Psyllid ID: psy6552

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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----
Protein Sequence
MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTECMNAEKETI
Secondary Structure (PSIPRED)
ccccccHHHHHccHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHccccEEHHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHcccEEEEEEccEEEEEEcccccccHHHHHHHHHHHHHccccccHHHHHHHccccHHHHHHHHHHHHHcccEEEEcccccccccEEccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHcccccccccccHHHHcccccHHHHHEEEEHHHHHHHHccccccEcHHHHHHHHHHHcccccccccccHHHHHHHHHHHccccccEEEEEEcccEEEEEEccHHccHHHHHHHHHHHHHccccEcHHHHHHHccccHHHHHHHHHHHHHcccEEEEcccccccEEEcHHHHHHHHccccccc
Coil and Loop (DISEMBL)
mrrragvgaiqKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASigvdplasrkGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKsrgkslqhqdiTNEDLLAAAKKLKIfgngfsiipigqgqylvqsipgelsldHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEgyawidtqspqehlywfpsLFTECMNAEKETI
Flexible Loop (DISEMBL)
mrrragvgaiqkqkleqekykdKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSrgkslqhqditnEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTECMNAEKETI
Low Complexity Region (SEG)
MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTECMNAEKETI
Disordered region (IsUnstruct)
**********************************************************KDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTECM*******
Disordered Region (DISOPRED)
**RRAGVGAIQ*********************EQLSQHLNTFRDK********************HFQEMCASIGVDPLASR***WSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVK**G******DITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFT**********
Disordered Region (DISEMBL)
**********QKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRL**********QDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTECMNAEKETI
Disordered Region (DISPRO)
****AGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRG*****QDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTECMNA*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQxxxxxxxxxxxxxxxxxxxxxYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTECMNAEKETI
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	254	2.2.26 [Sep-21-2011]
Q5U3V9	258	Vacuolar-sorting protein	yes	N/A	0.952	0.937	0.544	5e-77
Q9CZ28	258	Vacuolar-sorting protein	yes	N/A	0.960	0.945	0.54	8e-76
Q96H20	258	Vacuolar-sorting protein	yes	N/A	0.960	0.945	0.54	1e-75
Q5RK19	258	Vacuolar-sorting protein	yes	N/A	0.960	0.945	0.54	1e-75
Q5RJU0	257	Vacuolar-sorting protein	yes	N/A	0.937	0.926	0.549	2e-75
Q5M759	250	Vacuolar protein sorting-	yes	N/A	0.933	0.948	0.434	5e-53
Q54RC4	246	Vacuolar-sorting protein	yes	N/A	0.944	0.975	0.440	2e-52
O94663	252	Vacuolar-sorting protein	yes	N/A	0.925	0.932	0.320	1e-34
Q12483	233	Vacuolar-sorting protein	yes	N/A	0.897	0.978	0.325	7e-29
Q9LIJ4	120	Putative vacuolar protein	no	N/A	0.448	0.95	0.516	1e-26

>sp|Q5U3V9|SNF8_DANRE Vacuolar-sorting protein SNF8 OS=Danio rerio GN=snf8 PE=2 SV=2

 Score =  287 bits (735), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 135/248 (54%), Positives = 187/248 (75%), Gaps = 6/248 (2%)

Query: 2   RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
           RR  G GAI K+KL + KYK++G+ + E+Q+ Q+S+ L+TF+  LE FAS++K EI+K +
Sbjct: 3   RRGVGAGAIAKKKLAEAKYKERGSVLAEDQIAQMSKQLDTFKTHLEEFASKHKQEIRKSS 62

Query: 62  QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           QFR  FQEMCA+IGVDPLAS KGFWS +LG+GDFYYEL VQI+EVCLA  ++NGGLI LD
Sbjct: 63  QFRVQFQEMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLD 122

Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           EL  R++K RGK    QD++ +DL+ A KKLK  GNGF +IP+G G YLVQS+P EL++D
Sbjct: 123 ELHHRVLKGRGKFA--QDVSQDDLVRAIKKLKAMGNGFGMIPVG-GTYLVQSVPAELNMD 179

Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
           H++VLQ   ++ + +++VS +   L W  ERA H LD +++EG AW+D+Q+  E  YW P
Sbjct: 180 HTVVLQ--LAEKKGYVTVSEIRESLKWEKERACHVLDHLLKEGLAWLDSQAAGEPQYWLP 237

Query: 241 SLFTECMN 248
           +LF+E ++
Sbjct: 238 ALFSELLS 245

Component of the ESCRT-II complex, which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation. The ESCRT-II complex is probably involved in the recruitment of the ESCRT-III complex.
Danio rerio (taxid: 7955)

>sp|Q9CZ28|SNF8_MOUSE Vacuolar-sorting protein SNF8 OS=Mus musculus GN=Snf8 PE=2 SV=1

 Score =  283 bits (724), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 135/250 (54%), Positives = 187/250 (74%), Gaps = 6/250 (2%)

Query: 2   RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
           RR  G GAI K+KL + KYK++GT + E+QL Q+S+ L+ F+  LE FAS++K EI+K+ 
Sbjct: 3   RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query: 62  QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           +FR  FQ+MCA+IGVDPLAS KGFWS +LG+GDFYYEL VQI+EVCLA  ++NGGLI L+
Sbjct: 63  EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           EL  +++K RGK    QD++ +DL+ A KKLK  G GF IIP+G G YL+QS+P EL++D
Sbjct: 123 ELHQQVLKGRGKF--AQDVSQDDLIRAIKKLKALGTGFGIIPVG-GTYLIQSVPAELNMD 179

Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
           H++VL Q+A KN  +++VS +   L W TERA+  L+ +++EG AW+D Q+P E  YW P
Sbjct: 180 HTVVL-QLAEKN-GYVTVSEIKTSLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLP 237

Query: 241 SLFTECMNAE 250
           +LFT+  + E
Sbjct: 238 ALFTDLYSQE 247

Component of the endosomal sorting complex required for transport II (ESCRT-II), which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation. The ESCRT-II complex is probably involved in the recruitment of the ESCRT-III complex. The ESCRT-II complex may also play a role in transcription regulation by participating in derepression of transcription by RNA polymerase II, possibly via its interaction with ELL. Required for degradation of both endocytosed EGF and EGFR, but not for the EGFR ligand-mediated internalization.

Mus musculus (taxid: 10090)

>sp|Q96H20|SNF8_HUMAN Vacuolar-sorting protein SNF8 OS=Homo sapiens GN=SNF8 PE=1 SV=1

 Score =  282 bits (722), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 135/250 (54%), Positives = 187/250 (74%), Gaps = 6/250 (2%)

Query: 2   RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
           RR  G GAI K+KL + KYK++GT + E+QL Q+S+ L+ F+  LE FAS++K EI+K+ 
Sbjct: 3   RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query: 62  QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           +FR  FQ+MCA+IGVDPLAS KGFWS +LG+GDFYYEL VQI+EVCLA  ++NGGLI L+
Sbjct: 63  EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           EL  +++K RGK    QD++ +DL+ A KKLK  G GF IIP+G G YL+QS+P EL++D
Sbjct: 123 ELHQQVLKGRGKF--AQDVSQDDLIRAIKKLKALGTGFGIIPVG-GTYLIQSVPAELNMD 179

Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
           H++VL Q+A KN  +++VS +   L W TERA+  L+ +++EG AW+D Q+P E  YW P
Sbjct: 180 HTVVL-QLAEKN-GYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLP 237

Query: 241 SLFTECMNAE 250
           +LFT+  + E
Sbjct: 238 ALFTDLYSQE 247

Component of the endosomal sorting complex required for transport II (ESCRT-II), which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation. The ESCRT-II complex is probably involved in the recruitment of the ESCRT-III complex. The ESCRT-II complex may also play a role in transcription regulation by participating in derepression of transcription by RNA polymerase II, possibly via its interaction with ELL. Required for degradation of both endocytosed EGF and EGFR, but not for the EGFR ligand-mediated internalization. It is also required for the degradation of CXCR4.

Homo sapiens (taxid: 9606)

>sp|Q5RK19|SNF8_RAT Vacuolar-sorting protein SNF8 OS=Rattus norvegicus GN=Snf8 PE=1 SV=1

 Score =  282 bits (722), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 135/250 (54%), Positives = 187/250 (74%), Gaps = 6/250 (2%)

Query: 2   RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
           RR  G GAI K+KL + KYK++GT + E+QL Q+S+ L+ F+  LE FAS++K EI+K+ 
Sbjct: 3   RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query: 62  QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           +FR  FQ+MCA+IGVDPLAS KGFWS +LG+GDFYYEL VQI+EVCLA  ++NGGLI L+
Sbjct: 63  EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           EL  +++K RGK    QD++ +DL+ A KKLK  G GF IIP+G G YL+QS+P EL++D
Sbjct: 123 ELHQQVLKGRGKF--AQDVSQDDLIRAIKKLKALGTGFGIIPVG-GTYLIQSVPAELNMD 179

Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
           H++VL Q+A KN  +++VS +   L W TERA+  L+ +++EG AW+D Q+P E  YW P
Sbjct: 180 HTVVL-QLAEKN-GYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLP 237

Query: 241 SLFTECMNAE 250
           +LFT+  + E
Sbjct: 238 ALFTDLYSQE 247

Required for degradation of both endocytosed EGF and EGFR, but not for the EGFR ligand-mediated internalization (By similarity). Component of the endosomal sorting complex required for transport II (ESCRT-II), which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation. The ESCRT-II complex is probably involved in the recruitment of the ESCRT-III complex. The ESCRT-II complex may also play a role in transcription regulation by participating in derepression of transcription by RNA polymerase II, possibly via its interaction with ELL.

Rattus norvegicus (taxid: 10116)

>sp|Q5RJU0|SNF8_XENTR Vacuolar-sorting protein SNF8 OS=Xenopus tropicalis GN=snf8 PE=2 SV=1

 Score =  281 bits (720), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 134/244 (54%), Positives = 183/244 (75%), Gaps = 6/244 (2%)

Query: 2   RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
           RR  G GAI K+KL + KYK++GT + E+QL Q+S+ L  F+  LE FAS++K EI+K+ 
Sbjct: 3   RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLLQMSKQLEMFKTNLEEFASKHKQEIRKNP 62

Query: 62  QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           QFR  FQ+MCA+IGVDPLAS KGFWS +LG+GDFYYEL VQI+EVCLA  + NGGLI L 
Sbjct: 63  QFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHHNGGLITLA 122

Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           EL   ++K RGK    QD++ +D++ A KKLK+ GNGF IIP+G G YLVQS+P EL++D
Sbjct: 123 ELHQHVLKGRGKLA--QDVSQDDIIRAIKKLKVLGNGFGIIPVG-GSYLVQSVPAELNMD 179

Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
           H++VLQ   ++ +  ++V+ + + LNW TERA+H L+ +++EG AWID+Q+  E  YW P
Sbjct: 180 HTVVLQ--LAEKKGFVTVNEIKSSLNWETERAKHVLEHLLKEGLAWIDSQAQGEAQYWLP 237

Query: 241 SLFT 244
           +LFT
Sbjct: 238 ALFT 241

Component of the endosomal sorting complex required for transport II (ESCRT-II), which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation. The ESCRT-II complex is probably involved in the recruitment of the ESCRT-III complex.

Xenopus tropicalis (taxid: 8364)

>sp|Q5M759|VP221_ARATH Vacuolar protein sorting-associated protein 22 homolog 1 OS=Arabidopsis thaliana GN=VP22-1 PE=2 SV=2

 Score =  207 bits (528), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 106/244 (43%), Positives = 160/244 (65%), Gaps = 7/244 (2%)

Query: 1   MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD 60
           MRRR G+G +QK    +++Y+  G ++ + + + + + L+TFR +LE FA ++KN+I+K+
Sbjct: 1   MRRRPGIGGLQKAAAARDQYRLLGENVAKLRTDMMKEQLSTFRSQLEEFARKHKNDIRKN 60

Query: 61  AQFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILL 119
             FR  F EMCA+IGVDPLAS KGFW+ LLG+GDFYYEL VQI+EVC+ T   NGGLI L
Sbjct: 61  PAFRAQFHEMCANIGVDPLASNKGFWAELLGIGDFYYELGVQIIEVCMLTRSHNGGLISL 120

Query: 120 DELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSL 179
            EL   L + R K    + +T +D L A  KLK+ G+GF +I IG+ + LV+S+P EL+ 
Sbjct: 121 QELCNHLRQRRKKD--REAVTEDDCLRAISKLKVLGSGFEVITIGK-KKLVRSVPTELNK 177

Query: 180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT-QSPQEHLYW 238
           DH+ +L+   ++ +  + V  +   L+W++ R   AL+ +++EG A ID      +  YW
Sbjct: 178 DHNQILE--LAQGQGFVIVEEVQRRLSWTSGRVIDALETLLEEGLAMIDNGHKDGKCRYW 235

Query: 239 FPSL 242
           FP +
Sbjct: 236 FPCV 239

Component of the endosomal sorting complex required for transport II (ESCRT-II), which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The ESCRT-II complex is probably involved in the recruitment of the ESCRT-III complex.

Arabidopsis thaliana (taxid: 3702)

>sp|Q54RC4|SNF8_DICDI Vacuolar-sorting protein SNF8 OS=Dictyostelium discoideum GN=snf8 PE=3 SV=1

 Score =  206 bits (523), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 108/245 (44%), Positives = 164/245 (66%), Gaps = 5/245 (2%)

Query: 1   MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD 60
           MRR  G+ A QKQ   Q++ ++    +    + ++ + L  F++ LE FA+++K +I K+
Sbjct: 1   MRRGIGIQAAQKQTQTQKQLQNVSEQLNTENINKIKEQLLVFKENLEIFATKHKKDIIKN 60

Query: 61  AQFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILL 119
            +FR++FQ+MC  IGVDPLAS KGFW  +LG+GDFYY L VQI+E+CL     NGGL+ +
Sbjct: 61  PEFRKYFQDMCNMIGVDPLASNKGFWCQVLGVGDFYYTLGVQIIEICLKYRSSNGGLMEM 120

Query: 120 DELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSL 179
           D L   L K RGK+   Q+I+ +D+  +  KLK+ GNGF+II +  G+ LVQS+P EL+ 
Sbjct: 121 DTLAEHLRKLRGKN--SQEISCDDIECSISKLKVLGNGFNIIKVSGGKKLVQSVPCELNK 178

Query: 180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF 239
           DH+ ++  +A  N A I+ S++ ++L WS ER  + ++F++QE   WID QS  E +YWF
Sbjct: 179 DHTDII-ILAQDNNASITQSLVISKLKWSEERINNVINFLLQESMIWIDEQS-NETIYWF 236

Query: 240 PSLFT 244
           PSL++
Sbjct: 237 PSLWS 241

Component of the endosomal sorting complex required for transport II (ESCRT-II), which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation.

Dictyostelium discoideum (taxid: 44689)

>sp|O94663|SNF8_SCHPO Vacuolar-sorting protein dot2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=dot2 PE=3 SV=1

 Score =  147 bits (370), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 144/243 (59%), Gaps = 8/243 (3%)

Query: 1   MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD 60
           MR+R G+GA+   +   ++Y++ G  + E Q ++++  L+TF++ L++FA E+  EIK++
Sbjct: 1   MRKRIGIGALNDDEY-LKQYEEVGNELIEQQSDEIASQLSTFQEALKTFAREHATEIKQN 59

Query: 61  AQFRRHFQEMCASIGVDPL--ASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLIL 118
           +QFR  F ++   IG+DP    S +  W+ +GM +FYY+++V+++EVC AT  +NGGL+ 
Sbjct: 60  SQFRNTFVKLALKIGLDPFVSGSDESAWAAVGMNEFYYQVAVRVIEVCYATQMENGGLLS 119

Query: 119 LDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELS 178
           + ++  R +    ++  H+ +   D++ A   L   G GF +  I   QY ++S+P EL+
Sbjct: 120 VSQV-CRFLNEENEAFGHEWLRETDVVRAVDSLAPLGPGFVLEKIAGKQY-IRSLPLELN 177

Query: 179 LDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYW 238
            D ++VL+ V  +   ++++S+L +   W   R    L+ +V +   WID+Q   E  YW
Sbjct: 178 TDQNVVLEAV--EILGYVTISILRDNYAWERSRCIQVLNDLVSKSLLWIDSQGV-EMAYW 234

Query: 239 FPS 241
             S
Sbjct: 235 GAS 237

Component of the endosomal sorting complex required for transport II (ESCRT-II), which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation. The ESCRT-II complex is probably involved in the recruitment of the ESCRT-III complex. Negatively regulates meiotic spindle pole body maturation via indirect regulation of the pcp1 gene. Required for efficient entry into pre-meiotic S phase.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|Q12483|SNF8_YEAST Vacuolar-sorting protein SNF8 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SNF8 PE=1 SV=1

 Score =  127 bits (319), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 79/243 (32%), Positives = 128/243 (52%), Gaps = 15/243 (6%)

Query: 3   RRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQ 62
           ++ G+ A  +  L+  KY D   +I E Q  +L   L  F+++L  FA ++ +E++   +
Sbjct: 2   KQFGLAAFDE--LKDGKYNDVNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPE 59

Query: 63  FRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDEL 122
           FR  F  MC+SIG+DPL+       L  + DFYYE+ ++++E+C  T   NGG+I   EL
Sbjct: 60  FRSKFMHMCSSIGIDPLSLFDRDKHLFTVNDFYYEVCLKVIEICRQTKDMNGGVISFQEL 119

Query: 123 RTRLVKSRGKSLQHQDITNE-DLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDH 181
               V  R  ++   D+    D+L + +  +IF          +G+  ++S+P EL+ D 
Sbjct: 120 EK--VHFRKLNVGLDDLEKSIDMLKSLECFEIFQI--------RGKKFLRSVPNELTSDQ 169

Query: 182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS 241
           + +L+  +     + S+S+L   L W   R++ ALD MV  G  WID Q   E LYW PS
Sbjct: 170 TKILEICSIL--GYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGAEALYWDPS 227

Query: 242 LFT 244
             T
Sbjct: 228 WIT 230

Component of the endosomal sorting complex required for transport II (ESCRT-II), which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation. The ESCRT-II complex is probably involved in the recruitment of the ESCRT-III complex.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q9LIJ4|VP222_ARATH Putative vacuolar protein sorting-associated protein 22 homolog 2 OS=Arabidopsis thaliana GN=VP22-2 PE=5 SV=1

 Score =  119 bits (299), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 61/118 (51%), Positives = 83/118 (70%), Gaps = 4/118 (3%)

Query: 70  MCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVK 128
           MCA+IGVDPLAS KGFW+ LLG+GDFYYE+ VQI+EVC+ T   NGGLI L EL   L +
Sbjct: 1   MCANIGVDPLASNKGFWAELLGIGDFYYEIGVQIIEVCMLTRSHNGGLISLQELCNHLRQ 60

Query: 129 SRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQ 186
            R      + +T +D L A  KLK+ G+ F +I IG+ ++ V+S+P EL+ DH+ +L+
Sbjct: 61  RR--KTDREAVTEDDCLRAISKLKLLGSRFEVITIGKKKF-VRSVPTELNKDHNHILE 115

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	254
332024593	251	Vacuolar-sorting protein SNF8 [Acromyrme	0.972	0.984	0.724	1e-107
380010929	251	PREDICTED: vacuolar-sorting protein SNF8	0.972	0.984	0.716	1e-105
307167587	251	Vacuolar-sorting protein SNF8 [Camponotu	0.972	0.984	0.712	1e-105
328788910	251	PREDICTED: vacuolar-sorting protein SNF8	0.972	0.984	0.716	1e-105
307207318	251	Vacuolar-sorting protein SNF8 [Harpegnat	0.972	0.984	0.708	1e-105
322796202	250	hypothetical protein SINV_10899 [Solenop	0.972	0.988	0.700	1e-104
114051099	249	ELL complex EAP30 subunit [Bombyx mori]	0.980	1.0	0.686	1e-103
357614605	250	ELL complex EAP30 subunit [Danaus plexip	0.980	0.996	0.702	1e-103
345485615	251	PREDICTED: vacuolar-sorting protein SNF8	0.972	0.984	0.716	1e-103
242247603	249	ELL complex EAP30 subunit-like [Acyrthos	0.980	1.0	0.658	9e-99

>gi|332024593|gb|EGI64791.1| Vacuolar-sorting protein SNF8 [Acromyrmex echinatior]

 Score =  392 bits (1008), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 179/247 (72%), Positives = 214/247 (86%)

Query: 1   MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD 60
           MRR+AGVGAIQKQKLEQEKY+DKGT IQENQ EQ+++H+ TFR  LE FAS+YKNEIKK+
Sbjct: 1   MRRKAGVGAIQKQKLEQEKYRDKGTEIQENQFEQMTKHMETFRVNLEEFASKYKNEIKKN 60

Query: 61  AQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           AQFRR F EMCASIGVDPLAS KGFWS+LG+GDFYYEL+VQIVEVC+ATNYKNGGLI LD
Sbjct: 61  AQFRRQFTEMCASIGVDPLASGKGFWSVLGIGDFYYELAVQIVEVCMATNYKNGGLISLD 120

Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           ELRTRL+++RG+  +HQ+ITNEDLLAAAKKLKIFGNGFS++PIG+G++LVQSIPGELS+D
Sbjct: 121 ELRTRLIQARGRRKEHQEITNEDLLAAAKKLKIFGNGFSVVPIGRGKHLVQSIPGELSMD 180

Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
           H+ VL Q +    A++S S+L  EL W  +RAQ ALD M++EG AW+D Q+  E LYWFP
Sbjct: 181 HTAVLSQASLSTNAYVSKSILCKELKWEEDRAQKALDHMMKEGLAWLDRQAKDETLYWFP 240

Query: 241 SLFTECM 247
           SLFT C+
Sbjct: 241 SLFTACI 247

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380010929|ref|XP_003689568.1| PREDICTED: vacuolar-sorting protein SNF8-like isoform 1 [Apis florea] gi|380010931|ref|XP_003689569.1| PREDICTED: vacuolar-sorting protein SNF8-like isoform 2 [Apis florea]

 Score =  387 bits (994), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 177/247 (71%), Positives = 212/247 (85%)

Query: 1   MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD 60
           MRR+AGVGAIQKQKLEQEKYKDKGT IQENQ EQ+++ + TFR  LE FA++YKNEIKK+
Sbjct: 1   MRRKAGVGAIQKQKLEQEKYKDKGTEIQENQFEQMTKQMETFRVNLEEFATKYKNEIKKN 60

Query: 61  AQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           A+FRR F EMCASIGVDPLAS KGFWS+LG+GDFYYEL+VQIVEVC+ATNYKNGGLI LD
Sbjct: 61  ARFRRQFTEMCASIGVDPLASGKGFWSVLGIGDFYYELAVQIVEVCMATNYKNGGLISLD 120

Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           ELR RL+++RG+  +HQ+ITNEDLLAAAKKLKIFGNGFSI+PIG+G++LVQS+PGELS+D
Sbjct: 121 ELRARLIQARGRRKEHQEITNEDLLAAAKKLKIFGNGFSIVPIGRGKHLVQSVPGELSMD 180

Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
           H+ VLQQ +    A++S S+L  EL W ++R Q ALD MV+EG AW+D Q   E LYWFP
Sbjct: 181 HTAVLQQASLSGNAYVSRSMLCKELKWESDRTQKALDHMVKEGLAWLDEQGENETLYWFP 240

Query: 241 SLFTECM 247
           SLFT C+
Sbjct: 241 SLFTACI 247

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307167587|gb|EFN61131.1| Vacuolar-sorting protein SNF8 [Camponotus floridanus]

 Score =  386 bits (991), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 176/247 (71%), Positives = 213/247 (86%)

Query: 1   MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD 60
           MRR+AGVGAIQKQKLEQEKY+DK T IQENQ EQ+++H+ TFR  LE FAS++KNEIKK+
Sbjct: 1   MRRKAGVGAIQKQKLEQEKYRDKTTEIQENQFEQMTKHMETFRVNLEEFASKHKNEIKKN 60

Query: 61  AQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           A FRR F EMCASIGVDPLAS KGFWS+LG+GDFYYEL+VQIVEVC+ATNYKNGGLI LD
Sbjct: 61  AHFRRQFTEMCASIGVDPLASGKGFWSVLGIGDFYYELAVQIVEVCMATNYKNGGLISLD 120

Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           ELRTRL+++RG+  +HQ+ITNEDLLAAAKKL+IFGNGFS++PIG+G++LVQSIPGELS+D
Sbjct: 121 ELRTRLIQARGRRKEHQEITNEDLLAAAKKLRIFGNGFSVVPIGRGKHLVQSIPGELSMD 180

Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
           H+ VL+Q +    A++S S+L  EL W  +RAQ ALD M++EG AW+D QS  E LYWFP
Sbjct: 181 HTAVLRQASLSTNAYVSKSILCKELKWEKDRAQKALDHMMKEGLAWLDEQSEDEMLYWFP 240

Query: 241 SLFTECM 247
           SLFT C+
Sbjct: 241 SLFTACI 247

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328788910|ref|XP_003251206.1| PREDICTED: vacuolar-sorting protein SNF8 [Apis mellifera]

 Score =  386 bits (991), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 177/247 (71%), Positives = 212/247 (85%)

Query: 1   MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD 60
           MRR+AGVGAIQKQKLEQEKYKDKGT IQENQ EQ+++ + TFR  LE FA++YKNEIKK+
Sbjct: 1   MRRKAGVGAIQKQKLEQEKYKDKGTEIQENQFEQMTKQMETFRVNLEEFATKYKNEIKKN 60

Query: 61  AQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           A+FRR F EMCASIGVDPLAS KGFWS+LG+GDFYYEL+VQIVEVC+ATNYKNGGLI LD
Sbjct: 61  ARFRRQFTEMCASIGVDPLASGKGFWSVLGIGDFYYELAVQIVEVCMATNYKNGGLISLD 120

Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           ELR RL+++RG+  +HQ+ITNEDLLAAAKKLKIFGNGFSI+PIG+G++LVQS+PGELS+D
Sbjct: 121 ELRARLIQARGRRKEHQEITNEDLLAAAKKLKIFGNGFSIVPIGRGKHLVQSVPGELSMD 180

Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
           H+ VLQQ +    A++S S+L  EL W ++R Q ALD MV+EG AW+D Q   E LYWFP
Sbjct: 181 HTAVLQQASLSGNAYVSRSMLCKELKWESDRTQKALDHMVKEGLAWLDEQGENEILYWFP 240

Query: 241 SLFTECM 247
           SLFT C+
Sbjct: 241 SLFTACI 247

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307207318|gb|EFN85068.1| Vacuolar-sorting protein SNF8 [Harpegnathos saltator]

 Score =  385 bits (989), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 175/247 (70%), Positives = 213/247 (86%)

Query: 1   MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD 60
           MRR+AGVGAIQKQKLEQEKY+DKGT IQENQ EQ+++H+ TFR  LE FAS++KNEIKK+
Sbjct: 1   MRRKAGVGAIQKQKLEQEKYRDKGTEIQENQFEQMTKHMETFRVNLEEFASKHKNEIKKN 60

Query: 61  AQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           A+FRR F EMCASIGVDPLAS KGFWS+LG+GDFYYEL+VQIVEVC+ATNYKNGGLI LD
Sbjct: 61  ARFRRQFTEMCASIGVDPLASGKGFWSVLGIGDFYYELAVQIVEVCMATNYKNGGLISLD 120

Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           ELRTRL+++RG+  +HQ+ITNEDLLAAAKKL+IFGNGFS++PIG G+YLVQS+PGELS+D
Sbjct: 121 ELRTRLIQARGRRKEHQEITNEDLLAAAKKLRIFGNGFSVVPIGGGKYLVQSVPGELSMD 180

Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
           H+ VL Q +    A++S S+L  EL W  +RAQ AL+ M++EG AW+D Q+  E LYWFP
Sbjct: 181 HTAVLHQASLSANAYVSKSILCKELRWEEDRAQKALNHMMKEGLAWLDEQNESETLYWFP 240

Query: 241 SLFTECM 247
           SLFT C+
Sbjct: 241 SLFTACI 247

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322796202|gb|EFZ18778.1| hypothetical protein SINV_10899 [Solenopsis invicta]

 Score =  384 bits (987), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 173/247 (70%), Positives = 214/247 (86%)

Query: 1   MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD 60
           MRR+AGVGAIQKQKLEQEKY+DKGT IQENQ EQ+++H+ TFR  LE FAS++KNEI+K+
Sbjct: 1   MRRKAGVGAIQKQKLEQEKYRDKGTEIQENQFEQMTKHMETFRVNLEEFASKHKNEIRKN 60

Query: 61  AQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           A FRR F EMCASIGVDPLAS KGFWS+LG+G+FYYEL+VQIVEVC+ATNYKNGGLI LD
Sbjct: 61  AHFRRQFTEMCASIGVDPLASGKGFWSVLGIGEFYYELAVQIVEVCMATNYKNGGLISLD 120

Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           ELRTRL+++RG+  +HQ+ITNEDLLAAAKKL+IFGNGFS++PIG+G++LVQS+PGELS+D
Sbjct: 121 ELRTRLIQARGRRKEHQEITNEDLLAAAKKLRIFGNGFSVVPIGRGKHLVQSVPGELSMD 180

Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
           H+ VL+Q +    A++S S+L  EL W  +RAQ ALD M++EG AW+D Q+  E LYWFP
Sbjct: 181 HTAVLRQASLSTNAYVSKSILCRELKWEEDRAQKALDHMMKEGLAWLDKQAEDETLYWFP 240

Query: 241 SLFTECM 247
           SLFT C+
Sbjct: 241 SLFTACI 247

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|114051099|ref|NP_001040397.1| ELL complex EAP30 subunit [Bombyx mori] gi|95102746|gb|ABF51314.1| ELL complex EAP30 subunit isoform 1 [Bombyx mori] gi|411100662|gb|AFW03816.1| Vps22 [Bombyx mori]

 Score =  382 bits (980), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 171/249 (68%), Positives = 217/249 (87%)

Query: 1   MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD 60
           MRRRAGVGAIQK +LEQEKYK+KGT IQENQ +Q+S+ L  FR+ LE FAS++K+EIKK+
Sbjct: 1   MRRRAGVGAIQKHRLEQEKYKEKGTEIQENQFQQMSKQLEVFRENLEDFASKHKSEIKKN 60

Query: 61  AQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           AQFRR FQEMCA+IGVDPLAS KGFWS+LG+GDFYYEL VQIVEVCLATNYKNGGLI L+
Sbjct: 61  AQFRRQFQEMCAAIGVDPLASGKGFWSVLGIGDFYYELGVQIVEVCLATNYKNGGLITLE 120

Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           ELR+RL+ SRG++ +HQDITNEDLLAA KKL+IFGNGF+++PI +G++LVQS+PGEL++D
Sbjct: 121 ELRSRLIASRGRAKKHQDITNEDLLAAVKKLRIFGNGFTVVPISKGKWLVQSVPGELNMD 180

Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
            +LVLQ+ +    A +SVSVL ++L W+  RA++AL+ MV+EG AW+D+Q P+E LYWFP
Sbjct: 181 QTLVLQKASGLGTAWVSVSVLTSDLGWTEIRAENALNHMVREGLAWVDSQEPKETLYWFP 240

Query: 241 SLFTECMNA 249
           S+F EC++A
Sbjct: 241 SMFAECVSA 249

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357614605|gb|EHJ69169.1| ELL complex EAP30 subunit [Danaus plexippus]

 Score =  381 bits (979), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 175/249 (70%), Positives = 216/249 (86%)

Query: 1   MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD 60
           MRRRAGVGAIQKQ+LEQEKY++KG+ IQENQ +Q+S+ L+ FR+ LE FAS++KNEIKK+
Sbjct: 1   MRRRAGVGAIQKQRLEQEKYREKGSEIQENQFQQMSKQLDVFRENLEEFASKHKNEIKKN 60

Query: 61  AQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           AQFRR FQEMCA+IGVDPLAS KGFWS+LG+GDFYYEL VQIVEVCLATNYKNGGLI LD
Sbjct: 61  AQFRRQFQEMCAAIGVDPLASGKGFWSVLGIGDFYYELGVQIVEVCLATNYKNGGLITLD 120

Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           ELR+RL+ +RG++ +HQDITNEDLLAA KKLKIFGNGF+++ IG+G++LVQSIPGEL+LD
Sbjct: 121 ELRSRLIAARGRAKKHQDITNEDLLAAVKKLKIFGNGFTVVSIGKGKWLVQSIPGELNLD 180

Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
            +LVLQ+ +   +A IS SVL N+L W+  RAQ+AL+ MV+EG AW+D+Q   E LYWFP
Sbjct: 181 QTLVLQKASGLGKAWISKSVLINDLGWNETRAQNALNHMVKEGLAWVDSQDDNEILYWFP 240

Query: 241 SLFTECMNA 249
           S+F EC+ A
Sbjct: 241 SMFNECVTA 249

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345485615|ref|XP_003425304.1| PREDICTED: vacuolar-sorting protein SNF8-like [Nasonia vitripennis]

 Score =  381 bits (978), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 177/247 (71%), Positives = 209/247 (84%)

Query: 1   MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD 60
           MRR+ GVGAI KQK EQE+Y+DKGT +QENQ EQ+++ L TFR  LE FAS++KNEIKK+
Sbjct: 1   MRRKPGVGAIHKQKYEQERYRDKGTELQENQFEQMTKQLETFRINLEEFASKHKNEIKKN 60

Query: 61  AQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           AQFRR F EMCASIGVDPLAS KGFWS+LG+GDFYYEL+VQIVEVCLATNYKNGGLI LD
Sbjct: 61  AQFRRQFTEMCASIGVDPLASGKGFWSVLGIGDFYYELAVQIVEVCLATNYKNGGLISLD 120

Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           ELR RLV++RG+  +HQ+ITNEDLLA+AKKLKI GNGFS++PI +G+YLVQSIPGELS+D
Sbjct: 121 ELRDRLVRARGRRQEHQEITNEDLLASAKKLKILGNGFSVVPISKGKYLVQSIPGELSMD 180

Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
           H+ VLQQ ++   A IS S+L  EL W  ERAQ ALD MV+EG AWID Q+ +E LYWFP
Sbjct: 181 HTAVLQQTSNAGNAFISKSLLQKELKWEGERAQKALDHMVKEGLAWIDNQNEEEPLYWFP 240

Query: 241 SLFTECM 247
           SLFT C+
Sbjct: 241 SLFTACI 247

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242247603|ref|NP_001156166.1| ELL complex EAP30 subunit-like [Acyrthosiphon pisum] gi|239792933|dbj|BAH72744.1| ACYPI004419 [Acyrthosiphon pisum]

 Score =  365 bits (937), Expect = 9e-99,   Method: Compositional matrix adjust.
 Identities = 164/249 (65%), Positives = 208/249 (83%)

Query: 1   MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD 60
           MRRRAGVGAIQKQKLEQEKYKDKGT IQENQ EQ+++ +  FR  LE FA++YKNEIKK+
Sbjct: 1   MRRRAGVGAIQKQKLEQEKYKDKGTVIQENQFEQMTKQMEVFRGNLEEFATKYKNEIKKN 60

Query: 61  AQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           +QFRR FQEMC+SIGVDPLAS KGFWS+LG+GDFYYEL+VQIVEVC+AT+YKNGG+I LD
Sbjct: 61  SQFRRQFQEMCSSIGVDPLASGKGFWSVLGIGDFYYELAVQIVEVCMATSYKNGGIIGLD 120

Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           ELR RL+K+RG+++QHQ+IT +DLL AAKKLKIFGNGF +IP+G+GQY+VQS+PGELS+D
Sbjct: 121 ELRDRLIKARGRNIQHQEITVDDLLCAAKKLKIFGNGFCVIPVGKGQYMVQSVPGELSMD 180

Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
            + VL+ ++S     +S+S L  +LNW   RA +A+  MV EG  W+D+Q+  E  YWFP
Sbjct: 181 QTAVLKLLSSSGSPCVSLSSLKVQLNWEETRAVNAISQMVIEGLCWVDSQNEGEFSYWFP 240

Query: 241 SLFTECMNA 249
           ++F EC+ +
Sbjct: 241 AMFNECITS 249

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	254
FB|FBgn0260940	254	lsn "larsen" [Drosophila melan	0.956	0.956	0.592	1.3e-77
ZFIN|ZDB-GENE-041114-117	258	snf8 "SNF8, ESCRT-II complex s	0.960	0.945	0.548	3.7e-71
UNIPROTKB|Q08DR7	258	SNF8 "Uncharacterized protein"	0.960	0.945	0.544	7.7e-71
UNIPROTKB|I3L6X7	258	SNF8 "Uncharacterized protein"	0.960	0.945	0.544	1.6e-70
MGI|MGI:1343161	258	Snf8 "SNF8, ESCRT-II complex s	0.960	0.945	0.54	2.1e-70
UNIPROTKB|Q96H20	258	SNF8 "Vacuolar-sorting protein	0.960	0.945	0.54	3.3e-70
RGD|1310144	258	Snf8 "SNF8, ESCRT-II complex s	0.960	0.945	0.54	3.3e-70
UNIPROTKB|E2RTF6	258	SNF8 "Uncharacterized protein"	0.960	0.945	0.54	4.3e-70
UNIPROTKB|E1BZH7	258	SNF8 "Uncharacterized protein"	0.960	0.945	0.532	1.8e-69
WB|WBGene00016167	269	vps-22 [Caenorhabditis elegans	0.984	0.929	0.484	1.8e-64

FB|FBgn0260940 lsn "larsen" [Drosophila melanogaster (taxid:7227)]

 Score = 781 (280.0 bits), Expect = 1.3e-77, P = 1.3e-77
 Identities = 144/243 (59%), Positives = 190/243 (78%)

Query:     1 MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD 60
             MRRR G+GAIQ+QKL  EKYKDKGT +QENQLEQ+++ +  FR KLE FA ++K +I+K+
Sbjct:     1 MRRRVGLGAIQQQKLAAEKYKDKGTDLQENQLEQMTKQMEVFRVKLEEFAMKHKEDIRKN 60

Query:    61 AQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
             +QFR+ FQEMCA+IGVDPLA+ KGFWS+LGMGDFYYEL VQ+VEVCLA N+K GGL+ LD
Sbjct:    61 SQFRKQFQEMCAAIGVDPLATGKGFWSVLGMGDFYYELGVQVVEVCLAANHKTGGLMELD 120

Query:   121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
             +LR RL+ +RG+S  HQ+IT ED+L AAKKL IFGNGF +  +G+G+Y+VQSIPGELS++
Sbjct:   121 DLRRRLIAARGQSSVHQEITKEDILMAAKKLSIFGNGFVVHKLGKGKYIVQSIPGELSME 180

Query:   181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
              + +L   ++  +  ++ S L  +L W+  RAQ +LD ++ EG  WID Q+  E  YWFP
Sbjct:   181 ETNILNAASNTEQGCVTQSQLIKDLGWTDYRAQQSLDKVLGEGLCWIDKQAGDEPAYWFP 240

Query:   241 SLF 243
             SLF
Sbjct:   241 SLF 243

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0045450 "bicoid mRNA localization" evidence=IMP

GO:0042981 "regulation of apoptotic process" evidence=IMP

GO:0008283 "cell proliferation" evidence=IMP

GO:0008593 "regulation of Notch signaling pathway" evidence=IEP

GO:0010797 "regulation of multivesicular body size involved in endosome transport" evidence=IDA

ZFIN|ZDB-GENE-041114-117 snf8 "SNF8, ESCRT-II complex subunit, homolog (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 720 (258.5 bits), Expect = 3.7e-71, P = 3.7e-71
 Identities = 137/250 (54%), Positives = 189/250 (75%)

Query:     2 RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
             RR  G GAI K+KL + KYK++G+ + E+Q+ Q+S+ L+TF+  LE FAS++K EI+K +
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGSVLAEDQIAQMSKQLDTFKTHLEEFASKHKQEIRKSS 62

Query:    62 QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
             QFR  FQEMCA+IGVDPLAS KGFWS +LG+GDFYYEL VQI+EVCLA  ++NGGLI LD
Sbjct:    63 QFRVQFQEMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLD 122

Query:   121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
             EL  R++K RGK  Q  D++ +DL+ A KKLK  GNGF +IP+G G YLVQS+P EL++D
Sbjct:   123 ELHHRVLKGRGKFAQ--DVSQDDLVRAIKKLKAMGNGFGMIPVG-GTYLVQSVPAELNMD 179

Query:   181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
             H++VLQ +A K + +++VS +   L W  ERA H LD +++EG AW+D+Q+  E  YW P
Sbjct:   180 HTVVLQ-LAEK-KGYVTVSEIRESLKWEKERACHVLDHLLKEGLAWLDSQAAGEPQYWLP 237

Query:   241 SLFTECMNAE 250
             +LF+E ++ +
Sbjct:   238 ALFSELLSQD 247

GO:0006810 "transport" evidence=IEA

GO:0015031 "protein transport" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|Q08DR7 SNF8 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 717 (257.5 bits), Expect = 7.7e-71, P = 7.7e-71
 Identities = 136/250 (54%), Positives = 188/250 (75%)

Query:     2 RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
             RR  G GAI K+KL + KYK++GT + E+QL Q+S+ L+ F+  LE FAS++K EI+K+ 
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query:    62 QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
             +FR  FQ+MCA+IGVDPLAS KGFWS +LG+GDFYYEL VQI+EVCLA  ++NGGLI L+
Sbjct:    63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query:   121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
             EL  +++K RGK  Q  D++ +DL+ A KKLK  G GFSIIP+G G YL+QS+P EL++D
Sbjct:   123 ELHQQVLKGRGKFAQ--DVSQDDLIRAIKKLKALGTGFSIIPVG-GTYLIQSVPAELNMD 179

Query:   181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
             H++VLQ +A KN  +++VS +   L W TERA+  L+ +++EG AW+D Q+P E  YW P
Sbjct:   180 HTVVLQ-LAEKN-GYVTVSAIKASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLP 237

Query:   241 SLFTECMNAE 250
             +LFT+  + E
Sbjct:   238 ALFTDLYSQE 247

GO:0008134 "transcription factor binding" evidence=IEA

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

GO:0005667 "transcription factor complex" evidence=IEA

UNIPROTKB|I3L6X7 SNF8 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 714 (256.4 bits), Expect = 1.6e-70, P = 1.6e-70
 Identities = 136/250 (54%), Positives = 188/250 (75%)

Query:     2 RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
             RR  G GAI K+KL + KYK++GT + E+QL Q+S+ L+ F+  LE FAS++K EI+K+ 
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query:    62 QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
             +FR  FQ+MCA+IGVDPLAS KGFWS +LG+GDFYYEL VQI+EVCLA  ++NGGLI L+
Sbjct:    63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query:   121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
             EL  +++K RGK  Q  D++ +DL+ A KKLK  G GFSIIP+G G YL+QS+P EL++D
Sbjct:   123 ELHQQVLKGRGKFAQ--DVSQDDLIRAIKKLKALGTGFSIIPVG-GTYLIQSVPAELNMD 179

Query:   181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
             H++VLQ +A KN  +++VS +   L W TERA+  L+ +++EG AW+D Q+P E  YW P
Sbjct:   180 HTVVLQ-LAEKN-GYVTVSDIKASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLP 237

Query:   241 SLFTECMNAE 250
             +LFT+  + E
Sbjct:   238 ALFTDLYSQE 247

GO:0008134 "transcription factor binding" evidence=IEA

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

GO:0005667 "transcription factor complex" evidence=IEA

MGI|MGI:1343161 Snf8 "SNF8, ESCRT-II complex subunit, homolog (S. cerevisiae)" [Mus musculus (taxid:10090)]

 Score = 713 (256.0 bits), Expect = 2.1e-70, P = 2.1e-70
 Identities = 135/250 (54%), Positives = 187/250 (74%)

Query:     2 RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
             RR  G GAI K+KL + KYK++GT + E+QL Q+S+ L+ F+  LE FAS++K EI+K+ 
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query:    62 QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
             +FR  FQ+MCA+IGVDPLAS KGFWS +LG+GDFYYEL VQI+EVCLA  ++NGGLI L+
Sbjct:    63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query:   121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
             EL  +++K RGK  Q  D++ +DL+ A KKLK  G GF IIP+G G YL+QS+P EL++D
Sbjct:   123 ELHQQVLKGRGKFAQ--DVSQDDLIRAIKKLKALGTGFGIIPVG-GTYLIQSVPAELNMD 179

Query:   181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
             H++VLQ +A KN  +++VS +   L W TERA+  L+ +++EG AW+D Q+P E  YW P
Sbjct:   180 HTVVLQ-LAEKN-GYVTVSEIKTSLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLP 237

Query:   241 SLFTECMNAE 250
             +LFT+  + E
Sbjct:   238 ALFTDLYSQE 247

GO:0005634 "nucleus" evidence=IEA

GO:0005667 "transcription factor complex" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0005768 "endosome" evidence=IEA

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

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

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

GO:0006810 "transport" evidence=IEA

GO:0008134 "transcription factor binding" evidence=ISO

GO:0015031 "protein transport" evidence=IEA

GO:0016020 "membrane" evidence=IEA

UNIPROTKB|Q96H20 SNF8 "Vacuolar-sorting protein SNF8" [Homo sapiens (taxid:9606)]

 Score = 711 (255.3 bits), Expect = 3.3e-70, P = 3.3e-70
 Identities = 135/250 (54%), Positives = 187/250 (74%)

Query:     2 RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
             RR  G GAI K+KL + KYK++GT + E+QL Q+S+ L+ F+  LE FAS++K EI+K+ 
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query:    62 QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
             +FR  FQ+MCA+IGVDPLAS KGFWS +LG+GDFYYEL VQI+EVCLA  ++NGGLI L+
Sbjct:    63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query:   121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
             EL  +++K RGK  Q  D++ +DL+ A KKLK  G GF IIP+G G YL+QS+P EL++D
Sbjct:   123 ELHQQVLKGRGKFAQ--DVSQDDLIRAIKKLKALGTGFGIIPVG-GTYLIQSVPAELNMD 179

Query:   181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
             H++VLQ +A KN  +++VS +   L W TERA+  L+ +++EG AW+D Q+P E  YW P
Sbjct:   180 HTVVLQ-LAEKN-GYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLP 237

Query:   241 SLFTECMNAE 250
             +LFT+  + E
Sbjct:   238 ALFTDLYSQE 247

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

GO:0015031 "protein transport" evidence=IEA

GO:0031902 "late endosome membrane" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IDA

