEEC
T ss_pred             CHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhC-CCEEEec
Confidence            3678889999976  334778999999999999999999999997 9988543

>1mkm_A ICLR transcriptional regulator; structural genomics, winged helix-turn-helix, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.33 d.110.2.2

Probab=88.79  E-value=0.52  Score=41.59  Aligned_cols=58  Identities=19%  Similarity=0.216  Sum_probs=48.0

Q ss_pred             HHHHHHHhccCC-CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHH
Q psy10346          6 TEKILKYLDTNP-PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGN   66 (292)
Q Consensus         6 e~~iL~~L~~~~-~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~   66 (292)
                      ..+||..|...+ .....++|+.+|++.+.|.+.++.|+.. |+|...  ....|.|+...-
T Consensus        10 ~l~iL~~l~~~~~~~~~~ela~~~gl~~stv~r~l~~L~~~-G~v~~~--~~~~Y~lg~~~~   68 (249)
T 1mkm_A           10 AFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEK-GFVLRK--KDKRYVPGYKLI   68 (249)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEC--TTSCEEECTHHH
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CcEEEC--CCCcEEECHHHH
Confidence            456888886554 5788999999999999999999999987 999876  456799987643

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=88.19  E-value=0.27  Score=38.18  Aligned_cols=49  Identities=8%  Similarity=-0.037  Sum_probs=40.5

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcC----CCHHHHHHHHHHhhccCCcEEEee
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFN----EDHQKVVGGMKSIETLGEYLIVEP   53 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~----~~~~~v~~~~~~L~s~~glv~~e~   53 (292)
                      ..|..||..|-..+.++..++++.++    ++...|.+.+..|+.+ |+|.-+.
T Consensus        35 ~~e~~VL~~L~~~~~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~K-GlV~R~~   87 (99)
T 2k4b_A           35 NAELIVMRVIWSLGEARVDEIYAQIPQELEWSLATVKTLLGRLVKK-EMLSTEK   87 (99)
T ss_dssp             CSCSHHHHHHHHHSCEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHT-TSCEEEE
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHhcccCCCHhhHHHHHHHHHHC-CCEEEEe
Confidence            34667899997667788899999886    4689999999999987 9998754

>1wyd_A Hypothetical aspartyl-tRNA synthetase; archaea, LIGA; HET: EPE; 2.30A {Sulfolobus tokodaii}

Probab=88.06  E-value=0.36  Score=46.83  Aligned_cols=47  Identities=13%  Similarity=0.160  Sum_probs=39.5

Q ss_pred             CCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeec
Q psy10346        219 HLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVT  276 (292)
Q Consensus       219 ~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~  276 (292)
                      ..|+-+.+++.||++|.+.||.|+. .|.++++          ..|+||++.+|.|.+
T Consensus       133 ~~~~rs~i~~~ir~ff~~~gF~eV~-TP~l~~~----------~~e~~~~~f~~~~~~  179 (429)
T 1wyd_A          133 VIKIQSLALKAFRETLYKEGFIEIF-TPKIIAS----------ATEGGAQLFPVIYFG  179 (429)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCEECC-CCSEESS----------CSSTTCCCCEEEETT
T ss_pred             HHHHHHHHHHHHHHHHhhCCCEEEE-CCEEEee----------CCCCCceeEEEecCC
Confidence            4456788999999999999999986 5888776          689999999887654

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=87.70  E-value=1.4  Score=39.11  Aligned_cols=70  Identities=17%  Similarity=0.156  Sum_probs=53.4

Q ss_pred             HHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHH
Q psy10346          6 TEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVF   79 (292)
Q Consensus         6 e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~   79 (292)
                      -.+||..|.. .+.....++|+.+|++...|.+.+..|+.. |||.-.   ...|.|+...-.....-..-..+.
T Consensus        16 ~l~iL~~l~~~~~~~~~~eia~~~gl~~stv~r~l~~L~~~-G~v~~~---~~~Y~Lg~~~~~l~~~~~~~~~l~   86 (257)
T 2g7u_A           16 GFAVLLAFDAQRPNPTLAELATEAGLSRPAVRRILLTLQKL-GYVAGS---GGRWSLTPRVLSIGQHYSESHALI   86 (257)
T ss_dssp             HHHHHHTCSSSCSSCBHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEE---TTEEEECGGGHHHHTTCCHHHHHH
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEeC---CCEEEEcHHHHHHHHHhhccCcHH
Confidence            3467888864 345788999999999999999999999987 999865   378999988766554444433343

>1n9w_A Aspartyl-tRNA synthetase 2; biosynthetic protein; 2.30A {Thermus thermophilus} SCOP: b.40.4.1 d.104.1.1 PDB: 3kfu_A*

Probab=87.50  E-value=0.27  Score=47.60  Aligned_cols=47  Identities=15%  Similarity=0.117  Sum_probs=22.4

Q ss_pred             CChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecC
Q psy10346        220 LHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTD  277 (292)
Q Consensus       220 ~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~  277 (292)
                      .+.-+.+++.||++|.++||.|+. .|.++++          ..||||++-+|.|.+.
T Consensus       125 ~~~rs~i~~~ir~~f~~~gF~EV~-TPil~~~----------~~e~~~~~f~~~~~g~  171 (422)
T 1n9w_A          125 LKVQAALVRGFRRYLDRQDFTEIF-TPKVVRA----------GAEGGSGLFGVDYFEK  171 (422)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCEECC-CC-------------------------------
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEE-CCEEEEe----------CCCCCceeEEEeeCCC
Confidence            455678999999999999999996 5888876          6799999888766553

>3p9c_A Caffeic acid O-methyltransferase; S-adenosylmethionine dependent O-methyltransferase; HET: SAH; 1.80A {Lolium perenne} PDB: 3p9i_A* 3p9k_A*

Probab=87.33  E-value=1.1  Score=41.73  Aligned_cols=70  Identities=7%  Similarity=0.042  Sum_probs=53.8

Q ss_pred             HHHHHHHHHhccC--CCCChHHHHHhcCC--CHH---HHHHHHHHhhccCCcEEEeee------eEEEEEeChhHHHHhh
Q psy10346          4 DLTEKILKYLDTN--PPVDTLDLAKLFNE--DHQ---KVVGGMKSIETLGEYLIVEPL------SHKIWELTGEGNQVKD   70 (292)
Q Consensus         4 ~~e~~iL~~L~~~--~~~~~~ela~~~~~--~~~---~v~~~~~~L~s~~glv~~e~~------~~~~~~LTeEG~~yl~   70 (292)
                      ..+..|...|.+.  +..+.++||+.+|+  ++.   .+-+.+.-|.+. |+++....      ....|.+|+.++.++.
T Consensus        40 a~~Lgifd~L~~~g~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~-g~l~~~~~~~~~g~~~~~y~~t~~s~~l~~  118 (364)
T 3p9c_A           40 AIELGLLEILVAAGGKSLTPTEVAAKLPSAANPEAPDMVDRILRLLASY-NVVTCLVEEGKDGRLSRSYGAAPVCKFLTP  118 (364)
T ss_dssp             HHHHTHHHHHHHTTTCCBCHHHHHHTTTCTTCTTHHHHHHHHHHHHHHT-TSEEEEEEECSSSCEEEEEEECGGGGGSSC
T ss_pred             HHHCChHHHHhhcCCCCCCHHHHHHhcCCCCCccchhhHHHHHHHHHhC-CCEEEeccccCCCCcCCEEecCHHHHHHcC
Confidence            4566788888763  56889999999997  655   788999999987 99986532      1468999999987666


Q ss_pred             cCCh
Q psy10346         71 NGSH   74 (292)
Q Consensus        71 ~GlP   74 (292)
                      .++|
T Consensus       119 ~~~~  122 (364)
T 3p9c_A          119 NEDG  122 (364)
T ss_dssp             CTTS
T ss_pred             CCCC
Confidence            5544

>2xrn_A HTH-type transcriptional regulator TTGV; DNA-binding protein, tetramer gene regulator, cooperative DN binding, multidrug binding protein; 2.90A {Pseudomonas putida} PDB: 2xro_A

Probab=86.80  E-value=0.83  Score=40.17  Aligned_cols=62  Identities=15%  Similarity=0.105  Sum_probs=49.5

Q ss_pred             HHHHHHHhccCC-CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346          6 TEKILKYLDTNP-PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus         6 e~~iL~~L~~~~-~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl   69 (292)
                      -.+||..|...+ .....++|+.+|++...|.+.+..|+.. |||.-... ...|.|+.......
T Consensus         8 ~l~iL~~l~~~~~~~s~~ela~~~gl~~stv~r~l~~L~~~-G~v~~~~~-~~~Y~lg~~~~~lg   70 (241)
T 2xrn_A            8 AASIMRALGSHPHGLSLAAIAQLVGLPRSTVQRIINALEEE-FLVEALGP-AGGFRLGPALGQLI   70 (241)
T ss_dssp             HHHHHHHHHTCTTCEEHHHHHHHTTSCHHHHHHHHHHHHTT-TSEEECGG-GCEEEECSHHHHHH
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEeCC-CCeEEECHHHHHHH
Confidence            346888886544 5778999999999999999999999987 99986532 35799998776544

>2rkh_A Putative APHA-like transcription factor; ZP_00208345.1, STRU genomics, joint center for structural genomics, JCSG; 2.00A {Magnetospirillum magnetotacticum}

Probab=86.42  E-value=0.094  Score=45.25  Aligned_cols=66  Identities=8%  Similarity=0.061  Sum_probs=43.9

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhc----CCCHHHHHH----HHHHhhccCCcEEEee-----eeEEEEEeChhHHHHh
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLF----NEDHQKVVG----GMKSIETLGEYLIVEP-----LSHKIWELTGEGNQVK   69 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~----~~~~~~v~~----~~~~L~s~~glv~~e~-----~~~~~~~LTeEG~~yl   69 (292)
                      +++...||..|.... -..+++.+.+    .+...++-.    ++..|+.+ |+|++..     .+++.|.+|+.|++.+
T Consensus        12 ~~~~l~VLGlL~e~p-~h~Yei~~~i~~~~~~s~gSiY~~~~~~l~~Le~~-GlI~~~~~~~~rpektvY~ITe~Gr~~l   89 (180)
T 2rkh_A           12 EAVRLCALGTIASQP-MRYSELAGSVRHFTSRIMGPSLELMGISIELLRYE-GLVEAVDDGQGMEDDAMLAISAAGRREL   89 (180)
T ss_dssp             HHHHHHHHHHHHHSC-EEHHHHHHHHHHHHHHHHSCCGGGTTCCTHHHHHT-TSEECCC--------CEEEECHHHHHHH
T ss_pred             chHHHHHHHHHHhCC-CCHHHHHHHHHHHhccCCCCCchhHHHHHHHHHHC-CCeeeeecCCCCCccceeeeCHHHHHHH
Confidence            567888999987543 3455565432    122334455    88999876 9996544     5788999999999987


Q ss_pred             h
Q psy10346         70 D   70 (292)
Q Consensus        70 ~   70 (292)
                      .
T Consensus        90 ~   90 (180)
T 2rkh_A           90 H   90 (180)
T ss_dssp             H
T ss_pred             H
Confidence            4

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=85.79  E-value=0.68  Score=39.37  Aligned_cols=60  Identities=12%  Similarity=0.235  Sum_probs=44.6

Q ss_pred             cHHHHHHHHHhcc-----CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeCh
Q psy10346          3 SDLTEKILKYLDT-----NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG   63 (292)
Q Consensus         3 ~~~e~~iL~~L~~-----~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTe   63 (292)
                      ...|.+||..+..     +...+..++|+.+|++..+|.+.++.|+.+ |+|.........+.|++
T Consensus         4 t~~q~~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~l~~Le~~-G~i~~~~~~~r~i~~~~   68 (196)
T 3k2z_A            4 TERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHLIALEKK-GYIERKNGKPRALRISK   68 (196)
T ss_dssp             CHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHT-TSEECC---TTCCEESS
T ss_pred             CHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHHHHHHHHC-CCEEecCCCcceEEecC
Confidence            4568888887742     335678999999999999999999999987 99987655545555554

>2ijl_A AGR_C_4647P, molybdenum-binding transcriptional repressor; structural GE DNA-binding protein, PSI-2, PROT structure initiative; 2.30A {Agrobacterium tumefaciens str}

Probab=85.68  E-value=1.1  Score=36.59  Aligned_cols=62  Identities=5%  Similarity=-0.009  Sum_probs=44.0

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHh
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVK   69 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl   69 (292)
                      +.+++..+...+  +...-|+.+|+++.+|.+.++.||..-|.-=+++..    ...+.||++|+.++
T Consensus        28 ~L~~f~av~e~g--S~s~AA~~L~iSqsavS~~I~~LE~~lG~~Lf~R~~~G~~grg~~LT~~G~~ll   93 (135)
T 2ijl_A           28 KVELMQLIAETG--SISAAGRAMDMSYRRAWLLVDALNHMFRQPVICSQRGGKQGGGAALTVFGAELL   93 (135)
T ss_dssp             HHHHHHHHHHHS--CHHHHHHHTTCCHHHHHHHHHHHHHHBSSCSEEECCC------EEECHHHHHHH
T ss_pred             HHHHHHHHHHhC--CHHHHHHHHCcCHHHHHHHHHHHHHHHCCeeEEecCCCCCCCceeECHHHHHHH
Confidence            455666665544  345778889999999999999999765543333433    25799999999987

>2hgc_A YJCQ protein; SR346, structure, autostructure, NESG, PSI-2, northeast structural genomics consortium, protein structure initiative; NMR {Bacillus subtilis} SCOP: a.4.5.77

Probab=85.10  E-value=0.55  Score=37.05  Aligned_cols=75  Identities=15%  Similarity=0.130  Sum_probs=50.2

Q ss_pred             HHHHHHHHHhccCCC-CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee--EEE-----EEeChhHHHHhhcCChH
Q psy10346          4 DLTEKILKYLDTNPP-VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS--HKI-----WELTGEGNQVKDNGSHE   75 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~-~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~--~~~-----~~LTeEG~~yl~~GlPE   75 (292)
                      .+-++||+.|...+. ++    ++.+|++.......+..|... |||.--...  ...     ..+|.+|.+||++.|-=
T Consensus         5 ~iiYkIL~~L~~~~~~is----~e~l~Ise~~~~~il~~L~d~-GyI~Gv~~~~~~~~i~~~~~~IT~~GleYL~ENS~m   79 (102)
T 2hgc_A            5 KLRYAILKEIFEGNTPLS----ENDIGVTEDQFDDAVNFLKRE-GYIIGVHYSDDRPHLYKLGPELTEKGENYLKENGTW   79 (102)
T ss_dssp             CCHHHHHHHHHHHCSCCC----HHHHTSCHHHHHHHHHHHHHH-TSEECCEESSSSEECCSSCCEECHHHHHHHHHHTCS
T ss_pred             eeHHHHHHHHHhCCCcCC----HHhcCCCHHHHHHHHHHHHHC-CCccceEEEeCcceeeccCceECHHHHHHHHHChHH
Confidence            456899999976432 23    345799999999999999987 998753321  111     46999999999887655


Q ss_pred             HHHHhhcC
Q psy10346         76 VLVFNNVP   83 (292)
Q Consensus        76 ~rl~~~l~   83 (292)
                      .++++.++
T Consensus        80 kKa~k~lK   87 (102)
T 2hgc_A           80 SKAYKTIK   87 (102)
T ss_dssp             CCC-----
T ss_pred             HHHHHHHH
Confidence            55555554

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=85.09  E-value=0.8  Score=40.74  Aligned_cols=58  Identities=16%  Similarity=0.114  Sum_probs=46.3

Q ss_pred             HHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHH
Q psy10346          7 EKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQ   67 (292)
Q Consensus         7 ~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~   67 (292)
                      .+||..|.. .+.....++|+.+|++...+.+.+..|+.. |||.-....  .|.|+...-+
T Consensus        26 l~iL~~l~~~~~~~~~~eia~~~gl~kstv~r~l~tL~~~-G~v~~~~~~--~Y~lg~~~~~   84 (260)
T 2o0y_A           26 IDLLELFDAAHPTRSLKELVEGTKLPKTTVVRLVATMCAR-SVLTSRADG--SYSLGPEMLR   84 (260)
T ss_dssp             HHHHTTCBTTBSSBCHHHHHHHHCCCHHHHHHHHHHHHHT-TSEEECTTS--CEEECHHHHH
T ss_pred             HHHHHHHhhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEECCCC--eEEecHHHHH
Confidence            457777753 456788999999999999999999999987 999876433  8999876443

>2b0l_A GTP-sensing transcriptional pleiotropic repressor; CODY, DNA-binding, nucleotide-binding, transcript regulation, winged HTH motif.; 2.90A {Bacillus subtilis} SCOP: a.4.5.66

Probab=85.06  E-value=0.66  Score=35.94  Aligned_cols=47  Identities=17%  Similarity=0.239  Sum_probs=37.7

Q ss_pred             HHHHHHHhccCCCC-ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346          6 TEKILKYLDTNPPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP   53 (292)
Q Consensus         6 e~~iL~~L~~~~~~-~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~   53 (292)
                      ...|+..|..++.+ ...++|+.+|++...|..++..|++. |+|....
T Consensus        30 ~~~I~~~l~~g~~lps~~eLa~~lgVSr~tVr~al~~L~~~-GlI~~~~   77 (102)
T 2b0l_A           30 IEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESA-GVIESRS   77 (102)
T ss_dssp             HHHHTTSSBTTEEEECHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEE
T ss_pred             HHHHHhhhcCCCcCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEe
Confidence            45566555444445 77899999999999999999999987 9998766

>1tw3_A COMT, carminomycin 4-O-methyltransferase; anthracycline, methylate, tailoring enzyme, polyketide, S-adenosyl-L-homocystein; HET: SAH ERT; 2.35A {Streptomyces peucetius} SCOP: a.4.5.29 c.66.1.12 PDB: 1tw2_A*

Probab=85.01  E-value=1.3  Score=40.27  Aligned_cols=66  Identities=9%  Similarity=0.060  Sum_probs=52.3

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCCh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSH   74 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlP   74 (292)
                      ..+..|+..|. .+..+..++|+.+|+++..+.+.++-|.+. |+++...  ...|.+|+.++ ++..+.|
T Consensus        39 ~~~l~i~~~l~-~~~~t~~ela~~~~~~~~~l~r~L~~L~~~-g~~~~~~--~g~y~~t~~s~-~l~~~~~  104 (360)
T 1tw3_A           39 AATLRLVDHIL-AGARTVKALAARTDTRPEALLRLIRHLVAI-GLLEEDA--PGEFVPTEVGE-LLADDHP  104 (360)
T ss_dssp             HHHTTHHHHHH-TTCCBHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEE--TTEEEECTTGG-GGSTTST
T ss_pred             HHHhCHHHHHh-CCCCCHHHHHHHhCcCHHHHHHHHHHHHHC-CCEEecC--CCeEEeCHHHH-HHhcCCc
Confidence            45666788885 456788999999999999999999999997 9998643  34699999985 5555554

>3i53_A O-methyltransferase; CO-complex, rossmann-like fold; HET: SAH; 2.08A {Streptomyces carzinostaticus subsp} PDB: 3i58_A* 3i5u_A* 3i64_A*

Probab=84.99  E-value=0.9  Score=41.11  Aligned_cols=65  Identities=11%  Similarity=0.190  Sum_probs=53.8

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG   72 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G   72 (292)
                      ..+..|...|.+ +..+.+++|+.+|++...+-+++..|.+. |++...  ....|.+|+.++.+...+
T Consensus        25 a~~lglf~~l~~-g~~t~~elA~~~~~~~~~l~rlLr~l~~~-gl~~~~--~~~~y~~t~~s~~l~~~~   89 (332)
T 3i53_A           25 AATLRVADHIAA-GHRTAAEIASAAGAHADSLDRLLRHLVAV-GLFTRD--GQGVYGLTEFGEQLRDDH   89 (332)
T ss_dssp             HHHHTHHHHHHT-TCCBHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEC--TTSBEEECTTGGGGSTTC
T ss_pred             HHHcChHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHhC-CcEEec--CCCeEEcCHhHHHHhcCC
Confidence            456678888864 57888999999999999999999999997 998753  246799999999886554

>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A*

Probab=84.98  E-value=1.1  Score=41.38  Aligned_cols=61  Identities=10%  Similarity=0.109  Sum_probs=48.7

Q ss_pred             CC-cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeCh
Q psy10346          1 MA-SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG   63 (292)
Q Consensus         1 m~-~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTe   63 (292)
                      |. .....+||..|..++.++..++|+.+|++...|-+.++.|+.. |++...... .-|.|..
T Consensus         1 M~~~~r~~~Il~~L~~~~~~s~~eLa~~l~vS~~ti~r~l~~L~~~-G~~i~~~~g-~GY~l~~   62 (321)
T 1bia_A            1 MKDNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDW-GVDVFTVPG-KGYSLPE   62 (321)
T ss_dssp             CCCCHHHHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHT-TCCCEEETT-TEEECSS
T ss_pred             CCcchHHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHhC-CCcEEEecC-CCcEEee
Confidence            44 4677889999987777899999999999999999999999986 887543322 3677654

>3ig2_A Phenylalanyl-tRNA synthetase beta chain; phers, MCSG, structural genomics, midwest center for structural GE protein structure initiative; HET: MSE; 2.09A {Bacteroides fragilis}

Probab=84.95  E-value=0.8  Score=39.78  Aligned_cols=50  Identities=16%  Similarity=0.322  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCCC
Q psy10346        223 LMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKT  280 (292)
Q Consensus       223 l~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~  280 (292)
                      ..++.+.|+++|.++||.|+-+.+.+..+  .||.|..+.++      ++..|.+|-+
T Consensus         6 ~~~~~~~ir~~l~~~G~~Evitysf~~~~--~~~~~~~~~~~------~~v~l~NPls   55 (213)
T 3ig2_A            6 SNKLQNLVAEQLVGCGFNEILNNSLTRAA--YYDGLESYPSK------NLVMLLNPLS   55 (213)
T ss_dssp             HHHHHHHHHHHHHHTTCEECCCCSEECGG--GGTTCSSSCGG------GCEEBSSGGG
T ss_pred             HHHHHHHHHHHHHHCCCeEEeccccCCHH--HHHhhcccCcC------CeEEEeCCcc
Confidence            35789999999999999999888887554  58888765433      5677877644

>3l09_A Putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG, protein structure initiative transcription regulator; 2.81A {Jannaschia SP}

Probab=84.27  E-value=2.8  Score=38.19  Aligned_cols=62  Identities=6%  Similarity=0.010  Sum_probs=50.5

Q ss_pred             CCCCCh---HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHHHhhcCChHHHHHh
Q psy10346         16 NPPVDT---LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQVKDNGSHEVLVFN   80 (292)
Q Consensus        16 ~~~~~~---~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~yl~~GlPE~rl~~   80 (292)
                      ++.+..   ..+...+|++..+|-.++..|... |.++.++. -...|.||+.|++.+..|  ..|++.
T Consensus        40 g~~i~~~~Li~l~~~~Gi~~~avR~Al~RL~~~-G~l~~~~~Gr~~~Y~Lt~~g~~~l~~~--~~ri~~  105 (266)
T 3l09_A           40 VIEVSGVALSSFVERMGLQPQAMRVALHRLKRD-GWVESRRLGRVGFHRLSDSALTQTRAV--AGRIYG  105 (266)
T ss_dssp             CCCEEHHHHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEECHHHHHHHHTT--HHHHHS
T ss_pred             CCcccHHHHHHHHHHcCCCchHHHHHHHHHHHC-CCeeeeecCCcceEEECHHHHHHHHHH--HHHhcC
Confidence            444544   456778999999999999999986 99988653 344899999999999999  778887

>1zg3_A Isoflavanone 4'-O-methyltransferase; rossman fold, plant Pro transferase; HET: 2HI SAH; 2.35A {Medicago truncatula} PDB: 1zga_A* 1zhf_A* 1zgj_A*

Probab=84.23  E-value=1.7  Score=39.78  Aligned_cols=69  Identities=10%  Similarity=0.114  Sum_probs=53.6

Q ss_pred             HHHHHHHHHhccC-CCCChHHHHHhcCC---CHHHHHHHHHHhhccCCcEEEeee---e-----EEEEEeChhHHHHhhc
Q psy10346          4 DLTEKILKYLDTN-PPVDTLDLAKLFNE---DHQKVVGGMKSIETLGEYLIVEPL---S-----HKIWELTGEGNQVKDN   71 (292)
Q Consensus         4 ~~e~~iL~~L~~~-~~~~~~ela~~~~~---~~~~v~~~~~~L~s~~glv~~e~~---~-----~~~~~LTeEG~~yl~~   71 (292)
                      ..+..|+..|... +..+..++|+.+|+   ++..+-++++.|.+. |+++....   .     ...|.+|+.++ ++..
T Consensus        30 a~~lgif~~L~~~~~~~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~-gll~~~~~~~~~~~g~~~~~y~~t~~s~-~l~~  107 (358)
T 1zg3_A           30 AMELGIADAIHNHGKPMTLSELASSLKLHPSKVNILHRFLRLLTHN-GFFAKTIVKGKEGDEEEEIAYSLTPPSK-LLIS  107 (358)
T ss_dssp             HHHHTHHHHHHHHTSCEEHHHHHHHTTCCTTTHHHHHHHHHHHHHT-TSEEEEEECCSSSSCCCEEEEEECHHHH-TTCT
T ss_pred             HHHCChHhHHhhcCCCcCHHHHHHhcCCCCcchHHHHHHHHHHhhC-CcEEEecccccccCCCCCCEEeCCHHHH-HHhC
Confidence            4566788888653 46788999999999   588899999999997 99986510   1     47899999987 5666


Q ss_pred             CCh
Q psy10346         72 GSH   74 (292)
Q Consensus        72 GlP   74 (292)
                      +.|
T Consensus       108 ~~~  110 (358)
T 1zg3_A          108 GKP  110 (358)
T ss_dssp             TST
T ss_pred             CCC
Confidence            665

>1fp1_D Isoliquiritigenin 2'-O-methyltransferase; protein-substrate, protein-product complex; HET: SAH HCC; 1.82A {Medicago sativa} SCOP: a.4.5.29 c.66.1.12 PDB: 1fpq_A*

Probab=84.23  E-value=0.97  Score=41.78  Aligned_cols=69  Identities=7%  Similarity=0.161  Sum_probs=52.7

Q ss_pred             HHHHHHHHHhccCC-C---CChHHHHHhcCC------CHHHHHHHHHHhhccCCcEEEeee--e----EEEEEeChhHHH
Q psy10346          4 DLTEKILKYLDTNP-P---VDTLDLAKLFNE------DHQKVVGGMKSIETLGEYLIVEPL--S----HKIWELTGEGNQ   67 (292)
Q Consensus         4 ~~e~~iL~~L~~~~-~---~~~~ela~~~~~------~~~~v~~~~~~L~s~~glv~~e~~--~----~~~~~LTeEG~~   67 (292)
                      ..+..|+..|...+ .   .+..+||+.+|+      ++..+-++++.|.+. |+++....  .    ...|.+|+.++ 
T Consensus        44 a~~lgif~~L~~~g~pg~~~t~~eLA~~~~~~~~~~~~~~~l~rlLr~L~~~-gll~~~~~~~~~g~~~~~y~~t~~s~-  121 (372)
T 1fp1_D           44 AIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRMLRLLASY-SVLTSTTRTIEDGGAERVYGLSMVGK-  121 (372)
T ss_dssp             HHHTTHHHHHHTCSSTTCCBCHHHHHTTSCGGGCCTTHHHHHHHHHHHHHHT-TSEEEEEEECTTSCEEEEEEECTTGG-
T ss_pred             HHHCChHHHHHhcCCCCCCcCHHHHHHhcCCCCCCCcChHHHHHHHHHHhhC-CceEecccccCCCCcCCeEecCHHHH-
Confidence            34566778887544 4   788999999999      677899999999987 99986521  1    46899999987 


Q ss_pred             HhhcCCh
Q psy10346         68 VKDNGSH   74 (292)
Q Consensus        68 yl~~GlP   74 (292)
                      ++..+.|
T Consensus       122 ~L~~~~~  128 (372)
T 1fp1_D          122 YLVPDES  128 (372)
T ss_dssp             GGSTTCT
T ss_pred             HHhCCCC
Confidence            5656655

>3lst_A CALO1 methyltransferase; calicheamicin, enediyne, SAH, STRU genomics, PSI-2, protein structure initiative; HET: SAH; 2.40A {Micromonospora echinospora}

Probab=84.00  E-value=0.81  Score=41.93  Aligned_cols=62  Identities=15%  Similarity=0.179  Sum_probs=50.5

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN   71 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~   71 (292)
                      .+..|...|.+ +..+.+++|+.+|++...+-+++..|.+. |+++.   ....|.+|+.++.++..
T Consensus        43 ~~lglf~~l~~-g~~t~~elA~~~g~~~~~l~rlLr~l~~~-g~l~~---~~~~y~~t~~s~~l~~~  104 (348)
T 3lst_A           43 AAVGVADHLVD-GPRTPAELAAATGTDADALRRVLRLLAVR-DVVRE---SDGRFALTDKGAALRSD  104 (348)
T ss_dssp             HHHTGGGGGTT-SCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEE---ETTEEEECTTTGGGSTT
T ss_pred             HHcCchhHhhC-CCCCHHHHHHHhCcCHHHHHHHHHHHHhC-CCEEe---cCCEEecCHHHHHHhcC
Confidence            44556666653 56788999999999999999999999997 99986   45679999999887544

>2ip2_A Probable phenazine-specific methyltransferase; pyocyanin, phenazine-1-carboxy PHZM; 1.80A {Pseudomonas aeruginosa}

Probab=83.63  E-value=1.3  Score=39.89  Aligned_cols=65  Identities=9%  Similarity=0.089  Sum_probs=51.6

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCCh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSH   74 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlP   74 (292)
                      ..+..|+..|.+ +..+.+++|+.+|++...+-+.++-|.+. |++....  ...|.+|+.++.++  +.|
T Consensus        28 ~~~lgi~~~l~~-~~~t~~ela~~~~~~~~~l~r~Lr~L~~~-g~l~~~~--~~~y~~t~~s~~l~--~~~   92 (334)
T 2ip2_A           28 ATRLGLADLIES-GIDSDETLAAAVGSDAERIHRLMRLLVAF-EIFQGDT--RDGYANTPTSHLLR--DVE   92 (334)
T ss_dssp             HHHTTHHHHHHT-TCCSHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEET--TTEEEECHHHHTTS--SST
T ss_pred             HHHcCcHHHHhC-CCCCHHHHHHHhCcCHHHHHHHHHHHHhC-CceEecC--CCeEecCHHHHHHh--CCC
Confidence            345567777754 56888999999999999999999999997 9997542  25799999997554  554

>1qzz_A RDMB, aclacinomycin-10-hydroxylase; anthracycline, methyltransferase, polyketide, tailoring enzymes, structural proteomics in E spine; HET: SAM; 2.10A {Streptomyces purpurascens} SCOP: a.4.5.29 c.66.1.12 PDB: 1r00_A* 1xds_A* 1xdu_A*

Probab=83.11  E-value=0.99  Score=41.31  Aligned_cols=68  Identities=13%  Similarity=0.016  Sum_probs=51.6

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCCh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSH   74 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlP   74 (292)
                      ..+..|+..|. .+..+..++|+.+|+++..+.+.++-|.+. |++.........|.+|..++. +..+.|
T Consensus        36 ~~~l~i~~~l~-~~~~t~~eLA~~~g~~~~~l~r~Lr~L~~~-Gll~~~~~~~~~y~~t~~s~~-l~~~~~  103 (374)
T 1qzz_A           36 AATLRLVDHLL-AGADTLAGLADRTDTHPQALSRLVRHLTVV-GVLEGGEKQGRPLRPTRLGML-LADGHP  103 (374)
T ss_dssp             HHHTTHHHHHH-TTCCSHHHHHHHHTCCHHHHHHHHHHHHHT-TSEECCCC-CCCCEECTTGGG-GSTTCT
T ss_pred             HHHcChHHHHh-CCCCCHHHHHHHhCcCHHHHHHHHHHHhhC-CCEEEeCCCCeEEEEChHHHh-hcCCCc
Confidence            45666788884 466888999999999999999999999997 999753221227999999854 444443

>1stz_A Heat-inducible transcription repressor HRCA homol; circe element, structural genomics, BSGC structure FUN NIH, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.51 d.110.2.3

Probab=82.90  E-value=1.8  Score=40.51  Aligned_cols=65  Identities=22%  Similarity=0.328  Sum_probs=50.6

Q ss_pred             CcHHHHHHHH-----HhccCCCCChHHHHHhc--CCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHH
Q psy10346          2 ASDLTEKILK-----YLDTNPPVDTLDLAKLF--NEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQV   68 (292)
Q Consensus         2 ~~~~e~~iL~-----~L~~~~~~~~~ela~~~--~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~y   68 (292)
                      .+.-+++||.     +|..++++.+.++|+.+  |++...|-+.+..|+.. |++.- ....---..|+.|.++
T Consensus        15 l~eR~~~IL~~i~~~yl~~~~pV~s~~La~~~~l~VS~aTIRrDL~~LE~~-GlL~r-~HgsAgript~~g~r~   86 (338)
T 1stz_A           15 LNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYL-GYIYQ-PHTSAGRIPTDKGLRF   86 (338)
T ss_dssp             CCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHT-TSEEC-CSSCSCBEECHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCccHHHHHHHhCCCCCHHHHHHHHHHHHHC-CCEEE-ccCcceecCCcccchh
Confidence            4577889999     78888999999999998  89999999999999987 99873 2221112467777553

>3rkx_A Biotin-[acetyl-COA-carboxylase] ligase; biotin protein ligase, 3 domains, enzyme DNA binding, biotin coupling domains; 2.10A {Staphylococcus aureus} PDB: 3rir_A* 3rkw_A 3rky_A* 3v7c_A* 3v7s_A* 3v8j_A 3v7r_A 3v8k_A* 3v8l_A* 4dq2_A*