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

GO:0008134 "transcription factor binding" evidence=IDA

GO:0005829 "cytosol" evidence=TAS

GO:0016044 "cellular membrane organization" evidence=TAS

GO:0016197 "endosomal transport" evidence=TAS

RGD|1310144 Snf8 "SNF8, ESCRT-II complex subunit, homolog (S. cerevisiae)" [Rattus norvegicus (taxid:10116)]

 Score = 711 (255.3 bits), Expect = 3.3e-70, P = 3.3e-70
 Identities = 135/250 (54%), Positives = 187/250 (74%)

Query:     2 RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
             RR  G GAI K+KL + KYK++GT + E+QL Q+S+ L+ F+  LE FAS++K EI+K+ 
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query:    62 QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
             +FR  FQ+MCA+IGVDPLAS KGFWS +LG+GDFYYEL VQI+EVCLA  ++NGGLI L+
Sbjct:    63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query:   121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
             EL  +++K RGK  Q  D++ +DL+ A KKLK  G GF IIP+G G YL+QS+P EL++D
Sbjct:   123 ELHQQVLKGRGKFAQ--DVSQDDLIRAIKKLKALGTGFGIIPVG-GTYLIQSVPAELNMD 179

Query:   181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
             H++VLQ +A KN  +++VS +   L W TERA+  L+ +++EG AW+D Q+P E  YW P
Sbjct:   180 HTVVLQ-LAEKN-GYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLP 237

Query:   241 SLFTECMNAE 250
             +LFT+  + E
Sbjct:   238 ALFTDLYSQE 247

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0005667 "transcription factor complex" evidence=IEA;ISO

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

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

GO:0008134 "transcription factor binding" evidence=IEA;ISO

GO:0008150 "biological_process" evidence=ND

GO:0015031 "protein transport" evidence=IEA

GO:0031902 "late endosome membrane" evidence=IEA

UNIPROTKB|E2RTF6 SNF8 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 710 (255.0 bits), Expect = 4.3e-70, P = 4.3e-70
 Identities = 135/250 (54%), Positives = 187/250 (74%)

Query:     2 RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
             RR  G GAI K+KL + KYK++GT + E+QL Q+S+ L+ F+  LE FAS++K EI+K+ 
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query:    62 QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
             +FR  FQ+MCA+IGVDPLAS KGFWS +LG+GDFYYEL VQI+EVCLA  ++NGGLI L+
Sbjct:    63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query:   121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
             EL  +++K RGK  Q  D++ +DL+ A KKLK  G GF IIP+G G YL+QS+P EL++D
Sbjct:   123 ELHQQVLKGRGKFAQ--DVSQDDLIRAIKKLKALGTGFGIIPVG-GTYLIQSVPAELNMD 179

Query:   181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
             H++VLQ +A KN  +++VS +   L W TERA+  L+ +++EG AW+D Q+P E  YW P
Sbjct:   180 HTVVLQ-LAEKN-GYVTVSDIKASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLP 237

Query:   241 SLFTECMNAE 250
             +LFT+  + E
Sbjct:   238 ALFTDLYSQE 247

GO:0008134 "transcription factor binding" evidence=IEA

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

GO:0005667 "transcription factor complex" evidence=IEA

UNIPROTKB|E1BZH7 SNF8 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 704 (252.9 bits), Expect = 1.8e-69, P = 1.8e-69
 Identities = 133/250 (53%), Positives = 188/250 (75%)

Query:     2 RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
             RR  G GAI K+KL + KYK++GT + E+QL Q+S+ L+ F+  LE FAS++K EI+K+ 
Sbjct:     3 RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62

Query:    62 QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
             +FR  FQ+MCA+IGVDPLAS KGFWS +LG+GDFYYEL VQI+EVCLA  ++NGGLI L+
Sbjct:    63 EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122

Query:   121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
             EL  +++K RGK  Q  +++ +DLL A KKLK+ G+GF IIP+G G YL+QS+P EL++D
Sbjct:   123 ELHQQVLKGRGKFAQ--EVSQDDLLRAIKKLKVLGSGFGIIPVG-GTYLIQSVPAELNMD 179

Query:   181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
             H++VLQ +A K + +++V  + + L W  ERA+  L+ +++EG AW+DTQ+  E  YW P
Sbjct:   180 HTVVLQ-LAEK-KGYVTVGEIKSSLKWEVERAKQILEHLLKEGMAWLDTQAAGEPQYWLP 237

Query:   241 SLFTECMNAE 250
             +LFTE  + E
Sbjct:   238 ALFTELYSQE 247

GO:0005667 "transcription factor complex" evidence=IEA

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

GO:0008134 "transcription factor binding" evidence=IEA

WB|WBGene00016167 vps-22 [Caenorhabditis elegans (taxid:6239)]

 Score = 657 (236.3 bits), Expect = 1.8e-64, P = 1.8e-64
 Identities = 124/256 (48%), Positives = 180/256 (70%)

Query:     2 RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
             RRR GV AIQK++    K+  KG  +   QL Q SQ L      LE FA  +++EIKK++
Sbjct:     4 RRRIGVAAIQKKQETANKFAAKGDQMAGEQLVQFSQQLEQLSAGLEMFAQRHRDEIKKNS 63

Query:    62 QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
             QFRRHFQEMCAS+GVDPLAS KGFW+  LG GDFYYEL +QIVE+CL+T + NGG++ ++
Sbjct:    64 QFRRHFQEMCASVGVDPLASSKGFWAKALGFGDFYYELGIQIVEICLSTTHINGGIMTVE 123

Query:   121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
             E+R RL+++R ++ +   I+ +D+L A  KLK+ GNGF ++P+G G++LVQS+PGELS+D
Sbjct:   124 EIRNRLMRTRSRT-RKDTISTDDILRAVDKLKVLGNGFELVPLGGGRFLVQSVPGELSMD 182

Query:   181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
             HS VLQ   +++ A+++  ++ ++L W   RA  AL+ +V+EG AW D Q+     YWFP
Sbjct:   183 HSRVLQ--LAEDAAYVTKELIIDKLRWDEARASSALEHLVKEGLAWTDEQASDTTQYWFP 240

Query:   241 SLFTE--CMNAEKETI 254
             SLF +  C ++   ++
Sbjct:   241 SLFLQQYCHSSSSTSV 256

GO:0008340 "determination of adult lifespan" evidence=IMP

---

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)
Q9CZ28	SNF8_MOUSE	No assigned EC number	0.54	0.9606	0.9457	yes	N/A
O94663	SNF8_SCHPO	No assigned EC number	0.3209	0.9251	0.9325	yes	N/A
Q5RK19	SNF8_RAT	No assigned EC number	0.54	0.9606	0.9457	yes	N/A
Q96H20	SNF8_HUMAN	No assigned EC number	0.54	0.9606	0.9457	yes	N/A
Q5U3V9	SNF8_DANRE	No assigned EC number	0.5443	0.9527	0.9379	yes	N/A
Q12483	SNF8_YEAST	No assigned EC number	0.3251	0.8976	0.9785	yes	N/A
Q5RJU0	SNF8_XENTR	No assigned EC number	0.5491	0.9370	0.9260	yes	N/A
Q54RC4	SNF8_DICDI	No assigned EC number	0.4408	0.9448	0.9756	yes	N/A
Q5M759	VP221_ARATH	No assigned EC number	0.4344	0.9330	0.948	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	254
pfam04157	219	pfam04157, EAP30, EAP30/Vps36 family	9e-76

>gnl|CDD|217934 pfam04157, EAP30, EAP30/Vps36 family

 Score =  228 bits (584), Expect = 9e-76
 Identities = 100/225 (44%), Positives = 142/225 (63%), Gaps = 7/225 (3%)

Query: 5   AGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFR 64
            G+  I++ + EQ KY D G  +    LE L +    F + LESFA ++K+EIK + +FR
Sbjct: 1   VGIAGIERSREEQRKYNDLGLQLAFEDLEALMKQAKDFVELLESFAKKHKSEIKANPEFR 60

Query: 65  RHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRT 124
             FQ MCAS+GVDPLAS+KG   L G+GDFYYEL+VQIVE+CLAT  +NGG+I L +L  
Sbjct: 61  AQFQSMCASLGVDPLASKKG-SVLGGVGDFYYELAVQIVEICLATLKENGGIISLQDLYA 119

Query: 125 RLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIP-GELSLDHSL 183
              ++RG +   + ++ EDLL A KKL+  G GF ++ IG G  +VQS+P  ELS D + 
Sbjct: 120 LYNRARGGT---ELVSPEDLLKACKKLEKLGLGFKLVKIGSGVLVVQSVPKSELSEDQTK 176

Query: 184 VLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228
           +L ++A +    ++ S L  +L WS  RA+  L+   +EG  W D
Sbjct: 177 IL-ELAEELG-GVTASELAEKLGWSIGRAKEVLEKAEKEGLLWRD 219

This family includes EAP30 as well as the Vps36 protein. Vps36 is involved in Golgi to endosome trafficking. EAP30 is a subunit of the ELL complex. The ELL is an 80-kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. Length = 219

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	254
KOG3341|consensus	249		100.0
PF04157	223	EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP	100.0
KOG2760|consensus	432		100.0
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	96.76
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	96.73
PF05158	327	RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; Inter	96.61
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	96.52
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	96.21
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	95.91
PRK00135	188	scpB segregation and condensation protein B; Revie	95.31
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	95.13
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	95.05
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	94.7
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	94.66
PRK09334	86	30S ribosomal protein S25e; Provisional	94.58
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	94.49
COG3355	126	Predicted transcriptional regulator [Transcription	94.31
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	94.06
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	93.99
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	93.98
PHA02943	165	hypothetical protein; Provisional	93.95
COG2345	218	Predicted transcriptional regulator [Transcription	93.52
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	93.31
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	93.16
PF09397	65	Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541	93.09
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	92.97
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	92.88
PRK03573	144	transcriptional regulator SlyA; Provisional	92.81
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	92.66
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	92.58
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	92.23
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	92.18
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	92.1
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	92.0
PRK11169	164	leucine-responsive transcriptional regulator; Prov	91.88
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	91.78
COG4901	107	Ribosomal protein S25 [Translation, ribosomal stru	91.76
COG2512	258	Predicted membrane-associated trancriptional regul	91.74
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	91.32
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	91.06
PRK06266	178	transcription initiation factor E subunit alpha; V	91.04
PF03297	105	Ribosomal_S25: S25 ribosomal protein; InterPro: IP	90.98
PF09107	50	SelB-wing_3: Elongation factor SelB, winged helix	90.96
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	90.93
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	90.82
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	90.57
PRK10870	176	transcriptional repressor MprA; Provisional	90.53
smart00843	63	Ftsk_gamma This domain directs oriented DNA transl	90.51
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	90.5
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	90.4
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	90.37
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	90.22
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	90.21
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	89.98
PRK15466	166	carboxysome structural protein EutK; Provisional	89.64
PRK10512	614	selenocysteinyl-tRNA-specific translation factor;	89.4
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	89.04
PF04079	159	DUF387: Putative transcriptional regulators (Ypuh-	89.04
PRK13509	251	transcriptional repressor UlaR; Provisional	88.9
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	88.84
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	88.83
PF03965	115	Penicillinase_R: Penicillinase repressor; InterPro	88.75
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	88.65
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	88.59
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	88.57
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	88.37
PRK13777	185	transcriptional regulator Hpr; Provisional	88.08
PHA00738	108	putative HTH transcription regulator	88.0
COG1414	246	IclR Transcriptional regulator [Transcription]	87.96
PRK03902	142	manganese transport transcriptional regulator; Pro	87.67
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	87.57
PF05331	114	DUF742: Protein of unknown function (DUF742); Inte	87.4
PRK11569	274	transcriptional repressor IclR; Provisional	87.25
COG1522	154	Lrp Transcriptional regulators [Transcription]	86.83
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	86.7
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	86.6
COG3413	215	Predicted DNA binding protein [General function pr	86.55
COG4565	224	CitB Response regulator of citrate/malate metaboli	86.35
COG1846	126	MarR Transcriptional regulators [Transcription]	85.78
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	85.52
PRK09954	362	putative kinase; Provisional	85.41
PRK00215	205	LexA repressor; Validated	84.98
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	84.93
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	84.89
TIGR00281	186	segregation and condensation protein B. Shown to b	84.66
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	84.55
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	84.43
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	84.15
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	84.09
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	84.01
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	84.01
PRK11050	152	manganese transport regulator MntR; Provisional	83.72
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	83.67
PF13730	55	HTH_36: Helix-turn-helix domain	82.49
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	82.23
KOG1767|consensus	110		82.21
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	81.98
PF04558	164	tRNA_synt_1c_R1: Glutaminyl-tRNA synthetase, non-s	81.55
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	81.52
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	81.43
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	81.09
PF09743	272	DUF2042: Uncharacterized conserved protein (DUF204	80.94
PRK11014	141	transcriptional repressor NsrR; Provisional	80.91
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	80.82
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	80.63
PRK10263	1355	DNA translocase FtsK; Provisional	80.45
PF12324	77	HTH_15: Helix-turn-helix domain of alkylmercury ly	80.23

>KOG3341|consensus

Probab=100.00  E-value=1.2e-80  Score=533.42  Aligned_cols=246  Identities=53%  Similarity=0.931  Sum_probs=239.6

Q ss_pred             CCcchhhHHHhccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCccc
Q psy6552           1 MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLA   80 (254)
Q Consensus         1 mrR~vGi~~i~~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~   80 (254)
                      |||++|++||++.+ ...+|++.|+++.++|+.+|..||++|++.|++||+||+.+|++||+||++|+.||++|||||++
T Consensus         1 ~rrrvG~gAi~~~k-~~~ky~~~g~~l~e~Ql~q~~~Ql~~f~~~LeeFA~kH~~ei~knsqFR~~Fq~Mca~IGvDPla   79 (249)
T KOG3341|consen    1 MRRRVGLGAIQKKK-AAKKYKEVGTELAEQQLVQMSKQLEVFQEALEEFARKHKTEIRKNSQFRNQFQEMCASIGVDPLA   79 (249)
T ss_pred             CccchhhhHHhhHH-HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHcCCCccc
Confidence            89999999999997 89999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCcccc-ccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeE
Q psy6552          81 SRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFS  159 (254)
Q Consensus        81 s~kg~w~-~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~  159 (254)
                      ++||||+ ++|+|||||||+|||+|+|+++.+.|||+|++.||..++.+.|+..+  +.||+||++||+++|++||+||.
T Consensus        80 s~kgfw~~~lgvgdFYYelgVqviEvC~at~~~nGGlislqel~~~l~~~R~~~~--e~vt~dD~lrAi~kLk~LG~gFe  157 (249)
T KOG3341|consen   80 SGKGFWAELLGVGDFYYELGVQVIEVCLATKHTNGGLISLQELCNHLLQRRKKDH--EAVTEDDLLRAIDKLKVLGSGFE  157 (249)
T ss_pred             cCcchHHHHhhhHHHHHHHhhHHHHHHHHhhcccCCeeeHHHHHHHHHHHhcccc--hhccHHHHHHHHHHhhccCCCeE
Confidence            9999999 99999999999999999999999999999999999999999998866  89999999999999999999999


Q ss_pred             EEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552         160 IIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF  239 (254)
Q Consensus       160 l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~  239 (254)
                      |++++ |+++|||+|.|||+||+.||++|+  ..||||.+.|.++++|+..||+.+|++|+.+|++|+|.|.++|..|||
T Consensus       158 v~~ig-gK~~vrSVP~ELn~Dht~ILela~--~~gyvt~s~l~~~l~We~~Ra~qaLe~lv~egL~WiD~q~g~e~~YW~  234 (249)
T KOG3341|consen  158 VIKIG-GKKLVRSVPTELNMDHTVILELAE--ILGYVTISLLKANLGWERSRAIQALEHLVKEGLAWIDLQAGDEAAYWF  234 (249)
T ss_pred             EEEec-CEEeeecCcchhcccHHHHHHHHH--hcCceeHHHHHHhccchHHHHHHHHHHHHhccceeeeccCCcceeeec
Confidence            99999 999999999999999999999999  569999999999999999999999999999999999999888999999


Q ss_pred             cccccCccccccc
Q psy6552         240 PSLFTECMNAEKE  252 (254)
Q Consensus       240 p~lf~~~~~~~~~  252 (254)
                      |++|...++++..
T Consensus       235 ps~~~~~~~q~~~  247 (249)
T KOG3341|consen  235 PSLFTDQYAQRSL  247 (249)
T ss_pred             hhhhhHHHhhhhh
Confidence            9999999888753

>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex

Probab=100.00  E-value=1.5e-64  Score=445.43  Aligned_cols=218  Identities=46%  Similarity=0.788  Sum_probs=184.9

Q ss_pred             hhhHHHhccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCcccCCCc
Q psy6552           5 AGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKG   84 (254)
Q Consensus         5 vGi~~i~~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg   84 (254)
                      +||+||+++.++++++++.+.+.+.+.+++|.+|++.|++++++||+||+++|++||+||++|++||++|||||+++++ 
T Consensus         1 ~GI~~l~~~~~~~~~~~~~~~~~a~~dl~~L~~qa~~~~~~l~~fa~k~~~~i~~~~~~r~~f~~~~~~lGvdp~~s~~-   79 (223)
T PF04157_consen    1 VGIAGLQRRQEQKRQYNELGMQLAFQDLEALMSQAKDFVELLENFARKHKSEIKSDPEFRSQFQSMCASLGVDPLASSK-   79 (223)
T ss_dssp             --------------------TCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCSHHHHHHHHHHHHHHT--CHCCTT-
T ss_pred             CchHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCchHHHHHHHHHHHcCCCcccchh-
Confidence            6999999999999999999999999999999999999999999999999999999999999999999999999998888 


Q ss_pred             ccc-cc-ccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhc-CCCCCCCCCCHHHHHHHHHHhhhhCCCeEEE
Q psy6552          85 FWS-LL-GMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSR-GKSLQHQDITNEDLLAAAKKLKIFGNGFSII  161 (254)
Q Consensus        85 ~w~-~l-g~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~R-g~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~  161 (254)
                      +|+ .+ |.++||||||+||+|||..++++|||||+|+||||+|||+| |.    ++|||+||++||++|++||.||+++
T Consensus        80 ~~s~~l~~~~~f~~ELa~qi~e~c~~~~~~~GGii~L~dl~~~~nr~R~g~----~lISp~Di~~A~~~l~~lg~g~~l~  155 (223)
T PF04157_consen   80 FWSESLKGSGDFYYELAVQIAEVCLATRSKNGGIISLSDLYCRYNRARGGS----ELISPEDILRACKLLEVLGLGFRLR  155 (223)
T ss_dssp             CCCCCCSCHHHHHHHHHHHHHHHHHHHCCTTTSEEEHHHHHHHHHHCTTTS----ST--HHHHHHHHHHHCCCTSSEEEE
T ss_pred             hhhhccccchhHHHHHHHHHHHHHHHHHhcCCCEEEHHHHHHHHHHhcccC----CCcCHHHHHHHHHHHHHcCCCeEEE
Confidence            999 87 88999999999999999999999999999999999999999 66    7999999999999999999999999


Q ss_pred             EeCCceEEEEccC-CCCChhHHHHHHHh-hccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         162 PIGQGQYLVQSIP-GELSLDHSLVLQQV-ASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       162 ~~~sg~~vv~s~p-~els~D~~~il~l~-~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      +|+||++||+++| .++|.|+.+|++++ .. ..||+|+.+|++++||++.||+++|+.|+++|++|||
T Consensus       156 ~~~sg~~vv~s~~~~e~~~~~~~il~~~~~~-~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~~D  223 (223)
T PF04157_consen  156 KFGSGVKVVQSVPYSELSKDQSRILELAEEE-NGGGVTASELAEKLGWSVERAKEALEELEREGLLWRD  223 (223)
T ss_dssp             EETTTEEEEECST-CHH-HHHHHHHHHH--T-TTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEEEE
T ss_pred             EeCCCcEEEEeCCchhhhHHHHHHHHHHHhh-cCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEeeC
Confidence            9999999999999 88999999999999 32 4899999999999999999999999999999999999

The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.

>KOG2760|consensus

Probab=100.00  E-value=7e-45  Score=335.82  Aligned_cols=227  Identities=27%  Similarity=0.389  Sum_probs=199.2

Q ss_pred             cchhhHHHhccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHH---HHHHHhh---hhhhcCHHHHHHHHHHHHHcCC
Q psy6552           3 RRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLE---SFASEYK---NEIKKDAQFRRHFQEMCASIGV   76 (254)
Q Consensus         3 R~vGi~~i~~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~---~FA~kh~---~~I~~dp~fr~~f~~mc~~lGV   76 (254)
                      |++||+||+|+.+.|.+.++..  |.. +|+||+++|+.||+|+.   +||.|.+   ++|..|++.  .|.++..++||
T Consensus       196 r~vGI~giEr~~e~q~~~td~~--i~~-AFqDLskLMs~Akemv~Lsk~~~~Km~~~~g~i~dDetv--~~ks~llsLGI  270 (432)
T KOG2760|consen  196 RMVGISGIERSLEEQLKKTDKT--INN-AFQDLSKLMSLAKEMVSLSKSIAEKMKSKTGEIQDDETV--RFKSYLLSLGI  270 (432)
T ss_pred             eeechhHHHHHHHHHHHhcchh--HHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcCchhhh--hhHHhhhhhcc
Confidence            5799999999999998888874  555 99999999999999997   8888884   678888887  89999999999


Q ss_pred             C-cccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhC
Q psy6552          77 D-PLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFG  155 (254)
Q Consensus        77 d-Pl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg  155 (254)
                      + |++... |  -+....|+.+||+||.|+...+.++|||||+|.|+||+|||+||+    ++|||+|+.+||++|+.||
T Consensus       271 ~dpvt~~n-~--~~s~~~Y~~~Lakqlse~l~~~lee~ggmisLtdvY~~~NRaRG~----eLiSPedl~~ACe~le~l~  343 (432)
T KOG2760|consen  271 LDPVTKDN-F--GLSLSLYHQELAKQLSEFLRLPLEENGGMISLTDVYCRYNRARGT----ELISPEDLVNACELLEHLG  343 (432)
T ss_pred             CCcchhcc-c--cchHHHHHHHHHHHHHHHHhcchhhcCCEEEHHHHHHHHHHhccC----CCCCHHHHHHHHHHHHhcC
Confidence            8 998432 0  111248999999999999999999999999999999999999999    8999999999999999999


Q ss_pred             CCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhcc-CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCc
Q psy6552         156 NGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASK-NEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQE  234 (254)
Q Consensus       156 ~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~-~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e  234 (254)
                      .|+++++|+||+.|||...  .+ |..+++++.+.. ..+..|+++++..+||++..|+|+|..++++|.+|||++  .|
T Consensus       344 ~pl~L~kf~SGvlvvqlKs--~~-~~e~l~~~l~~V~~~etl~a~e~A~~l~is~~lakErLl~AE~~G~lcRD~s--~e  418 (432)
T KOG2760|consen  344 VPLRLRKFNSGVLVVQLKS--HS-DEEKLVDALEDVSKSETLTASELAKKLGISLGLAKERLLNAEDEGLLCRDDS--VE  418 (432)
T ss_pred             CceEEEEcCCceEEEEeec--cc-hHHHHHHHHHhccCcchhhHHHHHHHhCchHHHHHHHHHHHHhcCCeeeccC--cc
Confidence            9999999999999999775  44 666665555432 245678999999999999999999999999999999999  69


Q ss_pred             ccceecccccCc
Q psy6552         235 HLYWFPSLFTEC  246 (254)
Q Consensus       235 ~~yw~p~lf~~~  246 (254)
                      |+|||||+|...
T Consensus       419 GL~fY~N~f~e~  430 (432)
T KOG2760|consen  419 GLRFYPNLFMES  430 (432)
T ss_pred             ceeecccccccC
Confidence            999999999764

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

Probab=96.76  E-value=0.0073  Score=43.62  Aligned_cols=56  Identities=11%  Similarity=0.135  Sum_probs=46.2

Q ss_pred             HHHHHHHhhccCCC-cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552         181 HSLVLQQVASKNEA-HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP  240 (254)
Q Consensus       181 ~~~il~l~~~~~~g-~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p  240 (254)
                      ...||++.... ++ .+|+.+|+..+|.+..-+..+|..|+++|+++.+.+   .+.+|.-
T Consensus         8 ~~~IL~~L~~~-g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~---~~~~W~i   64 (68)
T smart00550        8 EEKILEFLENS-GDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGG---TPPLWKL   64 (68)
T ss_pred             HHHHHHHHHHC-CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCC---CCCceEe
Confidence            45788888843 23 399999999999999999999999999999999865   3457764

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

>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=96.73  E-value=0.0042  Score=41.33  Aligned_cols=47  Identities=17%  Similarity=0.232  Sum_probs=38.2

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA  225 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l  225 (254)
                      ||.-+..|+....+  .|.+|..+|++.+|+|..-+...|..|+++|++
T Consensus         1 l~~~~~~Il~~l~~--~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I   47 (48)
T PF13412_consen    1 LDETQRKILNYLRE--NPRITQKELAEKLGISRSTVNRYLKKLEEKGLI   47 (48)
T ss_dssp             --HHHHHHHHHHHH--CTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence            35556788888884  578999999999999999999999999999986

...

>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=96.61  E-value=0.076  Score=49.78  Aligned_cols=119  Identities=16%  Similarity=0.215  Sum_probs=89.3

Q ss_pred             HHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccC
Q psy6552          95 YYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIP  174 (254)
Q Consensus        95 y~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p  174 (254)
                      ..+|+.+|.+.|...  ..+..++..||...+          ...+..++..|++.|-.-| -+++++-+ |..+.+-++
T Consensus         7 ~~~~~~~l~~~~~~~--~~~~~~~~~~L~~~~----------~~~~~~~~~~~in~Ll~~~-~~~~~~~~-~~l~~~~~~   72 (327)
T PF05158_consen    7 LSELEKKLLELCREN--PSPKGFSQEDLQQLI----------PGLDLQELVKAINELLSSG-LLKLLKKG-GGLSYKAVS   72 (327)
T ss_dssp             HHHHHHHHHHHHHH-----SS-EEHHHHHHH-----------TTS-HHHHHHHHHHHHHHT-SEEEEE-S-SSEEEEE--
T ss_pred             HHHHHHHHHHHHHHh--cCCCCcCHHHHHhhc----------CCCCHHHHHHHHHHHHhCC-CEEEEEcC-CEEEEEEeC
Confidence            356888999999876  567899999999882          4679999999999987765 68888855 555555552


Q ss_pred             -------CCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         175 -------GELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       175 -------~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                             ..++.|+..|+.+++..+.-+|-..+|..+.|.........|..|+..+++=-
T Consensus        73 ~~~a~k~~~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~  132 (327)
T PF05158_consen   73 EEEAKKLKGLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKS  132 (327)
T ss_dssp             SSS-----SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHhhhcCCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEE
Confidence                   45788899999998876567899999999999999999999999999998743

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.

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

Probab=96.52  E-value=0.0088  Score=42.81  Aligned_cols=57  Identities=16%  Similarity=0.232  Sum_probs=43.6

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP  240 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p  240 (254)
                      .|++..... .+.+|+.++++.+|.|...|+..|+.|+++|.+-....-.+-..||.-
T Consensus         4 ~Il~~i~~~-~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~~~~W~l   60 (62)
T PF04703_consen    4 KILEYIKEQ-NGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRGKSTYWRL   60 (62)
T ss_dssp             CHHHHHHHH-TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSSS-EEEE
T ss_pred             HHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCcceeeee
Confidence            467777743 578999999999999999999999999999999776653344569964

>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=96.21  E-value=0.0063  Score=43.43  Aligned_cols=52  Identities=17%  Similarity=0.174  Sum_probs=44.9

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      +|..+..|+...-.  .|..|+.+|++.+|++...+..+|+.|++.|++-+...
T Consensus         6 Ls~~E~~vy~~Ll~--~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~   57 (68)
T PF01978_consen    6 LSENEAKVYLALLK--NGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEG   57 (68)
T ss_dssp             HHHHHHHHHHHHHH--HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             cCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence            66677777655432  58999999999999999999999999999999999975

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.

>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=95.91  E-value=0.027  Score=39.19  Aligned_cols=47  Identities=17%  Similarity=0.243  Sum_probs=41.7

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      +..|+++..  ..|.+|+.+|++.||.|..=++.-|..|++.|++-+--
T Consensus         2 ~~~Il~~l~--~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~   48 (57)
T PF08220_consen    2 QQQILELLK--EKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRTH   48 (57)
T ss_pred             HHHHHHHHH--HcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence            457888888  46999999999999999999999999999999987653

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

>PRK00135 scpB segregation and condensation protein B; Reviewed

Probab=95.31  E-value=0.17  Score=43.85  Aligned_cols=94  Identities=17%  Similarity=0.189  Sum_probs=73.1

Q ss_pred             eeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhh----hCCCeEEEEeCCceEEEEccCC---------------CC
Q psy6552         117 ILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKI----FGNGFSIIPIGQGQYLVQSIPG---------------EL  177 (254)
Q Consensus       117 i~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~----Lg~g~~l~~~~sg~~vv~s~p~---------------el  177 (254)
                      +++.++-..++           ++++++..+++.|..    -+.|++|+.++ |...+++.|.               .|
T Consensus        21 ls~~~La~~l~-----------~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~-~~y~l~tk~e~~~~v~~~~~~~~~~~L   88 (188)
T PRK00135         21 LSLEQLAEILE-----------LEPTEVQQLLEELQEKYEGDDRGLKLIEFN-DVYKLVTKEENADYLQKLVKTPIKQSL   88 (188)
T ss_pred             CCHHHHHHHHC-----------CCHHHHHHHHHHHHHHHhhCCCCEEEEEEC-CEEEEEEcHHHHHHHHHHhcccccCCC
Confidence            67777776643           467899999999843    27899999999 7777777552               46


Q ss_pred             ChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         178 SLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       178 s~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      |.-...+|.++..  .+.||-.+|++..|.+.   ..++..|++.|++-.
T Consensus        89 S~aaLEtLaiIay--~qPiTr~eI~~irGv~~---~~ii~~L~~~gLI~e  133 (188)
T PRK00135         89 SQAALEVLAIIAY--KQPITRIEIDEIRGVNS---DGALQTLLAKGLIKE  133 (188)
T ss_pred             CHHHHHHHHHHHH--cCCcCHHHHHHHHCCCH---HHHHHHHHHCCCeEE
Confidence            6555566766663  47899999999999996   688999999999875

>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=95.13  E-value=0.052  Score=36.76  Aligned_cols=46  Identities=22%  Similarity=0.367  Sum_probs=38.0

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      .||+..... .+.+|..+|++.+|+++.-+...|..|++.|++-.|.
T Consensus         7 ~iL~~l~~~-~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~dp   52 (52)
T PF09339_consen    7 RILEALAES-GGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVERDP   52 (52)
T ss_dssp             HHHHCHHCT-BSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEECS
T ss_pred             HHHHHHHcC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeecCc
Confidence            456655543 5668999999999999999999999999999998873

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.

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=95.05  E-value=0.095  Score=35.31  Aligned_cols=46  Identities=17%  Similarity=0.256  Sum_probs=38.6

Q ss_pred             CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552         194 AHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       194 g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      +.+|..++++.+|+++.-+...|+.|++.|++.....  +...||.++
T Consensus         9 ~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~--~~~~~~~~~   54 (66)
T smart00418        9 GELCVCELAEILGLSQSTVSHHLKKLREAGLVESRRE--GKRVYYSLT   54 (66)
T ss_pred             CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeec--CCEEEEEEc
Confidence            5789999999999999999999999999999997764  345555443

>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=94.70  E-value=0.19  Score=34.54  Aligned_cols=55  Identities=16%  Similarity=0.178  Sum_probs=43.1

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.||-.....+.+.+|+.+|++.+++++.-+...+..|++.|++.+....
T Consensus         3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~   57 (62)
T PF12802_consen    3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDP   57 (62)
T ss_dssp             STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred             cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence            5666777776666432223999999999999999999999999999999988653

...

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

Probab=94.66  E-value=0.051  Score=39.08  Aligned_cols=46  Identities=17%  Similarity=0.289  Sum_probs=36.4

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .|.+.+.  ..|.+|..+|+.+|++++.-.+..|+.+++.|.+-.-+.
T Consensus         4 ~i~~~l~--~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~   49 (69)
T PF09012_consen    4 EIRDYLR--ERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDM   49 (69)
T ss_dssp             HHHHHHH--HS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred             HHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence            4556666  468999999999999999999999999999999876543

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

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=94.58  E-value=0.15  Score=38.77  Aligned_cols=38  Identities=13%  Similarity=0.137  Sum_probs=34.8

Q ss_pred             CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE-EEeCC
Q psy6552         193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYA-WIDTQ  230 (254)
Q Consensus       193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l-wvD~q  230 (254)
                      ..+||++.|++.+++...+|+.+|.+|+++|++ .|...
T Consensus        39 ~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~   77 (86)
T PRK09334         39 EKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLYSKN   77 (86)
T ss_pred             CcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEecC
Confidence            579999999999999999999999999999998 66544

>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=94.49  E-value=0.19  Score=35.48  Aligned_cols=47  Identities=9%  Similarity=0.127  Sum_probs=40.5

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ..|.++.+  .++.++..+|++.+|.++.=+.+.|..|.+.|++..+..
T Consensus        11 ~~Iy~l~~--~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~y   57 (60)
T PF01325_consen   11 KAIYELSE--EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEPY   57 (60)
T ss_dssp             HHHHHHHH--CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHHc--CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCC
Confidence            35567777  578999999999999999999999999999999988754

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 ....

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=94.31  E-value=0.18  Score=41.13  Aligned_cols=54  Identities=19%  Similarity=0.144  Sum_probs=44.1

Q ss_pred             CChhHHHH-HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCC
Q psy6552         177 LSLDHSLV-LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSP  232 (254)
Q Consensus       177 ls~D~~~i-l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~  232 (254)
                      ++.....| ..+.+  ..|..|+++|++.++.+...+...|+.|+..|++-+-..+-
T Consensus        25 Ls~~Dv~v~~~LL~--~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~   79 (126)
T COG3355          25 LSELDVEVYKALLE--ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNL   79 (126)
T ss_pred             CcHHHHHHHHHHHh--hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeecc
Confidence            44433334 45565  36899999999999999999999999999999999987763

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=94.06  E-value=0.21  Score=32.64  Aligned_cols=47  Identities=19%  Similarity=0.193  Sum_probs=39.3

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ..++.....  .+++|+.+|++.+++++.-+...|..|.+.|++-...+
T Consensus         3 ~~il~~l~~--~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~~   49 (53)
T smart00420        3 QQILELLAQ--QGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVHG   49 (53)
T ss_pred             HHHHHHHHH--cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeec
Confidence            456666653  46799999999999999999999999999999876654

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=93.99  E-value=0.12  Score=35.29  Aligned_cols=52  Identities=15%  Similarity=0.176  Sum_probs=43.1

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      +|..|-.+|..+..  .|.+|..+|++.++.++.-+...+..|++.|++-+-..
T Consensus         1 lt~~q~~iL~~l~~--~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~   52 (59)
T PF01047_consen    1 LTPSQFRILRILYE--NGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERD   52 (59)
T ss_dssp             STHHHHHHHHHHHH--HSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccC
Confidence            35567778877774  46799999999999999999999999999999987654

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 ....

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=93.98  E-value=0.28  Score=36.23  Aligned_cols=54  Identities=26%  Similarity=0.228  Sum_probs=46.8

Q ss_pred             CCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         175 GELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       175 ~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ..++..+..|+.++.  ..|.+|..+|++.++++..-....|..|++.|++-+...
T Consensus         6 ~~l~~~~~~il~~l~--~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~   59 (101)
T smart00347        6 LGLTPTQFLVLRILY--EEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPS   59 (101)
T ss_pred             cCCCHHHHHHHHHHH--HcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCC
Confidence            347878888888887  357899999999999999999999999999999987654

>PHA02943 hypothetical protein; Provisional

Probab=93.95  E-value=0.19  Score=42.21  Aligned_cols=55  Identities=22%  Similarity=0.224  Sum_probs=47.1

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      ..||++..   .|..|.+++++.+|.|...|+-.|..|+++|.+-.=..  +-..||.-+
T Consensus        14 ~eILE~Lk---~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~--G~~tyw~l~   68 (165)
T PHA02943         14 IKTLRLLA---DGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEI--GRAAIWCLD   68 (165)
T ss_pred             HHHHHHHh---cCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEee--cceEEEEEC
Confidence            45677773   68999999999999999999999999999999988665  567888744

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=93.52  E-value=0.24  Score=43.96  Aligned_cols=49  Identities=22%  Similarity=0.279  Sum_probs=43.5

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCC
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSP  232 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~  232 (254)
                      ..|+.++.  ..|.+|+.+|++.+|+|+.-++.+|+.|+++|++-+-.+.+
T Consensus        14 ~~il~lL~--~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~   62 (218)
T COG2345          14 ERILELLK--KSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQG   62 (218)
T ss_pred             HHHHHHHh--ccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccC
Confidence            56788888  46899999999999999999999999999999998876654

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=93.31  E-value=0.42  Score=37.20  Aligned_cols=55  Identities=18%  Similarity=0.301  Sum_probs=44.9

Q ss_pred             CChhHHHHHHHhh--ccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVA--SKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~--~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..|-.+|..+.  ....|.+|..+|++.+++++.-.-..++.|++.|++.+-..+
T Consensus        23 ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~   79 (109)
T TIGR01889        23 LSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSE   79 (109)
T ss_pred             CCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCc
Confidence            6666766765543  222578999999999999999999999999999999986654

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.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=93.16  E-value=0.38  Score=35.56  Aligned_cols=46  Identities=24%  Similarity=0.343  Sum_probs=39.6

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      .|+++.... .+.+|+.+|++.+|.+..-+...|..|++.|++-.+.
T Consensus         9 ~Il~~l~~~-~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~   54 (91)
T smart00346        9 AVLRALAEE-PGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDG   54 (91)
T ss_pred             HHHHHHHhC-CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecC
Confidence            456666532 4789999999999999999999999999999999874

>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []

Probab=93.09  E-value=0.28  Score=35.45  Aligned_cols=47  Identities=21%  Similarity=0.260  Sum_probs=36.2

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      ...+++++-.  .+.+|++.|..+|++-..||...++.|+++|++==-+
T Consensus         8 y~~a~~~V~~--~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~~~   54 (65)
T PF09397_consen    8 YEEAVEFVIE--EGKASISLLQRKFRIGYNRAARIIDQLEEEGIVSPAN   54 (65)
T ss_dssp             HHHHHHHHHH--CTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE---
T ss_pred             HHHHHHHHHH--cCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCCC
Confidence            4566666663  4789999999999999999999999999999985433

Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.

>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=92.97  E-value=0.13  Score=39.77  Aligned_cols=64  Identities=13%  Similarity=0.272  Sum_probs=40.9

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE----eCCCCCcccceeccc
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI----DTQSPQEHLYWFPSL  242 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv----D~q~~~e~~yw~p~l  242 (254)
                      .++++..|+.+...  .|.++.++|+..+|+++.-.+..|..|.++|++..    |++.+....|||.++
T Consensus        11 yg~~~~~Il~~L~~--~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~~~~~yw~i~~   78 (105)
T PF02002_consen   11 YGEEAVRILDALLR--KGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERGWTRYYWYIDY   78 (105)
T ss_dssp             S-STTHHHHHHHHH--H--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE--------EEEEE-TH
T ss_pred             cCchHHHHHHHHHH--cCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCcEEEEEEEEcH
Confidence            34567788887763  47899999999999999999999999999999943    333223357888764

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.

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=92.88  E-value=0.33  Score=40.17  Aligned_cols=49  Identities=14%  Similarity=0.092  Sum_probs=43.4

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      ++.-...||.+.+  ..|..|..+|++.+|+|..-+...++.|+++|+++.
T Consensus         7 lD~~D~~Il~~Lq--~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~   55 (153)
T PRK11179          7 IDNLDRGILEALM--ENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITG   55 (153)
T ss_pred             cCHHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence            5555667888888  459999999999999999999999999999999984

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=92.81  E-value=0.55  Score=38.00  Aligned_cols=55  Identities=18%  Similarity=0.184  Sum_probs=45.6

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .++.-|-.+|..+... .+++|+.+|++.+++++.-....++.|++.|++.+-..+
T Consensus        28 glt~~q~~vL~~l~~~-~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~   82 (144)
T PRK03573         28 ELTQTHWVTLHNIHQL-PPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCA   82 (144)
T ss_pred             CCCHHHHHHHHHHHHc-CCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCC
Confidence            3666676776666532 467999999999999999999999999999999998664

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=92.66  E-value=0.67  Score=42.39  Aligned_cols=143  Identities=10%  Similarity=0.107  Sum_probs=83.3

Q ss_pred             cCHHHHHHHHHHHHHcCCCc-ccCCCcccc-cc-ccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCC
Q psy6552          59 KDAQFRRHFQEMCASIGVDP-LASRKGFWS-LL-GMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQ  135 (254)
Q Consensus        59 ~dp~fr~~f~~mc~~lGVdP-l~s~kg~w~-~l-g~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~  135 (254)
                      .+|.|  .++.+|..+|++| -     +.+ .+ |-...-..-+.+|++++--+-.+.    +--++.-.+++       
T Consensus        24 ~~p~f--S~R~fa~~~G~ss~s-----~L~~v~~Gkr~Ls~~~~~k~a~~l~L~~~E~----~yF~~lV~f~~-------   85 (271)
T TIGR02147        24 TDPAF--SWRFFAEKAGFSSTS-----YLNDIIKGKKNLTKRMIPKFAEALGLDEKEA----AYFEAMVNFGQ-------   85 (271)
T ss_pred             cCcCc--CHHHHHHHhCCCCHH-----HHHHHHcCCCCCCHHHHHHHHHHcCCCHHHH----HHHHHHHHHhc-------
Confidence            68888  7899999999985 2     111 11 111122333444444442211110    00011112232       


Q ss_pred             CCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCC--ChhHHHHHHHhhccCCCcc-cHHHHHHhcC--CCHH
Q psy6552         136 HQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGEL--SLDHSLVLQQVASKNEAHI-SVSVLNNELN--WSTE  210 (254)
Q Consensus       136 ~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~el--s~D~~~il~l~~~~~~g~v-t~~~l~~~l~--ws~~  210 (254)
                        .-|+++=.+|.+.+..+...-.++.++       ....+.  +=-+..|.+++.-  .++- ++..|++.++  +|.+
T Consensus        86 --ak~~~~k~~~~~~~~~~~~~~~~~~L~-------~~~~~y~~~W~~~virel~~~--~~~~~~~~~ia~~l~p~is~~  154 (271)
T TIGR02147        86 --AKTDTEKQQFFEEMQALKPRPRLRVLA-------ADQFEYYRHWYNSVIRELLGV--MPFADDPEELAKRCFPKISAE  154 (271)
T ss_pred             --cCCHHHHHHHHHHHHHHhhhchheecc-------HHHHHHHHHHHHHHHHHHhhc--CCCCCCHHHHHHHhCCCCCHH
Confidence              246777777777777664322222222       111111  1135778888884  4555 9999999999  9999


Q ss_pred             HHHHHHHHHHHcCcEEEeCC
Q psy6552         211 RAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       211 ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .+++.|+.|++-|++=.|..
T Consensus       155 ev~~sL~~L~~~glikk~~~  174 (271)
T TIGR02147       155 QVKESLDLLERLGLIKKNED  174 (271)
T ss_pred             HHHHHHHHHHHCCCeeECCC
Confidence            99999999999999998854

This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=92.58  E-value=0.58  Score=38.02  Aligned_cols=54  Identities=19%  Similarity=0.150  Sum_probs=46.2

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .++.-|-.||....  ..+.+|+.+|++.+++++.-.-..|+.|++.|++-+-..+
T Consensus        37 glt~~q~~vL~~l~--~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~   90 (144)
T PRK11512         37 DITAAQFKVLCSIR--CAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP   90 (144)
T ss_pred             CCCHHHHHHHHHHH--HcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCc
Confidence            36666777777665  2578999999999999999999999999999999997664

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=92.23  E-value=0.71  Score=37.42  Aligned_cols=62  Identities=13%  Similarity=0.149  Sum_probs=47.5

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHh----cCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceeccc
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNE----LNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSL  242 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~----l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~l  242 (254)
                      +++-+..|+.+.=  ..|.+|+.++.+.    .+|++.-..+.|..|++.|++=++..  +...+|.|..
T Consensus         2 Lt~~E~~VM~vlW--~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~--gr~~~Y~p~v   67 (130)
T TIGR02698         2 ISDAEWEVMRVVW--TLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEKE--GRKFIYTALV   67 (130)
T ss_pred             CCHHHHHHHHHHH--cCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeecC--CCcEEEEecC
Confidence            5555667777775  3567899995555    48999999999999999999988865  4556777643

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.

>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A)

Probab=92.18  E-value=0.51  Score=36.23  Aligned_cols=50  Identities=28%  Similarity=0.422  Sum_probs=41.3

Q ss_pred             CChhHHHHHHHhhcc--CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552         177 LSLDHSLVLQQVASK--NEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW  226 (254)
Q Consensus       177 ls~D~~~il~l~~~~--~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw  226 (254)
                      ++.-+..|++++...  ..-+|++.+|++.++.+....+.+|+.|..+|.+.
T Consensus        45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY   96 (102)
T PF08784_consen   45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIY   96 (102)
T ss_dssp             S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEe
Confidence            666788999998751  13479999999999999999999999999999875

RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.

>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=92.10  E-value=0.36  Score=33.60  Aligned_cols=47  Identities=21%  Similarity=0.276  Sum_probs=39.3

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ..|+....  ..+..|+.+|++.+|++..-+..+|..|++.|++=+..+
T Consensus        13 ~~Il~~L~--~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~~   59 (61)
T PF12840_consen   13 LRILRLLA--SNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVERE   59 (61)
T ss_dssp             HHHHHHHH--HCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHh--cCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecc
Confidence            45677663  268899999999999999999999999999999877654

...