Probab=81.44  E-value=1.6  Score=40.47  Aligned_cols=57  Identities=16%  Similarity=0.172  Sum_probs=44.4

Q ss_pred             HHHHHHHHhc--cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeCh
Q psy10346          5 LTEKILKYLD--TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG   63 (292)
Q Consensus         5 ~e~~iL~~L~--~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTe   63 (292)
                      ...+||..|.  ++..++.+++|+.+|++..+|-..++.|++. |++. +.....-|.|..
T Consensus         4 ~~~~iL~~L~~~~g~~~Sg~eLa~~lgvSr~aV~k~i~~L~~~-G~~i-~~~~~~GY~L~~   62 (323)
T 3rkx_A            4 YSQDVLQLLYKNKPNYISGQSIAESLNISRTAVKKVIDQLKLE-GCKI-DSVNHKGHLLQQ   62 (323)
T ss_dssp             HHHHHHHHHHHHTTSCBCHHHHHHHHTSCHHHHHHHHHHHHHT-TCEE-EEETTTEEEEEE
T ss_pred             HHHHHHHHHHhCCCCccCHHHHHHHHCCCHHHHHHHHHHHHhc-CCeE-EEeCCCeEEEec
Confidence            4568999994  3446788999999999999999999999986 8843 333445777664

>2gqq_A Leucine-responsive regulatory protein; helix-turn-helix, transcription; 3.20A {Escherichia coli} PDB: 2l4a_A

Probab=81.39  E-value=0.35  Score=39.92  Aligned_cols=48  Identities=13%  Similarity=0.257  Sum_probs=42.8

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      ..+..+||..|..++.+...++|+.+|++...|..+++.|++. |+|..
T Consensus        12 d~l~~~Il~~l~~~~~ls~~eLa~~lgvSr~~vr~al~~L~~~-Gli~~   59 (163)
T 2gqq_A           12 DRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQ-GFIQG   59 (163)
T ss_dssp             CSHHHHHHHHHHHCSSCCTTGGGTSSSCCTTTSSSTHHHHHHH-TSEEE
T ss_pred             hHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CcEEE
Confidence            4677889998888888877899999999999999999999987 99985

>1ylf_A RRF2 family protein; structural genomics, transcription regulator, P protein structure initiative; 2.50A {Bacillus cereus atcc 14579} SCOP: a.4.5.55

Probab=81.20  E-value=1.3  Score=36.11  Aligned_cols=58  Identities=14%  Similarity=0.033  Sum_probs=44.0

Q ss_pred             HHHHHHHhcc--CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhH
Q psy10346          6 TEKILKYLDT--NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEG   65 (292)
Q Consensus         6 e~~iL~~L~~--~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG   65 (292)
                      ..++|..|..  ++.+.+.++|+.+|++...|.+.+..|... |+|...+- .--|.|+...
T Consensus        16 Al~~L~~La~~~~~~~~~~~iA~~~~i~~~~l~kil~~L~~~-Glv~s~rG-~GGy~L~~~p   75 (149)
T 1ylf_A           16 AVHILSILKNNPSSLCTSDYMAESVNTNPVVIRKIMSYLKQA-GFVYVNRG-PGGAGLLKDL   75 (149)
T ss_dssp             HHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEC----CCEEESSCG
T ss_pred             HHHHHHHHHhCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CcEEEccC-CCceEeCCCh
Confidence            3556666653  345788999999999999999999999976 99987766 6668777554

>2l02_A Uncharacterized protein; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=81.18  E-value=3.7  Score=31.12  Aligned_cols=50  Identities=14%  Similarity=0.157  Sum_probs=41.1

Q ss_pred             HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEE
Q psy10346          8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKI   58 (292)
Q Consensus         8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~   58 (292)
                      .|-.+|.+.+..+..++++..|++...|..++-||.- +|=|.+++.....
T Consensus        12 ~VW~~L~~~~~~s~~el~k~t~l~d~el~lAIGWLaR-EdKI~~~~~~~~l   61 (82)
T 2l02_A           12 KVWHALNEADGISIPELARKVNLSVESTALAVGWLAR-ENKVVIERKNGLI   61 (82)
T ss_dssp             HHHHHHHHCCSBCHHHHHHHHTCCHHHHHHHHHHHHT-TTSEEEEEETTEE
T ss_pred             HHHHHHhccCCCCHHHHHHHhCCCHHHHHHHHHHHhc-cCceeEEeeCCEE
Confidence            5677887777888899999999999999999999975 5888887654433

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

Probab=81.12  E-value=2  Score=35.19  Aligned_cols=54  Identities=9%  Similarity=0.062  Sum_probs=40.8

Q ss_pred             CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChH
Q psy10346         19 VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHE   75 (292)
Q Consensus        19 ~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE   75 (292)
                      ++-.++|..+|++++.|.+.++.|+.. |+|+....  ....+-.++.+-+..+.||
T Consensus       140 ~t~~~lA~~lg~sr~tvsR~l~~L~~~-g~I~~~~~--~i~i~d~~~L~~~~~~~~e  193 (195)
T 3b02_A          140 VSHEEIADATASIRESVSKVLADLRRE-GLIATAYR--RVYLLDLAALEREAGSALE  193 (195)
T ss_dssp             CCHHHHHHTTTSCHHHHHHHHHHHHHH-TSEEEETT--EEEECCHHHHHHHHCSCCC
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHC-CCEEecCC--EEEEeCHHHHHHHhccccc
Confidence            456899999999999999999999987 99987653  3445555665555455444

>3ica_A Phenylalanyl-tRNA synthetase beta chain; APC61692.1, phenylalanyl-tRNA SYNT beta subunit, structural genomics, PSI-2; HET: TAM; 2.44A {Porphyromonas gingivalis}

Probab=80.49  E-value=1.4  Score=38.17  Aligned_cols=51  Identities=16%  Similarity=0.275  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCCCC
Q psy10346        223 LMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS  281 (292)
Q Consensus       223 l~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~~  281 (292)
                      ..++.+.|+++|.++||.|+-+.+.+..+  +||.+..+.++      ++..|.+|-+.
T Consensus         6 ~~~~~~~ir~~L~~~G~~Evitysf~s~~--~~~~~~~~~~~------~~v~l~NPls~   56 (213)
T 3ica_A            6 RYKWQTVVSEQLVGAGFNEILNNSLTAGS--YYEGLKSHPRE------MAVELMNPLSQ   56 (213)
T ss_dssp             HHHHHHHHHHHHHHTTCEECCCCSEEEGG--GGTTCSSSCGG------GCCBCSSBSCS
T ss_pred             HHHHHHHHHHHHHHCCCceeeeccCCCHH--HHhhhcccCcC------CeEEecCCccH
Confidence            45789999999999999999888887544  78888765333      34566666443

>3szp_A Transcriptional regulator, LYSR family; winged helix-turn helix, DNA-binding, transcription factor; 2.20A {Vibrio cholerae} PDB: 3t1b_B

Probab=80.36  E-value=1.7  Score=36.80  Aligned_cols=61  Identities=10%  Similarity=0.045  Sum_probs=45.5

Q ss_pred             HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD   70 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~   70 (292)
                      .+++..+.+.+  +...-|+.+++++.+|.+.++.||..-|. ..-.+....++||++|+.++.
T Consensus         6 l~~f~~v~~~~--s~t~AA~~L~isq~avS~~i~~LE~~lg~-~Lf~R~~~~~~lT~~G~~l~~   66 (291)
T 3szp_A            6 LNLFRLVVENG--SYTSTSKKTMIPVATITRRIQALEDSLNL-RLLNRHARKLTLTEAGERFYK   66 (291)
T ss_dssp             HHHHHHHHHHS--SHHHHHHHHTCCHHHHHHHHHHHHHHHTC-CCEEEETTEEEECHHHHHHHH
T ss_pred             HHHHHHHHhcC--CHHHHHHHhCCCHHHHHHHHHHHHHHhCC-ceEeecCCCcccCHhHHHHHH
Confidence            34444554433  35677888999999999999999976444 445556778999999999874

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	292
d1jjca_	266	d.104.1.1 (A:) Phenyl-tRNA synthetase (PheRS) alph	6e-21

>d1jjca_ d.104.1.1 (A:) Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS {Thermus thermophilus [TaxId: 274]} Length = 266

class: Alpha and beta proteins (a+b)
fold: Class II aaRS and biotin synthetases
superfamily: Class II aaRS and biotin synthetases
family: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
domain: Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS
species: Thermus thermophilus [TaxId: 274]

 Score = 87.4 bits (216), Expect = 6e-21
 Identities = 31/71 (43%), Positives = 41/71 (57%), Gaps = 1/71 (1%)

Query: 212 GISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHD 271
           G SL SG LHP+  +  E  +IF  +G+  +     VES F+NFDAL  P+ HPARD  D
Sbjct: 8   GASLFSGGLHPITLMERELVEIFRALGYQAVE-GPEVESEFFNFDALNIPEHHPARDMWD 66

Query: 272 TFFVTDPKTSE 282
           TF++T      
Sbjct: 67  TFWLTGEGFRL 77

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	292
d1jjca_	266	Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS	99.92
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	97.99
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	97.41
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	97.37
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	97.37
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	97.33
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	97.31
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	97.22
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	97.19
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	97.16
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	97.15
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	97.15
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	97.03
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	96.99
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	96.98
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	96.94
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	96.78
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	96.74
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	96.62
d1xmka1	73	Z-alpha domain of dsRNA-specific adenosine deamina	96.43
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	96.43
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	96.42
d1xmaa_	103	Predicted transcriptional regulator {Clostridium t	96.26
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	96.25
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	96.21
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	96.12
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	96.11
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	95.87
d1yg2a_	178	Hypothetical protein AphA {Vibrio cholerae [TaxId:	95.73
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	95.67
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	95.53
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	95.3
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	95.19
d2esha1	114	Hypothetical protein TM0937 {Thermotoga maritima [	95.0
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	94.93
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	94.85
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	94.57
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	94.1
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	94.02
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	94.01
d1okra_	120	Methicillin resistance regulatory protein MecI {St	94.01
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	93.98
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	93.93
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	93.89
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	93.85
d1fp2a1	101	Isoflavone O-methyltransferase {Alfalfa (Medicago	93.7
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	93.62
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	93.53
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	93.43
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	93.42
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	93.29
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	93.18
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	92.38
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	92.29
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	92.22
d1sd4a_	122	Penicillinase repressor BlaI {Staphylococcus aureu	91.65
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	91.32
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	91.09
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	90.07
d1zara1	89	Rio2 serine protein kinase N-terminal domain {Arch	89.01
d2p8ta1	69	Hypothetical protein PH0730 {Pyrococcus horikoshii	88.76
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	88.59
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	88.11
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	85.99
d2esna1	89	Probable LysR-type transcriptional regulator PA047	85.66
d1zyba1	73	Probable transcription regulator BT4300, C-termina	85.42
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	84.22
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	84.21
d1j75a_	57	Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}	83.99
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	83.74
d1kyza1	107	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltra	82.9
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	82.18
d2obpa1	81	Putative DNA-binding protein ReutB4095 {Ralstonia	81.15
d1ixca1	89	LysR-type regulatory protein CbnR {Ralstonia eutro	80.84
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	80.82
d1b9ma1	127	N-terminal domain of molybdate-dependent transcrip	80.16

>d1jjca_ d.104.1.1 (A:) Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a+b)
fold: Class II aaRS and biotin synthetases
superfamily: Class II aaRS and biotin synthetases
family: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
domain: Phenyl-tRNA synthetase (PheRS) alpha subunit, PheS
species: Thermus thermophilus [TaxId: 274]

Probab=99.92  E-value=7.9e-27  Score=213.11  Aligned_cols=74  Identities=42%  Similarity=0.670  Sum_probs=70.6

Q ss_pred             CCcccCCCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCC
Q psy10346        205 PYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPK  279 (292)
Q Consensus       205 ~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~  279 (292)
                      ++|+++||+.++.|+.|||++++++|+++|.+|||+++. ||+|||+|||||+||+|||||||++|||||++++.
T Consensus         1 kiDvtlPg~~~~~G~~HPl~~~~~~i~~if~~~GF~~~~-gp~ies~~~NFDaLn~P~dHPAR~~~DTfYi~~~~   74 (266)
T d1jjca_           1 RVDVSLPGASLFSGGLHPITLMERELVEIFRALGYQAVE-GPEVESEFFNFDALNIPEHHPARDMWDTFWLTGEG   74 (266)
T ss_dssp             CCCTTSCCCCCCCCBCCHHHHHHHHHHHHHHTTTCEECC-CCSEEEHHHHTGGGTCCTTSGGGGGSCCCBEECSS
T ss_pred             CcceeCCCCCCCCCCCChHHHHHHHHHHHHHHcCCeEee-CCccccchhhhhcccCCcccchhcccceEEEeccc
Confidence            479999999999999999999999999999999999985 89999999999999999999999999999999763

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=97.99  E-value=4.6e-06  Score=62.93  Aligned_cols=74  Identities=9%  Similarity=0.060  Sum_probs=62.4

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ++.+..||..|...+..+..++|+.+|++...|.+.++.|+.. |||+.+.    .....|.||++|++.++.-.+..+
T Consensus        15 ~p~r~~IL~~L~~~~~~~~~eLa~~l~is~~~vs~~l~~L~~~-glV~~~~~~~d~r~~~~~LT~~G~~~~~~~~~~~~   92 (100)
T d1ub9a_          15 NPVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERN-GLVKTYKVIADRPRTVVEITDFGMEEAKRFLSSLK   92 (100)
T ss_dssp             SHHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEEEECSSSCEEEEEECHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHhccCCCeeHHHHHHHHhhccccccHHHHHHhhh-ceeEEEEcCcCCccccccCCHHHHHHHHHHHHHHH
Confidence            4668899999977777888999999999999999999999987 9998764    446789999999988766555444

>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=97.41  E-value=0.0002  Score=56.63  Aligned_cols=73  Identities=16%  Similarity=0.189  Sum_probs=62.1

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..|..||..|...+.++..++|..++++++.|.+.+..|+.+ |||+.+.    .-...+.||+.|++..+.-.+-.+
T Consensus        36 ~~q~~vL~~l~~~~~~t~~~la~~l~~~~~~vsr~l~~L~~~-G~v~r~~~~~D~R~~~l~lT~~G~~~~~~~~~~~~  112 (141)
T d1lnwa_          36 PPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGR-NLVRRERNPSDQRSFQLFLTDEGLAIHQHAEAIMS  112 (141)
T ss_dssp             HHHHHHHHHHHSSTTCBHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEEECSSSSSSEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCccHhHHHHHHHHHHHh-hceeeeccCCCCcchhhccCHHHHHHHHHHHHHHH
Confidence            568889999987777899999999999999999999999987 9998755    446789999999998876655444

>d2fbia1 a.4.5.28 (A:5-140) Probable transcriptional regulator PA4135 {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 PA4135
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=97.37  E-value=0.00014  Score=57.10  Aligned_cols=72  Identities=14%  Similarity=0.096  Sum_probs=60.4

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      ..+..||..|..++.....++|...++++..|.+.++.|+.+ |||+.+..    -...+.||++|++..+.-.+..
T Consensus        30 ~~q~~vL~~l~~~~~~t~~~la~~~~i~~~~vs~~i~~L~~~-gli~r~~~~~D~R~~~l~lT~~G~~~~~~~~~~~  105 (136)
T d2fbia1          30 EQQWRVIRILRQQGEMESYQLANQACILRPSMTGVLARLERD-GIVRRWKAPKDQRRVYVNLTEKGQQCFVSMSGDM  105 (136)
T ss_dssp             HHHHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEeecCccCchhhhccCHHHHHHHHHHHHHH
Confidence            457889999988778888999999999999999999999987 99987543    3477899999999887655443

>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=97.37  E-value=0.00022  Score=56.06  Aligned_cols=73  Identities=21%  Similarity=0.204  Sum_probs=62.2

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..+|..|...+..+..++|..+|+++..|.+.+..|+.+ |||....    .-...+.||+.|+.++.+-.|...
T Consensus        30 ~~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~~L~~~-gli~r~~~~~D~R~~~i~LT~~G~~~~~~~~~~~~  106 (139)
T d2a61a1          30 PAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEAD-GYLTRTPDPADRRAYFLVITRKGEEVIEKVIERRE  106 (139)
T ss_dssp             HHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEEEEECHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHhc-CeeeeeeccCCCCeEEEEECHHHHHHHHHHHHHHH
Confidence            467889999977777888999999999999999999999987 9998765    446889999999998876655554

>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=97.33  E-value=0.00024  Score=55.38  Aligned_cols=89  Identities=18%  Similarity=0.185  Sum_probs=67.2

Q ss_pred             HHHHHHHHHhccC--CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDTN--PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~--~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..|..||..|...  +.++..++|+..+++++.|.++++.|+.+ |||.....    -...+.||++|++..++-.+...
T Consensus        29 ~~q~~vL~~l~~~~~~~it~~ela~~~~~~~~~vs~~l~~L~~~-g~v~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~~~  107 (135)
T d3broa1          29 GTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIK-KLLYRKVSGKDSRQKCLKLTKKANKLETIILSYMD  107 (135)
T ss_dssp             HHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECSSCTTSEEEEECHHHHTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCCHHHHHHHHCcCHhHHHHHHHHHHHH-HHHHHHhhhhhhhhhhhcccHHHHHHHHHHHHHHH
Confidence            5678899999654  44788999999999999999999999987 99987653    35689999999998887666555


Q ss_pred             HH-hhcCCCCCChHHHhh
Q psy10346         78 VF-NNVPSEGIGQKELLA   94 (292)
Q Consensus        78 l~-~~l~~~~~~~~el~~   94 (292)
                      -+ ..+ -.+++-+|+..
T Consensus       108 ~~~~~~-~~~l~~ee~~~  124 (135)
T d3broa1         108 SDQSQM-TSGLNKEEVVF  124 (135)
T ss_dssp             HHHHHH-TTTCCHHHHHH
T ss_pred             HHHHHH-HhCCCHHHHHH
Confidence            22 222 23555555443

>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=97.31  E-value=0.00025  Score=55.73  Aligned_cols=70  Identities=14%  Similarity=0.126  Sum_probs=59.8

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCCh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSH   74 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlP   74 (292)
                      ..|..||..|..++.++..++|+.++++.+.|.+.+..|+++ |||.-+.    .-...+.||+.|+++++.=.+
T Consensus        32 ~~q~~iL~~l~~~~~~t~~~La~~l~i~~~~vs~~v~~L~~~-gli~r~~~~~D~R~~~l~lT~~G~~~~~~~~~  105 (140)
T d2etha1          32 TTELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEKR-GLVVREMDPVDRRTYRVVLTEKGKEIFGEILS  105 (140)
T ss_dssp             HHHHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHHHHHHT-TSEEEEECTTTSSCEEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeeeeecccccchhhhhcCHHHHHHHHHHHH
Confidence            567889999988888899999999999999999999999987 9999755    334789999999998764433

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=97.22  E-value=0.00016  Score=53.33  Aligned_cols=60  Identities=15%  Similarity=0.143  Sum_probs=50.4

Q ss_pred             CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHhhcCChHHH
Q psy10346         17 PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus        17 ~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      +.++..++|+.+|+++..|.+.+..|+.+ |||.-.. .-...+.||++|++++++=.|+++
T Consensus        20 ~~lt~~eLa~~l~i~~~~vs~~l~~Le~~-GlV~r~~D~R~~~i~LT~~G~~~l~~~~~~~~   80 (85)
T d3ctaa1          20 AYLTSSKLADMLGISQQSASRIIIDLEKN-GYITRTVTKRGQILNITEKGLDVLYTEFADLS   80 (85)
T ss_dssp             EECCHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEECHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCeeeecccccccceECHHHHHHHHHHHHHHH
Confidence            34788999999999999999999999987 9998733 234668999999999988777774

>d1lj9a_ a.4.5.28 (A:) Transcriptional regulator SlyA {Enterococcus faecalis [TaxId: 1351]}

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 SlyA
species: Enterococcus faecalis [TaxId: 1351]

Probab=97.19  E-value=0.00033  Score=55.55  Aligned_cols=90  Identities=19%  Similarity=0.141  Sum_probs=69.5

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHhhcCChHHHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVKDNGSHEVLVF   79 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl~~GlPE~rl~   79 (292)
                      ..|..+|..|..++.++..++|..++++++.|.+.+..|+.+ |||......    ...+.||+.|+.+.+.-.+..+-+
T Consensus        29 ~~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~~L~~~-glI~r~~~~~D~R~~~l~LT~~G~~~~~~~~~~~~~~  107 (144)
T d1lj9a_          29 RGQYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIKRLEEQ-GFIYRQEDASNKKIKRIYATEKGKNVYPIIVRENQHS  107 (144)
T ss_dssp             TTHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECSSCTTCEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHCccHhhHHHHHHHHHhh-hcccccCCCCCCCccccccCHHHHHHHHHHHHHHHHH
Confidence            457789999977777888999999999999999999999987 999876643    458899999999988777766633


Q ss_pred             hhcCCCCCChHHHhh
Q psy10346         80 NNVPSEGIGQKELLA   94 (292)
Q Consensus        80 ~~l~~~~~~~~el~~   94 (292)
                      ...--.+++.+|+..
T Consensus       108 ~~~~~~~l~~ee~~~  122 (144)
T d1lj9a_         108 NQVALQGLSEVEISQ  122 (144)
T ss_dssp             HHHHTTTCCHHHHHH
T ss_pred             HHHHHhCCCHHHHHH
Confidence            221113566655544

>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=97.16  E-value=0.00028  Score=55.34  Aligned_cols=88  Identities=11%  Similarity=0.056  Sum_probs=68.8

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChHHHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHEVLVF   79 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE~rl~   79 (292)
                      ..+..||..|..++.++..++|...+++...|.+.++.|+.+ |||..+..    -...+.||++|+.+.++-.|-..-+
T Consensus        33 ~~q~~vL~~l~~~~~~t~~~La~~~~i~~~~vsr~i~~L~~~-glv~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~~~~~  111 (137)
T d1z91a1          33 YPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPMLKRMEQQ-GLITRKRSEEDERSVLISLTEDGALLKEKAVDIPGTI  111 (137)
T ss_dssp             HHHHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHHHHHHHH-TSEECCBCSSCTTSBEEEECHHHHSGGGGTTTHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHhhc-cceEEeecCCCCCeEEEEECHHHHHHHHHHHHHHHHH
Confidence            568899999977777888999999999999999999999987 99987544    3367899999999988877754433


Q ss_pred             hhcCCCCCChHHHhh
Q psy10346         80 NNVPSEGIGQKELLA   94 (292)
Q Consensus        80 ~~l~~~~~~~~el~~   94 (292)
                      ..+.  +.+.+|+..
T Consensus       112 ~~~~--~~~~ee~~~  124 (137)
T d1z91a1         112 LGLS--KQSGEDLKQ  124 (137)
T ss_dssp             HHHT--CCCTHHHHH
T ss_pred             HHHh--CCCHHHHHH
Confidence            3332  455555444

>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {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: Putative transcriptional regulator YusO
species: Bacillus subtilis [TaxId: 1423]

Probab=97.15  E-value=0.00024  Score=55.99  Aligned_cols=89  Identities=12%  Similarity=0.052  Sum_probs=67.3

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHhhcCChHHH-H
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVKDNGSHEVL-V   78 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl~~GlPE~r-l   78 (292)
                      ..+..||..|...+..+..++|...++++..|.+.++.|+.+ |||.-....    ...+.||++|+++++.=.+... .
T Consensus        35 ~~q~~iL~~l~~~~~~t~~~la~~~~i~~~~vs~~l~~L~~~-glv~r~~~~~D~R~~~v~lT~~G~~~~~~~~~~~~~~  113 (143)
T d1s3ja_          35 PAQLFVLASLKKHGSLKVSEIAERMEVKPSAVTLMADRLEQK-NLIARTHNTKDRRVIDLSLTDEGDIKFEEVLAGRKAI  113 (143)
T ss_dssp             HHHHHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEEECSSCTTSEEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHHHHHHHh-hhheeeeecCCCCceEEEECHHHHHHHHHHHHHHHHH
Confidence            567889999977767788999999999999999999999987 999865443    3678999999999876555544 2


Q ss_pred             HhhcCCCCCChHHHhh
Q psy10346         79 FNNVPSEGIGQKELLA   94 (292)
Q Consensus        79 ~~~l~~~~~~~~el~~   94 (292)
                      +..+- .+++-+|+..
T Consensus       114 ~~~~~-~~l~~~e~~~  128 (143)
T d1s3ja_         114 MARYL-SFLTEEEMLQ  128 (143)
T ss_dssp             HHHHH-TTSCHHHHHH
T ss_pred             HHHHH-hCCCHHHHHH
Confidence            22221 2455555544

>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=97.15  E-value=0.00031  Score=55.26  Aligned_cols=71  Identities=13%  Similarity=0.131  Sum_probs=60.9

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHE   75 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE   75 (292)
                      ..|..+|..|...+.++..++|...++++++|.+.+..|+.+ |+|+-...    -...+.||++|+...+.-.|.
T Consensus        34 ~~q~~vL~~l~~~~~~t~~ela~~~~i~~~~vs~~v~~L~~~-glv~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~  108 (138)
T d1jgsa_          34 AAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCK-GWVERLPNPNDKRGVLVKLTTGGAAICEQCHQL  108 (138)
T ss_dssp             HHHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECTTCSSCEEEEECHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhHHhCcCCCHHHHHHHHCCCHhHHHHHHHHHhhC-CCEEEeeccCCCCeeEEEECHHHHHHHHHHHHH
Confidence            567889999977777889999999999999999999999987 99986543    346899999999998776665

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

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 SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.03  E-value=0.00049  Score=53.83  Aligned_cols=73  Identities=14%  Similarity=0.157  Sum_probs=57.7

Q ss_pred             HHHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeE----EEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSH----KIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~----~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..+..+|..|.. ++..+..++|...+++++.|.+.++.|+.+ |+|.......    ..+.||++|+++++.-.+...
T Consensus        31 ~~~~~~L~~l~~~~~~~t~~~la~~l~i~~~~vs~~l~~L~~~-glI~~~~~~~D~R~~~l~lT~~G~~~~~~~~~~~~  108 (140)
T d3deua1          31 QTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDK-GLISRQTCASDRRAKRIKLTEKAEPLIAEMEEVIH  108 (140)
T ss_dssp             HHHHHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEC--------CEEEECGGGHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCccHHHHHHHHCCCHhHHHHHHHHHHhC-CCEEecccCCCCCceeeEECHHHHHHHHHHHHHHH
Confidence            467789998865 455778999999999999999999999987 9998655433    579999999999876555543

>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=96.99  E-value=0.00079  Score=52.39  Aligned_cols=89  Identities=16%  Similarity=0.091  Sum_probs=66.2

Q ss_pred             HHHHHHHHHhccCC-CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHhhcCChHHH-
Q psy10346          4 DLTEKILKYLDTNP-PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVKDNGSHEVL-   77 (292)
Q Consensus         4 ~~e~~iL~~L~~~~-~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl~~GlPE~r-   77 (292)
                      ..+..+|..|...+ .++..++|..+++++..|.+.++.|+.+ |+|+.....    ...+.||++|++.+++-.|... 
T Consensus        28 ~~q~~iL~~l~~~~~~~t~~~la~~~~~~~~~vs~~v~~L~~~-gli~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~~~~  106 (137)
T d2fbha1          28 QARWLVLLHLARHRDSPTQRELAQSVGVEGPTLARLLDGLESQ-GLVRRLAVAEDRRAKHIVLTPKADVLIADIEAIAAS  106 (137)
T ss_dssp             TTHHHHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEECCBTTBCSCEEEECTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHHc-CCccccCCCCCCCchhhhcCHHHHHHHHHHHHHHHH
Confidence            35778888886443 4778999999999999999999999987 999976543    3578999999999877666555 


Q ss_pred             HHhhcCCCCCChHHHhh
Q psy10346         78 VFNNVPSEGIGQKELLA   94 (292)
Q Consensus        78 l~~~l~~~~~~~~el~~   94 (292)
                      +...+- .+++-+|+..
T Consensus       107 ~~~~~~-~~l~~~e~~~  122 (137)
T d2fbha1         107 VRNDVL-TGIDESEQAL  122 (137)
T ss_dssp             HHHHHT-TTCCHHHHHH
T ss_pred             HHHHHH-hCCCHHHHHH
Confidence            222221 3556555444

>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=96.98  E-value=0.001  Score=52.47  Aligned_cols=71  Identities=13%  Similarity=0.071  Sum_probs=57.2

Q ss_pred             HHHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChH
Q psy10346          4 DLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHE   75 (292)
Q Consensus         4 ~~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE   75 (292)
                      ..+..||..|.. ++.++..++|...|+++..|.+.++.|+.+ |||.-...    -...+.||+.|++.++.-.+.
T Consensus        34 ~~q~~vL~~L~~~~g~~t~~~La~~~~~~~~~vs~~i~~L~~~-glv~r~~~~~DrR~~~i~LT~~G~~~~~~~~~~  109 (145)
T d2hr3a1          34 FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERG-GLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAK  109 (145)
T ss_dssp             HHHHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEEC------CCEEEECHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHc-CCeEeeeCccchhHHHhccCHHHHHHHHHHHHH
Confidence            567889999954 456889999999999999999999999987 99986443    346899999999987654443

>d2bv6a1 a.4.5.28 (A:5-140) Transcriptional regulator MgrA {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: Transcriptional regulator MgrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.94  E-value=0.00038  Score=54.53  Aligned_cols=70  Identities=17%  Similarity=0.159  Sum_probs=58.9

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCCh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSH   74 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlP   74 (292)
                      ..|..||..|..++..+..++|..++++.+.+.+.++.|+.+ |||+.+..    -...+.||+.|++....-.+
T Consensus        34 ~~q~~vL~~i~~~~~~t~~~la~~l~~~~~~~s~~l~~L~~~-Gli~r~~~~~D~R~~~l~lT~~G~~~~~~~~~  107 (136)
T d2bv6a1          34 YPQFLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQV-DLIKRERSEVDQREVFIHLTDKSETIRPELSN  107 (136)
T ss_dssp             HHHHHHHHHHHHSSEEEHHHHHHHTTCCTTTHHHHHHHHHHT-TSEEEEECSSSTTCEEEEECHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHCCCHhHHHHHHHHHHHC-CCEEEeecCCcccchhhccCHHHHHHHHHHHH
Confidence            467889999987778888999999999999999999999987 99987544    34688999999987665443

>d1p4xa1 a.4.5.28 (A:1-125) Staphylococcal accessory regulator A homolog, SarS {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: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.78  E-value=0.00047  Score=53.81  Aligned_cols=73  Identities=10%  Similarity=0.008  Sum_probs=60.4

Q ss_pred             HHHHHHHHHhcc--CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346          4 DLTEKILKYLDT--NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL   77 (292)
Q Consensus         4 ~~e~~iL~~L~~--~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r   77 (292)
                      ..|..||..|..  ++.++..++|...+++...|.+.++.|+.+ |+|.-..    .-...+.||++|++++++-.++..
T Consensus        34 ~~q~~iL~~l~~~~~~~~t~~eia~~~~~~~~~vs~~l~~L~~~-g~v~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~~~  112 (125)
T d1p4xa1          34 IKEFILLTYLFHQQENTLPFKKIVSDLCYKQSDLVQHIKVLVKH-SYISKVRSKIDERNTYISISEEQREKIAERVTLFD  112 (125)
T ss_dssp             HHHHHHHHHHHSCSCSEEEHHHHHHHSSSCGGGTHHHHHHHHHT-TSCEEEECSSSTTSEEEECCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCCcCHHHHHHHhCCCcchHHHHHHHHHHC-CCceeecccCCCCeEEEEECHHHHHHHHHHHHHHH
Confidence            468889999954  345678999999999999999999999987 9998866    446889999999999877666543

>d1p4xa2 a.4.5.28 (A:126-250) Staphylococcal accessory regulator A homolog, SarS {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: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.74  E-value=0.0011  Score=51.88  Aligned_cols=72  Identities=15%  Similarity=0.155  Sum_probs=58.3

Q ss_pred             HHHHHHHHHhcc--CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHH
Q psy10346          4 DLTEKILKYLDT--NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         4 ~~e~~iL~~L~~--~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      ..|..||..|..  ++.+...++|+.+++++..|.+.+..|+.+ |+|.-..    .-...+.||++|++++++=.|+.
T Consensus        33 ~~q~~vL~~l~~~~~~~~~~~~ia~~l~~~~~~vs~~v~~L~~~-glV~r~~~~~D~R~v~i~LT~~G~~~~~~l~~~~  110 (125)
T d1p4xa2          33 FVEFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQ-GYLIKERSTEDERKILIHMDDAQQDHAEQLLAQV  110 (125)
T ss_dssp             HHHHHHHHHHHTTTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHH-TSSEEEECSSSTTCEEEECCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCCCccHHHHHHHHCCCcchHHHHHHHHHhc-cCEeeeecCCCCCeEEEEECHHHHHHHHHHHHHH
Confidence            468889999943  345677899999999999999999999987 9997643    33678899999999887655553

>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=96.62  E-value=0.0011  Score=53.99  Aligned_cols=67  Identities=19%  Similarity=0.051  Sum_probs=55.3

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhc
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDN   71 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~   71 (292)
                      ..|..||..|..++.++..++|...+++...|.++++.|+.+ |||..+.    .-...+.||++|++.+.+
T Consensus        41 ~~q~~vL~~l~~~~~~t~~~la~~~~l~~~tvs~~i~rL~~~-gli~r~~~~~D~R~~~l~lT~~G~~~~~~  111 (162)
T d2fxaa1          41 INEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFSKKLEER-GYLRFSKRLNDKRNTYVQLTEEGTEVFWS  111 (162)
T ss_dssp             HHHHHHHHHHHHHTSEEHHHHHHHTTCCHHHHHHHHHHHHHH-TSEEEECC------CEEEECHHHHHHHHH
T ss_pred             HHHHHHHhhhccCCCcCHHHHHHHHcCCchhhHHHHHHHHHC-CCceeecccccCeeeeeccCHhHHHHHHH
Confidence            457789999977777788999999999999999999999987 9998644    335578999999987754