>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=92.00  E-value=0.55  Score=33.69  Aligned_cols=55  Identities=22%  Similarity=0.271  Sum_probs=40.8

Q ss_pred             CCChhHHHHHHHhhcc--CCC-cccHHHHHHhcCCC-HHHHHHHHHHHHHcCcEEEeCC
Q psy6552         176 ELSLDHSLVLQQVASK--NEA-HISVSVLNNELNWS-TERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       176 els~D~~~il~l~~~~--~~g-~vt~~~l~~~l~ws-~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      +|+.-|..||+.+...  ..| .-|+.+|++.+|++ +.-+...|..|++.|++=++..
T Consensus         3 ~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~   61 (65)
T PF01726_consen    3 ELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDPG   61 (65)
T ss_dssp             ---HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred             CCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCCC
Confidence            3677788888876431  123 47999999999996 9999999999999999988865

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.

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=91.88  E-value=0.38  Score=40.27  Aligned_cols=50  Identities=14%  Similarity=0.195  Sum_probs=44.0

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      .++.-..+||.+.+  ..|.+|..+|++.+|.|..-+...++.|+++|+++.
T Consensus        11 ~lD~~D~~IL~~Lq--~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~   60 (164)
T PRK11169         11 DLDRIDRNILNELQ--KDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG   60 (164)
T ss_pred             hHHHHHHHHHHHhc--cCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            35544668888888  569999999999999999999999999999999984

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

Probab=91.78  E-value=0.88  Score=31.24  Aligned_cols=49  Identities=16%  Similarity=0.183  Sum_probs=41.5

Q ss_pred             hhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         179 LDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       179 ~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ..+..|+..+.  ..+ ++..++++.++.+..-+...|+.|++.|++-+...
T Consensus         7 ~~~~~il~~l~--~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~   55 (78)
T cd00090           7 PTRLRILRLLL--EGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRRE   55 (78)
T ss_pred             hHHHHHHHHHH--HCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEe
Confidence            35667777766  245 99999999999999999999999999999998755

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.

>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]

Probab=91.76  E-value=0.22  Score=39.01  Aligned_cols=38  Identities=18%  Similarity=0.215  Sum_probs=34.4

Q ss_pred             CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ..+||+..|++.+|+....|+.+|.+|+++|.+-.=..
T Consensus        57 ~r~VTpy~la~r~gI~~SvAr~vLR~LeeeGvv~lvsk   94 (107)
T COG4901          57 ERVVTPYVLASRYGINGSVARIVLRHLEEEGVVQLVSK   94 (107)
T ss_pred             ceeecHHHHHHHhccchHHHHHHHHHHHhCCceeeecc
Confidence            57999999999999999999999999999998865444

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=91.74  E-value=0.41  Score=43.52  Aligned_cols=55  Identities=16%  Similarity=0.219  Sum_probs=49.5

Q ss_pred             CCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         175 GELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       175 ~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ..+++|...++++.... +|.++..+|.+.+|.|+.-....|..|++.|++=+=..
T Consensus       191 ~~L~~~e~~il~~i~~~-GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~  245 (258)
T COG2512         191 YDLNEDEKEILDLIRER-GGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKK  245 (258)
T ss_pred             CCCCHHHHHHHHHHHHh-CCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEe
Confidence            45999999999988865 77899999999999999999999999999999877655

>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=91.32  E-value=1.1  Score=31.18  Aligned_cols=49  Identities=16%  Similarity=0.190  Sum_probs=36.0

Q ss_pred             hhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         179 LDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       179 ~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      ..|-.||..+.. ..+..|..+|++.++.+..-+...|+.|++.|++=.-
T Consensus         3 ~~q~~vL~~l~~-~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~   51 (68)
T PF13463_consen    3 RPQWQVLRALAH-SDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKE   51 (68)
T ss_dssp             HHHHHHHHHHT---TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHc-cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence            345555554442 3689999999999999999999999999999999443

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

Probab=91.06  E-value=0.92  Score=29.96  Aligned_cols=41  Identities=27%  Similarity=0.380  Sum_probs=35.0

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA  225 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l  225 (254)
                      ..|+.+..   .|..++.+|++.+|.+..-...+|..|.+.|++
T Consensus         5 ~~Il~~L~---~~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV   45 (47)
T PF01022_consen    5 LRILKLLS---EGPLTVSELAEELGLSQSTVSHHLKKLREAGLV   45 (47)
T ss_dssp             HHHHHHHT---TSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHH---hCCCchhhHHHhccccchHHHHHHHHHHHCcCe
Confidence            35566666   378999999999999999999999999999986

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 ....

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=91.04  E-value=0.81  Score=39.26  Aligned_cols=45  Identities=9%  Similarity=0.064  Sum_probs=39.7

Q ss_pred             hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552         180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW  226 (254)
Q Consensus       180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw  226 (254)
                      ....|+.+.-  ..|.+|.++|+..+|++..-++..|..|.++|++-
T Consensus        23 ~~~~Vl~~L~--~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~   67 (178)
T PRK06266         23 EGFEVLKALI--KKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLAD   67 (178)
T ss_pred             cHhHHHHHHH--HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence            3566777666  35899999999999999999999999999999998

>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=90.98  E-value=0.38  Score=37.99  Aligned_cols=35  Identities=26%  Similarity=0.199  Sum_probs=32.7

Q ss_pred             CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      ..+||++.|++.++++..+|+.+|++|++.|++-.
T Consensus        57 ~K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~   91 (105)
T PF03297_consen   57 MKLITPSVLSERLKINGSLARKALRELESKGLIKP   91 (105)
T ss_dssp             SSCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEE
T ss_pred             CcEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEE
Confidence            57899999999999999999999999999998754

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.

>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []

Probab=90.96  E-value=1.2  Score=30.43  Aligned_cols=43  Identities=19%  Similarity=0.262  Sum_probs=37.8

Q ss_pred             HHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         186 QQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       186 ~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ++++  ..|.+|+.++.+.+|.|.--|...|+.+-+.|+.+++..
T Consensus         3 ~~~~--~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T~R~gd   45 (50)
T PF09107_consen    3 ELLQ--KNGEITVAEFRDLLGLSRKYAIPLLEYLDREGITRRVGD   45 (50)
T ss_dssp             HHHH--TTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHh--cCCcCcHHHHHHHHCccHHHHHHHHHHHhccCCEEEeCC
Confidence            4455  468999999999999999999999999999999999964

Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=90.93  E-value=1  Score=38.86  Aligned_cols=53  Identities=21%  Similarity=0.172  Sum_probs=46.8

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .++..+..++....  ..|.+|..+|++.++.++.-+...|..|++.|++-++..
T Consensus       140 ~ls~~~~~IL~~l~--~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~  192 (203)
T TIGR01884       140 GLSREELKVLEVLK--AEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGR  192 (203)
T ss_pred             CCCHHHHHHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence            46777788888887  347899999999999999999999999999999999863

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.

>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=90.82  E-value=0.35  Score=39.35  Aligned_cols=48  Identities=15%  Similarity=0.204  Sum_probs=43.1

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ...|++++.  ..|.+|..++...+|.+..-++.++.+|++.|-+..=..
T Consensus        14 k~rIvElVR--e~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~~G~   61 (127)
T PF06163_consen   14 KARIVELVR--EHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYRHGR   61 (127)
T ss_pred             HHHHHHHHH--HcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeCCC
Confidence            457899999  569999999999999999999999999999999998433

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=90.57  E-value=0.73  Score=35.30  Aligned_cols=44  Identities=18%  Similarity=0.318  Sum_probs=39.1

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW  226 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw  226 (254)
                      ...|+...+  ..|.+|..+|++.+|.++.-+...|..|+++|++.
T Consensus         5 D~~il~~L~--~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~   48 (108)
T smart00344        5 DRKILEELQ--KDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK   48 (108)
T ss_pred             HHHHHHHHH--HhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            456777777  35789999999999999999999999999999987

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

>PRK10870 transcriptional repressor MprA; Provisional

Probab=90.53  E-value=1.4  Score=37.48  Aligned_cols=55  Identities=18%  Similarity=0.152  Sum_probs=44.7

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.+|........+.+|+.+|++.+++++.-+...++.|++.|++-+-..+
T Consensus        53 Lt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~  107 (176)
T PRK10870         53 INETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESD  107 (176)
T ss_pred             CCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCC
Confidence            5555666665554322578999999999999999999999999999999997665

>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure

Probab=90.51  E-value=0.57  Score=33.64  Aligned_cols=46  Identities=22%  Similarity=0.223  Sum_probs=38.7

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      ...+++++-  ..+..|++.|..+|.+-..||...++.|+++|++=--
T Consensus         7 y~~a~~~V~--~~~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p~   52 (63)
T smart00843        7 YDEAVELVI--ETQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGPA   52 (63)
T ss_pred             HHHHHHHHH--HhCCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCCC
Confidence            345666666  3578999999999999999999999999999998543

Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=90.50  E-value=0.8  Score=36.71  Aligned_cols=55  Identities=15%  Similarity=0.156  Sum_probs=44.5

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      .|+.+..  ..|.+++.+|++.++.+..-+..+|..|.+.|++....+  +...||..+
T Consensus        20 ~IL~~L~--~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~--Gr~~~Y~l~   74 (117)
T PRK10141         20 GIVLLLR--ESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQ--GKWVHYRLS   74 (117)
T ss_pred             HHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEE--cCEEEEEEC
Confidence            4555554  246799999999999999999999999999999999988  455555544

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=90.40  E-value=1.2  Score=34.82  Aligned_cols=52  Identities=13%  Similarity=0.106  Sum_probs=43.7

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ++.-|-.+|....  ..|.+|+.+|++.++++..-+...|+.|++.|++-+-..
T Consensus        26 lt~~q~~iL~~l~--~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~   77 (118)
T TIGR02337        26 LTEQQWRILRILA--EQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKA   77 (118)
T ss_pred             CCHHHHHHHHHHH--HcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccC
Confidence            5556767777666  357899999999999999999999999999999998543

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.

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

Probab=90.37  E-value=0.6  Score=41.98  Aligned_cols=47  Identities=17%  Similarity=0.222  Sum_probs=43.3

Q ss_pred             hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      =|..|+++.+  ..|.+++++|++.|+.|.+=.+.=|..|++.|++-+=
T Consensus         6 R~~~Il~~l~--~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~   52 (253)
T COG1349           6 RHQKILELLK--EKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRV   52 (253)
T ss_pred             HHHHHHHHHH--HcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEE
Confidence            3778999999  5699999999999999999999999999999999883

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=90.22  E-value=0.81  Score=29.43  Aligned_cols=35  Identities=14%  Similarity=0.183  Sum_probs=32.2

Q ss_pred             cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      .+|..+|++.+|++..-+...|..|++.|++-.+.
T Consensus         8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~~   42 (48)
T smart00419        8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISREG   42 (48)
T ss_pred             ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence            48899999999999999999999999999997763

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

Probab=90.21  E-value=1.1  Score=30.12  Aligned_cols=41  Identities=17%  Similarity=0.234  Sum_probs=33.3

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcC
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEG  223 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G  223 (254)
                      ..++.+... ..+++|..+|++.+|.|..-....|..|.+.|
T Consensus         3 ~~il~~L~~-~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    3 KQILKLLLE-SKEPITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHH-TTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHH-cCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            456665522 35679999999999999999999999999999

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 ....

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=89.98  E-value=1.1  Score=37.67  Aligned_cols=61  Identities=18%  Similarity=0.187  Sum_probs=46.0

Q ss_pred             hhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE----EEeCCCCCcccceecc
Q psy6552         179 LDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA----WIDTQSPQEHLYWFPS  241 (254)
Q Consensus       179 ~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l----wvD~q~~~e~~yw~p~  241 (254)
                      +++-.|+.+.-  ..|.+|.++|+..+|++..-.+..|..|.+.|++    ..|+..+--+.||+.+
T Consensus        14 ~~~v~Vl~aL~--~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~   78 (158)
T TIGR00373        14 EEVGLVLFSLG--IKGEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRIN   78 (158)
T ss_pred             hhHHHHHHHHh--ccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeC
Confidence            34566677555  3578999999999999999999999999999998    3555532234556544

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.

>PRK15466 carboxysome structural protein EutK; Provisional

Probab=89.64  E-value=0.57  Score=39.75  Aligned_cols=40  Identities=15%  Similarity=0.302  Sum_probs=34.0

Q ss_pred             HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552         185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW  226 (254)
Q Consensus       185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw  226 (254)
                      ..+++  ...+.|+.+++.+|||+-++++.+|++|..+|.|-
T Consensus       116 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (166)
T PRK15466        116 ALLTS--VRQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLR  155 (166)
T ss_pred             HHHHH--HHccccHHHHHHHhCCcHHHHHHHHHHHHhccchh
Confidence            34445  24579999999999999999999999999999874

>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional

Probab=89.40  E-value=13  Score=37.80  Aligned_cols=169  Identities=11%  Similarity=0.122  Sum_probs=102.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHhhh-------hhhc-------CHHHHHHHHHHHHHcCCCcccCCCcccccc----ccchhH
Q psy6552          34 QLSQHLNTFRDKLESFASEYKN-------EIKK-------DAQFRRHFQEMCASIGVDPLASRKGFWSLL----GMGDFY   95 (254)
Q Consensus        34 ~L~~ql~~fk~~L~~FA~kh~~-------~I~~-------dp~fr~~f~~mc~~lGVdPl~s~kg~w~~l----g~gdfy   95 (254)
                      .++++.+...+.|+.|.++|..       ++++       .+-|..-...+|..=.   +....++|+.-    ..++-+
T Consensus       415 ~~~~~~~~~~~~l~~~h~~~p~~~g~~~~~l~~~~~~~~~~~~~~~~l~~l~~~~~---i~~~~~~~~~~~~~~~~~~~~  491 (614)
T PRK10512        415 VAARWQRKLLDTLATYHEQHRDEPGPGRERLRRMALPMEDEALVLLLIEKMRESGD---IHSHHGWLHLPDHKAGFSEEQ  491 (614)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCcccCCCHHHHHhhcccCCCHHHHHHHHHHHHhCCC---EEEeCCEEECCCCCCCCCHHH
Confidence            3455666667777788888743       2221       1112222233333211   22222344311    235667


Q ss_pred             HHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCC
Q psy6552          96 YELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPG  175 (254)
Q Consensus        96 ~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~  175 (254)
                      .++..+|.+.+..      .--.+.|++..+           .+.++++.+.+..|-..|   .+++++ +..|+.... 
T Consensus       492 ~~~~~~l~~~~~~------~p~~~~~~~~~l-----------~~~~~~~~~~l~~l~~~g---~lv~l~-~~~~~~~~~-  549 (614)
T PRK10512        492 QALWQKAEPLFGD------EPWWVRDLAKET-----------GTDEQAMRLTLRQAAQQG---IITAIV-KDRYYRNDR-  549 (614)
T ss_pred             HHHHHHHHHHHhc------CCCCHHHHHHHh-----------CCCHHHHHHHHHHHHHCC---CEEEec-CCEEECHHH-
Confidence            7777777775541      122344554432           356778888888887766   355666 444553332 


Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                       +..--..+.++.+  ..|.+|+.++.+.+|.|.-.|...|+.+-+.|+.-++..
T Consensus       550 -~~~~~~~~~~~~~--~~~~~~~~~~r~~~g~sRK~~i~lLE~~D~~~~T~r~g~  601 (614)
T PRK10512        550 -IVQFANMIRELDQ--ECGSTCAADFRDRLGVGRKLAIQILEYFDRIGFTRRRGN  601 (614)
T ss_pred             -HHHHHHHHHHHHh--hCCcEeHHHHHHHhCccHHHHHHHHHHhccCCCEEEECC
Confidence             3333345566666  468999999999999999999999999999999999864

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=89.04  E-value=1.2  Score=40.29  Aligned_cols=47  Identities=19%  Similarity=0.266  Sum_probs=41.0

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .||++.... .+.+|..+|++.+|+++.-+-..|..|++.|++-.|+.
T Consensus        29 ~IL~~~~~~-~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~   75 (271)
T PRK10163         29 AILQYLEKS-GGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQ   75 (271)
T ss_pred             HHHHHHHhC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence            557766543 56799999999999999999999999999999999865

>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]

Probab=89.04  E-value=1.9  Score=36.37  Aligned_cols=96  Identities=18%  Similarity=0.321  Sum_probs=64.5

Q ss_pred             eeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhh-hh---CCCeEEEEeCCceEEEEccCC---------------CC
Q psy6552         117 ILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLK-IF---GNGFSIIPIGQGQYLVQSIPG---------------EL  177 (254)
Q Consensus       117 i~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~-~L---g~g~~l~~~~sg~~vv~s~p~---------------el  177 (254)
                      +++.++...+           . +++++.++++.|. .+   +.|++|+.++ |....++.|.               .|
T Consensus        14 vs~~~La~~l-----------~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~-~~y~l~tk~~~~~~v~~~~~~~~~~~L   80 (159)
T PF04079_consen   14 VSIEELAEIL-----------G-SEDEVEEALEELQEEYNEEDRGLELVEVG-GGYRLQTKPEYAEYVEKLFKKPKPPKL   80 (159)
T ss_dssp             B-HHHHHHHC-----------T--HHHHHHHHHHHHHHHHHCT-SEEEEEET-TEEEEEE-GGGHHHHHHHHCTCCCHHH
T ss_pred             CCHHHHHHHh-----------C-CHHHHHHHHHHHHHHhccCCCCEEEEEEC-CEEEEEEhHHHHHHHHHHhccCccCCC
Confidence            6666666552           3 7899999999884 33   8999999999 8888888772               12


Q ss_pred             ChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         178 SLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       178 s~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      |.-...+|.++.-  ..-||-.++.+--|.+   +..+|..|++.|++..=..
T Consensus        81 S~aalEtLAiIAY--~QPiTr~eIe~IRGv~---s~~~i~~L~e~glI~~~gr  128 (159)
T PF04079_consen   81 SQAALETLAIIAY--KQPITRAEIEEIRGVN---SDSVIKTLLERGLIEEVGR  128 (159)
T ss_dssp             HHHHHHHHHHHHH--H-SEEHHHHHHHHTS-----HCHHHHHHHTTSEEEEEE
T ss_pred             CHHHHHHHHHHHh--cCCcCHHHHHHHcCCC---hHHHHHHHHHCCCEEecCc
Confidence            2222223444443  2579999999999987   7788999999999987653

The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=88.90  E-value=1  Score=40.44  Aligned_cols=45  Identities=18%  Similarity=0.256  Sum_probs=41.4

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      +..|+++..  ..|.+++.+|++.+|+|..-++.-|..|++.|++-+
T Consensus         7 ~~~Il~~l~--~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r   51 (251)
T PRK13509          7 HQILLELLA--QLGFVTVEKVIERLGISPATARRDINKLDESGKLKK   51 (251)
T ss_pred             HHHHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            567888888  569999999999999999999999999999999976

>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=88.84  E-value=1  Score=31.08  Aligned_cols=36  Identities=14%  Similarity=0.147  Sum_probs=34.1

Q ss_pred             CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         194 AHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       194 g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      +.+|..+|++.+|.+..-+...|..|+++|++..+.
T Consensus        24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~   59 (67)
T cd00092          24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG   59 (67)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            579999999999999999999999999999999875

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=88.83  E-value=0.97  Score=40.64  Aligned_cols=48  Identities=13%  Similarity=0.160  Sum_probs=42.5

Q ss_pred             hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      =+..|+++..  ..|.+++.+|++.|+.|..=++.-|..|+++|++-+=-
T Consensus         6 R~~~Il~~L~--~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~~   53 (256)
T PRK10434          6 RQAAILEYLQ--KQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTY   53 (256)
T ss_pred             HHHHHHHHHH--HcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
Confidence            3678899998  46899999999999999999999999999999886643

>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=88.75  E-value=0.95  Score=35.53  Aligned_cols=61  Identities=15%  Similarity=0.253  Sum_probs=43.9

Q ss_pred             ChhHHHHHHHhhccCCCcccHHHHHHhc----CCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceeccc
Q psy6552         178 SLDHSLVLQQVASKNEAHISVSVLNNEL----NWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSL  242 (254)
Q Consensus       178 s~D~~~il~l~~~~~~g~vt~~~l~~~l----~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~l  242 (254)
                      ++-+..|+++.=..  |.+|+.++.+.+    +|++.=..+.|..|++.|++-++..  +...+|.|..
T Consensus         2 s~~E~~IM~~lW~~--~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~--gr~~~Y~p~i   66 (115)
T PF03965_consen    2 SDLELEIMEILWES--GEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKI--GRAYVYSPLI   66 (115)
T ss_dssp             -HHHHHHHHHHHHH--SSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEE--TTCEEEEESS
T ss_pred             CHHHHHHHHHHHhC--CCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeec--CCceEEEeCC
Confidence            33456677777643  559999888755    6889999999999999999999976  3455566543

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 ....

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

Probab=88.65  E-value=1.5  Score=30.30  Aligned_cols=43  Identities=19%  Similarity=0.152  Sum_probs=35.3

Q ss_pred             CChhHHHHHHHhhccCCCc------ccHHHHHHhcCCCHHHHHHHHHHHHH
Q psy6552         177 LSLDHSLVLQQVASKNEAH------ISVSVLNNELNWSTERAQHALDFMVQ  221 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~------vt~~~l~~~l~ws~~ra~~~L~~l~~  221 (254)
                      |++.|..+|..|=.  .||      +|..+|++.+|+|+.=+.+.|..+++
T Consensus         1 LT~~Q~e~L~~A~~--~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~   49 (53)
T PF04967_consen    1 LTDRQREILKAAYE--LGYFDVPRRITLEELAEELGISKSTVSEHLRRAER   49 (53)
T ss_pred             CCHHHHHHHHHHHH--cCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            35567888888873  454      89999999999999999999988765

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

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=88.59  E-value=1.6  Score=34.65  Aligned_cols=45  Identities=16%  Similarity=0.131  Sum_probs=36.8

Q ss_pred             HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      +.++...+.+.+|..+|++.++.++......|..|.+.|++....
T Consensus        15 ~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~   59 (132)
T TIGR00738        15 LDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVR   59 (132)
T ss_pred             HHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecc
Confidence            344442224589999999999999999999999999999988753

This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=88.57  E-value=1.4  Score=29.33  Aligned_cols=37  Identities=22%  Similarity=0.187  Sum_probs=32.4

Q ss_pred             CCcc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         193 EAHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       193 ~g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      +..+ |..+|++.+|+|..-+..+|..|+++|++-+..
T Consensus        17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~   54 (60)
T smart00345       17 GDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRP   54 (60)
T ss_pred             CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            3456 899999999999999999999999999976543

>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=88.37  E-value=2.2  Score=31.46  Aligned_cols=54  Identities=13%  Similarity=0.099  Sum_probs=39.1

Q ss_pred             HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552         185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP  240 (254)
Q Consensus       185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p  240 (254)
                      +.++...+.+.+|..+|++.++.++......|..|.+.|++=--..  ..|-|+..
T Consensus        15 ~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G--~~GGy~L~   68 (83)
T PF02082_consen   15 LYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRG--RGGGYRLA   68 (83)
T ss_dssp             HHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETS--TTSEEEES
T ss_pred             HHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCC--CCCceeec
Confidence            3445433233599999999999999999999999999999644333  35677663

(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.

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=88.08  E-value=2.3  Score=36.72  Aligned_cols=54  Identities=13%  Similarity=0.089  Sum_probs=45.8

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .++.-|-.||..+.  ..+++|..+|++.++.++.-+...|+.|++.|++-+-..+
T Consensus        42 gLt~~q~~iL~~L~--~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~   95 (185)
T PRK13777         42 DLNINEHHILWIAY--HLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKE   95 (185)
T ss_pred             CCCHHHHHHHHHHH--hCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCC
Confidence            36767778887776  3578999999999999999999999999999999986554

>PHA00738 putative HTH transcription regulator

Probab=88.00  E-value=1.8  Score=34.37  Aligned_cols=55  Identities=20%  Similarity=0.258  Sum_probs=45.8

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      .|+++..  .++..++.+|++.++.+......+|..|.+.|++-....  +...||..+
T Consensus        16 ~IL~lL~--~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~--Gr~vyY~Ln   70 (108)
T PHA00738         16 KILELIA--ENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKE--GRTLYAKIR   70 (108)
T ss_pred             HHHHHHH--HcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEE--CCEEEEEEC
Confidence            4577665  345699999999999999999999999999999999988  566666544

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=87.96  E-value=1.5  Score=39.14  Aligned_cols=47  Identities=21%  Similarity=0.325  Sum_probs=40.4

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .||++.... .+.++..+|++.+|.++.-+...|..|++.|++..|..
T Consensus         8 ~iL~~l~~~-~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~   54 (246)
T COG1414           8 AILDLLAEG-PGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPE   54 (246)
T ss_pred             HHHHHHHhC-CCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence            466666543 44589999999999999999999999999999999975

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=87.67  E-value=1.8  Score=35.15  Aligned_cols=45  Identities=9%  Similarity=0.141  Sum_probs=38.8

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      .|+.+..  ..|++++++|++.+++++.-+...|..|++.|++..+.
T Consensus        12 ~I~~l~~--~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~~   56 (142)
T PRK03902         12 QIYLLIE--EKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEK   56 (142)
T ss_pred             HHHHHHh--cCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEec
Confidence            4455666  46899999999999999999999999999999998653

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=87.57  E-value=1.3  Score=39.73  Aligned_cols=47  Identities=13%  Similarity=0.210  Sum_probs=42.1

Q ss_pred             hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      -+..|+++..  ..|.+|+.+|++.|+.|.+=++.-|..|+++|++-+=
T Consensus         6 R~~~Il~~l~--~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~   52 (252)
T PRK10906          6 RHDAIIELVK--QQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRH   52 (252)
T ss_pred             HHHHHHHHHH--HcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3678899988  4689999999999999999999999999999999763

>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis

Probab=87.40  E-value=1.7  Score=34.75  Aligned_cols=53  Identities=13%  Similarity=0.219  Sum_probs=48.1

Q ss_pred             CCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         175 GELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       175 ~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ..++.++..|+++|.  .  ..|+.|++..++.+...++-.+-+|.+.|++-+-...
T Consensus        39 ~~l~pE~~~Il~lC~--~--~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v~~p~   91 (114)
T PF05331_consen   39 AGLGPEHRAILELCR--R--PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRVRAPA   91 (114)
T ss_pred             CCCCHHHHHHHHHHC--C--CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEEeCCC
Confidence            457888999999999  2  8999999999999999999999999999999997654

The function of these proteins is unknown.

>PRK11569 transcriptional repressor IclR; Provisional

Probab=87.25  E-value=1.6  Score=39.45  Aligned_cols=47  Identities=15%  Similarity=0.264  Sum_probs=40.7

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .||++.... .+.+|.++|++.+|.++.-+-..|..|++.|++-.|..
T Consensus        32 ~IL~~l~~~-~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~~   78 (274)
T PRK11569         32 KLLEWIAES-NGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVGE   78 (274)
T ss_pred             HHHHHHHhC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence            456666543 56799999999999999999999999999999998865

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=86.83  E-value=1.7  Score=35.20  Aligned_cols=49  Identities=18%  Similarity=0.161  Sum_probs=43.2

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      +++-...+|.+.+  ..+..+..+|++.+|.|+.-+...++.|+++|++-.
T Consensus         6 lD~~D~~IL~~L~--~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~   54 (154)
T COG1522           6 LDDIDRRILRLLQ--EDARISNAELAERVGLSPSTVLRRIKRLEEEGVIKG   54 (154)
T ss_pred             ccHHHHHHHHHHH--HhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceee
Confidence            6666778999999  457799999999999999999999999999998644

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=86.70  E-value=2  Score=38.28  Aligned_cols=46  Identities=22%  Similarity=0.267  Sum_probs=39.9

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .||++...  .+.+|.++|++.+|.++.-+-..|..|++.|++-.|..
T Consensus        18 ~IL~~l~~--~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~   63 (257)
T PRK15090         18 GILQALGE--EREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGE   63 (257)
T ss_pred             HHHHHhhc--CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence            55776653  35699999999999999999999999999999999854

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

Probab=86.60  E-value=1.7  Score=31.80  Aligned_cols=41  Identities=10%  Similarity=0.088  Sum_probs=32.4

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA  225 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l  225 (254)
                      ..||+.+.   .|..+.++|+...|.+..++...|+.|++.|++
T Consensus         9 ~~IL~~l~---~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI   49 (77)
T PF14947_consen    9 FDILKILS---KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLI   49 (77)
T ss_dssp             HHHHHHH----TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHH---cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCe
Confidence            45677776   478999999999999999999999999999999

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=86.55  E-value=3.6  Score=35.78  Aligned_cols=45  Identities=20%  Similarity=0.143  Sum_probs=39.0

Q ss_pred             CCChhHHHHHHHhhccCCCc------ccHHHHHHhcCCCHHHHHHHHHHHHHc
Q psy6552         176 ELSLDHSLVLQQVASKNEAH------ISVSVLNNELNWSTERAQHALDFMVQE  222 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~------vt~~~l~~~l~ws~~ra~~~L~~l~~~  222 (254)
                      +|++=|..+|..|=  ..||      +|..+||+.+|+|+.=+.++|+.+++.
T Consensus       155 ~LTdrQ~~vL~~A~--~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~K  205 (215)
T COG3413         155 DLTDRQLEVLRLAY--KMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERK  205 (215)
T ss_pred             cCCHHHHHHHHHHH--HcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            58877999999998  3465      999999999999999999999988753

>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]

Probab=86.35  E-value=2.1  Score=37.98  Aligned_cols=122  Identities=16%  Similarity=0.181  Sum_probs=75.7

Q ss_pred             HHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChh-
Q psy6552         102 IVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD-  180 (254)
Q Consensus       102 ive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D-  180 (254)
                      +++++.++.+..-    +.+....|.+.|-...-++.+|.+.|=.....-.+ ..            -....|+.++.- 
T Consensus        97 v~DYLiKPf~~eR----l~~aL~~y~~~r~~l~~~~~~sQ~~lD~l~~~~~k-~~------------~~~~LPkGi~~~T  159 (224)
T COG4565          97 VVDYLIKPFTFER----LQQALTRYRQKRHALESHQQLSQKELDQLFNIQSK-EQ------------PPDDLPKGLDELT  159 (224)
T ss_pred             chhheecceeHHH----HHHHHHHHHHHHHHHhhhcccCHHHHHHHHhcccc-cc------------CcccCCCCcCHHH
Confidence            4555555443221    55666666666633221256787766554443222 11            112345545422 


Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCC----Ccccceecc
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSP----QEHLYWFPS  241 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~----~e~~yw~p~  241 (254)
                      -..|.+..+. ..-..|++++++.+|.|..-|+..|+.|+..|.+-.+-+-+    .+..||.+.
T Consensus       160 l~~i~~~~~~-~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a~i~yG~vGRP~r~Y~~~~  223 (224)
T COG4565         160 LQKVREALKE-PDQELTAEELAQALGISRVTARRYLEYLVSNGILEAEIHYGKVGRPERRYRLKA  223 (224)
T ss_pred             HHHHHHHHhC-cCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeEEeeccccCCcceeeeccC
Confidence            1345555553 24679999999999999999999999999999999997543    457888764

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=85.78  E-value=3.3  Score=31.30  Aligned_cols=53  Identities=17%  Similarity=0.133  Sum_probs=43.5

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.++..+..  .+..+..+|++.+++++.-....|+.|++.|++.+-..+
T Consensus        20 lt~~q~~~L~~l~~--~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~   72 (126)
T COG1846          20 LTPPQYQVLLALYE--AGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDP   72 (126)
T ss_pred             CCHHHHHHHHHHHH--hCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCc
Confidence            55567777766663  355555999999999999999999999999999998775

>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities

Probab=85.52  E-value=2.1  Score=29.94  Aligned_cols=38  Identities=18%  Similarity=0.108  Sum_probs=32.6

Q ss_pred             CCcc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         193 EAHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       193 ~g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      +-.+ |..+|++.+|.|..-++++|..|.++|++-+-..
T Consensus        21 g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~   59 (64)
T PF00392_consen   21 GDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRPG   59 (64)
T ss_dssp             TSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred             CCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence            3468 9999999999999999999999999999988754

The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....

>PRK09954 putative kinase; Provisional

Probab=85.41  E-value=1.8  Score=40.38  Aligned_cols=43  Identities=14%  Similarity=0.170  Sum_probs=38.5

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA  225 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l  225 (254)
                      ..+||++.+  ..+++|..+|++.+|+|..-+...|..|+++|++
T Consensus         5 ~~~il~~l~--~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i   47 (362)
T PRK09954          5 EKEILAILR--RNPLIQQNEIADILQISRSRVAAHIMDLMRKGRI   47 (362)
T ss_pred             HHHHHHHHH--HCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence            456888888  4589999999999999999999999999999875

>PRK00215 LexA repressor; Validated

Probab=84.98  E-value=4.8  Score=34.54  Aligned_cols=55  Identities=15%  Similarity=0.188  Sum_probs=44.0

Q ss_pred             CChhHHHHHHHhhc---cCCCcccHHHHHHhcCC-CHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVAS---KNEAHISVSVLNNELNW-STERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~---~~~g~vt~~~l~~~l~w-s~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|..+|+.+..   ......|..+|++.+|+ ++.-+...|..|++.|++-++...
T Consensus         2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~   60 (205)
T PRK00215          2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR   60 (205)
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC
Confidence            34567778776542   11345899999999999 999999999999999999988764

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

Probab=84.93  E-value=1.7  Score=29.63  Aligned_cols=32  Identities=28%  Similarity=0.167  Sum_probs=29.1

Q ss_pred             ccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         196 ISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       196 vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      .|..+|++.+++|..-+..+|..|.+.|++=.
T Consensus        26 ~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~   57 (66)
T cd07377          26 PSERELAEELGVSRTTVREALRELEAEGLVER   57 (66)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            56999999999999999999999999998643

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

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=84.89  E-value=3.5  Score=35.56  Aligned_cols=46  Identities=15%  Similarity=0.203  Sum_probs=39.5

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      ..||.+...  .|.+|+.+|++.+|+++.-+...|+.|++.|++-+..
T Consensus         4 ~~IL~~L~~--~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~   49 (203)
T TIGR02702         4 EDILSYLLK--QGQATAAALAEALAISPQAVRRHLKDLETEGLIEYEA   49 (203)
T ss_pred             HHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEee
Confidence            456666652  4669999999999999999999999999999998773

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.

>TIGR00281 segregation and condensation protein B

Probab=84.66  E-value=11  Score=32.69  Aligned_cols=96  Identities=25%  Similarity=0.273  Sum_probs=68.4

Q ss_pred             eeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhh----CCCeEEEEeCCceEEEEccCC--------------CCC
Q psy6552         117 ILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIF----GNGFSIIPIGQGQYLVQSIPG--------------ELS  178 (254)
Q Consensus       117 i~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~L----g~g~~l~~~~sg~~vv~s~p~--------------els  178 (254)
                      +++.++-..++.        +  .++++..+++.|+.-    +.|++|+.++ |...+++.|.              .+|
T Consensus        18 ls~~~La~il~~--------~--~~~~~~~~l~~l~~~~~~~~~gl~l~~~~-~~y~l~tk~e~~~~i~~~~~~~~~~LS   86 (186)
T TIGR00281        18 VTLAELVRILGK--------E--KAEKLNAIMELLEDYLSRDTAGIEIIKFG-QSYSLVTKPAFADYIHRFLPAKLKNLN   86 (186)
T ss_pred             CCHHHHHHHhCC--------C--chHHHHHHHHHHHHHHhcCCCCEEEEEEC-CEEEEEEhHHHHHHHHHHhccccccCC
Confidence            677777766532        1  145677777777554    5689999999 8777777661              144


Q ss_pred             hhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         179 LDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       179 ~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      .-...+|.++.-  ..-||-.++.+--|.+   +..+|..|++.|++-+-
T Consensus        87 ~aaLEtLAIIAY--~QPITr~eIe~IRGv~---s~~~l~~L~ergLI~~~  131 (186)
T TIGR00281        87 SASLEVLAIIAY--KQPITRARINEIRGVK---SYQIVDDLVEKGLVVEL  131 (186)
T ss_pred             HHHHHHHHHHHH--cCCcCHHHHHHHcCCC---HHHHHHHHHHCCCeEec
Confidence            334444555553  3579999999999988   57899999999999775

Shown to be required for chromosome segregation and condensation in B. subtilis.

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=84.55  E-value=2.3  Score=33.85  Aligned_cols=42  Identities=7%  Similarity=0.058  Sum_probs=35.6

Q ss_pred             HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      ..++.. ..+.+|..+|++.+|.+...+..+|..|.+.|++-.
T Consensus        16 ~~la~~-~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~   57 (130)
T TIGR02944        16 TTLAQN-DSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTS   57 (130)
T ss_pred             HHHHhC-CCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence            344443 256899999999999999999999999999999855

The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=84.43  E-value=3.2  Score=35.24  Aligned_cols=48  Identities=17%  Similarity=0.235  Sum_probs=42.7

Q ss_pred             HHHHHHHhhccCCCcc-cHHHHHHhc--CCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         181 HSLVLQQVASKNEAHI-SVSVLNNEL--NWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       181 ~~~il~l~~~~~~g~v-t~~~l~~~l--~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      +..|.+++.  -.++- ++..|++.+  ++|.+.+++.|+.|++-|++=.|..
T Consensus        26 ~~~ir~l~~--l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~   76 (171)
T PF14394_consen   26 HPAIRELLP--LMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD   76 (171)
T ss_pred             HHHHHHHhh--cCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC
Confidence            567888888  45666 999999999  9999999999999999999999965

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=84.15  E-value=2.4  Score=38.43  Aligned_cols=48  Identities=19%  Similarity=0.261  Sum_probs=42.8

Q ss_pred             hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      -+..|+++.+  ..|.+|+.+|++.||.|..=++.-|..|++.|++-+-.
T Consensus        18 R~~~Il~~L~--~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~   65 (269)
T PRK09802         18 RREQIIQRLR--QQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAY   65 (269)
T ss_pred             HHHHHHHHHH--HcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEe
Confidence            4678888888  45889999999999999999999999999999998765

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=84.09  E-value=5.8  Score=36.57  Aligned_cols=74  Identities=15%  Similarity=0.139  Sum_probs=53.4

Q ss_pred             CCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHH-HhhccCCCcccHHHHHHhcCCCHHHHHHH
Q psy6552         137 QDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQ-QVASKNEAHISVSVLNNELNWSTERAQHA  215 (254)
Q Consensus       137 ~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~-l~~~~~~g~vt~~~l~~~l~ws~~ra~~~  215 (254)
                      ..|+.+++..+.+.++.   .+                ..++..+...+. ++..-.+|.++.+.++..+|++..-+.++
T Consensus       236 ~~I~~~~v~~~l~~~~~---~~----------------~~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~  296 (328)
T PRK00080        236 GVITKEIADKALDMLGV---DE----------------LGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDV  296 (328)
T ss_pred             CCCCHHHHHHHHHHhCC---Cc----------------CCCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHH
Confidence            46888888888865421   00                124444445554 55532267899999999999999999999


Q ss_pred             HH-HHHHcCcEEEeC
Q psy6552         216 LD-FMVQEGYAWIDT  229 (254)
Q Consensus       216 L~-~l~~~G~lwvD~  229 (254)
                      ++ .|++.|++....
T Consensus       297 ~e~~Li~~~li~~~~  311 (328)
T PRK00080        297 YEPYLIQQGFIQRTP  311 (328)
T ss_pred             hhHHHHHcCCcccCC
Confidence            99 899999997443

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=84.01  E-value=1.3  Score=37.96  Aligned_cols=46  Identities=7%  Similarity=-0.046  Sum_probs=41.2

Q ss_pred             hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      -+..|++++.  ..|.+++.+|++.+|.|..-++.=|..|+++|++-+
T Consensus         8 R~~~Il~~l~--~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r   53 (185)
T PRK04424          8 RQKALQELIE--ENPFITDEELAEKFGVSIQTIRLDRMELGIPELRER   53 (185)
T ss_pred             HHHHHHHHHH--HCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHHH
Confidence            4678899998  569999999999999999999999999999998744

>TIGR00498 lexA SOS regulatory protein LexA

Probab=84.01  E-value=3.1  Score=35.51  Aligned_cols=55  Identities=16%  Similarity=0.228  Sum_probs=45.0

Q ss_pred             CChhHHHHHHHhhcc--CCCc-ccHHHHHHhcCCC-HHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASK--NEAH-ISVSVLNNELNWS-TERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~--~~g~-vt~~~l~~~l~ws-~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|..||+.+.+.  ..|+ .|..+|++.+|.+ +.-+...|..|++.|++-.++..
T Consensus         4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~~   62 (199)
T TIGR00498         4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGK   62 (199)
T ss_pred             cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCCC
Confidence            666788898887632  1233 8899999999998 99999999999999999987653

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.

>PRK11050 manganese transport regulator MntR; Provisional

Probab=83.72  E-value=3.5  Score=34.13  Aligned_cols=44  Identities=11%  Similarity=0.110  Sum_probs=37.5

Q ss_pred             HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      +.+..  .+|.+++.+|++.+++++.-....|..|++.|++.++..
T Consensus        43 ~~~l~--~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~~   86 (152)
T PRK11050         43 ADLIA--EVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPY   86 (152)
T ss_pred             HHHHH--hcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            34455  357899999999999999999999999999999887643

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=83.67  E-value=3.3  Score=37.13  Aligned_cols=47  Identities=17%  Similarity=0.301  Sum_probs=40.1

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .||+..... .+.+|..+|++.+|.++.-+-..|..|++.|++-+|..
T Consensus        15 ~iL~~l~~~-~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~   61 (263)
T PRK09834         15 MVLRALNRL-DGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSAS   61 (263)
T ss_pred             HHHHHHHhc-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC
Confidence            456665432 45699999999999999999999999999999999965

>PF13730 HTH_36: Helix-turn-helix domain

Probab=82.49  E-value=5.2  Score=26.75  Aligned_cols=32  Identities=22%  Similarity=0.259  Sum_probs=29.1

Q ss_pred             CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552         194 AHISVSVLNNELNWSTERAQHALDFMVQEGYA  225 (254)
Q Consensus       194 g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l  225 (254)
                      -|-|.+.|++.+|.+..-...+|..|++.|++
T Consensus        24 ~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen   24 CFPSQETLAKDLGVSRRTVQRAIKELEEKGLI   55 (55)
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence            35688999999999999999999999999975

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=82.23  E-value=7.6  Score=27.37  Aligned_cols=42  Identities=17%  Similarity=0.189  Sum_probs=34.7

Q ss_pred             HHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         184 VLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       184 il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      ++++..   .+..|..+|++.+|.|..-+...|..|.+.|+.-..
T Consensus         5 il~~L~---~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~   46 (69)
T TIGR00122         5 LLALLA---DNPFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLT   46 (69)
T ss_pred             HHHHHH---cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence            444444   356889999999999999999999999999995544

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.

>KOG1767|consensus

Probab=82.21  E-value=1.9  Score=33.96  Aligned_cols=46  Identities=22%  Similarity=0.201  Sum_probs=36.9

Q ss_pred             hHHHHHHHhhcc-CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552         180 DHSLVLQQVASK-NEAHISVSVLNNELNWSTERAQHALDFMVQEGYA  225 (254)
Q Consensus       180 D~~~il~l~~~~-~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l  225 (254)
                      |+.+.-.+..+- ...+||++.|.+.+.+.-.+|+.+|.+|..+|++
T Consensus        44 dqatydkl~kevp~~k~it~svl~dRlkIngsLAr~alr~L~~kG~I   90 (110)
T KOG1767|consen   44 DQATYDKLLKEVPKYKLITPSVLSDRLKINGSLARAALRELSNKGVI   90 (110)
T ss_pred             cHHHHHHHHHhcccceeecHHHhhhhhhhchHHHHHHHHHHHhcchH
Confidence            555554454421 1458999999999999999999999999999986

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=81.98  E-value=3  Score=37.68  Aligned_cols=37  Identities=14%  Similarity=0.112  Sum_probs=34.9

Q ss_pred             CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      .|.++..+|++.+|.|+.-+.+++..|++.|++-.-.
T Consensus       196 egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~  232 (251)
T TIGR02787       196 EGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS  232 (251)
T ss_pred             cccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence            4899999999999999999999999999999998776

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.

>PF04558 tRNA_synt_1c_R1: Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 ; InterPro: IPR007639 The aminoacyl-tRNA synthetases (6

Probab=81.55  E-value=7.5  Score=32.94  Aligned_cols=98  Identities=20%  Similarity=0.240  Sum_probs=54.3

Q ss_pred             HHHHhhhhhhcCHHHHHHHHHHHHHcCCC-cccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHH
Q psy6552          49 FASEYKNEIKKDAQFRRHFQEMCASIGVD-PLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLV  127 (254)
Q Consensus        49 FA~kh~~~I~~dp~fr~~f~~mc~~lGVd-Pl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~n  127 (254)
                      |..+=..++-+||.+...|......-|++ |...+        .|..-|.||.++-.-+...         .+-+...+.
T Consensus        15 L~e~kAket~KN~kls~~L~~iI~ea~~~~~~dk~--------~g~LLy~lAtk~k~~~~~~---------r~~iv~~I~   77 (164)
T PF04558_consen   15 LSEKKAKETLKNKKLSASLKAIINEAGVDSGCDKK--------QGNLLYQLATKLKPQALPH---------RPFIVKYIV   77 (164)
T ss_dssp             --HHHHHHHTTSHHHHHHHHHHHHTS-TT----HH--------HHHHHHHHHHHHTT---TT---------HHHHHHHHH
T ss_pred             CChhhHHHHHhCHHHHHHHHHHHHHhcccCCCCHH--------HHHHHHHHHHhcCCCcchh---------HHHHHHHHH
Confidence            55566778889999999999999999988 66543        3677777877554433332         333333333


Q ss_pred             HhcCCCCCCCCCCHHHHHHHHHHhhhhCC-CeEEEEeC--CceEEE
Q psy6552         128 KSRGKSLQHQDITNEDLLAAAKKLKIFGN-GFSIIPIG--QGQYLV  170 (254)
Q Consensus       128 r~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~-g~~l~~~~--sg~~vv  170 (254)
                      ..       .+-|+..+-.|++.++.-+. ++..-.|+  .|+=|+
T Consensus        78 ~g-------klkt~~Ql~AA~~Yl~~~~~~~~d~~~Fe~~cGVGV~  116 (164)
T PF04558_consen   78 DG-------KLKTNLQLDAALKYLKSNPSEPIDVAEFEKACGVGVV  116 (164)
T ss_dssp             TT-------S--SHHHHHHHHHHHHHHGG-G--HHHHHHTTTTT--
T ss_pred             hC-------CCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHcCCCeE
Confidence            32       24466666666666666654 56655554  355444

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. This is a domain found N-terminal to the catalytic domain of glutaminyl-tRNA synthetase (6.1.1.18 from EC) in eukaryotes but not in Escherichia coli. This domain is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 3TL4_X.