>d1xmka1 a.4.5.19 (A:294-366) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.43  E-value=0.0016  Score=46.93  Aligned_cols=65  Identities=22%  Similarity=0.282  Sum_probs=56.9

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHH-HHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQ-KVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~-~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl   69 (292)
                      +.+.+||.+|.+.+...+..||+.+|++.. +|-+++.+|+.. |.|.-+...--.|.||+.+++.+
T Consensus         5 d~eekI~~~L~~~g~~~Al~iak~lGl~kakeVN~~LY~L~k~-g~v~k~~~tPP~W~L~~~~~Er~   70 (73)
T d1xmka1           5 EIKEKICDYLFNVSDSSALNLAKNIGLTKARDINAVLIDMERQ-GDVYRQGTTPPIWHLTDKKRERM   70 (73)
T ss_dssp             HHHHHHHHHHHHTCCEEHHHHHHHHCGGGHHHHHHHHHHHHHT-TSEEEECSSSCEEEECHHHHTTT
T ss_pred             HHHHHHHHHHHHcCCchHHHHHHHhCCCcHHHHhHHHHHHHHC-CCeecCCCCCCceeeecchhhhh
Confidence            578899999998888888999999999984 799999999976 99887777777999999998754

>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=96.43  E-value=0.00059  Score=52.44  Aligned_cols=71  Identities=11%  Similarity=0.093  Sum_probs=57.1

Q ss_pred             HHHHHHHHHhcc--CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChH
Q psy10346          4 DLTEKILKYLDT--NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHE   75 (292)
Q Consensus         4 ~~e~~iL~~L~~--~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE   75 (292)
                      ..|..||..|..  ++.+...++|...++++..|.+.++.|+.+ |||.-..    .-...+.||+.|++++++-.|+
T Consensus        33 ~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~tvs~~i~~Le~~-gli~r~~~~~D~R~~~i~LT~~G~~~~~~~~~~  109 (115)
T d2frha1          33 FEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQE-DYFDKKRNEHDERTVLILVNAQQRKKIESLLSR  109 (115)
T ss_dssp             HHHHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHT-TSSCCBCCSSSSCCCEEECCSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCCCHHHHHHHHCCCHhHHHHHHHHHHhh-hhheeeecccCCceEEEEECHHHHHHHHHHHHH
Confidence            457888888854  334678899999999999999999999987 9997643    3357789999999988765554

>d1r7ja_ a.4.5.49 (A:) Sso10a (SSO10449) {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Archaeal DNA-binding protein
domain: Sso10a (SSO10449)
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=96.42  E-value=0.0038  Score=46.53  Aligned_cols=61  Identities=16%  Similarity=0.132  Sum_probs=50.4

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN   71 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~   71 (292)
                      +-..||.++.++  +....+....|+++..+...+..|.++ |+|+.   ....|.||+.|+++++.
T Consensus         7 Ii~DIL~~~~~g--~~kT~i~~~aNLs~~~~~kyl~~L~~~-GLI~~---~~~~Y~iT~kG~~~L~~   67 (90)
T d1r7ja_           7 IIQAILEACKSG--SPKTRIMYGANLSYALTGRYIKMLMDL-EIIRQ---EGKQYMLTKKGEELLED   67 (90)
T ss_dssp             HHHHHHHHHTTC--BCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEE---ETTEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHhCC--CCccHHHHHcCCCHHHHHHHHHHHHHC-CCeee---cCCEEEECccHHHHHHH
Confidence            345788888644  356788889999999999999999987 99963   45789999999999853

>d1xmaa_ a.4.5.61 (A:) Predicted transcriptional regulator {Clostridium thermocellum [TaxId: 1515]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PadR-like
domain: Predicted transcriptional regulator
species: Clostridium thermocellum [TaxId: 1515]

Probab=96.26  E-value=0.0053  Score=46.29  Aligned_cols=66  Identities=14%  Similarity=0.130  Sum_probs=49.9

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHh--------cCCCHHHHHHHHHHhhccCCcEEEeee------eEEEEEeChhHHHHh
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKL--------FNEDHQKVVGGMKSIETLGEYLIVEPL------SHKIWELTGEGNQVK   69 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~--------~~~~~~~v~~~~~~L~s~~glv~~e~~------~~~~~~LTeEG~~yl   69 (292)
                      .++.-||..|..+. ..-.++.+.        .++++.+|-.+++.|+.+ |+|+.+..      .++.|.+|+.|++++
T Consensus         7 ~l~~~IL~lL~~~~-~~GYei~~~l~~~~~~~~~is~gslY~~L~rLe~~-GlI~~~~~~~~~g~~rk~Y~iT~~G~~~l   84 (103)
T d1xmaa_           7 YVDTIILSLLIEGD-SYGYEISKNIRIKTDELYVIKETTLYSAFARLEKN-GYIKSYYGEETQGKRRTYYRITPEGIKYY   84 (103)
T ss_dssp             THHHHHHHHHHHCC-EEHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHT-TSEEEEEEEEC--CEEEEEEECHHHHHHH
T ss_pred             cHHHHHHHHHhhCC-ccHHHHHHHHHHHcCCeecCCCCchHHHHHHHHHC-CCeEEEeeccCCCCCceEEEECHHHHHHH
Confidence            46778999997643 333555443        358899999999999987 99986533      367899999999988


Q ss_pred             hc
Q psy10346         70 DN   71 (292)
Q Consensus        70 ~~   71 (292)
                      .+
T Consensus        85 ~~   86 (103)
T d1xmaa_          85 KQ   86 (103)
T ss_dssp             HH
T ss_pred             HH
Confidence            64

>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=96.25  E-value=0.0031  Score=43.70  Aligned_cols=60  Identities=10%  Similarity=0.119  Sum_probs=47.2

Q ss_pred             CC-cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346          1 MA-SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT   62 (292)
Q Consensus         1 m~-~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT   62 (292)
                      |- .....+||..|.+++.++..++|+.+|++...|-+.+..|++. |+.. +.....-|+|+
T Consensus         1 Mk~~~~~~~iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~-G~~I-~~~~g~GY~L~   61 (63)
T d1biaa1           1 MKDNTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDW-GVDV-FTVPGKGYSLP   61 (63)
T ss_dssp             CCCCHHHHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHT-TCCC-EEETTTEEECS
T ss_pred             CCccHHHHHHHHHHHHCCcCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCcE-EEeCCCeEEeC
Confidence            44 4677899999988888899999999999999999999999986 8732 22222346664

>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=96.21  E-value=0.0043  Score=42.81  Aligned_cols=49  Identities=18%  Similarity=0.240  Sum_probs=45.0

Q ss_pred             CCcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346          1 MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI   50 (292)
Q Consensus         1 m~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~   50 (292)
                      |-....++||..|..++.....++|+.+|++.+.|..-++.|++. |+|.
T Consensus         2 ~lD~~D~~IL~~L~~~~r~s~~eiA~~l~ls~~~v~~Ri~rL~~~-GiI~   50 (63)
T d2cg4a1           2 LIDNLDRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQA-GIIT   50 (63)
T ss_dssp             CCCHHHHHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHHHHH-TSEE
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeE
Confidence            445788999999999888999999999999999999999999987 9987

>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=96.12  E-value=0.0058  Score=42.21  Aligned_cols=47  Identities=11%  Similarity=0.247  Sum_probs=43.8

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI   50 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~   50 (292)
                      .....+||..|..++.....++|+.+|++.+.|..-++.|+.. |+|.
T Consensus         4 D~~D~~IL~~L~~n~r~s~~~iA~~lgis~~tv~~Ri~~L~~~-giI~   50 (63)
T d2cfxa1           4 DQIDLNIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQLESF-GIIK   50 (63)
T ss_dssp             CHHHHHHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEE
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCee
Confidence            5788999999999999999999999999999999999999987 9986

>d1hsja1 a.4.5.28 (A:373-487) Staphylococcal accessory regulator A homolog, SarR {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: Staphylococcal accessory regulator A homolog, SarR
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.11  E-value=0.0014  Score=50.23  Aligned_cols=67  Identities=12%  Similarity=0.040  Sum_probs=54.6

Q ss_pred             HHHHHHHHHhc--cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe----eeeEEEEEeChhHHHHhhc
Q psy10346          4 DLTEKILKYLD--TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE----PLSHKIWELTGEGNQVKDN   71 (292)
Q Consensus         4 ~~e~~iL~~L~--~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e----~~~~~~~~LTeEG~~yl~~   71 (292)
                      ..|..||..|.  .++.++..++|..++++...|.+.++.|+.+ |||.-+    ..-...+.||++|++.++.
T Consensus        32 ~~q~~vL~~l~~~~~~~~t~~ela~~l~~~~~~vs~~i~~Le~~-gli~r~~~~~D~R~~~i~LT~~G~~~~~~  104 (115)
T d1hsja1          32 YEEIYILNHILRSESNEISSKEIAKCSEFKPYYLTKALQKLKDL-KLLSKKRSLQDERTVIVYVTDTQKANIQK  104 (115)
T ss_dssp             HHHHHHHHHHHTCSCSEEEHHHHHHSSCCCHHHHHHHHHHHHTT-TTSCCEECCSSSSCCEEECCSSHHHHHHH
T ss_pred             HHHHHHHHHHHccCCCCcCHHHHHHHHCCChhhHHHHHHHHHHc-CCeEEEeecCCCceEEEEECHHHHHHHHH
Confidence            46778898885  3445788999999999999999999999987 998743    3345788999999998753

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}

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 DR1159
species: Deinococcus radiodurans [TaxId: 1299]

Probab=95.87  E-value=0.0012  Score=54.02  Aligned_cols=73  Identities=11%  Similarity=-0.011  Sum_probs=58.5

Q ss_pred             HHHHHHHHHhccC---CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHhhcCChHH
Q psy10346          4 DLTEKILKYLDTN---PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVKDNGSHEV   76 (292)
Q Consensus         4 ~~e~~iL~~L~~~---~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl~~GlPE~   76 (292)
                      ..|..||..|...   +.+...++|..+++++..|.+.+..|+.+ |+|+-....    ...+.||+.|++.+..-.|..
T Consensus        62 ~~q~~vL~~L~~~~~~~~lt~~eLa~~l~i~~~tvsr~l~~Le~~-GlV~r~~~~~DrR~~~i~LT~~G~~l~~~~~~~~  140 (172)
T d2fbka1          62 AAGWDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRIVRLLEK-GLIERREDERDRRSASIRLTPQGRALVTHLLPAH  140 (172)
T ss_dssp             HHHHHHHHHHHHHCCSSCBCHHHHHHHCSCCSGGGSSHHHHHHHH-TSEECCC-------CCBEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhCCCCCcCHHHHHHHHCcCHhHHHHHHHHHHhC-CCeeeeccccchhhHHhhcCHHHHHHHHHHHHHH
Confidence            5677899888532   23688999999999999999999999987 999976543    566899999999988777666


Q ss_pred             H
Q psy10346         77 L   77 (292)
Q Consensus        77 r   77 (292)
                      .
T Consensus       141 ~  141 (172)
T d2fbka1         141 L  141 (172)
T ss_dssp             H
T ss_pred             H
Confidence            5

>d1yg2a_ a.4.5.61 (A:) Hypothetical protein AphA {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PadR-like
domain: Hypothetical protein AphA
species: Vibrio cholerae [TaxId: 666]

Probab=95.73  E-value=0.0075  Score=49.06  Aligned_cols=64  Identities=22%  Similarity=0.323  Sum_probs=47.9

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhc--------CCCHHHHHHHHHHhhccCCcEEEee------eeEEEEEeChhHHHHhh
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLF--------NEDHQKVVGGMKSIETLGEYLIVEP------LSHKIWELTGEGNQVKD   70 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~--------~~~~~~v~~~~~~L~s~~glv~~e~------~~~~~~~LTeEG~~yl~   70 (292)
                      +.+-||..|..+ +..-.++.+.+        ++++..|-.+++.|+.. |+|+.+.      ..++.|.+|++|++.+.
T Consensus         2 l~~~iLg~L~~~-~~~GYei~~~~~~~~~~~w~~s~g~iY~~L~kLe~~-Gli~~~~~~~~~~~~rk~Y~iT~~Gr~~l~   79 (178)
T d1yg2a_           2 LPHVILTVLSTR-DATGYDITKEFSASIGYFWKASHQQVYRELNKMGEQ-GLVTCVLEPQEGKPDRKVYSITQAGRSALG   79 (178)
T ss_dssp             HHHHHHHHHHHC-CBCHHHHHHHHTTGGGGTCCCCHHHHHHHHHHHHHT-TSEEECCC---------CEEECHHHHHHHH
T ss_pred             HHHHHHHHHhhC-CCCHHHHHHHHHHHhCCccCCCCCcHHHHHHHHHHC-CCeEEEeeecCCCCCceEEEECHHHHHHHH
Confidence            567899999764 34556665544        68899999999999987 9998743      25678999999999874

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein PH1932
domain: Hypothetical protein PH1932
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=95.67  E-value=0.01  Score=48.54  Aligned_cols=62  Identities=19%  Similarity=0.274  Sum_probs=53.0

Q ss_pred             CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee------EEEEEeChhH
Q psy10346          2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS------HKIWELTGEG   65 (292)
Q Consensus         2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~------~~~~~LTeEG   65 (292)
                      +++...+||..|. .++.+..++|+.+|+++.+|..-++.|+.. |+|.+....      ...|.+|..+
T Consensus        17 ~~p~R~~Il~~L~-~~~~s~~ela~~lg~s~~~v~~hl~~L~~~-glv~~~~~~~~~g~~~k~y~~~~~~   84 (190)
T d1ulya_          17 LEDTRRKILKLLR-NKEMTISQLSEILGKTPQTIYHHIEKLKEA-GLVEVKRTEMKGNLVEKYYGRTADV   84 (190)
T ss_dssp             HSHHHHHHHHHHT-TCCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEEEEETTEEEEEEEESSSE
T ss_pred             CCHHHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeEEEEeeccCCcceEEEEEcccc
Confidence            4577889999996 567788999999999999999999999986 999886554      5789999765

>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=95.53  E-value=0.018  Score=43.21  Aligned_cols=61  Identities=11%  Similarity=0.076  Sum_probs=49.8

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEG   65 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG   65 (292)
                      ..|.+|+.+|...+..+..++|+.+|++...|.+++..|+++ |+|.....    ....|..|+-+
T Consensus        20 ~~e~~v~~~L~~~g~~t~~eia~~~~i~~~~v~~~l~~L~~~-GlV~r~~~~~~~r~~~~~a~~~~   84 (109)
T d1sfxa_          20 PSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKR-GFVRREIVEKGWVGYIYSAEKPE   84 (109)
T ss_dssp             HHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEEESSSEEEEEEECCHH
T ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHhCCCcchHHHHHHHHHhC-CCEEEEeccCCCccccccCCCHH
Confidence            567888888887888899999999999999999999999987 99975432    23456777544

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=95.30  E-value=0.015  Score=45.18  Aligned_cols=62  Identities=13%  Similarity=0.161  Sum_probs=51.5

Q ss_pred             HHHHHHHHHhc-cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe----eeeEEEEEeChhHH
Q psy10346          4 DLTEKILKYLD-TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE----PLSHKIWELTGEGN   66 (292)
Q Consensus         4 ~~e~~iL~~L~-~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e----~~~~~~~~LTeEG~   66 (292)
                      ..+.+|+..|- .+++.+..++|+.+|++.++|.+.+..|+.+ |+|...    ......+.+|+.|.
T Consensus        26 ~~~~~i~~~L~~~~~plt~~ela~~l~vsk~~vs~~l~~L~~~-GlV~r~~~~~drr~~~~~~t~~g~   92 (151)
T d1ku9a_          26 KSVGAVYAILYLSDKPLTISDIMEELKISKGNVSMSLKKLEEL-GFVRKVWIKGERKNYYEAVDGFSS   92 (151)
T ss_dssp             HHHHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEECCTTCSSCEEEECCHHHH
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHhCCCcchHHHHHHHHHHC-CCEEEEEcCCCCceeEEeCCHHHH
Confidence            45678888884 4455788999999999999999999999987 999865    34557889999996

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.19  E-value=0.0099  Score=40.56  Aligned_cols=46  Identities=17%  Similarity=0.216  Sum_probs=42.3

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI   50 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~   50 (292)
                      ..+.+||..|..++.....++|..+|++.+.|..-++.|+.. |+|.
T Consensus         3 ~~D~kIl~~L~~n~r~s~~~lA~~~gls~~~v~~Ri~~L~~~-giI~   48 (60)
T d1i1ga1           3 ERDKIILEILEKDARTPFTEIAKKLGISETAVRKRVKALEEK-GIIE   48 (60)
T ss_dssp             SHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHH-TSSC
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeE
Confidence            467899999999999999999999999999999999999987 8874

>d2esha1 a.4.5.61 (A:4-117) Hypothetical protein TM0937 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PadR-like
domain: Hypothetical protein TM0937
species: Thermotoga maritima [TaxId: 2336]

Probab=95.00  E-value=0.019  Score=43.82  Aligned_cols=65  Identities=20%  Similarity=0.271  Sum_probs=47.2

Q ss_pred             HHHHHHHHhccCCCCChHHHHHhc---------CCCHHHHHHHHHHhhccCCcEEEeeee-----EEEEEeChhHHHHhh
Q psy10346          5 LTEKILKYLDTNPPVDTLDLAKLF---------NEDHQKVVGGMKSIETLGEYLIVEPLS-----HKIWELTGEGNQVKD   70 (292)
Q Consensus         5 ~e~~iL~~L~~~~~~~~~ela~~~---------~~~~~~v~~~~~~L~s~~glv~~e~~~-----~~~~~LTeEG~~yl~   70 (292)
                      ++.-||..|..+ +..-.++.+.+         .+++.+|-.+++.|+.+ |+|+.+..+     ++.|.+|++|++++.
T Consensus        11 l~~~iL~lL~~~-~~~GYei~~~i~~~~~~~~~~~~~gtiY~~L~rLe~~-G~I~~~~~~~~g~~rk~Y~IT~~G~~~l~   88 (114)
T d2esha1          11 LASTILLLVAEK-PSHGYELAERLAEFGIEIPGIGHMGNIYRVLADLEES-GFLSTEWDTTVSPPRKIYRITPQGKLYLR   88 (114)
T ss_dssp             HHHHHHHHHHHS-CBCHHHHHHHHHTTCCSSTTCCCCCCHHHHHHHHHHT-TSEEEEEECSSSSCEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHhcC-CccHHHHHHHHHHhcCCCcccCCCCcHHHHHHHHHHC-CCeEEEeecCCCCCcEEEEECHHHHHHHH
Confidence            456688888664 33445555532         23467899999999987 999876553     478999999999885


Q ss_pred             c
Q psy10346         71 N   71 (292)
Q Consensus        71 ~   71 (292)
                      +
T Consensus        89 ~   89 (114)
T d2esha1          89 E   89 (114)
T ss_dssp             H
T ss_pred             H
Confidence            3

>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=94.93  E-value=0.033  Score=41.47  Aligned_cols=63  Identities=14%  Similarity=0.276  Sum_probs=48.2

Q ss_pred             HHHHHHHHHh-ccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee-------EEEEEeChhHHH
Q psy10346          4 DLTEKILKYL-DTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS-------HKIWELTGEGNQ   67 (292)
Q Consensus         4 ~~e~~iL~~L-~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~-------~~~~~LTeEG~~   67 (292)
                      ..+..||..| ..+++++..++|..+|++...|.+.+..|+++ |+|.-....       ...|..++++.+
T Consensus        21 ~~~~~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~l~~L~~~-GlV~r~~~~~d~rg~~~~~~~~~~~~~~   91 (109)
T d2d1ha1          21 DTDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIEL-GLVVRTKTEGKKIGRPKYYYSISSNILE   91 (109)
T ss_dssp             HHHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEC-------CCEEEEECTTHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHCccHhHHHHHHHHHHHC-CCEEEeecCCCCCceeEEEeeCCHHHHH
Confidence            5678889877 45667888999999999999999999999987 999765432       233455555544

>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=94.85  E-value=0.015  Score=39.45  Aligned_cols=46  Identities=11%  Similarity=0.243  Sum_probs=42.2

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI   50 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~   50 (292)
                      +...+||..|..++.....++|..+|++...|..-++.|+.. |+|.
T Consensus         3 ~~D~~Il~~L~~n~r~s~~eiA~~l~ls~~~v~~Ri~~L~~~-giI~   48 (60)
T d2cyya1           3 EIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRES-GVIK   48 (60)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHH-TSSC
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeE
Confidence            567899999999888999999999999999999999999987 8875

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=94.57  E-value=0.047  Score=40.52  Aligned_cols=62  Identities=18%  Similarity=0.221  Sum_probs=51.6

Q ss_pred             CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee-EEEEEeChhH
Q psy10346          2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS-HKIWELTGEG   65 (292)
Q Consensus         2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~-~~~~~LTeEG   65 (292)
                      +++...+||..|.. ++.+..++|+.+|+++..|..-++.|+.. |+|+.++.- ..+|.|+++.
T Consensus        21 ~~p~Rl~Il~~L~~-~~~~v~ela~~l~is~stvS~HL~~L~~a-glV~~~r~G~~~~Y~l~~~~   83 (98)
T d1r1ta_          21 ADPNRLRLLSLLAR-SELCVGDLAQAIGVSESAVSHQLRSLRNL-RLVSYRKQGRHVYYQLQDHH   83 (98)
T ss_dssp             CCHHHHHHHHHHTT-CCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEESSHH
T ss_pred             CCHHHHHHHHHHHc-CCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CceEEEEECCEEEEEEChHH
Confidence            46777889998864 55788999999999999999999999986 999986554 4568898765

>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=94.10  E-value=0.031  Score=38.36  Aligned_cols=47  Identities=21%  Similarity=0.293  Sum_probs=38.0

Q ss_pred             HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL   54 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~   54 (292)
                      +.|+.+...++.+.+.++|+.+|+++.+|..+++.|+.. |||+.+.-
T Consensus        10 k~I~~l~~~~~~v~~~~iA~~L~vs~~SVs~mikrL~~~-GlV~~~~Y   56 (61)
T d2ev0a1          10 EQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKD-EYLIYEKY   56 (61)
T ss_dssp             HHHHHHHHHHSSCCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEC---
T ss_pred             HHHHHHHhcCCCccHHHHHHHhCCCchhHHHHHHHHHHC-CCEEEccC
Confidence            445665566778899999999999999999999999987 99987654

>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=94.02  E-value=0.046  Score=37.69  Aligned_cols=47  Identities=13%  Similarity=0.055  Sum_probs=39.1

Q ss_pred             HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL   54 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~   54 (292)
                      +.|+.....++.+...++|+.+|+++.+|..+++.|+.+ |+|+.+.-
T Consensus        12 ~~I~~L~~~~~~v~~~~iA~~L~vs~~SVt~mvkrL~~~-Glv~~~~y   58 (63)
T d2isya1          12 RTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERD-GLLRVAGD   58 (63)
T ss_dssp             HHHHHHHHTTCCCCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEECTT
T ss_pred             HHHHHHHhcCCCCcHHHHHHHhCCCchhHHHHHHHHHHC-CCEEEcCC
Confidence            345555556777888999999999999999999999987 99998754

>d1tw3a1 a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Carminomycin 4-O-methyltransferase
species: Streptomyces peucetius [TaxId: 1950]

Probab=94.01  E-value=0.036  Score=40.06  Aligned_cols=61  Identities=10%  Similarity=0.040  Sum_probs=50.4

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQV   68 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~y   68 (292)
                      .++..|...|. +++.+.+++|+.+|++++.+.+.+.-|.+. |+++  +.....|.+|+-|+-.
T Consensus        21 av~L~ifd~l~-~gp~s~~eLA~~~g~~~~~l~rlLr~l~a~-gl~~--e~~~~~y~lt~~s~~L   81 (85)
T d1tw3a1          21 AATLRLVDHIL-AGARTVKALAARTDTRPEALLRLIRHLVAI-GLLE--EDAPGEFVPTEVGELL   81 (85)
T ss_dssp             HHHTTHHHHHH-TTCCBHHHHHHHHTCCHHHHHHHHHHHHHT-TSEE--EEETTEEEECTTGGGG
T ss_pred             HHHcCcHHHhc-cCCCCHHHHHHHhCcChhHHHHHHHHHHHC-CCeE--ecCCCeEecCHHHHHh
Confidence            46667888885 567889999999999999999999999997 9986  3345689999998643

>d1okra_ a.4.5.39 (A:) Methicillin resistance regulatory protein MecI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Methicillin resistance regulatory protein MecI
species: Staphylococcus aureus [TaxId: 1280]

Probab=94.01  E-value=0.095  Score=39.58  Aligned_cols=91  Identities=12%  Similarity=0.114  Sum_probs=61.6

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHh----cCCCHHHHHHHHHHhhccCCcEEEeeee--EEEEEeChhHHHH--------
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKL----FNEDHQKVVGGMKSIETLGEYLIVEPLS--HKIWELTGEGNQV--------   68 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~----~~~~~~~v~~~~~~L~s~~glv~~e~~~--~~~~~LTeEG~~y--------   68 (292)
                      ++.|..||..|=..+.+...++...    .++++..|...+..|+.| |+|+.+..-  ..+..++.+....        
T Consensus         6 t~~E~~VM~~lW~~~~~t~~ei~~~l~~~~~~~~sTv~t~L~rL~~K-g~l~r~~~gr~~~Y~~~~~~~~~~~~~~~~~~   84 (120)
T d1okra_           6 SSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKK-GFIDRKKDNKIFQYYSLVEESDIKYKTSKNFI   84 (120)
T ss_dssp             CHHHHHHHHHHHHHSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHH-TSEEEEEETTEEEEEESSCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHcCCCCCHHHHHHHHhcccCccHHhHHHHHHHHHHC-CCeEEEecCCceEEeecCCHHHHHHHHHHHHH
Confidence            3678999999966667777665544    489999999999999987 999875542  2333444443321        


Q ss_pred             --hhcCChHHHHHhhcCCCCCChHHHhh
Q psy10346         69 --KDNGSHEVLVFNNVPSEGIGQKELLA   94 (292)
Q Consensus        69 --l~~GlPE~rl~~~l~~~~~~~~el~~   94 (292)
                        +-+|++...+..++...+++.+|+.+
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~ls~~el~~  112 (120)
T d1okra_          85 NKVYKGGFNSLVLNFVEKEDLSQDEIEE  112 (120)
T ss_dssp             HHHSTTCHHHHHHHHHHHSCCCHHHHHH
T ss_pred             HHHHcccHHHHHHHHHHccCCCHHHHHH
Confidence              22577766666666555666666554

>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=93.98  E-value=0.042  Score=38.57  Aligned_cols=60  Identities=7%  Similarity=0.092  Sum_probs=47.4

Q ss_pred             cHHHHHHHHHhcc-----CCCCChHHHHHhcCC-CHHHHHHHHHHhhccCCcEEEeeeeEEEEEeCh
Q psy10346          3 SDLTEKILKYLDT-----NPPVDTLDLAKLFNE-DHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG   63 (292)
Q Consensus         3 ~~~e~~iL~~L~~-----~~~~~~~ela~~~~~-~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTe   63 (292)
                      .+.|.+||..+..     +-..+..|+|+.+|+ +++.|-..+..|+.+ |+|+-.......+.|++
T Consensus         4 T~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~k-G~I~r~~~~~R~i~i~~   69 (71)
T d1jhfa1           4 TARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARK-GVIEIVSGASRGIRLLQ   69 (71)
T ss_dssp             CHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHT-TSEEECSSSSSCEEECC
T ss_pred             CHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHC-cCeecCCCCCceeEecC
Confidence            5678899988853     334678999999999 699999999999987 99998765555555554

>d2hzta1 a.4.5.69 (A:4-98) Putative transcriptional regulator YtcD {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtcD
species: Bacillus subtilis [TaxId: 1423]

Probab=93.93  E-value=0.089  Score=38.82  Aligned_cols=60  Identities=18%  Similarity=0.203  Sum_probs=47.6

Q ss_pred             HHHHHhccCCCCChHHHHHhc-CCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHh
Q psy10346          8 KILKYLDTNPPVDTLDLAKLF-NEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVK   69 (292)
Q Consensus         8 ~iL~~L~~~~~~~~~ela~~~-~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl   69 (292)
                      .||..|. .+.....++...+ |+++..+..-++.|+.. |+|.-...    ....|.||+.|+...
T Consensus        15 ~Il~~L~-~g~~rF~el~~~l~gis~~~Ls~rLk~Le~~-glv~r~~~~~~p~~veY~LT~~G~~L~   79 (95)
T d2hzta1          15 VILCHLT-HGKKRTSELKRLMPNITQKMLTQQLRELEAD-GVINRIVYNQVPPKVEYELSEYGRSLE   79 (95)
T ss_dssp             HHHHHHT-TCCBCHHHHHHHCTTSCHHHHHHHHHHHHHT-TSEEEEEECSSSCEEEEEECTTGGGGH
T ss_pred             HHHHHHH-cCCCCHHHHHHHhhcCChhHHHHHHHHHHHh-HHHhheeccccccchhhhhhhhHHHHH
Confidence            4677775 4556778898886 99999999999999997 99975433    257799999998754

>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=93.89  E-value=0.073  Score=39.20  Aligned_cols=63  Identities=11%  Similarity=0.174  Sum_probs=52.6

Q ss_pred             CCcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee-EEEEEeChhH
Q psy10346          1 MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS-HKIWELTGEG   65 (292)
Q Consensus         1 m~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~-~~~~~LTeEG   65 (292)
                      ++.+...+||..|.. ++....+++..+|+++..|..-++.|+.. |+|+.++.- ..+|.|+++.
T Consensus        15 L~d~~Rl~Il~~L~~-~~~~v~el~~~l~~s~~~vS~HL~~L~~~-glv~~~r~G~~~~Y~l~~~~   78 (94)
T d1r1ua_          15 LGDYNRIRIMELLSV-SEASVGHISHQLNLSQSNVSHQLKLLKSV-HLVKAKRQGQSMIYSLDDIH   78 (94)
T ss_dssp             TCSHHHHHHHHHHHH-CCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEESSHH
T ss_pred             hCCHHHHHHHHHHHc-CCccHHHHHHHHCCCHHHHHHHHHHHHHC-CceEEEEECCEEEEEECcHH
Confidence            356778889999975 45678999999999999999999999986 999986654 4678999764

>d2fswa1 a.4.5.69 (A:3-104) Hypothetical protein PG0823 {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein PG0823
species: Porphyromonas gingivalis [TaxId: 837]

Probab=93.85  E-value=0.077  Score=39.71  Aligned_cols=60  Identities=12%  Similarity=0.124  Sum_probs=47.1

Q ss_pred             HHHHHhccCCCCChHHHHHhc-CCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHh
Q psy10346          8 KILKYLDTNPPVDTLDLAKLF-NEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVK   69 (292)
Q Consensus         8 ~iL~~L~~~~~~~~~ela~~~-~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl   69 (292)
                      .||..|. .+.....++...+ |+++..+..-++.|++. |+|.-+...    ...|.||+.|++.+
T Consensus        24 ~Il~~L~-~g~~rF~el~~~l~gIs~~~Ls~rLkeL~~~-glv~r~~~~~~p~~veY~LT~~G~~L~   88 (102)
T d2fswa1          24 LIIFQIN-RRIIRYGELKRAIPGISEKMLIDELKFLCGK-GLIKKKQYPEVPPRVEYSLTPLGEKVL   88 (102)
T ss_dssp             HHHHHHT-TSCEEHHHHHHHSTTCCHHHHHHHHHHHHHT-TSEEEEEECSSSCEEEEEECHHHHTTH
T ss_pred             HHHHHHc-cCCCCHHHHHhhCcccchhHHHHHHHHHHHC-CceeecccCCCCCeehhhhhHhHHHHH
Confidence            4666775 3455678898886 99999999999999997 999754432    56899999998743

>d1fp2a1 a.4.5.29 (A:8-108) Isoflavone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Isoflavone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=93.70  E-value=0.038  Score=41.50  Aligned_cols=67  Identities=12%  Similarity=0.189  Sum_probs=51.6

Q ss_pred             HHHHHHHHHhcc-CCCCChHHHHHhcCCCH---HHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346          4 DLTEKILKYLDT-NPPVDTLDLAKLFNEDH---QKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG   72 (292)
Q Consensus         4 ~~e~~iL~~L~~-~~~~~~~ela~~~~~~~---~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G   72 (292)
                      +++..|...|.. ++..+.+++|..+++++   ..+-+.+.-|.+. |+++........|.||+-++ ++-.|
T Consensus        29 aveLgi~d~l~~~~~p~t~~eLa~~~~~~~~~~~~L~RlLR~L~~~-gi~~~~~~~~~~Y~lt~~s~-~Lv~~   99 (101)
T d1fp2a1          29 AVEMNIPNIIQNHGKPISLSNLVSILQVPSSKIGNVRRLMRYLAHN-GFFEIITKEEESYALTVASE-LLVRG   99 (101)
T ss_dssp             HHHTTHHHHHHHHTSCEEHHHHHHHHTCCGGGHHHHHHHHHHHHHT-TSEEEEESSSEEEEECHHHH-TTSTT
T ss_pred             HHHcCcHHHHHHcCCCCCHHHHHHHcCCCCccchHHHHHHHHHHhC-CceeeecCCCCeEecCHHHH-HhhcC
Confidence            456667777753 45678899999999864   4477888999887 99987776777899999997 55444