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=81.52  E-value=3.7  Score=33.12  Aligned_cols=44  Identities=7%  Similarity=0.101  Sum_probs=36.8

Q ss_pred             HHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         184 VLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       184 il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      ++.+|.....+.+|..+|++.+++++.-....|..|.+.|++-.
T Consensus        14 l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s   57 (135)
T TIGR02010        14 MLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKS   57 (135)
T ss_pred             HHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEE
Confidence            35666543345799999999999999999999999999998854

This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.

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

Probab=81.43  E-value=3.7  Score=36.31  Aligned_cols=45  Identities=16%  Similarity=0.268  Sum_probs=39.0

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      .||++.... .+.+|..+|++.+|.++.-+-..|..|++.|++-.|
T Consensus        13 ~IL~~l~~~-~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~   57 (248)
T TIGR02431        13 AVIEAFGAE-RPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSD   57 (248)
T ss_pred             HHHHHHhcC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            567766543 567999999999999999999999999999999775

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.

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=81.09  E-value=4  Score=36.36  Aligned_cols=46  Identities=17%  Similarity=0.277  Sum_probs=41.4

Q ss_pred             hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      -+..|+++..  ..+++|+.+|++.|++|..-++.-|..|+..|++-+
T Consensus         5 R~~~Il~~l~--~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r   50 (240)
T PRK10411          5 RQQAIVDLLL--NHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILR   50 (240)
T ss_pred             HHHHHHHHHH--HcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            3667888888  468999999999999999999999999999999877

>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms

Probab=80.94  E-value=13  Score=33.97  Aligned_cols=123  Identities=14%  Similarity=0.244  Sum_probs=81.6

Q ss_pred             HHHHHHHHcCCCcccCCCccccccccchhH--HHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHH
Q psy6552          66 HFQEMCASIGVDPLASRKGFWSLLGMGDFY--YELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNED  143 (254)
Q Consensus        66 ~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy--~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~D  143 (254)
                      -.+.++..=.+|-+.+..|       ..|.  .+|..+|.+-|..    +||=+++.||-..+           .|..+.
T Consensus        29 iv~kL~~~~~ldli~T~dG-------keyiT~~~L~~EI~~el~~----~gGRv~~~dL~~~L-----------nVd~~~   86 (272)
T PF09743_consen   29 IVNKLIEKKLLDLIHTTDG-------KEYITPEQLEKEIKDELYV----HGGRVNLVDLAQAL-----------NVDLDH   86 (272)
T ss_pred             HHHHHHHcCCeeEEEECCC-------CEEECHHHHHHHHHHHHHH----cCCceEHHHHHHhc-----------CcCHHH
Confidence            4456666667785543321       2343  4688888876653    79999999998664           488999


Q ss_pred             HHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHH-HHHHH
Q psy6552         144 LLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQ-HALDF  218 (254)
Q Consensus       144 i~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~-~~L~~  218 (254)
                      |.+.++.+-+=..++.+  ++ |. ++....  ++.--..+-+..+  +.|.+|.++|+..++.+.+-.+ ..+..
T Consensus        87 ie~~~~~i~~~~~~~~l--~~-ge-lit~~Y--ld~l~~Eine~Lq--e~G~vsi~eLa~~~~Lp~efl~~~li~~  154 (272)
T PF09743_consen   87 IERRAQEIVKSDKSLQL--VQ-GE-LITDSY--LDSLAEEINEKLQ--ESGQVSISELAKQYDLPSEFLKEELISK  154 (272)
T ss_pred             HHHHHHHHHhCCCcEEE--EC-CE-EccHHH--HHHHHHHHHHHHH--HcCeEeHHHHHHhcCCcHHHHHHHHhhh
Confidence            99999998776555543  33 43 332222  2222234445555  4699999999999999999988 44433

Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=80.91  E-value=6.1  Score=32.05  Aligned_cols=45  Identities=11%  Similarity=0.071  Sum_probs=38.3

Q ss_pred             CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552         193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF  239 (254)
Q Consensus       193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~  239 (254)
                      +..+|..+|++.+|.|+.-.+++|..|.++|++..-...  .|-|..
T Consensus        23 g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~--~GG~~l   67 (141)
T PRK11014         23 GRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGK--NGGIRL   67 (141)
T ss_pred             CCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCC--CCCeee
Confidence            447899999999999999999999999999999988764  344444

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

Probab=80.82  E-value=3.8  Score=30.38  Aligned_cols=46  Identities=17%  Similarity=0.292  Sum_probs=37.0

Q ss_pred             HHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         184 VLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       184 il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      |+.+...  .+.++..+|++.+|.+..-...+|..|+++|++=++...
T Consensus         5 Il~~L~~--~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~   50 (80)
T PF13601_consen    5 ILALLYA--NEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEF   50 (80)
T ss_dssp             HHHHHHH--HSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-
T ss_pred             HHHHHhh--cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEec
Confidence            4444442  468999999999999999999999999999999999875

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

Probab=80.63  E-value=3.6  Score=25.51  Aligned_cols=30  Identities=13%  Similarity=0.234  Sum_probs=25.6

Q ss_pred             ccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552         196 ISVSVLNNELNWSTERAQHALDFMVQEGYA  225 (254)
Q Consensus       196 vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l  225 (254)
                      +|..+|++.+|.+++-+...|..+.++|++
T Consensus         3 mtr~diA~~lG~t~ETVSR~l~~l~~~glI   32 (32)
T PF00325_consen    3 MTRQDIADYLGLTRETVSRILKKLERQGLI   32 (32)
T ss_dssp             --HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             cCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence            678999999999999999999999999985

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 ....

>PRK10263 DNA translocase FtsK; Provisional

Probab=80.45  E-value=4.5  Score=44.45  Aligned_cols=88  Identities=16%  Similarity=0.107  Sum_probs=60.2

Q ss_pred             CCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEc-----cCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHH
Q psy6552         138 DITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQS-----IPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERA  212 (254)
Q Consensus       138 ~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s-----~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra  212 (254)
                      -||.+||.+-++.++.-|.+--+..+-.+..--.+     ...+.+.-...+++++-  ..+.+|++.|.++|.+-..||
T Consensus      1247 fvsD~Ei~~vv~~~k~~~~p~y~~~~~~~~~~~~~~~~~~~~~~~D~l~~~a~~~v~--~~~~~S~S~lQR~~~iGynRA 1324 (1355)
T PRK10263       1247 FVRDQEVHAVVQDWKARGRPQYVDGITSDSESEGGAGGFDGAEELDPLFDQAVQFVT--EKRKASISGVQRQFRIGYNRA 1324 (1355)
T ss_pred             cCCHHHHHHHHHHHHhcCCCchhhhhcccccccccccCcCCCccccHHHHHHHHHHH--hcCccCHHHHHHHhhcChHHH
Confidence            69999999999999988755322222100000000     00111112356677777  468899999999999999999


Q ss_pred             HHHHHHHHHcCcEEE
Q psy6552         213 QHALDFMVQEGYAWI  227 (254)
Q Consensus       213 ~~~L~~l~~~G~lwv  227 (254)
                      ...++.|+++|++==
T Consensus      1325 ariid~lE~~Giv~p 1339 (1355)
T PRK10263       1325 ARIIEQMEAQGIVSE 1339 (1355)
T ss_pred             HHHHHHHHHCCcCCC
Confidence            999999999999854

>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4

Probab=80.23  E-value=3.3  Score=30.90  Aligned_cols=43  Identities=28%  Similarity=0.363  Sum_probs=28.8

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .+|.+..  .+.-||++.|+..+||+.+..+.+|..+-   -.-.|++
T Consensus        28 ~LLr~LA--~G~PVt~~~LA~a~g~~~e~v~~~L~~~p---~tEyD~~   70 (77)
T PF12324_consen   28 PLLRLLA--KGQPVTVEQLAAALGWPVEEVRAALAAMP---DTEYDDQ   70 (77)
T ss_dssp             HHHHHHT--TTS-B-HHHHHHHHT--HHHHHHHHHH-T---TSEEETT
T ss_pred             HHHHHHH--cCCCcCHHHHHHHHCCCHHHHHHHHHhCC---CceEcCC
Confidence            3455555  46789999999999999999999998863   2445555

99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	254
2zme_A	258	Integrated Structural And Functional Model Of The H		1e-76
3cuq_A	234	Integrated Structural And Functional Model Of The H		3e-69
1u5t_A	233	Structure Of The Escrt-Ii Endosomal Trafficking Com		5e-30

>pdb|2ZME|A Chain A, Integrated Structural And Functional Model Of The Human Escrt-Ii Complex Length = 258

Iteration: 1
 Score =  282 bits (722), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 135/250 (54%), Positives = 187/250 (74%), Gaps = 6/250 (2%)
Query: 2   RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
           RR  G GAI K+KL + KYK++GT + E+QL Q+S+ L+ F+  LE FAS++K EI+K+ 
Sbjct: 3   RRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNP 62
Query: 62  QFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLD 120
           +FR  FQ+MCA+IGVDPLAS KGFWS +LG+GDFYYEL VQI+EVCLA  ++NGGLI L+
Sbjct: 63  EFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLE 122
Query: 121 ELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD 180
           EL  +++K RGK    QD++ +DL+ A KKLK  G GF IIP+G G YL+QS+P EL++D
Sbjct: 123 ELHQQVLKGRGKF--AQDVSQDDLIRAIKKLKALGTGFGIIPVG-GTYLIQSVPAELNMD 179
Query: 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240
           H++VL Q+A KN  +++VS +   L W TERA+  L+ +++EG AW+D Q+P E  YW P
Sbjct: 180 HTVVL-QLAEKN-GYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLP 237
Query: 241 SLFTECMNAE 250
           +LFT+  + E
Sbjct: 238 ALFTDLYSQE 247

>pdb|3CUQ|A Chain A, Integrated Structural And Functional Model Of The Human Escrt-Ii Complex Length = 234

Iteration: 1
 Score =  258 bits (658), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 123/228 (53%), Positives = 171/228 (75%), Gaps = 6/228 (2%)
Query: 24  GTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRK 83
           GT + E+QL Q+S+ L+ F+  LE FAS++K EI+K+ +FR  FQ+MCA+IGVDPLAS K
Sbjct: 1   GTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQDMCATIGVDPLASGK 60
Query: 84  GFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNE 142
           GFWS +LG+GDFYYEL VQI+EVCLA  ++NGGLI L+EL  +++K RGK    QD++ +
Sbjct: 61  GFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLEELHQQVLKGRGKF--AQDVSQD 118
Query: 143 DLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLN 202
           DL+ A KKLK  G GF IIP+G G YL+QS+P EL++DH++VL Q+A KN  +++VS + 
Sbjct: 119 DLIRAIKKLKALGTGFGIIPVG-GTYLIQSVPAELNMDHTVVL-QLAEKN-GYVTVSEIK 175
Query: 203 NELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTECMNAE 250
             L W TERA+  L+ +++EG AW+D Q+P E  YW P+LFT+  + E
Sbjct: 176 ASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLPALFTDLYSQE 223

>pdb|1U5T|A Chain A, Structure Of The Escrt-Ii Endosomal Trafficking Complex Length = 233

Iteration: 1
 Score =  127 bits (319), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 79/243 (32%), Positives = 128/243 (52%), Gaps = 15/243 (6%)
Query: 3   RRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQ 62
           ++ G+ A  +  L+  KY D   +I E Q  +L   L  F+++L  FA ++ +E++   +
Sbjct: 2   KQFGLAAFDE--LKDGKYNDVNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPE 59
Query: 63  FRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDEL 122
           FR  F  MC+SIG+DPL+       L  + DFYYE+ ++++E+C  T   NGG+I   EL
Sbjct: 60  FRSKFMHMCSSIGIDPLSLFDRDKHLFTVNDFYYEVCLKVIEICRQTKDMNGGVISFQEL 119
Query: 123 RTRLVKSRGKSLQHQDITNE-DLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDH 181
               V  R  ++   D+    D+L + +  +IF          +G+  ++S+P EL+ D 
Sbjct: 120 EK--VHFRKLNVGLDDLEKSIDMLKSLECFEIFQI--------RGKKFLRSVPNELTSDQ 169
Query: 182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS 241
           + +L+  +     + S+S+L   L W   R++ ALD MV  G  WID Q   E LYW PS
Sbjct: 170 TKILEICSIL--GYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGAEALYWDPS 227
Query: 242 LFT 244
             T
Sbjct: 228 WIT 230

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	254
1u5t_A	233	Appears to BE functionally related to SNF7; SNF8P;	1e-103
3cuq_A	234	Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nu	1e-100
3cuq_B	218	Vacuolar protein-sorting-associated protein 36; ES	2e-22
1w7p_D	566	VPS36P, YLR417W; ESCRT-II complex, endosomal prote	8e-16
1u5t_B	169	Defective in vacuolar protein sorting; VPS36P; ESC	4e-09
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-05

>1u5t_A Appears to BE functionally related to SNF7; SNF8P; ESCRT, endosomal, trafficking, protein complex, transport protein; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54 PDB: 1w7p_A Length = 233

 Score =  298 bits (765), Expect = e-103
 Identities = 79/243 (32%), Positives = 123/243 (50%), Gaps = 13/243 (5%)

Query: 3   RRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQ 62
           ++ G+ A  + K    KY D   +I E Q  +L   L  F+++L  FA ++ +E++   +
Sbjct: 2   KQFGLAAFDELK--DGKYNDVNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPE 59

Query: 63  FRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDEL 122
           FR  F  MC+SIG+DPL+       L  + DFYYE+ ++++E+C  T   NGG+I   EL
Sbjct: 60  FRSKFMHMCSSIGIDPLSLFDRDKHLFTVNDFYYEVCLKVIEICRQTKDMNGGVISFQEL 119

Query: 123 RTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHS 182
                +         ++  +DL  +   LK     F I  I  G+  ++S+P EL+ D +
Sbjct: 120 EKVHFRKL-------NVGLDDLEKSIDMLKSLE-CFEIFQIR-GKKFLRSVPNELTSDQT 170

Query: 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSL 242
            +L+        + S+S+L   L W   R++ ALD MV  G  WID Q   E LYW PS 
Sbjct: 171 KILE--ICSILGYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGAEALYWDPSW 228

Query: 243 FTE 245
            T 
Sbjct: 229 ITR 231

>3cuq_A Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nucleus, protein transport, transc transcription regulation, transport, endosome; 2.61A {Homo sapiens} PDB: 2zme_A Length = 234

 Score =  291 bits (746), Expect = e-100
 Identities = 120/228 (52%), Positives = 169/228 (74%), Gaps = 6/228 (2%)

Query: 24  GTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRK 83
           GT + E+QL Q+S+ L+ F+  LE FAS++K EI+K+ +FR  FQ+MCA+IGVDPLAS K
Sbjct: 1   GTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQDMCATIGVDPLASGK 60

Query: 84  GFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNE 142
           GFWS +LG+GDFYYEL VQI+EVCLA  ++NGGLI L+EL  +++K RGK    QD++ +
Sbjct: 61  GFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLEELHQQVLKGRGKF--AQDVSQD 118

Query: 143 DLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLN 202
           DL+ A KKLK  G GF IIP+G G YL+QS+P EL++DH++VLQ   ++   +++VS + 
Sbjct: 119 DLIRAIKKLKALGTGFGIIPVG-GTYLIQSVPAELNMDHTVVLQ--LAEKNGYVTVSEIK 175

Query: 203 NELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTECMNAE 250
             L W TERA+  L+ +++EG AW+D Q+P E  YW P+LFT+  + E
Sbjct: 176 ASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLPALFTDLYSQE 223

>3cuq_B Vacuolar protein-sorting-associated protein 36; ESCRT, MBV, VPS, nucleus, protein transport, transc transcription regulation, transport, endosome; 2.61A {Homo sapiens} PDB: 2zme_B Length = 218

 Score = 90.8 bits (225), Expect = 2e-22
 Identities = 39/220 (17%), Positives = 87/220 (39%), Gaps = 19/220 (8%)

Query: 30  NQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLL 89
           ++L   ++ +      + +   + + +I +D   R  F+    S+G+    +R+ + S  
Sbjct: 14  SKLMIKAKEMVELSKSIANKIKDKQGDITEDETIR--FKSYLLSMGIANPVTRETYGS-- 69

Query: 90  GMGDFYY-ELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAA 148
             G  Y+ +L+ Q+  +      + GG++ L E+   + ++RG  L    ++ EDL+ A 
Sbjct: 70  --GTQYHMQLAKQLAGILQVPLEERGGIMSLTEVYCLVNRARGMEL----LSPEDLVNAC 123

Query: 149 KKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSV--LNNELN 206
           K L+       +     G  +++      S     ++           S++       + 
Sbjct: 124 KMLEALKLPLRLRVFDSGVMVIELQ----SHKEEEMVASALETVSEKGSLTSEEFAKLVG 179

Query: 207 WSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTEC 246
            S   A+  L    + G+   D     E L ++P+LF   
Sbjct: 180 MSVLLAKERLLLAEKMGHLCRDDSV--EGLRFYPNLFMTQ 217

>1w7p_D VPS36P, YLR417W; ESCRT-II complex, endosomal protein sorting, protein transpo; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54 Length = 566

 Score = 75.5 bits (184), Expect = 8e-16
 Identities = 40/256 (15%), Positives = 89/256 (34%), Gaps = 22/256 (8%)

Query: 2   RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDA 61
             R G+ +++K +  Q    D   +     L +L     +    +E         +K   
Sbjct: 320 LSRIGISSLEKSRENQLLNNDILFNNALTDLNKLM----SLATSIERLYKNSNITMKTKT 375

Query: 62  QFRRHFQEMCASIGVDPLAS--RKGFWSLLGMGDFYYELSVQIVEVCLA-----TNYKNG 114
              +    +       PL    R+ F +      F  E++ +I E  L+      +  N 
Sbjct: 376 LNLQDESTVNEPKTRRPLLILDREKFLN---KELFLDEIAREIYEFTLSEFKDLNSDTNY 432

Query: 115 GLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNG-FSIIPIGQGQYLVQSI 173
            +I L +L     KS         I+  ++  A ++ +  G     ++ + +    V S 
Sbjct: 433 MIITLVDLYAMYNKSMRIGTGL--ISPMEMREACERFEHLGLNELKLVKVNKRILCVTSE 490

Query: 174 PGELSLDHSL-VLQQVASKNEAHISVSV--LNNELNWSTERAQHALDFMVQEGYAWIDTQ 230
             ++  +  + ++      +   ++  +   N++ NW+       L   V EG   ID Q
Sbjct: 491 KFDVVKEKLVDLIGDNPGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCVDEGDLLIDKQ 550

Query: 231 SPQEHLYWFPSLFTEC 246
                +Y++ + +   
Sbjct: 551 L--SGIYYYKNSYWPS 564

>1u5t_B Defective in vacuolar protein sorting; VPS36P; ESCRT, endosomal, trafficking, protein complex, transport protein; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54 Length = 169

 Score = 53.4 bits (128), Expect = 4e-09
 Identities = 27/160 (16%), Positives = 62/160 (38%), Gaps = 13/160 (8%)

Query: 94  FYYELSVQIVEVCLA-----TNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAA 148
           F  E++ +I E  L+      +  N  +I L +L     KS         I+  ++  A 
Sbjct: 12  FLDEIAREIYEFTLSEFKDLNSDTNYMIITLVDLYAMYNKSMRIGTGL--ISPMEMREAC 69

Query: 149 KKLKIFGNG-FSIIPIGQGQYLVQSIPGELSLDHSL-VLQQVASKNEAHISVSV--LNNE 204
           ++ +  G     ++ + +    V S   ++  +  + ++      +   ++  +   N++
Sbjct: 70  ERFEHLGLNELKLVKVNKRILCVTSEKFDVVKEKLVDLIGDNPGSDLLRLTQILSSNNSK 129

Query: 205 LNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFT 244
            NW+       L   V EG   ID Q     +Y++ + + 
Sbjct: 130 SNWTLGILMEVLQNCVDEGDLLIDKQL--SGIYYYKNSYW 167

>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 = 44.8 bits (105), Expect = 1e-05
 Identities = 36/310 (11%), Positives = 83/310 (26%), Gaps = 100/310 (32%)

Query: 15  LEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQE----- 69
           +   K + +  S+         Q    + D  + FA    + ++   + R+   E     
Sbjct: 95  MSPIKTEQRQPSMMTRMYI--EQRDRLYNDN-QVFAKYNVSRLQPYLKLRQALLELRPAK 151

Query: 70  ------M------------CASIGVDPLASRKGFWSLLG-----------MGDFYYELSV 100
                 +            C S  V      K FW  L            +    Y++  
Sbjct: 152 NVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDP 211

Query: 101 QIVEVC---------------------LATNYKNGGLILLDELRTR------------LV 127
                                       +  Y+N  L++L  ++              L+
Sbjct: 212 NWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYEN-CLLVLLNVQNAKAWNAFNLSCKILL 270

Query: 128 KSRGKSL-------QHQDITNEDL---LAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGEL 177
            +R K +           I+ +     L   +   +        P        Q +P E+
Sbjct: 271 TTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRP--------QDLPREV 322

Query: 178 SLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQE--H 235
              +   L  +A      +  +  +N  + + ++    ++       + ++   P E   
Sbjct: 323 LTTNPRRLSIIAESIRDGL--ATWDNWKHVNCDKLTTIIE-------SSLNVLEPAEYRK 373

Query: 236 LYWFPSLFTE 245
           ++   S+F  
Sbjct: 374 MFDRLSVFPP 383

>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 = 42.5 bits (99), Expect = 9e-05
 Identities = 37/227 (16%), Positives = 82/227 (36%), Gaps = 61/227 (26%)

Query: 34  QLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASI----GVDPL--------AS 81
           +  +H   ++D L  F    ++    +    +  Q+M  SI     +D +         +
Sbjct: 10  ETGEHQYQYKDILSVF----EDAFVDNFDC-KDVQDMPKSILSKEEIDHIIMSKDAVSGT 64

Query: 82  RKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQD-IT 140
            + FW+LL   +   +   + VE  L  NYK     L+  ++T     R  S+  +  I 
Sbjct: 65  LRLFWTLLSKQEEMVQ---KFVEEVLRINYK----FLMSPIKTE---QRQPSMMTRMYIE 114

Query: 141 NEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISV-- 198
             D        +++ +           Y V  +   L L  +  L ++  +   ++ +  
Sbjct: 115 QRD--------RLYNDNQVFAK-----YNVSRLQPYLKLRQA--LLEL--RPAKNVLIDG 157

Query: 199 ------SVLNNELNWSTERAQHALDFMVQEGYAWID---TQSPQEHL 236
                 + +  ++   + + Q  +DF +     W++     SP+  L
Sbjct: 158 VLGSGKTWVALDV-CLSYKVQCKMDFKI----FWLNLKNCNSPETVL 199

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	254
3cuq_A	234	Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nu	100.0
1u5t_A	233	Appears to BE functionally related to SNF7; SNF8P;	100.0
3cuq_B	218	Vacuolar protein-sorting-associated protein 36; ES	100.0
1w7p_D	566	VPS36P, YLR417W; ESCRT-II complex, endosomal prote	100.0
1u5t_B	169	Defective in vacuolar protein sorting; VPS36P; ESC	100.0
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	96.82
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	96.57
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	96.46
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	96.09
3i71_A	68	Ethanolamine utilization protein EUTK; helix-turn-	96.07
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	96.0
1p6r_A	82	Penicillinase repressor; transcription regulation,	95.84
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	95.82
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	95.64
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	95.28
2kko_A	108	Possible transcriptional regulatory protein (possi	95.25
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	95.25
3jth_A	98	Transcription activator HLYU; transcription factor	95.22
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	94.85
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	94.74
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	94.74
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	94.71
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	94.69
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	94.66
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	94.64
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	94.58
1ku9_A	152	Hypothetical protein MJ223; putative transcription	94.58
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	94.52
3r0a_A	123	Putative transcriptional regulator; structural gen	94.31
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	94.3
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	94.24
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	94.15
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	94.14
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	94.07
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	94.06
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	94.03
2pex_A	153	Transcriptional regulator OHRR; transcription regu	94.02
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	94.0
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	93.98
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	93.93
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	93.93
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	93.9
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	93.89
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	93.86
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	93.85
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	93.84
1sfx_A	109	Conserved hypothetical protein AF2008; structural	93.79
2gxg_A	146	146AA long hypothetical transcriptional regulator;	93.77
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	93.75
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	93.71
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	93.69
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	93.67
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	93.63
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	93.6
3s2w_A	159	Transcriptional regulator, MARR family; structural	93.58
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	93.54
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	93.5
2nnn_A	140	Probable transcriptional regulator; structural gen	93.46
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	93.42
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	93.4
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	93.38
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	93.3
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	93.25
1z91_A	147	Organic hydroperoxide resistance transcriptional;	93.23
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	93.23
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	93.1
3bja_A	139	Transcriptional regulator, MARR family, putative;	93.04
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	92.98
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	92.95
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	92.82
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	92.76
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	92.76
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	92.76
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	92.75
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	92.74
1t6s_A	162	Conserved hypothetical protein; A winged helix-tur	92.74
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	92.71
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	92.69
3nqo_A	189	MARR-family transcriptional regulator; structural	92.58
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	92.51
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	92.45
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	92.43
2z99_A	219	Putative uncharacterized protein; winged helix dom	92.42
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	92.42
2w25_A	150	Probable transcriptional regulatory protein; trans	92.18
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	92.14
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	92.03
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	92.02
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	91.96
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	91.92
1okr_A	123	MECI, methicillin resistance regulatory protein ME	91.91
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	91.85
2eth_A	154	Transcriptional regulator, putative, MAR family; M	91.74
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	91.53
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	91.5
3f3x_A	144	Transcriptional regulator, MARR family, putative;	91.49
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	91.31
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	91.06
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	91.05
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	91.03
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	91.0
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	90.99
2fxa_A	207	Protease production regulatory protein HPR; protea	90.9
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	90.75
1lva_A	258	Selenocysteine-specific elongation factor; winged-	90.62
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	90.59
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	90.54
2xzm_8	143	RPS25E,; ribosome, translation; 3.93A {Tetrahymena	90.25
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	90.16
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	89.99
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	89.94
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	89.82
2c9l_Y	63	EB1, zebra, BZLF1 trans-activator protein; viral p	89.79
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	89.35
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	88.75
2ve8_A	73	FTSK, DNA translocase FTSK; nucleotide-binding, ch	88.49
1y0u_A	96	Arsenical resistance operon repressor, putative; s	88.32
2pg4_A	95	Uncharacterized protein; structural genomics, join	88.27
3u5c_Z	108	RP45, S31, YS23, 40S ribosomal protein S25-A; tran	88.14
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	87.92
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	87.91
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	87.5
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	87.39
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	87.26
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	86.9
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	86.88
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	86.32
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	86.11
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	85.62
1mkm_A	249	ICLR transcriptional regulator; structural genomic	85.41
2h09_A	155	Transcriptional regulator MNTR; transcription regu	85.18
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	85.06
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	84.93
2vn2_A	128	DNAD, chromosome replication initiation protein; D	84.63
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	84.41
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	84.22
3iz6_V	108	40S ribosomal protein S25 (S25E); eukaryotic ribos	84.2
1hsj_A	487	Fusion protein consisting of staphylococcus access	83.94
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	83.88
3nw0_A	238	Non-structural maintenance of chromosomes element	83.65
3i5g_C	159	Myosin catalytic light chain LC-1, mantle muscle;	82.93
1yyv_A	131	Putative transcriptional regulator; reductive meth	82.87
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	82.64
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	82.6
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	82.32
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	82.22
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	82.11
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	81.94
4fx0_A	148	Probable transcriptional repressor protein; helix-	80.94
2g7u_A	257	Transcriptional regulator; ICLR family, structural	80.41
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	80.15

>3cuq_A Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nucleus, protein transport, transc transcription regulation, transport, endosome; 2.61A {Homo sapiens} PDB: 2zme_A

Probab=100.00  E-value=1.1e-80  Score=547.67  Aligned_cols=221  Identities=54%  Similarity=1.002  Sum_probs=206.2

Q ss_pred             ccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCcccCCCcccc-ccccchhHHHHHHHH
Q psy6552          24 GTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQI  102 (254)
Q Consensus        24 g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~-~lg~gdfy~eLavqi  102 (254)
                      |+++.++++++|++||++||++|++||+||+++|++||+||++|++||++||||||+++||||+ ++|+|||||||||||
T Consensus         1 g~~l~~~~~~~~~~Ql~~F~~~L~~FA~kH~~eI~~dp~fR~~F~~mc~siGVDPlas~kg~ws~~lG~gdfy~eLavqI   80 (234)
T 3cuq_A            1 GTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQDMCATIGVDPLASGKGFWSEMLGVGDFYYELGVQI   80 (234)
T ss_dssp             ---------CTTHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHTCCTTSCTTSHHHHHHCHHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCHHHHHHHHHHHHHcCCCcccCCcchhhhhcCcchHHHHHHHHH
Confidence            4568888999999999999999999999999999999999999999999999999999999999 999999999999999


Q ss_pred             HHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHH
Q psy6552         103 VEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHS  182 (254)
Q Consensus       103 ve~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~  182 (254)
                      +|+|.+||++|||||+|+||+|++||+||..+  ++|||+||+|||++|++||+||+|++|+ |++||||+|.|+|+||+
T Consensus        81 vEvC~~tr~~nGGli~L~el~~~~~r~Rg~~~--~~IS~dDi~rAik~L~~LG~g~~v~~~~-g~~~VqSvp~el~~D~~  157 (234)
T 3cuq_A           81 IEVCLALKHRNGGLITLEELHQQVLKGRGKFA--QDVSQDDLIRAIKKLKALGTGFGIIPVG-GTYLIQSVPAELNMDHT  157 (234)
T ss_dssp             HHHHHHHHHHHSSEEEHHHHHHHHHHTTTTCC--SSCCHHHHHHHHHHHGGGBTTCEEEEET-TEEEEECSCCCCCHHHH
T ss_pred             HHHHHHHHHhcCCeeEHHHHHHHHHHhcCCcc--CccCHHHHHHHHHHHHhcCCCeEEEEEC-CEEEEEeCCCccchHHH
Confidence            99999999999999999999999999999866  7999999999999999999999999999 99999999999999999


Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecccccCcccc
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTECMNA  249 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~lf~~~~~~  249 (254)
                      .||++|+  ..||||+++|++++||+++||+++|++|+++|++|||+|.++|+.|||||+|.+..++
T Consensus       158 ~vLela~--~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~GllwvD~q~~ge~~Yw~P~lf~~~~~~  222 (234)
T 3cuq_A          158 VVLQLAE--KNGYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHYWLPALFTDLYSQ  222 (234)
T ss_dssp             HHHHHHT--TTSEECHHHHHHHHTCCHHHHHHHHHHHHHHTSCEEESSSSSSCEEECTTSSCCCCCC
T ss_pred             HHHHHHH--hcCcCcHHHHHHHhCCCHHHHHHHHHHHHhCCCEEEeCCCCCcceeecchhhcccccc
Confidence            9999999  6799999999999999999999999999999999999997678999999999976654

>1u5t_A Appears to BE functionally related to SNF7; SNF8P; ESCRT, endosomal, trafficking, protein complex, transport protein; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54 PDB: 1w7p_A

Probab=100.00  E-value=1.5e-80  Score=546.95  Aligned_cols=230  Identities=34%  Similarity=0.628  Sum_probs=205.1

Q ss_pred             CcchhhHHHhccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCccc-
Q psy6552           2 RRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLA-   80 (254)
Q Consensus         2 rR~vGi~~i~~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~-   80 (254)
                      ||+|||+||+  ++++++|+++|+++.++++++|++||++||++|++||+||+++|++||+||++|++||++||||||+ 
T Consensus         1 rr~~G~~a~~--~~~~~~~~~~g~~l~~~~~~~l~~Ql~~F~~~L~~FA~kHk~eI~~dp~fR~~F~~mc~siGVDPLa~   78 (233)
T 1u5t_A            1 MKQFGLAAFD--ELKDGKYNDVNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPEFRSKFMHMCSSIGIDPLSL   78 (233)
T ss_dssp             ---------------------CCSHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTTTTTCHHHHHHHHHHHHHHTCCHHHH
T ss_pred             CCCccHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhhcccCHHHHHHHHHHHHHcCCCCCcc
Confidence            6889999999  6789999999999999999999999999999999999999999999999999999999999999999 


Q ss_pred             CCCcccc-ccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeE
Q psy6552          81 SRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFS  159 (254)
Q Consensus        81 s~kg~w~-~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~  159 (254)
                      |+||  + ++|+|||||||||||+|+|.+||++|||||+|+||+|++||+       ++|||+||++||++|++| .||+
T Consensus        79 s~kg--~~~lg~gdfy~eLavqIvEvC~~tr~~nGGli~l~el~~~~~r~-------~~IS~dDi~rAik~L~~L-~gf~  148 (233)
T 1u5t_A           79 FDRD--KHLFTVNDFYYEVCLKVIEICRQTKDMNGGVISFQELEKVHFRK-------LNVGLDDLEKSIDMLKSL-ECFE  148 (233)
T ss_dssp             TTSS--GGGTTHHHHHHHHHHHHHHHHHHHTTTSSSCEEHHHHHHTTTTT-------TTCCHHHHHHHHHHHTTT-CCCC
T ss_pred             CCcc--ccccCcchHHHHHHHHHHHHHHHHHHhcCCeeEHHHHHHHHHhh-------cCCCHHHHHHHHHHhhhc-cCeE
Confidence            9998  7 999999999999999999999999999999999999999997       589999999999999999 9999


Q ss_pred             EEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552         160 IIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF  239 (254)
Q Consensus       160 l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~  239 (254)
                      +++++ |++||||+|.|+|+||+.||++|+  ..||||+++|++++||+++||+++|++|+++|++|||+|.++|+.|||
T Consensus       149 v~~v~-g~~~vqsvp~el~~D~~~vLe~a~--~~g~vt~~~L~~~lgW~~~Ra~~~L~~l~~~G~lwvD~q~~~e~~Yw~  225 (233)
T 1u5t_A          149 IFQIR-GKKFLRSVPNELTSDQTKILEICS--ILGYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGAEALYWD  225 (233)
T ss_dssp             EEEET-TEEEECCSSSCCCTTHHHHHHTTT--TTSCCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEEECSSSSSCEEEC
T ss_pred             EEEEC-CEEEEEeCCCccchHHHHHHHHHH--hcCcCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCCCCCccceec
Confidence            99999 999999999999999999999999  679999999999999999999999999999999999999756899999


Q ss_pred             cccccCc
Q psy6552         240 PSLFTEC  246 (254)
Q Consensus       240 p~lf~~~  246 (254)
                      ||+|.+.
T Consensus       226 P~lf~~~  232 (233)
T 1u5t_A          226 PSWITRQ  232 (233)
T ss_dssp             GGGGGCC
T ss_pred             hhhhhcc
Confidence            9999853

>3cuq_B Vacuolar protein-sorting-associated protein 36; ESCRT, MBV, VPS, nucleus, protein transport, transc transcription regulation, transport, endosome; 2.61A {Homo sapiens} PDB: 2zme_B

Probab=100.00  E-value=2.9e-61  Score=422.21  Aligned_cols=203  Identities=19%  Similarity=0.290  Sum_probs=187.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhc-------CHHHHHHHHHHHHHcCCC-cccCCCccccccccchhHHHHH
Q psy6552          28 QENQLEQLSQHLNTFRDKLESFASEYKNEIKK-------DAQFRRHFQEMCASIGVD-PLASRKGFWSLLGMGDFYYELS   99 (254)
Q Consensus        28 ~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~~-------dp~fr~~f~~mc~~lGVd-Pl~s~kg~w~~lg~gdfy~eLa   99 (254)
                      ..++|+||+++|++|++|+. +|++++.++++       |+  ..+|++||++|||| |+++ +|||   +.|+||||||
T Consensus         6 ~~~af~DL~~LM~~Ak~mv~-la~~~~~~~~~~~~~~~~~e--~~~f~~m~~slGvd~Pl~~-~~~~---s~~~f~~ELa   78 (218)
T 3cuq_B            6 ISEAFEDLSKLMIKAKEMVE-LSKSIANKIKDKQGDITEDE--TIRFKSYLLSMGIANPVTR-ETYG---SGTQYHMQLA   78 (218)
T ss_dssp             SHHHHHHHHHHHHHHHHHHH-HHHGGGCC----------CC--SHHHHHHHHHHTCCCHHHH-TTSS---CSCHHHHHHH
T ss_pred             HHHHHHhHHHHHHHHHHHHH-HHHHHHHHHhccCCCCCchH--HHHHHHHHHHcCCCCcchh-hccC---cccHHHHHHH
Confidence            34599999999999999996 78888766653       33  36899999999999 9996 5888   4689999999


Q ss_pred             HHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCCh
Q psy6552         100 VQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSL  179 (254)
Q Consensus       100 vqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~  179 (254)
                      |||+|||.+++++|||||+|.||||+|||+||.    ++|||+||++||++|++||+||+|++|+||++|||++|.+++.
T Consensus        79 ~qi~e~c~~~~~~~GG~I~L~dl~~~~nraRG~----~lVSp~Dl~~A~~~l~~Lg~~~~l~~~~sg~~vvqs~~~~~~~  154 (218)
T 3cuq_B           79 KQLAGILQVPLEERGGIMSLTEVYCLVNRARGM----ELLSPEDLVNACKMLEALKLPLRLRVFDSGVMVIELQSHKEEE  154 (218)
T ss_dssp             HHHHHHHHHHHHHTTSEEEHHHHHHHHHHTCSS----SCCCHHHHHHHHHTTTTTTCSEEEEECTTSBEEEEETTCCGGG
T ss_pred             HHHHHHHHHHHHhCCCeEEHHHHHHHHHHHcCC----CCCCHHHHHHHHHHHHHcCCCEEEEEECCCcEEEEcCCCchHH
Confidence            999999999999999999999999999999998    8999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecccccC
Q psy6552         180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTE  245 (254)
Q Consensus       180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~lf~~  245 (254)
                      |++.|+++++  ..||||+.+|++++||++.||+++|++|+++|++|||++  .++.|||||+|.+
T Consensus       155 ~~~~il~~~~--~~g~vt~~~la~~l~ws~~~a~e~L~~~e~~G~l~~D~~--~eg~~y~pn~f~~  216 (218)
T 3cuq_B          155 MVASALETVS--EKGSLTSEEFAKLVGMSVLLAKERLLLAEKMGHLCRDDS--VEGLRFYPNLFMT  216 (218)
T ss_dssp             GHHHHHHHHH--HTSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEES--SSCEEEEECGGGC
T ss_pred             HHHHHHHHHH--HCCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCEEEECC--CCceEEehhhccc
Confidence            9999999999  569999999999999999999999999999999999997  6899999999985

>1w7p_D VPS36P, YLR417W; ESCRT-II complex, endosomal protein sorting, protein transpo; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54

Probab=100.00  E-value=3.2e-49  Score=384.36  Aligned_cols=219  Identities=17%  Similarity=0.211  Sum_probs=141.0

Q ss_pred             cchhhHHHhccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh-------cCH--HHHHHHHHHHHH
Q psy6552           3 RRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIK-------KDA--QFRRHFQEMCAS   73 (254)
Q Consensus         3 R~vGi~~i~~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~-------~dp--~fr~~f~~mc~~   73 (254)
                      +++||+||+|+.+++++.++.   +..++|+||+++|++|++|+. +|++++.+++       .|+  +-..+|..++  
T Consensus       321 ~~~GI~gler~~e~~~~~~~~---~i~~Af~DL~~LM~~AkemV~-La~~~~~~~~~~~~~~s~~~~~~e~~~~~s~L--  394 (566)
T 1w7p_D          321 SRIGISSLEKSRENQLLNNDI---LFNNALTDLNKLMSLATSIER-LYKNSNITMKTKTLNLQDESTVNEPKTRRPLL--  394 (566)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             cccCcHHHHHHHHHHHHHHHH---HHHHHHHhHHHHHHHHHHHHH-HHHHHHHHHhhcccCCCCCccchhhHhhHhhc--
Confidence            569999999999998888887   455699999999999999996 5666655553       221  1122444444  


Q ss_pred             cCCCcccCCCccccccc-cchhHHHHHHHHHHHhhhhh----hh-cCCceeHHHHHHHHHHh-c-CCCCCCCCCCHHHHH
Q psy6552          74 IGVDPLASRKGFWSLLG-MGDFYYELSVQIVEVCLATN----YK-NGGLILLDELRTRLVKS-R-GKSLQHQDITNEDLL  145 (254)
Q Consensus        74 lGVdPl~s~kg~w~~lg-~gdfy~eLavqive~c~~~r----~~-nGGii~L~dl~~~~nr~-R-g~~~~~~~IS~~Di~  145 (254)
                          |++..     ++| .++|||||||||+|||.+++    ++ |||||+|.||||+|||+ | |.    ++|||+||+
T Consensus       395 ----~Vtrd-----~~~s~~~f~~ELA~qI~E~c~~~~~~~l~~~nGGmItL~DL~~~~NRa~R~g~----elISp~Dll  461 (566)
T 1w7p_D          395 ----ILDRE-----KFLNKELFLDEIAREIYEFTLSEFKDLNSDTNYMIITLVDLYAMYNKSMRIGT----GLISPMEMR  461 (566)
T ss_dssp             -----CCSS-----CCCCHHHHHHHHHHHHHHHHHHTTCCSSCSCCCCEEEHHHHHHHHHHHTTTTT----CCCCHHHHH
T ss_pred             ----ccchh-----hcCChhHHHHHHHHHHHHHHHhhhcccchhcCcCeEEHHHHHHHHHHhccCCC----CccCHHHHH
Confidence                88854     333 47999999999999999999    88 99999999999999999 9 55    799999999


Q ss_pred             HHHHHhhhhCCCeE-EEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcC-------CCHHHHHHHHH
Q psy6552         146 AAAKKLKIFGNGFS-IIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELN-------WSTERAQHALD  217 (254)
Q Consensus       146 rA~~~L~~Lg~g~~-l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~-------ws~~ra~~~L~  217 (254)
                      +||++|++||+||+ |++|+||+.|+ ++|.+ +.|+.+|+++++  ..||||+.+|++++|       |++.||+++|+
T Consensus       462 ~A~~~le~Lg~~~~~L~~~~sgvlVv-s~~~~-~~~~~~il~l~~--~~g~vT~~~la~~lg~~~~~~~Ws~~~A~e~L~  537 (566)
T 1w7p_D          462 EACERFEHLGLNELKLVKVNKRILCV-TSEKF-DVVKEKLVDLIG--DNPGSDLLRLTQILSSNNSKSNWTLGILMEVLQ  537 (566)
T ss_dssp             HHHTTGGGGTCTTCEEEECSSSCEEE-ESSCH-HHHHHHHHHHHT--TSTTCCHHHHHHHHSCSSSCCCBCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCeEEEEEECCEEEEE-cCCCc-hHHHHHHHHHHH--hcCCcCHHHHHHHhCCccccCcccHHHHHHHHH
Confidence            99999999999999 99999888776 99977 889999999999  579999999999999       99999999999


Q ss_pred             HHHHcCcEEEeCCCCCcccceecccccCc
Q psy6552         218 FMVQEGYAWIDTQSPQEHLYWFPSLFTEC  246 (254)
Q Consensus       218 ~l~~~G~lwvD~q~~~e~~yw~p~lf~~~  246 (254)
                      +|+++|++|||+|.  ++.|||||+|...
T Consensus       538 ~~e~eG~l~rDd~~--~G~~yypNlf~~~  564 (566)
T 1w7p_D          538 NCVDEGDLLIDKQL--SGIYYYKNSYWPS  564 (566)
T ss_dssp             HHHHTTSEEEEEET--TEEEEEECCSSCC
T ss_pred             HHHHcCCEEEECCC--CceEEehhhcccc
Confidence            99999999999994  6999999999854

>1u5t_B Defective in vacuolar protein sorting; VPS36P; ESCRT, endosomal, trafficking, protein complex, transport protein; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54

Probab=100.00  E-value=9e-42  Score=288.05  Aligned_cols=143  Identities=21%  Similarity=0.298  Sum_probs=129.9

Q ss_pred             chhHHHHHHHHHHHhh---h-hhhhcCC-ceeHHHHHHHHHHh-c-CCCCCCCCCCHHHHHHHHHHhhhhCCC-eEEEEe
Q psy6552          92 GDFYYELSVQIVEVCL---A-TNYKNGG-LILLDELRTRLVKS-R-GKSLQHQDITNEDLLAAAKKLKIFGNG-FSIIPI  163 (254)
Q Consensus        92 gdfy~eLavqive~c~---~-~r~~nGG-ii~L~dl~~~~nr~-R-g~~~~~~~IS~~Di~rA~~~L~~Lg~g-~~l~~~  163 (254)
                      .+||+||||||+|+|.   + ++++||| ||+|.||||+|||+ | |.    ++|||+||++||++|++||+| |+|++|
T Consensus        10 ~~f~~ELa~qi~e~c~~~~~~~~~~~GG~~I~L~dl~~~~nra~R~g~----~lISp~Dl~~A~~~l~~Lg~~~~~l~~~   85 (169)
T 1u5t_B           10 ELFLDEIAREIYEFTLSEFKDLNSDTNYMIITLVDLYAMYNKSMRIGT----GLISPMEMREACERFEHLGLNELKLVKV   85 (169)
T ss_dssp             TTHHHHHHHHHHHHHHTTTTTSSSCCCCCCEETTHHHHHHHHTTTSSS----CCCCHHHHHHHHTTTGGGTCCSCEEEEE
T ss_pred             hHHHHHHHHHHHHHHhhcchhhHHhcCceeEEHHHHHHHHHHhhcCCC----CccCHHHHHHHHHHHHhcCCCeEEEEEE
Confidence            5999999999999999   7 9999999 99999999999999 9 45    799999999999999999999 999999