>d1qzza1 a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase RdmB {Streptomyces purpurascens [TaxId: 1924]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Aclacinomycin-10-hydroxylase RdmB
species: Streptomyces purpurascens [TaxId: 1924]

Probab=93.62  E-value=0.028  Score=41.49  Aligned_cols=62  Identities=13%  Similarity=-0.010  Sum_probs=52.2

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHH
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQ   67 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~   67 (292)
                      +++..|...|. .++.+.+++|...|+++..+.+.+.-|.+. |+++-.+...-.|.+|+.|+-
T Consensus        27 aveL~ifd~L~-~gp~t~~eLA~~~g~~~~~l~rLlr~L~a~-gll~~~~d~~~~~~~t~~g~l   88 (92)
T d1qzza1          27 AATLRLVDHLL-AGADTLAGLADRTDTHPQALSRLVRHLTVV-GVLEGGEKQGRPLRPTRLGML   88 (92)
T ss_dssp             HHHTTHHHHHH-TTCCSHHHHHHHHTCCHHHHHHHHHHHHHT-TSEECCCC-CCCCEECTTGGG
T ss_pred             HHHcCchHHHh-CCCCCHHHHHHHHCcCchHHHHHHHHHHHC-CCeeeecCCCceecccHHHHh
Confidence            45667788886 467899999999999999999999999998 999877666678999999865

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Cadmium efflux system accessory protein CadC
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.53  E-value=0.039  Score=41.72  Aligned_cols=64  Identities=13%  Similarity=0.102  Sum_probs=51.2

Q ss_pred             CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee-EEEEEeChhHH
Q psy10346          2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS-HKIWELTGEGN   66 (292)
Q Consensus         2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~-~~~~~LTeEG~   66 (292)
                      +++...+||..|...++....+++..+|++.+.|..-++.|+.. |+|+.++.- ..+|.|+++.-
T Consensus        29 adp~Rl~Il~~L~~~~~~~v~ela~~l~~s~s~vS~HL~~L~~a-Glv~~~r~G~~~~Y~l~~~~i   93 (108)
T d1u2wa1          29 ADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQ-GVVNFRKEGKLALYSLGDEHI   93 (108)
T ss_dssp             HSHHHHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEC----CCEEEESCHHH
T ss_pred             CCHHHHHHHHHHHhCCCccHHHHHHHHccChhHHHHHHHHHHHC-CeeEEEEECCEEEEEECHHHH
Confidence            35667789988866677778999999999999999999999986 999996554 45789998763

>d1z7ua1 a.4.5.69 (A:1-108) Hypothetical protein EF0647 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein EF0647
species: Enterococcus faecalis [TaxId: 1351]

Probab=93.43  E-value=0.13  Score=38.79  Aligned_cols=60  Identities=13%  Similarity=0.167  Sum_probs=46.3

Q ss_pred             HHHHHhccCCCCChHHHHHhc-CCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHh
Q psy10346          8 KILKYLDTNPPVDTLDLAKLF-NEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVK   69 (292)
Q Consensus         8 ~iL~~L~~~~~~~~~ela~~~-~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl   69 (292)
                      .||..|.. +.....++...+ |+++..+..-++.|+.. |+|.-....    ...|.||+-|+..+
T Consensus        23 ~Il~~L~~-g~~RF~el~~~l~gIS~~~Ls~rLk~L~~~-glv~R~~~~~~p~~veY~LT~~G~~L~   87 (108)
T d1z7ua1          23 SLMDELFQ-GTKRNGELMRALDGITQRVLTDRLREMEKD-GLVHRESFNELPPRVEYTLTPEGYALY   87 (108)
T ss_dssp             HHHHHHHH-SCBCHHHHHHHSTTCCHHHHHHHHHHHHHH-TSEEEEEECCSSCEEEEEECHHHHHHH
T ss_pred             HHHHHHHc-CCCCHHHHHHHCcCCChhHHHHHHHHHHHC-CcceeeccCCCcceehhhhchhHHHHH
Confidence            35666643 445678888886 89999999999999997 998754332    56799999999754

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF1790-like
domain: Transcriptional regulatory protein PF1790
species: Pyrococcus furiosus [TaxId: 2261]

Probab=93.42  E-value=0.036  Score=45.50  Aligned_cols=65  Identities=12%  Similarity=0.136  Sum_probs=53.5

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee------EEEEEeChhHHHHh
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS------HKIWELTGEGNQVK   69 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~------~~~~~LTeEG~~yl   69 (292)
                      .+.-.+||..|.. ++.+..++|..+|+++..|..-++.|+.. |+|+.....      ...|.||+.|...+
T Consensus        14 ~~~R~~Il~~L~~-~~~~~~ela~~l~~s~~~v~~HL~~L~~~-Glv~~~~~~~~~G~~~~~y~l~~~~~~~~   84 (194)
T d2p4wa1          14 NETRRRILFLLTK-RPYFVSELSRELGVGQKAVLEHLRILEEA-GLIESRVEKIPRGRPRKYYMIKKGLRLEI   84 (194)
T ss_dssp             SHHHHHHHHHHHH-SCEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECCBTTBCCCEEEEECTTEEEEE
T ss_pred             CHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeEEEEeecCCCCceEEEEecccceeee
Confidence            4566789998864 56788999999999999999999999986 999976543      46899999876543

>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=93.29  E-value=0.047  Score=37.85  Aligned_cols=45  Identities=13%  Similarity=0.232  Sum_probs=40.9

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      ..+||..|..++.++..++|+.+|++..+|.+.+..|.+. |+|..
T Consensus         8 ~~~Il~~l~~~g~~sr~eLa~~~glS~~Tv~~~l~~L~~~-Glv~e   52 (71)
T d1z05a1           8 AGRVYKLIDQKGPISRIDLSKESELAPASITKITRELIDA-HLIHE   52 (71)
T ss_dssp             HHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEE
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEE
Confidence            4679999988888999999999999999999999999987 99863

>d1yyva1 a.4.5.69 (A:9-122) Putative transcriptional regulator YtfH {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtfH
species: Salmonella typhimurium [TaxId: 90371]

Probab=93.18  E-value=0.12  Score=39.40  Aligned_cols=60  Identities=22%  Similarity=0.227  Sum_probs=47.6

Q ss_pred             HHHHHhccCCCCChHHHHHhc-CCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHh
Q psy10346          8 KILKYLDTNPPVDTLDLAKLF-NEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVK   69 (292)
Q Consensus         8 ~iL~~L~~~~~~~~~ela~~~-~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl   69 (292)
                      .||..|.. +.....++...+ |++...+..-++.|+.. |+|.-...    ....|.||+.|+..+
T Consensus        28 ~Il~~L~~-g~~RF~el~~~l~gis~~~Ls~rL~~Le~~-glv~R~~~~~~p~~veY~LT~~G~~L~   92 (114)
T d1yyva1          28 LILVALRD-GTHRFSDLRRKMGGVSEKMLAQSLQALEQD-GFLNRVSYPVVPPHVEYSLTPLGEQVS   92 (114)
T ss_dssp             HHHHHGGG-CCEEHHHHHHHSTTCCHHHHHHHHHHHHHH-TCEEEEEECSSSCEEEEEECHHHHHHH
T ss_pred             HHHHHHhc-CCCCHHHHHHHccccchhHHHHHHHHHHHH-HHHhhcccCCCCchhHhHhhHhHHHHH
Confidence            46777753 455668898887 89999999999999997 99975443    357899999999854

>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=92.38  E-value=0.14  Score=35.75  Aligned_cols=61  Identities=15%  Similarity=0.117  Sum_probs=49.0

Q ss_pred             HHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHH
Q psy10346          5 LTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQV   68 (292)
Q Consensus         5 ~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~y   68 (292)
                      .-.+||..+.. .+.+...++|+.+|++.+.+.+.+..|... |++.-..  ...|.|+...-+.
T Consensus         6 r~l~IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~tL~~~-g~l~~~~--~g~y~lG~~l~~l   67 (75)
T d1mkma1           6 KAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEK-GFVLRKK--DKRYVPGYKLIEY   67 (75)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEECT--TSCEEECTHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEECC--CCCEeecHHHHHH
Confidence            34578888865 456888999999999999999999999987 9998653  3569998776443

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, 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: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=92.29  E-value=0.099  Score=38.23  Aligned_cols=64  Identities=22%  Similarity=0.273  Sum_probs=51.9

Q ss_pred             HHHHHHHHHhc-----cCCCCChHHHHHhcCC--CHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346          4 DLTEKILKYLD-----TNPPVDTLDLAKLFNE--DHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus         4 ~~e~~iL~~L~-----~~~~~~~~ela~~~~~--~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl   69 (292)
                      +.++.||.++.     .+.++.+.++++..|+  +...|-..+..|+.+ |||.- .....-...|+.|-+|-
T Consensus         4 ~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~~LE~~-G~l~~-~h~s~GriPT~~g~r~y   74 (87)
T d1stza1           4 DRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYL-GYIYQ-PHTSAGRIPTDKGLRFY   74 (87)
T ss_dssp             HHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHT-TSEEC-CSSCSCBEECHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHHHHHHC-CcccC-CCCCCCCcccHHHHHHH
Confidence            56788888774     3667899999999776  588999999999987 99874 66666678999998764

>d2gxba1 a.4.5.19 (A:140-198) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.22  E-value=0.16  Score=34.63  Aligned_cols=55  Identities=18%  Similarity=0.338  Sum_probs=41.5

Q ss_pred             HHHHHHHhcc---CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEe
Q psy10346          6 TEKILKYLDT---NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWEL   61 (292)
Q Consensus         6 e~~iL~~L~~---~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~L   61 (292)
                      |.+||..|..   +..+..-.+|.+++++...|-+++.+|+.+ |.+.-+.-+--.|++
T Consensus         1 Eq~vl~~l~~lg~~~~~tA~~LA~kl~vpKk~iNr~LYsL~~k-gkl~k~~gtPPlWr~   58 (59)
T d2gxba1           1 EQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKK-GKLQKEAGTPPLWKI   58 (59)
T ss_dssp             HHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEECSSSCEEEE
T ss_pred             ChHHHHHHHhcCCccchhHHHHHHHhCCcHHHHHHHHHHHHHc-cchhhcCCCCCCccc
Confidence            5677766654   455677999999999999999999999986 887755544444433

>d1sd4a_ a.4.5.39 (A:) Penicillinase repressor BlaI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Penicillinase repressor BlaI
species: Staphylococcus aureus [TaxId: 1280]

Probab=91.65  E-value=0.41  Score=36.34  Aligned_cols=91  Identities=11%  Similarity=0.103  Sum_probs=64.8

Q ss_pred             cHHHHHHHHHhccCCCCChHHHHHh----cCCCHHHHHHHHHHhhccCCcEEEeeeeEE-EEEe--ChhH------HHHh
Q psy10346          3 SDLTEKILKYLDTNPPVDTLDLAKL----FNEDHQKVVGGMKSIETLGEYLIVEPLSHK-IWEL--TGEG------NQVK   69 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~~~~~ela~~----~~~~~~~v~~~~~~L~s~~glv~~e~~~~~-~~~L--TeEG------~~yl   69 (292)
                      ++.|..|+..|=+.+++++.++...    .++.+..|...+..|..| |+|+.+..-.. .|..  |++.      ++.+
T Consensus         5 s~~E~~VM~~lW~~~~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~K-g~l~~~~~gr~~~Y~~~v~~~~~~~~~~~~~~   83 (122)
T d1sd4a_           5 SMAEWDVMNIIWDKKSVSANEIVVEIQKYKEVSDKTIRTLITRLYKK-EIIKRYKSENIYFYSSNIKEDDIKMKTAKTFL   83 (122)
T ss_dssp             CHHHHHHHHHHHHSSSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHT-TSEEEEEETTEEEEEECSCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHcCCCCCHHHHHHHhhccCCCcHhHHHHHHHHHHhh-hceeeeccCCeEEEeecCCHHHHHHHHHHHHH
Confidence            5788999999966667777655443    578899999999999987 99998665333 3322  3322      2334


Q ss_pred             h---cCChHHHHHhhcCCCCCChHHHhh
Q psy10346         70 D---NGSHEVLVFNNVPSEGIGQKELLA   94 (292)
Q Consensus        70 ~---~GlPE~rl~~~l~~~~~~~~el~~   94 (292)
                      +   +|++..-+..++....++.+|+.+
T Consensus        84 ~~~~~gs~~~lv~~~~~~~~ls~~el~e  111 (122)
T d1sd4a_          84 NKLYGGDMKSLVLNFAKNEELNNKEIEE  111 (122)
T ss_dssp             HHHHTTCHHHHHHHHHHTTCSCHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHhCCCCCHHHHHH
Confidence            3   889988888888766688777665

>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=91.32  E-value=0.19  Score=34.72  Aligned_cols=45  Identities=13%  Similarity=0.220  Sum_probs=41.1

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      ...||..|..++.++-.++|..+|++..+|.+.+..|.+. |+|..
T Consensus         7 ~~~Il~~i~~~g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~-glv~e   51 (70)
T d1z6ra1           7 AGAVYRLIDQLGPVSRIDLSRLAQLAPASITKIVHEMLEA-HLVQE   51 (70)
T ss_dssp             HHHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHHHHHHHH-TSEEE
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEe
Confidence            4579999999999999999999999999999999999987 99864

>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=91.09  E-value=0.11  Score=35.46  Aligned_cols=44  Identities=23%  Similarity=0.415  Sum_probs=37.5

Q ss_pred             HHHHHHHHHhccC-CCCChHHHHHhcCCCHHHHHHHHHHhhccCCc
Q psy10346          4 DLTEKILKYLDTN-PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEY   48 (292)
Q Consensus         4 ~~e~~iL~~L~~~-~~~~~~ela~~~~~~~~~v~~~~~~L~s~~gl   48 (292)
                      .-..+||..|.+. +.++..++|+.+|++...|.+.+..|++. |+
T Consensus         7 eR~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L~~~-G~   51 (65)
T d1j5ya1           7 ERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSL-GY   51 (65)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHHH-TC
T ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHHC-CC
Confidence            4456789988654 45899999999999999999999999987 86

>d2f2ea1 a.4.5.69 (A:5-146) Hypothetical protein PA1607 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein PA1607
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=90.07  E-value=0.35  Score=38.05  Aligned_cols=60  Identities=12%  Similarity=0.122  Sum_probs=47.1

Q ss_pred             HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe---eeeEEEEEeChhHHHHh
Q psy10346          8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE---PLSHKIWELTGEGNQVK   69 (292)
Q Consensus         8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e---~~~~~~~~LTeEG~~yl   69 (292)
                      .||..|. .+.....++...+|+++..+..-++.|+.. |+|.-.   .-....|.||+.|++..
T Consensus        24 ~Il~~l~-~G~~rf~el~~~lgis~~vLs~rL~~L~~~-gLv~r~~~~~p~r~~Y~LT~~G~~L~   86 (142)
T d2f2ea1          24 LIVRDAF-EGLTRFGEFQKSLGLAKNILAARLRNLVEH-GVMVAVPAESGSHQEYRLTDKGRALF   86 (142)
T ss_dssp             HHHHHHH-TTCCSHHHHHHHHCCCHHHHHHHHHHHHHT-TSEEEEECSSSSCEEEEECHHHHTTH
T ss_pred             HHHHHHH-cCCCCHHHHHHHhhccHHHHHHHHHHHHHh-cceeeecCCCCCeeEEecCcCcchHH
Confidence            4667775 356677899999999999999999999987 998741   22346799999998754

>d1zara1 a.4.5.56 (A:2-90) Rio2 serine protein kinase N-terminal domain {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Rio2 serine protein kinase N-terminal domain
domain: Rio2 serine protein kinase N-terminal domain
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=89.01  E-value=0.49  Score=34.66  Aligned_cols=66  Identities=12%  Similarity=-0.028  Sum_probs=53.8

Q ss_pred             cHHHHHHHHHhccCC---C-CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346          3 SDLTEKILKYLDTNP---P-VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~---~-~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl   69 (292)
                      ++.+.+||.+++.+-   + +-.+.+++..+++++.+...+..|... ++|.-....-.=|.||-.|-+||
T Consensus        10 ~~~dfRvL~aiE~gmrnhE~VP~~lI~~~a~l~~~~~~~~L~~L~k~-kLv~~~~~~Y~GYrLT~~GYD~L   79 (89)
T d1zara1          10 GKHSWRIMDAIFKNLWDYEYVPLQLISSHARIGEEKARNILKYLSDL-RVVQNRQKDYEGSTFTFIGLSLY   79 (89)
T ss_dssp             CHHHHHHHHHHHTTTTTCSSEEHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEECSSSCEEEECHHHHHHH
T ss_pred             CHHHHHHHHHHHhccccCccccHHHHHHHHCCCHHHHHHHHHHHHHc-CCeeccCCCcceEEeeccChHHH
Confidence            467889999997422   2 455778888999999999999999876 89976665557899999999987

>d2p8ta1 a.4.5.72 (A:14-82) Hypothetical protein PH0730 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PH0730 N-terminal domain-like
domain: Hypothetical protein PH0730
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=88.76  E-value=0.57  Score=32.73  Aligned_cols=50  Identities=14%  Similarity=0.250  Sum_probs=42.4