Q ss_pred             CCceEEEEccCCCCChhH--HHHHHHhhccCCCc----ccHH-H-HHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcc
Q psy6552         164 GQGQYLVQSIPGELSLDH--SLVLQQVASKNEAH----ISVS-V-LNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEH  235 (254)
Q Consensus       164 ~sg~~vv~s~p~els~D~--~~il~l~~~~~~g~----vt~~-~-l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~  235 (254)
                      +||++|+.+    .+.|+  +.++++++.. .|+    +|+. + +++++||++.||+++|++++++|++|||+|.  ++
T Consensus        86 ~sg~~V~~~----~~~d~~~~~il~~~~~~-~g~d~~~vt~~~~~la~~~~ws~~~a~e~L~~~e~~G~l~~D~~~--~G  158 (169)
T 1u5t_B           86 NKRILCVTS----EKFDVVKEKLVDLIGDN-PGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCVDEGDLLIDKQL--SG  158 (169)
T ss_dssp             TTTEEEEES----SCSHHHHHHHHHHHHHS-CSBCHHHHHHHHHTSCTTCCCCHHHHHHHHHHHHHHTSEEEEECS--SC
T ss_pred             CCeeEEEeC----CChhHHHHHHHHHHHhc-CCCCcccccHHHHHHHHHhCCCHHHHHHHHHHHHHcCCEEEECCC--Cc
Confidence            988888833    34455  8899999854 589    9999 9 9999999999999999999999999999995  56


Q ss_pred             cceecccccC
Q psy6552         236 LYWFPSLFTE  245 (254)
Q Consensus       236 ~yw~p~lf~~  245 (254)
                      .+||||+|..
T Consensus       159 ~~y~~N~f~~  168 (169)
T 1u5t_B          159 IYYYKNSYWP  168 (169)
T ss_dssp             EEEEECCSSC
T ss_pred             ceEEeeecCc
Confidence            8888999875

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=96.82  E-value=0.0029  Score=45.97  Aligned_cols=59  Identities=10%  Similarity=0.077  Sum_probs=48.5

Q ss_pred             HHHHHHHhhcc----CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552         181 HSLVLQQVASK----NEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF  239 (254)
Q Consensus       181 ~~~il~l~~~~----~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~  239 (254)
                      +..||+++...    .++.+|+.+|++.+|+|..-++..|..|++.|++-++-...+-..+|+
T Consensus         6 ~~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~Le~kG~I~R~~ggr~~~~~~~   68 (77)
T 2jt1_A            6 VTKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQLHDVGVLEKVNAGKGVPGLWR   68 (77)
T ss_dssp             HHHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEESCSSSSCCEEE
T ss_pred             HHHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCCCCcHHHHH
Confidence            56788877632    147899999999999999999999999999999999976444567776

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=96.57  E-value=0.0063  Score=43.65  Aligned_cols=58  Identities=14%  Similarity=0.168  Sum_probs=46.2

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      ..|+++...  .|.+|..+|++.+|+|..-+...|..|++.|++-.+....+.+.||..+
T Consensus         3 ~~Il~~L~~--~~~~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~~~~~~~gr~~~y~l~   60 (81)
T 2htj_A            3 NEILEFLNR--HNGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQRSPLRRGMATYWFLK   60 (81)
T ss_dssp             HHHHHHHHH--SCCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEECCSSSSSCEEEES
T ss_pred             HHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeccCCCCcEEEEEC
Confidence            456777663  4679999999999999999999999999999998765432455677643

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=96.46  E-value=0.0087  Score=41.85  Aligned_cols=53  Identities=9%  Similarity=0.000  Sum_probs=41.2

Q ss_pred             CCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         174 PGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       174 p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      |..+++-...||++.... .+.+|..+|++.+|++..-+...|..|+++|++..
T Consensus         5 ~~~m~~~~~~IL~~L~~~-~~~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~~   57 (67)
T 2heo_A            5 LSTGDNLEQKILQVLSDD-GGPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSS   57 (67)
T ss_dssp             ----CHHHHHHHHHHHHH-CSCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cccccHHHHHHHHHHHHc-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEec
Confidence            444554355788887643 46899999999999999999999999999999654

>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=96.09  E-value=0.0048  Score=45.14  Aligned_cols=46  Identities=13%  Similarity=0.109  Sum_probs=41.2

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHH-HHHHHHHHHHHcCcEEEe
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTE-RAQHALDFMVQEGYAWID  228 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~-ra~~~L~~l~~~G~lwvD  228 (254)
                      +..||.+..  ..|..|+.+|++.+|+++. -+..+|..|+++|++..-
T Consensus        13 ~~~IL~~Lk--~~g~~ta~eiA~~Lgit~~~aVr~hL~~Le~eGlV~~~   59 (79)
T 1xmk_A           13 KEKICDYLF--NVSDSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQ   59 (79)
T ss_dssp             HHHHHHHHH--HTCCEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHH--HcCCcCHHHHHHHcCCCcHHHHHHHHHHHHHCCCEEec
Confidence            568888888  4588999999999999999 889999999999999854

>3i71_A Ethanolamine utilization protein EUTK; helix-turn-helix, unknown function; HET: FLC; 2.10A {Escherichia coli}

Probab=96.07  E-value=0.017  Score=39.87  Aligned_cols=42  Identities=14%  Similarity=0.269  Sum_probs=35.7

Q ss_pred             HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      ..+++  ...+.|+.+++..|||+-+.|+.+|+.|..+|.+---
T Consensus        10 all~s--~~QGMTaGEVAA~f~w~Le~ar~aLeqLf~~G~LRKR   51 (68)
T 3i71_A           10 ALLTS--VRQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLRKR   51 (68)
T ss_dssp             HHHHH--CTTCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHH--HhccccHHHHHHHhCCcHHHHHHHHHHHHhcchhhhh
Confidence            34445  3567999999999999999999999999999988654

>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=96.00  E-value=0.0082  Score=43.32  Aligned_cols=59  Identities=12%  Similarity=0.143  Sum_probs=45.9

Q ss_pred             ChhH-HHHHHHhhccC-CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552         178 SLDH-SLVLQQVASKN-EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF  239 (254)
Q Consensus       178 s~D~-~~il~l~~~~~-~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~  239 (254)
                      +.|. ..||++...+. +..+|+.+|++.+|.+..-+...|..|+++|++.+-..   .+-||+
T Consensus        12 ~~~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~~G~I~~~g~---~~~~W~   72 (77)
T 1qgp_A           12 YQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAG---TPPLWK   72 (77)
T ss_dssp             HHHHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHHHHTSEEEECS---SSCEEE
T ss_pred             CHHHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCC---CCCceE
Confidence            3343 67888877441 22899999999999999999999999999999988643   235565

>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=95.84  E-value=0.021  Score=40.72  Aligned_cols=63  Identities=17%  Similarity=0.281  Sum_probs=51.5

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcC----CCHHHHHHHHHHHHHcCcEEEeCCCCCcccceeccc
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELN----WSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSL  242 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~----ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~l  242 (254)
                      .++.-+..|+..+.  ..|.+|+.+|++.++    |++.-....|+.|++.|++-+...  +...+|.|..
T Consensus         6 ~lt~~e~~vL~~L~--~~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r~~~--gr~~~y~~~~   72 (82)
T 1p6r_A            6 QISDAELEVMKVIW--KHSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKE--GRVFVYTPNI   72 (82)
T ss_dssp             CCCHHHHHHHHHHH--TSSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEE--TTEEEEEESC
T ss_pred             CCCHHHHHHHHHHH--cCCCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEEec--CCEEEEEeec
Confidence            36767788888887  357899999999986    999999999999999999999865  3455666654

>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=95.82  E-value=0.02  Score=41.86  Aligned_cols=57  Identities=11%  Similarity=0.121  Sum_probs=44.8

Q ss_pred             HHHHHHHhhccC-CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552         181 HSLVLQQVASKN-EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP  240 (254)
Q Consensus       181 ~~~il~l~~~~~-~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p  240 (254)
                      +..||++...+. +..+|+.+|++.+|.+..-+..+|..|+++|++.+-..   .+-||+-
T Consensus        12 ~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G~I~~~g~---~~~~W~i   69 (81)
T 1qbj_A           12 EQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAG---TPPLWKI   69 (81)
T ss_dssp             HHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEESS---SSCEEEE
T ss_pred             HHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCC---CCCeeEE
Confidence            457888887441 12899999999999999999999999999999997543   2355553

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=95.64  E-value=0.022  Score=41.29  Aligned_cols=45  Identities=16%  Similarity=0.054  Sum_probs=40.9

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      ..|+++++  ..|.+|+++|++.|+.|+.-.+.-|+.|++.|++-+-
T Consensus         5 ~~Il~~L~--~~g~vsv~eLa~~l~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            5 IQVRDLLA--LRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHH--HSCSBCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHH--HcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            45788887  4699999999999999999999999999999999886

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=95.28  E-value=0.024  Score=42.07  Aligned_cols=45  Identities=16%  Similarity=0.034  Sum_probs=40.7

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      ..|+++++  ..|.+|+++|++.|+.|..-.+.-|+.|++.|++-+-
T Consensus         5 ~~Il~~L~--~~g~vsv~eLA~~l~VS~~TIRrDL~~Le~~G~l~R~   49 (87)
T 2k02_A            5 MEVRDMLA--LQGRMEAKQLSARLQTPQPLIDAMLERMEAMGKVVRI   49 (87)
T ss_dssp             HHHHHHHH--HSCSEEHHHHHHHTTCCHHHHHHHHHHHHTTCCSEEE
T ss_pred             HHHHHHHH--HcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            35778887  4699999999999999999999999999999999886

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=95.25  E-value=0.072  Score=40.13  Aligned_cols=77  Identities=17%  Similarity=0.148  Sum_probs=58.9

Q ss_pred             CCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHH
Q psy6552         137 QDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHAL  216 (254)
Q Consensus       137 ~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L  216 (254)
                      ..++.+++.++.+.++.|+.+.                      ...|+.+..   .|.+|+.+|++.+|+++.-+...|
T Consensus         5 ~~~~~~~~~~~~~~~~al~~~~----------------------r~~IL~~L~---~~~~s~~eLa~~lgis~stvs~~L   59 (108)
T 2kko_A            5 SDRKAALLDQVARVGKALANGR----------------------RLQILDLLA---QGERAVEAIATATGMNLTTASANL   59 (108)
T ss_dssp             CCTHHHHHHHHHHHHHHHTTST----------------------THHHHHHHT---TCCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             CccChhhHHHHHHHHHHhCCHH----------------------HHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHH
Confidence            3467778888888888887222                      234666655   267899999999999999999999


Q ss_pred             HHHHHcCcEEEeCCCCCcccceec
Q psy6552         217 DFMVQEGYAWIDTQSPQEHLYWFP  240 (254)
Q Consensus       217 ~~l~~~G~lwvD~q~~~e~~yw~p  240 (254)
                      ..|++.|++-+...  +...||..
T Consensus        60 ~~L~~~GlV~~~~~--gr~~~y~l   81 (108)
T 2kko_A           60 QALKSGGLVEARRE--GTRQYYRI   81 (108)
T ss_dssp             HHHHHHTSEEEEEE--TTEEEEEE
T ss_pred             HHHHHCCCeEEEEe--CCEEEEEE
Confidence            99999999988754  34455543

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=95.25  E-value=0.062  Score=38.87  Aligned_cols=55  Identities=16%  Similarity=0.164  Sum_probs=44.7

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF  239 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~  239 (254)
                      +..|+.+..  ..+.+|..+|++.+|+++.-+...|..|++.|++-+...  +...||.
T Consensus        26 ~~~il~~l~--~~~~~s~~ela~~l~is~~tvs~~l~~L~~~glv~~~~~--~r~~~y~   80 (99)
T 3cuo_A           26 RLLILCMLS--GSPGTSAGELTRITGLSASATSQHLARMRDEGLIDSQRD--AQRILYS   80 (99)
T ss_dssp             HHHHHHHHT--TCCSEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEEC--SSCEEEE
T ss_pred             HHHHHHHHH--hCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEec--CCEEEEE
Confidence            556777666  456899999999999999999999999999999988764  3344443

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=95.22  E-value=0.065  Score=39.20  Aligned_cols=54  Identities=19%  Similarity=0.292  Sum_probs=44.5

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP  240 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p  240 (254)
                      ..|+.+..  . |.+|+.+|++.+|++..-+..+|..|++.|++-+...  +...||..
T Consensus        26 ~~Il~~L~--~-~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~--g~~~~y~l   79 (98)
T 3jth_A           26 LQILCMLH--N-QELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTRKE--AQTVYYTL   79 (98)
T ss_dssp             HHHHHHTT--T-SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECC--TTCCEEEE
T ss_pred             HHHHHHHh--c-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe--CCEEEEEE
Confidence            45666666  3 7899999999999999999999999999999998876  44555543

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=94.85  E-value=0.12  Score=39.67  Aligned_cols=53  Identities=17%  Similarity=0.103  Sum_probs=45.7

Q ss_pred             CChhHHHHHHHh-hccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQV-ASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~-~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.||... .  ..|.+|+.+|++.+|+++.-+...|..|++.|++-+....
T Consensus        35 l~~~~~~iL~~l~~--~~~~~t~~~la~~l~~s~~~vs~~l~~L~~~glv~r~~~~   88 (146)
T 2fbh_A           35 LSQARWLVLLHLAR--HRDSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLAVA   88 (146)
T ss_dssp             CTTTHHHHHHHHHH--CSSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCB
T ss_pred             CCHHHHHHHHHHHH--cCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCeeecCCC
Confidence            565677787777 5  3678999999999999999999999999999999997653

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=94.74  E-value=0.062  Score=39.47  Aligned_cols=54  Identities=15%  Similarity=0.257  Sum_probs=44.2

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      ..||++..  ..| +|+.+|++.+|.|+.-+...|..|+++|++..=..   .+-.|+-+
T Consensus        20 ~~IL~lL~--~~g-~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~~~---~PP~W~~~   73 (82)
T 1oyi_A           20 CEAIKTIG--IEG-ATAAQLTRQLNMEKREVNKALYDLQRSAMVYSSDD---IPPRWFMT   73 (82)
T ss_dssp             HHHHHHHS--SST-EEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEECSS---SSCEEESC
T ss_pred             HHHHHHHH--HcC-CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCC---CCCcceec
Confidence            46678887  356 99999999999999999999999999999988543   45556543

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=94.74  E-value=0.094  Score=37.22  Aligned_cols=54  Identities=15%  Similarity=0.180  Sum_probs=45.5

Q ss_pred             CChhHHHHHHHhhccCC-CcccHHHHHHhc-----CCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNE-AHISVSVLNNEL-----NWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~-g~vt~~~l~~~l-----~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-...|+++.... . +.+|+.+|++.+     +++..=+...|+.|++.|++-+....
T Consensus        15 ~t~~r~~IL~~l~~~-~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~~~~~   74 (83)
T 2fu4_A           15 VTLPRLKILEVLQEP-DNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFE   74 (83)
T ss_dssp             CCHHHHHHHHHHTSG-GGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEEECG
T ss_pred             cCHHHHHHHHHHHhC-CCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEEEeeC
Confidence            344567788888743 4 789999999999     99999999999999999999988763

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=94.71  E-value=0.07  Score=41.12  Aligned_cols=54  Identities=22%  Similarity=0.258  Sum_probs=45.3

Q ss_pred             CCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         174 PGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       174 p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      +..++.-+-.||....  ..| +|+.+|++.+|+++.-+...|..|++.|++-+-..
T Consensus        33 ~~~lt~~~~~iL~~l~--~~~-~t~~eLa~~l~~s~~tvs~~l~~L~~~Glv~r~~~   86 (146)
T 3tgn_A           33 EVALTNTQEHILMLLS--EES-LTNSELARRLNVSQAAVTKAIKSLVKEGMLETSKD   86 (146)
T ss_dssp             SSCCCHHHHHHHHHHT--TCC-CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC---
T ss_pred             ccCCCHHHHHHHHHHH--hCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEeccC
Confidence            3447878888888887  457 99999999999999999999999999999987554

>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=94.69  E-value=0.098  Score=40.00  Aligned_cols=55  Identities=5%  Similarity=0.108  Sum_probs=46.1

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.||......+.+.+|+.+|++.+++++.-+...|+.|++.|++-+...+
T Consensus        29 lt~~~~~vL~~l~~~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~~~   83 (139)
T 3eco_A           29 ITNEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRYVDA   83 (139)
T ss_dssp             CCHHHHHHHHHHHHSTTTCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             CCHHHHHHHHHHHhcCCCCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecCCC
Confidence            6767777877666432258999999999999999999999999999999987654

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=94.66  E-value=0.082  Score=40.83  Aligned_cols=55  Identities=11%  Similarity=0.122  Sum_probs=46.3

Q ss_pred             CCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         175 GELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       175 ~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ..++..+-.||.....  .|.+|+.+|++.+++++.-+...|+.|++.|++-+...+
T Consensus        27 ~~lt~~q~~iL~~l~~--~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   81 (145)
T 3g3z_A           27 QDLNYNLFAVLYTLAT--EGSRTQKHIGEKWSLPKQTVSGVCKTLAGQGLIEWQEGE   81 (145)
T ss_dssp             TTCCHHHHHHHHHHHH--HCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECCCS
T ss_pred             cCCCHHHHHHHHHHHH--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeccCC
Confidence            3477778888877763  356999999999999999999999999999999986543

>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=94.64  E-value=0.18  Score=37.60  Aligned_cols=78  Identities=15%  Similarity=0.261  Sum_probs=57.5

Q ss_pred             CCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHH
Q psy6552         137 QDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHAL  216 (254)
Q Consensus       137 ~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L  216 (254)
                      ..++++++......++.|+.+                      -...|+.+..   .|..|+.+|++.+|++..-...+|
T Consensus         6 ~~~~~~~~~~~~~~~~~l~~~----------------------~r~~IL~~L~---~~~~~~~ela~~l~is~stvs~~L   60 (106)
T 1r1u_A            6 SEINTDTLERVTEIFKALGDY----------------------NRIRIMELLS---VSEASVGHISHQLNLSQSNVSHQL   60 (106)
T ss_dssp             ---CHHHHHHHHHHHHHTCSH----------------------HHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhCCH----------------------HHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHH
Confidence            467888888888888877632                      2345555555   256899999999999999999999


Q ss_pred             HHHHHcCcEEEeCCCCCcccceecc
Q psy6552         217 DFMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       217 ~~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      ..|++.|++-+...  +...||..+
T Consensus        61 ~~L~~~Glv~~~~~--gr~~~y~l~   83 (106)
T 1r1u_A           61 KLLKSVHLVKAKRQ--GQSMIYSLD   83 (106)
T ss_dssp             HHHHHTTSEEEEEE--TTEEEEEES
T ss_pred             HHHHHCCCeEEEEe--CCEEEEEEC
Confidence            99999999988764  344555543

>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=94.58  E-value=0.073  Score=41.11  Aligned_cols=53  Identities=13%  Similarity=0.236  Sum_probs=45.7

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.||....  ..|.+|+.+|++.+++++.-+...|+.|++.|++-+...+
T Consensus        34 lt~~q~~vL~~l~--~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~   86 (140)
T 3hsr_A           34 LTYTGYIVLMAIE--NDEKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVRTREE   86 (140)
T ss_dssp             CCHHHHHHHHHSC--TTCEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCHHHHHHHHHHH--HcCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCeEecCCC
Confidence            6767888888776  3588999999999999999999999999999999998654

>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=94.58  E-value=0.15  Score=39.01  Aligned_cols=54  Identities=15%  Similarity=0.115  Sum_probs=44.0

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-+..++.+.... .|.+|+.+|++.+|+++.-+...|..|++.|++-+....
T Consensus        24 l~~~~~~il~~L~~~-~~~~t~~ela~~l~~~~stvs~~l~~L~~~G~v~r~~~~   77 (152)
T 1ku9_A           24 LNKSVGAVYAILYLS-DKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIK   77 (152)
T ss_dssp             CCHHHHHHHHHHHHC-SSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCT
T ss_pred             CChhHHHHHHHHHHc-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecC
Confidence            455566676665322 467999999999999999999999999999999998654

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=94.52  E-value=0.084  Score=40.67  Aligned_cols=54  Identities=11%  Similarity=0.140  Sum_probs=45.5

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .++..+-.||.....  .|.+|+.+|++.+++++.-+...|+.|++.|++-+...+
T Consensus        34 ~lt~~~~~iL~~l~~--~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~   87 (143)
T 3oop_A           34 DVTPEQWSVLEGIEA--NEPISQKEIALWTKKDTPTVNRIVDVLLRKELIVREIST   87 (143)
T ss_dssp             SSCHHHHHHHHHHHH--HSSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCCHHHHHHHHHHHH--cCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCeeccCCC
Confidence            367778888877763  378999999999999999999999999999999987554

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=94.31  E-value=0.1  Score=40.25  Aligned_cols=52  Identities=12%  Similarity=0.147  Sum_probs=43.0

Q ss_pred             CChhHHHHHHHhhccCCCc-ccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         177 LSLDHSLVLQQVASKNEAH-ISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~-vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      ++.-+..|+...... .+. +|+.+|++.+++++.-+...|+.|++.|++-+..
T Consensus        24 Lt~~e~~il~~L~~~-~~~~~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~r~~   76 (123)
T 3r0a_A           24 LTKADLNVMKSFLNE-PDRWIDTDALSKSLKLDVSTVQRSVKKLHEKEILQRSQ   76 (123)
T ss_dssp             CCHHHHHHHHHHHHS-TTCCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHHHHHC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeeC
Confidence            565566777665533 344 9999999999999999999999999999999864

>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=94.30  E-value=0.12  Score=39.35  Aligned_cols=53  Identities=19%  Similarity=0.147  Sum_probs=45.1

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.++.....  .|.+|+.+|++.+++++.-+...|..|++.|++-+....
T Consensus        32 lt~~~~~iL~~l~~--~~~~~~~~la~~l~~~~~tvs~~l~~L~~~gli~r~~~~   84 (138)
T 1jgs_A           32 ITAAQFKVLCSIRC--AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP   84 (138)
T ss_dssp             SCHHHHHHHHHHHH--HSSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECT
T ss_pred             CCHHHHHHHHHHHh--cCCCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCCc
Confidence            67677777777663  467999999999999999999999999999999986543

>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=94.24  E-value=0.15  Score=39.43  Aligned_cols=53  Identities=11%  Similarity=0.152  Sum_probs=45.5

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.||.....  .|.+|+.+|++.+|+++.-+...|..|++.|++-+....
T Consensus        38 lt~~~~~iL~~l~~--~~~~t~~ela~~l~~~~~~vs~~l~~Le~~Glv~r~~~~   90 (152)
T 3bj6_A           38 VTVGQRAILEGLSL--TPGATAPQLGAALQMKRQYISRILQEVQRAGLIERRTNP   90 (152)
T ss_dssp             CCHHHHHHHHHHHH--STTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCS
T ss_pred             CCHHHHHHHHHHHh--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCc
Confidence            56667777777663  468999999999999999999999999999999997654

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=94.15  E-value=0.12  Score=39.42  Aligned_cols=53  Identities=19%  Similarity=0.302  Sum_probs=45.7

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.++.....  .|.+|+.+|++.+++++.-+...|..|++.|++-+....
T Consensus        29 l~~~~~~iL~~l~~--~~~~~~~ela~~l~is~~~vs~~l~~L~~~gli~~~~~~   81 (142)
T 3bdd_A           29 ISLTRYSILQTLLK--DAPLHQLALQERLQIDRAAVTRHLKLLEESGYIIRKRNP   81 (142)
T ss_dssp             SCHHHHHHHHHHHH--HCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCHHHHHHHHHHHh--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCC
Confidence            66677778777763  367999999999999999999999999999999987654

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=94.14  E-value=0.046  Score=41.23  Aligned_cols=62  Identities=15%  Similarity=0.243  Sum_probs=50.1

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcC----CCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELN----WSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~----ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      .++.-+..|+..+-.  .|.+|+.+|++.++    |++.-....|+.|++.|++-+...  +....|+|.
T Consensus        32 ~LT~~e~~VL~~L~~--~~~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~R~~~--gR~~~Y~p~   97 (99)
T 2k4b_A           32 NVSNAELIVMRVIWS--LGEARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEKE--GRKFVYRPL   97 (99)
T ss_dssp             CCCCSCSHHHHHHHH--HSCEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCEEEEE--TTEEEEECC
T ss_pred             CCCHHHHHHHHHHHh--CCCCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEEEEeC--CCEEEEEEe
Confidence            466667778887763  46899999999985    899999999999999999999865  455666663

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=94.07  E-value=0.18  Score=34.55  Aligned_cols=46  Identities=7%  Similarity=0.194  Sum_probs=40.8

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      ..+|+.+..+ +|++.++..+.++|.+++-...+|..|++.|++-+.
T Consensus        13 ~~lL~yIr~s-GGildI~~~a~kygV~kdeV~~~LrrLe~KGLI~le   58 (59)
T 2xvc_A           13 RELLDYIVNN-GGFLDIEHFSKVYGVEKQEVVKLLEALKNKGLIAVE   58 (59)
T ss_dssp             HHHHHHHHHT-TSEEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHc-CCEEeHHHHHHHhCCCHHHHHHHHHHHHHCCCeecc
Confidence            4567777765 899999999999999999999999999999998663

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=94.06  E-value=0.13  Score=39.83  Aligned_cols=54  Identities=17%  Similarity=0.214  Sum_probs=46.0

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .++..+-.||.....  .|.+|+.+|++.+++++.-+...|..|++.|++-+....
T Consensus        39 ~l~~~~~~iL~~l~~--~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   92 (150)
T 2rdp_A           39 PITPPQFVALQWLLE--EGDLTVGELSNKMYLACSTTTDLVDRMERNGLVARVRDE   92 (150)
T ss_dssp             SSCHHHHHHHHHHHH--HCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             CCCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecCCC
Confidence            367678788777663  368999999999999999999999999999999986543

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=94.03  E-value=0.089  Score=40.02  Aligned_cols=52  Identities=13%  Similarity=0.141  Sum_probs=45.2

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ++..+-.++.....  .|.+|+.+|++.+|+++.-+...|..|++.|++-+...
T Consensus        27 l~~~~~~iL~~l~~--~~~~~~~ela~~l~~s~~tvs~~l~~L~~~glv~~~~~   78 (138)
T 3bpv_A           27 LTDAQVACLLRIHR--EPGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQD   78 (138)
T ss_dssp             CCHHHHHHHHHHHH--STTCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeecC
Confidence            66677778777763  47899999999999999999999999999999998654

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=94.02  E-value=0.14  Score=39.79  Aligned_cols=53  Identities=17%  Similarity=0.139  Sum_probs=44.5

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.||.....  .|.+|+.+|++.+++++.-+...|..|++.|++-+....
T Consensus        45 l~~~~~~iL~~l~~--~~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~   97 (153)
T 2pex_A           45 LTYPQYLVMLVLWE--TDERSVSEIGERLYLDSATLTPLLKRLQAAGLVTRTRAA   97 (153)
T ss_dssp             CCHHHHHHHHHHHH--SCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCHHHHHHHHHHHh--CCCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecCCc
Confidence            66667777777663  467999999999999999999999999999999997543

>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=94.00  E-value=0.13  Score=39.50  Aligned_cols=53  Identities=15%  Similarity=0.249  Sum_probs=45.0

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.++.....  .|.+|+.+|++.+++++.-+...|..|++.|++-+...+
T Consensus        27 lt~~~~~iL~~l~~--~~~~t~~~la~~l~~s~~~vs~~l~~Le~~gli~r~~~~   79 (144)
T 1lj9_A           27 LTRGQYLYLVRVCE--NPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDA   79 (144)
T ss_dssp             CTTTHHHHHHHHHH--STTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCHHHHHHHHHHHH--CcCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeecCC
Confidence            56567777776663  478999999999999999999999999999999987543

>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=93.98  E-value=0.19  Score=36.65  Aligned_cols=53  Identities=25%  Similarity=0.307  Sum_probs=46.0

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHH----HHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVL----NNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l----~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .++..|-.||....  ..|.+|..+|    ++.+++++.-+...|+.|++.|++.+...
T Consensus         5 ~lt~~q~~iL~~l~--~~~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r~~~   61 (99)
T 1tbx_A            5 PFFYPEAIVLAYLY--DNEGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKERQE   61 (99)
T ss_dssp             SSBCHHHHHHHHHT--TCTTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCHHHHHHHHHHH--HcCCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEEEec
Confidence            46777888887776  3578999999    99999999999999999999999998754

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=93.93  E-value=0.19  Score=39.20  Aligned_cols=52  Identities=15%  Similarity=0.111  Sum_probs=44.9

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ++.-+-.||....  ..|.+|+.+|++.+|+++.-+...|..|++.|++-+...
T Consensus        41 lt~~~~~iL~~l~--~~~~~t~~ela~~l~i~~~tvs~~l~~Le~~Glv~r~~~   92 (155)
T 3cdh_A           41 LRVPEWRVLACLV--DNDAMMITRLAKLSLMEQSRMTRIVDQMDARGLVTRVAD   92 (155)
T ss_dssp             CCHHHHHHHHHHS--SCSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC-
T ss_pred             CCHHHHHHHHHHH--HCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccC
Confidence            5666778887776  357899999999999999999999999999999998644

>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=93.93  E-value=0.12  Score=40.27  Aligned_cols=53  Identities=11%  Similarity=0.133  Sum_probs=45.6

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.||.....  .|.+|+.+|++.+++++.-+...|..|++.|++-+....
T Consensus        35 l~~~~~~iL~~l~~--~~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~   87 (155)
T 1s3j_A           35 VTPAQLFVLASLKK--HGSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNT   87 (155)
T ss_dssp             CCHHHHHHHHHHHH--HSEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecCCC
Confidence            66667778777763  468999999999999999999999999999999987553

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=93.90  E-value=0.094  Score=40.55  Aligned_cols=54  Identities=11%  Similarity=0.216  Sum_probs=44.8

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .++..+-.+|.....  .|.+|+.+|++.+++++.-+...|..|++.|++-+...+
T Consensus        37 ~l~~~~~~iL~~l~~--~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   90 (148)
T 3nrv_A           37 GIGMTEWRIISVLSS--ASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHS   90 (148)
T ss_dssp             TCCHHHHHHHHHHHH--SSSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC----
T ss_pred             CCCHHHHHHHHHHHc--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeecCC
Confidence            478778888877763  579999999999999999999999999999999987543

>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=93.89  E-value=0.2  Score=38.17  Aligned_cols=55  Identities=11%  Similarity=0.132  Sum_probs=44.8

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.+|......+.+.+|+.+|++.+++++.-+...|+.|++.|++-+....
T Consensus        32 lt~~~~~iL~~l~~~~~~~~~~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~~~   86 (141)
T 3bro_A           32 LTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVSG   86 (141)
T ss_dssp             CCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCcchHHHHHHHHHHCCCEEeeCCC
Confidence            6666777777665331227999999999999999999999999999999886543

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=93.86  E-value=0.35  Score=37.21  Aligned_cols=95  Identities=8%  Similarity=0.092  Sum_probs=70.5

Q ss_pred             eeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcc
Q psy6552         117 ILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHI  196 (254)
Q Consensus       117 i~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~v  196 (254)
                      .+..|+...           -.++++.+.+.++.+...|.   ++++..+. ++.+..  +..--..+.++++.  .|.+
T Consensus        21 ~~~~~la~~-----------~~~~~~~~~~~l~~l~~~G~---l~~i~~~~-~~~~~~--~~~~~~~l~~~~~~--~~~i   81 (121)
T 2pjp_A           21 WWVRDLAKE-----------TGTDEQAMRLTLRQAAQQGI---ITAIVKDR-YYRNDR--IVEFANMIRDLDQE--CGST   81 (121)
T ss_dssp             EEHHHHHHH-----------TTCCHHHHHHHHHHHHHTTS---EEEEETTE-EEEHHH--HHHHHHHHHHHHHH--HSSE
T ss_pred             CCHHHHHHH-----------hCCCHHHHHHHHHHHHHCCC---EEEecCCc-eECHHH--HHHHHHHHHHHHHH--CCCc
Confidence            466666654           35789999999999988884   44444243 443332  33333456777773  5899


Q ss_pred             cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         197 SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       197 t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      |+.++.+.+|.|.-.|...|+.+-+.|+..+...
T Consensus        82 t~ae~Rd~lg~sRK~ai~lLE~~Dr~g~TrR~gd  115 (121)
T 2pjp_A           82 CAADFRDRLGVGRKLAIQILEYFDRIGFTRRRGN  115 (121)
T ss_dssp             EHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEETT
T ss_pred             cHHHHHHHHCCcHHHHHHHHHHHhhcCCeEeeCC
Confidence            9999999999999999999999999999998753

>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=93.85  E-value=0.3  Score=36.15  Aligned_cols=55  Identities=11%  Similarity=-0.013  Sum_probs=47.8

Q ss_pred             cCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         173 IPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       173 ~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      .+..++.+|..|+..+...+..+++..+|+..++.+..-....|+.|+..|++-+
T Consensus        14 k~~~Lt~~q~~Vl~~I~~~g~~gi~qkeLa~~~~l~~~tvt~iLk~LE~kglIkr   68 (91)
T 2dk5_A           14 KMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKA   68 (91)
T ss_dssp             CCCCSCSSHHHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             hhcCCCHHHHHHHHHHHHcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            3456888999999998854245899999999999999999999999999999983

>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=93.84  E-value=0.13  Score=37.83  Aligned_cols=53  Identities=11%  Similarity=0.248  Sum_probs=43.0

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP  240 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p  240 (254)
                      .|+.+..   .|..|+.+|++.+|++..-...+|..|++.|++-+...  +...||..
T Consensus        27 ~Il~~L~---~~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~--g~~~~y~l   79 (102)
T 3pqk_A           27 MLVCTLV---EGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRN--IKQIFYRL   79 (102)
T ss_dssp             HHHHHHH---TCCBCHHHHHHHHTCCTTHHHHHHHHHHHTTSEEEECS--SSCCEEEE
T ss_pred             HHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe--CCEEEEEE
Confidence            4555555   25699999999999999999999999999999998876  44555553

>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=93.79  E-value=0.1  Score=37.93  Aligned_cols=52  Identities=13%  Similarity=0.247  Sum_probs=44.1

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ++.-+..|+.....  .|.+|+.+|++.+|+++.-+...|..|++.|++-+...
T Consensus        18 l~~~~~~il~~l~~--~~~~s~~ela~~l~is~~tv~~~l~~L~~~glv~~~~~   69 (109)
T 1sfx_A           18 FKPSDVRIYSLLLE--RGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIV   69 (109)
T ss_dssp             CCHHHHHHHHHHHH--HCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEee
Confidence            55556777777763  46799999999999999999999999999999988654

>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=93.77  E-value=0.28  Score=37.50  Aligned_cols=52  Identities=17%  Similarity=0.133  Sum_probs=44.7

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.|+.... .  |.+|+.+|++.+|+++.-+...|..|++.|++-+....
T Consensus        35 l~~~~~~iL~~l~-~--~~~~~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~   86 (146)
T 2gxg_A           35 LSYLDFLVLRATS-D--GPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRVRDR   86 (146)
T ss_dssp             CCHHHHHHHHHHT-T--SCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCHHHHHHHHHHh-c--CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeecCC
Confidence            6666777877776 3  67999999999999999999999999999999986543

>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=93.75  E-value=0.12  Score=40.91  Aligned_cols=49  Identities=16%  Similarity=0.123  Sum_probs=43.3

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      ++.-+..|+.+.+  ..|.+|..+|++.+|.|..-+...|..|++.|++.+
T Consensus         6 ld~~d~~il~~L~--~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   54 (152)
T 2cg4_A            6 IDNLDRGILEALM--GNARTAYAELAKQFGVSPETIHVRVEKMKQAGIITG   54 (152)
T ss_dssp             CCHHHHHHHHHHH--HCTTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             cCHHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcce
Confidence            5655668888887  358899999999999999999999999999999985

>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=93.71  E-value=0.18  Score=40.31  Aligned_cols=54  Identities=17%  Similarity=0.160  Sum_probs=44.4

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.||..+... .+.+|+.+|++.+++++.-+...|+.|++.|++-+....
T Consensus        51 lt~~q~~vL~~L~~~-~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~GlV~r~~~~  104 (166)
T 3deu_A           51 LTQTHWVTLHNIHQL-PPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCA  104 (166)
T ss_dssp             CCHHHHHHHHHHHHS-CSSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC---
T ss_pred             CCHHHHHHHHHHHHc-CCCCCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEeeCCC
Confidence            666777787776632 567999999999999999999999999999999987553

>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=93.69  E-value=0.076  Score=40.94  Aligned_cols=54  Identities=7%  Similarity=0.114  Sum_probs=41.4

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .++.-+-.||.....  .|.+|+.+|++.+|+++.-+...|+.|++.|++-+...+
T Consensus        34 ~lt~~~~~vL~~l~~--~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~   87 (142)
T 3ech_A           34 DLTPPDVHVLKLIDE--QRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNP   87 (142)
T ss_dssp             CCCHHHHHHHHHHHH--TTTCCHHHHHHHHC---CHHHHHHHHHHHTTSEEC----
T ss_pred             CCCHHHHHHHHHHHh--CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeeccCC
Confidence            377778888877773  478999999999999999999999999999999987654

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=93.67  E-value=0.17  Score=39.82  Aligned_cols=52  Identities=15%  Similarity=0.139  Sum_probs=44.9

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ++.-+-.||.....  .|.+|..+|++.+|+++.-+...|..|++.|++-+...
T Consensus        50 lt~~~~~iL~~l~~--~~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~  101 (162)
T 3cjn_A           50 LSTAKMRALAILSA--KDGLPIGTLGIFAVVEQSTLSRALDGLQADGLVRREVD  101 (162)
T ss_dssp             CCHHHHHHHHHHHH--SCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             CCHHHHHHHHHHHH--CCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecCC
Confidence            56667778777763  47899999999999999999999999999999998754

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=93.63  E-value=0.14  Score=40.40  Aligned_cols=49  Identities=14%  Similarity=0.186  Sum_probs=42.9

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      ++.-+..|+.+.+  ..|.+|..+|++.+|.|+.-+...|..|++.|++.+
T Consensus         7 ld~~d~~il~~L~--~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   55 (151)
T 2dbb_A            7 LDRVDMQLVKILS--ENSRLTYRELADILNTTRQRIARRIDKLKKLGIIRK   55 (151)
T ss_dssp             CCHHHHHHHHHHH--HCTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCHHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            5555667888877  358899999999999999999999999999999984

>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=93.60  E-value=0.15  Score=39.19  Aligned_cols=56  Identities=13%  Similarity=0.179  Sum_probs=42.3

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      ..|+.+...  .|..|+.+|++.+|++..-+...|..|++.|++-+...  +...||..+
T Consensus        45 l~IL~~L~~--~~~~s~~eLa~~l~is~stvs~~L~~L~~~Glv~~~~~--gr~~~y~l~  100 (122)
T 1u2w_A           45 AKITYALCQ--DEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKE--GKLALYSLG  100 (122)
T ss_dssp             HHHHHHHHH--SSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC------CCEEEES
T ss_pred             HHHHHHHHH--CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEE--CCEEEEEEC
Confidence            356665552  46799999999999999999999999999999998755  344555543

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=93.58  E-value=0.12  Score=40.68  Aligned_cols=53  Identities=19%  Similarity=0.283  Sum_probs=44.7

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.||.....  .|.+|+.+|++.+++++.-+...|+.|++.|++-+...+
T Consensus        48 lt~~q~~vL~~l~~--~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~  100 (159)
T 3s2w_A           48 IGSGQFPFLMRLYR--EDGINQESLSDYLKIDKGTTARAIQKLVDEGYVFRQRDE  100 (159)
T ss_dssp             CCTTTHHHHHHHHH--SCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             CCHHHHHHHHHHHH--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence            55556777776653  478999999999999999999999999999999987554

>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=93.54  E-value=0.42  Score=34.44  Aligned_cols=57  Identities=23%  Similarity=0.253  Sum_probs=44.5

Q ss_pred             hHHHHHHHhhccC-CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552         180 DHSLVLQQVASKN-EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF  239 (254)
Q Consensus       180 D~~~il~l~~~~~-~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~  239 (254)
                      ++..|..++.... ++++|+.+|+.+||.++.-+..+|-.|++.|.++.=...   +-.|+
T Consensus        13 ~~~~v~~~i~~L~~~~~~Ta~~IAkkLg~sK~~vNr~LY~L~kkG~V~~~~~~---PP~W~   70 (75)
T 1sfu_A           13 IFSLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPSN---PPKWF   70 (75)
T ss_dssp             HHHHHHHHHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCS---SCEEE
T ss_pred             HHHHHHHHHHhCCCCcchHHHHHHHHHCCCHHHHHHHHHHHHHCCCEecCCCC---CCCcc
Confidence            4666666665433 445999999999999999999999999999999877553   44454

>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=93.50  E-value=0.15  Score=40.37  Aligned_cols=53  Identities=17%  Similarity=0.199  Sum_probs=45.9

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.||..+..  .|.+|+.+|++.+++++.-+...|+.|++.|++-+...+
T Consensus        44 lt~~q~~iL~~l~~--~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   96 (162)
T 3k0l_A           44 ISLPQFTALSVLAA--KPNLSNAKLAERSFIKPQSANKILQDLLANGWIEKAPDP   96 (162)
T ss_dssp             CCHHHHHHHHHHHH--CTTCCHHHHHHHHTSCGGGHHHHHHHHHHTTSEEEEECC
T ss_pred             CCHHHHHHHHHHHH--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCeEecCCC
Confidence            66678788877763  478999999999999999999999999999999987654

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=93.46  E-value=0.13  Score=39.00  Aligned_cols=52  Identities=8%  Similarity=0.056  Sum_probs=45.0

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ++..+-.||.....  .|.+|..+|++.+|+++.-+...|..|++.|++-+...
T Consensus        36 l~~~~~~iL~~l~~--~~~~t~~ela~~l~~~~~tvs~~l~~L~~~glv~r~~~   87 (140)
T 2nnn_A           36 LTPTQWAALVRLGE--TGPCPQNQLGRLTAMDAATIKGVVERLDKRGLIQRSAD   87 (140)
T ss_dssp             CCHHHHHHHHHHHH--HSSBCHHHHHHHTTCCHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCC
Confidence            67677788777763  46899999999999999999999999999999998644

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=93.42  E-value=0.14  Score=39.89  Aligned_cols=53  Identities=17%  Similarity=0.258  Sum_probs=43.6

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.||..+..  .|.+|+.+|++.+++++.-+...|+.|++.|++-+...+
T Consensus        39 lt~~q~~iL~~l~~--~~~~~~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~   91 (149)
T 4hbl_A           39 ITYSQYLVMLTLWE--ENPQTLNSIGRHLDLSSNTLTPMLKRLEQSGWVKRERQQ   91 (149)
T ss_dssp             CCHHHHHHHHHHHH--SSSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC----
T ss_pred             CCHHHHHHHHHHHH--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeCCCC
Confidence            66677788777763  478999999999999999999999999999999987553

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=93.40  E-value=0.26  Score=38.40  Aligned_cols=61  Identities=11%  Similarity=0.115  Sum_probs=48.8

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcC----CCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELN----WSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP  240 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~----ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p  240 (254)
                      ++.-+-.|+...-.. .|.+|+.+|++.++    |++.-....|+.|++.|++-+...  +...+|+|
T Consensus         7 lt~~e~~vL~~L~~~-~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~r~~~--~r~~~~~~   71 (138)
T 2g9w_A            7 LGDLERAVMDHLWSR-TEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRD--DRAHRYAP   71 (138)
T ss_dssp             CCHHHHHHHHHHHTC-SSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC-----CCEEEE
T ss_pred             CCHHHHHHHHHHHhc-CCCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHCCCEEEEec--CCeEEEEe
Confidence            676778888888732 47899999999997    999999999999999999999865  34445555

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=93.38  E-value=0.17  Score=40.32  Aligned_cols=54  Identities=11%  Similarity=0.095  Sum_probs=45.9

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .++.-+-.||..+..  .|.+|+.+|++.+|+++.-+...|+.|++.|++-+....
T Consensus        42 ~lt~~~~~iL~~L~~--~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~   95 (168)
T 2nyx_A           42 NITIPQFRTLVILSN--HGPINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHP   95 (168)
T ss_dssp             SCCHHHHHHHHHHHH--HCSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHH--cCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence            367678788777763  368999999999999999999999999999999986543

>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=93.30  E-value=0.16  Score=39.14  Aligned_cols=54  Identities=11%  Similarity=0.114  Sum_probs=44.8

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.||..+... .|.+|+.+|++.+|+++.-+...|..|++.|++-+....
T Consensus        33 l~~~~~~iL~~l~~~-~~~~~~~~la~~l~i~~~~vs~~l~~Le~~glv~r~~~~   86 (147)
T 2hr3_A           33 VQFSQLVVLGAIDRL-GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP   86 (147)
T ss_dssp             HHHHHHHHHHHHHHT-TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCHHHHHHHHHHHHc-CCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeCCCC
Confidence            566677777777631 578999999999999999999999999999999987553

>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=93.25  E-value=0.18  Score=39.66  Aligned_cols=49  Identities=10%  Similarity=0.144  Sum_probs=42.7

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      ++.-+..|+.+.+  ..|.+|..+|++.+|.|+.-+...|..|++.|++-+
T Consensus         3 ld~~d~~il~~L~--~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   51 (144)
T 2cfx_A            3 LDQIDLNIIEELK--KDSRLSMRELGRKIKLSPPSVTERVRQLESFGIIKQ   51 (144)
T ss_dssp             CCHHHHHHHHHHH--HCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            5555667888877  358899999999999999999999999999999974

>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=93.23  E-value=0.17  Score=38.91  Aligned_cols=53  Identities=15%  Similarity=0.171  Sum_probs=45.1

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.|+.....  .|.+|+.+|++.+++++.-+...|..|++.|++-+....
T Consensus        38 l~~~~~~iL~~l~~--~~~~~~~~la~~l~~~~~tvs~~l~~L~~~glv~r~~~~   90 (147)
T 1z91_A           38 ITYPQYLALLLLWE--HETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSE   90 (147)
T ss_dssp             CCHHHHHHHHHHHH--HSEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCBCS
T ss_pred             CCHHHHHHHHHHHH--CCCCCHHHHHHHHCCCcCcHHHHHHHHHHCCCEEeccCC
Confidence            66667777776663  468999999999999999999999999999999986543

>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=93.23  E-value=0.2  Score=38.41  Aligned_cols=56  Identities=20%  Similarity=0.286  Sum_probs=45.8

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .++.-+-.+|........+.+|+.+|++.+++++.-+...|+.|++.|++-+...+
T Consensus        34 ~lt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   89 (127)
T 2frh_A           34 SISFEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNE   89 (127)
T ss_dssp             CCCHHHHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCS
T ss_pred             CCCHHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCC
Confidence            36777777776665322378999999999999999999999999999999985443

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=93.10  E-value=0.25  Score=38.33  Aligned_cols=49  Identities=20%  Similarity=0.230  Sum_probs=42.6

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      ++.-+-.||.....  .|.+|+.+|++.+++++.-+...|..|++.|++-+
T Consensus        39 lt~~~~~iL~~l~~--~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r   87 (154)
T 2qww_A           39 LTIQQLAMINVIYS--TPGISVADLTKRLIITGSSAAANVDGLISLGLVVK   87 (154)
T ss_dssp             CCHHHHHHHHHHHH--STTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHH--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            56567777776663  46799999999999999999999999999999999

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}

Probab=93.04  E-value=0.13  Score=39.06  Aligned_cols=52  Identities=19%  Similarity=0.279  Sum_probs=44.9

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ++..+-.|+.....  .|.+|+.+|++.+++++.-+...|..|++.|++-+...
T Consensus        31 l~~~~~~iL~~l~~--~~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~   82 (139)
T 3bja_A           31 ISYVQFGVIQVLAK--SGKVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMTEKN   82 (139)
T ss_dssp             CCHHHHHHHHHHHH--SCSEEHHHHHHHCSSCCTTHHHHHHHHHHTTSEEEEEC
T ss_pred             CCHHHHHHHHHHHH--cCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCeeeccC
Confidence            67677788777763  47899999999999999999999999999999988644

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=92.98  E-value=0.16  Score=41.56  Aligned_cols=52  Identities=13%  Similarity=0.142  Sum_probs=43.1

Q ss_pred             cCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552         173 IPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW  226 (254)
Q Consensus       173 ~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw  226 (254)
                      .+..++.-+..|+.+.+.  .|.+|..+|++.+|+|+.-+...|+.|++.|++-
T Consensus        11 ~~~~ld~~d~~IL~~L~~--~~~~s~~eLA~~lglS~~tv~~~l~~L~~~G~I~   62 (171)
T 2ia0_A           11 SEIHLDDLDRNILRLLKK--DARLTISELSEQLKKPESTIHFRIKKLQERGVIE   62 (171)
T ss_dssp             ---CCCHHHHHHHHHHHH--CTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CcCCCCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            344466656788888873  5789999999999999999999999999999994

>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=92.95  E-value=0.19  Score=38.00  Aligned_cols=62  Identities=10%  Similarity=0.092  Sum_probs=49.6

Q ss_pred             CCCChhHHHHHHHhhccCCCcccHHHHHHhcC----CCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552         175 GELSLDHSLVLQQVASKNEAHISVSVLNNELN----WSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP  240 (254)
Q Consensus       175 ~els~D~~~il~l~~~~~~g~vt~~~l~~~l~----ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p  240 (254)
                      ..++.-|-.|+...-.  .|.+|+.+|++.++    |++.-....|+.|++.|++-+...  +....|+|
T Consensus         6 ~~Lt~~q~~vL~~L~~--~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~~~--~r~~~~~~   71 (126)
T 1sd4_A            6 VEISMAEWDVMNIIWD--KKSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKS--ENIYFYSS   71 (126)
T ss_dssp             CCCCHHHHHHHHHHHH--SSSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEE--TTEEEEEE
T ss_pred             CCCCHHHHHHHHHHHh--cCCCCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEEeC--CCeEEEEE
Confidence            3477778888887763  47899999999986    899999999999999999999764  23444544

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=92.82  E-value=0.17  Score=38.47  Aligned_cols=52  Identities=12%  Similarity=0.061  Sum_probs=44.3

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ++..+-.++.....  .|.+|..+|++.+++++.-+...|..|++.|++-+...
T Consensus        34 lt~~~~~iL~~l~~--~~~~t~~ela~~l~~s~~~vs~~l~~Le~~glv~r~~~   85 (142)
T 2fbi_A           34 LTEQQWRVIRILRQ--QGEMESYQLANQACILRPSMTGVLARLERDGIVRRWKA   85 (142)
T ss_dssp             CCHHHHHHHHHHHH--HCSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeecC
Confidence            56667777776663  36799999999999999999999999999999998654

>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi}

Probab=92.76  E-value=0.23  Score=39.16  Aligned_cols=53  Identities=17%  Similarity=0.177  Sum_probs=44.4

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.||..+..  .|.+|+.+|++.+++++.-+...|+.|++.|++-+...+
T Consensus        51 lt~~q~~vL~~l~~--~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~~~~  103 (161)
T 3e6m_A           51 LPTPKLRLLSSLSA--YGELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSISD  103 (161)
T ss_dssp             CCHHHHHHHHHHHH--HSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC--
T ss_pred             CCHHHHHHHHHHHh--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCc
Confidence            56667777777663  368999999999999999999999999999999987553

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=92.76  E-value=0.19  Score=39.36  Aligned_cols=52  Identities=13%  Similarity=0.173  Sum_probs=43.0

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ++..+-.||..+..  .|.+|..+|++.+|+++.-+...|..|++.|++-+...
T Consensus        47 lt~~~~~iL~~l~~--~~~~t~~ela~~l~is~~tvs~~l~~Le~~glv~r~~~   98 (162)
T 2fa5_A           47 MAIPEWRVITILAL--YPGSSASEVSDRTAMDKVAVSRAVARLLERGFIRRETH   98 (162)
T ss_dssp             CCHHHHHHHHHHHH--STTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC---
T ss_pred             CCHHHHHHHHHHHh--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeecC
Confidence            56567777777663  47899999999999999999999999999999998543

>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=92.76  E-value=0.14  Score=39.75  Aligned_cols=54  Identities=9%  Similarity=0.086  Sum_probs=42.8

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.||...... .+.+|+.+|++.+++++.-+...|+.|++.|++-+....
T Consensus        37 lt~~q~~vL~~l~~~-~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv~r~~~~   90 (150)
T 3fm5_A           37 LRVRSYSVLVLACEQ-AEGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLDP   90 (150)
T ss_dssp             CCHHHHHHHHHHHHS-TTCCCSHHHHHHHTCCHHHHHHHHHHHHTTTSEEC----
T ss_pred             CCHHHHHHHHHHHhC-CCCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeeCCc
Confidence            666677777766433 457999999999999999999999999999999886543

>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=92.75  E-value=0.19  Score=38.51  Aligned_cols=53  Identities=23%  Similarity=0.180  Sum_probs=45.0

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.|+.....  .|.+|+.+|++.+++++.-+...|..|++.|++-+...+
T Consensus        35 l~~~~~~iL~~l~~--~~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~~   87 (142)
T 2bv6_A           35 LTYPQFLVLTILWD--ESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSE   87 (142)
T ss_dssp             CCHHHHHHHHHHHH--SSEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEECS
T ss_pred             CCHHHHHHHHHHHH--cCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeecCC
Confidence            56567777777663  478999999999999999999999999999999887653

>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=92.74  E-value=0.17  Score=38.70  Aligned_cols=52  Identities=13%  Similarity=0.093  Sum_probs=44.8

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ++..+-.|+.....  .|.+|..+|++.+++++.-+...|..|++.|++-+...
T Consensus        31 l~~~~~~iL~~l~~--~~~~~~~~la~~l~~s~~tvs~~l~~L~~~glv~r~~~   82 (145)
T 2a61_A           31 ITPAQFDILQKIYF--EGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPD   82 (145)
T ss_dssp             CCHHHHHHHHHHHH--HCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecCC
Confidence            66667778777663  46899999999999999999999999999999998754

>1t6s_A Conserved hypothetical protein; A winged helix-turn-helix, structural genomics, BSGC structu by NIH, protein structure initiative, PSI; 1.95A {Chlorobium tepidum tls} SCOP: a.4.5.60 a.4.5.60

Probab=92.74  E-value=0.34  Score=39.85  Aligned_cols=99  Identities=20%  Similarity=0.209  Sum_probs=73.6

Q ss_pred             CCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhh----hCCCeEEEEeCCceEEEEccCCCCChh---------
Q psy6552         114 GGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKI----FGNGFSIIPIGQGQYLVQSIPGELSLD---------  180 (254)
Q Consensus       114 GGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~----Lg~g~~l~~~~sg~~vv~s~p~els~D---------  180 (254)
                      |-=+++.+|-..+.         ..++++++..+++.|..    -+.|++|+.++ |..-+++.|. +..-         
T Consensus        20 ~~pvs~~~La~~~~---------~~~~~~~v~~~l~~L~~~y~~~~rg~~l~~v~-~gy~l~t~~~-~~~~v~~~~~~~~   88 (162)
T 1t6s_A           20 EEPVNLQTLSQITA---------HKFTPSELQEAVDELNRDYEATGRTFRIHAIA-GGYRFLTEPE-FADLVRQLLAPVI   88 (162)
T ss_dssp             SSCBCHHHHHHHTT---------CCCCHHHHHHHHHHHHHHHHHHTCSEEEEEET-TEEEEEECGG-GHHHHHHHHSCHH
T ss_pred             CCCCCHHHHHHHhC---------cCCCHHHHHHHHHHHHHHhhhCCCCEEEEEEC-CEEEEEEcHH-HHHHHHHHhcccc
Confidence            33388888877653         23799999999998843    37899999999 7788888883 2210         


Q ss_pred             H-------HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         181 H-------SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       181 ~-------~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      .       ..+|.++..  .+-||-.+|++..|.+   +...+..|++.|++..-
T Consensus        89 ~~~LS~aaLEtLaiIay--~qPiTR~eI~~irGv~---~~~~v~~L~e~glI~e~  138 (162)
T 1t6s_A           89 QRRLSRSMLEVLAVVAW--HQPVTKGEIQQIRGAS---PDYSIDRLLARGLIEVR  138 (162)
T ss_dssp             HHHHHHHHHHHHHHHHH--HCSEEHHHHHHHHTCC---CCSHHHHHHHTTSEEEE
T ss_pred             cCccCHHHHHHHHHHHH--cCCcCHHHHHHHHCCC---HHHHHHHHHHCCCEEEc
Confidence            0       113444442  3689999999999999   77899999999999863

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=92.71  E-value=0.3  Score=38.65  Aligned_cols=54  Identities=17%  Similarity=0.159  Sum_probs=44.7

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.+|...... .+.+|+.+|++.+++++.-+...++.|++.|++-+...+
T Consensus        29 Lt~~q~~vL~~L~~~-~~~~~~~eLa~~l~~~~~tvs~~v~~Le~~GlV~R~~~~   82 (151)
T 4aik_A           29 LTQTHWVTLYNINRL-PPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLITRHTSA   82 (151)
T ss_dssp             CCHHHHHHHHHHHHS-CTTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCHHHHHHHHHHHHc-CCCCcHHHHHHHHCcCHHHHHHHHHHHHhCCCeEeecCC
Confidence            666676676655432 567899999999999999999999999999999987664

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=92.69  E-value=0.27  Score=36.43  Aligned_cols=47  Identities=19%  Similarity=0.114  Sum_probs=39.7

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ...|+.+..   .|.+|+.+|++.+|+++.-+...|..|++.|++-+...
T Consensus        23 r~~IL~~L~---~~~~~~~ela~~l~is~~tv~~~l~~L~~~gli~~~~~   69 (114)
T 2oqg_A           23 RWEILTELG---RADQSASSLATRLPVSRQAIAKHLNALQACGLVESVKV   69 (114)
T ss_dssp             HHHHHHHHH---HSCBCHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEec
Confidence            445666664   35699999999999999999999999999999988654

>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=92.58  E-value=0.33  Score=39.67  Aligned_cols=55  Identities=9%  Similarity=0.178  Sum_probs=46.1

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.||..+.....|.+|+.+|++.+++++.-+...|..|++.|++-+....
T Consensus        39 lt~~q~~vL~~L~~~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~   93 (189)
T 3nqo_A           39 LTSRQYMTILSILHLPEEETTLNNIARKMGTSKQNINRLVANLEKNGYVDVIPSP   93 (189)
T ss_dssp             SCHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCHHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence            6667777777665322578999999999999999999999999999999997654

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=92.51  E-value=0.24  Score=37.66  Aligned_cols=54  Identities=15%  Similarity=0.168  Sum_probs=43.0

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP  240 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p  240 (254)
                      ..|+.+..   .|.+|+.+|++.+|++..-+..+|..|++.|++-+...  +...||..
T Consensus        21 ~~Il~~L~---~~~~~~~eLa~~l~is~~tvs~hL~~L~~~GlV~~~~~--gr~~~y~l   74 (118)
T 3f6o_A           21 RAVLGRLS---RGPATVSELAKPFDMALPSFMKHIHFLEDSGWIRTHKQ--GRVRTCAI   74 (118)
T ss_dssp             HHHHHHHH---TCCEEHHHHHTTCCSCHHHHHHHHHHHHHTTSEEEEEE--TTEEEEEE
T ss_pred             HHHHHHHH---hCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEec--CCEEEEEE
Confidence            34556555   36789999999999999999999999999999988765  34455543

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=92.45  E-value=0.18  Score=40.60  Aligned_cols=47  Identities=15%  Similarity=0.191  Sum_probs=41.5

Q ss_pred             hhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         179 LDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       179 ~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      .-...|+.+.+  ..|.+|..+|++.+|.|..-+...|+.|++.|++.+
T Consensus         3 ~~d~~il~~L~--~~~~~s~~~la~~lg~s~~tv~~rl~~L~~~g~i~~   49 (162)
T 3i4p_A            3 RLDRKILRILQ--EDSTLAVADLAKKVGLSTTPCWRRIQKMEEDGVIRR   49 (162)
T ss_dssp             HHHHHHHHHHT--TCSCSCHHHHHHHHTCCHHHHHHHHHHHHHTTSSCC
T ss_pred             HHHHHHHHHHH--HCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence            33457888888  568999999999999999999999999999999874

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=92.43  E-value=0.25  Score=39.50  Aligned_cols=50  Identities=14%  Similarity=0.165  Sum_probs=43.5

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      +++.-+..|+.+.+  ..|.+|..+|++.+|+|..-+...|..|++.|++-+
T Consensus         7 ~ld~~~~~il~~L~--~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   56 (162)
T 2p5v_A            7 TLDKTDIKILQVLQ--ENGRLTNVELSERVALSPSPCLRRLKQLEDAGIVRQ   56 (162)
T ss_dssp             CCCHHHHHHHHHHH--HCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEee
Confidence            36665678888887  357899999999999999999999999999999974

>2z99_A Putative uncharacterized protein; winged helix domain, cell cycle, cell division, chromosome partition, cytoplasm; 2.30A {Mycobacterium tuberculosis}

Probab=92.42  E-value=1.1  Score=38.63  Aligned_cols=109  Identities=10%  Similarity=0.033  Sum_probs=77.5

Q ss_pred             HHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhh----hCCCeEEEEeCCceEEEEccCC-
Q psy6552         101 QIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKI----FGNGFSIIPIGQGQYLVQSIPG-  175 (254)
Q Consensus       101 qive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~----Lg~g~~l~~~~sg~~vv~s~p~-  175 (254)
                      .++|.++=.   .|-=+++.+|-..+.           ++++++..+++.|..    -+.|++|+.++ |..-+++.|. 
T Consensus        18 ~~iEAlLf~---a~epvs~~~La~~l~-----------~~~~~v~~~l~~L~~~y~~~~rGiel~~v~-~gy~l~T~~e~   82 (219)
T 2z99_A           18 RVLEALLLV---IDTPVTADALAAATE-----------QPVYRVAAKLQLMADELTGRDSGIDLRHTS-EGWRMYTRARF   82 (219)
T ss_dssp             HHHHHHHHH---CSSCBCHHHHHHHHT-----------SCHHHHHHHHHHHHHHHHHTTCSEEEEEET-TEEEEEECGGG
T ss_pred             HHHHHHHHH---cCCCCCHHHHHHHHC-----------cCHHHHHHHHHHHHHHHhhCCCCEEEEEEC-CEEEEEEcHHH
Confidence            345544432   233488888887652           588999999988843    37899999999 7778888772 


Q ss_pred             --------------CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         176 --------------ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       176 --------------els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                                    .+|.-...+|.++..  .+-||-.+|++..|.+.   ...+..|++.|++..-.
T Consensus        83 ~~~v~~~~~~~~~~~Ls~aaLEtLaiIAy--~QPITR~eI~~irGv~~---~~~v~~Lle~gLI~e~G  145 (219)
T 2z99_A           83 APYVEKLLLDGARTKLTRAALETLAVVAY--RQPVTRARVSAVRGVNV---DAVMRTLLARGLITEVG  145 (219)
T ss_dssp             HHHHHHHHHHHHSCCCCHHHHHHHHHHHH--HCSEEHHHHHHHHTSCC---HHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHhcccccCccCHHHHHHHHHHHH--cCCcCHHHHHHHHCCCH---HHHHHHHHHCCCEEEcc
Confidence                          122111224444443  36899999999999997   57899999999998754

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=92.42  E-value=0.26  Score=38.66  Aligned_cols=55  Identities=13%  Similarity=0.180  Sum_probs=45.2

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.+|.+......|.+|+.+|++.+++++.-....++.|++.|++-+-..+
T Consensus        33 Lt~~q~~vL~~L~~~~~~~~t~~eLa~~l~~~~~tvs~~v~~Le~~Glv~r~~~~   87 (147)
T 4b8x_A           33 LTFARYEALVLLTFSKSGELPMSKIGERLMVHPTSVTNTVDRLVRSGLVAKRPNP   87 (147)
T ss_dssp             CCHHHHHHHHHHHTSGGGEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             CCHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCEEEeecC
Confidence            6666777766553222578999999999999999999999999999999987664

>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=92.18  E-value=0.29  Score=38.54  Aligned_cols=49  Identities=14%  Similarity=0.152  Sum_probs=42.2

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      ++.-+..||.+.+  ..|.+|..+|++.+|+|+.-+...|..|++.|++-+
T Consensus         5 ld~~~~~iL~~L~--~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   53 (150)
T 2w25_A            5 LDDIDRILVRELA--ADGRATLSELATRAGLSVSAVQSRVRRLESRGVVQG   53 (150)
T ss_dssp             CCHHHHHHHHHHH--HCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCHHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            5555567888777  357899999999999999999999999999999964

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=92.14  E-value=0.37  Score=37.09  Aligned_cols=77  Identities=17%  Similarity=0.203  Sum_probs=58.6

Q ss_pred             CCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHH
Q psy6552         138 DITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALD  217 (254)
Q Consensus       138 ~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~  217 (254)
                      ..+++++......++.|+.+                      -...|+.+..   .|..|+.+|++.+|++..-...+|.
T Consensus        27 ~~~~~~~~~~~~~~kaL~~~----------------------~rl~IL~~L~---~~~~s~~ela~~lgis~stvs~~L~   81 (122)
T 1r1t_A           27 AIAPEVAQSLAEFFAVLADP----------------------NRLRLLSLLA---RSELCVGDLAQAIGVSESAVSHQLR   81 (122)
T ss_dssp             CCCHHHHHHHHHHHHHHCCH----------------------HHHHHHHHHT---TCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHhHHHHHHHHHHHhCCH----------------------HHHHHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45777888888888877622                      2345666555   2568999999999999999999999


Q ss_pred             HHHHcCcEEEeCCCCCcccceecc
Q psy6552         218 FMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       218 ~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      .|++.|++-+...  +...||.++
T Consensus        82 ~Le~~Glv~~~~~--gr~~~y~l~  103 (122)
T 1r1t_A           82 SLRNLRLVSYRKQ--GRHVYYQLQ  103 (122)
T ss_dssp             HHHHTTSEEEEEE--TTEEEEEES
T ss_pred             HHHHCCCeEEEEe--CCEEEEEEC
Confidence            9999999998765  345555543

>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=92.03  E-value=0.25  Score=38.75  Aligned_cols=48  Identities=10%  Similarity=0.063  Sum_probs=41.5

Q ss_pred             ChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         178 SLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       178 s~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      +.-+..|+.+.+  ..|.+|..+|++.+|.|+.-+...|..|++.|++-+
T Consensus         2 d~~~~~il~~L~--~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   49 (150)
T 2pn6_A            2 DEIDLRILKILQ--YNAKYSLDEIAREIRIPKATLSYRIKKLEKDGVIKG   49 (150)
T ss_dssp             CHHHHHHHHHHT--TCTTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSSCC
T ss_pred             ChHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEE
Confidence            334567788887  468899999999999999999999999999999875

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=92.02  E-value=0.23  Score=39.42  Aligned_cols=56  Identities=14%  Similarity=0.137  Sum_probs=43.5

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .++.-|-.||..+...+.+.+|+.+|++.+++++.-+...|+.|++.|++-+....
T Consensus        43 glt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   98 (168)
T 3u2r_A           43 ELSAQQYNTLRLLRSVHPEGMATLQIADRLISRAPDITRLIDRLDDRGLVLRTRKP   98 (168)
T ss_dssp             TCCHHHHHHHHHHHHHTTSCEEHHHHHHHC---CTHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCHHHHHHHHHHHhcCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEeecCCC
Confidence            36777877877766432368999999999999999999999999999999987553

>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=91.96  E-value=0.44  Score=35.44  Aligned_cols=46  Identities=15%  Similarity=0.286  Sum_probs=37.7

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      ..|+..... .+..+|..+|++.+|.|..-+.++|..|+++|++-..
T Consensus        21 l~Il~~l~~-~g~~~s~~eLa~~lgvs~~tV~~~L~~L~~~GlV~~~   66 (110)
T 1q1h_A           21 IDVLRILLD-KGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYR   66 (110)
T ss_dssp             HHHHHHHHH-HCSCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             HHHHHHHHH-cCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            345544421 2337999999999999999999999999999999887

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=91.92  E-value=0.2  Score=39.18  Aligned_cols=54  Identities=19%  Similarity=0.247  Sum_probs=44.0

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.||..... ..+.+|+.+|++.+++++.-+...|..|++.|++-+....
T Consensus        45 l~~~~~~iL~~L~~-~~~~~~~~ela~~l~i~~~tvs~~l~~Le~~Gli~r~~~~   98 (160)
T 3boq_A           45 LSLAKFDAMAQLAR-NPDGLSMGKLSGALKVTNGNVSGLVNRLIKDGMVVKAMSA   98 (160)
T ss_dssp             CCHHHHHHHHHHHH-CTTCEEHHHHHHHCSSCCSCHHHHHHHHHHHTSEEEC---
T ss_pred             CCHHHHHHHHHHHH-cCCCCCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeecCC
Confidence            66667778777722 3578999999999999999999999999999999996543

>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=91.91  E-value=0.19  Score=37.86  Aligned_cols=53  Identities=15%  Similarity=0.228  Sum_probs=45.6

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcC----CCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELN----WSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~----ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .++.-+..||.....  .|.+|+.+|++.++    |++.-+...|+.|++.|++-+...
T Consensus         7 ~lt~~~~~vL~~l~~--~~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~r~~~   63 (123)
T 1okr_A            7 EISSAEWEVMNIIWM--KKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKD   63 (123)
T ss_dssp             CCCHHHHHHHHHHHH--HSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEE
T ss_pred             cCCHHHHHHHHHHHh--CCCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHCCCeEEEec
Confidence            477777888887763  47899999999999    999999999999999999998754

>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=91.85  E-value=0.2  Score=38.80  Aligned_cols=49  Identities=10%  Similarity=0.195  Sum_probs=41.3

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      ++.-+..|+...+  ..|.+|..+|++.+|.|..-+...|..|++.|++-+
T Consensus         2 ld~~~~~il~~L~--~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   50 (141)
T 1i1g_A            2 IDERDKIILEILE--KDARTPFTEIAKKLGISETAVRKRVKALEEKGIIEG   50 (141)
T ss_dssp             CCSHHHHHHHHHH--HCTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSCC
T ss_pred             CCHHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEec
Confidence            4444667777776  357899999999999999999999999999999853

>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=91.74  E-value=0.43  Score=37.16  Aligned_cols=52  Identities=10%  Similarity=0.075  Sum_probs=44.5

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ++.-+-.||..+..  .|.+|+.+|++.+++++.-+...|..|++.|++-+...
T Consensus        42 lt~~~~~iL~~l~~--~~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~   93 (154)
T 2eth_A           42 MKTTELYAFLYVAL--FGPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMD   93 (154)
T ss_dssp             SBHHHHHHHHHHHH--HCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCC
Confidence            66667778777663  36799999999999999999999999999999998654

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=91.53  E-value=0.54  Score=33.92  Aligned_cols=52  Identities=17%  Similarity=0.201  Sum_probs=42.0

Q ss_pred             CChhHHHHH-HHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVL-QQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il-~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ++..+-.++ .+..  ..+.+|+.+|++.+|.++.-+...|..|++.|++-+...
T Consensus        19 l~~~~~~~l~~l~~--~~~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~~~~~   71 (109)
T 2d1h_A           19 ITDTDVAVLLKMVE--IEKPITSEELADIFKLSKTTVENSLKKLIELGLVVRTKT   71 (109)
T ss_dssp             CCHHHHHHHHHHHH--HCSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             CCHHHHHHHHHHHH--cCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeecc
Confidence            554454444 4444  257899999999999999999999999999999998754

>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=91.50  E-value=0.28  Score=38.78  Aligned_cols=49  Identities=4%  Similarity=0.069  Sum_probs=42.9

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      ++.-+..|+.+.+.  .|.+|..+|++.+|.|..-+...|..|++.|++-+
T Consensus         5 ld~~~~~il~~L~~--~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~   53 (151)
T 2cyy_A            5 LDEIDKKIIKILQN--DGKAPLREISKITGLAESTIHERIRKLRESGVIKK   53 (151)
T ss_dssp             CCHHHHHHHHHHHH--CTTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCC
T ss_pred             cCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            66556688888873  57899999999999999999999999999999864

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=91.49  E-value=0.33  Score=37.21  Aligned_cols=52  Identities=21%  Similarity=0.160  Sum_probs=43.7

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..+-.||..+..  .|. |+.+|++.+++++.-+...|..|++.|++-+...+
T Consensus        35 lt~~~~~iL~~l~~--~~~-~~~~la~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   86 (144)
T 3f3x_A           35 LSYLDFSILKATSE--EPR-SMVYLANRYFVTQSAITAAVDKLEAKGLVRRIRDS   86 (144)
T ss_dssp             CCHHHHHHHHHHHH--SCE-EHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCHHHHHHHHHHHH--CCC-CHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCC
Confidence            66667778777663  345 99999999999999999999999999999986543

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=91.06  E-value=0.3  Score=37.56  Aligned_cols=50  Identities=12%  Similarity=0.062  Sum_probs=43.0

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhc--CCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNEL--NWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l--~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      ++.-...||++...  .|..|+.+|++.+  |+|..-+...|..|++.|++-.-
T Consensus        11 md~~d~~IL~~L~~--~g~~s~~eLA~~l~~giS~~aVs~rL~~Le~~GLV~~~   62 (111)
T 3b73_A           11 MTIWDDRILEIIHE--EGNGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPL   62 (111)
T ss_dssp             CCHHHHHHHHHHHH--HSCBCHHHHHTSTTCCSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             cCHHHHHHHHHHHH--cCCCCHHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEec
Confidence            44445678888873  4799999999999  99999999999999999999873

>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=91.05  E-value=0.28  Score=38.09  Aligned_cols=48  Identities=13%  Similarity=0.192  Sum_probs=42.2

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      ++.-|-.+|... .  .|.+|+.+|++.+++++.-+...|+.|++.|++-+
T Consensus        36 lt~~q~~iL~~l-~--~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r   83 (151)
T 3kp7_A           36 ISAEQSHVLNML-S--IEALTVGQITEKQGVNKAAVSRRVKKLLNAELVKL   83 (151)
T ss_dssp             CCHHHHHHHHHH-H--HSCBCHHHHHHHHCSCSSHHHHHHHHHHHTTSEEC
T ss_pred             CCHHHHHHHHHH-H--cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            566677777766 3  47899999999999999999999999999999998

>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=91.03  E-value=0.5  Score=33.85  Aligned_cols=47  Identities=6%  Similarity=0.079  Sum_probs=38.9

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      +..|+.....  .|.+|..+|++.+|+++.-....|..|++.|++-+..
T Consensus        18 ~~~iL~~L~~--~~~~~~~ela~~l~is~~tvs~~l~~L~~~gli~~~~   64 (100)
T 1ub9_A           18 RLGIMIFLLP--RRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYK   64 (100)
T ss_dssp             HHHHHHHHHH--HSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHh--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            4456665542  3679999999999999999999999999999998643

>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=91.00  E-value=0.23  Score=38.42  Aligned_cols=55  Identities=13%  Similarity=0.099  Sum_probs=38.0

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.||........|.+|+.+|++.+++++.-+...|+.|++.|++-+...+
T Consensus        39 lt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~   93 (148)
T 3jw4_A           39 LNSQQGRMIGYIYENQESGIIQKDLAQFFGRRGASITSMLQGLEKKGYIERRIPE   93 (148)
T ss_dssp             CCHHHHHHHHHHHHHTTTCCCHHHHHHC------CHHHHHHHHHHTTSBCCC---
T ss_pred             CCHHHHHHHHHHHhCCCCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeeCCC
Confidence            6666777776665332378999999999999999999999999999999886543

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=90.99  E-value=0.26  Score=39.08  Aligned_cols=52  Identities=17%  Similarity=0.305  Sum_probs=41.3

Q ss_pred             CChhHHHH-HHHhhcc--CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         177 LSLDHSLV-LQQVASK--NEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       177 ls~D~~~i-l~l~~~~--~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      +|.++..+ +.+....  +..+.|+++|++.+|+++.-+...|..|++.|++-|.
T Consensus        30 Ls~~E~~lLl~L~~~~~~g~~~ps~~~LA~~~~~s~~~v~~~L~~L~~KGlI~i~   84 (135)
T 2v79_A           30 LNETELILLLKIKMHLEKGSYFPTPNQLQEGMSISVEECTNRLRMFIQKGFLFIE   84 (135)
T ss_dssp             CCHHHHHHHHHHHHHHTTTCCSCCHHHHHTTSSSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             CCHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            67666544 3333321  2468999999999999999999999999999999993

>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=90.90  E-value=0.38  Score=40.16  Aligned_cols=53  Identities=13%  Similarity=0.066  Sum_probs=45.3

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.||..+..  .|.+|+.+|++.+++++.-+...|+.|++.|++-+...+
T Consensus        46 Lt~~q~~iL~~L~~--~~~~t~~eLa~~l~i~~stvs~~l~~Le~~GlV~r~~~~   98 (207)
T 2fxa_A           46 LNINEHHILWIAYQ--LNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRL   98 (207)
T ss_dssp             CCHHHHHHHHHHHH--HTSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC-
T ss_pred             CCHHHHHHHHHHHH--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence            66667778777663  368999999999999999999999999999999997654

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

Probab=90.75  E-value=0.47  Score=35.63  Aligned_cols=78  Identities=14%  Similarity=0.207  Sum_probs=60.1

Q ss_pred             CCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHH
Q psy6552         137 QDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHAL  216 (254)
Q Consensus       137 ~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L  216 (254)
                      ..++++++.+....++.|+.                      ..+..|+.+..  . +..|..+|++.+|++..-+...|
T Consensus        12 ~~~~~~~~~~~~~~~~~l~~----------------------~~~~~il~~L~--~-~~~s~~ela~~l~is~stvsr~l   66 (119)
T 2lkp_A           12 APLDSQAAAQVASTLQALAT----------------------PSRLMILTQLR--N-GPLPVTDLAEAIGMEQSAVSHQL   66 (119)
T ss_dssp             SCCHHHHHHHHHHHHHHHCC----------------------HHHHHHHHHHH--H-CCCCHHHHHHHHSSCHHHHHHHH
T ss_pred             cccCHHHHHHHHHHHHHhCC----------------------HHHHHHHHHHH--H-CCCCHHHHHHHHCcCHHHHHHHH
Confidence            56778888888888887652                      23556666665  2 56899999999999999999999


Q ss_pred             HHHHHcCcEEEeCCCCCcccceecc
Q psy6552         217 DFMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       217 ~~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      ..|++.|++-++..  +...||.+.
T Consensus        67 ~~Le~~Glv~~~~~--~r~~~~~~~   89 (119)
T 2lkp_A           67 RVLRNLGLVVGDRA--GRSIVYSLY   89 (119)
T ss_dssp             HHHHHHCSEEEEEE--TTEEEEEES
T ss_pred             HHHHHCCCEEEEec--CCEEEEEEc
Confidence            99999999988754  344555443

>1lva_A Selenocysteine-specific elongation factor; winged-helix, translation; 2.12A {Moorella thermoacetica} SCOP: a.4.5.35 a.4.5.35 a.4.5.35 a.4.5.35 PDB: 2uwm_A 2ply_A 1wsu_A

Probab=90.62  E-value=7.7  Score=33.43  Aligned_cols=170  Identities=14%  Similarity=0.168  Sum_probs=102.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhhh-------hhh------cCHH-HHHHHHHHHHHcCCCcccCCCcccccc----ccchh
Q psy6552          33 EQLSQHLNTFRDKLESFASEYKN-------EIK------KDAQ-FRRHFQEMCASIGVDPLASRKGFWSLL----GMGDF   94 (254)
Q Consensus        33 ~~L~~ql~~fk~~L~~FA~kh~~-------~I~------~dp~-fr~~f~~mc~~lGVdPl~s~kg~w~~l----g~gdf   94 (254)
                      +...++.+...+.|..|-++|..       +++      -++. |..-+..+|.. |.  +....++++.-    ....-
T Consensus        62 ~~~~~~~~~l~~~L~~~H~~~P~~~G~~~~~L~~~~~~~~~~~l~~~ll~~l~~~-g~--l~~~~~~v~l~~h~~~~~~~  138 (258)
T 1lva_A           62 ERYQAWWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSRE-GR--LQLAANTVALAGFTPSFSET  138 (258)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCTTSSCEEHHHHHHHHCTTSCHHHHHHHHHHHHHT-TS--EEEETTEEEETTCCCCCCHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhCCCccCCCHHHHHHhccccCCHHHHHHHHHHHHHC-CC--EEecCCEEeCCCCccCCCHH
Confidence            34444455566778888888842       332      1222 22122223222 32  33333444322    23456


Q ss_pred             HHHHHHHHHHHhhhhhhhcCCcee--HHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEc
Q psy6552          95 YYELSVQIVEVCLATNYKNGGLIL--LDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQS  172 (254)
Q Consensus        95 y~eLavqive~c~~~r~~nGGii~--L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s  172 (254)
                      +..+..+|.+.+.+     +|+-+  +.|+...           -.+.++++...++.|-..|.   |+.+. +..|+..
T Consensus       139 ~~~~~~~i~~~~~~-----~g~~pp~~~dl~~~-----------l~~~~~~~~~~l~~l~~~g~---lv~l~-~~~~~~~  198 (258)
T 1lva_A          139 QKKLLKDLEDKYRV-----SRWQPPSFKEVAGS-----------FNLDPSELEELLHYLVREGV---LVKIN-DEFYWHR  198 (258)
T ss_dssp             HHHHHHHHHHHHHH-----HTTSCCBHHHHHHH-----------TTCCHHHHHHHHHHHHHTTS---EEESS-SSBEEEH
T ss_pred             HHHHHHHHHHHHHH-----CCCCCCCHHHHHhH-----------hCCCHHHHHHHHHHHHHCCC---EEEec-CCeEEcH
Confidence            66677777766632     55433  4454432           24678888888888887773   55666 3334433


Q ss_pred             cCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         173 IPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       173 ~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ..  +..--..+.+++ .  .|.+|+.+..+.+|.|.-.|...|+.+-+.|+..+...
T Consensus       199 ~~--~~~~~~~l~~~~-~--~~~it~a~~Rd~lg~SRK~aIplLE~~Dr~g~TrR~gd  251 (258)
T 1lva_A          199 QA--LGEAREVIKNLA-S--TGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGD  251 (258)
T ss_dssp             HH--HHHHHHHHHHHH-T--TSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HH--HHHHHHHHHHHH-h--cCCcCHHHHHHHhCCcHHHHHHHHHHHhhcCceeeeCC
Confidence            32  332234455555 3  48999999999999999999999999999999999854

>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=90.59  E-value=0.67  Score=34.78  Aligned_cols=55  Identities=11%  Similarity=-0.003  Sum_probs=47.8

Q ss_pred             CCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         175 GELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       175 ~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      ..++.++..|+.++++....+|+..+|+...+.+.......|..|+..|++=.=.
T Consensus        33 ~~Lt~~E~lVy~~I~~aGn~GIw~kdL~~~tnL~~~~vtkiLK~LE~k~lIK~Vk   87 (95)
T 2yu3_A           33 KGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVK   87 (95)
T ss_dssp             CSCSHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             cCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEEEec
Confidence            4688889999999986545679999999999999999999999999999986533

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=90.54  E-value=0.58  Score=35.88  Aligned_cols=51  Identities=10%  Similarity=0.091  Sum_probs=41.0

Q ss_pred             CChhHHHHHHH----hhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         177 LSLDHSLVLQQ----VASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       177 ls~D~~~il~l----~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      ++.-+..+|..    ++  ..+.+|..+|++.+|+++.-+...|..|++.|++-++.
T Consensus        11 lt~~~~~~L~~l~~l~~--~~~~~s~~ela~~l~is~~tv~~~l~~Le~~Gli~r~~   65 (139)
T 2x4h_A           11 LSRREFSYLLTIKRYND--SGEGAKINRIAKDLKIAPSSVFEEVSHLEEKGLVKKKE   65 (139)
T ss_dssp             CCHHHHHHHHHHHHHHT--TTSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             cCHHHHHHHHHHHHHHh--cCCCcCHHHHHHHhCCChHHHHHHHHHHHHCCCEEecC
Confidence            45444444433    33  35789999999999999999999999999999999875

>2xzm_8 RPS25E,; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_8

Probab=90.25  E-value=0.27  Score=39.58  Aligned_cols=47  Identities=13%  Similarity=0.109  Sum_probs=37.2

Q ss_pred             hHHHHHHHhhcc-CC-CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552         180 DHSLVLQQVASK-NE-AHISVSVLNNELNWSTERAQHALDFMVQEGYAW  226 (254)
Q Consensus       180 D~~~il~l~~~~-~~-g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw  226 (254)
                      |..+.=.+..+- .. .+||++.|++.|+++..+|+.+|++|+..|++-
T Consensus        46 Dk~tydKL~KEVpk~gKlITpsvlseRlkI~gSLARkaLreL~~kGlIk   94 (143)
T 2xzm_8           46 EKKNVESIINNPSKVGKVLTVSTVVEKLKVNGSLARQLMRTMADRKLVE   94 (143)
T ss_dssp             CHHHHHHHHTCCTTSCSEECHHHHHHHHCBCHHHHHHHHHHHHHTTSEE
T ss_pred             cHHHHHHHHHHhcccceeecHHHHHHHhcchHHHHHHHHHHHHHCCCEE
Confidence            444444444321 24 689999999999999999999999999999985

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=89.99  E-value=0.47  Score=38.74  Aligned_cols=54  Identities=17%  Similarity=0.112  Sum_probs=46.5

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP  240 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p  240 (254)
                      ..|+|+..   .|.+|+..|++.+|.|...|+-+|..|+++|++--=..  +-..||--
T Consensus        14 ~~ILE~Lk---~G~~~t~~Iak~LGlShg~aq~~Ly~LeREG~V~~Vk~--GK~ayw~L   67 (165)
T 2vxz_A           14 RDILALLA---DGCKTTSLIQQRLGLSHGRAKALIYVLEKEGRVTRVAF--GNVALVCL   67 (165)
T ss_dssp             HHHHHHHT---TCCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSCEEEEE--TTEEEEES
T ss_pred             HHHHHHHH---hCCccHHHHHHHhCCcHHHHHHHHHHHHhcCceEEEEE--ccEEEEEe
Confidence            46788887   48999999999999999999999999999999876655  56788864

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=89.94  E-value=0.48  Score=38.00  Aligned_cols=55  Identities=13%  Similarity=0.147  Sum_probs=44.0

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP  240 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p  240 (254)
                      ...||.+..   .|..|+.+|++.+|++..-+...|..|++.|++.+...  +...||..
T Consensus        60 R~~IL~~L~---~~~~t~~eLa~~lgls~stvs~hL~~L~~aGlV~~~~~--Gr~~~y~l  114 (151)
T 3f6v_A           60 RRRLVQLLT---SGEQTVNNLAAHFPASRSAISQHLRVLTEAGLVTPRKD--GRFRYYRL  114 (151)
T ss_dssp             HHHHHHHGG---GCCEEHHHHHTTSSSCHHHHHHHHHHHHHTTSEEEEEE--TTEEEEEE
T ss_pred             HHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEec--CCEEEEEE
Confidence            345666665   25699999999999999999999999999999998754  34455543

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=89.82  E-value=0.41  Score=41.57  Aligned_cols=53  Identities=11%  Similarity=0.049  Sum_probs=46.5

Q ss_pred             CCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         174 PGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       174 p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      +..++..+-.+|+....  .|.+|..+|++.+|.++.-+...|..|++.|++.++
T Consensus       147 ~~~L~~~~~~IL~~L~~--~~~~s~~eLA~~lglsksTv~r~L~~Le~~GlV~r~  199 (244)
T 2wte_A          147 MRDYSREEMKLLNVLYE--TKGTGITELAKMLDKSEKTLINKIAELKKFGILTQK  199 (244)
T ss_dssp             HSCCCHHHHHHHHHHHH--HTCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            34578778888887653  367999999999999999999999999999999998

>2c9l_Y EB1, zebra, BZLF1 trans-activator protein; viral protein, epstein-BARR virus, EBV; 2.25A {Human herpesvirus 4} SCOP: h.1.3.1 PDB: 2c9n_Y

Probab=89.79  E-value=0.22  Score=33.62  Aligned_cols=39  Identities=21%  Similarity=0.474  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCc
Q psy6552          40 NTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDP   78 (254)
Q Consensus        40 ~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdP   78 (254)
                      ++|+..|+.|-.--..+-.+|.-+|--+.+||-+|.||.
T Consensus        18 akfkn~lqh~r~vaaaks~en~rlr~l~kqmcpsldvds   56 (63)
T 2c9l_Y           18 AKFKQLLQHYREVAAAKSSENDRLRLLLKQMCPSLDVDS   56 (63)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCCHHH
T ss_pred             HHHHHHHHHHHHHHHhhcccchHHHHHHHHhCCcccccc
Confidence            456666655544444445567788999999999999993

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=89.35  E-value=0.52  Score=34.24  Aligned_cols=35  Identities=3%  Similarity=-0.031  Sum_probs=32.0

Q ss_pred             cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .+|+.+|++.++.++.-+...|..|++.|++ .|..
T Consensus        30 ~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv-~~~~   64 (95)
T 2qvo_A           30 DVYIQYIASKVNSPHSYVWLIIKKFEEAKMV-ECEL   64 (95)
T ss_dssp             CEEHHHHHHHSSSCHHHHHHHHHHHHHTTSE-EEEE
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCcCc-cCCC
Confidence            3999999999999999999999999999999 5543

>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=88.75  E-value=0.59  Score=36.04  Aligned_cols=44  Identities=9%  Similarity=0.146  Sum_probs=37.8

Q ss_pred             HHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         184 VLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       184 il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      ++.+...  .|.+|+.+|++.+|+++.-+...|..|++.|++-+..
T Consensus        13 i~~l~~~--~~~~~~~ela~~l~vs~~tvs~~l~~Le~~Glv~r~~   56 (142)
T 1on2_A           13 IYMLIEE--KGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEK   56 (142)
T ss_dssp             HHHHHHH--HSSCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHhh--cCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEee
Confidence            3455542  4679999999999999999999999999999999874

>2ve8_A FTSK, DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA-binding, winged helix, bacterial cell division; HET: DNA; 1.4A {Pseudomonas aeruginosa} SCOP: a.4.5.67 PDB: 2ve9_A* 2j5o_A*

Probab=88.49  E-value=1.1  Score=32.16  Aligned_cols=48  Identities=17%  Similarity=0.157  Sum_probs=40.1

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ...+++++-.  .+..|++.|..+|.+-..||...++.|+++|++=--+.
T Consensus        12 y~~A~~~V~~--~~~aS~S~lQR~lrIGYnRAArlid~lE~~GiVgp~~g   59 (73)
T 2ve8_A           12 YDEAVRFVTE--SRRASISAVQRKLKIGYNRAARMIEAMEMAGVVTPMNT   59 (73)
T ss_dssp             HHHHHHHHHH--HCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSBCCCCT
T ss_pred             HHHHHHHHHh--cCCccHHHHHHHHccChHHHHHHHHHHHHCCcCCcccC
Confidence            4566676663  47899999999999999999999999999999855443

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=88.32  E-value=1.3  Score=31.98  Aligned_cols=45  Identities=11%  Similarity=-0.020  Sum_probs=38.8

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      ...|+.+.  .  |.+|+.+|++.+|++..-+...|..|++.|++-+..
T Consensus        33 r~~Il~~L--~--~~~~~~eLa~~l~is~~tv~~~L~~L~~~Glv~~~~   77 (96)
T 1y0u_A           33 RRKILRML--D--KGRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIERVG   77 (96)
T ss_dssp             HHHHHHHH--H--TTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHH--c--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEC
Confidence            45566666  2  469999999999999999999999999999998875

>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=88.27  E-value=0.6  Score=33.77  Aligned_cols=36  Identities=14%  Similarity=0.060  Sum_probs=33.5

Q ss_pred             cccHHHHHHhcCCCHHH-HHHHHHHHHHcCcEEEeCC
Q psy6552         195 HISVSVLNNELNWSTER-AQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       195 ~vt~~~l~~~l~ws~~r-a~~~L~~l~~~G~lwvD~q  230 (254)
                      .+|+.+|++.+++++.- +...|+.|++.|++-.|..
T Consensus        30 ~~t~~eLa~~l~is~~t~vs~~l~~Le~~Glv~~~~~   66 (95)
T 2pg4_A           30 EPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVKEETL   66 (95)
T ss_dssp             CCCHHHHHHHHCCCHHHHHTTHHHHHHHTTSEEEEEE
T ss_pred             CCCHHHHHHHHCCCchHHHHHHHHHHHHCCCeecCCC
Confidence            79999999999999999 9999999999999996654

>3u5c_Z RP45, S31, YS23, 40S ribosomal protein S25-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_V 3o30_Q 3o2z_Q 3u5g_Z