Q ss_pred             CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346         17 PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD   70 (292)
Q Consensus        17 ~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~   70 (292)
                      .++--..+|+.+|+.--.|-.-+.-|.+. |+|.+..   .=..||++|++.++
T Consensus        16 qPiGRr~La~~L~l~Er~vRte~~~Lk~~-gLI~~~~---~Gm~lTe~G~~~l~   65 (69)
T d2p8ta1          16 EPLGRKQISERLELGEGSVRTLLRKLSHL-DIIRSKQ---RGHFLTLKGKEIRD   65 (69)
T ss_dssp             SCBCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEC-----CEEECHHHHHHHH
T ss_pred             CCccHHHHHHHcCCcHHHHHHHHHHHHHC-CCeeeeC---CCCEECHhHHHHHH
Confidence            45777899999999999999999999987 9999875   66789999999875

>d1xd7a_ a.4.5.55 (A:) Hypothetical protein ywnA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein ywnA
species: Bacillus subtilis [TaxId: 1423]

Probab=88.59  E-value=0.31  Score=36.97  Aligned_cols=57  Identities=12%  Similarity=0.063  Sum_probs=46.1

Q ss_pred             HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346          4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT   62 (292)
Q Consensus         4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT   62 (292)
                      +..-.+|..|..++.++++++|+..|+++.-|.+.+..|... |+|+..+-..--| |+
T Consensus         4 ~~Av~~L~~la~~~~~ss~~IA~~~~~~~~~v~kIl~~L~~a-glV~s~rG~~GGy-La   60 (127)
T d1xd7a_           4 AVAIHILSLISMDEKTSSEIIADSVNTNPVVVRRMISLLKKA-DILTSRAGVPGAS-LK   60 (127)
T ss_dssp             HHHHHHHHHHHTCSCCCHHHHHHHHTSCHHHHHHHHHHHHHT-TSEECCSSSSSCE-ES
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHh-CcccccCCCCCcc-cc
Confidence            345668888887778999999999999999999999999875 9999766544444 54

>d1sfua_ a.4.5.19 (A:) 34L {Yaba-like disease virus, YLDV [TaxId: 132475]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: 34L
species: Yaba-like disease virus, YLDV [TaxId: 132475]

Probab=88.11  E-value=0.41  Score=33.62  Aligned_cols=47  Identities=15%  Similarity=0.219  Sum_probs=38.1

Q ss_pred             HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL   54 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~   54 (292)
                      +++|..|..++.+...+||.++|++...|-+.+.+|+.. |.|..+..
T Consensus        13 k~~l~~L~~~~~~tA~~LAk~Lg~~Kk~VNr~LY~L~~~-G~v~~~~~   59 (70)
T d1sfua_          13 KKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKE-DTVKMVPS   59 (70)
T ss_dssp             HHHHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEECC
T ss_pred             HHHHHhcCCCCCchHHHHHHHhCCCHHHHHHHHHHHHHC-CCeecCCC
Confidence            445555655666788999999999999999999999986 99876544

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=85.99  E-value=0.25  Score=33.42  Aligned_cols=43  Identities=23%  Similarity=0.237  Sum_probs=37.1

Q ss_pred             HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe
Q psy10346          8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE   52 (292)
Q Consensus         8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e   52 (292)
                      +||+.|..+ +++-.++|+.+|++...|...+..|.+. |+|.-.
T Consensus         3 ~Il~~i~~~-pisr~eLa~~~gls~~TVs~~v~~L~~~-GlV~e~   45 (62)
T d2hoea1           3 RILKRIMKS-PVSRVELAEELGLTKTTVGEIAKIFLEK-GIVVEE   45 (62)
T ss_dssp             CSHHHHHHS-CBCHHHHHHHHTCCHHHHHHHHHHHHHH-TSEEEE
T ss_pred             HHHHHHHHC-CcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEC
Confidence            478888754 5788999999999999999999999987 999754

>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=85.66  E-value=0.46  Score=33.99  Aligned_cols=61  Identities=5%  Similarity=-0.104  Sum_probs=46.0

Q ss_pred             HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346          7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD   70 (292)
Q Consensus         7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~   70 (292)
                      .+++..+.+.+  +....|+.+|+++.+|.+.++.|+..-|. ..-.+....+.||+.|+.++.
T Consensus        11 L~~f~~v~~~g--s~t~AA~~l~isq~avs~~l~~lE~~~g~-~Lf~R~~~~~~lT~~g~~l~~   71 (89)
T d2esna1          11 LLVFDALYRHR--NVGTAASELAISASAFSHALGRLRQGLDD-ELFLRQGNRMQPTQRAEHLAA   71 (89)
T ss_dssp             HHHHHHHHHHS--SHHHHHHHHTCCHHHHHHHHHHHHHHHTS-CCEEEETTEEEECHHHHHHHH
T ss_pred             HHHHHHHHHhC--CHHHHHHHHCCCCcHhhHHHHHHHhcCCc-eeEEECCCceeECHHHHHHHH
Confidence            34555554443  45677888999999999999999987664 444456789999999998863

>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=85.42  E-value=0.89  Score=31.37  Aligned_cols=52  Identities=15%  Similarity=0.290  Sum_probs=40.5

Q ss_pred             cHHHHHHHHHhcc-----CCC----CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee
Q psy10346          3 SDLTEKILKYLDT-----NPP----VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS   55 (292)
Q Consensus         3 ~~~e~~iL~~L~~-----~~~----~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~   55 (292)
                      .+++.+|...|-.     ++.    ++-+++|.-+|+..+.|.++++.|+.. |+|+.....
T Consensus         3 ~dv~~Rla~~Ll~~~~~~~~~~~i~lt~~elA~~lg~sr~tvsr~l~~l~~~-g~I~~~~~~   63 (73)
T d1zyba1           3 LDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQDN-GLIELHRKE   63 (73)
T ss_dssp             CSHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHHTSCHHHHHHHHHHHHHT-TSCEEETTE
T ss_pred             CCHHHHHHHHHHHhhhhhCCCeEeecCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEecCCE
Confidence            4677788777632     122    466899999999999999999999986 999876543

>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=84.22  E-value=0.6  Score=31.62  Aligned_cols=38  Identities=8%  Similarity=0.110  Sum_probs=32.8

Q ss_pred             CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEE
Q psy10346         19 VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHK   57 (292)
Q Consensus        19 ~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~   57 (292)
                      ++-+++|.-+|+..+.|.+.++.|+.. |+|++....-.
T Consensus        30 lt~~~lA~~~G~sRetvsr~L~~l~~~-glI~~~~~~I~   67 (69)
T d1i5za1          30 ITRQEIGQIVGCSRETVGRILKMLEDQ-NLISAHGKTIV   67 (69)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEETTEEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEcCCEEE
Confidence            456899999999999999999999986 99998765543

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.21  E-value=0.69  Score=32.16  Aligned_cols=48  Identities=8%  Similarity=0.163  Sum_probs=39.1

Q ss_pred             cHHHHHHHHHhccCCC---CChHHHHHhc-CCCHHHHHHHHHHhhccCCcEEE
Q psy10346          3 SDLTEKILKYLDTNPP---VDTLDLAKLF-NEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         3 ~~~e~~iL~~L~~~~~---~~~~ela~~~-~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      .+.+.+||.+++....   +...++++++ |++...|..++..|.+. |+|=.
T Consensus         5 s~~q~~V~~~i~s~~~~eGi~~~el~~~l~~~~~~~i~~aid~L~~e-G~IYs   56 (69)
T d1dpua_           5 TVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNE-GHIYS   56 (69)
T ss_dssp             CHHHHHHHHHHHHCCCTTTEEHHHHHHHSTTSCHHHHHHHHHHHHHT-TSEEE
T ss_pred             CHHHHHHHHHHHhCCCccCcCHHHHHHHccCCCHHHHHHHHHHHHhC-Cceec
Confidence            4788999999965332   5668998887 89999999999999986 98753

>d1j75a_ a.4.5.19 (A:) Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Dlm-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.99  E-value=0.87  Score=30.28  Aligned_cols=47  Identities=19%  Similarity=0.227  Sum_probs=39.4

Q ss_pred             HHHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346          4 DLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV   51 (292)
Q Consensus         4 ~~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~   51 (292)
                      ++|++||..|.+ +.++.+..+++++.++...+-+.+..|... +=|..
T Consensus         1 ~LEQkILQVL~dagspvk~~ql~k~cqVpkk~lNqVL~rlkke-~kVsl   48 (57)
T d1j75a_           1 NLEQKILQVLSDDGGPVKIGQLVKKCQVPKKTLNQVLYRLKKE-DRVSS   48 (57)
T ss_dssp             CHHHHHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHHHT-TSEEE
T ss_pred             CHHHHHHHHHHhcCCchHHHHHHHHHCCCHHHHHHHHHHHHhc-ccccc
Confidence            478999999965 556788999999999999999999999864 55544

>d2dk5a1 a.4.5.85 (A:8-85) DNA-directed RNA polymerase III subunit RPC6, RPO3F {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: RPO3F domain-like
domain: DNA-directed RNA polymerase III subunit RPC6, RPO3F
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.74  E-value=0.36  Score=34.54  Aligned_cols=48  Identities=8%  Similarity=0.067  Sum_probs=39.9

Q ss_pred             HHHHHHHHHhccCC--CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe
Q psy10346          4 DLTEKILKYLDTNP--PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE   52 (292)
Q Consensus         4 ~~e~~iL~~L~~~~--~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e   52 (292)
                      +.|+.|+.++++.+  .+.+.++-.+.|+++..|-+.+++|+++ ++|+.-
T Consensus        13 ~~E~lVY~~I~~ag~~GIW~~dir~ktnL~~~~l~K~LK~Lesk-~lIK~V   62 (78)
T d2dk5a1          13 NQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESK-KLIKAV   62 (78)
T ss_dssp             SSHHHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEE
T ss_pred             HHHHHHHHHHHHccccceeHHHHHHHcCCCHHHHHHHHHHHHhc-CCceee
Confidence            46778888886533  3677999999999999999999999997 899863

>d1kyza1 a.4.5.29 (A:13-119) Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=82.90  E-value=2.7  Score=31.35  Aligned_cols=67  Identities=9%  Similarity=0.163  Sum_probs=50.2

Q ss_pred             HHHHHHHHHhccCC---CCChHHHHHhcCCC----HHHHHHHHHHhhccCCcEEEeeee------EEEEEeChhHHHHhh
Q psy10346          4 DLTEKILKYLDTNP---PVDTLDLAKLFNED----HQKVVGGMKSIETLGEYLIVEPLS------HKIWELTGEGNQVKD   70 (292)
Q Consensus         4 ~~e~~iL~~L~~~~---~~~~~ela~~~~~~----~~~v~~~~~~L~s~~glv~~e~~~------~~~~~LTeEG~~yl~   70 (292)
                      ++|..|...|.+.|   .....+++..++.+    +..+-|.++.|.+. |+++.....      ...|.||+-++-.++
T Consensus        27 AieLgI~DiI~~~G~~~~ls~~eia~~l~~~~p~~~~~L~RilR~Las~-~vf~~~~~~~~dg~~~~~Y~LTpvsk~Lv~  105 (107)
T d1kyza1          27 ALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLLACY-IILTCSVRTQQDGKVQRLYGLATVAKYLVK  105 (107)
T ss_dssp             HHHTTHHHHHHTTCTTCCBCHHHHHHTSSCCCTTHHHHHHHHHHHHHHT-TSEEEEEEECTTSCEEEEEEECHHHHHHSC
T ss_pred             HHHcCCHHHHHHcCCCCCCCHHHHHHhcCCCCCcchHHHHHHHHHHHhc-CceEEeeecCCCCCeeeEEecchhHHhhcC
Confidence            56777888887644   35668999888764    34688999999987 999875443      468999999987655


Q ss_pred             c
Q psy10346         71 N   71 (292)
Q Consensus        71 ~   71 (292)
                      +
T Consensus       106 d  106 (107)
T d1kyza1         106 N  106 (107)
T ss_dssp             C
T ss_pred             C
Confidence            3

>d1q1ha_ a.4.5.41 (A:) Transcription factor E/IIe-alpha, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcription factor E/IIe-alpha, N-terminal domain
domain: Transcription factor E/IIe-alpha, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=82.18  E-value=0.95  Score=32.98  Aligned_cols=49  Identities=14%  Similarity=0.217  Sum_probs=40.1

Q ss_pred             HHHHHHh-ccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeE
Q psy10346          7 EKILKYL-DTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSH   56 (292)
Q Consensus         7 ~~iL~~L-~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~   56 (292)
                      .+|++.| +.++.++-+++|+++|+....|-+++..|... |+|+..+...
T Consensus        21 ~~v~~~L~~~~~evtDe~iA~~tgi~in~VRk~Ly~L~~~-~L~~y~R~kd   70 (88)
T d1q1ha_          21 IDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQ-GFVSYRKTRD   70 (88)
T ss_dssp             HHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHH-TSCEEEEEC-
T ss_pred             HHHHHHHHhccCcCCHHHHHHHhCCcHHHHHHHHHHHHhC-CceEEEEeec
Confidence            4577666 34566788999999999999999999999987 9998876654

>d2obpa1 a.4.5.71 (A:12-92) Putative DNA-binding protein ReutB4095 {Ralstonia eutropha [TaxId: 106590]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ReutB4095-like
domain: Putative DNA-binding protein ReutB4095
species: Ralstonia eutropha [TaxId: 106590]

Probab=81.15  E-value=1.5  Score=31.21  Aligned_cols=63  Identities=16%  Similarity=0.079  Sum_probs=49.2

Q ss_pred             HHHHHHhcc------CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe--eeeEEEEEeChhHHHHhh
Q psy10346          7 EKILKYLDT------NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE--PLSHKIWELTGEGNQVKD   70 (292)
Q Consensus         7 ~~iL~~L~~------~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e--~~~~~~~~LTeEG~~yl~   70 (292)
                      -.||..|-.      ++.++...+++..+++-+.+-+.+..|.+- |++.+.  +.-.-.-.||++|++...
T Consensus         7 vavL~~L~eA~~e~~g~~WSLaklsKra~~PMS~LRR~LTqL~~a-Gl~~t~~~edG~G~A~Lt~~G~~lca   77 (81)
T d2obpa1           7 VEVLLVLREAGIENGATPWSLPKIAKRAQLPMSVLRRVLTQLQAA-GLADVSVEADGRGHASLTQEGAALAA   77 (81)
T ss_dssp             HHHHHHHHHHTSSTTCCCCBHHHHHHHHTCCHHHHHHHHHHHHHT-TSEEEEECTTSCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHhccCCCCCccHHHHHhhcCCcHHHHHHHHHHHhhc-CceeeeeccCCcceeeccHHHHHHHH
Confidence            345665621      335778899999999999999999999986 998874  445677899999998653

>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=80.84  E-value=0.56  Score=33.54  Aligned_cols=61  Identities=18%  Similarity=0.139  Sum_probs=42.9

Q ss_pred             HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346          6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK   69 (292)
Q Consensus         6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl   69 (292)
                      +.+++..+...+  +...-|..+|+++.+|.+.++.|+..-|.- .-.+....+.||+.|+.++
T Consensus         5 ~L~~f~~v~e~g--s~~~AA~~L~isq~avs~~i~~LE~~lg~~-Lf~R~~~~~~lT~~G~~l~   65 (89)
T d1ixca1           5 QLKYFIAVAEAG--NMAAAAKRLHVSQPPITRQMQALEADLGVV-LLERSHRGIELTAAGHAFL   65 (89)
T ss_dssp             HHHHHHHHHHHS--SHHHHHHHHTCCHHHHHHHHHHHHHHHTSC-CBC-----CCBCHHHHHHH
T ss_pred             HHHHHHHHHHhC--CHHHHHHHhCCChHHHHHHHHHHHhcCCce-eeEecCCccCccHhHHHHH
Confidence            445666665544  456778889999999999999999875543 3445678899999999876

>d3bwga1 a.4.5.6 (A:5-82) Transcriptional regulator YydK {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional regulator YydK
species: Bacillus subtilis [TaxId: 1423]

Probab=80.82  E-value=1.4  Score=30.50  Aligned_cols=43  Identities=9%  Similarity=0.006  Sum_probs=35.1

Q ss_pred             CCCC-ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346         16 NPPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW   59 (292)
Q Consensus        16 ~~~~-~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~   59 (292)
                      +..+ +-.++|..+|++...|..++..|++. |+|......-.++
T Consensus        19 G~~LPse~~La~~~~vSr~tvr~Al~~L~~~-Gli~~~~g~G~~V   62 (78)
T d3bwga1          19 GDKLPVLETLMAQFEVSKSTITKSLELLEQK-GAIFQVRGSGIFV   62 (78)
T ss_dssp             TCBCCCHHHHHHHTTCCHHHHHHHHHHHHHT-TSEEEETTTEEEE
T ss_pred             cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CcEEEEcCcEEEE
Confidence            4445 45789999999999999999999987 9999876655444