Probab=88.14  E-value=0.22  Score=38.33  Aligned_cols=38  Identities=29%  Similarity=0.225  Sum_probs=33.9

Q ss_pred             CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ...||++.|++.|++...+|+.+|++|+..|++-.=..
T Consensus        57 ~KlITpsvlseRlkI~gSLAR~aLreL~~kGlIk~V~k   94 (108)
T 3u5c_Z           57 YRYVSVSVLVDRLKIGGSLARIALRHLEKEGIIKPISK   94 (108)
T ss_dssp             CSSBSHHHHHHTTCCCTTHHHHHHHHHSSSSSCEEEEC
T ss_pred             CeEEeHHHhhhhhhhhHHHHHHHHHHHHHCCCEEEEec
Confidence            57899999999999999999999999999999764333

>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=87.92  E-value=1.2  Score=38.63  Aligned_cols=56  Identities=18%  Similarity=0.262  Sum_probs=46.3

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .++.-|-.||......+++.+|+.+|++.+++++.-....++.|++.|++-+-..+
T Consensus       155 gLt~~q~~vL~~L~~~~~~~~t~~eLa~~l~i~~~tvt~~v~rLe~~GlV~R~~~~  210 (250)
T 1p4x_A          155 TLSFVEFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERST  210 (250)
T ss_dssp             SSCHHHHHHHHHHHTTTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECS
T ss_pred             CCCHHHHHHHHHHHhCCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeeCCC
Confidence            36777877877766331235999999999999999999999999999999997665

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=87.91  E-value=0.82  Score=38.51  Aligned_cols=49  Identities=10%  Similarity=0.079  Sum_probs=41.6

Q ss_pred             hHH-HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         180 DHS-LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       180 D~~-~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      |.- .|+.+.+  ..|.+|..+|++.+++++.-+...|..|+++|++-+...
T Consensus         6 dYL~~I~~l~~--~~~~~~~~~lA~~l~vs~~tvs~~l~~Le~~GlV~r~~~   55 (214)
T 3hrs_A            6 DYLKCLYELGT--RHNKITNKEIAQLMQVSPPAVTEMMKKLLAEELLIKDKK   55 (214)
T ss_dssp             HHHHHHHHTTS--SCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHHHHHh--cCCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCEEEecC
Confidence            543 4456555  478999999999999999999999999999999988754

>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=87.50  E-value=0.94  Score=38.70  Aligned_cols=47  Identities=9%  Similarity=0.099  Sum_probs=40.1

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .||++.... .+.+|..+|++.+|+++.-+...|..|++.|++.+|..
T Consensus        10 ~iL~~l~~~-~~~~s~~ela~~~gl~~stv~r~l~~L~~~G~v~~~~~   56 (241)
T 2xrn_A           10 SIMRALGSH-PHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALGP   56 (241)
T ss_dssp             HHHHHHHTC-TTCEEHHHHHHHTTSCHHHHHHHHHHHHTTTSEEECGG
T ss_pred             HHHHHHHhC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence            466766532 45799999999999999999999999999999999853

>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=87.39  E-value=1.5  Score=32.36  Aligned_cols=44  Identities=7%  Similarity=0.042  Sum_probs=38.0

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .||..+.   .| ++...|+..+|.++..+...|+.|++.|++-++..
T Consensus        12 ~IL~~i~---~~-~~~t~La~~~~ls~~~~~~~l~~L~~~GLI~~~~~   55 (95)
T 1r7j_A           12 AILEACK---SG-SPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEGK   55 (95)
T ss_dssp             HHHHHHT---TC-BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHH---cC-CCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEECC
Confidence            4456565   35 99999999999999999999999999999998843

>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=87.26  E-value=1.3  Score=33.17  Aligned_cols=45  Identities=11%  Similarity=0.107  Sum_probs=38.1

Q ss_pred             HHHHHhhccCCCcccHHHHHHhc-CCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNEL-NWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l-~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .||....  . |.+|..+|++.+ |++..-....|..|++.|++-+...
T Consensus        26 ~IL~~L~--~-~~~~~~eLa~~l~~is~~tvs~~L~~Le~~GlI~r~~~   71 (112)
T 1z7u_A           26 SLMDELF--Q-GTKRNGELMRALDGITQRVLTDRLREMEKDGLVHRESF   71 (112)
T ss_dssp             HHHHHHH--H-SCBCHHHHHHHSTTCCHHHHHHHHHHHHHHTSEEEEEE
T ss_pred             HHHHHHH--h-CCCCHHHHHHHhccCCHHHHHHHHHHHHHCCCEEEeec
Confidence            4555444  2 679999999999 9999999999999999999988654

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=86.90  E-value=1.9  Score=32.92  Aligned_cols=36  Identities=14%  Similarity=0.072  Sum_probs=33.1

Q ss_pred             CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      ++.+|..+|++.+|+++.-....|..|.+.|++-..
T Consensus        24 ~~~~s~~ela~~~~i~~~~v~~il~~L~~~Glv~~~   59 (129)
T 2y75_A           24 EGPTSLKSIAQTNNLSEHYLEQLVSPLRNAGLVKSI   59 (129)
T ss_dssp             SCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEec
Confidence            467999999999999999999999999999997654

>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=86.88  E-value=1.8  Score=32.01  Aligned_cols=45  Identities=13%  Similarity=0.123  Sum_probs=38.0

Q ss_pred             HHHHHhhccCCCcccHHHHHHhc-CCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNEL-NWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l-~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .||....   .|..+..+|++.+ |+++.-....|..|++.|++-+-..
T Consensus        18 ~IL~~L~---~~~~~~~eLa~~l~~is~~tls~~L~~Le~~GlI~r~~~   63 (107)
T 2hzt_A           18 VILXHLT---HGKKRTSELKRLMPNITQKMLTQQLRELEADGVINRIVY   63 (107)
T ss_dssp             HHHHHHT---TCCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHH---hCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeec
Confidence            3555444   3679999999999 9999999999999999999987644

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=86.32  E-value=1.4  Score=31.90  Aligned_cols=59  Identities=14%  Similarity=0.085  Sum_probs=49.7

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      +++-..+||++..+. +.-+++.+|+..+|.+..-...+|..|-.+|.+.-     ..+-||-|.
T Consensus        17 ~~d~eekVLe~Lkea-G~PlkageIae~~GvdKKeVdKaik~LKkEgkI~S-----PkRCyw~~~   75 (80)
T 2lnb_A           17 EGHLEQRILQVLTEA-GSPVKLAQLVKECQAPKRELNQVLYRMKKELKVSL-----TSPATWCLG   75 (80)
T ss_dssp             HHHHHHHHHHHHHHH-TSCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE-----EETTEEEES
T ss_pred             cchHHHHHHHHHHHc-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCccC-----CCCceeeCC
Confidence            343367899999876 67899999999999999999999999999999642     367899886

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=86.11  E-value=1.4  Score=30.08  Aligned_cols=36  Identities=17%  Similarity=0.337  Sum_probs=29.3

Q ss_pred             hhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhC
Q psy6552         109 TNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFG  155 (254)
Q Consensus       109 ~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg  155 (254)
                      ....+||++.++++-..|           -|+++|++.+.+.|+.-|
T Consensus        18 yIr~sGGildI~~~a~ky-----------gV~kdeV~~~LrrLe~KG   53 (59)
T 2xvc_A           18 YIVNNGGFLDIEHFSKVY-----------GVEKQEVVKLLEALKNKG   53 (59)
T ss_dssp             HHHHTTSEEEHHHHHHHH-----------CCCHHHHHHHHHHHHHTT
T ss_pred             HHHHcCCEEeHHHHHHHh-----------CCCHHHHHHHHHHHHHCC
Confidence            345689999988876553           489999999999999877

>3r4k_A Transcriptional regulator, ICLR family; DNA/RNA-binding 3-helical bundle, profilin-like, structural joint center for structural genomics, JCSG; 2.46A {Ruegeria SP}

Probab=85.62  E-value=0.79  Score=39.67  Aligned_cols=47  Identities=11%  Similarity=0.061  Sum_probs=40.1

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .||++.... .+.+|..+|++.+|.++.-+-..|..|++.|++-.|..
T Consensus        10 ~IL~~l~~~-~~~lsl~eia~~lgl~ksT~~RlL~tL~~~G~v~~~~~   56 (260)
T 3r4k_A           10 TLLTYFNHG-RLEIGLSDLTRLSGMNKATVYRLMSELQEAGFVEQVEG   56 (260)
T ss_dssp             HHHTTCBTT-BSEEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEECSS
T ss_pred             HHHHHHhhC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence            355555532 57899999999999999999999999999999999865

>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=85.41  E-value=2  Score=36.70  Aligned_cols=46  Identities=17%  Similarity=0.273  Sum_probs=39.6

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      ..||++.... .+.+|..+|++.+|+++.-+...|..|++.|++..|
T Consensus        11 l~iL~~l~~~-~~~~~~~ela~~~gl~~stv~r~l~~L~~~G~v~~~   56 (249)
T 1mkm_A           11 FEILDFIVKN-PGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK   56 (249)
T ss_dssp             HHHHHHHHHC-SSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHhC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEC
Confidence            3567665532 457999999999999999999999999999999998

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=85.18  E-value=1.1  Score=35.04  Aligned_cols=43  Identities=9%  Similarity=0.008  Sum_probs=36.4

Q ss_pred             HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      +.+...  .|.+|+.+|++.+|++..-....|..|++.|++-+..
T Consensus        46 ~~~l~~--~~~~~~~~la~~l~vs~~tvs~~l~~Le~~Glv~r~~   88 (155)
T 2h09_A           46 SDLIRE--VGEARQVDMAARLGVSQPTVAKMLKRLATMGLIEMIP   88 (155)
T ss_dssp             HHHHHH--HSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEET
T ss_pred             HHHHHh--CCCcCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEec
Confidence            344442  4679999999999999999999999999999987763

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=85.06  E-value=1.1  Score=39.14  Aligned_cols=46  Identities=17%  Similarity=0.164  Sum_probs=37.8

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      .||++.... .+.+|..+|++.+|+++.-+-..|..|++.|++-.|.
T Consensus        34 ~IL~~l~~~-~~~ltl~eia~~lgl~ksTv~RlL~tL~~~G~v~~~~   79 (275)
T 3mq0_A           34 RILDLVAGS-PRDLTAAELTRFLDLPKSSAHGLLAVMTELDLLARSA   79 (275)
T ss_dssp             HHHHHHHHC-SSCEEHHHHHHHHTCC--CHHHHHHHHHHTTSEEECT
T ss_pred             HHHHHHhhC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC
Confidence            356665543 5679999999999999999999999999999999985

>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=84.93  E-value=2.5  Score=31.23  Aligned_cols=38  Identities=16%  Similarity=0.157  Sum_probs=34.2

Q ss_pred             CCcccHHHHHHhc-CCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         193 EAHISVSVLNNEL-NWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       193 ~g~vt~~~l~~~l-~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .|..+..+|++.+ |++..-....|..|++.|++-+-..
T Consensus        36 ~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~   74 (107)
T 2fsw_A           36 RRIIRYGELKRAIPGISEKMLIDELKFLCGKGLIKKKQY   74 (107)
T ss_dssp             TSCEEHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             hCCcCHHHHHHHcccCCHHHHHHHHHHHHHCCCEEEeec
Confidence            3679999999999 5999999999999999999987644

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=84.63  E-value=2.3  Score=32.85  Aligned_cols=55  Identities=13%  Similarity=0.115  Sum_probs=41.5

Q ss_pred             CCChhHHHHH-HHhhcc--CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         176 ELSLDHSLVL-QQVASK--NEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       176 els~D~~~il-~l~~~~--~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .++..+-.++ -+....  ...+.|+++|++.+|.+..-+..+|+.|++.|++-+...
T Consensus        29 gLt~~e~~vll~L~~~~~~~~~~ps~~~LA~~l~~s~~~V~~~l~~Le~kGlI~~~~~   86 (128)
T 2vn2_A           29 GLGEGELVLLLHMQSFFEEGVLFPTPAELAERMTVSAAECMEMVRRLLQKGMIAIEEH   86 (128)
T ss_dssp             TCCHHHHHHHHHHHHHHTTTCSSCCHHHHHHTSSSCHHHHHHHHHHHHHTTSSEECC-
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeE
Confidence            4665555453 333211  245799999999999999999999999999999999543

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=84.41  E-value=1.5  Score=36.21  Aligned_cols=55  Identities=16%  Similarity=0.126  Sum_probs=43.0

Q ss_pred             CCChhHHHHHHHhhcc--CCC-cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         176 ELSLDHSLVLQQVASK--NEA-HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       176 els~D~~~il~l~~~~--~~g-~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      +++.-|..+|+.+.+.  ..| ..|..+|++.+|++..-+...|..|++.|++-++..
T Consensus         2 ~lt~~q~~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~l~~Le~~G~i~~~~~   59 (196)
T 3k2z_A            2 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHLIALEKKGYIERKNG   59 (196)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECC--
T ss_pred             CcCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHHHHHHHHCCCEEecCC
Confidence            3677788887765321  124 599999999999999988999999999999988854

>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=84.22  E-value=1.2  Score=33.25  Aligned_cols=37  Identities=11%  Similarity=0.088  Sum_probs=33.5

Q ss_pred             CCcc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         193 EAHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       193 ~g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      ++.+ |..+|++.+|+|..-++++|..|+++|++-+-.
T Consensus        40 g~~lps~~eLa~~lgVSr~tVr~al~~L~~~GlI~~~~   77 (102)
T 2b0l_A           40 NEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS   77 (102)
T ss_dssp             TEEEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCcCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            4456 999999999999999999999999999998765

>3iz6_V 40S ribosomal protein S25 (S25E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=84.20  E-value=0.22  Score=38.42  Aligned_cols=37  Identities=22%  Similarity=0.231  Sum_probs=33.2

Q ss_pred             CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552         193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT  229 (254)
Q Consensus       193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~  229 (254)
                      ...||++.|++.|++...+|+.+|++|+..|++-.=.
T Consensus        58 ~KlITpsvlseRlkI~gSLAR~aLreL~~kGlIk~V~   94 (108)
T 3iz6_V           58 YKQITPSVLSERLRINGSLARQAIKDLESRGAIRVVS   94 (108)
T ss_dssp             HSSEEEHHHHHHHHTCCHHHHHHHHHHHHHHTSCEEC
T ss_pred             CeEEeHHHHHhhhcccHHHHHHHHHHHHHCCCEEEEe
Confidence            4689999999999999999999999999999875433

>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=83.94  E-value=1.7  Score=40.10  Aligned_cols=58  Identities=10%  Similarity=0.051  Sum_probs=47.6

Q ss_pred             CCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         174 PGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       174 p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      +..++.-|-.||........+.+|..+|++.+++++......|+.|++.|++-|-...
T Consensus       399 ~~~lt~~q~~vl~~l~~~~~~~~~~~~l~~~~~~~~~~~t~~~~~le~~g~v~r~~~~  456 (487)
T 1hsj_A          399 KFNLNYEEIYILNHILRSESNEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKRSL  456 (487)
T ss_dssp             SCCCCHHHHHHHHHHHTCSCSEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEECC
T ss_pred             hcCCCHHHHHHHHHHHhCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecCCC
Confidence            4558877878877766211278999999999999999999999999999999886543

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=83.88  E-value=0.76  Score=36.91  Aligned_cols=54  Identities=9%  Similarity=0.007  Sum_probs=43.7

Q ss_pred             CChhHHHHHHHhhccCC-CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVLQQVASKNE-AHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~-g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ++.-+-.||......+. +++|+.+|++.+++++.-+...|+.|++.|++-+...
T Consensus        67 lt~~~~~iL~~L~~~~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~  121 (181)
T 2fbk_A           67 LNAAGWDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRIVRLLEKGLIERRED  121 (181)
T ss_dssp             CCHHHHHHHHHHHHHCCSSCBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC-
T ss_pred             CCHHHHHHHHHHHHcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCEEecCC
Confidence            66667777776654311 2599999999999999999999999999999998654

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=83.65  E-value=10  Score=32.56  Aligned_cols=112  Identities=12%  Similarity=0.095  Sum_probs=64.9

Q ss_pred             cCCceeHHHHHHHHHHhcCCCCCCCCC---CHHHHHHHHH-HhhhhCCCeEEEEeC---CceEEEEccCC---C------
Q psy6552         113 NGGLILLDELRTRLVKSRGKSLQHQDI---TNEDLLAAAK-KLKIFGNGFSIIPIG---QGQYLVQSIPG---E------  176 (254)
Q Consensus       113 nGGii~L~dl~~~~nr~Rg~~~~~~~I---S~~Di~rA~~-~L~~Lg~g~~l~~~~---sg~~vv~s~p~---e------  176 (254)
                      +-|+|+..|+..++.+-.....  ..+   .-+|++..|+ .|.+|+  |+|+...   +|..|.-.|..   +      
T Consensus        16 srg~l~~~~~~~l~~~~~~~~~--~~~~~~~l~~~I~~IN~~L~~l~--~~Ir~~~~q~~g~~~y~lVN~~~d~~~klaT   91 (238)
T 3nw0_A           16 THGVLEEWDVKRLQTHCYKVHD--RNATVDKLEDFINNINSVLESLY--IEIKRGVTEDDGRPIYALVNLATTSISKMAT   91 (238)
T ss_dssp             HSSEEEHHHHHHHHHHHHHHC----CCCCCCHHHHHHHHHHHHGGGT--EEEEEEECTTTCCEEEEEEESSSCTTHHHHT
T ss_pred             cCCCCCHHHHHHHHHHHHHhcC--CcccHHHHHHHHHHHHHHhhhcC--cEEEEeecCCCCCEEEEEEeCCCCHHHhhcc
Confidence            3688888888777776321111  122   4566666664 457766  5555553   35544444442   1      


Q ss_pred             -CChhH----HHHHHHhhccCCCcccHHHHHH---h---cCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         177 -LSLDH----SLVLQQVASKNEAHISVSVLNN---E---LNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       177 -ls~D~----~~il~l~~~~~~g~vt~~~l~~---~---l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                       ++.++    ..+++.+-.++.|.++..++-.   .   -+.++..|++.|..|+++|++...
T Consensus        92 ~yt~~Ei~~fk~lle~i~~s~~~~~s~~~~lnl~~~~~~k~l~~~eae~lL~~lv~~gWl~~~  154 (238)
T 3nw0_A           92 DFAENELDLFRKALELIIDSETGFASSTNILNLVDQLKGKKMRKKEAEQVLQKFVQNKWLIEK  154 (238)
T ss_dssp             TSCHHHHHHHHHHHHHHHHSSSSCEEHHHHHGGGTTCSSSCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHHHHHHHHhCCCCceeHHHHHHHHhhcccCCCCHHHHHHHHHHHHHhcchhhh
Confidence             12221    1224333322367777654332   2   478999999999999999999874

>3i5g_C Myosin catalytic light chain LC-1, mantle muscle; rigor-like, squid, muscle myosin, contractIle protein; 2.60A {Todarodes pacificus} PDB: 3i5f_C 3i5h_C 3i5i_C

Probab=82.93  E-value=5.7  Score=31.08  Aligned_cols=93  Identities=14%  Similarity=0.287  Sum_probs=52.3

Q ss_pred             HHHHHHHHHHHHHH-H-hhhhhhcCHHHHHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCC
Q psy6552          38 HLNTFRDKLESFAS-E-YKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGG  115 (254)
Q Consensus        38 ql~~fk~~L~~FA~-k-h~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGG  115 (254)
                      |++.+|+....|=. + ..+.|..+     +|..++.+||+.|-..                   +|-++. ..-..+.|
T Consensus         7 qi~elre~F~~fD~~~d~dG~I~~~-----El~~~lr~lG~~~t~~-------------------el~~~~-~~d~~~~g   61 (159)
T 3i5g_C            7 EIEEVREVFDLFDFWDGRDGDVDAA-----KVGDLLRCLGMNPTEA-------------------QVHQHG-GTKKMGEK   61 (159)
T ss_dssp             HHHHHHHHHHHHHHHTTSSSCEEGG-----GHHHHHHHTTCCCCHH-------------------HHHTTT-CCSSTTSC
T ss_pred             HHHHHHHHHHHHCcCCCCCCeECHH-----HHHHHHHHcCCCCCHH-------------------HHHHHH-cccccCCC
Confidence            34445555555533 1 22345433     5677888999987431                   111111 12233457


Q ss_pred             ceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCe
Q psy6552         116 LILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGF  158 (254)
Q Consensus       116 ii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~  158 (254)
                      -|+..+.+..+.+.....   ..-++++|.+|.+.+.+=|.|+
T Consensus        62 ~i~f~eFl~~~~~~~~~~---~~~~~~~l~~aF~~fD~d~~G~  101 (159)
T 3i5g_C           62 AYKLEEILPIYEEMSSKD---TGTAADEFMEAFKTFDREGQGL  101 (159)
T ss_dssp             EECHHHHHHHHHHHTTCC---TTCCHHHHHHHHHHHCTTSSSE
T ss_pred             cccHHHHHHHHHHhhccc---ccchHHHHHHHHHHHhcCCCCc
Confidence            788888877776654331   2456777888877776655554

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=82.87  E-value=2.6  Score=32.69  Aligned_cols=38  Identities=16%  Similarity=0.157  Sum_probs=34.5

Q ss_pred             CCcccHHHHHHhc-CCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         193 EAHISVSVLNNEL-NWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       193 ~g~vt~~~l~~~l-~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .|..+..+|++.+ |++..-....|..|++.|++-+-..
T Consensus        46 ~g~~~~~eLa~~l~gis~~tls~~L~~Le~~GlV~r~~~   84 (131)
T 1yyv_A           46 DGTHRFSDLRRXMGGVSEXMLAQSLQALEQDGFLNRVSY   84 (131)
T ss_dssp             GCCEEHHHHHHHSTTCCHHHHHHHHHHHHHHTCEEEEEE
T ss_pred             cCCCCHHHHHHHhccCCHHHHHHHHHHHHHCCcEEEEec
Confidence            3679999999999 7999999999999999999997644

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=82.64  E-value=1.5  Score=37.81  Aligned_cols=38  Identities=8%  Similarity=-0.024  Sum_probs=35.3

Q ss_pred             CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .+.+|..+|++.+|.++.-+-..|..|++.|++..|..
T Consensus        36 ~~~~~~~eia~~~gl~kstv~r~l~tL~~~G~v~~~~~   73 (260)
T 2o0y_A           36 HPTRSLKELVEGTKLPKTTVVRLVATMCARSVLTSRAD   73 (260)
T ss_dssp             BSSBCHHHHHHHHCCCHHHHHHHHHHHHHTTSEEECTT
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCC
Confidence            46799999999999999999999999999999999853

>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=82.60  E-value=3.7  Score=32.29  Aligned_cols=45  Identities=13%  Similarity=0.155  Sum_probs=38.3

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .||..+.   .|..+..+|++.+|++..-....|..|++.|++-+-..
T Consensus        28 ~IL~~L~---~g~~~~~eLa~~lgis~~tls~~L~~Le~~GlI~r~~~   72 (146)
T 2f2e_A           28 LIVRDAF---EGLTRFGEFQKSLGLAKNILAARLRNLVEHGVMVAVPA   72 (146)
T ss_dssp             HHHHHHH---TTCCSHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEEec
Confidence            3455454   36799999999999999999999999999999998654

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=82.32  E-value=2  Score=31.43  Aligned_cols=45  Identities=13%  Similarity=0.094  Sum_probs=37.5

Q ss_pred             CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552         194 AHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       194 g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      |..|+.+|++.+|.+..-+..+|..|++. ++-....  +...||..+
T Consensus        40 ~~~~~~ela~~l~is~stvs~hL~~L~~~-lv~~~~~--gr~~~y~l~   84 (99)
T 2zkz_A           40 KALNVTQIIQILKLPQSTVSQHLCKMRGK-VLKRNRQ--GLEIYYSIN   84 (99)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHBTT-TBEEEEE--TTEEEEECC
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHH-hhhheEe--CcEEEEEEC
Confidence            67999999999999999999999999999 8876654  455666543

>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=82.22  E-value=2.5  Score=35.06  Aligned_cols=46  Identities=15%  Similarity=0.284  Sum_probs=40.5

Q ss_pred             hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      -+..|+.+..  . |.+|..+|++.+|.|+.-+...|..|++.|++-+.
T Consensus        21 ~~~~IL~~L~--~-~~~s~~eLA~~lglS~stv~~~l~~Le~~GlI~~~   66 (192)
T 1uly_A           21 TRRKILKLLR--N-KEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVK   66 (192)
T ss_dssp             HHHHHHHHHT--T-CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHH--c-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            3456777777  2 67999999999999999999999999999999886

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=82.11  E-value=4.2  Score=31.90  Aligned_cols=53  Identities=17%  Similarity=0.163  Sum_probs=44.0

Q ss_pred             ChhHHHHHHHhhccCCCcccHHHHHHhc-----CCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         178 SLDHSLVLQQVASKNEAHISVSVLNNEL-----NWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       178 s~D~~~il~l~~~~~~g~vt~~~l~~~l-----~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      +.--..||++.... .+.+|+.+|.+.+     +++..=.-..|+.|++.|++-.=+..
T Consensus        21 T~qR~~Il~~L~~~-~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~   78 (145)
T 2fe3_A           21 TPQRHAILEYLVNS-MAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYG   78 (145)
T ss_dssp             CHHHHHHHHHHHHC-SSCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEEEECCT
T ss_pred             CHHHHHHHHHHHhC-CCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEEEEeeC
Confidence            33456788877654 6799999999988     89999999999999999999887663

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=81.94  E-value=3.8  Score=32.08  Aligned_cols=39  Identities=5%  Similarity=0.018  Sum_probs=35.7

Q ss_pred             CCcccHHHHHHhc-CCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         193 EAHISVSVLNNEL-NWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       193 ~g~vt~~~l~~~l-~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .|..+..+|++.+ |++.......|..|++.|++-+-..+
T Consensus        37 ~g~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~GLV~R~~~~   76 (131)
T 4a5n_A           37 DGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYH   76 (131)
T ss_dssp             TSCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEEC
T ss_pred             cCCcCHHHHHHHhcccCHHHHHHHHHHHHHCCCEEEEecC
Confidence            4789999999999 99999999999999999999987543

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=80.94  E-value=2.7  Score=32.81  Aligned_cols=49  Identities=14%  Similarity=0.222  Sum_probs=37.1

Q ss_pred             CChhHHHHHHHhhccC---CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552         177 LSLDHSLVLQQVASKN---EAHISVSVLNNELNWSTERAQHALDFMVQEGYA  225 (254)
Q Consensus       177 ls~D~~~il~l~~~~~---~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l  225 (254)
                      ++.-|-.+|.......   .|.+|+.+|++.+++++.-....|+.|++.|++
T Consensus        31 Lt~~q~~vL~~l~~~~~~~~~~~t~~eLa~~l~~~~~tvsr~v~~Le~~glV   82 (148)
T 4fx0_A           31 LTNTQFSTLAVISLSEGSAGIDLTMSELAARIGVERTTLTRNLEVMRRDGLV   82 (148)
T ss_dssp             CCHHHHHHHHHHHC---------CHHHHHHHHTCCHHHHHHHHHHHHHTTSB
T ss_pred             CCHHHHHHHHHHHHhcCCCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCE
Confidence            5656777766654321   356999999999999999999999999999998

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=80.41  E-value=2.1  Score=36.72  Aligned_cols=45  Identities=18%  Similarity=0.164  Sum_probs=38.5

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      .||++.... .+.+|..+|++.+|+++.-+...|..|++.|++..|
T Consensus        18 ~iL~~l~~~-~~~~~~~eia~~~gl~~stv~r~l~~L~~~G~v~~~   62 (257)
T 2g7u_A           18 AVLLAFDAQ-RPNPTLAELATEAGLSRPAVRRILLTLQKLGYVAGS   62 (257)
T ss_dssp             HHHHTCSSS-CSSCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHhC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            455555422 467999999999999999999999999999999998

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=80.15  E-value=4  Score=31.42  Aligned_cols=49  Identities=16%  Similarity=0.141  Sum_probs=41.7

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhc-----CCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNEL-----NWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l-----~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ..||++.... .+.+|+++|.+.+     +++..=.-..|+.|++.|++-.=+..
T Consensus        14 ~~Il~~l~~~-~~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~~~~~   67 (131)
T 2o03_A           14 AAISTLLETL-DDFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLVDTLHTD   67 (131)
T ss_dssp             HHHHHHHHHC-CSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTTSEEEEECT
T ss_pred             HHHHHHHHhC-CCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCEEEEEeC
Confidence            4677777644 6799999999988     89999999999999999999876653

---

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	254
d1u5ta1	145	a.4.5.54 (A:20-164) Vacuolar sorting protein SNF8	5e-64
d1u5ta2	68	a.4.5.54 (A:165-232) Vacuolar sorting protein SNF8	2e-23

>d1u5ta1 a.4.5.54 (A:20-164) Vacuolar sorting protein SNF8 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 145

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar sorting protein SNF8
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score =  194 bits (495), Expect = 5e-64
 Identities = 47/153 (30%), Positives = 77/153 (50%), Gaps = 9/153 (5%)

Query: 24  GTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRK 83
             +I E Q  +L   L  F+++L  FA ++ +E++   +FR  F  MC+SIG+DPL+   
Sbjct: 2   NKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPEFRSKFMHMCSSIGIDPLSLFD 61

Query: 84  GFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNED 143
               L  + DFYYE+ ++++E+C  T   NGG+I   EL     +          +  +D
Sbjct: 62  RDKHLFTVNDFYYEVCLKVIEICRQTKDMNGGVISFQELEKVHFRKLN-------VGLDD 114

Query: 144 LLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGE 176
           L  +   LK     F I  I  G+  ++S+P E
Sbjct: 115 LEKSIDMLKSLE-CFEIFQIR-GKKFLRSVPNE 145

>d1u5ta2 a.4.5.54 (A:165-232) Vacuolar sorting protein SNF8 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 68

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar sorting protein SNF8
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 87.9 bits (218), Expect = 2e-23
 Identities = 27/69 (39%), Positives = 37/69 (53%), Gaps = 2/69 (2%)

Query: 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHL 236
           L+ D + +L+ + S    + S+S+L   L W   R++ ALD MV  G  WID Q   E L
Sbjct: 1   LTSDQTKILE-ICSIL-GYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGAEAL 58

Query: 237 YWFPSLFTE 245
           YW PS  T 
Sbjct: 59  YWDPSWITR 67

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	254
d1u5ta1	145	Vacuolar sorting protein SNF8 {Baker's yeast (Sacc	100.0
d1u5tb1	94	Vacuolar protein sorting-associated protein VPS36	99.88
d1u5ta2	68	Vacuolar sorting protein SNF8 {Baker's yeast (Sacc	99.88
d1u5tb2	75	Vacuolar protein sorting-associated protein VPS36	96.42
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	95.74
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	95.71
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	95.25
d2htja1	73	P fimbrial regulatory protein PapI {Escherichia co	95.01
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	95.0
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	94.88
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	94.67
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	94.6
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	94.58
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.49
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	94.33
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	94.31
d1okra_	120	Methicillin resistance regulatory protein MecI {St	94.28
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	94.25
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	94.23
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	93.89
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	93.76
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	93.69
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	93.58
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	93.55
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	93.53
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	93.46
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	93.4
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	93.2
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	93.02
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	92.88
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	92.63
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	92.61
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	92.48
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	92.31
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	92.09
d1p6ra_	82	Penicillinase repressor BlaI {Bacillus licheniform	92.04
d2ve8a1	67	DNA translocase FtsK {Pseudomonas aeruginosa [TaxI	91.84
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	91.84
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	91.83
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	91.63
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	91.48
d2j5pa1	69	DNA translocase FtsK {Escherichia coli [TaxId: 562	91.37
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	91.22
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	90.89
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	90.88
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	90.53
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	89.49
d1sd4a_	122	Penicillinase repressor BlaI {Staphylococcus aureu	89.48
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	89.36
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	89.34
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	89.2
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	89.04
d1xmka1	73	Z-alpha domain of dsRNA-specific adenosine deamina	87.59
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	87.3
d1wdcc_	152	Myosin Regulatory Chain {Bay scallop (Aequipecten	87.1
d1s6la1	60	Alkylmercury lyase MerB {Escherichia coli [TaxId:	86.58
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	86.4
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	86.24
d1t6sa1	85	Segregation and condensation protein B, ScpB {Chlo	86.03
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	85.37
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	84.68
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	84.35
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	83.73
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	83.68
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	83.14
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	80.93

>d1u5ta1 a.4.5.54 (A:20-164) Vacuolar sorting protein SNF8 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar sorting protein SNF8
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=100.00  E-value=1.2e-54  Score=353.18  Aligned_cols=145  Identities=32%  Similarity=0.589  Sum_probs=137.3

Q ss_pred             cccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHH
Q psy6552          23 KGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQI  102 (254)
Q Consensus        23 ~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqi  102 (254)
                      +|++|.+.|+++|+.||++||+.|++||++|+++|++||+||++|++||++||||||++++++|+++|+|||||||||||
T Consensus         1 l~~~l~e~q~~ql~~QL~vF~~~L~~FA~kH~~eI~~np~FR~~F~~MC~~iGVDPLas~~~~~~~lg~gDFYyEL~VqI   80 (145)
T d1u5ta1           1 VNKTILEKQSVELRDQLMVFQERLVEFAKKHNSELQASPEFRSKFMHMCSSIGIDPLSLFDRDKHLFTVNDFYYEVCLKV   80 (145)
T ss_dssp             CCSHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTTTTTCHHHHHHHHHHHHHHTCCHHHHTTSSGGGTTHHHHHHHHHHHH
T ss_pred             CchhHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHhhcCHHHHHHHHHHHHHhCCChhhcCCCccccccccchHHHHHHHH
Confidence            36789999999999999999999999999999999999999999999999999999999999777999999999999999


Q ss_pred             HHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCC
Q psy6552         103 VEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGE  176 (254)
Q Consensus       103 ve~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~e  176 (254)
                      +|+|++||+.|||||+|.||...+.|.       ..||.+||+||+++|++|| ||.+++++ |+++|+|+|.|
T Consensus        81 vEvC~~tr~~NGGli~l~el~~~~~~~-------~~is~dDi~rAi~~L~~Lg-G~~v~~ig-gk~~v~SVP~E  145 (145)
T d1u5ta1          81 IEICRQTKDMNGGVISFQELEKVHFRK-------LNVGLDDLEKSIDMLKSLE-CFEIFQIR-GKKFLRSVPNE  145 (145)
T ss_dssp             HHHHHHHTTTSSSCEEHHHHHHTTTTT-------TTCCHHHHHHHHHHHTTTC-CCCEEEET-TEEEECCSSSC
T ss_pred             HHHHHHhhhcCCCEeEHHHHHHHHHhh-------cCCCHHHHHHHHHhhcccC-CcEEEEEC-CEEEEEeCCCC
Confidence            999999999999999999998877765       3689999999999999996 99999999 99999999975

>d1u5tb1 a.4.5.54 (B:396-489) Vacuolar protein sorting-associated protein VPS36 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar protein sorting-associated protein VPS36
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.88  E-value=3.9e-23  Score=155.33  Aligned_cols=79  Identities=19%  Similarity=0.195  Sum_probs=72.6

Q ss_pred             chhHHHHHHHHHHHhhhhhhhcCC-----ceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCC-CeEEEEeCC
Q psy6552          92 GDFYYELSVQIVEVCLATNYKNGG-----LILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGN-GFSIIPIGQ  165 (254)
Q Consensus        92 gdfy~eLavqive~c~~~r~~nGG-----ii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~-g~~l~~~~s  165 (254)
                      ..||.|||+||+|+|....+..||     ||+|.||||+|||+||.+.  ++|||+|+++||++|++|+. |++|++|+|
T Consensus        10 ~lyh~ELArqlae~l~~~~k~~~g~~~~~mItL~Dly~~~NRaR~~G~--eLiSP~D~~~Ac~~~e~l~L~p~~Lr~f~s   87 (94)
T d1u5tb1          10 ELFLDEIAREIYEFTLSEFKDLNSDTNYMIITLVDLYAMYNKSMRIGT--GLISPMEMREACERFEHLGLNELKLVKVNK   87 (94)
T ss_dssp             TTHHHHHHHHHHHHHHTTTTTSSSCCCCCCEETTHHHHHHHHTTTSSS--CCCCHHHHHHHHTTTGGGTCCSCEEEEETT
T ss_pred             hHHHHHHHHHHHHHHHhhhhhhCCCCCcceeeHHHHHHHHHHhhhcCC--cccCHHHHHHHHHHHHhCCCCceEEEEecC
Confidence            589999999999999998876666     9999999999999994333  89999999999999999998 999999999


Q ss_pred             ceEEEEc
Q psy6552         166 GQYLVQS  172 (254)
Q Consensus       166 g~~vv~s  172 (254)
                      |+.||||
T Consensus        88 gvlvv~s   94 (94)
T d1u5tb1          88 RILCVTS   94 (94)
T ss_dssp             TEEEEES
T ss_pred             ceEEeeC
Confidence            9999986

>d1u5ta2 a.4.5.54 (A:165-232) Vacuolar sorting protein SNF8 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar sorting protein SNF8
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.88  E-value=1.1e-23  Score=149.68  Aligned_cols=67  Identities=39%  Similarity=0.635  Sum_probs=63.7

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecccccC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTE  245 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~lf~~  245 (254)
                      ||+||++||++|+  ..||||+++|.+++||+.+||+.+|++|+++|++|||+|+++|..||||+||..
T Consensus         1 Ls~Dqt~vLe~a~--~~G~Vt~s~l~~~lgW~~~Ra~~aLd~lv~eGl~WvD~Q~~~e~~YWfPsl~~~   67 (68)
T d1u5ta2           1 LTSDQTKILEICS--ILGYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGAEALYWDPSWITR   67 (68)
T ss_dssp             CCTTHHHHHHTTT--TTSCCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEEECSSSSSCEEECGGGGGC
T ss_pred             CCchHHHHHHHHH--HcCceeHHHHHHHhCCCHHHHHHHHHHHHhcCcEEEecCCCCCceeeChHhhcc
Confidence            6889999999999  569999999999999999999999999999999999999877999999999975

>d1u5tb2 a.4.5.54 (B:490-564) Vacuolar protein sorting-associated protein VPS36 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar protein sorting-associated protein VPS36
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.42  E-value=0.0037  Score=42.75  Aligned_cols=59  Identities=22%  Similarity=0.277  Sum_probs=43.9

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhc-------CCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceeccc
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNEL-------NWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSL  242 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l-------~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~l  242 (254)
                      ..+++++++..  ++...-.|-+.|       +|+.....|+|+.++.+|-+.+|+|. +...||+.+.
T Consensus         7 k~ki~~~i~~~--pG~DlLqlT~~ln~~~~~nnW~iGvi~EVlqncv~eG~lliDeQi-SGi~YY~N~~   72 (75)
T d1u5tb2           7 KEKLVDLIGDN--PGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCVDEGDLLIDKQL-SGIYYYKNSY   72 (75)
T ss_dssp             HHHHHHHHHHS--CSBCHHHHHHHHHTSCTTCCCCHHHHHHHHHHHHHHTSEEEEECS-SCEEEEECCS
T ss_pred             HHHHHHHHhcC--CCccHHHHHHHHcccCCcccchHHHHHHHHHHHHhccceeeehhh-cceeeeeecc
Confidence            35788888854  555555555444       59999999999999999999999996 3444444433

>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=95.74  E-value=0.013  Score=42.85  Aligned_cols=50  Identities=14%  Similarity=0.271  Sum_probs=43.3

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      ++.-+..|+...-.  .|..|+.+|++.+|++...+..+|+.|++.|++-+-
T Consensus        18 lt~~e~~v~~~L~~--~g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~r~   67 (109)
T d1sfxa_          18 FKPSDVRIYSLLLE--RGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRRE   67 (109)
T ss_dssp             CCHHHHHHHHHHHH--HCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHh--cCCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEEEE
Confidence            66667777666552  589999999999999999999999999999999864

>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=95.71  E-value=0.0084  Score=43.41  Aligned_cols=76  Identities=18%  Similarity=0.221  Sum_probs=60.6

Q ss_pred             CCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHH
Q psy6552         137 QDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHAL  216 (254)
Q Consensus       137 ~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L  216 (254)
                      ..++|+.+....+.|+.||.|.++                      .|+.+..   .|..|+.+|++.+|++..-...+|
T Consensus         3 ~~~~pe~~~~la~~~kaL~~p~Rl----------------------~Il~~L~---~~~~~v~ela~~l~is~stvS~HL   57 (98)
T d1r1ta_           3 QAIAPEVAQSLAEFFAVLADPNRL----------------------RLLSLLA---RSELCVGDLAQAIGVSESAVSHQL   57 (98)
T ss_dssp             CCCCHHHHHHHHHHHHHHCCHHHH----------------------HHHHHHT---TCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhCCHHHH----------------------HHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHH
Confidence            358899888888999998855543                      3555554   356899999999999999999999


Q ss_pred             HHHHHcCcEEEeCCCCCccccee
Q psy6552         217 DFMVQEGYAWIDTQSPQEHLYWF  239 (254)
Q Consensus       217 ~~l~~~G~lwvD~q~~~e~~yw~  239 (254)
                      ..|.+.|++.....  +...||.
T Consensus        58 ~~L~~aglV~~~r~--G~~~~Y~   78 (98)
T d1r1ta_          58 RSLRNLRLVSYRKQ--GRHVYYQ   78 (98)
T ss_dssp             HHHHHTTSEEEEEE--TTEEEEE
T ss_pred             HHHHHCCceEEEEE--CCEEEEE
Confidence            99999999988765  4555555

>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=95.25  E-value=0.03  Score=38.25  Aligned_cols=47  Identities=17%  Similarity=0.295  Sum_probs=41.0

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .||+..... .+.+|.++|++.+|.++.-+-..|..|++.|++-.|++
T Consensus         9 ~IL~~~a~~-~~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~~~~   55 (75)
T d1mkma1           9 EILDFIVKN-PGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKD   55 (75)
T ss_dssp             HHHHHHHHC-SSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECTT
T ss_pred             HHHHHHHhC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCC
Confidence            567765543 67899999999999999999999999999999999854

>d2htja1 a.4.5.73 (A:1-73) P fimbrial regulatory protein PapI {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FaeA-like
domain: P fimbrial regulatory protein PapI
species: Escherichia coli [TaxId: 562]

Probab=95.01  E-value=0.042  Score=36.93  Aligned_cols=58  Identities=14%  Similarity=0.169  Sum_probs=47.5

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      +.||+.....  +.-+..++++.+|.|...|+-.|..|+++|++-+----.+-..|||--
T Consensus         3 n~Il~fl~~~--~~~~T~EIAea~gvsaYQARyYL~~Lekegki~RsPlRrGa~TlW~~~   60 (73)
T d2htja1           3 NEILEFLNRH--NGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQRSPLRRGMATYWFLK   60 (73)
T ss_dssp             HHHHHHHHHS--CCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEECCSSSSSCEEEES
T ss_pred             hHHHHHHHhc--CCccHHHHHHHhhhHHHHHHHHHHHHHHhcCcccChhhhhhHHHHHHh
Confidence            4678877743  445889999999999999999999999999999875443667899853

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.00  E-value=0.026  Score=37.41  Aligned_cols=46  Identities=15%  Similarity=0.091  Sum_probs=40.4

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      ...++++.+  +.+++|.++|++.+|.|..-+...|..|.+.|+.-.-
T Consensus         7 ~~~iL~~L~--~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G~~I~~   52 (63)
T d1biaa1           7 PLKLIALLA--NGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFT   52 (63)
T ss_dssp             HHHHHHHHT--TSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCCEE
T ss_pred             HHHHHHHHH--HCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCCcEEE
Confidence            457888888  5789999999999999999999999999999985443

>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=94.88  E-value=0.045  Score=41.21  Aligned_cols=62  Identities=15%  Similarity=0.133  Sum_probs=46.9

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF  239 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~  239 (254)
                      ++.-+..|+.+.-.+ .+.+|+.+|++.+|.++.-+...|..|++.|++.+...+...+.||+
T Consensus        24 l~~~~~~i~~~L~~~-~~plt~~ela~~l~vsk~~vs~~l~~L~~~GlV~r~~~~~drr~~~~   85 (151)
T d1ku9a_          24 LNKSVGAVYAILYLS-DKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIKGERKNYYE   85 (151)
T ss_dssp             CCHHHHHHHHHHHHC-SSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTTCSSCEEE
T ss_pred             CCHHHHHHHHHHHhC-CCCcCHHHHHHHhCCCcchHHHHHHHHHHCCCEEEEEcCCCCceeEE
Confidence            444466666554322 45699999999999999999999999999999999877632334444

>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=94.67  E-value=0.043  Score=37.37  Aligned_cols=45  Identities=16%  Similarity=0.220  Sum_probs=39.3

Q ss_pred             CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552         193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP  240 (254)
Q Consensus       193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p  240 (254)
                      +.++|+.+|+.++|.++-.+-.+|-.|.+.|.+..-...   +-.||.
T Consensus        22 ~~~~tA~~LAk~Lg~~Kk~VNr~LY~L~~~G~v~~~~~t---PP~W~~   66 (70)
T d1sfua_          22 NDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPSN---PPKWFK   66 (70)
T ss_dssp             TCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCS---SCEEEE
T ss_pred             CCCchHHHHHHHhCCCHHHHHHHHHHHHHCCCeecCCCc---CCcccc
Confidence            679999999999999999999999999999999998764   445553

>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=94.60  E-value=0.035  Score=36.68  Aligned_cols=48  Identities=17%  Similarity=0.157  Sum_probs=41.3

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW  226 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw  226 (254)
                      +++-...||+..+.  .+..|..+|++.+|+|..-+...++.|+++|++-
T Consensus         3 lD~~D~~IL~~L~~--~~r~s~~eiA~~l~ls~~~v~~Ri~rL~~~GiI~   50 (63)
T d2cg4a1           3 IDNLDRGILEALMG--NARTAYAELAKQFGVSPETIHVRVEKMKQAGIIT   50 (63)
T ss_dssp             CCHHHHHHHHHHHH--CTTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEE
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            44445678888873  5899999999999999999999999999999875

>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=94.58  E-value=0.024  Score=39.73  Aligned_cols=39  Identities=23%  Similarity=0.227  Sum_probs=35.9

Q ss_pred             CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         192 NEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       192 ~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ..|++|+.+|++.+++++..+...|..|+++|++.+...
T Consensus        18 ~~~~lt~~eLa~~l~i~~~~vs~~l~~Le~~GlV~r~~D   56 (85)
T d3ctaa1          18 NRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRTVT   56 (85)
T ss_dssp             SEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeecc
Confidence            367999999999999999999999999999999999543

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=94.49  E-value=0.027  Score=36.96  Aligned_cols=43  Identities=12%  Similarity=0.283  Sum_probs=38.8

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA  225 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l  225 (254)
                      ..+|+.+.+.  .|.+|..+|++.+|+|+.-+...|+.|+++|++
T Consensus         5 D~kIl~~L~~--n~r~s~~~lA~~~gls~~~v~~Ri~~L~~~giI   47 (60)
T d1i1ga1           5 DKIILEILEK--DARTPFTEIAKKLGISETAVRKRVKALEEKGII   47 (60)
T ss_dssp             HHHHHHHHHH--CTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSS
T ss_pred             HHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            4678888883  589999999999999999999999999999987

>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=94.33  E-value=0.047  Score=36.08  Aligned_cols=49  Identities=10%  Similarity=0.140  Sum_probs=42.4

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      ++.-...||...+.  .|.+|..+|++.+|+|+.-+...++.|+++|++..
T Consensus         3 lD~~D~~IL~~L~~--n~r~s~~~iA~~lgis~~tv~~Ri~~L~~~giI~~   51 (63)
T d2cfxa1           3 LDQIDLNIIEELKK--DSRLSMRELGRKIKLSPPSVTERVRQLESFGIIKQ   51 (63)
T ss_dssp             CCHHHHHHHHHHHH--CSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence            55556778888883  58999999999999999999999999999999853

>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=94.31  E-value=0.051  Score=39.16  Aligned_cols=53  Identities=17%  Similarity=0.179  Sum_probs=43.5

Q ss_pred             CChhHHHHHH-HhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQ-QVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~-l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-+-.||. +..  ..|.+|+.+|++.+|+++.-+...|..|++.|++.+....
T Consensus        19 Ls~~~~~iL~~L~~--~~~~~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV~r~~~~   72 (109)
T d2d1ha1          19 ITDTDVAVLLKMVE--IEKPITSEELADIFKLSKTTVENSLKKLIELGLVVRTKTE   72 (109)
T ss_dssp             CCHHHHHHHHHHHH--HCSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC-
T ss_pred             cCHHHHHHHHHHHH--cCCCCCHHHHHHHHCccHhHHHHHHHHHHHCCCEEEeecC
Confidence            6655666664 445  2578999999999999999999999999999999987654

>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=94.28  E-value=0.034  Score=40.97  Aligned_cols=64  Identities=13%  Similarity=0.215  Sum_probs=52.4

Q ss_pred             CCCCChhHHHHHHHhhccCCCcccHHHHHHhc----CCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552         174 PGELSLDHSLVLQQVASKNEAHISVSVLNNEL----NWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       174 p~els~D~~~il~l~~~~~~g~vt~~~l~~~l----~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      +++++.-+..|+.+.=.  .|.+|+.+|.+.+    +|++.=....|..|++.|++=+...  +...+|.|.
T Consensus         2 ~~~lt~~E~~VM~~lW~--~~~~t~~ei~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~r~~~--gr~~~Y~~~   69 (120)
T d1okra_           2 TYEISSAEWEVMNIIWM--KKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKD--NKIFQYYSL   69 (120)
T ss_dssp             CCCCCHHHHHHHHHHHH--HSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEE--TTEEEEEES
T ss_pred             CCCCCHHHHHHHHHHHc--CCCCCHHHHHHHHhcccCccHHhHHHHHHHHHHCCCeEEEec--CCceEEeec
Confidence            35688778888888763  4789999977665    8999999999999999999999876  466777765

>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=94.25  E-value=0.041  Score=39.02  Aligned_cols=50  Identities=6%  Similarity=0.030  Sum_probs=42.1

Q ss_pred             hhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         179 LDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       179 ~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .-+-.|+.+...  .|.+|+.+|++.+|+++.-....|..|++.|++-+-..
T Consensus        16 p~r~~IL~~L~~--~~~~~~~eLa~~l~is~~~vs~~l~~L~~~glV~~~~~   65 (100)
T d1ub9a_          16 PVRLGIMIFLLP--RRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKV   65 (100)
T ss_dssp             HHHHHHHHHHHH--HSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHhcc--CCCeeHHHHHHHHhhccccccHHHHHHhhhceeEEEEc
Confidence            345667777763  47899999999999999999999999999999976543

>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=94.23  E-value=0.093  Score=38.74  Aligned_cols=56  Identities=11%  Similarity=0.146  Sum_probs=46.6

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .++..|-.||......+++.+|+.+|++.++++...+...|+.|++.|++.+-..+
T Consensus        26 glt~~q~~vL~~l~~~~~~~it~~ela~~~~~~~~~vs~~l~~L~~~g~v~r~~~~   81 (135)
T d3broa1          26 DLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVSG   81 (135)
T ss_dssp             TCCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCHHHHHHHHHHHHcCCCCCCHHHHHHHHCcCHhHHHHHHHHHHHHHHHHHHhhh
Confidence            37777877776655433567999999999999999999999999999999877654

>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=93.89  E-value=0.13  Score=38.43  Aligned_cols=55  Identities=7%  Similarity=0.090  Sum_probs=47.8

Q ss_pred             CCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         175 GELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       175 ~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ..++.-|-.||....  ..+.+|+.+|++.+++++.-+...++.|++.|++.+...+
T Consensus        32 ~~lt~~q~~vL~~l~--~~~~~t~~~la~~l~~~~~~vsr~l~~L~~~G~v~r~~~~   86 (141)
T d1lnwa_          32 LDLTPPDVHVLKLID--EQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNP   86 (141)
T ss_dssp             CCCCHHHHHHHHHHH--SSTTCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCCCHHHHHHHHHHH--HCCCCCHHHHHHHHCccHhHHHHHHHHHHHhhceeeeccC
Confidence            347777888887776  3467999999999999999999999999999999988765

>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=93.76  E-value=0.057  Score=40.07  Aligned_cols=57  Identities=9%  Similarity=0.216  Sum_probs=48.8

Q ss_pred             CCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         175 GELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       175 ~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ..++..|-.||......+.|.+|+.+|++.+++++..+...|..|++.|++-+-...
T Consensus        30 ~~Lt~~q~~iL~~l~~~~~~~~t~~eia~~~~~~~~~vs~~l~~L~~~g~v~r~~~~   86 (125)
T d1p4xa1          30 VDMTIKEFILLTYLFHQQENTLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSK   86 (125)
T ss_dssp             CSSCHHHHHHHHHHHSCSCSEEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEEECS
T ss_pred             cCCCHHHHHHHHHHHHhccCCcCHHHHHHHhCCCcchHHHHHHHHHHCCCceeeccc
Confidence            348888888887665433578999999999999999999999999999999988765

>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=93.69  E-value=0.073  Score=38.91  Aligned_cols=58  Identities=10%  Similarity=0.051  Sum_probs=47.8

Q ss_pred             CCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         174 PGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       174 p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      +..++..|-.+|......+.+.+|+.+|++.+++++.-+...|+.|++.|++-+-..+
T Consensus        27 ~~~Lt~~q~~vL~~l~~~~~~~~t~~ela~~l~~~~~~vs~~i~~Le~~gli~r~~~~   84 (115)
T d1hsja1          27 KFNLNYEEIYILNHILRSESNEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKRSL   84 (115)
T ss_dssp             SCCCCHHHHHHHHHHHTCSCSEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEECC
T ss_pred             hcCCCHHHHHHHHHHHccCCCCcCHHHHHHHHCCChhhHHHHHHHHHHcCCeEEEeec
Confidence            3458888888877654323678999999999999999999999999999999876554

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=93.58  E-value=0.055  Score=35.25  Aligned_cols=44  Identities=2%  Similarity=0.108  Sum_probs=39.2

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW  226 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw  226 (254)
                      ...++...+.  .+.+|..+|++.+|.|..-+...|..|+++|++-
T Consensus         5 D~~Il~~L~~--n~r~s~~eiA~~l~ls~~~v~~Ri~~L~~~giI~   48 (60)
T d2cyya1           5 DKKIIKILQN--DGKAPLREISKITGLAESTIHERIRKLRESGVIK   48 (60)
T ss_dssp             HHHHHHHHHH--CTTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            4577888884  5899999999999999999999999999999875

>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=93.55  E-value=0.12  Score=38.38  Aligned_cols=56  Identities=18%  Similarity=0.262  Sum_probs=47.3

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .+|..|-.||......+.+.+|+.+|++.+++++.-+...++.|++.|++.+-..+
T Consensus        30 ~Ls~~q~~vL~~l~~~~~~~~~~~~ia~~l~~~~~~vs~~v~~L~~~glV~r~~~~   85 (125)
T d1p4xa2          30 TLSFVEFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERST   85 (125)
T ss_dssp             SSCHHHHHHHHHHHTTTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECS
T ss_pred             CCCHHHHHHHHHHHHccCCCccHHHHHHHHCCCcchHHHHHHHHHhccCEeeeecC
Confidence            47877888877764333568999999999999999999999999999999977654

>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=93.53  E-value=0.095  Score=35.38  Aligned_cols=54  Identities=15%  Similarity=0.204  Sum_probs=44.8

Q ss_pred             CChhHHHHHHHhhcc--C-CCcccHHHHHHhcCC-CHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         177 LSLDHSLVLQQVASK--N-EAHISVSVLNNELNW-STERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       177 ls~D~~~il~l~~~~--~-~g~vt~~~l~~~l~w-s~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      |+.-|..||+.+..-  . +-..|..+|++.+|| |+.-+...|..|++.|++=++..
T Consensus         3 LT~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~kG~I~r~~~   60 (71)
T d1jhfa1           3 LTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSG   60 (71)
T ss_dssp             CCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEECSS
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHCcCeecCCC
Confidence            677788888876421  1 336999999999999 89999999999999999999854

>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=93.46  E-value=0.049  Score=36.51  Aligned_cols=46  Identities=11%  Similarity=0.052  Sum_probs=40.6

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      ...|+.++..  .|.+|..+|++.+|.|..=+...+..|+++|++-..
T Consensus         8 ~~~Il~~l~~--~g~~sr~eLa~~~glS~~Tv~~~l~~L~~~Glv~e~   53 (71)
T d1z05a1           8 AGRVYKLIDQ--KGPISRIDLSKESELAPASITKITRELIDAHLIHET   53 (71)
T ss_dssp             HHHHHHHHHH--HCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHH--cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3578888884  488999999999999999999999999999998643

>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=93.40  E-value=0.048  Score=35.99  Aligned_cols=45  Identities=9%  Similarity=0.137  Sum_probs=38.2

Q ss_pred             HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      ..|+++.+  ..|.++..+|++.+|.++.=+.+.+..|.+.|++-..
T Consensus        10 k~I~~l~~--~~~~v~~~~iA~~L~vs~~SVs~mikrL~~~GlV~~~   54 (61)
T d2ev0a1          10 EQIYMLIE--EKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYE   54 (61)
T ss_dssp             HHHHHHHH--HHSSCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             HHHHHHHh--cCCCccHHHHHHHhCCCchhHHHHHHHHHHCCCEEEc
Confidence            35566666  3689999999999999999999999999999997654

>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=93.20  E-value=0.14  Score=34.55  Aligned_cols=50  Identities=24%  Similarity=0.420  Sum_probs=43.3

Q ss_pred             CChhHHHHHHHhhcc-CCCcccHHHHHHhc-CCCHHHHHHHHHHHHHcCcEE
Q psy6552         177 LSLDHSLVLQQVASK-NEAHISVSVLNNEL-NWSTERAQHALDFMVQEGYAW  226 (254)
Q Consensus       177 ls~D~~~il~l~~~~-~~g~vt~~~l~~~l-~ws~~ra~~~L~~l~~~G~lw  226 (254)
                      |+.-|..|+.+.+.. ..-++++.+|++.| |.+..-.+++++.|..+|.+.
T Consensus         4 Ls~~q~~V~~~i~s~~~~eGi~~~el~~~l~~~~~~~i~~aid~L~~eG~IY   55 (69)
T d1dpua_           4 LTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIY   55 (69)
T ss_dssp             SCHHHHHHHHHHHHCCCTTTEEHHHHHHHSTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHHHHhCCCccCcCHHHHHHHccCCCHHHHHHHHHHHHhCCcee
Confidence            677788998887643 23479999999999 899999999999999999998

>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=93.02  E-value=0.26  Score=34.80  Aligned_cols=75  Identities=16%  Similarity=0.239  Sum_probs=56.6

Q ss_pred             CHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH
Q psy6552         140 TNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFM  219 (254)
Q Consensus       140 S~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l  219 (254)
                      .+|.+.+..+.|+.||.|.++                      .|+.+..   .|-.++.+|++.+|++..-...+|..|
T Consensus         1 n~d~~e~~a~~fkaL~d~~Rl----------------------~Il~~L~---~~~~~v~el~~~l~~s~~~vS~HL~~L   55 (94)
T d1r1ua_           1 NTDTLERVTEIFKALGDYNRI----------------------RIMELLS---VSEASVGHISHQLNLSQSNVSHQLKLL   55 (94)
T ss_dssp             CHHHHHHHHHHHHHTCSHHHH----------------------HHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHhCCHHHH----------------------HHHHHHH---cCCccHHHHHHHHCCCHHHHHHHHHHH
Confidence            367777788888877755432                      3455554   245899999999999999999999999


Q ss_pred             HHcCcEEEeCCCCCcccceecc
Q psy6552         220 VQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       220 ~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      .+.|++-.-..  +...||..+
T Consensus        56 ~~~glv~~~r~--G~~~~Y~l~   75 (94)
T d1r1ua_          56 KSVHLVKAKRQ--GQSMIYSLD   75 (94)
T ss_dssp             HHTTSEEEEEE--TTEEEEEES
T ss_pred             HHCCceEEEEE--CCEEEEEEC
Confidence            99999988765  455666543

>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=92.88  E-value=0.13  Score=38.26  Aligned_cols=54  Identities=19%  Similarity=0.161  Sum_probs=46.0

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      +++..|-.+|.....  .|.+|+++|++.+++++.-+...+..|++.|++.+-..+
T Consensus        31 ~Lt~~q~~vL~~l~~--~~~~t~~ela~~~~i~~~~vs~~v~~L~~~glv~r~~~~   84 (138)
T d1jgsa_          31 DITAAQFKVLCSIRC--AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP   84 (138)
T ss_dssp             TSCHHHHHHHHHHHH--HSSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECT
T ss_pred             CCCHHHHHHHHhHHh--CcCCCHHHHHHHHCCCHhHHHHHHHHHhhCCCEEEeecc
Confidence            477778888777764  368999999999999999999999999999999975443

>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=92.63  E-value=0.17  Score=33.45  Aligned_cols=46  Identities=9%  Similarity=0.099  Sum_probs=40.4

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .|.++-+  ..|.++..+||+.+|.++.=+.+.+..|.++|++-.+..
T Consensus        13 ~I~~L~~--~~~~v~~~~iA~~L~vs~~SVt~mvkrL~~~Glv~~~~y   58 (63)
T d2isya1          13 TIYDLEE--EGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGD   58 (63)
T ss_dssp             HHHHHHH--TTCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTT
T ss_pred             HHHHHHh--cCCCCcHHHHHHHhCCCchhHHHHHHHHHHCCCEEEcCC
Confidence            5566666  478999999999999999999999999999999987754

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=92.61  E-value=0.11  Score=34.20  Aligned_cols=44  Identities=16%  Similarity=0.265  Sum_probs=37.6

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA  225 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l  225 (254)
                      +..|+++..+. .+++|+.+|++.||.|..=.+.-|+.|.+.|+.
T Consensus         9 ~~~Il~~L~~~-~~~vs~~~La~~l~VS~~TI~rdi~~L~~~G~~   52 (65)
T d1j5ya1           9 LKSIVRILERS-KEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYN   52 (65)
T ss_dssp             HHHHHHHHHHC-SSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTCC
T ss_pred             HHHHHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence            45677776543 678999999999999999999999999999973

>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=92.48  E-value=0.19  Score=37.00  Aligned_cols=54  Identities=19%  Similarity=0.115  Sum_probs=44.0

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.+|...... .+.+|+++|+..+++++.-+...+..|++.|++.+-..+
T Consensus        26 lt~~q~~iL~~l~~~-~~~~t~~~la~~~~~~~~~vs~~v~~L~~~gli~r~~~~   79 (137)
T d2fbha1          26 LSQARWLVLLHLARH-RDSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLAVA   79 (137)
T ss_dssp             CTTTHHHHHHHHHHC-SSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCB
T ss_pred             CCHHHHHHHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHHHHcCCccccCCC
Confidence            455566666544322 457999999999999999999999999999999988775

>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=92.31  E-value=0.17  Score=37.39  Aligned_cols=55  Identities=18%  Similarity=0.179  Sum_probs=43.8

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .++..|-.+|..+... .+.+|+.+|++.++++..-+...|..|++.|++.+=..+
T Consensus        28 glt~~~~~~L~~l~~~-~~~~t~~~la~~l~i~~~~vs~~l~~L~~~glI~~~~~~   82 (140)
T d3deua1          28 ELTQTHWVTLHNIHQL-PPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCA   82 (140)
T ss_dssp             TCCHHHHHHHHHHHHS-CSSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC---
T ss_pred             CCCHHHHHHHHHHHHc-CCCccHHHHHHHHCCCHhHHHHHHHHHHhCCCEEecccC
Confidence            4676777777665432 578999999999999999999999999999999865543

>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=92.09  E-value=0.16  Score=37.95  Aligned_cols=54  Identities=11%  Similarity=0.114  Sum_probs=43.9

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.+|...... .|.+|+.+|++.+|+++.-+...|+.|++.|++-+-..+
T Consensus        32 lt~~q~~vL~~L~~~-~g~~t~~~La~~~~~~~~~vs~~i~~L~~~glv~r~~~~   85 (145)
T d2hr3a1          32 VQFSQLVVLGAIDRL-GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP   85 (145)
T ss_dssp             HHHHHHHHHHHHHHT-TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCHHHHHHHHHHHHc-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeeeCc
Confidence            555677776655433 567999999999999999999999999999999887664

>d1p6ra_ a.4.5.39 (A:) Penicillinase repressor BlaI {Bacillus licheniformis [TaxId: 1402]}

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: Bacillus licheniformis [TaxId: 1402]

Probab=92.04  E-value=0.26  Score=34.06  Aligned_cols=63  Identities=14%  Similarity=0.227  Sum_probs=50.5

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHH----HhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceeccc
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLN----NELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSL  242 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~----~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~l  242 (254)
                      .+++-+..|++++=  ..|.+|+.++.    +..+|+..=..+.|..|++.|++=++.+  +...+|.|..
T Consensus         6 ~Ls~~E~~IM~~lW--~~~~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~KG~l~~~k~--gr~~~Y~p~i   72 (82)
T d1p6ra_           6 QISDAELEVMKVIW--KHSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKE--GRVFVYTPNI   72 (82)
T ss_dssp             CCCHHHHHHHHHHH--TSSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEE--TTEEEEEESC
T ss_pred             CCCHHHHHHHHHHH--hCCCCCHHHHHHHhccccCCcHhHHHHHHHHHHHCCCeEEEec--CCeEEEEecC
Confidence            37767778888876  35789999965    4569999999999999999999999987  4566666654

>d2ve8a1 a.4.5.67 (A:745-811) DNA translocase FtsK {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FtsK C-terminal domain-like
domain: DNA translocase FtsK
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=91.84  E-value=0.12  Score=34.83  Aligned_cols=44  Identities=18%  Similarity=0.209  Sum_probs=38.1

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW  226 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw  226 (254)
                      ...+++++..  .+..|++.|..+|++-..||...++.|++.|++=
T Consensus         6 y~~a~~~V~~--~~kaS~S~lQR~l~IGYnRAariid~LE~~GiVs   49 (67)
T d2ve8a1           6 YDEAVRFVTE--SRRASISAVQRKLKIGYNRAARMIEAMEMAGVVT   49 (67)
T ss_dssp             HHHHHHHHHH--HCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSBC
T ss_pred             HHHHHHHHHH--hCcccHHHHHHHHhcchHHHHHHHHHHHHCcCCC
Confidence            4556677764  3789999999999999999999999999999984

>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=91.84  E-value=0.15  Score=37.75  Aligned_cols=55  Identities=15%  Similarity=0.143  Sum_probs=47.5

Q ss_pred             CCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         175 GELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       175 ~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ..++..|-.+|..+..  .|.+|+.+|++.+++++.-+...++.|++.|++-+...+
T Consensus        29 ~gLt~~q~~vL~~l~~--~~~~t~~~La~~~~i~~~~vsr~i~~L~~~glv~r~~~~   83 (137)
T d1z91a1          29 LNITYPQYLALLLLWE--HETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSE   83 (137)
T ss_dssp             TCCCHHHHHHHHHHHH--HSEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCBCS
T ss_pred             cCcCHHHHHHHHHHHc--CCCCCHHHHHHHHCcCHHHHHHHHHHHhhccceEEeecC
Confidence            3477778888777763  478999999999999999999999999999999988765

>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=91.83  E-value=0.18  Score=36.56  Aligned_cols=56  Identities=20%  Similarity=0.286  Sum_probs=46.6

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .+|..|-.+|......+.|.+|+.+|++.+++++.-....+..|++.|++-+-..+
T Consensus        30 ~Ls~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~tvs~~i~~Le~~gli~r~~~~   85 (115)
T d2frha1          30 SISFEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNE   85 (115)
T ss_dssp             CCCHHHHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCS
T ss_pred             CCCHHHHHHHHHHHcCCCCCCCHHHHHHHHCCCHhHHHHHHHHHHhhhhheeeecc
Confidence            47777777765554333677999999999999999999999999999999888765

>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=91.63  E-value=0.2  Score=33.39  Aligned_cols=45  Identities=9%  Similarity=0.010  Sum_probs=40.4

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      ...|+.++.  ..|.+|..+|++.+|.|..=....++.|+++|++--
T Consensus         7 ~~~Il~~i~--~~g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~glv~e   51 (70)
T d1z6ra1           7 AGAVYRLID--QLGPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQE   51 (70)
T ss_dssp             HHHHHHHHH--SSCSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            456888888  569999999999999999999999999999998863

>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=91.48  E-value=0.19  Score=37.25  Aligned_cols=54  Identities=9%  Similarity=0.091  Sum_probs=46.0

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      +++..+-.+|.....  .|.+|+.+|++.++.++.-+...+..|++.|++.+=..+
T Consensus        29 ~lt~~q~~iL~~l~~--~~~~t~~~La~~l~i~~~~vs~~v~~L~~~gli~r~~~~   82 (140)
T d2etha1          29 DMKTTELYAFLYVAL--FGPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDP   82 (140)
T ss_dssp             HSBHHHHHHHHHHHH--HCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECT
T ss_pred             CCCHHHHHHHHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeeecc
Confidence            367677777776663  478999999999999999999999999999999977664

>d2j5pa1 a.4.5.67 (A:1261-1329) DNA translocase FtsK {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FtsK C-terminal domain-like
domain: DNA translocase FtsK
species: Escherichia coli [TaxId: 562]

Probab=91.37  E-value=0.16  Score=34.40  Aligned_cols=44  Identities=18%  Similarity=0.231  Sum_probs=38.8

Q ss_pred             HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552         181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW  226 (254)
Q Consensus       181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw  226 (254)
                      ...+++++-.  .+..|++.|..+|++-..||...++.|+++|++=
T Consensus         9 y~~a~~~V~~--~~kaS~S~lQR~l~IGYnRAariid~LE~~GiVs   52 (69)
T d2j5pa1           9 FDQAVQFVTE--KRKASISGVQRQFRIGYNRAARIIEQMEAQGIVS   52 (69)
T ss_dssp             HHHHHHHHHH--TTEEEHHHHHHHHTCCHHHHHHHHHHHHHHTSBC
T ss_pred             HHHHHHHHHH--hCcccHHHHHHHHhccchHHHHHHHHHHHCCcCC
Confidence            5667777773  4789999999999999999999999999999964

>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=91.22  E-value=0.15  Score=37.72  Aligned_cols=53  Identities=11%  Similarity=0.062  Sum_probs=45.8

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..|-.+|.....  .|.+|+.+|++.+++++.-+...|+.|++.|++.+-..+
T Consensus        28 lt~~q~~vL~~l~~--~~~~t~~~la~~~~i~~~~vs~~i~~L~~~gli~r~~~~   80 (136)
T d2fbia1          28 LTEQQWRVIRILRQ--QGEMESYQLANQACILRPSMTGVLARLERDGIVRRWKAP   80 (136)
T ss_dssp             CCHHHHHHHHHHHH--HCSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeecC
Confidence            67778888887763  478999999999999999999999999999999776554

>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=90.89  E-value=0.26  Score=36.85  Aligned_cols=53  Identities=15%  Similarity=0.249  Sum_probs=45.4

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..|-.+|.....  .+++|+.+|++.++.++.-....|..|++.|++.+-..+
T Consensus        27 lt~~q~~iL~~i~~--~~~~t~~~la~~l~i~~~tvs~~l~~L~~~glI~r~~~~   79 (144)
T d1lj9a_          27 LTRGQYLYLVRVCE--NPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDA   79 (144)
T ss_dssp             CTTTHHHHHHHHHH--STTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCHHHHHHHHHHHh--CCCCCHHHHHHHHCccHhhHHHHHHHHHhhhcccccCCC
Confidence            66678777766653  467999999999999999999999999999999987665

>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=90.88  E-value=0.19  Score=37.20  Aligned_cols=53  Identities=23%  Similarity=0.180  Sum_probs=46.7

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++..|-.+|..+..  .+++|+.+|++.++.++.-....+..|++.|++.+-..+
T Consensus        32 lt~~q~~vL~~i~~--~~~~t~~~la~~l~~~~~~~s~~l~~L~~~Gli~r~~~~   84 (136)
T d2bv6a1          32 LTYPQFLVLTILWD--ESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSE   84 (136)
T ss_dssp             CCHHHHHHHHHHHH--SSEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEECS
T ss_pred             CCHHHHHHHHHHHc--CCCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEEeecC
Confidence            67778888887773  478999999999999999999999999999999987665

>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=90.53  E-value=0.21  Score=37.02  Aligned_cols=53  Identities=13%  Similarity=0.093  Sum_probs=44.8

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.+|..+..  .|.+|+++|++.++.++.-....|+.|++.|++.+=...
T Consensus        28 lt~~q~~iL~~i~~--~~~~t~~~la~~l~i~~~tvs~~l~~L~~~gli~r~~~~   80 (139)
T d2a61a1          28 ITPAQFDILQKIYF--EGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDP   80 (139)
T ss_dssp             CCHHHHHHHHHHHH--HCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHhCCCcccchHHHHHHHhcCeeeeeecc
Confidence            66667777776663  478999999999999999999999999999999876543

>d2g9wa1 a.4.5.39 (A:3-124) Hypothetical protein Rv1846c {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Hypothetical protein Rv1846c
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=89.49  E-value=0.61  Score=34.11  Aligned_cols=63  Identities=11%  Similarity=0.103  Sum_probs=47.7

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhc----CCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceeccc
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNEL----NWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSL  242 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l----~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~l  242 (254)
                      |++-...|+++.=.. ++.+|+.++.+.+    +|++.=..+.|..|++.|++=++..  +...+|.|..
T Consensus         5 L~~~E~~IM~~lW~~-g~~~t~~eI~~~l~~~~~~~~sTV~T~L~rL~~Kg~l~~~~~--gr~~~Y~~~i   71 (122)
T d2g9wa1           5 LGDLERAVMDHLWSR-TEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRD--DRAHRYAPVH   71 (122)
T ss_dssp             CCHHHHHHHHHHHTC-SSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC-----CCEEEESS
T ss_pred             CCHHHHHHHHHHHcC-CCCccHHHHHHHHhccCCCcHHHHHHHHHHHHHCCCEEEeec--CCeEEEEeCC
Confidence            665667788887632 3468999998766    7999999999999999999999976  4556666654

>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=89.48  E-value=0.38  Score=35.36  Aligned_cols=62  Identities=10%  Similarity=0.089  Sum_probs=49.3

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHh----cCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNE----LNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS  241 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~----l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~  241 (254)
                      ++|+-...|++++=.  .|.+|+.++.+.    .+|++.=..+.|..|++.|++=+..+  +...+|.|.
T Consensus         3 ~ls~~E~~VM~~lW~--~~~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~Kg~l~~~~~--gr~~~Y~~~   68 (122)
T d1sd4a_           3 EISMAEWDVMNIIWD--KKSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKS--ENIYFYSSN   68 (122)
T ss_dssp             CCCHHHHHHHHHHHH--SSSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEE--TTEEEEEEC
T ss_pred             CCCHHHHHHHHHHHc--CCCCCHHHHHHHhhccCCCcHhHHHHHHHHHHhhhceeeecc--CCeEEEeec
Confidence            366566778887763  578999987765    59999999999999999999999877  455666654

>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=89.36  E-value=0.31  Score=37.61  Aligned_cols=54  Identities=13%  Similarity=0.081  Sum_probs=46.3

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      .++.-|-.||.++..  .|.+|+.+|++.+++++.-+...+..|++.|++-+-..+
T Consensus        38 ~Lt~~q~~vL~~l~~--~~~~t~~~la~~~~l~~~tvs~~i~rL~~~gli~r~~~~   91 (162)
T d2fxaa1          38 DLNINEHHILWIAYQ--LNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRL   91 (162)
T ss_dssp             TCCHHHHHHHHHHHH--HTSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC-
T ss_pred             CCCHHHHHHHhhhcc--CCCcCHHHHHHHHcCCchhhHHHHHHHHHCCCceeeccc
Confidence            367678888887763  467999999999999999999999999999999987654

>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=89.34  E-value=0.32  Score=35.23  Aligned_cols=75  Identities=13%  Similarity=0.174  Sum_probs=54.9

Q ss_pred             CCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHH-hhccCCCcccHHHHHHhcCCCHHHHHHHHH
Q psy6552         139 ITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQ-VASKNEAHISVSVLNNELNWSTERAQHALD  217 (254)
Q Consensus       139 IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l-~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~  217 (254)
                      +.++|+.++.+.|+.||.|-++                      .|+.. +.   .|..|+.+|++.+|.+..-+..+|.
T Consensus        13 l~~~d~~~~~~~~kaLadp~Rl----------------------~Il~~L~~---~~~~~v~ela~~l~~s~s~vS~HL~   67 (108)
T d1u2wa1          13 LQTVDISGVSQILKAIADENRA----------------------KITYALCQ---DEELCVCDIANILGVTIANASHHLR   67 (108)
T ss_dssp             HHTTTHHHHHHHHHHHHSHHHH----------------------HHHHHHHH---SSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             cChhhHHHHHHHHHHhCCHHHH----------------------HHHHHHHh---CCCccHHHHHHHHccChhHHHHHHH
Confidence            4566778888888877744332                      34443 34   4679999999999999999999999


Q ss_pred             HHHHcCcEEEeCCCCCcccceec
Q psy6552         218 FMVQEGYAWIDTQSPQEHLYWFP  240 (254)
Q Consensus       218 ~l~~~G~lwvD~q~~~e~~yw~p  240 (254)
                      .|.+.|++-.-.+  +...||..
T Consensus        68 ~L~~aGlv~~~r~--G~~~~Y~l   88 (108)
T d1u2wa1          68 TLYKQGVVNFRKE--GKLALYSL   88 (108)
T ss_dssp             HHHHTTSEEEC------CCEEEE
T ss_pred             HHHHCCeeEEEEE--CCEEEEEE
Confidence            9999999988776  45566654

>d1lvaa3 a.4.5.35 (A:511-574) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal fragment of elongation factor SelB
domain: C-terminal fragment of elongation factor SelB
species: Moorella thermoacetica [TaxId: 1525]

Probab=89.20  E-value=0.73  Score=30.10  Aligned_cols=52  Identities=15%  Similarity=0.171  Sum_probs=39.5

Q ss_pred             CChhHHHHHHHh----hccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         177 LSLDHSLVLQQV----ASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       177 ls~D~~~il~l~----~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      +|.||..+.+-+    .....---++.+++..+|.+...+++.|..|.+.|.+..=
T Consensus         1 ls~~q~~l~~~I~~~~~~~g~~PP~vrdl~~~l~~~e~~~~~lL~~l~~~G~lvkI   56 (64)
T d1lvaa3           1 FSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKI   56 (64)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTSCCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEES
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            466776554432    2111234789999999999999999999999999999863

>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=89.04  E-value=0.4  Score=35.43  Aligned_cols=53  Identities=11%  Similarity=0.133  Sum_probs=44.4

Q ss_pred             CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ++.-|-.+|.....  .|.+|+.+|++.+++++.-+...++.|++.|++-+-..+
T Consensus        33 lt~~q~~iL~~l~~--~~~~t~~~la~~~~i~~~~vs~~l~~L~~~glv~r~~~~   85 (143)
T d1s3ja_          33 VTPAQLFVLASLKK--HGSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNT   85 (143)
T ss_dssp             CCHHHHHHHHHHHH--HSEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             CCHHHHHHHHHHHH--CCCCCHHHHHHHHCcCHHHHHHHHHHHHHhhhheeeeec
Confidence            55567777776663  468999999999999999999999999999999766543

>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=87.59  E-value=0.31  Score=33.21  Aligned_cols=52  Identities=12%  Similarity=0.078  Sum_probs=43.5

Q ss_pred             ChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHH-HHHHHHHHHHcCcEEEeCCC
Q psy6552         178 SLDHSLVLQQVASKNEAHISVSVLNNELNWSTER-AQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       178 s~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~r-a~~~L~~l~~~G~lwvD~q~  231 (254)
                      .+-+..|+++...  .|..|+-.|+.++|.+..+ .-.+|..|++.|.++.....
T Consensus         4 ~d~eekI~~~L~~--~g~~~Al~iak~lGl~kakeVN~~LY~L~k~g~v~k~~~t   56 (73)
T d1xmka1           4 AEIKEKICDYLFN--VSDSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQGTT   56 (73)
T ss_dssp             HHHHHHHHHHHHH--TCCEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEECSS
T ss_pred             HHHHHHHHHHHHH--cCCchHHHHHHHhCCCcHHHHhHHHHHHHHCCCeecCCCC
Confidence            3345788888884  5789999999999999975 88889999999999987654

>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=87.30  E-value=1.5  Score=28.42  Aligned_cols=50  Identities=10%  Similarity=0.116  Sum_probs=41.3

Q ss_pred             HHHHHHhhcc-CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         182 SLVLQQVASK-NEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       182 ~~il~l~~~~-~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      ..|+.+.... +...+|+.+|+..|+.++-.+-.+|-.|+..|.+|....+
T Consensus         2 q~vl~~l~~lg~~~~~tA~~LA~kl~vpKk~iNr~LYsL~~kgkl~k~~gt   52 (59)
T d2gxba1           2 QRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGT   52 (59)
T ss_dssp             HHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECSS
T ss_pred             hHHHHHHHhcCCccchhHHHHHHHhCCcHHHHHHHHHHHHHccchhhcCCC
Confidence            3455554432 2568999999999999999999999999999999998765

>d1wdcc_ a.39.1.5 (C:) Myosin Regulatory Chain {Bay scallop (Aequipecten irradians) [TaxId: 31199]}

class: All alpha proteins
fold: EF Hand-like
superfamily: EF-hand
family: Calmodulin-like
domain: Myosin Regulatory Chain
species: Bay scallop (Aequipecten irradians) [TaxId: 31199]

Probab=87.10  E-value=1.1  Score=32.97  Aligned_cols=92  Identities=17%  Similarity=0.282  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHHHHH--hhhhhhcCHHHHHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCC
Q psy6552          38 HLNTFRDKLESFASE--YKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGG  115 (254)
Q Consensus        38 ql~~fk~~L~~FA~k--h~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGG  115 (254)
                      |+..+++....|-..  ..+.|..     .+|..++.++|+.|-.  .                 ++-++ ...-..+.|
T Consensus         5 qi~~l~~~F~~fD~~~~~dG~I~~-----~el~~~l~~lG~~~t~--~-----------------e~~~~-~~~~~~~~~   59 (152)
T d1wdcc_           5 EIDDLKDVFELFDFWDGRDGAVDA-----FKLGDVCRCLGINPRN--E-----------------DVFAV-GGTHKMGEK   59 (152)
T ss_dssp             HHHHHHHHHHHHHHHTCSSSCEEG-----GGHHHHHHHTTCCCCH--H-----------------HHHHT-TCCSSTTSC
T ss_pred             HHHHHHHHHHHHCcCCCCCCeECH-----HHHHHHHHHhccCccH--h-----------------hhhhh-hhhhccccc
Confidence            445556655555321  1223433     3667888899998721  1                 22222 222334567


Q ss_pred             ceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCe
Q psy6552         116 LILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGF  158 (254)
Q Consensus       116 ii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~  158 (254)
                      -|+..+....+.+....    ..-+.+++.+|.+.+..=|.|+
T Consensus        60 ~i~~~eFl~~~~~~~~~----~~~~~~~l~~aF~~~D~~~~G~   98 (152)
T d1wdcc_          60 SLPFEEFLPAYEGLMDC----EQGTFADYMEAFKTFDREGQGF   98 (152)
T ss_dssp             EECHHHHHHHHHHHTTS----CCCCHHHHHHHHHTTCSSSSSE
T ss_pred             ccccccccccccccccc----chhHHHhhhhhhhccccccCcc
Confidence            88888888888776544    4567888888888877666553

>d1s6la1 a.4.5.79 (A:21-80) Alkylmercury lyase MerB {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MerB N-terminal domain-like
domain: Alkylmercury lyase MerB
species: Escherichia coli [TaxId: 562]

Probab=86.58  E-value=0.24  Score=32.40  Aligned_cols=29  Identities=24%  Similarity=0.424  Sum_probs=26.1

Q ss_pred             CCCcccHHHHHHhcCCCHHHHHHHHHHHH
Q psy6552         192 NEAHISVSVLNNELNWSTERAQHALDFMV  220 (254)
Q Consensus       192 ~~g~vt~~~l~~~l~ws~~ra~~~L~~l~  220 (254)
                      .+.-||+..|+..+||+.++.+.+|+.+-
T Consensus        13 ~G~PVs~~~LA~alg~~~~eV~~aL~~~p   41 (60)
T d1s6la1          13 KGRPVSRTTLAGILDWPAERVAAVLEQAT   41 (60)
T ss_dssp             TTCCBCHHHHHHHHTCCHHHHHHHHTTCC
T ss_pred             CCCCcCHHHHHHHhCCCHHHHHHHHHhCC
Confidence            36789999999999999999999998764

>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Putative transcriptional regulator RHA1 ro03477
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=86.40  E-value=0.53  Score=31.06  Aligned_cols=38  Identities=13%  Similarity=0.211  Sum_probs=34.0

Q ss_pred             CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      +-.++..+|++.+|.+..-++++|..|+++|++-+=..
T Consensus        23 G~~l~~~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~~   60 (69)
T d2hs5a1          23 GARLSEPDICAALDVSRNTVREAFQILIEDRLVAHELN   60 (69)
T ss_dssp             TCEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             cCccCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEcC
Confidence            34678999999999999999999999999999987644

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF1790-like
domain: Transcriptional regulatory protein PF1790
species: Pyrococcus furiosus [TaxId: 2261]

Probab=86.24  E-value=0.59  Score=36.69  Aligned_cols=43  Identities=19%  Similarity=0.151  Sum_probs=36.9

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID  228 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD  228 (254)
                      .||.++.   .|..|+.+|++.+|.|+.-+..+|..|++.|++=..
T Consensus        19 ~Il~~L~---~~~~~~~ela~~l~~s~~~v~~HL~~L~~~Glv~~~   61 (194)
T d2p4wa1          19 RILFLLT---KRPYFVSELSRELGVGQKAVLEHLRILEEAGLIESR   61 (194)
T ss_dssp             HHHHHHH---HSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            4566665   367999999999999999999999999999999654

>d1t6sa1 a.4.5.60 (A:1-85) Segregation and condensation protein B, ScpB {Chlorobium tepidum [TaxId: 1097]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ScpB/YpuH-like
domain: Segregation and condensation protein B, ScpB
species: Chlorobium tepidum [TaxId: 1097]

Probab=86.03  E-value=1.9  Score=29.37  Aligned_cols=52  Identities=25%  Similarity=0.331  Sum_probs=42.2

Q ss_pred             cCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhh----hCCCeEEEEeCCceEEEEccC
Q psy6552         113 NGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKI----FGNGFSIIPIGQGQYLVQSIP  174 (254)
Q Consensus       113 nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~----Lg~g~~l~~~~sg~~vv~s~p  174 (254)
                      .|.=+++.++...+.         ..+|+++|..+++.|..    -+.||+|+.++ |....++.|
T Consensus        19 s~~Pls~~~L~~~l~---------~~~~~~~i~~~l~~L~~~y~~~~~g~el~~~~-~gy~~~tk~   74 (85)
T d1t6sa1          19 SEEPVNLQTLSQITA---------HKFTPSELQEAVDELNRDYEATGRTFRIHAIA-GGYRFLTEP   74 (85)
T ss_dssp             CSSCBCHHHHHHHTT---------CCCCHHHHHHHHHHHHHHHHHHTCSEEEEEET-TEEEEEECG
T ss_pred             cCCCCCHHHHHHHHc---------cCCCHHHHHHHHHHHHHHHhcCCCcEEEEEEC-CEEEEEEhH
Confidence            466788888877664         25899999999988854    47899999999 778888887

>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=85.37  E-value=0.43  Score=31.06  Aligned_cols=44  Identities=14%  Similarity=0.279  Sum_probs=37.1

Q ss_pred             HHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         184 VLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       184 il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ||.+..  . |.+|..+|++.+|.|+.-....++.|+++|++..-..
T Consensus         4 Il~~i~--~-~pisr~eLa~~~gls~~TVs~~v~~L~~~GlV~e~~~   47 (62)
T d2hoea1           4 ILKRIM--K-SPVSRVELAEELGLTKTTVGEIAKIFLEKGIVVEEKD   47 (62)
T ss_dssp             SHHHHH--H-SCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             HHHHHH--H-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCC
Confidence            556665  2 3599999999999999999999999999999976543

>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=84.68  E-value=0.66  Score=35.99  Aligned_cols=42  Identities=14%  Similarity=0.280  Sum_probs=36.5

Q ss_pred             HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      .||.+..   .|..|+.+|++.+|.++.-+..+|..|++.|++=.
T Consensus        23 ~Il~~L~---~~~~s~~ela~~lg~s~~~v~~hl~~L~~~glv~~   64 (190)
T d1ulya_          23 KILKLLR---NKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEV   64 (190)
T ss_dssp             HHHHHHT---TCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            4566665   46799999999999999999999999999999943

>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=84.35  E-value=1.4  Score=30.09  Aligned_cols=52  Identities=12%  Similarity=0.022  Sum_probs=46.0

Q ss_pred             CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552         176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI  227 (254)
Q Consensus       176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv  227 (254)
                      .+++++..|+.+++..+..++...+|....|.+.......|..|+..+++=-
T Consensus        10 ~l~~~E~lVY~~I~~ag~~GIW~~dir~ktnL~~~~l~K~LK~Lesk~lIK~   61 (78)
T d2dk5a1          10 GSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKA   61 (78)
T ss_dssp             CSCSSHHHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHHHHHHccccceeHHHHHHHcCCCHHHHHHHHHHHHhcCCcee
Confidence            4777888999998876667899999999999999999999999999998743

>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=83.73  E-value=0.8  Score=30.74  Aligned_cols=37  Identities=14%  Similarity=0.232  Sum_probs=34.0

Q ss_pred             Ccc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         194 AHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       194 g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      ..+ |..+|++.||.|..-++++|..|+.+|++-.-..
T Consensus        20 ~~LPse~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g   57 (78)
T d3bwga1          20 DKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQVRG   57 (78)
T ss_dssp             CBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEcC
Confidence            356 8999999999999999999999999999998865

>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=83.68  E-value=1.2  Score=30.88  Aligned_cols=56  Identities=16%  Similarity=0.227  Sum_probs=42.7

Q ss_pred             CCChhHHHHHHHhhcc---CCCcccHHHHHHh--cCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552         176 ELSLDHSLVLQQVASK---NEAHISVSVLNNE--LNWSTERAQHALDFMVQEGYAWIDTQS  231 (254)
Q Consensus       176 els~D~~~il~l~~~~---~~g~vt~~~l~~~--l~ws~~ra~~~L~~l~~~G~lwvD~q~  231 (254)
                      +|++-|..||..+-+.   .+--++..+|++.  +++|++=.+..|..|++.|++-.+...
T Consensus         1 ~Lt~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~~LE~~G~l~~~h~s   61 (87)
T d1stza1           1 KLNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQPHTS   61 (87)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEECCSSC
T ss_pred             CcCHHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHHHHHHCCcccCCCCC
Confidence            3565677776654211   2556999999998  557899999999999999999887653

>d1hw1a1 a.4.5.6 (A:5-78) Fatty acid responsive transcription factor FadR, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Fatty acid responsive transcription factor FadR, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=83.14  E-value=0.64  Score=31.23  Aligned_cols=37  Identities=11%  Similarity=0.201  Sum_probs=33.4

Q ss_pred             Ccc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         194 AHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       194 g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      -.+ |..+|++.||.|..-++++|..|+++|++-+--.
T Consensus        25 ~~LPs~~eLa~~~~vSr~tvr~Al~~L~~~G~i~~~~g   62 (74)
T d1hw1a1          25 TILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHG   62 (74)
T ss_dssp             SBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEeC
Confidence            357 8999999999999999999999999999987744

>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=80.93  E-value=1.7  Score=30.28  Aligned_cols=38  Identities=5%  Similarity=-0.016  Sum_probs=35.8

Q ss_pred             CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552         193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ  230 (254)
Q Consensus       193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q  230 (254)
                      .|..|+.+|++..|.++......|+.|...|++=.|+.
T Consensus        38 ~gp~t~~eLA~~~g~~~~~l~rLlr~L~a~gll~~~~d   75 (92)
T d1qzza1          38 AGADTLAGLADRTDTHPQALSRLVRHLTVVGVLEGGEK   75 (92)
T ss_dssp             TTCCSHHHHHHHHTCCHHHHHHHHHHHHHTTSEECCCC
T ss_pred             CCCCCHHHHHHHHCcCchHHHHHHHHHHHCCCeeeecC
Confidence            47899999999999999999999999999999998876